Citrus Sinensis ID: 016936

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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
Protein Sequence
MAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDYSA
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccEEEEccccccccHHHHHHHHHHHHHHHcccccccccEEEEEEEcccccEEEEEEccHHHHHHHHHccccEEccEEEEEccccccccccccccccccccccccHHHHccccccccccccccEEEEccccccccHHHHHHHHHHcccEEEEEEEEccccccccEEEEEEEccHHHHHHHHHHHcccccccEEEEEEEcccccccccHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccEEEEEcccccccccccHHHHHHHHHHHHHHHcccccEEEEEEcccccccccccccEEEEEEEccHHHHHHHHHHHcccEEcccEEEEEEccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccccEEEEccccccccHHHHHHHHHHHHHHHcccccccccEEEEEEEcccccEEEEEEEcHHHHHHHHHcccEEEccEEEEEEcccccccccccccccccccccccccccccccccccccccccEEEEEcccccccHHHHHHHHHccccEEEEEEEEccccccEEEEEEEEEccHHHHHHHHHHHcccEEccEEcEEEEccccccccccHHcccccccccccHHHHHHcccccccccccccccccccccEEEEEcccccHHHccccHHHHHHHHHHHHHHHHcccEEEEEEcccccccccccccEEEEEEEccHHHHHHHHHHHccccccccEEEEEEEcHHHHccccccc
Coil and Loop (DISEMBL)
maqnmlpfgatqlgafplmpvQVMTQQATRHARRvyvgglpplanEQAIATFFSQVMTaiggnsagpgdAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAvrvrrptdynptlaaalgpgqpspnlnLAAVGLasgaiggaegpdrvfvgglpyyfTETQIKELLESFgtlhgfdlvkdrdtgnskgygfcvyqdpavtDIACAALNglkmgdktLTVRRatassgqsktEQESILAQAQQHIAIQKMALQTsgmntlgggmslFGETLAKVLCLTEAITadaladdeEYEEILEDMREECgkygtlvnvviprpdqnggetpgvgKVFLEYYDAvgcataknalsgrkfggntvnafyypedkyfnkdysa
Flexible Loop (DISEMBL)
MAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATassgqskteQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNvviprpdqnggeTPGVGKVFLEYYDAVGCATAknalsgrkfggntvnafyypedkyfnkdysa
Low Complexity Region (SEG)
MAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESilaqaqqhiaiqKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITadaladdeeyeeiledmreeCGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDYSA
Disordered region (IsUnstruct)
*******FGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEM*************GIIFEGVAVRVRRPTDYNPTLAAAL********LNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTL*************************HIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADAL*******************YGTLVNVVIP********TPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYF******
Disordered Region (DISOPRED)
**********************************VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVR****************************************DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR*******************************************SLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFN**Y**
Disordered Region (DISEMBL)
MAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV*******************QAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDYSA
Disordered Region (DISPRO)
****MLPFG*******PLMPVQ******TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFN*****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDYSA
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	380	2.2.26 [Sep-21-2011]
Q8L716	589	Splicing factor U2af larg	yes	no	0.960	0.619	0.707	1e-158
Q9ZR39	555	Splicing factor U2af larg	N/A	no	0.957	0.655	0.702	1e-157
Q9ZR40	573	Splicing factor U2af larg	N/A	no	0.960	0.636	0.701	1e-157
O23212	573	Splicing factor U2af larg	no	no	0.965	0.640	0.671	1e-148
Q2QKB4	543	Splicing factor U2af larg	N/A	no	0.963	0.674	0.684	1e-145
Q2QZL4	548	Splicing factor U2af larg	yes	no	0.963	0.667	0.681	1e-145
Q2R0Q1	574	Splicing factor U2af larg	no	no	0.955	0.632	0.655	1e-142
Q2QKB3	591	Splicing factor U2af larg	N/A	no	0.8	0.514	0.632	1e-111
Q24562	416	Splicing factor U2AF 50 k	yes	no	0.884	0.807	0.409	2e-70
P26368	475	Splicing factor U2AF 65 k	yes	no	0.892	0.713	0.423	3e-66

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

 Score =  556 bits (1434), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 268/379 (70%), Positives = 306/379 (80%), Gaps = 14/379 (3%)

Query: 1   MAQNMLPF-GATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTA 59
           M  NM P     QLGA P++PVQ MTQQATRHARRVYVGGLPP ANEQ+++TFFSQVM+A
Sbjct: 222 MFSNMFPMVPGQQLGALPVLPVQAMTQQATRHARRVYVGGLPPTANEQSVSTFFSQVMSA 281

Query: 60  IGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNP 119
           IGGN+AGPGDAVVNVYINHEKKFAFVEMR+VEEASNAMALDGII EGV V+VRRPTDYNP
Sbjct: 282 IGGNTAGPGDAVVNVYINHEKKFAFVEMRSVEEASNAMALDGIILEGVPVKVRRPTDYNP 341

Query: 120 TLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTL 179
           +LAA LGP QP+PNLNL AVGL+SG+ GG EGPDR+FVGGLPYYFTE QI+ELLESFG L
Sbjct: 342 SLAATLGPSQPNPNLNLGAVGLSSGSTGGLEGPDRIFVGGLPYYFTEVQIRELLESFGPL 401

Query: 180 HGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTE 239
            GF+LVKDR+TGNSKGY FCVYQDP+VTDIACAALNG+KMGDKTLTVRRA   + Q K E
Sbjct: 402 RGFNLVKDRETGNSKGYAFCVYQDPSVTDIACAALNGIKMGDKTLTVRRAIQGAIQPKPE 461

Query: 240 QESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYE 299
           QE +L  AQQ IA+Q++  Q  G             T  K++CLT+ +TAD L DDEEY 
Sbjct: 462 QEEVLLYAQQQIALQRLMFQPGG-------------TPTKIVCLTQVVTADDLRDDEEYA 508

Query: 300 EILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFG 359
           EI+EDMR+E GK+G LVNVVIPRP+ +   TPGVGKVFLEY D  G + A++ ++GRKFG
Sbjct: 509 EIMEDMRQEGGKFGNLVNVVIPRPNPDHDPTPGVGKVFLEYADVDGSSKARSGMNGRKFG 568

Query: 360 GNTVNAFYYPEDKYFNKDY 378
           GN V A YYPEDKY   DY
Sbjct: 569 GNQVVAVYYPEDKYAQGDY 587

Necessary for the splicing of pre-mRNA.
Arabidopsis thaliana (taxid: 3702)

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

 Score =  554 bits (1427), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 265/377 (70%), Positives = 302/377 (80%), Gaps = 13/377 (3%)

Query: 4   NMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGN 63
           NM P  ++Q GA P+MPVQ MTQQATRHARRVYVGGLPP ANEQ++ATFFS VM AIGGN
Sbjct: 192 NMFPLASSQFGALPMMPVQAMTQQATRHARRVYVGGLPPTANEQSVATFFSHVMYAIGGN 251

Query: 64  SAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAA 123
           +AGPGDAVVNVYINHEKKFAFVEMR+VEEASNAMALDG+IFEG  V+VRRP+DYNP+LAA
Sbjct: 252 TAGPGDAVVNVYINHEKKFAFVEMRSVEEASNAMALDGVIFEGGPVKVRRPSDYNPSLAA 311

Query: 124 ALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFD 183
            LGP QPSPNLNLAAVG   G+ GG EGPDR+FVGGLPYYFTE+QI+ELLESFG L GFD
Sbjct: 312 TLGPSQPSPNLNLAAVGSTPGSSGGLEGPDRIFVGGLPYYFTESQIRELLESFGQLRGFD 371

Query: 184 LVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESI 243
           LVKDR+TGNSKGY FCVYQD +VTDIACAALNG+KMGDKTLTVRRA   + Q   EQES+
Sbjct: 372 LVKDRETGNSKGYAFCVYQDVSVTDIACAALNGIKMGDKTLTVRRANQGTTQPNPEQESV 431

Query: 244 LAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILE 303
           L  AQQ IA+Q+  LQ   + T             KVLCLTE +T D L DD++Y++ILE
Sbjct: 432 LLHAQQQIALQRFMLQPGALAT-------------KVLCLTEVVTVDELNDDDDYQDILE 478

Query: 304 DMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTV 363
           DMR EC K+G LVNVVIPRP+ NG  TPG+GKVFLEY D  G + A+  L+GRKFGGN V
Sbjct: 479 DMRTECEKFGALVNVVIPRPNPNGVPTPGLGKVFLEYADVDGSSKARQGLNGRKFGGNQV 538

Query: 364 NAFYYPEDKYFNKDYSA 380
            A +YPE+K+   DY A
Sbjct: 539 VAVFYPENKFSEGDYEA 555

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

Nicotiana plumbaginifolia (taxid: 4092)

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

 Score =  553 bits (1425), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 265/378 (70%), Positives = 306/378 (80%), Gaps = 13/378 (3%)

Query: 1   MAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAI 60
           M  NM P  + Q GA P+MP+Q MTQQATRHARRVYVGGLP  ANEQ++ATFFS VM+AI
Sbjct: 207 MFPNMFPLASGQFGALPVMPIQAMTQQATRHARRVYVGGLPAHANEQSVATFFSHVMSAI 266

Query: 61  GGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPT 120
           GGN+AGPGDAVVNVYIN+EKKFAFVEMR+VEEASNAMALDGIIFEG   +VRRP+DYNP+
Sbjct: 267 GGNTAGPGDAVVNVYINYEKKFAFVEMRSVEEASNAMALDGIIFEGAPCKVRRPSDYNPS 326

Query: 121 LAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLH 180
           LAA LGP QP+PNLNLAAVGL+ G+ GG EGPDR+FVGGLPYYFTE QI+ELLESFG L 
Sbjct: 327 LAATLGPSQPNPNLNLAAVGLSPGSAGGLEGPDRIFVGGLPYYFTEAQIRELLESFGPLR 386

Query: 181 GFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQ 240
           GFDLVKDR+TGNSKGY FCVYQD +VTDIACAALNG+KMGDKTLTVRRA   + Q K EQ
Sbjct: 387 GFDLVKDRETGNSKGYAFCVYQDVSVTDIACAALNGIKMGDKTLTVRRANQGTTQPKPEQ 446

Query: 241 ESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEE 300
           ES+L  AQQ IA+Q++ LQ + + T             KVL LTE I+AD L DDE+Y++
Sbjct: 447 ESVLLHAQQQIALQRLMLQPATLAT-------------KVLSLTEVISADELNDDEDYQD 493

Query: 301 ILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGG 360
           ILEDMR ECGK+G+LVNVVIPRP  NG  TPGVGKVFLEY D    + A+ +L+GRKFGG
Sbjct: 494 ILEDMRTECGKFGSLVNVVIPRPSPNGEPTPGVGKVFLEYADVDSSSKARQSLNGRKFGG 553

Query: 361 NTVNAFYYPEDKYFNKDY 378
           N V A +YPE+K++  DY
Sbjct: 554 NQVVAVFYPENKFYEGDY 571

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

Nicotiana plumbaginifolia (taxid: 4092)

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

 Score =  526 bits (1354), Expect = e-148,   Method: Compositional matrix adjust.
 Identities = 256/381 (67%), Positives = 294/381 (77%), Gaps = 14/381 (3%)

Query: 1   MAQNMLPFGATQ-LGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTA 59
           M  NM P    Q  G   +MP+Q MTQQATRHARRVYVGGL P ANEQ++ATFFSQVM A
Sbjct: 206 MFPNMFPLPTGQSFGGLSMMPIQAMTQQATRHARRVYVGGLSPTANEQSVATFFSQVMAA 265

Query: 60  IGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNP 119
           +GGN+AGPGDAVVNVYINHEKKFAFVEMR+VEEASNAM+LDGIIFEG  V+VRRP+DYNP
Sbjct: 266 VGGNTAGPGDAVVNVYINHEKKFAFVEMRSVEEASNAMSLDGIIFEGAPVKVRRPSDYNP 325

Query: 120 TLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTL 179
           +LAA LGP QPSP+LNLAAVGL  GA GG EGPDR+FVGGLPYYFTE+Q++ELLESFG L
Sbjct: 326 SLAATLGPSQPSPHLNLAAVGLTPGASGGLEGPDRIFVGGLPYYFTESQVRELLESFGGL 385

Query: 180 HGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTE 239
            GFDLVKDR+TGNSKGY FCVYQD +VTDIACAALNG+KMGDKTLTVRRA   +   K E
Sbjct: 386 KGFDLVKDRETGNSKGYAFCVYQDLSVTDIACAALNGIKMGDKTLTVRRANQGTMLQKPE 445

Query: 240 QESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYE 299
           QE++L  AQQ IA Q++ LQ   + T              V+CLT+ +T D L DDEEY 
Sbjct: 446 QENVLLHAQQQIAFQRVMLQPGAVATT-------------VVCLTQVVTEDELRDDEEYG 492

Query: 300 EILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFG 359
           +I+EDMR+E GK+G L NVVIPRP  NG    G+GKVFL+Y D  G   A+  ++GRKFG
Sbjct: 493 DIMEDMRQEGGKFGALTNVVIPRPSPNGEPVAGLGKVFLKYADTDGSTRARFGMNGRKFG 552

Query: 360 GNTVNAFYYPEDKYFNKDYSA 380
           GN V A YYPEDK+   DY A
Sbjct: 553 GNEVVAVYYPEDKFEQGDYGA 573

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 =  514 bits (1325), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 260/380 (68%), Positives = 297/380 (78%), Gaps = 14/380 (3%)

Query: 1   MAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAI 60
           M  NMLPF   Q+    + P Q MTQQATRHARRVYVGGLPP ANEQ++A +F+QVM AI
Sbjct: 176 MFPNMLPFADGQINPLVMQP-QAMTQQATRHARRVYVGGLPPSANEQSVAIYFNQVMAAI 234

Query: 61  GGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPT 120
           GGN+AGPGDAV+NVYINH+KKFAFVEMR+VEEASNAMALDGI+FEG  V+VRRPTDYNP+
Sbjct: 235 GGNTAGPGDAVLNVYINHDKKFAFVEMRSVEEASNAMALDGILFEGAPVKVRRPTDYNPS 294

Query: 121 LAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLH 180
           LAAALGP QPS NLNLAAVGL  G+ GG EGPDR+FVGGLPYYFTE Q++ELLESFG L 
Sbjct: 295 LAAALGPSQPSSNLNLAAVGLTPGSAGGLEGPDRIFVGGLPYYFTEAQVRELLESFGPLR 354

Query: 181 GFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQ 240
           GFDLVKDR+TGNSKGY FCVYQD  VTDIACAALNG+KMGDKTLTVRRA   S Q + EQ
Sbjct: 355 GFDLVKDRETGNSKGYAFCVYQDLNVTDIACAALNGIKMGDKTLTVRRANQGSAQPRPEQ 414

Query: 241 ESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEE 300
           E+IL QAQQ + +QK+  Q   + T             KV+CLT+ +TAD L DDEEYE+
Sbjct: 415 ENILLQAQQQVQLQKLVYQVGALPT-------------KVVCLTQVVTADELKDDEEYED 461

Query: 301 ILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGG 360
           I+EDMR E GKYG LV VVIPRP  +G    GVGKVFLEY D  G   AK A+ GRKFGG
Sbjct: 462 IMEDMRLEAGKYGNLVKVVIPRPHPSGEPVSGVGKVFLEYADVDGSTKAKTAMHGRKFGG 521

Query: 361 NTVNAFYYPEDKYFNKDYSA 380
           N V A +YPE+K+ ++DY A
Sbjct: 522 NPVVAVFYPENKFADEDYDA 541

Necessary for the splicing of pre-mRNA.

Triticum aestivum (taxid: 4565)

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

 Score =  513 bits (1322), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 259/380 (68%), Positives = 297/380 (78%), Gaps = 14/380 (3%)

Query: 1   MAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAI 60
           M  NMLP G  Q     + P Q MTQQATRHARRVYVGGLPP ANEQ++A +F+QVM AI
Sbjct: 183 MFPNMLPMGVGQFNPLVIQP-QAMTQQATRHARRVYVGGLPPTANEQSVAIYFNQVMAAI 241

Query: 61  GGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPT 120
           GGN+AGPGDAV+NVYINH+KKFAFVEMR+VEEASNAMALDGI+FEG  V+VRRPTDYNP+
Sbjct: 242 GGNTAGPGDAVLNVYINHDKKFAFVEMRSVEEASNAMALDGILFEGAPVKVRRPTDYNPS 301

Query: 121 LAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLH 180
           LAAALGP QPSPNLNLAAVGL  G+ GG EGPDR+FVGGLPYYFTE Q++ELLESFG L 
Sbjct: 302 LAAALGPSQPSPNLNLAAVGLTPGSAGGLEGPDRIFVGGLPYYFTEAQVRELLESFGPLR 361

Query: 181 GFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQ 240
           GFDLVKDR+TGNSKGY FCVYQD  VTDIACAALNG+KMGDKTLTVRRA   + Q + EQ
Sbjct: 362 GFDLVKDRETGNSKGYAFCVYQDLNVTDIACAALNGIKMGDKTLTVRRANQGAAQPRPEQ 421

Query: 241 ESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEE 300
           ESIL QAQQ + +QK+  Q   + T             KV+CLT+ ++AD L DDEEYE+
Sbjct: 422 ESILLQAQQQVQLQKLVYQVGALPT-------------KVVCLTQVVSADELKDDEEYED 468

Query: 301 ILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGG 360
           I+EDMR E GKYG L+ VVIPRPD +G    GVGKVFLEY D  G   AK A+ GRKFGG
Sbjct: 469 IMEDMRLEAGKYGNLIKVVIPRPDPSGLPVAGVGKVFLEYADVDGATKAKTAMHGRKFGG 528

Query: 361 NTVNAFYYPEDKYFNKDYSA 380
           N V A +YPE+K+ + +Y A
Sbjct: 529 NPVVAVFYPENKFSSAEYDA 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-142,   Method: Compositional matrix adjust.
 Identities = 247/377 (65%), Positives = 285/377 (75%), Gaps = 14/377 (3%)

Query: 5   MLP--FGATQLGAFPL-MPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIG 61
           MLP  F  TQ    PL +  Q MTQQATRHARRVYVGGLPP ANE  +A +F+QVM A+G
Sbjct: 207 MLPNMFNLTQTPFTPLVIQPQAMTQQATRHARRVYVGGLPPTANEHTVAVYFNQVMAAVG 266

Query: 62  GNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTL 121
           GN+AGPGDAV+NVYINH+KKFAFVEMR+VEEASNAMALDGI+FEG  V+VRRPTDYNP+L
Sbjct: 267 GNTAGPGDAVLNVYINHDKKFAFVEMRSVEEASNAMALDGIMFEGAPVKVRRPTDYNPSL 326

Query: 122 AAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHG 181
           AAALGP QP+PNLNLAAVGL  G+ GG EGPDR+FVGGLPYYFTE Q++ELLESFG L G
Sbjct: 327 AAALGPSQPNPNLNLAAVGLTPGSAGGLEGPDRIFVGGLPYYFTEAQVRELLESFGPLRG 386

Query: 182 FDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQE 241
           FDLVKDR+TGNSKGY FCVYQD  VTDIACAALNG+KMGDKTLTVRRA   + Q + EQE
Sbjct: 387 FDLVKDRETGNSKGYAFCVYQDLNVTDIACAALNGIKMGDKTLTVRRANQGASQPRPEQE 446

Query: 242 SILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEI 301
           S+L   QQ   +QK+  Q  G           G    KV+CLT+ ++ D L DDEEYE+I
Sbjct: 447 SMLLHVQQQAQMQKLMFQVGG-----------GALPTKVVCLTQVVSPDELRDDEEYEDI 495

Query: 302 LEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGN 361
           ++DMREE  +YG LV VVIPRPD +G    GVG+VFLE+ D      AKN + GRKF  N
Sbjct: 496 VQDMREEGCRYGNLVKVVIPRPDPSGAPVAGVGRVFLEFADVESSTKAKNGMHGRKFANN 555

Query: 362 TVNAFYYPEDKYFNKDY 378
            V A +YPEDK+    Y
Sbjct: 556 QVVAVFYPEDKFAEGQY 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 =  403 bits (1035), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 208/329 (63%), Positives = 245/329 (74%), Gaps = 25/329 (7%)

Query: 1   MAQNMLP--FGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMT 58
           M  NMLP       LG  PL     MTQQATRHARRVYVGGLPP+ANEQ +A FF+QVM 
Sbjct: 243 MFPNMLPNLVNVPALGQ-PL----AMTQQATRHARRVYVGGLPPIANEQTVAVFFNQVMA 297

Query: 59  AIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYN 118
           AIGGN+   G AVVNVYINH+KKFAFVEMR+VEEASNAMALDGI+FEG  V+VRRPTDYN
Sbjct: 298 AIGGNTFALGHAVVNVYINHDKKFAFVEMRSVEEASNAMALDGIMFEGAPVKVRRPTDYN 357

Query: 119 PTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGT 178
           P+ AAALGP QP+PNLNLAAVGL  GA GG EGPDR+FVGGLPYYFTE Q++ELLE+FG 
Sbjct: 358 PSQAAALGPSQPNPNLNLAAVGLTPGAGGGLEGPDRIFVGGLPYYFTEAQVRELLETFGP 417

Query: 179 LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKT 238
           L GFD+VKD++TGNSKGY FC+Y+D  VTDIACAALNG+++GD+TLTVRRA     + + 
Sbjct: 418 LRGFDIVKDKETGNSKGYAFCLYKDGTVTDIACAALNGIQLGDRTLTVRRAN-QGAEPRP 476

Query: 239 EQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETL-AKVLCLTEAITADALADDEE 297
           EQE+IL QAQQ   ++++  +              G TL  KV+CLT+ ++AD L DDEE
Sbjct: 477 EQENILLQAQQEAQMKRLVYEV-------------GRTLTTKVVCLTQVVSADDLRDDEE 523

Query: 298 YEEILEDMREECGKY---GTLVNVVIPRP 323
           Y +ILEDM  E  KY    T+    I RP
Sbjct: 524 YNDILEDMTLEGHKYVPHSTIAESFIIRP 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 =  266 bits (680), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 150/366 (40%), Positives = 212/366 (57%), Gaps = 30/366 (8%)

Query: 17  PLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI 76
           P   V V+    TR ARR+YVG +P    E+ +  FF+Q M  +G   A  G  V+   I
Sbjct: 77  PQTAVPVVGSTITRQARRLYVGNIPFGVTEEEMMEFFNQQMHLVGLAQAA-GSPVLACQI 135

Query: 77  NHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPG-QPSPNLN 135
           N +K FAF+E R+++E + AMA DGI  +G ++++RRP DY P       PG   +P + 
Sbjct: 136 NLDKNFAFLEFRSIDETTQAMAFDGINLKGQSLKIRRPHDYQPM------PGITDTPAIK 189

Query: 136 LAAVGLASGAIGGA--EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNS 193
            A V  +SG I     + P ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG S
Sbjct: 190 PAVV--SSGVISTVVPDSPHKIFIGGLPNYLNDDQVKELLLSFGKLRAFNLVKDAATGLS 247

Query: 194 KGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAI 253
           KGY FC Y D ++TD + A LNG+++GDK L V+RA+  +  ++    +           
Sbjct: 248 KGYAFCEYVDLSITDQSIAGLNGMQLGDKKLIVQRASVGAKNAQNAANT----------T 297

Query: 254 QKMALQTSGM-NTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKY 312
           Q + LQ  G+ N +  G         +VLCL   +T D L D+EEYE+ILED++EEC KY
Sbjct: 298 QSVMLQVPGLSNVVTSGPP------TEVLCLLNMVTPDELRDEEEYEDILEDIKEECTKY 351

Query: 313 GTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK 372
           G + +V IPRP + G E PG GKVF+E+   + C  A+ AL+GRKF    V   Y+  DK
Sbjct: 352 GVVRSVEIPRPIE-GVEVPGCGKVFVEFNSVLDCQKAQQALTGRKFSDRVVVTSYFDPDK 410

Query: 373 YFNKDY 378
           Y  +++
Sbjct: 411 YHRREF 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 =  252 bits (644), Expect = 3e-66,   Method: Compositional matrix adjust.
 Identities = 152/359 (42%), Positives = 210/359 (58%), Gaps = 20/359 (5%)

Query: 20  PVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE 79
           PV V+  Q TR ARR+YVG +P    E+A+  FF+  M  +GG +  PG+ V+ V IN +
Sbjct: 136 PVPVVGSQMTRQARRLYVGNIPFGITEEAMMDFFNAQMR-LGGLTQAPGNPVLAVQINQD 194

Query: 80  KKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAV 139
           K FAF+E R+V+E + AMA DGIIF+G ++++RRP DY P       PG  S N ++   
Sbjct: 195 KNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPL------PGM-SENPSVYVP 247

Query: 140 GLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC 199
           G+ S  +   +   ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG SKGY FC
Sbjct: 248 GVVSTVV--PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFC 305

Query: 200 VYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQ 259
            Y D  VTD A A LNG+++GDK L V+RA+  +      + + L      I    + LQ
Sbjct: 306 EYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA------KNATLVSPPSTINQTPVTLQ 359

Query: 260 TSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVV 319
             G+ +    M   G    +VLCL   +  + L DDEEYEEI+ED+R+EC KYG + ++ 
Sbjct: 360 VPGLMSSQVQM---GGHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIE 416

Query: 320 IPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 378
           IPRP  +G E PG GK+F+E+     C  A   L+GRKF    V   Y   D Y  +D+
Sbjct: 417 IPRP-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	380
359497050	410	PREDICTED: splicing factor U2af large su	0.884	0.819	0.744	1e-159
388520789	527	unknown [Lotus japonicus]	0.989	0.713	0.719	1e-159
297840477	589	hypothetical protein ARALYDRAFT_475241 [	0.960	0.619	0.712	1e-157
30696485	589	Splicing factor U2af large subunit B [Ar	0.960	0.619	0.707	1e-156
12323333	568	putative U2 snRNP auxiliary factor; 1909	0.960	0.642	0.707	1e-156
156070797	558	unknown [Solanum bulbocastanum]	0.960	0.654	0.698	1e-155
75338883	555	RecName: Full=Splicing factor U2af large	0.957	0.655	0.702	1e-155
22655131	589	putative U2 snRNP auxiliary factor [Arab	0.960	0.619	0.704	1e-155
75338884	573	RecName: Full=Splicing factor U2af large	0.960	0.636	0.701	1e-155
188998293	554	U2 snRNP auxiliary factor large subunit	0.965	0.662	0.694	1e-155

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

 Score =  567 bits (1462), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 283/380 (74%), Positives = 303/380 (79%), Gaps = 44/380 (11%)

Query: 1   MAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAI 60
           M QNM PFGATQLGA PLMPVQ MTQQATRHARRVYVGGLPPLANEQ IATFFSQVMTAI
Sbjct: 75  MIQNMFPFGATQLGALPLMPVQAMTQQATRHARRVYVGGLPPLANEQTIATFFSQVMTAI 134

Query: 61  GGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPT 120
           GGNSAGPGDAVVNVYINHEKKFAFVEMR+VEEASNAMALDGI+FEGV+VRVRRPTDYNP+
Sbjct: 135 GGNSAGPGDAVVNVYINHEKKFAFVEMRSVEEASNAMALDGIMFEGVSVRVRRPTDYNPS 194

Query: 121 LAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLH 180
           LAAALGP QPSP+LNLAAVGL  G IGGAEGPDR+FVGGLPYYFTE QI+ELLESFG L 
Sbjct: 195 LAAALGPSQPSPHLNLAAVGLMPGVIGGAEGPDRIFVGGLPYYFTEEQIRELLESFGPLR 254

Query: 181 GFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQ 240
           GFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  SGQ+K+EQ
Sbjct: 255 GFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATVGSGQAKSEQ 314

Query: 241 ESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEE 300
           ++ILAQAQQHIAIQK+ALQ  G+N  G                                 
Sbjct: 315 DNILAQAQQHIAIQKIALQAGGLNLPGA-------------------------------- 342

Query: 301 ILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGG 360
                       G LV+VVIPRP  NG   PGVGKVFLEY D  G ++A+NALSGRKFGG
Sbjct: 343 ------------GALVHVVIPRPSPNGDLIPGVGKVFLEYSDTAGSSSARNALSGRKFGG 390

Query: 361 NTVNAFYYPEDKYFNKDYSA 380
           N V+A YYPEDKY++ DY A
Sbjct: 391 NVVSAVYYPEDKYYDGDYGA 410

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  567 bits (1460), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 274/381 (71%), Positives = 320/381 (83%), Gaps = 5/381 (1%)

Query: 2   AQNMLPFGATQ--LGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTA 59
           AQN   FG +Q  +GA  LM VQ MTQQATRHARRVY+GGLPPL NEQ+IATFFS VMTA
Sbjct: 146 AQNFSLFGISQPQIGALSLMQVQPMTQQATRHARRVYIGGLPPLTNEQSIATFFSHVMTA 205

Query: 60  IGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNP 119
           IGGNSAG GD+VVNVYINHEKKFAF+EMRTVEEASNAM+LDGI+FEGV+VRVRRPTDYNP
Sbjct: 206 IGGNSAGAGDSVVNVYINHEKKFAFLEMRTVEEASNAMSLDGIVFEGVSVRVRRPTDYNP 265

Query: 120 TLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTL 179
           TLAAALGP QPSP LNL+AVGL+ G IGG +G DR+FVGGLPYYF E QI+ELL++FG L
Sbjct: 266 TLAAALGPCQPSPYLNLSAVGLSGGTIGGTDGLDRIFVGGLPYYFAEEQIRELLQAFGPL 325

Query: 180 HGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTE 239
             FDLV+D++TGNSKGYGFC+YQDPAVTD+ACA+LNGLK+GDKTLTVRRAT  SG SKTE
Sbjct: 326 RSFDLVRDKETGNSKGYGFCIYQDPAVTDMACASLNGLKVGDKTLTVRRATV-SGHSKTE 384

Query: 240 QESILAQAQQHIAIQKMALQTSGMNTLGGGM--SLFGETLAKVLCLTEAITADALADDEE 297
           QE I AQAQQ+I +QK+AL+  G+N  G     +   E+  KVLCLTEAIT D L D+ E
Sbjct: 385 QEHIFAQAQQNITMQKVALEVVGLNIPGVERVPTTIDESATKVLCLTEAITTDELMDNGE 444

Query: 298 YEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRK 357
           YEEI+EDMR+ECGK+GTL+NVVIPRP+ +G +TPG+GKVFLEY D      AK+AL+GRK
Sbjct: 445 YEEIVEDMRDECGKFGTLMNVVIPRPNPSGEQTPGIGKVFLEYSDTAASFAAKSALNGRK 504

Query: 358 FGGNTVNAFYYPEDKYFNKDY 378
           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|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 =  561 bits (1447), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 270/379 (71%), Positives = 307/379 (81%), Gaps = 14/379 (3%)

Query: 1   MAQNMLPF-GATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTA 59
           M  NM P     QLGA P++PVQ MTQQATRHARRVYVGGLPP ANEQ++ATFFSQVM+A
Sbjct: 222 MFPNMFPMVPGQQLGALPVLPVQAMTQQATRHARRVYVGGLPPTANEQSVATFFSQVMSA 281

Query: 60  IGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNP 119
           IGGN+AGPGDAVVNVYINHEKKFAFVEMR+VEEASNAMALDGII EGV V+VRRPTDYNP
Sbjct: 282 IGGNTAGPGDAVVNVYINHEKKFAFVEMRSVEEASNAMALDGIILEGVPVKVRRPTDYNP 341

Query: 120 TLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTL 179
           +LAA LGP QP+PNLNLAAVGL+SG+ GG EGPDR+FVGGLPYYFTE QI+ELLESFG L
Sbjct: 342 SLAATLGPSQPNPNLNLAAVGLSSGSTGGLEGPDRIFVGGLPYYFTEVQIRELLESFGPL 401

Query: 180 HGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTE 239
            GF+LVKDR+TGNSKGY FCVYQDP+VTDIACAALNG+KMGDKTLTVRRA     Q K E
Sbjct: 402 RGFNLVKDRETGNSKGYAFCVYQDPSVTDIACAALNGIKMGDKTLTVRRAIQGVIQPKPE 461

Query: 240 QESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYE 299
           QE +L  AQQ IA+Q++ LQ  G             T  K++CLT+ +TAD L DDEEY 
Sbjct: 462 QEEVLLHAQQQIALQRLMLQPGG-------------TPTKIVCLTQVVTADDLRDDEEYA 508

Query: 300 EILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFG 359
           +I+EDMR+E GK+G LVNVVIPRP+ +   TPGVGKVFLEY D  G + A++ ++GRKFG
Sbjct: 509 DIMEDMRQEGGKFGNLVNVVIPRPNPDHDPTPGVGKVFLEYADVDGSSKARSGMNGRKFG 568

Query: 360 GNTVNAFYYPEDKYFNKDY 378
           GN V A YYPEDKY   DY
Sbjct: 569 GNQVVAVYYPEDKYLQGDY 587

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|30696485|ref|NP_176287.3| Splicing factor U2af large subunit B [Arabidopsis thaliana] gi|209572798|sp|Q8L716.2|U2A2B_ARATH RecName: Full=Splicing factor U2af large subunit B; 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|332195625|gb|AEE33746.1| Splicing factor U2af large subunit B [Arabidopsis thaliana]

 Score =  556 bits (1434), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 268/379 (70%), Positives = 306/379 (80%), Gaps = 14/379 (3%)

Query: 1   MAQNMLPF-GATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTA 59
           M  NM P     QLGA P++PVQ MTQQATRHARRVYVGGLPP ANEQ+++TFFSQVM+A
Sbjct: 222 MFSNMFPMVPGQQLGALPVLPVQAMTQQATRHARRVYVGGLPPTANEQSVSTFFSQVMSA 281

Query: 60  IGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNP 119
           IGGN+AGPGDAVVNVYINHEKKFAFVEMR+VEEASNAMALDGII EGV V+VRRPTDYNP
Sbjct: 282 IGGNTAGPGDAVVNVYINHEKKFAFVEMRSVEEASNAMALDGIILEGVPVKVRRPTDYNP 341

Query: 120 TLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTL 179
           +LAA LGP QP+PNLNL AVGL+SG+ GG EGPDR+FVGGLPYYFTE QI+ELLESFG L
Sbjct: 342 SLAATLGPSQPNPNLNLGAVGLSSGSTGGLEGPDRIFVGGLPYYFTEVQIRELLESFGPL 401

Query: 180 HGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTE 239
            GF+LVKDR+TGNSKGY FCVYQDP+VTDIACAALNG+KMGDKTLTVRRA   + Q K E
Sbjct: 402 RGFNLVKDRETGNSKGYAFCVYQDPSVTDIACAALNGIKMGDKTLTVRRAIQGAIQPKPE 461

Query: 240 QESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYE 299
           QE +L  AQQ IA+Q++  Q  G             T  K++CLT+ +TAD L DDEEY 
Sbjct: 462 QEEVLLYAQQQIALQRLMFQPGG-------------TPTKIVCLTQVVTADDLRDDEEYA 508

Query: 300 EILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFG 359
           EI+EDMR+E GK+G LVNVVIPRP+ +   TPGVGKVFLEY D  G + A++ ++GRKFG
Sbjct: 509 EIMEDMRQEGGKFGNLVNVVIPRPNPDHDPTPGVGKVFLEYADVDGSSKARSGMNGRKFG 568

Query: 360 GNTVNAFYYPEDKYFNKDY 378
           GN V A YYPEDKY   DY
Sbjct: 569 GNQVVAVYYPEDKYAQGDY 587

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|12323333|gb|AAG51641.1|AC018908_7 putative U2 snRNP auxiliary factor; 19096-22891 [Arabidopsis thaliana]

 Score =  556 bits (1434), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 268/379 (70%), Positives = 306/379 (80%), Gaps = 14/379 (3%)

Query: 1   MAQNMLPF-GATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTA 59
           M  NM P     QLGA P++PVQ MTQQATRHARRVYVGGLPP ANEQ+++TFFSQVM+A
Sbjct: 201 MFSNMFPMVPGQQLGALPVLPVQAMTQQATRHARRVYVGGLPPTANEQSVSTFFSQVMSA 260

Query: 60  IGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNP 119
           IGGN+AGPGDAVVNVYINHEKKFAFVEMR+VEEASNAMALDGII EGV V+VRRPTDYNP
Sbjct: 261 IGGNTAGPGDAVVNVYINHEKKFAFVEMRSVEEASNAMALDGIILEGVPVKVRRPTDYNP 320

Query: 120 TLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTL 179
           +LAA LGP QP+PNLNL AVGL+SG+ GG EGPDR+FVGGLPYYFTE QI+ELLESFG L
Sbjct: 321 SLAATLGPSQPNPNLNLGAVGLSSGSTGGLEGPDRIFVGGLPYYFTEVQIRELLESFGPL 380

Query: 180 HGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTE 239
            GF+LVKDR+TGNSKGY FCVYQDP+VTDIACAALNG+KMGDKTLTVRRA   + Q K E
Sbjct: 381 RGFNLVKDRETGNSKGYAFCVYQDPSVTDIACAALNGIKMGDKTLTVRRAIQGAIQPKPE 440

Query: 240 QESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYE 299
           QE +L  AQQ IA+Q++  Q  G             T  K++CLT+ +TAD L DDEEY 
Sbjct: 441 QEEVLLYAQQQIALQRLMFQPGG-------------TPTKIVCLTQVVTADDLRDDEEYA 487

Query: 300 EILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFG 359
           EI+EDMR+E GK+G LVNVVIPRP+ +   TPGVGKVFLEY D  G + A++ ++GRKFG
Sbjct: 488 EIMEDMRQEGGKFGNLVNVVIPRPNPDHDPTPGVGKVFLEYADVDGSSKARSGMNGRKFG 547

Query: 360 GNTVNAFYYPEDKYFNKDY 378
           GN V A YYPEDKY   DY
Sbjct: 548 GNQVVAVYYPEDKYAQGDY 566

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  554 bits (1427), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 264/378 (69%), Positives = 302/378 (79%), Gaps = 13/378 (3%)

Query: 1   MAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAI 60
           M  NM P  A Q GA P+MPVQ MTQQATRHARRVYVGGLPP ANEQ++ATFFS VM AI
Sbjct: 192 MFSNMFPLAAGQFGALPIMPVQAMTQQATRHARRVYVGGLPPTANEQSVATFFSHVMYAI 251

Query: 61  GGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPT 120
           GGN+AGPGDAVVNVYINHEKKFAFVEMR+VEEASNAMALDG++FEG  V+VRRP+DYNP+
Sbjct: 252 GGNTAGPGDAVVNVYINHEKKFAFVEMRSVEEASNAMALDGVVFEGGPVKVRRPSDYNPS 311

Query: 121 LAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLH 180
           LAA LGP QPSPNLNLAAVGL  G+ GG EGPDR+FVGGLPYYFTE+QI+ELLESFG L 
Sbjct: 312 LAATLGPSQPSPNLNLAAVGLTPGSSGGLEGPDRIFVGGLPYYFTESQIRELLESFGQLR 371

Query: 181 GFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQ 240
           GFDLVKDR+TGNSKGY FCVYQD +VTDIACAALNG+KMGDKTLTVRRA   + Q   EQ
Sbjct: 372 GFDLVKDRETGNSKGYAFCVYQDVSVTDIACAALNGIKMGDKTLTVRRANQGTTQPNPEQ 431

Query: 241 ESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEE 300
           ES+L  AQQ IA+Q+  LQ   + T             KVLCLTE ++ D L DD++Y++
Sbjct: 432 ESVLLHAQQQIALQRFMLQPGALAT-------------KVLCLTEVVSVDELKDDDDYQD 478

Query: 301 ILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGG 360
           ILEDMR ECGK+G L+NVVIPRP+ NG  TPG+GKVFLEY D    + A+  L+GRKFGG
Sbjct: 479 ILEDMRIECGKFGALLNVVIPRPNPNGEPTPGLGKVFLEYADVDSSSKARQGLNGRKFGG 538

Query: 361 NTVNAFYYPEDKYFNKDY 378
           N V A +YPE+K+   DY
Sbjct: 539 NQVIAVFYPENKFSEGDY 556

Source: Solanum bulbocastanum

Species: Solanum bulbocastanum

Genus: Solanum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  554 bits (1427), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 265/377 (70%), Positives = 302/377 (80%), Gaps = 13/377 (3%)

Query: 4   NMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGN 63
           NM P  ++Q GA P+MPVQ MTQQATRHARRVYVGGLPP ANEQ++ATFFS VM AIGGN
Sbjct: 192 NMFPLASSQFGALPMMPVQAMTQQATRHARRVYVGGLPPTANEQSVATFFSHVMYAIGGN 251

Query: 64  SAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAA 123
           +AGPGDAVVNVYINHEKKFAFVEMR+VEEASNAMALDG+IFEG  V+VRRP+DYNP+LAA
Sbjct: 252 TAGPGDAVVNVYINHEKKFAFVEMRSVEEASNAMALDGVIFEGGPVKVRRPSDYNPSLAA 311

Query: 124 ALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFD 183
            LGP QPSPNLNLAAVG   G+ GG EGPDR+FVGGLPYYFTE+QI+ELLESFG L GFD
Sbjct: 312 TLGPSQPSPNLNLAAVGSTPGSSGGLEGPDRIFVGGLPYYFTESQIRELLESFGQLRGFD 371

Query: 184 LVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESI 243
           LVKDR+TGNSKGY FCVYQD +VTDIACAALNG+KMGDKTLTVRRA   + Q   EQES+
Sbjct: 372 LVKDRETGNSKGYAFCVYQDVSVTDIACAALNGIKMGDKTLTVRRANQGTTQPNPEQESV 431

Query: 244 LAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILE 303
           L  AQQ IA+Q+  LQ   + T             KVLCLTE +T D L DD++Y++ILE
Sbjct: 432 LLHAQQQIALQRFMLQPGALAT-------------KVLCLTEVVTVDELNDDDDYQDILE 478

Query: 304 DMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTV 363
           DMR EC K+G LVNVVIPRP+ NG  TPG+GKVFLEY D  G + A+  L+GRKFGGN V
Sbjct: 479 DMRTECEKFGALVNVVIPRPNPNGVPTPGLGKVFLEYADVDGSSKARQGLNGRKFGGNQV 538

Query: 364 NAFYYPEDKYFNKDYSA 380
            A +YPE+K+   DY A
Sbjct: 539 VAVFYPENKFSEGDYEA 555

Source: Nicotiana plumbaginifolia

Species: Nicotiana plumbaginifolia

Genus: Nicotiana

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|22655131|gb|AAM98156.1| putative U2 snRNP auxiliary factor [Arabidopsis thaliana]

 Score =  553 bits (1426), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 267/379 (70%), Positives = 305/379 (80%), Gaps = 14/379 (3%)

Query: 1   MAQNMLPF-GATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTA 59
           M  NM P     QLGA P++PVQ MTQQATRHA RVYVGGLPP ANEQ+++TFFSQVM+A
Sbjct: 222 MFSNMFPMVPGQQLGALPVLPVQAMTQQATRHAPRVYVGGLPPTANEQSVSTFFSQVMSA 281

Query: 60  IGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNP 119
           IGGN+AGPGDAVVNVYINHEKKFAFVEMR+VEEASNAMALDGII EGV V+VRRPTDYNP
Sbjct: 282 IGGNTAGPGDAVVNVYINHEKKFAFVEMRSVEEASNAMALDGIILEGVPVKVRRPTDYNP 341

Query: 120 TLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTL 179
           +LAA LGP QP+PNLNL AVGL+SG+ GG EGPDR+FVGGLPYYFTE QI+ELLESFG L
Sbjct: 342 SLAATLGPSQPNPNLNLGAVGLSSGSTGGLEGPDRIFVGGLPYYFTEVQIRELLESFGPL 401

Query: 180 HGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTE 239
            GF+LVKDR+TGNSKGY FCVYQDP+VTDIACAALNG+KMGDKTLTVRRA   + Q K E
Sbjct: 402 RGFNLVKDRETGNSKGYAFCVYQDPSVTDIACAALNGIKMGDKTLTVRRAIQGAIQPKPE 461

Query: 240 QESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYE 299
           QE +L  AQQ IA+Q++  Q  G             T  K++CLT+ +TAD L DDEEY 
Sbjct: 462 QEEVLLYAQQQIALQRLMFQPGG-------------TPTKIVCLTQVVTADDLRDDEEYA 508

Query: 300 EILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFG 359
           EI+EDMR+E GK+G LVNVVIPRP+ +   TPGVGKVFLEY D  G + A++ ++GRKFG
Sbjct: 509 EIMEDMRQEGGKFGNLVNVVIPRPNPDHDPTPGVGKVFLEYADVDGSSKARSGMNGRKFG 568

Query: 360 GNTVNAFYYPEDKYFNKDY 378
           GN V A YYPEDKY   DY
Sbjct: 569 GNQVVAVYYPEDKYAQGDY 587

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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 =  553 bits (1425), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 265/378 (70%), Positives = 306/378 (80%), Gaps = 13/378 (3%)

Query: 1   MAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAI 60
           M  NM P  + Q GA P+MP+Q MTQQATRHARRVYVGGLP  ANEQ++ATFFS VM+AI
Sbjct: 207 MFPNMFPLASGQFGALPVMPIQAMTQQATRHARRVYVGGLPAHANEQSVATFFSHVMSAI 266

Query: 61  GGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPT 120
           GGN+AGPGDAVVNVYIN+EKKFAFVEMR+VEEASNAMALDGIIFEG   +VRRP+DYNP+
Sbjct: 267 GGNTAGPGDAVVNVYINYEKKFAFVEMRSVEEASNAMALDGIIFEGAPCKVRRPSDYNPS 326

Query: 121 LAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLH 180
           LAA LGP QP+PNLNLAAVGL+ G+ GG EGPDR+FVGGLPYYFTE QI+ELLESFG L 
Sbjct: 327 LAATLGPSQPNPNLNLAAVGLSPGSAGGLEGPDRIFVGGLPYYFTEAQIRELLESFGPLR 386

Query: 181 GFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQ 240
           GFDLVKDR+TGNSKGY FCVYQD +VTDIACAALNG+KMGDKTLTVRRA   + Q K EQ
Sbjct: 387 GFDLVKDRETGNSKGYAFCVYQDVSVTDIACAALNGIKMGDKTLTVRRANQGTTQPKPEQ 446

Query: 241 ESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEE 300
           ES+L  AQQ IA+Q++ LQ + + T             KVL LTE I+AD L DDE+Y++
Sbjct: 447 ESVLLHAQQQIALQRLMLQPATLAT-------------KVLSLTEVISADELNDDEDYQD 493

Query: 301 ILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGG 360
           ILEDMR ECGK+G+LVNVVIPRP  NG  TPGVGKVFLEY D    + A+ +L+GRKFGG
Sbjct: 494 ILEDMRTECGKFGSLVNVVIPRPSPNGEPTPGVGKVFLEYADVDSSSKARQSLNGRKFGG 553

Query: 361 NTVNAFYYPEDKYFNKDY 378
           N V A +YPE+K++  DY
Sbjct: 554 NQVVAVFYPENKFYEGDY 571

Source: Nicotiana plumbaginifolia

Species: Nicotiana plumbaginifolia

Genus: Nicotiana

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  553 bits (1425), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 264/380 (69%), Positives = 302/380 (79%), Gaps = 13/380 (3%)

Query: 1   MAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAI 60
           M  NM P  A Q GA P+MPVQ MTQQATRHARRVYVGGLPP ANEQ++ATFFS VM AI
Sbjct: 186 MFSNMFPVAAGQFGALPVMPVQAMTQQATRHARRVYVGGLPPTANEQSVATFFSHVMYAI 245

Query: 61  GGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPT 120
           GGN+AGPGDAVVNVYINHEKKFAFVEMR+VEEASNAMALDG+IFEG  V+VRRP+DYNP+
Sbjct: 246 GGNTAGPGDAVVNVYINHEKKFAFVEMRSVEEASNAMALDGVIFEGGPVKVRRPSDYNPS 305

Query: 121 LAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLH 180
           LAA LGP QPSPNLNLAAVGL  G+ GG EGPDR+FVGGLPYYFTE+QI+ELLESFG L 
Sbjct: 306 LAATLGPSQPSPNLNLAAVGLTPGSSGGLEGPDRIFVGGLPYYFTESQIRELLESFGQLR 365

Query: 181 GFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQ 240
           GFDLVKDR+TGNSKGY FCVYQD +VTDIACAALNG+KMGDKTLTVRRA     Q   EQ
Sbjct: 366 GFDLVKDRETGNSKGYAFCVYQDVSVTDIACAALNGIKMGDKTLTVRRANQGITQPNPEQ 425

Query: 241 ESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEE 300
           ES+L  AQQ IA+Q+  LQ   + T             K+LCLT+ ++ D L DD++Y++
Sbjct: 426 ESVLLHAQQQIALQRFMLQPGALAT-------------KILCLTQVVSVDELKDDDDYQD 472

Query: 301 ILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGG 360
           ILEDMR ECGK+G L+NVVIPRP+ NG  TPG+GKVFLEY D    + A+  L+GRKFGG
Sbjct: 473 ILEDMRIECGKFGALLNVVIPRPNPNGEPTPGLGKVFLEYADVDSSSKARQGLNGRKFGG 532

Query: 361 NTVNAFYYPEDKYFNKDYSA 380
           N V A +YPE+K+   DY A
Sbjct: 533 NQVIAVFYPENKFSEGDYEA 552

Source: Solanum melongena

Species: Solanum melongena

Genus: Solanum

Family: Solanaceae

Order: Solanales

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	380
TAIR|locus:2206001	589	AT1G60900 [Arabidopsis thalian	0.960	0.619	0.649	4.8e-126
TAIR|locus:2115280	573	ATU2AF65A [Arabidopsis thalian	0.965	0.640	0.619	4.7e-119
UNIPROTKB|Q24JZ8	475	U2AF2 "Uncharacterized protein	0.892	0.713	0.381	5.1e-58
MGI|MGI:98886	475	U2af2 "U2 small nuclear ribonu	0.892	0.713	0.378	2.2e-57
RGD|1597319	475	LOC690372 "similar to U2 (RNU2	0.892	0.713	0.378	2.2e-57
UNIPROTKB|P26368	475	U2AF2 "Splicing factor U2AF 65	0.892	0.713	0.378	2.8e-57
UNIPROTKB|E2R0G3	471	U2AF2 "Uncharacterized protein	0.881	0.711	0.378	1.2e-56
ZFIN|ZDB-GENE-050706-131	470	u2af2a "U2 small nuclear RNA a	0.897	0.725	0.373	8.6e-56
FB|FBgn0005411	416	U2af50 "U2 small nuclear ribop	0.884	0.807	0.377	9.9e-55
ZFIN|ZDB-GENE-040426-1881	475	u2af2b "U2 small nuclear RNA a	0.884	0.707	0.373	1.5e-53

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

 Score = 1238 (440.9 bits), Expect = 4.8e-126, P = 4.8e-126
 Identities = 246/379 (64%), Positives = 280/379 (73%)

Query:     1 MAQNMLPF-GATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTA 59
             M  NM P     QLGA P++PVQ MTQQATRHARRVYVGGLPP ANEQ+++TFFSQVM+A
Sbjct:   222 MFSNMFPMVPGQQLGALPVLPVQAMTQQATRHARRVYVGGLPPTANEQSVSTFFSQVMSA 281

Query:    60 IGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNP 119
             IGGN+AGPGDAVVNVYINHEKKFAFVEMR+VEEASNAMALDGII EGV V+VRRPTDYNP
Sbjct:   282 IGGNTAGPGDAVVNVYINHEKKFAFVEMRSVEEASNAMALDGIILEGVPVKVRRPTDYNP 341

Query:   120 TLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTL 179
             +LAA LGP QP+PNLNL AVGL+SG+ GG EGPDR+FVGGLPYYFTE QI+ELLESFG L
Sbjct:   342 SLAATLGPSQPNPNLNLGAVGLSSGSTGGLEGPDRIFVGGLPYYFTEVQIRELLESFGPL 401

Query:   180 HGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTE 239
              GF+LVKDR+TGNSKGY FCVYQDP+VTDIACAALNG+KMGDKTLTVRRA   + Q K E
Sbjct:   402 RGFNLVKDRETGNSKGYAFCVYQDPSVTDIACAALNGIKMGDKTLTVRRAIQGAIQPKPE 461

Query:   240 QESXXXXXXXXXXXXKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITXXXXXXXXXXX 299
             QE             ++  Q  G  T             K++CLT+ +T           
Sbjct:   462 QEEVLLYAQQQIALQRLMFQPGGTPT-------------KIVCLTQVVTADDLRDDEEYA 508

Query:   300 XXXXXXXXXCGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFG 359
                       GK+G LVNVVIPRP+ +   TPGVGKVFLEY D  G + A++ ++GRKFG
Sbjct:   509 EIMEDMRQEGGKFGNLVNVVIPRPNPDHDPTPGVGKVFLEYADVDGSSKARSGMNGRKFG 568

Query:   360 GNTVNAFYYPEDKYFNKDY 378
             GN V A YYPEDKY   DY
Sbjct:   569 GNQVVAVYYPEDKYAQGDY 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 = 1172 (417.6 bits), Expect = 4.7e-119, P = 4.7e-119
 Identities = 236/381 (61%), Positives = 270/381 (70%)

Query:     1 MAQNMLPFGATQ-LGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTA 59
             M  NM P    Q  G   +MP+Q MTQQATRHARRVYVGGL P ANEQ++ATFFSQVM A
Sbjct:   206 MFPNMFPLPTGQSFGGLSMMPIQAMTQQATRHARRVYVGGLSPTANEQSVATFFSQVMAA 265

Query:    60 IGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNP 119
             +GGN+AGPGDAVVNVYINHEKKFAFVEMR+VEEASNAM+LDGIIFEG  V+VRRP+DYNP
Sbjct:   266 VGGNTAGPGDAVVNVYINHEKKFAFVEMRSVEEASNAMSLDGIIFEGAPVKVRRPSDYNP 325

Query:   120 TLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTL 179
             +LAA LGP QPSP+LNLAAVGL  GA GG EGPDR+FVGGLPYYFTE+Q++ELLESFG L
Sbjct:   326 SLAATLGPSQPSPHLNLAAVGLTPGASGGLEGPDRIFVGGLPYYFTESQVRELLESFGGL 385

Query:   180 HGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTE 239
              GFDLVKDR+TGNSKGY FCVYQD +VTDIACAALNG+KMGDKTLTVRRA   +   K E
Sbjct:   386 KGFDLVKDRETGNSKGYAFCVYQDLSVTDIACAALNGIKMGDKTLTVRRANQGTMLQKPE 445

Query:   240 QESXXXXXXXXXXXXKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITXXXXXXXXXXX 299
             QE+            ++ LQ   + T              V+CLT+ +T           
Sbjct:   446 QENVLLHAQQQIAFQRVMLQPGAVATT-------------VVCLTQVVTEDELRDDEEYG 492

Query:   300 XXXXXXXXXCGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFG 359
                       GK+G L NVVIPRP  NG    G+GKVFL+Y D  G   A+  ++GRKFG
Sbjct:   493 DIMEDMRQEGGKFGALTNVVIPRPSPNGEPVAGLGKVFLKYADTDGSTRARFGMNGRKFG 552

Query:   360 GNTVNAFYYPEDKYFNKDYSA 380
             GN V A YYPEDK+   DY A
Sbjct:   553 GNEVVAVYYPEDKFEQGDYGA 573

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISM;IEA

GO:0006397 "mRNA processing" evidence=IEA

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

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

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

 Score = 596 (214.9 bits), Expect = 5.1e-58, P = 5.1e-58
 Identities = 137/359 (38%), Positives = 193/359 (53%)

Query:    20 PVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE 79
             PV V+  Q TR ARR+YVG +P    E+A+  FF+  M  +GG +  PG+ V+ V IN +
Sbjct:   136 PVPVVGSQMTRQARRLYVGNIPFGITEEAMMDFFNAQMR-LGGLTQAPGNPVLAVQINQD 194

Query:    80 KKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAV 139
             K FAF+E R+V+E + AMA DGIIF+G ++++RRP DY P       PG  S N ++   
Sbjct:   195 KNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPL------PGM-SENPSVYVP 247

Query:   140 GLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC 199
             G+ S  +   +   ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG SKGY FC
Sbjct:   248 GVVSTVV--PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFC 305

Query:   200 VYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESXXXXXXXXXXXXKMALQ 259
              Y D  VTD A A LNG+++GDK L V+RA+  +      + +             + LQ
Sbjct:   306 EYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA------KNATLVSPLSTINQTPVTLQ 359

Query:   260 TSGMNTLGGGMSLFGETLAKVLCLTEAITXXXXXXXXXXXXXXXXXXXXCGKYGTLVNVV 319
               G+  +   + + G    +VLCL   +                     CGKYG + ++ 
Sbjct:   360 VPGL--MSSQVQMGGHP-TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECGKYGLVKSIE 416

Query:   320 IPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 378
             IPRP  +G E PG GK+F+E+     C  A   L+GRKF    V   Y   D Y  +D+
Sbjct:   417 IPRP-VDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHRRDF 474

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

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

GO:0019899 "enzyme binding" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

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

 Score = 590 (212.7 bits), Expect = 2.2e-57, P = 2.2e-57
 Identities = 136/359 (37%), Positives = 192/359 (53%)

Query:    20 PVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE 79
             PV V+  Q TR ARR+YVG +P    E+A+  FF+  M  +GG +  PG+ V+ V IN +
Sbjct:   136 PVPVVGSQMTRQARRLYVGNIPFGITEEAMMDFFNAQMR-LGGLTQAPGNPVLAVQINQD 194

Query:    80 KKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAV 139
             K FAF+E R+V+E + AMA DGIIF+G ++++RRP DY P       PG  S N ++   
Sbjct:   195 KNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPL------PGM-SENPSVYVP 247

Query:   140 GLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC 199
             G+ S  +   +   ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG SKGY FC
Sbjct:   248 GVVSTVV--PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFC 305

Query:   200 VYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESXXXXXXXXXXXXKMALQ 259
              Y D  VTD A A LNG+++GDK L V+RA+  +      + +             + LQ
Sbjct:   306 EYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA------KNATLVSLPSTINQTPVTLQ 359

Query:   260 TSGMNTLGGGMSLFGETLAKVLCLTEAITXXXXXXXXXXXXXXXXXXXXCGKYGTLVNVV 319
               G+  +   + + G    +VLCL   +                     C KYG + ++ 
Sbjct:   360 VPGL--MSSQVQMGGHP-TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIE 416

Query:   320 IPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 378
             IPRP  +G E PG GK+F+E+     C  A   L+GRKF    V   Y   D Y  +D+
Sbjct:   417 IPRP-VDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHRRDF 474

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=ISO

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IDA

GO:0016607 "nuclear speck" evidence=TAS

GO:0019899 "enzyme binding" evidence=ISO

GO:0030529 "ribonucleoprotein complex" evidence=IEA

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

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

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

 Score = 590 (212.7 bits), Expect = 2.2e-57, P = 2.2e-57
 Identities = 136/359 (37%), Positives = 192/359 (53%)

Query:    20 PVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE 79
             PV V+  Q TR ARR+YVG +P    E+A+  FF+  M  +GG +  PG+ V+ V IN +
Sbjct:   136 PVPVVGSQMTRQARRLYVGNIPFGITEEAMMDFFNAQMR-LGGLTQAPGNPVLAVQINQD 194

Query:    80 KKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAV 139
             K FAF+E R+V+E + AMA DGIIF+G ++++RRP DY P       PG  S N ++   
Sbjct:   195 KNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPL------PGM-SENPSVYVP 247

Query:   140 GLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC 199
             G+ S  +   +   ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG SKGY FC
Sbjct:   248 GVVSTVV--PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFC 305

Query:   200 VYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESXXXXXXXXXXXXKMALQ 259
              Y D  VTD A A LNG+++GDK L V+RA+  +      + +             + LQ
Sbjct:   306 EYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA------KNATLVSLPSTINQTPVTLQ 359

Query:   260 TSGMNTLGGGMSLFGETLAKVLCLTEAITXXXXXXXXXXXXXXXXXXXXCGKYGTLVNVV 319
               G+  +   + + G    +VLCL   +                     C KYG + ++ 
Sbjct:   360 VPGL--MSSQVQMGGHP-TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIE 416

Query:   320 IPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 378
             IPRP  +G E PG GK+F+E+     C  A   L+GRKF    V   Y   D Y  +D+
Sbjct:   417 IPRP-VDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHRRDF 474

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0019899 "enzyme binding" evidence=IEA

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

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

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

 Score = 589 (212.4 bits), Expect = 2.8e-57, P = 2.8e-57
 Identities = 136/359 (37%), Positives = 192/359 (53%)

Query:    20 PVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE 79
             PV V+  Q TR ARR+YVG +P    E+A+  FF+  M  +GG +  PG+ V+ V IN +
Sbjct:   136 PVPVVGSQMTRQARRLYVGNIPFGITEEAMMDFFNAQMR-LGGLTQAPGNPVLAVQINQD 194

Query:    80 KKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAV 139
             K FAF+E R+V+E + AMA DGIIF+G ++++RRP DY P       PG  S N ++   
Sbjct:   195 KNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPL------PGM-SENPSVYVP 247

Query:   140 GLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC 199
             G+ S  +   +   ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG SKGY FC
Sbjct:   248 GVVSTVV--PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFC 305

Query:   200 VYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESXXXXXXXXXXXXKMALQ 259
              Y D  VTD A A LNG+++GDK L V+RA+  +      + +             + LQ
Sbjct:   306 EYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA------KNATLVSPPSTINQTPVTLQ 359

Query:   260 TSGMNTLGGGMSLFGETLAKVLCLTEAITXXXXXXXXXXXXXXXXXXXXCGKYGTLVNVV 319
               G+  +   + + G    +VLCL   +                     C KYG + ++ 
Sbjct:   360 VPGL--MSSQVQMGGHP-TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIE 416

Query:   320 IPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 378
             IPRP  +G E PG GK+F+E+     C  A   L+GRKF    V   Y   D Y  +D+
Sbjct:   417 IPRP-VDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHRRDF 474

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

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

GO:0005515 "protein binding" evidence=IPI

GO:0019899 "enzyme binding" evidence=IPI

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

GO:0006397 "mRNA processing" evidence=TAS

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

GO:0005681 "spliceosomal complex" evidence=IDA

GO:0005654 "nucleoplasm" evidence=TAS

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

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

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

GO:0008380 "RNA splicing" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

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

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

 Score = 583 (210.3 bits), Expect = 1.2e-56, P = 1.2e-56
 Identities = 136/359 (37%), Positives = 191/359 (53%)

Query:    20 PVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE 79
             PV V+  Q TR ARR+YVG +P    E+A+  FF+  M  +GG +  PG+ V+ V IN +
Sbjct:   136 PVPVVGSQMTRQARRLYVGNIPFGITEEAMMDFFNAQMR-LGGLTQAPGNPVLAVQINQD 194

Query:    80 KKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAV 139
             K FAF+E R+V+E + AMA DGIIF+G ++++RRP DY P       PG  S N ++   
Sbjct:   195 KNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPL------PGM-SENPSVYVP 247

Query:   140 GLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC 199
             G+ S  +   +   ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG SKGY FC
Sbjct:   248 GVVSTVV--PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFC 305

Query:   200 VYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESXXXXXXXXXXXXKMALQ 259
              Y D  VTD A A LNG+++GDK L V+RA+  +  +                   + LQ
Sbjct:   306 EYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAKNA----------TLSTINQTPVTLQ 355

Query:   260 TSGMNTLGGGMSLFGETLAKVLCLTEAITXXXXXXXXXXXXXXXXXXXXCGKYGTLVNVV 319
               G+  +   + + G    +VLCL   +                     C KYG + ++ 
Sbjct:   356 VPGL--MSSQVQMGGHP-TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIE 412

Query:   320 IPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 378
             IPRP  +G E PG GK+F+E+     C  A   L+GRKF    V   Y   D Y  +D+
Sbjct:   413 IPRP-VDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHRRDF 470

GO:0006397 "mRNA processing" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

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

 Score = 575 (207.5 bits), Expect = 8.6e-56, P = 8.6e-56
 Identities = 134/359 (37%), Positives = 190/359 (52%)

Query:    20 PVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE 79
             PV V+  Q TR ARR+YVG +P    E+++  FF+  M  +GG +  PG+ V+ V IN +
Sbjct:   129 PVPVVGSQMTRQARRLYVGNIPFGITEESMMDFFNAQMR-LGGLTQAPGNPVLAVQINQD 187

Query:    80 KKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAV 139
             K FAF+E R+V+E + AMA DGIIF+G ++++RRP DY P    +  P    P  +L  V
Sbjct:   188 KNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPG-SLP-V 245

Query:   140 GLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC 199
             G+ S  +   +   ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG SKGY FC
Sbjct:   246 GVVSTVV--PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFC 303

Query:   200 VYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESXXXXXXXXXXXXKMALQ 259
              Y D  ++D A A LNG+++GDK L V+RA  S G   T                 + LQ
Sbjct:   304 EYVDVNISDQAIAGLNGMQLGDKKLLVQRA--SVGSKNT--------TLTGINQTPVTLQ 353

Query:   260 TSGMNTLGGGMSLFGETLAKVLCLTEAITXXXXXXXXXXXXXXXXXXXXCGKYGTLVNVV 319
               G+  +   ++  G    +VLCL   +                     C KYG + ++ 
Sbjct:   354 VPGL--MNSSVNQMGGIPTEVLCLMNMVAPEELLDDEEYEEIVEDVRDECSKYGQVKSIE 411

Query:   320 IPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 378
             IPRP  +G + PG GK+F+E+        A   L+GRKF    V   Y   D Y  +D+
Sbjct:   412 IPRP-VDGLDIPGTGKIFVEFMSVFDSQKAMQGLTGRKFANRVVVTKYCDPDAYHRRDF 469

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0046660 "female sex differentiation" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

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

 Score = 565 (203.9 bits), Expect = 9.9e-55, P = 9.9e-55
 Identities = 138/366 (37%), Positives = 194/366 (53%)

Query:    17 PLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI 76
             P   V V+    TR ARR+YVG +P    E+ +  FF+Q M  +G   A  G  V+   I
Sbjct:    77 PQTAVPVVGSTITRQARRLYVGNIPFGVTEEEMMEFFNQQMHLVGLAQAA-GSPVLACQI 135

Query:    77 NHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPG-QPSPNLN 135
             N +K FAF+E R+++E + AMA DGI  +G ++++RRP DY P       PG   +P + 
Sbjct:   136 NLDKNFAFLEFRSIDETTQAMAFDGINLKGQSLKIRRPHDYQPM------PGITDTPAIK 189

Query:   136 LAAVGLASGAIGGA--EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNS 193
              A V  +SG I     + P ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG S
Sbjct:   190 PAVV--SSGVISTVVPDSPHKIFIGGLPNYLNDDQVKELLLSFGKLRAFNLVKDAATGLS 247

Query:   194 KGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESXXXXXXXXXXX 253
             KGY FC Y D ++TD + A LNG+++GDK L V+RA+  +   K  Q +           
Sbjct:   248 KGYAFCEYVDLSITDQSIAGLNGMQLGDKKLIVQRASVGA---KNAQNAANTTQS----- 299

Query:   254 XKMALQTSGM-NTLGGGMSLFGETLAKVLCLTEAITXXXXXXXXXXXXXXXXXXXXCGKY 312
               + LQ  G+ N +  G         +VLCL   +T                    C KY
Sbjct:   300 --VMLQVPGLSNVVTSGPP------TEVLCLLNMVTPDELRDEEEYEDILEDIKEECTKY 351

Query:   313 GTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK 372
             G + +V IPRP + G E PG GKVF+E+   + C  A+ AL+GRKF    V   Y+  DK
Sbjct:   352 GVVRSVEIPRPIE-GVEVPGCGKVFVEFNSVLDCQKAQQALTGRKFSDRVVVTSYFDPDK 410

Query:   373 YFNKDY 378
             Y  +++
Sbjct:   411 YHRREF 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-040426-1881 u2af2b "U2 small nuclear RNA auxiliary factor 2b" [Danio rerio (taxid:7955)]

 Score = 554 (200.1 bits), Expect = 1.5e-53, P = 1.5e-53
 Identities = 134/359 (37%), Positives = 186/359 (51%)

Query:    20 PVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE 79
             PV V+  Q TR ARR+YVG +P    E+++  FF+  M  +GG +  PG+ V+ V IN +
Sbjct:   139 PVPVVGSQMTRQARRLYVGNIPFGITEESMMDFFNAQMR-LGGLTQAPGNPVLAVQINQD 197

Query:    80 KKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAV 139
             K FAF+E R+V+E + AMA DGIIF+  ++++RRP DY P       PG  S N ++   
Sbjct:   198 KNFAFLEFRSVDETTQAMAFDGIIFQAQSLKIRRPHDYQPL------PGM-SENPSVYVP 250

Query:   140 GLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC 199
             G+ S  +   +   ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG SKGY FC
Sbjct:   251 GVVSTVV--PDSIHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFC 308

Query:   200 VYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESXXXXXXXXXXXXKMALQ 259
              Y D  V D A A LNG+++ DK L V+RA  S G       S             + LQ
Sbjct:   309 EYVDVNVNDQAIAGLNGMQLADKKLLVQRA--SVGAKNATMTSINET--------PVTLQ 358

Query:   260 TSGMNTLGGGMSLFGETLAKVLCLTEAITXXXXXXXXXXXXXXXXXXXXCGKYGTLVNVV 319
               G+ +    M   G    +VLCL   +                     C KYG + ++ 
Sbjct:   359 VPGLTS--NPMIQMGGIPTEVLCLMNMVAPEELIDDEEYEEIVEDVKEECSKYGQVKSIE 416

Query:   320 IPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 378
             IPRP  +G + PG GK+F+E+        A   L+GRKF    V   Y   D Y  +D+
Sbjct:   417 IPRP-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)
Q24562	U2AF2_DROME	No assigned EC number	0.4098	0.8842	0.8076	yes	no
Q2QZL4	U2A2B_ORYSJ	No assigned EC number	0.6815	0.9631	0.6678	yes	no
Q9ZR39	U2A2A_NICPL	No assigned EC number	0.7029	0.9578	0.6558	N/A	no
Q8L716	U2A2B_ARATH	No assigned EC number	0.7071	0.9605	0.6196	yes	no
Q9ZR40	U2A2B_NICPL	No assigned EC number	0.7010	0.9605	0.6369	N/A	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	380
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	1e-165
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	3e-41
cd12230	82	cd12230, RRM1_U2AF65, RNA recognition motif 1 foun	4e-40
cd12232	89	cd12232, RRM3_U2AF65, RNA recognition motif 3 foun	2e-37
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	9e-26
cd12465	88	cd12465, RRM_UHMK1, RNA recognition motif found in	1e-19
smart00360	73	smart00360, RRM, RNA recognition motif	1e-18
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	2e-16
cd12374	85	cd12374, RRM_UHM_SPF45_PUF60, RNA recognition moti	7e-16
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	1e-15
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	2e-15
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	2e-15
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	2e-14
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	3e-14
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	4e-14
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	1e-13
cd12648	98	cd12648, RRM3_UHM_PUF60, RNA recognition motif 3 i	4e-13
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	8e-13
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	1e-12
cd12285	85	cd12285, RRM3_RBM39_like, RNA recognition motif 3	6e-12
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	7e-12
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	7e-12
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	8e-12
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	8e-12
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	8e-12
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	1e-11
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	4e-11
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	6e-11
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	9e-11
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	9e-11
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	1e-10
cd12647	96	cd12647, RRM_UHM_SPF45, RNA recognition motif in U	2e-10
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	2e-10
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	3e-10
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	4e-10
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	5e-10
smart00360	73	smart00360, RRM, RNA recognition motif	8e-10
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
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	3e-09
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	4e-09
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	4e-09
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	4e-09
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	4e-09
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	4e-09
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	8e-09
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	9e-09
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	1e-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
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	3e-08
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	3e-08
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	3e-08
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	6e-08
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	8e-08
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	8e-08
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	1e-07
cd12282	91	cd12282, RRM2_TatSF1_like, RNA recognition motif 2	1e-07
cd12666	77	cd12666, RRM2_RAVER2, RNA recognition motif 2 in v	1e-07
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	2e-07
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	2e-07
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	2e-07
cd12665	77	cd12665, RRM2_RAVER1, RNA recognition motif 2 foun	2e-07
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	2e-07
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	2e-07
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	4e-07
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	4e-07
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	4e-07
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	5e-07
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	5e-07
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	6e-07
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	6e-07
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	6e-07
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	6e-07
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	8e-07
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	1e-06
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	1e-06
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	2e-06
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	2e-06
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	2e-06
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	2e-06
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	3e-06
cd12661	77	cd12661, RRM3_hnRNPM, RNA recognition motif 3 in v	3e-06
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	4e-06
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	4e-06
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	5e-06
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	5e-06
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	5e-06
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	6e-06
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	7e-06
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	7e-06
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	8e-06
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	8e-06
smart00360	73	smart00360, RRM, RNA recognition motif	9e-06
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	9e-06
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	9e-06
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	9e-06
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	1e-05
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	1e-05
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	1e-05
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	1e-05
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	1e-05
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	1e-05
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	1e-05
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	1e-05
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	1e-05
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	2e-05
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	2e-05
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	2e-05
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	2e-05
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	2e-05
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	3e-05
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	3e-05
cd12287	102	cd12287, RRM_U2AF35_like, RNA recognition motif in	3e-05
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	3e-05
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	3e-05
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	3e-05
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	3e-05
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	3e-05
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	4e-05
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	4e-05
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	4e-05
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	4e-05
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	4e-05
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	4e-05
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	4e-05
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	5e-05
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	5e-05
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	5e-05
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	6e-05
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	7e-05
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	7e-05
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	7e-05
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	8e-05
cd12631	84	cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif	9e-05
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	1e-04
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	1e-04
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	1e-04
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	1e-04
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	1e-04
cd12587	71	cd12587, RRM1_PSF, RNA recognition motif 1 in vert	1e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-04
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	1e-04
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	1e-04
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	1e-04
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	2e-04
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	2e-04
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	2e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-04
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	2e-04
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	2e-04
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	2e-04
cd12368	75	cd12368, RRM3_RBM45, RNA recognition motif 3 in RN	2e-04
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	2e-04
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	2e-04
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	2e-04
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	2e-04
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	2e-04
cd12291	72	cd12291, RRM1_La, RNA recognition motif 1 in La au	2e-04
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	3e-04
cd12385	76	cd12385, RRM1_hnRNPM_like, RNA recognition motif 1	3e-04
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	3e-04
cd12662	77	cd12662, RRM3_MYEF2, RNA recognition motif 3 in ve	3e-04
cd12439	79	cd12439, RRM_TRMT2A, RNA recognition motif in tRNA	3e-04
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	3e-04
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	4e-04
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	4e-04
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	5e-04
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	5e-04
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	5e-04
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	6e-04
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	7e-04
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	7e-04
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	8e-04
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	8e-04
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	9e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	0.001
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	0.001
cd12584	80	cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in	0.001
cd12279	74	cd12279, RRM_TUT1, RNA recognition motif in speckl	0.001
cd12610	84	cd12610, RRM1_SECp43, RNA recognition motif 1 in t	0.001
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	0.001
cd12596	70	cd12596, RRM1_SRSF6, RNA recognition motif 1 in ve	0.001
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	0.002
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	0.002
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	0.002
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	0.002
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	0.002
cd12534	83	cd12534, RRM_SARFH, RNA recognition motif in Droso	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
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	0.002
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	0.002
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	0.002
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	0.002
cd12595	70	cd12595, RRM1_SRSF5, RNA recognition motif 1 in ve	0.003
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	0.003
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	0.003
cd12594	74	cd12594, RRM1_SRSF4, RNA recognition motif 1 in ve	0.003
cd12487	78	cd12487, RRM1_DND1, RNA recognition motif 1 found	0.003
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	0.003
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	0.004
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	0.004
cd12598	72	cd12598, RRM1_SRSF9, RNA recognition motif 1 in ve	0.004
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	0.004
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	0.004
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	0.004

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

 Score =  471 bits (1214), Expect = e-165
 Identities = 166/361 (45%), Positives = 212/361 (58%), Gaps = 14/361 (3%)

Query: 19  MPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH 78
           +PV    QQATR ARR+YVGG+PP   E+A+  FF+ +M A G + A  G  V +V IN 
Sbjct: 162 LPVLPYQQQATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNINK 221

Query: 79  EKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAA 138
           EK FAF+E RTVEEA+ AMALD II+  V +++RRP DY P         Q +P+ N   
Sbjct: 222 EKNFAFLEFRTVEEATFAMALDSIIYSNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKN 281

Query: 139 VGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGF 198
           V     +    +  DR+++G LP Y  E QIKELLESFG L  F+L+KD  TG SKGY F
Sbjct: 282 VEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAF 341

Query: 199 CVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQ-AQQHIAIQKMA 257
           C Y+DP+VTD+A AALNG   GD  L V+RA   + Q+  +  + +A       A+ +  
Sbjct: 342 CEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVGANQATIDTSNGMAPVTLLAKALSQSI 401

Query: 258 LQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVN 317
           LQ              G    KV+ LT  +T D L DDEEYEEI ED++ E  KYG L+N
Sbjct: 402 LQI-------------GGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLIN 448

Query: 318 VVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKD 377
           +VIPRP+ +   TPGVGKVFLEY D      A   ++GRKF    V A +Y ED Y   D
Sbjct: 449 IVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKFNDRVVVAAFYGEDCYKAGD 508

Query: 378 Y 378
           Y
Sbjct: 509 Y 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 =  139 bits (353), Expect = 3e-41
 Identities = 49/77 (63%), Positives = 61/77 (79%)

Query: 153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA 212
           +++F+GGLP Y +E Q+KELLESFG L  F+LVKD  TG SKGY FC Y DP+VTD A A
Sbjct: 1   NKIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIA 60

Query: 213 ALNGLKMGDKTLTVRRA 229
            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 =  136 bits (346), Expect = 4e-40
 Identities = 48/83 (57%), Positives = 61/83 (73%), Gaps = 1/83 (1%)

Query: 32  ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 91
           ARR+YVG LPP   E+ +  FF+Q M A G N   PG+ V++V IN EK FAFVE RTVE
Sbjct: 1   ARRLYVGNLPPGITEEELVDFFNQAMLAAGLN-QAPGNPVLSVQINPEKNFAFVEFRTVE 59

Query: 92  EASNAMALDGIIFEGVAVRVRRP 114
           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 =  129 bits (328), Expect = 2e-37
 Identities = 50/85 (58%), Positives = 64/85 (75%)

Query: 279 KVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFL 338
           +VLCL   +T + L DDEEYEEILED++EECGKYG +++VVIPRP+  G + PGVGKVF+
Sbjct: 2   RVLCLLNMVTPEELEDDEEYEEILEDVKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFV 61

Query: 339 EYYDAVGCATAKNALSGRKFGGNTV 363
           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 =  107 bits (269), Expect = 9e-26
 Identities = 95/412 (23%), Positives = 148/412 (35%), Gaps = 93/412 (22%)

Query: 20  PVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI--- 76
             + +T+ A R  R V+V  L   A E+ +  FFS+V         G    V +V     
Sbjct: 78  TKEPLTE-AERDDRTVFVLQLALKARERDLYEFFSKV---------GK---VRDVQCIKD 124

Query: 77  ---NHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPN 133
                 K  A+VE   VE    A+AL G +  G  + V+  +      AA     QP   
Sbjct: 125 RNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPIIVQ-SSQAEKNRAAKAATHQP--- 180

Query: 134 LNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNS 193
                        G      +++VG L +  TE +++++ E FG +    L +D +TG S
Sbjct: 181 -------------GDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRS 227

Query: 194 KGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKT--EQESILAQAQQHI 251
           KG+GF  + D      A   +NG ++  + + V  A  S+         E I  Q Q   
Sbjct: 228 KGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQDSTYLLDAANTFEDIDKQQQMGK 287

Query: 252 AI----------------QKMALQTSGMNTLGGGMSLFGE-----TLAKVLCLTEAITAD 290
            +                    L   G  +    M                  T A+   
Sbjct: 288 NLNTEEREQLMEKLDRDDGDGGLLIPGTGSKIALMQKLQRDGIIDPNIPSRYATGALAIM 347

Query: 291 AL------------------------ADDEE---YEEILEDMREECGKYGTLVNVVIPRP 323
           A                         A +EE     EIL+D++EEC KYG +V++ +   
Sbjct: 348 ARNSFVPSTNNNLATTCLVLSNMFDPATEEEPNFDNEILDDVKEECSKYGGVVHIYVDTK 407

Query: 324 DQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFN 375
           +         GK++L++        A  AL+GR FGG  + A +   D Y  
Sbjct: 408 NSA-------GKIYLKFSSVDAALAAFQALNGRYFGGKMITAAFVVNDVYDM 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 = 82.3 bits (203), Expect = 1e-19
 Identities = 39/90 (43%), Positives = 57/90 (63%), Gaps = 6/90 (6%)

Query: 280 VLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLE 339
           VL L   +    L ++EEYE+I+ED++EEC KYG +V+++IP+      E PG G+VF+E
Sbjct: 5   VLRLLNVLDDAHLQNEEEYEDIIEDIKEECQKYGPVVSLLIPK------ENPGKGQVFVE 58

Query: 340 YYDAVGCATAKNALSGRKFGGNTVNAFYYP 369
           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 = 79.2 bits (196), Expect = 1e-18
 Identities = 27/73 (36%), Positives = 42/73 (57%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
            +FVG LP   TE +++EL   FG +    LV+D++TG SKG+ F  ++     + A  A
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 214 LNGLKMGDKTLTV 226
           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 = 72.7 bits (179), Expect = 2e-16
 Identities = 32/72 (44%), Positives = 40/72 (55%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           VFVG +PY  TE Q+ E+    G +  F LV DRDTG  KGYGFC ++D      A   L
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60

Query: 215 NGLKMGDKTLTV 226
           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 = 7e-16
 Identities = 30/91 (32%), Positives = 48/91 (52%), Gaps = 7/91 (7%)

Query: 279 KVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFL 338
           K+L L   +T       E  E++ +++ EEC KYG ++NV++     +      V ++F+
Sbjct: 2   KILVLRNMVTPG-----EIDEDLKDEIEEECEKYGKVLNVIV-HEVASSEADDAV-RIFV 54

Query: 339 EYYDAVGCATAKNALSGRKFGGNTVNAFYYP 369
           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 = 1e-15
 Identities = 27/73 (36%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           +FVG LP   TE  ++EL   FG +    +V+D+D G SKG+ F  ++ P   + A  AL
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKD-GKSKGFAFVEFESPEDAEKALEAL 59

Query: 215 NGLKMGDKTLTVR 227
           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 = 70.2 bits (172), Expect = 2e-15
 Identities = 33/75 (44%), Positives = 43/75 (57%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           VFVG +PY  TE Q+K++    G +  F LV DR+TG  KGYGFC Y+D      A   L
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 215 NGLKMGDKTLTVRRA 229
           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|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General function prediction only]

 Score = 76.1 bits (186), Expect = 2e-15
 Identities = 33/111 (29%), Positives = 56/111 (50%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
            +FVG LPY  TE  ++EL + FG +    LV+DR+TG S+G+ F  ++     + A   
Sbjct: 117 TLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEE 176

Query: 214 LNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMN 264
           LNG ++  + L V++A  +S        ++ A   + ++  K  L     N
Sbjct: 177 LNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDN 227

Length = 306

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

 Score = 67.7 bits (166), Expect = 2e-14
 Identities = 28/72 (38%), Positives = 44/72 (61%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           +++GGLPY  TE  I  +   +G +   +LV+D+ TG SKG+ F  Y+D   T +A   L
Sbjct: 12  IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71

Query: 215 NGLKMGDKTLTV 226
           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|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins

 Score = 67.3 bits (165), Expect = 3e-14
 Identities = 29/76 (38%), Positives = 42/76 (55%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
            ++VG LPY  TE  +K+L   FG +    ++ DR+TG S+G+GF   +     + A   
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 214 LNGLKMGDKTLTVRRA 229
           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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 66.5 bits (163), Expect = 4e-14
 Identities = 27/71 (38%), Positives = 40/71 (56%), Gaps = 1/71 (1%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           +FVG LP   TE  +K+L   FG +    +V+D  TG SKG+ F  ++D    + A  AL
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDE-TGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 215 NGLKMGDKTLT 225
           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|240753 cd12307, RRM_NIFK_like, RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) and similar proteins

 Score = 64.9 bits (159), Expect = 1e-13
 Identities = 22/73 (30%), Positives = 39/73 (53%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           V++G LP+ F E ++++    FGT+    L + + TG SKGY F  ++ P V  I    +
Sbjct: 2   VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETM 61

Query: 215 NGLKMGDKTLTVR 227
           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 = 64.3 bits (157), Expect = 4e-13
 Identities = 27/82 (32%), Positives = 43/82 (52%), Gaps = 1/82 (1%)

Query: 299 EEILEDMREECGKYGTLVNVVIPRPDQNGGETPGV-GKVFLEYYDAVGCATAKNALSGRK 357
           +++  ++ EECGK+G +  V+I +  Q   E   +  K+F+E+        A  AL+GR 
Sbjct: 17  DDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSLPSEAEKAIQALNGRW 76

Query: 358 FGGNTVNAFYYPEDKYFNKDYS 379
           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 = 62.9 bits (153), Expect = 8e-13
 Identities = 25/73 (34%), Positives = 41/73 (56%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           +++G LP+ F E ++K+    FGT+    + + + TGNSK YGF  + +P V  IA  ++
Sbjct: 2   IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61

Query: 215 NGLKMGDKTLTVR 227
           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 = 62.7 bits (153), Expect = 1e-12
 Identities = 25/67 (37%), Positives = 36/67 (53%)

Query: 160 LPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM 219
           LP   T+ +++ L E+ G +    +V+DR TG S GYGF  Y D      A   LNG ++
Sbjct: 8   LPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNGFEI 67

Query: 220 GDKTLTV 226
            +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 = 60.6 bits (148), Expect = 6e-12
 Identities = 21/82 (25%), Positives = 36/82 (43%), Gaps = 7/82 (8%)

Query: 288 TADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCA 347
                 +DE  +EI ED+ EEC K+G + ++ +        +    G V++++       
Sbjct: 11  DPAEETEDEWDDEIKEDVLEECSKFGPVEHIKVD-------KNSPEGVVYVKFKTVEAAQ 63

Query: 348 TAKNALSGRKFGGNTVNAFYYP 369
               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|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General function prediction only]

 Score = 65.4 bits (158), Expect = 7e-12
 Identities = 40/187 (21%), Positives = 69/187 (36%), Gaps = 24/187 (12%)

Query: 19  MPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH 78
                  Q++      ++VG LP    E+ +   F +               V  V +  
Sbjct: 102 SESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGP------------VKRVRLVR 149

Query: 79  EKK------FAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPS 131
           +++      FAFVE  + E A  A+  L+G   EG  +RV++    +   +        +
Sbjct: 150 DRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQPRSEL-----SN 204

Query: 132 PNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTG 191
                 A  L+ G     E  D ++VG LP    E ++ +L +S G +    L   +D  
Sbjct: 205 NLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGK 264

Query: 192 NSKGYGF 198
             K   F
Sbjct: 265 IPKSRSF 271

Length = 306

>gnl|CDD|240835 cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 60.4 bits (147), Expect = 7e-12
 Identities = 30/75 (40%), Positives = 38/75 (50%)

Query: 156 FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN 215
            VG LP  FT+ Q +EL+  FG +    LV    TG SKGYGF  Y   A    A   L+
Sbjct: 3   CVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQLD 62

Query: 216 GLKMGDKTLTVRRAT 230
           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|241094 cd12650, RRM1_Hu, RNA recognition motif 1 in the Hu proteins family

 Score = 60.1 bits (146), Expect = 8e-12
 Identities = 28/70 (40%), Positives = 40/70 (57%)

Query: 160 LPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM 219
           LP   T+ +I+ L  S G +    L++D+ TG S GYGF  Y DP   + A   LNGL++
Sbjct: 9   LPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTLNGLRL 68

Query: 220 GDKTLTVRRA 229
            +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|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate Hu-antigen C (HuC)

 Score = 60.5 bits (146), Expect = 8e-12
 Identities = 34/79 (43%), Positives = 42/79 (53%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           + V  LP   T+ + K L  S G +    LV+D+ TG S GYGF  Y DP   D A   L
Sbjct: 6   LIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINTL 65

Query: 215 NGLKMGDKTLTVRRATASS 233
           NGLK+  KT+ V  A  SS
Sbjct: 66  NGLKLQTKTIKVSYARPSS 84

This subgroup corresponds to the RRM1 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 84

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

 Score = 60.3 bits (147), Expect = 8e-12
 Identities = 30/73 (41%), Positives = 42/73 (57%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
            VFVG +P   ++  I++LLE  G +  +  VKD  TG  K +GFC ++DP     A   
Sbjct: 2   TVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALRL 61

Query: 214 LNGLKMGDKTLTV 226
           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 = 1e-11
 Identities = 26/76 (34%), Positives = 41/76 (53%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           R++V  +    +E  IK + E+FG +    L  D +TG  KGYGF  Y++P     A A+
Sbjct: 2   RIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIAS 61

Query: 214 LNGLKMGDKTLTVRRA 229
           +N   +G + L V +A
Sbjct: 62  MNLFDLGGQQLRVGKA 77

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

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

 Score = 58.2 bits (141), Expect = 4e-11
 Identities = 28/76 (36%), Positives = 44/76 (57%), Gaps = 1/76 (1%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           ++FVGGLP   TE + KE    FG +    L++D DTG S+G+GF  +   +  +   +A
Sbjct: 1   KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSA 60

Query: 214 LNGLKMGDKTLTVRRA 229
              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|240858 cd12412, RRM_DAZL_BOULE, RNA recognition motif in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE

 Score = 57.7 bits (140), Expect = 6e-11
 Identities = 26/78 (33%), Positives = 41/78 (52%), Gaps = 2/78 (2%)

Query: 152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 211
           P+R+FVGG+P   TE ++++    FG++    ++ DR  G SKGYGF  ++     +   
Sbjct: 2   PNRIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRA-GVSKGYGFVTFETQEDAEKIL 60

Query: 212 AALNGLKMGDKTLTVRRA 229
           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 = 57.2 bits (139), Expect = 9e-11
 Identities = 25/79 (31%), Positives = 43/79 (54%)

Query: 152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 211
            +++FV GL    TE +++ L   FG +    L+KD +TG S+G+GF  ++     D A 
Sbjct: 1   GNKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAI 60

Query: 212 AALNGLKMGDKTLTVRRAT 230
             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 = 57.2 bits (138), Expect = 9e-11
 Identities = 23/79 (29%), Positives = 45/79 (56%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           ++F+GGL +   E  ++++   +G +    +VKDR+T  S+G+GF  +++P     A  A
Sbjct: 2   KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMA 61

Query: 214 LNGLKMGDKTLTVRRATAS 232
           +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|240730 cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins

 Score = 56.5 bits (137), Expect = 1e-10
 Identities = 24/71 (33%), Positives = 37/71 (52%)

Query: 156 FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN 215
           +VG L +  TE  ++ + E FG +    L +D +TG SKGYGF  + D      A   LN
Sbjct: 2   YVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLN 61

Query: 216 GLKMGDKTLTV 226
           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|241091 cd12647, RRM_UHM_SPF45, RNA recognition motif in UHM domain of 45 kDa-splicing factor (SPF45) and similar proteins

 Score = 56.9 bits (138), Expect = 2e-10
 Identities = 27/83 (32%), Positives = 43/83 (51%), Gaps = 4/83 (4%)

Query: 295 DEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALS 354
           DE+ E    +++EEC KYG +  V+I        +   V ++F+E+        A   L+
Sbjct: 17  DEDLEP---EVKEECSKYGKVTKVLIFEIPGASPDDEAV-RIFVEFERVESAIKAVVDLN 72

Query: 355 GRKFGGNTVNAFYYPEDKYFNKD 377
           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|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate Hu-antigen D (HuD)

 Score = 56.3 bits (135), Expect = 2e-10
 Identities = 31/79 (39%), Positives = 42/79 (53%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           + V  LP   T+ + + L  S G +    LV+D+ TG S GYGF  Y DP   + A   L
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 215 NGLKMGDKTLTVRRATASS 233
           NGL++  KT+ V  A  SS
Sbjct: 65  NGLRLQTKTIKVSYARPSS 83

This subgroup corresponds to the RRM1 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells, as well as the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 83

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

 Score = 55.9 bits (134), Expect = 3e-10
 Identities = 30/75 (40%), Positives = 41/75 (54%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           + V  LP   T+ ++K L  S G +    LV+D+ TG S GYGF  Y DP   + A   L
Sbjct: 7   LIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 66

Query: 215 NGLKMGDKTLTVRRA 229
           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|240771 cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP A and hnRNP D subfamilies and similar proteins

 Score = 55.3 bits (134), Expect = 4e-10
 Identities = 21/58 (36%), Positives = 33/58 (56%)

Query: 156 FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           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|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 60.0 bits (145), Expect = 5e-10
 Identities = 31/78 (39%), Positives = 43/78 (55%)

Query: 160 LPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM 219
           LP   T+ +I+ L  S G +    LV+D+ TG S GYGF  Y  P   + A  +LNGL++
Sbjct: 11  LPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRL 70

Query: 220 GDKTLTVRRATASSGQSK 237
            +KT+ V  A  SS   K
Sbjct: 71  QNKTIKVSYARPSSDSIK 88

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

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

 Score = 54.5 bits (132), Expect = 8e-10
 Identities = 25/85 (29%), Positives = 41/85 (48%), Gaps = 19/85 (22%)

Query: 34  RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFVEM 87
            ++VG LPP   E+ +   FS+          G    V +V +  +K+      FAFVE 
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKF---------GK---VESVRLVRDKETGKSKGFAFVEF 48

Query: 88  RTVEEASNAM-ALDGIIFEGVAVRV 111
            + E+A  A+ AL+G   +G  ++V
Sbjct: 49  ESEEDAEKALEALNGKELDGRPLKV 73

Length = 73

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

 Score = 53.9 bits (130), Expect = 1e-09
 Identities = 26/73 (35%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           V+VGG+PYY TE +I+      G +   DL+   DTG  +G  F  ++       A  AL
Sbjct: 1   VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRA-LAL 59

Query: 215 NGLKMGDKTLTVR 227
           +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 = 59.3 bits (143), Expect = 1e-09
 Identities = 34/92 (36%), Positives = 53/92 (57%), Gaps = 4/92 (4%)

Query: 292 LADDEEYEEILE-DMREECGKYGTLVNVVIPRPDQNGGETPG--VGKVFLEYYDAVGCAT 348
           +   ++ +E LE ++REECGK+G  V+ VI   ++ G E     + K+F+E+ D++    
Sbjct: 522 MVTPQDIDEFLEGEIREECGKFGV-VDRVIINFEKQGEEEDAEIIVKIFVEFSDSMEVDR 580

Query: 349 AKNALSGRKFGGNTVNAFYYPEDKYFNKDYSA 380
           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|240861 cd12415, RRM3_RBM28_like, RNA recognition motif 3 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 53.0 bits (128), Expect = 3e-09
 Identities = 26/80 (32%), Positives = 39/80 (48%), Gaps = 5/80 (6%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           VF+  LP+  TE ++KEL   FG +    +VKD+ TG+SKG  F  ++          A 
Sbjct: 3   VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAA 62

Query: 215 N-----GLKMGDKTLTVRRA 229
           +     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 = 52.3 bits (126), Expect = 4e-09
 Identities = 25/84 (29%), Positives = 39/84 (46%), Gaps = 18/84 (21%)

Query: 35  VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-----NHEKKFAFVEMRT 89
           ++VG LPP   E+ +   FS+          G    + +V I        K FAFVE  +
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKF---------GE---IESVRIVRDKDGKSKGFAFVEFES 48

Query: 90  VEEASNAM-ALDGIIFEGVAVRVR 112
            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|240838 cd12392, RRM2_SART3, RNA recognition motif 2 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 52.8 bits (127), Expect = 4e-09
 Identities = 20/75 (26%), Positives = 43/75 (57%), Gaps = 1/75 (1%)

Query: 152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 211
             ++FV GLP+  T+ ++++L +  G +    LV +R +G  KG  +  Y++ +    A 
Sbjct: 2   KHKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNR-SGKPKGLAYVEYENESSASQAV 60

Query: 212 AALNGLKMGDKTLTV 226
             ++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|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 = 52.5 bits (127), Expect = 4e-09
 Identities = 22/63 (34%), Positives = 34/63 (53%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           ++FVG LP   TE  ++ L E +G +    +++D+DTG SKG  F  +        A  A
Sbjct: 1   KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEA 60

Query: 214 LNG 216
           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 = 4e-09
 Identities = 23/63 (36%), Positives = 36/63 (57%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           R+FV  LP+  TE +++EL E+FG +    L  D++T  SKG+ F  +  P     A + 
Sbjct: 1   RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSE 60

Query: 214 LNG 216
           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 = 52.2 bits (126), Expect = 4e-09
 Identities = 23/72 (31%), Positives = 41/72 (56%), Gaps = 1/72 (1%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           VFVG LP+   E ++++  E  G +    +V+DR TG  KG+G+ +++      +A   L
Sbjct: 2   VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALAL-KL 60

Query: 215 NGLKMGDKTLTV 226
           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 = 51.5 bits (124), Expect = 8e-09
 Identities = 23/62 (37%), Positives = 37/62 (59%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           ++FVGGLPY+ T+  +++    FG +    ++ DR TG S+GYGF  ++D    + AC  
Sbjct: 2   KIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKD 61

Query: 214 LN 215
            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|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2 and similar proteins

 Score = 51.6 bits (124), Expect = 9e-09
 Identities = 21/63 (33%), Positives = 36/63 (57%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
            +FVG L +   +  +K   E FGT+ G  ++ DR+TG S+G+G+  ++ P     A  A
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 214 LNG 216
           ++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|241213 cd12769, RRM1_HuR, RNA recognition motif 1 in vertebrate Hu-antigen R (HuR)

 Score = 51.2 bits (122), Expect = 1e-08
 Identities = 26/78 (33%), Positives = 41/78 (52%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           + V  LP   T+ +++ L  S G +    L++D+  G+S GYGF  Y +    + A   L
Sbjct: 4   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTL 63

Query: 215 NGLKMGDKTLTVRRATAS 232
           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|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: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           V+V  L     + ++KEL   +G +    ++KD D G SKG+GF  +++      A   L
Sbjct: 4   VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKD-DEGKSKGFGFVNFENHEAAQKAVEEL 62

Query: 215 NGLKMGDKTLTVRRA 229
           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 = 55.1 bits (132), Expect = 3e-08
 Identities = 53/212 (25%), Positives = 84/212 (39%), Gaps = 31/212 (14%)

Query: 22  QVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVY---INH 78
           Q   QQA     RVYVG +     E  I   F            GP  ++   +      
Sbjct: 97  QQQRQQALAIMCRVYVGSISFELREDTIRRAFDPF---------GPIKSINMSWDPATGK 147

Query: 79  EKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLA 137
            K FAFVE    E A  A+  ++G +  G  ++V RP++            Q  P +++ 
Sbjct: 148 HKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNM----------PQAQPIIDMV 197

Query: 138 AVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYG 197
                      A+  +R++V  +    +ET IK + E+FG +    L +       KGYG
Sbjct: 198 Q--------EEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYG 249

Query: 198 FCVYQDPAVTDIACAALNGLKMGDKTLTVRRA 229
           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|240778 cd12332, RRM1_p54nrb_like, RNA recognition motif 1 in the p54nrb/PSF/PSP1 family

 Score = 50.0 bits (120), Expect = 3e-08
 Identities = 27/80 (33%), Positives = 39/80 (48%), Gaps = 13/80 (16%)

Query: 34  RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEA 93
           R++VG LP    E+     FS+            G+ V  V++N EK F F+ + T   A
Sbjct: 3   RLFVGNLPNDITEEEFKELFSKY-----------GE-VSEVFLNKEKGFGFIRLDTRTNA 50

Query: 94  SNA-MALDGIIFEGVAVRVR 112
             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|240774 cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 49.9 bits (120), Expect = 3e-08
 Identities = 17/60 (28%), Positives = 30/60 (50%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           ++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|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 = 49.9 bits (120), Expect = 3e-08
 Identities = 24/79 (30%), Positives = 35/79 (44%), Gaps = 13/79 (16%)

Query: 35  VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEAS 94
           VYVG LP    E+ +   FS            P  A+  V +  +K +AFV   T E A+
Sbjct: 3   VYVGNLPHGLTEEELQRTFS------------PFGAIEEVRVFKDKGYAFVRFDTHEAAA 50

Query: 95  NAM-ALDGIIFEGVAVRVR 112
            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|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 = 49.5 bits (118), Expect = 6e-08
 Identities = 25/79 (31%), Positives = 42/79 (53%), Gaps = 2/79 (2%)

Query: 151 GPD--RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 208
           GP+   +F+  LP  F + ++ ++   FG +    +  DR T  SK +GF  + +PA   
Sbjct: 1   GPEGCNLFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQ 60

Query: 209 IACAALNGLKMGDKTLTVR 227
            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|241093 cd12649, RRM1_SXL, RNA recognition motif 1 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 48.9 bits (117), Expect = 8e-08
 Identities = 22/67 (32%), Positives = 35/67 (52%)

Query: 160 LPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM 219
           LP   T+ + + L  + G +    +V+D+ TG S G+GF  YQ       A   LNGL++
Sbjct: 8   LPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLNGLQL 67

Query: 220 GDKTLTV 226
            +K + V
Sbjct: 68  QNKRIKV 74

This subfamily corresponds to the RRM1 of SXL which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 81

>gnl|CDD|241021 cd12577, RRM1_Hrp1p, RNA recognition motif 1 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 48.7 bits (116), Expect = 8e-08
 Identities = 16/55 (29%), Positives = 31/55 (56%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 209
           +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|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 48.8 bits (117), Expect = 1e-07
 Identities = 19/75 (25%), Positives = 33/75 (44%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           +FV  LPY  T+ Q++E     G +    +VKD+ +   +G+G+  +        A    
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 215 NGLKMGDKTLTVRRA 229
              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|240728 cd12282, RRM2_TatSF1_like, RNA recognition motif 2 in HIV Tat-specific factor 1 (Tat-SF1) and similar proteins

 Score = 48.8 bits (117), Expect = 1e-07
 Identities = 27/82 (32%), Positives = 38/82 (46%), Gaps = 13/82 (15%)

Query: 290 DALADDEEYEEILEDMREECGKYGTLVNVVI-PR-PDQNGGETPGVGKV-FLEYYDAVGC 346
           +   D     E+ +D+REEC K+G +  VV+  R PD       GV  V F E  +A   
Sbjct: 14  EFEEDPTLINELRDDLREECEKFGQVKKVVVFDRHPD-------GVASVKFKEPEEA--- 63

Query: 347 ATAKNALSGRKFGGNTVNAFYY 368
                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|241110 cd12666, RRM2_RAVER2, RNA recognition motif 2 in vertebrate ribonucleoprotein PTB-binding 2 (raver-2)

 Score = 48.4 bits (115), Expect = 1e-07
 Identities = 25/71 (35%), Positives = 36/71 (50%)

Query: 157 VGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNG 216
           V  LP  FT  + +EL+ ++G +    LV    TG+SKGYGF  Y        A   L G
Sbjct: 4   VTNLPISFTLEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKARLELLG 63

Query: 217 LKMGDKTLTVR 227
            ++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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 47.6 bits (114), Expect = 2e-07
 Identities = 24/78 (30%), Positives = 36/78 (46%), Gaps = 18/78 (23%)

Query: 35  VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE-----KKFAFVEMRT 89
           ++VG LPP   E+ +   FS+          GP   + ++ I  +     K FAFVE   
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKF---------GP---IESIRIVRDETGRSKGFAFVEFED 48

Query: 90  VEEASNAM-ALDGIIFEG 106
            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|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 47.8 bits (114), Expect = 2e-07
 Identities = 20/50 (40%), Positives = 27/50 (54%)

Query: 157 VGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAV 206
           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|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 = 47.6 bits (114), Expect = 2e-07
 Identities = 25/72 (34%), Positives = 39/72 (54%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           +F+  LP  FT+  + +L   FG +    +  D++TG SK +GF  Y +P     A  A+
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 215 NGLKMGDKTLTV 226
           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|241109 cd12665, RRM2_RAVER1, RNA recognition motif 2 found in vertebrate ribonucleoprotein PTB-binding 1 (raver-1)

 Score = 47.6 bits (113), Expect = 2e-07
 Identities = 27/70 (38%), Positives = 37/70 (52%)

Query: 157 VGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNG 216
           +  LP  +T+ Q +EL+  FG L    LV    TG+SKGYGF  Y        A + L G
Sbjct: 4   IANLPPTYTQQQFEELVRPFGNLERCFLVYSETTGHSKGYGFVEYMKKDSAARAKSDLLG 63

Query: 217 LKMGDKTLTV 226
            ++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|240816 cd12370, RRM1_PUF60, RNA recognition motif 1 in (U)-binding-splicing factor PUF60 and similar proteins

 Score = 47.4 bits (113), Expect = 2e-07
 Identities = 22/75 (29%), Positives = 37/75 (49%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           RV+VG + +   E  I++    FG +   D+  D  T   KG+ F  Y+ P    +A   
Sbjct: 2   RVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQ 61

Query: 214 LNGLKMGDKTLTVRR 228
           +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|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 47.5 bits (113), Expect = 2e-07
 Identities = 25/78 (32%), Positives = 39/78 (50%), Gaps = 1/78 (1%)

Query: 152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 211
           P+R+FVGG+ +   E  +++    +GT+    +V DR  G SKGYGF  ++         
Sbjct: 2   PNRIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDR-AGVSKGYGFVTFETQEDAQKIL 60

Query: 212 AALNGLKMGDKTLTVRRA 229
              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|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 46.8 bits (112), Expect = 4e-07
 Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 1/76 (1%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           R+ V  LP Y TE +++E  ES G +    +++ RD G S+ +GF  ++       A   
Sbjct: 2   RIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRD-GKSRRFGFVGFKSEEDAQQAVKY 60

Query: 214 LNGLKMGDKTLTVRRA 229
            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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 46.4 bits (111), Expect = 4e-07
 Identities = 24/77 (31%), Positives = 35/77 (45%), Gaps = 17/77 (22%)

Query: 35  VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEK----KFAFVEMRTV 90
           +YV  LPP   E+ +  FFS            P   V  V +   K     FAFVE  + 
Sbjct: 1   LYVRNLPPSVTEEDLREFFS------------PYGKVEGVRLVRNKDRPRGFAFVEFASP 48

Query: 91  EEASNAMA-LDGIIFEG 106
           E+A  A+  L+G++ +G
Sbjct: 49  EDAEAALKKLNGLVLDG 65

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

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

 Score = 46.9 bits (111), Expect = 4e-07
 Identities = 27/80 (33%), Positives = 42/80 (52%), Gaps = 1/80 (1%)

Query: 148 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 207
           G EG + +F+  LP  FT+T + +    FG +    +  D+ T  SK +GF  Y +P   
Sbjct: 1   GPEGCN-LFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSA 59

Query: 208 DIACAALNGLKMGDKTLTVR 227
             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|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins

 Score = 46.5 bits (111), Expect = 5e-07
 Identities = 25/84 (29%), Positives = 34/84 (40%), Gaps = 15/84 (17%)

Query: 34  RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE----KKFAFVEMRT 89
            +YVG LP    E+ +   F Q                  V  + E    + F FVEM T
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTS----------ARVITDRETGRSRGFGFVEMET 50

Query: 90  VEEASNAM-ALDGIIFEGVAVRVR 112
            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|240782 cd12336, RRM_RBM7_like, RNA recognition motif in RNA-binding protein 7 (RBM7) and similar proteins

 Score = 46.5 bits (111), Expect = 5e-07
 Identities = 21/73 (28%), Positives = 34/73 (46%), Gaps = 1/73 (1%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           +FVG L    TE  + EL    G L G  + KD + G  K + F  ++       A   L
Sbjct: 4   LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPN-GKPKSFAFVTFKHEVSVPYAIQLL 62

Query: 215 NGLKMGDKTLTVR 227
           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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 46.0 bits (110), Expect = 6e-07
 Identities = 21/70 (30%), Positives = 36/70 (51%), Gaps = 2/70 (2%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           ++V  LP   TE  ++E    +G + G  LV+++D    +G+ F  +  P   + A   L
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD--RPRGFAFVEFASPEDAEAALKKL 58

Query: 215 NGLKMGDKTL 224
           NGL +  +TL
Sbjct: 59  NGLVLDGRTL 68

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

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

 Score = 46.7 bits (111), Expect = 6e-07
 Identities = 21/52 (40%), Positives = 31/52 (59%), Gaps = 1/52 (1%)

Query: 152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD 203
           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|241010 cd12566, RRM2_MRD1, RNA recognition motif 2 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 46.6 bits (111), Expect = 6e-07
 Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 3/64 (4%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           R+FV  LPY   E  +++L   FG L    +  D+ +G SKG+ + ++ DP   + A  A
Sbjct: 4   RLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDP---EDAVKA 60

Query: 214 LNGL 217
              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|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins

 Score = 46.5 bits (111), Expect = 6e-07
 Identities = 20/71 (28%), Positives = 35/71 (49%)

Query: 156 FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN 215
           FV  L Y  TE++++   E +G +    LV+D+ TG  +GY F  ++       A    +
Sbjct: 5   FVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYAD 64

Query: 216 GLKMGDKTLTV 226
           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|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 46.2 bits (110), Expect = 8e-07
 Identities = 21/76 (27%), Positives = 38/76 (50%), Gaps = 1/76 (1%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           ++FVGGLP   TET +++    FGT+    ++ D +    +G+GF  ++     D     
Sbjct: 4   KIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVV-N 62

Query: 214 LNGLKMGDKTLTVRRA 229
            +   +  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|241011 cd12567, RRM3_RBM19, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 45.5 bits (108), Expect = 1e-06
 Identities = 23/65 (35%), Positives = 32/65 (49%), Gaps = 4/65 (6%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP--AVTDIAC 211
           R+F+  L Y  TE  +++L   +G L    L  D+ T   KG+ F  Y  P  AV   A 
Sbjct: 4   RLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVK--AF 61

Query: 212 AALNG 216
           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|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8 (NOL8) and similar proteins

 Score = 45.2 bits (108), Expect = 1e-06
 Identities = 23/78 (29%), Positives = 40/78 (51%), Gaps = 3/78 (3%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA-C- 211
           R+FVGGL    TE+ ++E    FGT+   +++K +D G  +G+ + +    +   +  C 
Sbjct: 1   RLFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAY-IDLRTSEAQLKKCK 59

Query: 212 AALNGLKMGDKTLTVRRA 229
           + LNG K     L +  A
Sbjct: 60  STLNGTKWKGSVLKIEEA 77

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

 Score = 45.3 bits (108), Expect = 2e-06
 Identities = 23/74 (31%), Positives = 34/74 (45%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           V+VG L    TE  + EL    G +    + KDR T   +GYGF  +      D A   +
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 215 NGLKMGDKTLTVRR 228
           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|240839 cd12393, RRM_ZCRB1, RNA recognition motif in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins

 Score = 45.0 bits (107), Expect = 2e-06
 Identities = 21/75 (28%), Positives = 36/75 (48%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           V+V  LP+  T   + ++   +G +    +VKD++T  SKG  F ++ D         AL
Sbjct: 4   VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKAL 63

Query: 215 NGLKMGDKTLTVRRA 229
           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|241022 cd12578, RRM1_hnRNPA_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 45.1 bits (107), Expect = 2e-06
 Identities = 21/78 (26%), Positives = 39/78 (50%), Gaps = 1/78 (1%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           ++F+GGL Y  T+  +K     +G +    ++KD +T  S+G+GF  +   +  D A  A
Sbjct: 1   KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNA 60

Query: 214 LNGLKMGDKTLTVRRATA 231
               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|240825 cd12379, RRM2_I_PABPs, RNA recognition motif 2 found in type I polyadenylate-binding proteins

 Score = 44.8 bits (107), Expect = 2e-06
 Identities = 19/76 (25%), Positives = 33/76 (43%), Gaps = 1/76 (1%)

Query: 151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA 210
           G   +F+  L        + +   +FG +    +  D + G SKGYGF  ++       A
Sbjct: 1   GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVATD-ENGGSKGYGFVHFETEEAAVRA 59

Query: 211 CAALNGLKMGDKTLTV 226
              +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|240781 cd12335, RRM2_SF3B4, RNA recognition motif 2 in splicing factor 3B subunit 4 (SF3B4) and similar proteins

 Score = 44.6 bits (106), Expect = 3e-06
 Identities = 25/76 (32%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 155 VFVGGLPYYFTETQIKELLESFGT-LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           +F+G L     E  + +   +FG  L    +++D DTGNSKG+ F  Y     +D A  A
Sbjct: 4   LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63

Query: 214 LNGLKMGDKTLTVRRA 229
           +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|241105 cd12661, RRM3_hnRNPM, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 44.6 bits (105), Expect = 3e-06
 Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 2/74 (2%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           ++FV  LP+ FT   +K+     G +   D+    + G SKG G   ++ P V + AC  
Sbjct: 1   QIFVRNLPFDFTWKMLKDKFNECGHVLYADI--KMENGKSKGCGVVRFESPEVAERACRM 58

Query: 214 LNGLKMGDKTLTVR 227
           +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|240778 cd12332, RRM1_p54nrb_like, RNA recognition motif 1 in the p54nrb/PSF/PSP1 family

 Score = 43.8 bits (104), Expect = 4e-06
 Identities = 25/74 (33%), Positives = 35/74 (47%), Gaps = 6/74 (8%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           R+FVG LP   TE + KEL   +G +    L K+      KG+GF         + A A 
Sbjct: 3   RLFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE------KGFGFIRLDTRTNAEKAKAE 56

Query: 214 LNGLKMGDKTLTVR 227
           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|240689 cd12243, RRM1_MSSP, RNA recognition motif 1 in the c-myc gene single-strand binding proteins (MSSP) family

 Score = 43.8 bits (104), Expect = 4e-06
 Identities = 20/64 (31%), Positives = 31/64 (48%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           V++ GLP   T+  +++L + FG +     + D+ T   KGYGF  +  P     A   L
Sbjct: 3   VYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEGL 62

Query: 215 NGLK 218
           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|241030 cd12586, RRM1_PSP1, RNA recognition motif 1 in vertebrate paraspeckle protein 1 (PSP1)

 Score = 43.8 bits (103), Expect = 5e-06
 Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 6/74 (8%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           R+FVG LP   TE   K+L E +G      + +DR      G+GF   +   + +IA A 
Sbjct: 3   RLFVGNLPTDITEEDFKKLFEKYGEPSEVFINRDR------GFGFIRLESRTLAEIAKAE 56

Query: 214 LNGLKMGDKTLTVR 227
           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|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins

 Score = 43.9 bits (104), Expect = 5e-06
 Identities = 24/77 (31%), Positives = 34/77 (44%), Gaps = 2/77 (2%)

Query: 152 PD--RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 209
           PD  ++FVG LP+  TE ++KE  + FG +    +      G    +GF V+ DP     
Sbjct: 1   PDSHQLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQK 60

Query: 210 ACAALNGLKMGDKTLTV 226
             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|240783 cd12337, RRM1_SRSF4_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins

 Score = 43.5 bits (103), Expect = 5e-06
 Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 8/76 (10%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           RV++G LPY   E  ++   + +G +        R+     G+GF  ++DP   D A   
Sbjct: 1   RVYIGRLPYRARERDVERFFKGYGRI--------REINLKNGFGFVEFEDPRDADDAVYE 52

Query: 214 LNGLKMGDKTLTVRRA 229
           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|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 43.5 bits (103), Expect = 6e-06
 Identities = 20/57 (35%), Positives = 35/57 (61%), Gaps = 1/57 (1%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA 210
           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|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins family

 Score = 43.5 bits (103), Expect = 7e-06
 Identities = 24/75 (32%), Positives = 38/75 (50%), Gaps = 6/75 (8%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCV---YQDPAVTDIAC 211
           +FV  LP    E+ + +L   FG +    +++D  T   KGYGF     Y++      A 
Sbjct: 4   IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYS---AI 60

Query: 212 AALNGLKMGDKTLTV 226
           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|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 = 7e-06
 Identities = 21/70 (30%), Positives = 33/70 (47%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           +FVG L        ++     FG +    +VKD  TG SKGYGF  +      + A  ++
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 215 NGLKMGDKTL 224
           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|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate Hu-antigen D (HuD)

 Score = 43.5 bits (102), Expect = 8e-06
 Identities = 23/76 (30%), Positives = 40/76 (52%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           +FV  L     E+ + +L   FG ++   +++D +T   KG+GF    +     +A A+L
Sbjct: 6   IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 215 NGLKMGDKTLTVRRAT 230
           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|240854 cd12408, RRM_eIF3G_like, RNA recognition motif in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins

 Score = 42.9 bits (102), Expect = 8e-06
 Identities = 17/52 (32%), Positives = 26/52 (50%)

Query: 165 TETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNG 216
            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|214636 smart00360, RRM, RNA recognition motif

 Score = 43.0 bits (102), Expect = 9e-06
 Identities = 17/62 (27%), Positives = 32/62 (51%), Gaps = 3/62 (4%)

Query: 303 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNT 362
           E++RE   K+G + +V + R D+  G++ G    F+E+        A  AL+G++  G  
Sbjct: 14  EELRELFSKFGKVESVRLVR-DKETGKSKGFA--FVEFESEEDAEKALEALNGKELDGRP 70

Query: 363 VN 364
           + 
Sbjct: 71  LK 72

Length = 73

>gnl|CDD|240671 cd12225, RRM1_2_CID8_like, RNA recognition motif 1 and 2 (RRM1, RRM2) in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 43.1 bits (102), Expect = 9e-06
 Identities = 25/83 (30%), Positives = 36/83 (43%), Gaps = 16/83 (19%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN----HEKKFAFVEMR 88
           R ++VGG+    +E  +  FFS      G         V  V +     H  +FAFVE  
Sbjct: 1   RTIHVGGIDGSLSEDDLKEFFS----NCG--------EVTRVRLCGDRQHSARFAFVEFA 48

Query: 89  TVEEASNAMALDGIIFEGVAVRV 111
             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|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 = 43.2 bits (102), Expect = 9e-06
 Identities = 21/65 (32%), Positives = 33/65 (50%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           ++FVG +P    E  ++ L E FG ++   ++KD+ TG  KG  F  Y        A +A
Sbjct: 7   KLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKAQSA 66

Query: 214 LNGLK 218
           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|241082 cd12638, RRM3_CELF1_2, RNA recognition motif 3 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 43.5 bits (102), Expect = 9e-06
 Identities = 25/80 (31%), Positives = 41/80 (51%), Gaps = 2/80 (2%)

Query: 150 EGPD--RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 207
           EGP+   +F+  LP  F +  + ++   FG +    +  D+ T  SK +GF  Y +P   
Sbjct: 3   EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSA 62

Query: 208 DIACAALNGLKMGDKTLTVR 227
             A  A+NG ++G K L V+
Sbjct: 63  QAAIQAMNGFQIGMKRLKVQ 82

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

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

 Score = 42.6 bits (101), Expect = 1e-05
 Identities = 22/85 (25%), Positives = 38/85 (44%), Gaps = 17/85 (20%)

Query: 34  RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE-----KKFAFVEMR 88
           R++VGG+PP   E+ +  FFS+              +V +V I  +     K + FV   
Sbjct: 4   RIFVGGIPPDTTEEELRDFFSRF------------GSVKDVKIITDRAGVSKGYGFVTFE 51

Query: 89  TVEEASNAMALDGIIFEGVAVRVRR 113
           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|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 46.5 bits (110), Expect = 1e-05
 Identities = 27/103 (26%), Positives = 42/103 (40%), Gaps = 6/103 (5%)

Query: 130 PSPNLNLAAVGLASGAIGGAEGPDR------VFVGGLPYYFTETQIKELLESFGTLHGFD 183
                  A  G  +G   GA+          +FV  L     ET + +L   FG +    
Sbjct: 241 AQRASPPATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVK 300

Query: 184 LVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV 226
           +++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|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 43.1 bits (101), Expect = 1e-05
 Identities = 14/55 (25%), Positives = 30/55 (54%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 208
           ++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|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 42.7 bits (100), Expect = 1e-05
 Identities = 16/55 (29%), Positives = 33/55 (60%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 208
           ++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|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 43.0 bits (101), Expect = 1e-05
 Identities = 18/57 (31%), Positives = 30/57 (52%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA 210
           ++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|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 42.7 bits (101), Expect = 1e-05
 Identities = 19/73 (26%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           +FV  L Y     ++KE+ +  G +   D+ +D++ G S+G G   ++ P     A +  
Sbjct: 1   IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKE-GKSRGMGVVQFEHPIEAVQAISMF 59

Query: 215 NGLKMGDKTLTVR 227
           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|240853 cd12407, RRM_FOX1_like, RNA recognition motif in vertebrate RNA binding protein fox-1 homologs and similar proteins

 Score = 42.4 bits (100), Expect = 1e-05
 Identities = 20/78 (25%), Positives = 40/78 (51%), Gaps = 4/78 (5%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLV-KDRDTGNSKGYGFCVYQDPAVTDIACA 212
           R+ V  +P+ F +  ++++   FG +   +++  +R    SKG+GF  + + A  D A  
Sbjct: 2   RLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNER---GSKGFGFVTFANSADADRARE 58

Query: 213 ALNGLKMGDKTLTVRRAT 230
            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|240683 cd12237, RRM_snRNP35, RNA recognition motif found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K) and similar proteins

 Score = 43.0 bits (102), Expect = 1e-05
 Identities = 19/49 (38%), Positives = 27/49 (55%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD 203
           +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|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 = 1e-05
 Identities = 18/51 (35%), Positives = 29/51 (56%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP 204
           ++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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 41.7 bits (99), Expect = 2e-05
 Identities = 10/63 (15%), Positives = 20/63 (31%), Gaps = 8/63 (12%)

Query: 306 REECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNA 365
            +    +G +  + + +              F+E+        A   L+G  FGG  +  
Sbjct: 2   YKLFSPFGNVEKIKLLKKKPG--------FAFVEFSTEEAAEKAVQYLNGVLFGGRPLRV 53

Query: 366 FYY 368
            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|240809 cd12363, RRM_TRA2, RNA recognition motif in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins

 Score = 42.2 bits (100), Expect = 2e-05
 Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 2/72 (2%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           VF  GL  Y TE  ++E+   +G +    +V D+ TG S+G+GF  ++       A   L
Sbjct: 4   VF--GLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERL 61

Query: 215 NGLKMGDKTLTV 226
           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|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate Hu-antigen B (HuB)

 Score = 42.4 bits (99), Expect = 2e-05
 Identities = 22/79 (27%), Positives = 40/79 (50%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           +FV  L     E+ + ++   FG +    +++D +T   KG+GF    +     +A A+L
Sbjct: 6   IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 215 NGLKMGDKTLTVRRATASS 233
           NG ++GD+ L V   T  +
Sbjct: 66  NGYRLGDRVLQVSFKTNKT 84

This subgroup corresponds to the RRM3 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 86

>gnl|CDD|241086 cd12642, RRM_TRA2A, RNA recognition motif in transformer-2 protein homolog alpha (TRA-2 alpha) and similar proteins

 Score = 42.3 bits (99), Expect = 2e-05
 Identities = 21/70 (30%), Positives = 38/70 (54%)

Query: 157 VGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNG 216
           V GL  Y TE  ++E+   +G L G ++V D+ TG S+G+ F  ++    +  A    NG
Sbjct: 4   VFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANG 63

Query: 217 LKMGDKTLTV 226
           +++  + + 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|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 42.0 bits (98), Expect = 2e-05
 Identities = 20/60 (33%), Positives = 34/60 (56%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           ++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|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 41.4 bits (97), Expect = 3e-05
 Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 6/74 (8%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           R+FVG LP   TE ++++L E +G      + KD      KG+GF   +   + +IA A 
Sbjct: 3   RLFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKD------KGFGFIRLETRTLAEIAKAE 56

Query: 214 LNGLKMGDKTLTVR 227
           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|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 42.0 bits (98), Expect = 3e-05
 Identities = 26/76 (34%), Positives = 35/76 (46%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           VFVG L    T   IK     FG +    +VKD  TG SKGYGF  + +    + A   +
Sbjct: 4   VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63

Query: 215 NGLKMGDKTLTVRRAT 230
            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|240733 cd12287, RRM_U2AF35_like, RNA recognition motif in U2 small nuclear ribonucleoprotein auxiliary factor U2AF 35 kDa subunit (U2AF35) and similar proteins

 Score = 42.2 bits (100), Expect = 3e-05
 Identities = 19/86 (22%), Positives = 38/86 (44%), Gaps = 4/86 (4%)

Query: 284 TEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDA 343
              +T       E ++E  ED+  E  ++G + ++V+     N G+   +G V++++   
Sbjct: 21  QGVLTLSEEEIQEHFDEFYEDVFLELSRFGEIEDLVVC---DNLGDHL-LGNVYVKFETE 76

Query: 344 VGCATAKNALSGRKFGGNTVNAFYYP 369
                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|240819 cd12373, RRM_SRSF3_like, RNA recognition motif in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins

 Score = 41.5 bits (98), Expect = 3e-05
 Identities = 26/82 (31%), Positives = 39/82 (47%), Gaps = 18/82 (21%)

Query: 34  RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK---FAFVEMRTV 90
           +VYVG L P A ++ +   F +          GP   + +V++   +    FAFVE    
Sbjct: 1   KVYVGNLGPRATKRELEDEFEKY---------GP---LRSVWV--ARNPPGFAFVEFEDP 46

Query: 91  EEASNAM-ALDGIIFEGVAVRV 111
            +A +A+ ALDG    G  VRV
Sbjct: 47  RDAEDAVRALDGRRICGNRVRV 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|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding protein Musashi homolog 2 (Musashi-2 ) and similar proteins

 Score = 41.6 bits (97), Expect = 3e-05
 Identities = 16/55 (29%), Positives = 31/55 (56%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 208
           ++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|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate Hu-antigen R (HuR)

 Score = 41.6 bits (97), Expect = 3e-05
 Identities = 23/79 (29%), Positives = 40/79 (50%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           +F+  L     E  + ++   FG +    +++D +T   KG+GF    +     +A A+L
Sbjct: 4   IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63

Query: 215 NGLKMGDKTLTVRRATASS 233
           NG ++GDK L V   T+ S
Sbjct: 64  NGYRLGDKILQVSFKTSKS 82

This subgroup corresponds to the RRM3 of HuR, also termed ELAV-like protein 1 (ELAV-1), the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 84

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

 Score = 41.6 bits (97), Expect = 3e-05
 Identities = 26/76 (34%), Positives = 35/76 (46%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           VFVG L    T   IK     FG +    +VKD  TG SKGYGF  + +    + A   +
Sbjct: 4   VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63

Query: 215 NGLKMGDKTLTVRRAT 230
            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|240833 cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 41.1 bits (97), Expect = 3e-05
 Identities = 23/73 (31%), Positives = 35/73 (47%), Gaps = 1/73 (1%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           +FV  LP+  T   +K+L    G +   D+  D D G SKG+G  +++ P     A    
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDND-GRSKGFGTVLFESPEDAQRAIEMF 59

Query: 215 NGLKMGDKTLTVR 227
           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|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily

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

Query: 303 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNT 362
           ED+RE   K+G + +V I R      +    G  F+E+        A  AL+G++  G  
Sbjct: 13  EDLRELFSKFGEIESVRIVRDKDGKSK----GFAFVEFESPEDAEKALEALNGKELDGRK 68

Query: 363 VNA 365
           +  
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|241205 cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 41.6 bits (97), Expect = 4e-05
 Identities = 19/60 (31%), Positives = 33/60 (55%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           ++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|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering time control protein FCA and similar proteins

 Score = 41.5 bits (97), Expect = 4e-05
 Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 3/79 (3%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           ++FVG +P   TE +++ + E  G +    ++KD+ TG+ +G  F  Y      D A  A
Sbjct: 1   KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRA 60

Query: 214 LNG---LKMGDKTLTVRRA 229
           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|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 = 4e-05
 Identities = 19/58 (32%), Positives = 30/58 (51%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 211
           ++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|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 42.2 bits (99), Expect = 4e-05
 Identities = 21/72 (29%), Positives = 31/72 (43%), Gaps = 3/72 (4%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           +FV  LPY  TE  +      FG++     V D+ TG +KG GF  ++D    +   A L
Sbjct: 4   LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYN---ACL 60

Query: 215 NGLKMGDKTLTV 226
                   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|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4; Provisional

 Score = 42.7 bits (100), Expect = 4e-05
 Identities = 19/85 (22%), Positives = 42/85 (49%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           ++F+GGL +   +  +++    FG +    ++ DR+TG S+G+GF  + D      A + 
Sbjct: 36  KLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISE 95

Query: 214 LNGLKMGDKTLTVRRATASSGQSKT 238
           ++G ++  + + V  A       + 
Sbjct: 96  MDGKELNGRHIRVNPANDRPSAPRA 120

Length = 144

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

 Score = 41.1 bits (96), Expect = 4e-05
 Identities = 23/76 (30%), Positives = 36/76 (47%), Gaps = 2/76 (2%)

Query: 153 DR-VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 211
           DR +FVG L     E  + EL    G L    + KD++ G  K +GF  ++       A 
Sbjct: 1   DRTLFVGNLECRVREEILYELFLQAGPLTKVTICKDKE-GKPKSFGFVCFKHSESVPYAI 59

Query: 212 AALNGLKMGDKTLTVR 227
           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|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 41.0 bits (96), Expect = 5e-05
 Identities = 19/54 (35%), Positives = 31/54 (57%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 208
           +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|240772 cd12326, RRM1_hnRNPA0, RNA recognition motif 1 found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 40.9 bits (96), Expect = 5e-05
 Identities = 16/76 (21%), Positives = 34/76 (44%), Gaps = 1/76 (1%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           ++FVGGL    +++ ++     +G L    ++ D +T  S+G+GF  +      D     
Sbjct: 4   KLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEAD-EAME 62

Query: 214 LNGLKMGDKTLTVRRA 229
                +    + ++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|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33 (Cyp33) and similar proteins

 Score = 40.7 bits (96), Expect = 5e-05
 Identities = 18/75 (24%), Positives = 35/75 (46%), Gaps = 6/75 (8%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           ++VGGL     E  +      FG +    +  D +T   +G+ F  +++P   + A AA+
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEP---EDAAAAI 57

Query: 215 ---NGLKMGDKTLTV 226
              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|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor 3B subunit 4 (SF3B4) and similar proteins

 Score = 40.7 bits (96), Expect = 6e-05
 Identities = 26/86 (30%), Positives = 38/86 (44%), Gaps = 19/86 (22%)

Query: 35  VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMR 88
           VYVG L     E+ +   F Q         AGP   VVNV+I         + + FVE  
Sbjct: 1   VYVGNLDEKVTEELLWELFIQ---------AGP---VVNVHIPKDRVTQAHQGYGFVEFL 48

Query: 89  TVEEASNAMA-LDGIIFEGVAVRVRR 113
           + 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|240791 cd12345, RRM2_SECp43_like, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 40.7 bits (96), Expect = 7e-05
 Identities = 25/77 (32%), Positives = 39/77 (50%), Gaps = 1/77 (1%)

Query: 155 VFVGGLPYYFTETQIKELLES-FGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           +FVG L    T+  ++E   + + ++ G  +V D  TG SKGYGF  + D    D A   
Sbjct: 4   IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALTE 63

Query: 214 LNGLKMGDKTLTVRRAT 230
           +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|241024 cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 40.7 bits (95), Expect = 7e-05
 Identities = 13/50 (26%), Positives = 28/50 (56%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD 203
           ++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|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP DL) and similar proteins

 Score = 40.4 bits (94), Expect = 7e-05
 Identities = 21/50 (42%), Positives = 27/50 (54%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD 203
           +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|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen C (HuC)

 Score = 40.5 bits (94), Expect = 8e-05
 Identities = 23/82 (28%), Positives = 41/82 (50%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           +FV  L     E+ + +L   FG +    +++D  T   KG+GF    +     +A A+L
Sbjct: 4   IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63

Query: 215 NGLKMGDKTLTVRRATASSGQS 236
           NG ++GD+ L V   T+   ++
Sbjct: 64  NGYRLGDRVLQVSFKTSKQHKA 85

This subgroup corresponds to the RRM3 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 85

>gnl|CDD|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 = 40.5 bits (95), Expect = 9e-05
 Identities = 13/46 (28%), Positives = 28/46 (60%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC 199
           ++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|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33 (Cyp33) and similar proteins

 Score = 39.5 bits (93), Expect = 1e-04
 Identities = 19/69 (27%), Positives = 32/69 (46%), Gaps = 18/69 (26%)

Query: 35 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGP-GDAV-VNVYINHEKK----FAFVEMR 88
          +YVGGL    +E+ +   F             P GD   + + +++E +    FAFVE  
Sbjct: 1  LYVGGLAEEVDEKVLHAAFI------------PFGDIKDIQIPLDYETQKHRGFAFVEFE 48

Query: 89 TVEEASNAM 97
            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|241058 cd12614, RRM1_PUB1, RNA recognition motif 1 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 40.2 bits (94), Expect = 1e-04
 Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 5/77 (6%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKG--YGFCVYQDPAVTDIACA 212
           ++VG L    TE  +K++ +  G +    ++ D+   N+KG  YGF  Y      +IA  
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDK---NNKGVNYGFVEYHQSHDAEIALQ 57

Query: 213 ALNGLKMGDKTLTVRRA 229
            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|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP DL) and similar proteins

 Score = 40.0 bits (93), Expect = 1e-04
 Identities = 23/76 (30%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           ++F+GGL +  ++  + E L  FG +    +  D  TG S+G+GF +++D A  D     
Sbjct: 1   KMFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVD-KVLE 59

Query: 214 LNGLKMGDKTLTVRRA 229
           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|240719 cd12273, RRM1_NEFsp, RNA recognition motif 1 in vertebrate putative RNA exonuclease NEF-sp

 Score = 39.7 bits (93), Expect = 1e-04
 Identities = 15/75 (20%), Positives = 30/75 (40%), Gaps = 4/75 (5%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
            V+ G  P  F  + +K L E+ G +    ++          + F  +++     +A   
Sbjct: 1   TVYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTVQ----PHAFITFENLEAAQLAIET 56

Query: 214 LNGLKMGDKTLTVRR 228
           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|241016 cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 39.6 bits (92), Expect = 1e-04
 Identities = 17/58 (29%), Positives = 30/58 (51%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 211
           ++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|241031 cd12587, RRM1_PSF, RNA recognition motif 1 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

 Score = 39.5 bits (92), Expect = 1e-04
 Identities = 25/74 (33%), Positives = 36/74 (48%), Gaps = 6/74 (8%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           R+FVG LP   TE + K+L   +G      + K       KG+GF   +  A+ +IA A 
Sbjct: 3   RLFVGNLPADITEDEFKKLFAKYGEPGEVFINK------GKGFGFIKLESRALAEIAKAE 56

Query: 214 LNGLKMGDKTLTVR 227
           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|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 43.6 bits (103), Expect = 1e-04
 Identities = 19/74 (25%), Positives = 32/74 (43%), Gaps = 1/74 (1%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           +FV  L        + +    FG +    +  D + G S+GYGF  ++       A   +
Sbjct: 91  IFVKNLDKSVDNKALFDTFSKFGNILSCKVATD-ENGKSRGYGFVHFEKEESAKAAIQKV 149

Query: 215 NGLKMGDKTLTVRR 228
           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|241025 cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 39.7 bits (92), Expect = 1e-04
 Identities = 14/50 (28%), Positives = 29/50 (58%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD 203
           ++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|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 = 1e-04
 Identities = 18/57 (31%), Positives = 28/57 (49%), Gaps = 1/57 (1%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP-AVTDI 209
           ++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|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 = 1e-04
 Identities = 21/73 (28%), Positives = 33/73 (45%), Gaps = 2/73 (2%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           VFVG +P    E ++  L E  G ++   L+ D   G ++GY F  Y +      A   L
Sbjct: 4   VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFS-GLNRGYAFVTYTNKEAAQRAVKQL 62

Query: 215 NGLKM-GDKTLTV 226
           +  ++   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|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 = 39.1 bits (92), Expect = 2e-04
 Identities = 26/84 (30%), Positives = 41/84 (48%), Gaps = 19/84 (22%)

Query: 35  VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE------KKFAFVEMR 88
           V+VG +P  A E+ +   FS+V         GP   VV+  +  +      K + F E  
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEV---------GP---VVSFRLVTDRDTGKPKGYGFCEFE 48

Query: 89  TVEEASNAM-ALDGIIFEGVAVRV 111
            +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|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 39.1 bits (91), Expect = 2e-04
 Identities = 24/81 (29%), Positives = 38/81 (46%), Gaps = 15/81 (18%)

Query: 34  RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFV--EMRTVE 91
           R++VG LPP   E+ +   F +   A              ++I+ +K F F+  E RT+ 
Sbjct: 3   RLFVGNLPPDITEEEMRKLFEKYGKA------------GEIFIHKDKGFGFIRLETRTLA 50

Query: 92  EASNAMALDGIIFEGVAVRVR 112
           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|240819 cd12373, RRM_SRSF3_like, RNA recognition motif in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins

 Score = 39.5 bits (93), Expect = 2e-04
 Identities = 18/73 (24%), Positives = 36/73 (49%), Gaps = 5/73 (6%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           +V+VG L    T+ ++++  E +G L    + +     N  G+ F  ++DP   + A  A
Sbjct: 1   KVYVGNLGPRATKRELEDEFEKYGPLRSVWVAR-----NPPGFAFVEFEDPRDAEDAVRA 55

Query: 214 LNGLKMGDKTLTV 226
           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|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 43.3 bits (102), Expect = 2e-04
 Identities = 27/94 (28%), Positives = 45/94 (47%), Gaps = 10/94 (10%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           ++V  L     E +++EL   FG +    ++KD  +G S+G+ F  ++       A   +
Sbjct: 181 LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDG-SGRSRGFAFVNFEKHEDAAKAVEEM 239

Query: 215 NGLKMGD----KTLTVRRATASSGQSKTEQESIL 244
           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|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 39.5 bits (93), Expect = 2e-04
 Identities = 16/81 (19%), Positives = 35/81 (43%), Gaps = 9/81 (11%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSK---GYGFCVYQDPAVTDIAC 211
           ++V  L +   E  ++ +   FG +    + K +D    +   G+ F  ++D +      
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDAS------ 56

Query: 212 AALNGLKMGDKTLTVRRATAS 232
           +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|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II polyadenylate-binding proteins

 Score = 39.2 bits (92), Expect = 2e-04
 Identities = 19/72 (26%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           +FVG + Y  T  +++E  +S GT++   ++ D+ TG  KG+ +  + D +  + A   L
Sbjct: 2   IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENAL-LL 60

Query: 215 NGLKMGDKTLTV 226
           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|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 39.7 bits (92), Expect = 2e-04
 Identities = 18/60 (30%), Positives = 32/60 (53%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           ++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|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: 164 FTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLK 218
            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|240846 cd12400, RRM_Nop6, RNA recognition motif in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and similar proteins

 Score = 39.3 bits (92), Expect = 2e-04
 Identities = 17/56 (30%), Positives = 24/56 (42%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA 210
           +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|241118 cd12674, RRM1_Nop4p, RNA recognition motif 1 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 39.4 bits (92), Expect = 2e-04
 Identities = 19/77 (24%), Positives = 32/77 (41%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           +FV  L +  T+  + +       +    +V D +TG S+GYGF  +        A A L
Sbjct: 2   LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 215 NGLKMGDKTLTVRRATA 231
              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|241020 cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins

 Score = 39.3 bits (92), Expect = 2e-04
 Identities = 18/53 (33%), Positives = 29/53 (54%)

Query: 156 FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 208
           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|240801 cd12355, RRM_RBM18, RNA recognition motif in eukaryotic RNA-binding protein 18 and similar proteins

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 22/79 (27%), Positives = 36/79 (45%), Gaps = 3/79 (3%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDR---DTGNSKGYGFCVYQDPAVTDIA 210
           R+++G L    TE  + +L   +G +  FD +  +     G  +GY F  ++     + A
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 211 CAALNGLKMGDKTLTVRRA 229
             +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|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 = 2e-04
 Identities = 23/82 (28%), Positives = 36/82 (43%), Gaps = 15/82 (18%)

Query: 35  VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK----FAFVEMRTV 90
           +YVG L     E+ I   FS+          G    ++ + ++   K    F FVE  T 
Sbjct: 1   LYVGNLSFYTTEEQIYELFSR---------CGDIKRII-MGLDRFTKTPCGFCFVEYYTR 50

Query: 91  EEASNAMA-LDGIIFEGVAVRV 111
           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|240737 cd12291, RRM1_La, RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins

 Score = 39.1 bits (92), Expect = 2e-04
 Identities = 21/82 (25%), Positives = 34/82 (41%), Gaps = 17/82 (20%)

Query: 35  VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI--NHEKKF---AFVEMRT 89
           VYV G P  A    I  FF +               V N+ +  + +KKF    FVE +T
Sbjct: 2   VYVKGFPKDATLDDIQEFFEKFGK------------VNNIRMRRDLDKKFKGSVFVEFKT 49

Query: 90  VEEASNAMALDGIIFEGVAVRV 111
            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|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 = 3e-04
 Identities = 27/89 (30%), Positives = 37/89 (41%), Gaps = 21/89 (23%)

Query: 31  HARRVYVGGLPP-LANEQAIATFFSQVMT------AIGGNSAGPGDAVVNVYINHEKKFA 83
           H+R ++V  LP    +   +   FSQV        AI   +  P              FA
Sbjct: 1   HSRCLFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIA-PNGQPRG------------FA 47

Query: 84  FVEMRTVEEASNAM-ALDGIIFEGVAVRV 111
           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|240831 cd12385, RRM1_hnRNPM_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 38.9 bits (91), Expect = 3e-04
 Identities = 21/75 (28%), Positives = 36/75 (48%), Gaps = 2/75 (2%)

Query: 154 RVFVGGLPYYFTETQIKELL-ESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA 212
           RVF+  +PY      +K+L  E  G +   +L KD + G S+G G   ++D      A  
Sbjct: 1   RVFISNIPYDLKWQDLKDLFREKVGEVTYVELFKD-EEGKSRGCGVVEFKDKESVQKALE 59

Query: 213 ALNGLKMGDKTLTVR 227
            +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|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 38.8 bits (91), Expect = 3e-04
 Identities = 16/63 (25%), Positives = 28/63 (44%)

Query: 157 VGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNG 216
           +G L  +  E  I       G +    +++++ TG S GYGF  +      + A  +LNG
Sbjct: 4   MGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSLNG 63

Query: 217 LKM 219
             +
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|241106 cd12662, RRM3_MYEF2, RNA recognition motif 3 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 38.9 bits (90), Expect = 3e-04
 Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 2/74 (2%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           ++FV  LP+  T  ++KE     G +  F  +K  + G SKG G   +  P   + AC  
Sbjct: 1   QIFVRNLPFDLTWQKLKEKFSQCGHVM-FAEIK-MENGKSKGCGTVRFDSPESAEKACRL 58

Query: 214 LNGLKMGDKTLTVR 227
           +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|240885 cd12439, RRM_TRMT2A, RNA recognition motif in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and similar proteins

 Score = 38.8 bits (91), Expect = 3e-04
 Identities = 17/79 (21%), Positives = 30/79 (37%), Gaps = 5/79 (6%)

Query: 153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA 212
            +V +  LP Y    Q+K+ L+       F   K +     + + F  ++       A  
Sbjct: 6   FKVEIKNLPKYIGFKQLKKFLKK----QLFKPHKIKLLKR-QDFAFVTFRSEEERQKALE 60

Query: 213 ALNGLKMGDKTLTVRRATA 231
            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|240894 cd12448, RRM2_gar2, RNA recognition motif 2 in yeast protein gar2 and similar proteins

 Score = 38.5 bits (90), Expect = 3e-04
 Identities = 21/63 (33%), Positives = 31/63 (49%), Gaps = 3/63 (4%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           +FVG L +   E  I E    +G +    L  D D+G  KG+G   Y + +  + A AAL
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFG---YVEFSSQEAAQAAL 57

Query: 215 NGL 217
           + 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|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 = 4e-04
 Identities = 18/73 (24%), Positives = 37/73 (50%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           + VG L     +  +KE+  ++GT+   DL  DR+    +GY +  ++ P   + A   +
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 215 NGLKMGDKTLTVR 227
           +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|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 = 4e-04
 Identities = 22/77 (28%), Positives = 41/77 (53%), Gaps = 2/77 (2%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           ++V GLP   T+ ++++L   +G +    +++D+ TG S+G GF  +      + A   L
Sbjct: 3   LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGL 62

Query: 215 NGLKM--GDKTLTVRRA 229
           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|241095 cd12651, RRM2_SXL, RNA recognition motif 2 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 38.3 bits (89), Expect = 5e-04
 Identities = 18/62 (29%), Positives = 35/62 (56%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           ++V  LP   TE +++++ E++G +   +L++D+ TG  +G  F  Y        A ++L
Sbjct: 3   LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSL 62

Query: 215 NG 216
           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|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 38.1 bits (88), Expect = 5e-04
 Identities = 17/55 (30%), Positives = 31/55 (56%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 208
           ++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|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 38.3 bits (88), Expect = 5e-04
 Identities = 18/60 (30%), Positives = 31/60 (51%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           +++ 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|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 41.1 bits (96), Expect = 6e-04
 Identities = 32/110 (29%), Positives = 48/110 (43%), Gaps = 6/110 (5%)

Query: 142 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 201
           +S +I GA     ++V GLP   T+ +++ +   FG +    ++ D  TG SKG GF  +
Sbjct: 83  SSDSIKGAN----LYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRF 138

Query: 202 QDPAVTDIACAALNGLKMGDKT--LTVRRATASSGQSKTEQESILAQAQQ 249
                 D A   LNG      T  +TV+ A   S  +     S L   Q 
Sbjct: 139 DKRDEADRAIKTLNGTTPSGCTEPITVKFANNPSSSNSKGLLSQLEAVQN 188

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

>gnl|CDD|241018 cd12574, RRM1_DAZAP1, RNA recognition motif 1 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 37.9 bits (88), Expect = 7e-04
 Identities = 16/51 (31%), Positives = 31/51 (60%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP 204
           ++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|240757 cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins

 Score = 37.7 bits (88), Expect = 7e-04
 Identities = 21/67 (31%), Positives = 34/67 (50%), Gaps = 3/67 (4%)

Query: 294 DDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNAL 353
           D+  Y    +D+R    KYG + +V IPR D+   E+ G    F+ +YD      A +A+
Sbjct: 4   DNLTYRTTPDDLRRVFEKYGEVGDVYIPR-DRYTRESRGFA--FVRFYDKRDAEDAMDAM 60

Query: 354 SGRKFGG 360
            G++  G
Sbjct: 61  DGKELDG 67

This subfamily corresponds to the RRM of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or splicing component, 35 kDa (splicing factor SC35 or SC-35), is a prototypical SR protein that plays important roles in the alternative splicing of pre-mRNA. It is also involved in transcription elongation by directly or indirectly mediating the recruitment of elongation factors to the C-terminal domain of polymerase II. SRSF2 is exclusively localized in the nucleus and is restricted to nuclear processes. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. The RRM is responsible for the specific recognition of 5'-SSNG-3' (S=C/G) RNA. In the regulation of alternative splicing events, it specifically binds to cis-regulatory elements on the pre-mRNA. The RS domain modulates SRSF2 activity through phosphorylation, directly contacts RNA, and promotes protein-protein interactions with the spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a novel mammalian SR splicing factor encoded by a PR264/SC35 functional retropseudogene. SRSF8 is localized in the nucleus and does not display the same activity as PR264/SC35. It functions as an essential splicing factor in complementing a HeLa cell S100 extract deficient in SR proteins. Like SRSF2, SRSF8 contains a single N-terminal RRM and a C-terminal RS domain. . Length = 73

>gnl|CDD|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 = 8e-04
 Identities = 25/78 (32%), Positives = 34/78 (43%), Gaps = 12/78 (15%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVK------DRDTGNSKGYGFCVYQDPAVTD 208
           ++VG L +Y TE QI EL    G       +K      DR T    G+ F  Y      +
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGD------IKRIIMGLDRFTKTPCGFCFVEYYTREDAE 54

Query: 209 IACAALNGLKMGDKTLTV 226
            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|241096 cd12652, RRM2_Hu, RNA recognition motif 2 in the Hu proteins family

 Score = 37.7 bits (88), Expect = 8e-04
 Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 2/77 (2%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           ++V GLP   T+ +++ L   +G +    ++ D  TG S+G GF  +      + A  AL
Sbjct: 3   LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62

Query: 215 NGLKMGDKT--LTVRRA 229
           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|240829 cd12383, RRM_RBM42, RNA recognition motif in RNA-binding protein 42 (RBM42) and similar proteins

 Score = 37.6 bits (88), Expect = 9e-04
 Identities = 24/78 (30%), Positives = 41/78 (52%), Gaps = 4/78 (5%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           R+FVG L    T+  +      + +     +V+D+ TG SKGYGF  + DP   D   A 
Sbjct: 8   RIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPN--DYLKAM 65

Query: 214 --LNGLKMGDKTLTVRRA 229
             +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|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 40.6 bits (95), Expect = 0.001
 Identities = 53/241 (21%), Positives = 94/241 (39%), Gaps = 31/241 (12%)

Query: 35  VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEAS 94
           +YV  L P  NE  +   F++     G  ++    AV+       + FAFV     E+A+
Sbjct: 181 LYVKNLDPSVNEDKLRELFAK----FGEITSA---AVMKDGSGRSRGFAFVNFEKHEDAA 233

Query: 95  NAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQP----SPNLNLAAVGLASGAIGGA 149
            A+  ++G                       +G  Q        L      L       A
Sbjct: 234 KAVEEMNGKKI----------GLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKA 283

Query: 150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 209
           +G + ++V  L    T+ +++EL    G +    ++ D + G S+G+GF  + +P   + 
Sbjct: 284 QGVN-LYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFSNPEEANR 341

Query: 210 ACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGG 269
           A   ++G  +G K L V  A     Q K ++ + L    Q + +Q    Q    + +GG 
Sbjct: 342 AVTEMHGRMLGGKPLYVALA-----QRKEQRRAHL--QDQFMQLQPRMRQLPMGSPMGGA 394

Query: 270 M 270
           M
Sbjct: 395 M 395

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

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

 Score = 36.8 bits (86), Expect = 0.001
 Identities = 18/80 (22%), Positives = 28/80 (35%), Gaps = 15/80 (18%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVV------NVYINHEKKFAFVE 86
           R +YV  L    +E  +   FS+          G  +++                FAFV 
Sbjct: 1   REIYVRNLDFKLDEDDLRGIFSK---------FGEVESIRIPKKQDEKQGRLNNGFAFVT 51

Query: 87  MRTVEEASNAMALDGIIFEG 106
            +    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|241028 cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 37.3 bits (86), Expect = 0.001
 Identities = 16/50 (32%), Positives = 27/50 (54%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD 203
           ++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|240725 cd12279, RRM_TUT1, RNA recognition motif in speckle targeted PIP5K1A-regulated poly(A) polymerase (Star-PAP) and similar proteins

 Score = 37.0 bits (86), Expect = 0.001
 Identities = 21/82 (25%), Positives = 35/82 (42%), Gaps = 13/82 (15%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-FAFVEMRTVE 91
           R V+V G     +E+ +  +FS           GP   V+NV ++ +K  +A VE  + E
Sbjct: 3   RSVFVSGFKRGTSEEQLMDYFSAF---------GP---VMNVIMDKDKGVYAIVEFDSKE 50

Query: 92  EASNAMALDGIIFEGVAVRVRR 113
                ++       G  +RVR 
Sbjct: 51  GVDKVLSEPQHTLNGHRLRVRP 72

This subfamily corresponds to the RRM of Star-PAP, also termed RNA-binding motif protein 21 (RBM21), which is a ubiquitously expressed U6 snRNA-specific terminal uridylyltransferase (U6-TUTase) essential for cell proliferation. Although it belongs to the well-characterized poly(A) polymerase protein superfamily, Star-PAP is highly divergent from both, the poly(A) polymerase (PAP) and the terminal uridylyl transferase (TUTase), identified within the editing complexes of trypanosomes. Star-PAP predominantly localizes at nuclear speckles and catalyzes RNA-modifying nucleotidyl transferase reactions. It functions in mRNA biosynthesis and may be regulated by phosphoinositides. It binds to glutathione S-transferase (GST)-PIPKIalpha. Star-PAP preferentially uses ATP as a nucleotide substrate and possesses PAP activity that is stimulated by PtdIns4,5P2. It contains an N-terminal C2H2-type zinc finger motif followed by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a split PAP domain linked by a proline-rich region, a PAP catalytic and core domain, a PAP-associated domain, an RS repeat, and a nuclear localization signal (NLS). . Length = 74

>gnl|CDD|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 36.9 bits (86), Expect = 0.001
 Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 1/64 (1%)

Query: 155 VFVGGLPYYFTETQIKELLESFG-TLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           +++G L  Y  E  IK    S G T+    +++++ TG   GY F  + D A  +     
Sbjct: 2   LWMGDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLHK 61

Query: 214 LNGL 217
           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|240789 cd12343, RRM1_2_CoAA_like, RNA recognition motif 1 and 2 in RRM-containing coactivator activator/modulator (CoAA) and similar proteins

 Score = 36.4 bits (85), Expect = 0.001
 Identities = 21/79 (26%), Positives = 33/79 (41%), Gaps = 15/79 (18%)

Query: 34  RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEA 93
           +++VG LP     + +   F +  T          D V        K + FV M   E+A
Sbjct: 1   KLFVGNLPDATTSEELRALFEKYGTVT------ECDVV--------KNYGFVHMEEEEDA 46

Query: 94  SNAM-ALDGIIFEGVAVRV 111
            +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|241040 cd12596, RRM1_SRSF6, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 6 (SRSF6)

 Score = 36.4 bits (84), Expect = 0.001
 Identities = 23/76 (30%), Positives = 33/76 (43%), Gaps = 8/76 (10%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           RV++G L Y+  E  I+     +G L   DL          GYGF  ++D    D A   
Sbjct: 1   RVYIGRLSYHVREKDIQRFFGGYGKLLEIDL--------KNGYGFVEFEDSRDADDAVYE 52

Query: 214 LNGLKMGDKTLTVRRA 229
           LNG  +  + + V  A
Sbjct: 53  LNGKDLCGERVIVEHA 68

This subfamily corresponds to the RRM1 of SRSF6, also termed pre-mRNA-splicing factor SRp55, which is an essential splicing regulatory serine/arginine (SR) protein that preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. For instance, it does not bind to the purine-rich sequence in the calcitonin-specific ESE, but binds to a region adjacent to the purine tract. Moreover, cellular levels of SRSF6 may control tissue-specific alternative splicing of the calcitonin/ calcitonin gene-related peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal SR domains rich in serine-arginine dipeptides. . Length = 70

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

 Score = 36.4 bits (85), Expect = 0.002
 Identities = 17/61 (27%), Positives = 31/61 (50%), Gaps = 4/61 (6%)

Query: 303 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNT 362
           ED+++   K+G + ++ I R     G + G    F+E+ D      A  AL+G++ GG  
Sbjct: 13  EDLKDLFSKFGPIESIRIVR--DETGRSKGFA--FVEFEDEEDAEKALEALNGKELGGRE 68

Query: 363 V 363
           +
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|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 = 36.8 bits (86), Expect = 0.002
 Identities = 21/86 (24%), Positives = 36/86 (41%), Gaps = 19/86 (22%)

Query: 35  VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFVEMR 88
           ++V GL     E+ +   FS+          G    V  V +  + +      F FV   
Sbjct: 4   LFVSGLSTRTTEKELEALFSKF---------GR---VEEVLLMKDPETGESRGFGFVTFE 51

Query: 89  TVEEASNAM-ALDGIIFEGVAVRVRR 113
           +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|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering time control protein FCA and similar proteins

 Score = 36.7 bits (85), Expect = 0.002
 Identities = 23/79 (29%), Positives = 40/79 (50%), Gaps = 4/79 (5%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           ++FVG L    TE +++E+   +G +    +++D +   S+G  F  Y    +   A  A
Sbjct: 1   KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRD-EMKQSRGCAFVKYSSKEMAQAAIKA 59

Query: 214 LNGL---KMGDKTLTVRRA 229
           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|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 36.4 bits (84), Expect = 0.002
 Identities = 22/73 (30%), Positives = 34/73 (46%), Gaps = 8/73 (10%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           ++FVG LP   TE +I+ L E +G +   D++K+        YGF    D    D A   
Sbjct: 2   KLFVGNLPPEATEQEIRSLFEQYGKVLECDIIKN--------YGFVHMDDKTAADEAIRN 53

Query: 214 LNGLKMGDKTLTV 226
           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|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 36.7 bits (84), Expect = 0.002
 Identities = 18/60 (30%), Positives = 32/60 (53%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           +++ 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|240978 cd12534, RRM_SARFH, RNA recognition motif in Drosophila melanogaster RNA-binding protein cabeza and similar proteins

 Score = 36.6 bits (85), Expect = 0.002
 Identities = 22/58 (37%), Positives = 25/58 (43%), Gaps = 8/58 (13%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTL-----HGFD---LVKDRDTGNSKGYGFCVYQDP 204
           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|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: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 211
           ++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: 294 DDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNAL 353
            DE++E  L++  E  G+ G +  + I        +    G V++ +  +   A A   L
Sbjct: 1   KDEDFERELKEEEEYFGEVGKINKIYIDDVGYENHK---RGNVYITFERSEDAARAIVDL 57

Query: 354 SGRKFGGNTVNA 365
           +GR F G  V A
Sbjct: 58  NGRYFDGRLVKA 69

Length = 70

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

 Score = 36.2 bits (84), Expect = 0.002
 Identities = 16/57 (28%), Positives = 27/57 (47%), Gaps = 1/57 (1%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA 210
            V++G L +  TE  ++E  +    +    L  D++TG  KG+G   + D    D A
Sbjct: 1   TVYIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLDAA 56

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

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

 Score = 36.5 bits (85), Expect = 0.002
 Identities = 21/77 (27%), Positives = 34/77 (44%), Gaps = 7/77 (9%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           R+F+       TE  ++E    FG +    +VKD+ T  SKG  +  +   A    A  A
Sbjct: 5   RLFIV-CGKSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKF---AKASSAARA 60

Query: 214 ---LNGLKMGDKTLTVR 227
              +NG  +G  T  ++
Sbjct: 61  MEEMNGKCLGGDTKPLK 77

This subfamily corresponds to the RRM1 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 81

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

 Score = 36.1 bits (84), Expect = 0.002
 Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD 203
           VFV  L Y   E ++++L    G +    LVK+   G SKGY +  +++
Sbjct: 2   VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNY-KGKSKGYAYVEFEN 49

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

>gnl|CDD|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 36.1 bits (83), Expect = 0.002
 Identities = 17/54 (31%), Positives = 30/54 (55%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 208
           +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

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

 Score = 36.1 bits (83), Expect = 0.003
 Identities = 21/78 (26%), Positives = 37/78 (47%), Gaps = 8/78 (10%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           RVF+G L     E  ++   + +G +   DL         +G+GF  + DP   D A   
Sbjct: 1   RVFIGRLNPAAREKDVERFFKGYGRIRDIDL--------KRGFGFVEFDDPRDADDAVYE 52

Query: 214 LNGLKMGDKTLTVRRATA 231
           L+G ++ ++ +T+  A A
Sbjct: 53  LDGKELCNERVTIEHARA 70

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

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

 Score = 36.2 bits (83), Expect = 0.003
 Identities = 22/77 (28%), Positives = 39/77 (50%), Gaps = 2/77 (2%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           ++V GLP   T+ ++++L   +G +    ++ D+ TG S+G GF  +      + A   L
Sbjct: 5   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 64

Query: 215 NGLKMGDKT--LTVRRA 229
           NG K       +TV+ A
Sbjct: 65  NGQKPSGAAEPITVKFA 81

This subgroup corresponds to the RRM2 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells and also regulates the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

>gnl|CDD|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like proteins mainly from plants

 Score = 36.2 bits (84), Expect = 0.003
 Identities = 22/76 (28%), Positives = 34/76 (44%), Gaps = 5/76 (6%)

Query: 155 VFVGGLPYYFTETQIK-ELLESF---GTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA 210
           +FV G      E  I+  L E F   G +    +  DR+TG SKG+ +  ++     + A
Sbjct: 2   IFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKA 61

Query: 211 CAALNGLKMGDKTLTV 226
              L+G  +G   L V
Sbjct: 62  -LELDGSDLGGGNLVV 76

This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 4 (SRSF4)

 Score = 35.7 bits (82), Expect = 0.003
 Identities = 19/66 (28%), Positives = 28/66 (42%), Gaps = 8/66 (12%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           RV++G L Y   E  ++   + +G +   DL          GYGF  + D    D A   
Sbjct: 1   RVYIGRLSYQARERDVERFFKGYGKILEVDL--------KNGYGFVEFDDLRDADDAVYE 52

Query: 214 LNGLKM 219
           LNG  +
Sbjct: 53  LNGKDL 58

This subgroup corresponds to the RRM1 of SRSF4, also termed pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing factor, arginine/serine-rich 4 (SFRS4). SRSF4 is a splicing regulatory serine/arginine (SR) protein that plays an important role in both constitutive splicing and alternative splicing of many pre-mRNAs. For instance, it interacts with heterogeneous nuclear ribonucleoproteins, hnRNP G and hnRNP E2, and further regulates the 5' splice site of tau exon 10, whose misregulation causes frontotemporal dementia. SFSF4 also induces production of HIV-1 vpr mRNA through the inhibition of the 5'-splice site of exon 3. In addition, it activates splicing of the cardiac troponin T (cTNT) alternative exon by direct interactions with the cTNT exon 5 enhancer RNA. SRSF4 can shuttle between the nucleus and cytoplasm. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine-rich region, an internal region homologous to the RRM, and a very long, highly phosphorylated C-terminal SR domains rich in serine-arginine dipeptides. . Length = 74

>gnl|CDD|240931 cd12487, RRM1_DND1, RNA recognition motif 1 found in vertebrate dead end protein homolog 1 (DND1)

 Score = 35.9 bits (83), Expect = 0.003
 Identities = 22/76 (28%), Positives = 39/76 (51%), Gaps = 2/76 (2%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           VF+G +P    E ++  L +S GTL+ F L+    +G ++G+ +  Y D      A A L
Sbjct: 4   VFIGKIPQDVYEDRLIPLFQSVGTLYEFRLMMTF-SGLNRGFAYAKYSDRRGASAAIATL 62

Query: 215 NGLKMGD-KTLTVRRA 229
           +  ++ +   L V R+
Sbjct: 63  HNYELPEGCCLLVCRS 78

This subgroup corresponds to the RRM1 of DND1, also termed RNA-binding motif, single-stranded-interacting protein 4, an RNA-binding protein that is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. For instance, DND1 binds cell cycle inhibitor, P27 (p27Kip1, CDKN1B), and cell cycle regulator and tumor suppressor, LATS2 (large tumor suppressor, homolog 2 of Drosophila). It helps maintain their protein expression through blocking the inhibitory function of microRNAs (miRNA) from these transcripts. DND1 may also impose another level of translational regulation to modulate expression of critical factors in embryonic stem (ES) cells. DND1 interacts specifically with apolipoprotein B editing complex 3 (APOBEC3), a multi-functional protein inhibiting retroviral replication. The DND1-APOBEC3 interaction may play a role in maintaining viability of germ cells and for preventing germ cell tumor development. DND1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

>gnl|CDD|240784 cd12338, RRM1_SRSF1_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 35.8 bits (83), Expect = 0.003
 Identities = 24/83 (28%), Positives = 33/83 (39%), Gaps = 18/83 (21%)

Query: 34  RVYVGGLPPLANEQAIATFFSQ----VMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRT 89
           R+YVG LP    E+ I   F +        +     GP              FAFVE   
Sbjct: 1   RIYVGNLPGDIRERDIEDLFYKYGPIKAIDLKNRRRGPP-------------FAFVEFED 47

Query: 90  VEEASNAM-ALDGIIFEGVAVRV 111
             +A +A+   DG  F+G  +RV
Sbjct: 48  PRDAEDAVRGRDGYDFDGYRLRV 70

This subgroup corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C), and plant pre-mRNA-splicing factor SF2 (SR1). SRSF1 is a shuttling SR protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF9 has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. It can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. Both, SRSF1 and SRSF9, contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RS domains rich in serine-arginine dipeptides. In contrast, SF2 contains two N-terminal RRMs and a C-terminal PSK domain rich in proline, serine and lysine residues. . Length = 72

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

 Score = 35.3 bits (82), Expect = 0.004
 Identities = 18/70 (25%), Positives = 34/70 (48%)

Query: 157 VGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNG 216
           V  L Y  T   ++ + E +G +    + +DR T  S+G+ F  + D    + A  A++G
Sbjct: 3   VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDG 62

Query: 217 LKMGDKTLTV 226
            ++  + L V
Sbjct: 63  KELDGRELRV 72

This subfamily corresponds to the RRM of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or splicing component, 35 kDa (splicing factor SC35 or SC-35), is a prototypical SR protein that plays important roles in the alternative splicing of pre-mRNA. It is also involved in transcription elongation by directly or indirectly mediating the recruitment of elongation factors to the C-terminal domain of polymerase II. SRSF2 is exclusively localized in the nucleus and is restricted to nuclear processes. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. The RRM is responsible for the specific recognition of 5'-SSNG-3' (S=C/G) RNA. In the regulation of alternative splicing events, it specifically binds to cis-regulatory elements on the pre-mRNA. The RS domain modulates SRSF2 activity through phosphorylation, directly contacts RNA, and promotes protein-protein interactions with the spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a novel mammalian SR splicing factor encoded by a PR264/SC35 functional retropseudogene. SRSF8 is localized in the nucleus and does not display the same activity as PR264/SC35. It functions as an essential splicing factor in complementing a HeLa cell S100 extract deficient in SR proteins. Like SRSF2, SRSF8 contains a single N-terminal RRM and a C-terminal RS domain. . Length = 73

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

 Score = 35.6 bits (83), Expect = 0.004
 Identities = 22/89 (24%), Positives = 36/89 (40%), Gaps = 20/89 (22%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFVE 86
             + + GL  L  E+ I    S +              + +V +  +K       FAFVE
Sbjct: 3   NTLILRGLDLLTTEEDILQALSAI----------ASVPIKDVRLIRDKLTGTSRGFAFVE 52

Query: 87  MRTVEEASNAM----ALDGIIFEGVAVRV 111
             ++E+A+  M     LD  + +G  VRV
Sbjct: 53  FPSLEDATQWMDALNNLDPFVIDGRVVRV 81

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

>gnl|CDD|241042 cd12598, RRM1_SRSF9, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 9 (SRSF9)

 Score = 35.5 bits (82), Expect = 0.004
 Identities = 18/73 (24%), Positives = 32/73 (43%), Gaps = 3/73 (4%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           R++VG LP    E  +++L   +G +   +L   ++      + F  ++DP   + A   
Sbjct: 1   RIYVGNLPSDVREKDLEDLFYKYGRIRDIEL---KNRRGLVPFAFVRFEDPRDAEDAVFG 57

Query: 214 LNGLKMGDKTLTV 226
            NG   G   L V
Sbjct: 58  RNGYDFGQCRLRV 70

This subgroup corresponds to the RRM1 of SRSF9, also termed pre-mRNA-splicing factor SRp30C. SRSF9 is an essential splicing regulatory serine/arginine (SR) protein that has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. SRSF9 can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by an unusually short C-terminal RS domains rich in serine-arginine dipeptides. . Length = 72

>gnl|CDD|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related protein 7 (LARP7) and similar proteins

 Score = 35.8 bits (83), Expect = 0.004
 Identities = 19/61 (31%), Positives = 30/61 (49%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           V+V  LP   T   +K +   +GT+    L + + TG+ KG+ F  ++ P     AC  L
Sbjct: 2   VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61

Query: 215 N 215
           N
Sbjct: 62  N 62

This subfamily corresponds to the RRM1 of LARP7, also termed La ribonucleoprotein domain family member 7, or P-TEFb-interaction protein for 7SK stability (PIP7S), an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. LARP7 is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP). It intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. It plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. LARP7 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminal region, which mediates binding to the U-rich 3' terminus of 7SK RNA. LARP7 also carries another putative RRM domain at its C-terminus. . Length = 80

>gnl|CDD|240700 cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, epithelial splicing regulatory proteins (ESRPs), Drosophila RNA-binding protein Fusilli, RNA-binding protein 12 (RBM12) and similar proteins

 Score = 35.2 bits (82), Expect = 0.004
 Identities = 18/72 (25%), Positives = 29/72 (40%), Gaps = 16/72 (22%)

Query: 35  VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI--NHEKKF---AFVEMRT 89
           V + GLP  A E+ I  FFS           G       ++I  + + +    A+VE  +
Sbjct: 2   VRLRGLPFSATEEDIRDFFS-----------GLDIPPDGIHIVYDDDGRPTGEAYVEFAS 50

Query: 90  VEEASNAMALDG 101
            E+A  A+    
Sbjct: 51  PEDARRALRKHN 62

The family includes RRM domains in the hnRNP H protein family, G-rich sequence factor 1 (GRSF-1), ESRPs (also termed RBM35), Drosophila Fusilli, RBM12 (also termed SWAN), RBM12B, RBM19 (also termed RBD-1) and similar proteins. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. Fusilli shows high sequence homology to ESRPs. It can regulate endogenous FGFR2 splicing and functions as a splicing factor. The biological roles of both, RBM12 and RBM12B, remain unclear. RBM19 is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. Members in this family contain 2~6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

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

 Score = 35.9 bits (82), Expect = 0.004
 Identities = 19/64 (29%), Positives = 34/64 (53%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           ++V GLP   T+ ++++L   +G +    ++ D+ TG S+G GF  +      + A   L
Sbjct: 8   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 67

Query: 215 NGLK 218
           NG K
Sbjct: 68  NGQK 71

This subgroup corresponds to the RRM2 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 90

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	380
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	100.0
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	100.0
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	100.0
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	100.0
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	100.0
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	100.0
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	100.0
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	100.0
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	100.0
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	100.0
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	100.0
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	100.0
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	100.0
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	100.0
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	100.0
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	100.0
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	100.0
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.97
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.97
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.96
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.95
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.95
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.95
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.95
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.94
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.93
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.91
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.91
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.91
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.9
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.9
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.9
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.89
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.89
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.87
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.86
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.85
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.85
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.85
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.83
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.83
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.83
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.81
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.78
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.77
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.77
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.76
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.74
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.72
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.7
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.7
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	99.68
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.67
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.65
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.61
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.61
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.58
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.57
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.56
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.53
KOG0122	270	consensus Translation initiation factor 3, subunit	99.53
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.52
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.52
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.5
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.47
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.45
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.45
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.45
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.43
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.43
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.43
PLN03120	260	nucleic acid binding protein; Provisional	99.43
PLN03120	260	nucleic acid binding protein; Provisional	99.41
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.41
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.39
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.39
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	99.37
smart00362	72	RRM_2 RNA recognition motif.	99.37
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.36
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.34
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.34
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.33
smart00360	71	RRM RNA recognition motif.	99.33
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.32
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.32
PLN03213	759	repressor of silencing 3; Provisional	99.32
PLN03121	243	nucleic acid binding protein; Provisional	99.32
PLN03121	243	nucleic acid binding protein; Provisional	99.32
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.31
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	99.3
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.3
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.28
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.27
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.26
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.26
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.24
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.24
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.24
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.24
KOG0122	270	consensus Translation initiation factor 3, subunit	99.24
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.2
smart00361	70	RRM_1 RNA recognition motif.	99.19
smart00362	72	RRM_2 RNA recognition motif.	99.18
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	99.16
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.15
smart00361	70	RRM_1 RNA recognition motif.	99.11
PLN03213	759	repressor of silencing 3; Provisional	99.1
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.07
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.06
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.01
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.0
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	98.99
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.95
smart00360	71	RRM RNA recognition motif.	98.94
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.94
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.93
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	98.92
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.85
KOG1996	378	consensus mRNA splicing factor [RNA processing and	98.84
KOG4210	285	consensus Nuclear localization sequence binding pr	98.8
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.8
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	98.8
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	98.78
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	98.76
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.71
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	98.69
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.69
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.68
KOG0226	290	consensus RNA-binding proteins [General function p	98.67
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.67
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	98.66
KOG0226	290	consensus RNA-binding proteins [General function p	98.61
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.59
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.5
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.47
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	98.45
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.43
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.4
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.39
KOG4210	285	consensus Nuclear localization sequence binding pr	98.36
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	98.35
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.34
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.31
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.3
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	98.27
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	98.26
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.23
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	98.16
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.15
KOG0151	877	consensus Predicted splicing regulator, contains R	98.14
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.11
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.07
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.06
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.04
KOG0151	877	consensus Predicted splicing regulator, contains R	97.97
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.77
KOG1995	351	consensus Conserved Zn-finger protein [General fun	97.73
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.69
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.59
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.59
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.45
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	97.44
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	97.39
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.32
KOG2314	698	consensus Translation initiation factor 3, subunit	97.26
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.25
KOG1995	351	consensus Conserved Zn-finger protein [General fun	97.22
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.22
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	97.21
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.07
KOG3152	278	consensus TBP-binding protein, activator of basal	97.03
KOG2314	698	consensus Translation initiation factor 3, subunit	96.83
KOG1855	484	consensus Predicted RNA-binding protein [General f	96.77
KOG1996	378	consensus mRNA splicing factor [RNA processing and	96.66
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	96.64
KOG1855	484	consensus Predicted RNA-binding protein [General f	96.3
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.27
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	96.2
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	96.12
KOG3152	278	consensus TBP-binding protein, activator of basal	96.0
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	95.96
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	95.94
KOG2135	526	consensus Proteins containing the RNA recognition	95.57
KOG2135	526	consensus Proteins containing the RNA recognition	94.85
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	94.84
KOG2068	327	consensus MOT2 transcription factor [Transcription	94.66
KOG2591	684	consensus c-Mpl binding protein, contains La domai	94.44
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	94.38
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	94.18
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	94.08
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	94.07
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	93.9
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	93.75
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	92.94
KOG2068	327	consensus MOT2 transcription factor [Transcription	92.7
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	92.41
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	92.4
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	92.37
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	91.97
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	91.38
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	90.84
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	90.81
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	90.62
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	90.12
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	89.83
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	87.95
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	87.15
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	85.53
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	84.94
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	84.27
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	83.28

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

Probab=100.00  E-value=1.2e-49  Score=394.70  Aligned_cols=344  Identities=47%  Similarity=0.747  Sum_probs=269.5

Q ss_pred             ccchhhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHHHcCCc
Q 016936           23 VMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGI  102 (380)
Q Consensus        23 ~~~~~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai~l~~~  102 (380)
                      .+.++.++..++|||+|||+.+|+++|+++|++++...+.....++.+|..+.+.+++|||||+|.+.++|..||+|++.
T Consensus       166 ~~~~~~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~~~~kg~afVeF~~~e~A~~Al~l~g~  245 (509)
T TIGR01642       166 PYQQQATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNINKEKNFAFLEFRTVEEATFAMALDSI  245 (509)
T ss_pred             ccCccCCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEECCCCCEEEEEeCCHHHHhhhhcCCCe
Confidence            44557789999999999999999999999999998777655555566789999999999999999999999999999999


Q ss_pred             eecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEE
Q 016936          103 IFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGF  182 (380)
Q Consensus       103 ~i~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v  182 (380)
                      .+.|++|+|.++..+..............+..+......+..........++|||+|||..+++++|+++|+.||.|..+
T Consensus       246 ~~~g~~l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~  325 (509)
T TIGR01642       246 IYSNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAF  325 (509)
T ss_pred             EeeCceeEecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEE
Confidence            99999999998776653221111111111111111111111222234556899999999999999999999999999999


Q ss_pred             EEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccCCCCChhHHHHHHHHHHHHHHHHHHHhhhcC
Q 016936          183 DLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSG  262 (380)
Q Consensus       183 ~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  262 (380)
                      .++.++.+|.++|||||+|.+.++|..|++.|+|..+.|+.|.|.++.................      ..   .....
T Consensus       326 ~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~~~~~~~~~~~~~~~------~~---~~~~~  396 (509)
T TIGR01642       326 NLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVGANQATIDTSNGMAP------VT---LLAKA  396 (509)
T ss_pred             EEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccCCCCCCccccccccc------cc---ccccc
Confidence            9999988899999999999999999999999999999999999999865433221111100000      00   00000


Q ss_pred             ccccCCCCCccCCccceEEEEeccCCcccCCChHHHHHHHHHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeec
Q 016936          263 MNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYD  342 (380)
Q Consensus       263 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~  342 (380)
                      .   ..........++.++.|.|+++.+++.++.+|.++.++|+++|++||.|.+|.|++........+|.|+|||+|.+
T Consensus       397 ~---~~~~~~~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~  473 (509)
T TIGR01642       397 L---SQSILQIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYAD  473 (509)
T ss_pred             c---hhhhccccCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeeccCcCCCcCCCcceEEEEECC
Confidence            0   0000011245789999999999999999999999999999999999999999998865444445678899999999


Q ss_pred             hhhHHHHHHHHcCcccCCeEEEEEeccccccccccC
Q 016936          343 AVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY  378 (380)
Q Consensus       343 ~~~A~~A~~~l~g~~i~gr~l~v~~~~~~~~~~~~~  378 (380)
                      +++|++|++.|||++|+|+.|.|.|++++.|+.+.|
T Consensus       474 ~e~A~~A~~~lnGr~~~gr~v~~~~~~~~~~~~~~~  509 (509)
T TIGR01642       474 VRSAEKAMEGMNGRKFNDRVVVAAFYGEDCYKAGDY  509 (509)
T ss_pred             HHHHHHHHHHcCCCEECCeEEEEEEeCHHHhhccCC
Confidence            999999999999999999999999999999999987

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

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

Probab=100.00  E-value=8.9e-42  Score=331.33  Aligned_cols=322  Identities=27%  Similarity=0.407  Sum_probs=233.6

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecCce
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  108 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g~~  108 (380)
                      ...|+|||+|||+++++++|+++|++||.|...      ..+.+...++++|||||+|.+.++|.+|+ .+||..|.|++
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV------~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~  178 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSI------NMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRN  178 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEE------EEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecce
Confidence            567899999999999999999999999984321      01111123568999999999999999999 79999999999


Q ss_pred             EEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC
Q 016936          109 VRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDR  188 (380)
Q Consensus       109 i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~  188 (380)
                      |+|.++.......          .....        ........++|||+|||.++++++|+++|+.||.|.+|++.+++
T Consensus       179 IkV~rp~~~p~a~----------~~~~~--------~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~  240 (612)
T TIGR01645       179 IKVGRPSNMPQAQ----------PIIDM--------VQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAP  240 (612)
T ss_pred             eeecccccccccc----------ccccc--------ccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecC
Confidence            9998754331110          00000        00112234699999999999999999999999999999999998


Q ss_pred             CCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccCCCCC--------hhHHHHHHH---HHH--HHHHHHH
Q 016936          189 DTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQS--------KTEQESILA---QAQ--QHIAIQK  255 (380)
Q Consensus       189 ~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~~~~~--------~~~~~~~~~---~~~--~~~~~~~  255 (380)
                      .++.++|||||+|.+.++|.+|++.||+..++|+.|+|.++.......        .+.......   .+.  .......
T Consensus       241 ~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi~pP~~~~~pa~~~~~p~aaa~Aaaaa~a~~~a~~~~~~  320 (612)
T TIGR01645       241 TGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTPPDALLQPATVSAIPAAAAVAAAAATAKIMAAEAVAG  320 (612)
T ss_pred             CCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecCCCccccCCCCCCCCCchHHHHHHHHhhhhhhhhhhhhc
Confidence            889999999999999999999999999999999999999977532111        000000000   000  0000000


Q ss_pred             HH-hh--------------------------------------------hcC-cc-----cc------------CCCC--
Q 016936          256 MA-LQ--------------------------------------------TSG-MN-----TL------------GGGM--  270 (380)
Q Consensus       256 ~~-~~--------------------------------------------~~~-~~-----~~------------~~~~--  270 (380)
                      .. ..                                            ..+ +.     .+            +...  
T Consensus       321 ~a~~g~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  400 (612)
T TIGR01645       321 AAVLGPRAQSPATPSSSLPTDIGNKAVVSSAKKEAEEVPPLPQAAPAVVKPGPMEIPTPVPPPGLAIPSLVAPPGLVAPT  400 (612)
T ss_pred             ccccccccCCCccccccccccccccccccccCCcccCCCCCccccccccCCCCcccccCCCCccccccccCCCccccCCC
Confidence            00 00                                            000 00     00            0000  


Q ss_pred             --------------------------------------------------------------------------------
Q 016936          271 --------------------------------------------------------------------------------  270 (380)
Q Consensus       271 --------------------------------------------------------------------------------  270 (380)
                                                                                                      
T Consensus       401 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  480 (612)
T TIGR01645       401 EINPSFLASPRKKMKREKLPVTFGALDDTLAWKEPSKEDQTSEDGKMLAIMGEAAAALALEPKKKKKEKEGEELQPKLVM  480 (612)
T ss_pred             cCchhhhcCcccccccccccccccccccchhccccchhhhhhhhhhhcccchhhHHHHhhhhhHHhhhhhhhhhcccccc
Confidence                                                                                            


Q ss_pred             --------------------------CccCCccceEEEEeccCCcccCCChHHHHHHHHHHHHhhcccCCeEEEEecCCC
Q 016936          271 --------------------------SLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPD  324 (380)
Q Consensus       271 --------------------------~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~~f~~~G~I~~v~i~~~~  324 (380)
                                                .......+++++|.|+++.+++.+     ++++||+++|++||.|.+|.|....
T Consensus       481 ~~~~~~~~~~~~~~i~~~~~~~~~~~~l~rp~~S~vVvL~NMv~~~elde-----dl~eDV~eEC~K~G~V~~v~I~~~~  555 (612)
T TIGR01645       481 NSEDASLASQEGMSIRGNSARHLVMQKLMRTNRSNVIVLRNMVTPQDIDE-----FLEGEIREECGKFGVVDRVIINFEK  555 (612)
T ss_pred             cccccccccccccccccchhhHHHHHhhcCCCCCCEEEEeCCCChHHhHH-----HHHHHHHHHhhcCceeEEEEEecCC
Confidence                                      000123578899999998877643     3668999999999999999998854


Q ss_pred             CC-CCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEeccccccccccCCC
Q 016936          325 QN-GGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDYSA  380 (380)
Q Consensus       325 ~~-~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~~~~~~~~~~~  380 (380)
                      .. .....+.|.+||+|++.++|.+|+..||||+|+||.|.++|+++++|..++|++
T Consensus       556 ~~~~~~~~~~g~VfV~F~~~~~A~~A~~~LnGR~F~GR~V~a~~yd~~~f~~~~l~~  612 (612)
T TIGR01645       556 QGEEEDAEIIVKIFVEFSDSMEVDRAKAALDGRFFGGRTVVAEAYDQILFDHADLSG  612 (612)
T ss_pred             CCccccccceEEEEEEECCHHHHHHHHHHhcCCeECCeEEEEEEcCHHHhhccccCC
Confidence            32 111234567899999999999999999999999999999999999999999986

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

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

Probab=100.00  E-value=4e-42  Score=336.38  Aligned_cols=313  Identities=27%  Similarity=0.437  Sum_probs=236.1

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe------cCCCcEEEEEeCCHHHHHHHHHcC
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAMALD  100 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~------~~~~g~afV~f~~~~~a~~ai~l~  100 (380)
                      .++++.++|||+|||..+++++|+++|++||.            |.++.+      ++++|||||+|.+.++|.+||.++
T Consensus        84 ~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~------------v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~l~  151 (457)
T TIGR01622        84 EAERDDRTVFVLQLALKARERDLYEFFSKVGK------------VRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALALT  151 (457)
T ss_pred             ccccCCcEEEEeCCCCCCCHHHHHHHHHhcCC------------eeEEEEeecCCCCCcceEEEEEECCHHHHHHHHHhC
Confidence            45778899999999999999999999999997            455544      456899999999999999999999


Q ss_pred             CceecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCee
Q 016936          101 GIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLH  180 (380)
Q Consensus       101 ~~~i~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~  180 (380)
                      +..+.|++|.|.++...........                 ..........++|||+|||..+++++|+++|++||.|.
T Consensus       152 g~~~~g~~i~v~~~~~~~~~~~~~~-----------------~~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~  214 (457)
T TIGR01622       152 GQMLLGRPIIVQSSQAEKNRAAKAA-----------------THQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIE  214 (457)
T ss_pred             CCEECCeeeEEeecchhhhhhhhcc-----------------cccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeE
Confidence            9999999999987533211100000                 00000011257999999999999999999999999999


Q ss_pred             EEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccCCCCChhHHHH----------H-HHHHHH
Q 016936          181 GFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQES----------I-LAQAQQ  249 (380)
Q Consensus       181 ~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~----------~-~~~~~~  249 (380)
                      .|.++.++.+|.++|||||+|.+.++|.+|+..|+|..+.|+.|.|.++.............          . ......
T Consensus       215 ~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  294 (457)
T TIGR01622       215 DVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQDSTYLLDAANTFEDIDKQQQMGKNLNTEER  294 (457)
T ss_pred             EEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccCCCccccchhhhccccccccCCcCCCccch
Confidence            99999998888999999999999999999999999999999999999976332111100000          0 000000


Q ss_pred             HHHHHHHHhhh--cCccccCC----------------------------------CCCcc---CCccceEEEEeccCCcc
Q 016936          250 HIAIQKMALQT--SGMNTLGG----------------------------------GMSLF---GETLAKVLCLTEAITAD  290 (380)
Q Consensus       250 ~~~~~~~~~~~--~~~~~~~~----------------------------------~~~~~---~~~~~~~~~l~~~~~~~  290 (380)
                      ......+....  ++...++.                                  .....   ...+++|+.|.|+++..
T Consensus       295 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~l~n~~~~~  374 (457)
T TIGR01622       295 EQLMEKLDRDDGDGGLLIPGTGSKIALMQKLQRDGIIDPNIPSRYATGALAIMARNSFVPSTNNNLATTCLVLSNMFDPA  374 (457)
T ss_pred             HHHHHhhccCCCCccccCCCccchhhhhccccccccccccccccccccccccccCCCCCCcccCCCCCcEEEEecCCCCc
Confidence            00000000000  00000000                                  00000   23678899999999998


Q ss_pred             cCCChHHHHHHHHHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEeccc
Q 016936          291 ALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPE  370 (380)
Q Consensus       291 ~~~~~~~~~~~~~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~  370 (380)
                      +..++.++.++++||+++|++||.|+.|.+.....       .|++||+|.+.++|.+|+..|||++|+||.|.++|+++
T Consensus       375 ~~~~~~~~~~~~~dv~~e~~k~G~v~~v~v~~~~~-------~G~~fV~F~~~e~A~~A~~~lnGr~f~gr~i~~~~~~~  447 (457)
T TIGR01622       375 TEEEPNFDNEILDDVKEECSKYGGVVHIYVDTKNS-------AGKIYLKFSSVDAALAAFQALNGRYFGGKMITAAFVVN  447 (457)
T ss_pred             ccccchHHHHHHHHHHHHHHhcCCeeEEEEeCCCC-------ceeEEEEECCHHHHHHHHHHhcCcccCCeEEEEEEEcH
Confidence            88888899999999999999999999999975432       37889999999999999999999999999999999999


Q ss_pred             ccccc
Q 016936          371 DKYFN  375 (380)
Q Consensus       371 ~~~~~  375 (380)
                      +.|..
T Consensus       448 ~~~~~  452 (457)
T TIGR01622       448 DVYDM  452 (457)
T ss_pred             HHHHh
Confidence            98864

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.

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=100.00  E-value=1.2e-40  Score=315.30  Aligned_cols=289  Identities=19%  Similarity=0.275  Sum_probs=211.2

Q ss_pred             ccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe------cCCCcEEEEEeCCHHHHHHHH-HcCCce
Q 016936           31 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-ALDGII  103 (380)
Q Consensus        31 ~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~------~~~~g~afV~f~~~~~a~~ai-~l~~~~  103 (380)
                      +..+|||+|||.++++++|+++|++||+            |.++++      ++++|||||+|.+.++|.+|| .+++..
T Consensus         2 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~------------i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~   69 (352)
T TIGR01661         2 SKTNLIVNYLPQTMTQEEIRSLFTSIGE------------IESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLR   69 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHccCC------------EEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEE
Confidence            4689999999999999999999999998            444443      457799999999999999999 799999


Q ss_pred             ecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEE
Q 016936          104 FEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFD  183 (380)
Q Consensus       104 i~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~  183 (380)
                      +.|++|+|.++.....                             .....+|||+|||..+++++|+++|++||.|..++
T Consensus        70 l~g~~i~v~~a~~~~~-----------------------------~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~  120 (352)
T TIGR01661        70 LQNKTIKVSYARPSSD-----------------------------SIKGANLYVSGLPKTMTQHELESIFSPFGQIITSR  120 (352)
T ss_pred             ECCeeEEEEeeccccc-----------------------------ccccceEEECCccccCCHHHHHHHHhccCCEEEEE
Confidence            9999999998643211                             11225899999999999999999999999999999


Q ss_pred             EeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCC--eEEEEEEcccCCCCChhHHHHHHHH----HHH--------
Q 016936          184 LVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD--KTLTVRRATASSGQSKTEQESILAQ----AQQ--------  249 (380)
Q Consensus       184 l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g--~~i~v~~~~~~~~~~~~~~~~~~~~----~~~--------  249 (380)
                      ++.+..++.++|||||+|.+.++|++|++.|||..+.|  .+|.|.++.................    ...        
T Consensus       121 ~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  200 (352)
T TIGR01661       121 ILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKFANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTIL  200 (352)
T ss_pred             EEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCCCCcCCchhcCchhhcccCcccCCCCccccc
Confidence            99987788999999999999999999999999998877  6788888765431110000000000    000        


Q ss_pred             -------------------HHHHHHH-----Hhhhc-----CccccC----------CCCCc-cCCccceEEEEeccCCc
Q 016936          250 -------------------HIAIQKM-----ALQTS-----GMNTLG----------GGMSL-FGETLAKVLCLTEAITA  289 (380)
Q Consensus       250 -------------------~~~~~~~-----~~~~~-----~~~~~~----------~~~~~-~~~~~~~~~~l~~~~~~  289 (380)
                                         .......     .....     ....+.          .+... .......++.+.|+...
T Consensus       201 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~  280 (352)
T TIGR01661       201 TAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAAQRASPPATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPD  280 (352)
T ss_pred             cccCCCCccCcccccccCcchhhhhhhhhhhhcccccccccccCCCccccccccccccCCCCCCCCCCCcEEEEeCCCCC
Confidence                               0000000     00000     000000          00000 00122335666664322


Q ss_pred             ccCCChHHHHHHHHHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEecc
Q 016936          290 DALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYP  369 (380)
Q Consensus       290 ~~~~~~~~~~~~~~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~  369 (380)
                                .+.++|+++|++||.|.++.++++..++. ++  |+|||+|.+.++|.+|++.|||+.|+||.|+|.|+.
T Consensus       281 ----------~~e~~L~~~F~~fG~v~~v~i~~d~~t~~-sk--G~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~  347 (352)
T TIGR01661       281 ----------TDETVLWQLFGPFGAVQNVKIIRDLTTNQ-CK--GYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKT  347 (352)
T ss_pred             ----------CCHHHHHHHHHhCCCeEEEEEeEcCCCCC-cc--ceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcc
Confidence                      22369999999999999999999876654 44  566999999999999999999999999999999998


Q ss_pred             cccc
Q 016936          370 EDKY  373 (380)
Q Consensus       370 ~~~~  373 (380)
                      .+.+
T Consensus       348 ~~~~  351 (352)
T TIGR01661       348 NKAY  351 (352)
T ss_pred             CCCC
Confidence            7643

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

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

Probab=100.00  E-value=2.8e-36  Score=292.82  Aligned_cols=249  Identities=19%  Similarity=0.296  Sum_probs=196.4

Q ss_pred             CccccchhhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe-----cCCCcEEEEEeCCHHHHH
Q 016936           20 PVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-----NHEKKFAFVEMRTVEEAS   94 (380)
Q Consensus        20 ~~~~~~~~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~-----~~~~g~afV~f~~~~~a~   94 (380)
                      |++.+........++|||+|||++++|++|+++|+++|.|            .++++     ++++|||||+|.+.++|+
T Consensus        46 Pp~~~~~~~p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I------------~~vrl~~D~sG~sRGfaFV~F~~~e~A~  113 (578)
T TIGR01648        46 PPPGWSGVQPGRGCEVFVGKIPRDLYEDELVPLFEKAGPI------------YELRLMMDFSGQNRGYAFVTFCGKEEAK  113 (578)
T ss_pred             CCCcccCCCCCCCCEEEeCCCCCCCCHHHHHHHHHhhCCE------------EEEEEEECCCCCccceEEEEeCCHHHHH
Confidence            3334444445567999999999999999999999999984            44443     568999999999999999


Q ss_pred             HHH-HcCCceec-CceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHH
Q 016936           95 NAM-ALDGIIFE-GVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKEL  172 (380)
Q Consensus        95 ~ai-~l~~~~i~-g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~  172 (380)
                      +|| .||+..+. |+.|.|.++..                                   .++|||+|||+.+++++|.+.
T Consensus       114 ~Ai~~lng~~i~~Gr~l~V~~S~~-----------------------------------~~rLFVgNLP~~~TeeeL~ee  158 (578)
T TIGR01648       114 EAVKLLNNYEIRPGRLLGVCISVD-----------------------------------NCRLFVGGIPKNKKREEILEE  158 (578)
T ss_pred             HHHHHcCCCeecCCcccccccccc-----------------------------------CceeEeecCCcchhhHHHHHH
Confidence            999 79998886 67777765321                                   258999999999999999999


Q ss_pred             HHhcCC-eeEEEEe-eCCCCCCCceEEEEEEcChhHHHHHHHHhCC--CeeCCeEEEEEEcccCCCCChhHHHHHHHHHH
Q 016936          173 LESFGT-LHGFDLV-KDRDTGNSKGYGFCVYQDPAVTDIACAALNG--LKMGDKTLTVRRATASSGQSKTEQESILAQAQ  248 (380)
Q Consensus       173 F~~~G~-i~~v~l~-~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g--~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~  248 (380)
                      |++++. +..+.+. ...+.++++|||||+|.++++|.+|+..|+.  ..+.|+.|.|.|+.+.......          
T Consensus       159 Fskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~VdwA~p~~~~d~~----------  228 (578)
T TIGR01648       159 FSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVDWAEPEEEVDED----------  228 (578)
T ss_pred             hhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccceEecCceEEEEeeccccccccc----------
Confidence            999864 4444333 3334567899999999999999999998763  4678999999998654221100          


Q ss_pred             HHHHHHHHHhhhcCccccCCCCCccCCccceEEEEeccCCcccCCChHHHHHHHHHHHHhhccc--CCeEEEEecCCCCC
Q 016936          249 QHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKY--GTLVNVVIPRPDQN  326 (380)
Q Consensus       249 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~~f~~~--G~I~~v~i~~~~~~  326 (380)
                                               .....+++.+.|....          .++++|+++|++|  |.|++|.+++    
T Consensus       229 -------------------------~~~~~k~LfVgNL~~~----------~tee~L~~~F~~f~~G~I~rV~~~r----  269 (578)
T TIGR01648       229 -------------------------VMAKVKILYVRNLMTT----------TTEEIIEKSFSEFKPGKVERVKKIR----  269 (578)
T ss_pred             -------------------------ccccccEEEEeCCCCC----------CCHHHHHHHHHhcCCCceEEEEeec----
Confidence                                     0223456777764321          1226999999999  9999998764    


Q ss_pred             CCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEecccc
Q 016936          327 GGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  371 (380)
Q Consensus       327 ~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~~  371 (380)
                             ++|||+|.+.++|.+|++.|||..|+|+.|+|+|+...
T Consensus       270 -------gfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~Akp~  307 (578)
T TIGR01648       270 -------DYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKPV  307 (578)
T ss_pred             -------CeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEccCC
Confidence                   47899999999999999999999999999999999763

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=6.9e-36  Score=299.01  Aligned_cols=274  Identities=20%  Similarity=0.313  Sum_probs=208.1

Q ss_pred             ccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecCceE
Q 016936           31 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  109 (380)
Q Consensus        31 ~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g~~i  109 (380)
                      ..++|||+|||.++++++|+++|+.||.|....       +.....++++|||||+|.+.++|.+|+ .+++..+.++.|
T Consensus        87 ~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~-------i~~~~~g~skg~afV~F~~~e~A~~Ai~~lng~~~~~~~i  159 (562)
T TIGR01628        87 GVGNIFVKNLDKSVDNKALFDTFSKFGNILSCK-------VATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEV  159 (562)
T ss_pred             CCCceEEcCCCccCCHHHHHHHHHhcCCcceeE-------eeecCCCCcccEEEEEECCHHHHHHHHHHhcccEecCceE
Confidence            456899999999999999999999999854311       111112457899999999999999999 899999999999


Q ss_pred             EEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCC
Q 016936          110 RVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRD  189 (380)
Q Consensus       110 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~  189 (380)
                      .|.+...+.....                        ......++|||+|||.++++++|+++|+.||.|..+.+..+. 
T Consensus       160 ~v~~~~~~~~~~~------------------------~~~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~-  214 (562)
T TIGR01628       160 YVGRFIKKHEREA------------------------APLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDG-  214 (562)
T ss_pred             EEecccccccccc------------------------ccccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECC-
Confidence            9976443322110                        011223689999999999999999999999999999999985 


Q ss_pred             CCCCceEEEEEEcChhHHHHHHHHhCCCeeC----CeEEEEEEcccCCCCChhHHHHHHHHHHHHHHHHHHHhhhcCccc
Q 016936          190 TGNSKGYGFCVYQDPAVTDIACAALNGLKMG----DKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNT  265 (380)
Q Consensus       190 ~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~----g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  265 (380)
                      ++.++|||||.|.+.++|.+|++.++|..+.    |+.+.|.++..+.     ++................         
T Consensus       215 ~g~~~G~afV~F~~~e~A~~Av~~l~g~~i~~~~~g~~l~v~~a~~k~-----er~~~~~~~~~~~~~~~~---------  280 (562)
T TIGR01628       215 SGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRA-----EREAELRRKFEELQQERK---------  280 (562)
T ss_pred             CCCcccEEEEEECCHHHHHHHHHHhCCcEecccccceeeEeecccChh-----hhHHHHHhhHHhhhhhhh---------
Confidence            6899999999999999999999999999999    9999999875432     221111111111100000         


Q ss_pred             cCCCCCccCCccceEEEEeccCCcccCCChHHHHHHHHHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhh
Q 016936          266 LGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVG  345 (380)
Q Consensus       266 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~  345 (380)
                              .......+.+.|....          .+.++|+++|++||.|.+|+++.+. ++. ++  |+|||+|++.++
T Consensus       281 --------~~~~~~~l~V~nl~~~----------~~~~~L~~~F~~~G~i~~~~i~~d~-~g~-~~--g~gfV~f~~~~~  338 (562)
T TIGR01628       281 --------MKAQGVNLYVKNLDDT----------VTDEKLRELFSECGEITSAKVMLDE-KGV-SR--GFGFVCFSNPEE  338 (562)
T ss_pred             --------cccCCCEEEEeCCCCc----------cCHHHHHHHHHhcCCeEEEEEEECC-CCC-cC--CeEEEEeCCHHH
Confidence                    0122233555553221          1226999999999999999999874 332 44  566999999999


Q ss_pred             HHHHHHHHcCcccCCeEEEEEeccccc
Q 016936          346 CATAKNALSGRKFGGNTVNAFYYPEDK  372 (380)
Q Consensus       346 A~~A~~~l~g~~i~gr~l~v~~~~~~~  372 (380)
                      |.+|+..|||+.|+|++|.|.|+..+.
T Consensus       339 A~~A~~~~~g~~~~gk~l~V~~a~~k~  365 (562)
T TIGR01628       339 ANRAVTEMHGRMLGGKPLYVALAQRKE  365 (562)
T ss_pred             HHHHHHHhcCCeeCCceeEEEeccCcH
Confidence            999999999999999999999998753

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

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

Probab=100.00  E-value=5.1e-36  Score=299.98  Aligned_cols=249  Identities=19%  Similarity=0.341  Sum_probs=201.7

Q ss_pred             eEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe------cCCCcEEEEEeCCHHHHHHHH-HcCCceecC
Q 016936           34 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  106 (380)
Q Consensus        34 ~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~------~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g  106 (380)
                      +|||+|||.++||++|+++|++||.            |.++++      .+++|||||+|.+.++|++|+ .+++..+.|
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~------------v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~g   69 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGP------------VLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGG   69 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCC------------EEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            6999999999999999999999998            444444      456799999999999999999 799999999


Q ss_pred             ceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEee
Q 016936          107 VAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVK  186 (380)
Q Consensus       107 ~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~  186 (380)
                      ++|+|.|+......                           ......+|||+|||.++++++|+++|+.||.|..|++..
T Consensus        70 k~i~i~~s~~~~~~---------------------------~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~  122 (562)
T TIGR01628        70 KPIRIMWSQRDPSL---------------------------RRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVAT  122 (562)
T ss_pred             eeEEeecccccccc---------------------------cccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeee
Confidence            99999995421100                           011235899999999999999999999999999999998


Q ss_pred             CCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccCCCCChhHHHHHHHHHHHHHHHHHHHhhhcCcccc
Q 016936          187 DRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTL  266 (380)
Q Consensus       187 ~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  266 (380)
                      +. +|+++|||||+|.+.++|.+|++.++|..+.|+.|.|.....+.....                             
T Consensus       123 ~~-~g~skg~afV~F~~~e~A~~Ai~~lng~~~~~~~i~v~~~~~~~~~~~-----------------------------  172 (562)
T TIGR01628       123 DE-NGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKKHEREA-----------------------------  172 (562)
T ss_pred             cC-CCCcccEEEEEECCHHHHHHHHHHhcccEecCceEEEecccccccccc-----------------------------
Confidence            85 688999999999999999999999999999999999987543321110                             


Q ss_pred             CCCCCccCCccceEEEEeccCCcccCCChHHHHHHHHHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhH
Q 016936          267 GGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGC  346 (380)
Q Consensus       267 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A  346 (380)
                            ......+.+.+.|....          .+.++|+++|++||.|.++.+.++.. +   +..|+|||+|.+.++|
T Consensus       173 ------~~~~~~~~l~V~nl~~~----------~tee~L~~~F~~fG~i~~~~i~~~~~-g---~~~G~afV~F~~~e~A  232 (562)
T TIGR01628       173 ------APLKKFTNLYVKNLDPS----------VNEDKLRELFAKFGEITSAAVMKDGS-G---RSRGFAFVNFEKHEDA  232 (562)
T ss_pred             ------ccccCCCeEEEeCCCCc----------CCHHHHHHHHHhcCCEEEEEEEECCC-C---CcccEEEEEECCHHHH
Confidence                  00222234555553211          12269999999999999999988753 2   2346779999999999


Q ss_pred             HHHHHHHcCcccC----CeEEEEEecccc
Q 016936          347 ATAKNALSGRKFG----GNTVNAFYYPED  371 (380)
Q Consensus       347 ~~A~~~l~g~~i~----gr~l~v~~~~~~  371 (380)
                      .+|++.|||..|.    |+.|.|.++...
T Consensus       233 ~~Av~~l~g~~i~~~~~g~~l~v~~a~~k  261 (562)
T TIGR01628       233 AKAVEEMNGKKIGLAKEGKKLYVGRAQKR  261 (562)
T ss_pred             HHHHHHhCCcEecccccceeeEeecccCh
Confidence            9999999999999    999999988654

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

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

Probab=100.00  E-value=6.6e-38  Score=289.74  Aligned_cols=330  Identities=25%  Similarity=0.353  Sum_probs=248.4

Q ss_pred             CCCCccccchhhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHH
Q 016936           17 PLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNA   96 (380)
Q Consensus        17 ~~~~~~~~~~~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~a   96 (380)
                      |..........++++.||||+-.|+..+++.||.+||+..|++..      +.+|-+.....++|.|||+|.+.+++..|
T Consensus       164 p~r~~~~~l~~eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrd------VriI~Dr~s~rskgi~Yvef~D~~sVp~a  237 (549)
T KOG0147|consen  164 PPREASRILSPEERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRD------VRIIGDRNSRRSKGIAYVEFCDEQSVPLA  237 (549)
T ss_pred             CcccccccCCchHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcce------eEeeccccchhhcceeEEEEecccchhhH
Confidence            444444555578999999999999999999999999999999532      22333333456789999999999999999


Q ss_pred             HHcCCceecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCC-CEEEEcCCCCCCCHHHHHHHHHh
Q 016936           97 MALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGP-DRVFVGGLPYYFTETQIKELLES  175 (380)
Q Consensus        97 i~l~~~~i~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~l~V~nlp~~~t~~~l~~~F~~  175 (380)
                      |.|.|..+.|.+|.|..+..-... ....               .+....++...+ ..+||+||.+.+++++|+.+|++
T Consensus       238 iaLsGqrllg~pv~vq~sEaeknr-~a~~---------------s~a~~~k~~~~p~~rl~vgnLHfNite~~lr~ifep  301 (549)
T KOG0147|consen  238 IALSGQRLLGVPVIVQLSEAEKNR-AANA---------------SPALQGKGFTGPMRRLYVGNLHFNITEDMLRGIFEP  301 (549)
T ss_pred             hhhcCCcccCceeEecccHHHHHH-HHhc---------------cccccccccccchhhhhhcccccCchHHHHhhhccC
Confidence            999999999999999864321111 1100               000011111222 23999999999999999999999


Q ss_pred             cCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccCCCCChh-----HHH-----HHHH
Q 016936          176 FGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKT-----EQE-----SILA  245 (380)
Q Consensus       176 ~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~~~~~~~-----~~~-----~~~~  245 (380)
                      ||.|..|.++.|..+|+++|||||+|.+.++|++|+..|||.++.|+.|+|.....+...+..     +.+     ....
T Consensus       302 fg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r~~~~~a~~~~~d~D~~d~~gl~~  381 (549)
T KOG0147|consen  302 FGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTERVDTKEAAVTQFDFDEDDRQGLSL  381 (549)
T ss_pred             cccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeeecccccccccccccchhhcccccc
Confidence            999999999999889999999999999999999999999999999999999976665433311     000     0000


Q ss_pred             HHHHHHHHHHHHhhhcCc---------------------cccCCC-CCccCC-------ccceEEEEeccCCcccCCChH
Q 016936          246 QAQQHIAIQKMALQTSGM---------------------NTLGGG-MSLFGE-------TLAKVLCLTEAITADALADDE  296 (380)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~---------------------~~~~~~-~~~~~~-------~~~~~~~l~~~~~~~~~~~~~  296 (380)
                      ......++........+.                     ..++.. ....+.       .++.|+.|+|++++....+.+
T Consensus       382 ~~~g~~Ql~~kla~~~~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~p~~~~p~~~i~t~C~lL~nMFdpstete~n  461 (549)
T KOG0147|consen  382 GSGGRNQLMAKLAEGKGRSLPSTAISALLLLAKLASAAQFNGVVRVRSVDPADASPAFDIPTQCLLLSNMFDPSTETEPN  461 (549)
T ss_pred             ccccHHHHHHHHhccCCccccchhhhHHHhccccchHHhhcCCcCccccCccccccccCCccHHHHHhhcCCcccccCcc
Confidence            000001111111111000                     000000 111122       789999999999999999999


Q ss_pred             HHHHHHHHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEeccccccccc
Q 016936          297 EYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNK  376 (380)
Q Consensus       297 ~~~~~~~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~~~~~~~  376 (380)
                      |-.++++|+.+.|++||.|.+|.+.+++.        |++||.|.+.+.|..|+.+|||+||.||.|.+.|.+.+.|+..
T Consensus       462 ~d~eI~edV~Eec~k~g~v~hi~vd~ns~--------g~VYvrc~s~~~A~~a~~alhgrWF~gr~Ita~~~~~~~Y~~~  533 (549)
T KOG0147|consen  462 WDQEIREDVIEECGKHGKVCHIFVDKNSA--------GCVYVRCPSAEAAGTAVKALHGRWFAGRMITAKYLPLERYHSK  533 (549)
T ss_pred             hhhHHHHHHHHHHHhcCCeeEEEEccCCC--------ceEEEecCcHHHHHHHHHHHhhhhhccceeEEEEeehhhhhhh
Confidence            99999999999999999999999988763        6999999999999999999999999999999999999998864

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

Probab=100.00  E-value=3e-37  Score=289.50  Aligned_cols=340  Identities=48%  Similarity=0.833  Sum_probs=289.5

Q ss_pred             CCCCCccccchhhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHH
Q 016936           16 FPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASN   95 (380)
Q Consensus        16 ~~~~~~~~~~~~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~   95 (380)
                      .+..|.+.+..+.+...+.++|+++|..+.++....+|..--...+.+..+.++.+..+.++..+++||++|.+.++|..
T Consensus       159 ~~~~~~~~~~~~~t~q~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~n~~~nfa~ie~~s~~~at~  238 (500)
T KOG0120|consen  159 LPQLPTPPMDSQATRQARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQLNLEKNFAFIEFRSISEATE  238 (500)
T ss_pred             cccCCCCccCcchhhhhhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeeecccccceeEEecCCCchhh
Confidence            56677788888999999999999999999999999999998888887777777889999999999999999999999999


Q ss_pred             HHHcCCceecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHh
Q 016936           96 AMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLES  175 (380)
Q Consensus        96 ai~l~~~~i~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~  175 (380)
                      |+.+++..+.|.++++..+..++..........+      ....+.....+....+...+||++||...++.+++++...
T Consensus       239 ~~~~~~~~f~g~~~~~~r~~d~~~~p~~~~~~~~------~~~~~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~  312 (500)
T KOG0120|consen  239 AMALDGIIFEGRPLKIRRPHDYQPVPGITLSPSQ------LGKVGLLPASTDVPDSPNKIFVGGLPLYLTEDQVKELLDS  312 (500)
T ss_pred             hhcccchhhCCCCceecccccccCCccchhhhcc------ccccCCcccccCcccccchhhhccCcCccCHHHHHHHHHh
Confidence            9999999999999999988887765443333222      1112233344455667789999999999999999999999


Q ss_pred             cCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccCCCCChhHHHHHHHHHHHHHHHHH
Q 016936          176 FGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQK  255 (380)
Q Consensus       176 ~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  255 (380)
                      ||.+....++.+..+|.++||||.+|.+......|++.|||+.+++..+.|..+.........+.. . . +.       
T Consensus       313 fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~~~~~~~~~-~-~-~~-------  382 (500)
T KOG0120|consen  313 FGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGASNANVNFN-I-S-QS-------  382 (500)
T ss_pred             cccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhccchhccccCC-c-c-cc-------
Confidence            999999999999888999999999999999999999999999999999999998765433322222 0 0 00       


Q ss_pred             HHhhhcCccccCCCC--CccCCccceEEEEeccCCcccCCChHHHHHHHHHHHHhhcccCCeEEEEecCCCCCCCCCCCc
Q 016936          256 MALQTSGMNTLGGGM--SLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGV  333 (380)
Q Consensus       256 ~~~~~~~~~~~~~~~--~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~  333 (380)
                              ..++...  ......++.+++|.|+++++++.++.+|.++.|+++..|++||.|.+|.+++....+...+|.
T Consensus       383 --------~~~~i~~~~~q~~g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr~~~~~~~~~G~  454 (500)
T KOG0120|consen  383 --------QVPGIPLLMTQMAGIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSVEIPRPYPDENPVPGT  454 (500)
T ss_pred             --------ccccchhhhcccCCCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEEecCCCCCCCCcCCCc
Confidence                    1111111  133478899999999999999999999999999999999999999999999986677778899


Q ss_pred             cEEEEEeechhhHHHHHHHHcCcccCCeEEEEEeccccccccccCC
Q 016936          334 GKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDYS  379 (380)
Q Consensus       334 g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~~~~~~~~~~  379 (380)
                      |.+||+|++.+++++|+++|+|++|.||+|.++|+++++||+++|+
T Consensus       455 GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYydeDkY~~r~~~  500 (500)
T KOG0120|consen  455 GKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYDEDKYHAREFE  500 (500)
T ss_pred             ccEEEEecChHHHHHHHHHccCceeCCcEEEEEecCHHHhhccccC
Confidence            9999999999999999999999999999999999999999999985

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

Probab=100.00  E-value=1.3e-35  Score=290.13  Aligned_cols=290  Identities=17%  Similarity=0.146  Sum_probs=205.9

Q ss_pred             ccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHHH---cCCceecCc
Q 016936           31 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA---LDGIIFEGV  107 (380)
Q Consensus        31 ~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai~---l~~~~i~g~  107 (380)
                      ++++|||+|||+++++++|+++|++||.            |.++.+.+++++|||+|.+.++|.+|+.   +++..+.|+
T Consensus         1 ps~vv~V~nLp~~~te~~L~~~f~~fG~------------V~~v~i~~~k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~   68 (481)
T TIGR01649         1 PSPVVHVRNLPQDVVEADLVEALIPFGP------------VSYVMMLPGKRQALVEFEDEESAKACVNFATSVPIYIRGQ   68 (481)
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhcCC------------eeEEEEECCCCEEEEEeCchHHHHHHHHHhhcCCceEcCe
Confidence            5799999999999999999999999998            7778888899999999999999999994   578999999


Q ss_pred             eEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeC
Q 016936          108 AVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKD  187 (380)
Q Consensus       108 ~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~  187 (380)
                      +|+|.|+..........   .    .          ..........+|||.||++.+++++|+++|+.||.|.+|.+.++
T Consensus        69 ~l~v~~s~~~~~~~~~~---~----~----------~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~  131 (481)
T TIGR01649        69 PAFFNYSTSQEIKRDGN---S----D----------FDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTK  131 (481)
T ss_pred             EEEEEecCCcccccCCC---C----c----------ccCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEec
Confidence            99999976543221100   0    0          00111223358999999999999999999999999999999876


Q ss_pred             CCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCC--eEEEEEEcccCCCC-----Chh----------HHHHHHHHHHHH
Q 016936          188 RDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD--KTLTVRRATASSGQ-----SKT----------EQESILAQAQQH  250 (380)
Q Consensus       188 ~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g--~~i~v~~~~~~~~~-----~~~----------~~~~~~~~~~~~  250 (380)
                      .  +  +|+|||+|.+.++|.+|++.|||..+.+  +.|+|.++....-.     ...          ++..........
T Consensus       132 ~--~--~~~afVef~~~~~A~~A~~~Lng~~i~~~~~~l~v~~sk~~~l~v~~~~~~s~dyt~~~l~~~~~~~~~~~~~~  207 (481)
T TIGR01649       132 N--N--VFQALVEFESVNSAQHAKAALNGADIYNGCCTLKIEYAKPTRLNVKYNDDDSRDYTNPDLPGRRDPGLDQTHRQ  207 (481)
T ss_pred             C--C--ceEEEEEECCHHHHHHHHHHhcCCcccCCceEEEEEEecCCCceeEecccCCCCCcCCCCCCCCCCCcCccccc
Confidence            3  2  4689999999999999999999999954  58999988753210     000          000000000000


Q ss_pred             HHHHHHHh------hhcCcccc-----------------------C-----CCCC-------ccCCccceEEEEeccCCc
Q 016936          251 IAIQKMAL------QTSGMNTL-----------------------G-----GGMS-------LFGETLAKVLCLTEAITA  289 (380)
Q Consensus       251 ~~~~~~~~------~~~~~~~~-----------------------~-----~~~~-------~~~~~~~~~~~l~~~~~~  289 (380)
                       .......      ...+.+..                       .     ...+       .....+..++.+.|....
T Consensus       208 -~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nL~~~  286 (481)
T TIGR01649       208 -RQPALLGQHPSSYGHDGYSSHGGPLAPLAGGDRMGPPHGPPSRYRPAYEAAPLAPAISSYGPAGGGPGSVLMVSGLHQE  286 (481)
T ss_pred             -cccccccCCCccCCCcccccCCCCCCcccccccCCCcccCCCCCcccccccccCccccccCCCCCCCCCEEEEeCCCCC
Confidence             0000000      00000000                       0     0000       001234557777775321


Q ss_pred             ccCCChHHHHHHHHHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEecc
Q 016936          290 DALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYP  369 (380)
Q Consensus       290 ~~~~~~~~~~~~~~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~  369 (380)
                      .         .++++|+++|++||.|.+|+++++.+        |+|||+|.+.++|.+|++.|||..|.|++|+|+++.
T Consensus       287 ~---------vt~~~L~~lF~~yG~V~~vki~~~~~--------g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~  349 (481)
T TIGR01649       287 K---------VNCDRLFNLFCVYGNVERVKFMKNKK--------ETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSK  349 (481)
T ss_pred             C---------CCHHHHHHHHHhcCCeEEEEEEeCCC--------CEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcc
Confidence            0         12269999999999999999988642        578999999999999999999999999999999985


Q ss_pred             cc
Q 016936          370 ED  371 (380)
Q Consensus       370 ~~  371 (380)
                      .+
T Consensus       350 ~~  351 (481)
T TIGR01649       350 QQ  351 (481)
T ss_pred             cc
Confidence            54

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

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

Probab=100.00  E-value=2.4e-35  Score=265.64  Aligned_cols=246  Identities=19%  Similarity=0.318  Sum_probs=208.0

Q ss_pred             cccchhhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe------cCCCcEEEEEeCCHHHHHH
Q 016936           22 QVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASN   95 (380)
Q Consensus        22 ~~~~~~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~------~~~~g~afV~f~~~~~a~~   95 (380)
                      +.+........|.|||+.||.++.|+||.-+|.+.|.            |.++++      +.++|||||.|.+.++|++
T Consensus        73 P~weg~~p~~G~EVfvGkIPrD~~EdeLvplfEkiG~------------I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~  140 (506)
T KOG0117|consen   73 PGWEGPPPPRGCEVFVGKIPRDVFEDELVPLFEKIGK------------IYELRLMMDPFSGDNRGYAFVTFCTKEEAQE  140 (506)
T ss_pred             CcccCCCCCCCceEEecCCCccccchhhHHHHHhccc------------eeeEEEeecccCCCCcceEEEEeecHHHHHH
Confidence            3477777799999999999999999999999999998            555555      3568999999999999999


Q ss_pred             HH-HcCCceec-CceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHH
Q 016936           96 AM-ALDGIIFE-GVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELL  173 (380)
Q Consensus        96 ai-~l~~~~i~-g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F  173 (380)
                      |+ .||+..|+ |+.|.|..+..                                   .++|||+|+|+.+++++|++.+
T Consensus       141 Aik~lnn~Eir~GK~igvc~Sva-----------------------------------n~RLFiG~IPK~k~keeIlee~  185 (506)
T KOG0117|consen  141 AIKELNNYEIRPGKLLGVCVSVA-----------------------------------NCRLFIGNIPKTKKKEEILEEM  185 (506)
T ss_pred             HHHHhhCccccCCCEeEEEEeee-----------------------------------cceeEeccCCccccHHHHHHHH
Confidence            99 79998875 68898876332                                   2699999999999999999999


Q ss_pred             HhcCC-eeEEEEeeCCC-CCCCceEEEEEEcChhHHHHHHHHhC-C-CeeCCeEEEEEEcccCCCCChhHHHHHHHHHHH
Q 016936          174 ESFGT-LHGFDLVKDRD-TGNSKGYGFCVYQDPAVTDIACAALN-G-LKMGDKTLTVRRATASSGQSKTEQESILAQAQQ  249 (380)
Q Consensus       174 ~~~G~-i~~v~l~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~-g-~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~  249 (380)
                      ++.++ |..|.+...++ ..+++|||||+|.++..|..|..+|- + ..+.|..+.|.||.+........          
T Consensus       186 ~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwgn~~tVdWAep~~e~ded~----------  255 (506)
T KOG0117|consen  186 KKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIKLWGNAITVDWAEPEEEPDEDT----------  255 (506)
T ss_pred             HhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCCceeecCCcceeeccCcccCCChhh----------
Confidence            99987 77777777654 46899999999999999999999874 3 58899999999998764332210          


Q ss_pred             HHHHHHHHhhhcCccccCCCCCccCCccceEEEEeccCCcccCCChHHHHHHHHHHHHhhcccCCeEEEEecCCCCCCCC
Q 016936          250 HIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGE  329 (380)
Q Consensus       250 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~~f~~~G~I~~v~i~~~~~~~~~  329 (380)
                                               -...+++.+.|+          ...+|++.|+++|++||.|++|+.+++      
T Consensus       256 -------------------------ms~VKvLYVRNL----------~~~tTeE~lk~~F~~~G~veRVkk~rD------  294 (506)
T KOG0117|consen  256 -------------------------MSKVKVLYVRNL----------MESTTEETLKKLFNEFGKVERVKKPRD------  294 (506)
T ss_pred             -------------------------hhheeeeeeecc----------chhhhHHHHHHHHHhccceEEeecccc------
Confidence                                     234567777773          334456899999999999999999864      


Q ss_pred             CCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEeccc
Q 016936          330 TPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPE  370 (380)
Q Consensus       330 ~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~  370 (380)
                           +|||.|.+.++|.+|++.|||+.|+|..|.|.+|.+
T Consensus       295 -----YaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP  330 (506)
T KOG0117|consen  295 -----YAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKP  330 (506)
T ss_pred             -----eeEEeecchHHHHHHHHHhcCceecCceEEEEecCC
Confidence                 779999999999999999999999999999999987

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

Probab=100.00  E-value=5.4e-35  Score=246.02  Aligned_cols=293  Identities=18%  Similarity=0.276  Sum_probs=215.4

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecCce
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  108 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g~~  108 (380)
                      ...+.|-|--||..+|+++++.+|...|.|..++      .|.+...+.+.||+||.|.+++||++|+ .+||..+..+.
T Consensus        39 ~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScK------LvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KT  112 (360)
T KOG0145|consen   39 ESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCK------LVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKT  112 (360)
T ss_pred             cccceeeeeecccccCHHHHHHHhhcccceeeee------eeeccccccccccceeeecChHHHHHHHhhhcceeeccce
Confidence            3445589999999999999999999999954432      2344445667899999999999999999 89999999999


Q ss_pred             EEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC
Q 016936          109 VRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDR  188 (380)
Q Consensus       109 i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~  188 (380)
                      |+|.++......                             -...+|||.+||+..|..+|..+|++||.|..-+++.|.
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            999986553211                             122589999999999999999999999999988999998


Q ss_pred             CCCCCceEEEEEEcChhHHHHHHHHhCCCeeCC--eEEEEEEcccCCCCChhHH--HHH-----------HHHHHHHHHH
Q 016936          189 DTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD--KTLTVRRATASSGQSKTEQ--ESI-----------LAQAQQHIAI  253 (380)
Q Consensus       189 ~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g--~~i~v~~~~~~~~~~~~~~--~~~-----------~~~~~~~~~~  253 (380)
                      .+|.++|.+||+|....+|+.||..|||..-.|  .+|.|+++..........-  .-.           ..+.++ ..+
T Consensus       164 vtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepItVKFannPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r-~r~  242 (360)
T KOG0145|consen  164 VTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPITVKFANNPSQKTNQALLSQLYQSPARRYGGPMHHQAQR-FRL  242 (360)
T ss_pred             ccceecceeEEEecchhHHHHHHHhccCCCCCCCCCCeEEEecCCcccccchhhhHHhhcCccccCCCcccchhhh-hcc
Confidence            899999999999999999999999999987755  4799998865432111000  000           000000 000


Q ss_pred             HHH------HhhhcCccccC------CCCCccCCccceEEEEeccCCcccCCChHHHHHHHHHHHHhhcccCCeEEEEec
Q 016936          254 QKM------ALQTSGMNTLG------GGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIP  321 (380)
Q Consensus       254 ~~~------~~~~~~~~~~~------~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~~f~~~G~I~~v~i~  321 (380)
                      ..+      ....+.+...+      ...+. ......|+.+-|.....+.          .-|.++|++||.|..|+++
T Consensus       243 ~~~~~~~~~~~rfsP~~~d~m~~l~~~~lp~-~~~~g~ciFvYNLspd~de----------~~LWQlFgpFGAv~nVKvi  311 (360)
T KOG0145|consen  243 DNLLNPHAAQARFSPMTIDGMSGLAGVNLPG-GPGGGWCIFVYNLSPDADE----------SILWQLFGPFGAVTNVKVI  311 (360)
T ss_pred             ccccchhhhhccCCCccccccceeeeeccCC-CCCCeeEEEEEecCCCchH----------hHHHHHhCcccceeeEEEE
Confidence            000      00111111111      11111 2233567766664333221          4799999999999999999


Q ss_pred             CCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEeccccc
Q 016936          322 RPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  372 (380)
Q Consensus       322 ~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~~~  372 (380)
                      ++..+   .+|.|++||.+.+.++|..|+..|||+.+++|.|.|+|.+.+.
T Consensus       312 rD~tt---nkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFKtnk~  359 (360)
T KOG0145|consen  312 RDFTT---NKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTNKA  359 (360)
T ss_pred             ecCCc---ccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEecCCC
Confidence            98754   3455666999999999999999999999999999999987654

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

Probab=100.00  E-value=2.9e-34  Score=257.47  Aligned_cols=172  Identities=24%  Similarity=0.390  Sum_probs=145.0

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCce-e
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGII-F  104 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~-i  104 (380)
                      .++.+.-++||+-||..|+|.||+++|.+||.+.+.      .++.|..++.++|||||.|.+.++|.+|+ +||++. |
T Consensus        29 ~~d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~ei------nl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktl  102 (510)
T KOG0144|consen   29 NPDGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEI------NLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTL  102 (510)
T ss_pred             CCCchhhhheeccCCccccHHHHHHHHHHhCceeEE------EeecccccCcccceEEEEeccHHHHHHHHHHhhccccc
Confidence            456777889999999999999999999999985442      23445555677899999999999999999 898865 6


Q ss_pred             cC--ceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEE
Q 016936          105 EG--VAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGF  182 (380)
Q Consensus       105 ~g--~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v  182 (380)
                      -|  .+|+|.++.....+.                            ...++|||+.|++.+++.+++++|++||.|++|
T Consensus       103 pG~~~pvqvk~Ad~E~er~----------------------------~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~  154 (510)
T KOG0144|consen  103 PGMHHPVQVKYADGERERI----------------------------VEERKLFVGMLSKQCTENEVREIFSRFGHIEDC  154 (510)
T ss_pred             CCCCcceeecccchhhhcc----------------------------ccchhhhhhhccccccHHHHHHHHHhhCccchh
Confidence            56  789999865432221                            122689999999999999999999999999999


Q ss_pred             EEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCC-eeCC--eEEEEEEcccCC
Q 016936          183 DLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGL-KMGD--KTLTVRRATASS  233 (380)
Q Consensus       183 ~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~-~~~g--~~i~v~~~~~~~  233 (380)
                      .|++|+ .+.+||||||.|.+.+.|..||+.|||. .+.|  .+|.|+|+.+..
T Consensus       155 ~ilrd~-~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkFADtqk  207 (510)
T KOG0144|consen  155 YILRDP-DGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKFADTQK  207 (510)
T ss_pred             hheecc-cccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEecccCC
Confidence            999996 5999999999999999999999999985 5555  579999998865

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

Probab=100.00  E-value=3.5e-34  Score=251.73  Aligned_cols=324  Identities=27%  Similarity=0.424  Sum_probs=236.5

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecC
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  106 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g  106 (380)
                      +-.-.|+|||+.|.+++.|+.|+..|..||+|...+-      --+-.+.++||||||+|.-+|.|+.|+ .+|+..+.|
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            3456799999999999999999999999998543210      001124678999999999999999999 799999999


Q ss_pred             ceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEee
Q 016936          107 VAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVK  186 (380)
Q Consensus       107 ~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~  186 (380)
                      |.|+|.++.+-          .+.++......        .++..-.+|||..+..+++++||+..|+.||+|..|.+-+
T Consensus       183 RNiKVgrPsNm----------pQAQpiID~vq--------eeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr  244 (544)
T KOG0124|consen  183 RNIKVGRPSNM----------PQAQPIIDMVQ--------EEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLAR  244 (544)
T ss_pred             ccccccCCCCC----------cccchHHHHHH--------HHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeec
Confidence            99999876542          11111111100        1123346999999999999999999999999999999999


Q ss_pred             CCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccCCCC---C-----hhHHHHHHHHHH--HHHHHHHH
Q 016936          187 DRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQ---S-----KTEQESILAQAQ--QHIAIQKM  256 (380)
Q Consensus       187 ~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~~~~---~-----~~~~~~~~~~~~--~~~~~~~~  256 (380)
                      ++..+.++||+|++|.+..+-..|+..||=+.++|.-++|..+......   +     .+........+-  +.......
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            9988899999999999999999999999999999999999986554311   0     000000000000  00000000


Q ss_pred             Hhhh----------------------------------------------------------------------------
Q 016936          257 ALQT----------------------------------------------------------------------------  260 (380)
Q Consensus       257 ~~~~----------------------------------------------------------------------------  260 (380)
                      +...                                                                            
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                                                                            


Q ss_pred             ------------------cCccccCCC------CCccCCccceEEEEeccCCcccCCChHHHHHHHHHHHHhhcccCCeE
Q 016936          261 ------------------SGMNTLGGG------MSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLV  316 (380)
Q Consensus       261 ------------------~~~~~~~~~------~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~~f~~~G~I~  316 (380)
                                        .++...|..      .-......+++++|.|+++++++.++.+     .+|++.|++||.|.
T Consensus       405 e~eelqpkl~~~~~L~~QE~msI~G~sARhlvMqkLmR~~~S~VivLRNMV~P~DiDe~Le-----gEi~EECgKfG~V~  479 (544)
T KOG0124|consen  405 EEEELQPKLERPEMLSEQEHMSISGSSARHLVMQKLMRKQESTVIVLRNMVDPKDIDEDLE-----GEITEECGKFGAVN  479 (544)
T ss_pred             hHhhhcccccCHHHhhhhhCccccCccHHHHHHHHHhccccCcEEEEeccCChhhhhhHHH-----HHHHHHHhccccee
Confidence                              000000000      0001456688999999999998766554     68999999999999


Q ss_pred             EEEecCCCCCCCCCCC-ccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEeccccccccccCCC
Q 016936          317 NVVIPRPDQNGGETPG-VGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDYSA  380 (380)
Q Consensus       317 ~v~i~~~~~~~~~~~g-~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~~~~~~~~~~~  380 (380)
                      +|.|.....++...-. .-..||+|+...++.+|.++|+|++|+||++..+.++-..|.+++|++
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            9999876654421000 123699999999999999999999999999999999999999999986

>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=9.7e-34  Score=239.94  Aligned_cols=236  Identities=23%  Similarity=0.394  Sum_probs=182.6

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHHHcCCceecCce
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVA  108 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai~l~~~~i~g~~  108 (380)
                      +.+.|||||+||+.++||+-|..+|++.|.            |..+++.         |+                   .
T Consensus         3 ~~~prtlyvgnld~~vte~~i~~lf~qig~------------v~~~k~i---------~~-------------------e   42 (321)
T KOG0148|consen    3 SDEPRTLYVGNLDSTVTEDFIATLFNQIGS------------VTKTKVI---------FD-------------------E   42 (321)
T ss_pred             CCCCceEEeeccChhhHHHHHHHHHHhccc------------cccceee---------hh-------------------h
Confidence            467899999999999999999999999998            5554433         22                   6


Q ss_pred             EEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC
Q 016936          109 VRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDR  188 (380)
Q Consensus       109 i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~  188 (380)
                      |+|.|+.....         +..+               .....-.|||+.|...++-++|++.|.+||.|.++++++|.
T Consensus        43 ~~v~wa~~p~n---------Qsk~---------------t~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~   98 (321)
T KOG0148|consen   43 LKVNWATAPGN---------QSKP---------------TSNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDM   98 (321)
T ss_pred             hccccccCccc---------CCCC---------------ccccceeEEehhcchhcchHHHHHHhccccccccceEeecc
Confidence            67777544210         0000               11223589999999999999999999999999999999999


Q ss_pred             CCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccCCCCChhHHHHHHHHHHHHHHHHHHHhhhcCccccCC
Q 016936          189 DTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGG  268 (380)
Q Consensus       189 ~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  268 (380)
                      .+++++|||||.|.+.++|++||..|||.=|++|.|+-.|+..+........          ........+.        
T Consensus        99 ~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATRKp~e~n~~~----------ltfdeV~NQs--------  160 (321)
T KOG0148|consen   99 NTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATRKPSEMNGKP----------LTFDEVYNQS--------  160 (321)
T ss_pred             cCCcccceeEEeccchHHHHHHHHHhCCeeeccceeeccccccCccccCCCC----------ccHHHHhccC--------
Confidence            9999999999999999999999999999999999999999976541110000          0011111111        


Q ss_pred             CCCccCCccceEEEEeccCC-cccCCChHHHHHHHHHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHH
Q 016936          269 GMSLFGETLAKVLCLTEAIT-ADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCA  347 (380)
Q Consensus       269 ~~~~~~~~~~~~~~l~~~~~-~~~~~~~~~~~~~~~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~  347 (380)
                           ...++.++ +.++.. +.+           ++|++.|++||.|.+|+++++.         |+|||+|.+.|.|.
T Consensus       161 -----sp~NtsVY-~G~I~~~lte-----------~~mr~~Fs~fG~I~EVRvFk~q---------GYaFVrF~tkEaAa  214 (321)
T KOG0148|consen  161 -----SPDNTSVY-VGNIASGLTE-----------DLMRQTFSPFGPIQEVRVFKDQ---------GYAFVRFETKEAAA  214 (321)
T ss_pred             -----CCCCceEE-eCCcCccccH-----------HHHHHhcccCCcceEEEEeccc---------ceEEEEecchhhHH
Confidence                 13333333 344333 322           5899999999999999999875         69999999999999


Q ss_pred             HHHHHHcCcccCCeEEEEEeccccc
Q 016936          348 TAKNALSGRKFGGNTVNAFYYPEDK  372 (380)
Q Consensus       348 ~A~~~l~g~~i~gr~l~v~~~~~~~  372 (380)
                      +||..|||..|+|+.++++|-.+..
T Consensus       215 hAIv~mNntei~G~~VkCsWGKe~~  239 (321)
T KOG0148|consen  215 HAIVQMNNTEIGGQLVRCSWGKEGD  239 (321)
T ss_pred             HHHHHhcCceeCceEEEEeccccCC
Confidence            9999999999999999999988743

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

Probab=100.00  E-value=3e-32  Score=266.46  Aligned_cols=303  Identities=17%  Similarity=0.182  Sum_probs=201.2

Q ss_pred             cceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCC--CcEEEEEeCCHHHHHHHH-HcCCceecC--
Q 016936           32 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE--KKFAFVEMRTVEEASNAM-ALDGIIFEG--  106 (380)
Q Consensus        32 ~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~--~g~afV~f~~~~~a~~ai-~l~~~~i~g--  106 (380)
                      ..+|||+||++.+|+++|+++|+.||.            |..+.+.+.  .++|||+|.+.++|.+|+ .|||..|.+  
T Consensus        96 ~~~v~v~nl~~~vt~~~L~~~F~~~G~------------V~~v~i~~~~~~~~afVef~~~~~A~~A~~~Lng~~i~~~~  163 (481)
T TIGR01649        96 VLRVIVENPMYPITLDVLYQIFNPYGK------------VLRIVTFTKNNVFQALVEFESVNSAQHAKAALNGADIYNGC  163 (481)
T ss_pred             eEEEEEcCCCCCCCHHHHHHHHhccCC------------EEEEEEEecCCceEEEEEECCHHHHHHHHHHhcCCcccCCc
Confidence            347999999999999999999999998            555555433  369999999999999999 799999975  


Q ss_pred             ceEEEecCCCCCccc------ccc-----C-CCCCCCCC----cccc-------------c----------------cc-
Q 016936          107 VAVRVRRPTDYNPTL------AAA-----L-GPGQPSPN----LNLA-------------A----------------VG-  140 (380)
Q Consensus       107 ~~i~v~~~~~~~~~~------~~~-----~-~~~~~~~~----~~~~-------------~----------------~~-  140 (380)
                      ..|+|.|+.......      ...     . +.......    ....             .                .+ 
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            578888876433211      000     0 00000000    0000             0                00 


Q ss_pred             ---CCC---------C--------CCCCCCCCCEEEEcCCCC-CCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEE
Q 016936          141 ---LAS---------G--------AIGGAEGPDRVFVGGLPY-YFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC  199 (380)
Q Consensus       141 ---~~~---------~--------~~~~~~~~~~l~V~nlp~-~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV  199 (380)
                         .+.         .        .........+|||+|||+ .+++++|+++|+.||.|.+|++++++     +|+|||
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        000112446999999997 69999999999999999999998763     589999


Q ss_pred             EEcChhHHHHHHHHhCCCeeCCeEEEEEEcccCCCCChhHHH-HHHHHHHHHHHHHHHHhhhcCccccCCCCCccCCccc
Q 016936          200 VYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQE-SILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLA  278 (380)
Q Consensus       200 ~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  278 (380)
                      +|.+.++|+.|+..|||..+.|++|+|.++............ .......+...    .........+..........++
T Consensus       319 ~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~~~~~~~~~~~~~~~~~~~d~~----~~~~~r~~~~~~~~~~~~~~ps  394 (481)
T TIGR01649       319 EMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQNVQPPREGQLDDGLTSYKDYS----SSRNHRFKKPGSANKNNIQPPS  394 (481)
T ss_pred             EECCHHHHHHHHHHhCCCEECCceEEEEEcccccccCCCCCcCcCCCccccccc----CCccccCCCcccccccccCCCC
Confidence            999999999999999999999999999997654322111000 00000000000    0000000000000000112355


Q ss_pred             eEEEEeccCCcccCCChHHHHHHHHHHHHhhcccCC--eEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCc
Q 016936          279 KVLCLTEAITADALADDEEYEEILEDMREECGKYGT--LVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGR  356 (380)
Q Consensus       279 ~~~~l~~~~~~~~~~~~~~~~~~~~~L~~~f~~~G~--I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~  356 (380)
                      ..+.+.|....          .+.++|+++|+.||.  |..+++.+... +  .+  |+|||+|.+.++|.+|+..|||+
T Consensus       395 ~~L~v~NLp~~----------~tee~L~~lF~~~G~~~i~~ik~~~~~~-~--~~--~~gfVeF~~~e~A~~Al~~ln~~  459 (481)
T TIGR01649       395 ATLHLSNIPLS----------VSEEDLKELFAENGVHKVKKFKFFPKDN-E--RS--KMGLLEWESVEDAVEALIALNHH  459 (481)
T ss_pred             cEEEEecCCCC----------CCHHHHHHHHHhcCCccceEEEEecCCC-C--cc--eeEEEEcCCHHHHHHHHHHhcCC
Confidence            67777774321          112699999999998  88888876442 2  23  46699999999999999999999


Q ss_pred             ccCCeE------EEEEeccc
Q 016936          357 KFGGNT------VNAFYYPE  370 (380)
Q Consensus       357 ~i~gr~------l~v~~~~~  370 (380)
                      .|+|+.      |+|+|+..
T Consensus       460 ~l~~~~~~~~~~lkv~fs~~  479 (481)
T TIGR01649       460 QLNEPNGSAPYHLKVSFSTS  479 (481)
T ss_pred             ccCCCCCCccceEEEEeccC
Confidence            999985      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).

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

Probab=100.00  E-value=1.5e-32  Score=253.01  Aligned_cols=326  Identities=16%  Similarity=0.230  Sum_probs=219.0

Q ss_pred             cceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecCceEE
Q 016936           32 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVR  110 (380)
Q Consensus        32 ~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g~~i~  110 (380)
                      ..||||++||++++.++|.++|+.+|+|..+..      |..--...++||+||.|.-.+|++.|+ .+++..+.|+.|+
T Consensus         5 g~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~v------Vt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~   78 (678)
T KOG0127|consen    5 GATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVV------VTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILN   78 (678)
T ss_pred             CceEEEecCCCccchhHHHHhhhcccCcceeEE------ecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceecc
Confidence            379999999999999999999999999754310      111112346899999999999999999 7999999999999


Q ss_pred             EecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCC
Q 016936          111 VRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDT  190 (380)
Q Consensus       111 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~  190 (380)
                      |..+..+..+...+.+........   .......-........+|.|+|||+.+...+|+.+|+.||.|.++.|++.++ 
T Consensus        79 v~~A~~R~r~e~~~~~e~~~veK~---~~q~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~d-  154 (678)
T KOG0127|consen   79 VDPAKKRARSEEVEKGENKAVEKP---IEQKRPTKAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKD-  154 (678)
T ss_pred             cccccccccchhcccccchhhhcc---cccCCcchhhccCccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCC-
Confidence            998766544432111111000000   0000000000111246899999999999999999999999999999998875 


Q ss_pred             CCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccCCCCChhHHHHHHHHHHHHHHHHHHHhhhcCcc----cc
Q 016936          191 GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMN----TL  266 (380)
Q Consensus       191 ~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~  266 (380)
                      |+-.|||||+|....+|..|++.+|+..|.||+|-|.||.++..........-..-.....-............    -.
T Consensus       155 gklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed  234 (678)
T KOG0127|consen  155 GKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDKDTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEED  234 (678)
T ss_pred             CCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeecccccccccchhhhhhhhhccchhhhcccccccccccchhc
Confidence            66669999999999999999999999999999999999998876554332110000000000000000000000    00


Q ss_pred             C---------------------C------CCC----ccCCccceEEEE---ecc--CCcccCCChHHHHHHHHHHHHhhc
Q 016936          267 G---------------------G------GMS----LFGETLAKVLCL---TEA--ITADALADDEEYEEILEDMREECG  310 (380)
Q Consensus       267 ~---------------------~------~~~----~~~~~~~~~~~l---~~~--~~~~~~~~~~~~~~~~~~L~~~f~  310 (380)
                      +                     .      ...    +......+-...   ...  .....++.|.+|.++++.|.++|+
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            0                     0      000    000000000011   111  112224557788888899999999


Q ss_pred             ccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHH-----cC-cccCCeEEEEEeccc
Q 016936          311 KYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNAL-----SG-RKFGGNTVNAFYYPE  370 (380)
Q Consensus       311 ~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l-----~g-~~i~gr~l~v~~~~~  370 (380)
                      +||.|.++.++.++.+++ +  .|+|||.|.+..+|+.||...     .| ..|.||.|+|..+-.
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 KFGEVKYAIIVKDKDTGH-S--KGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGRLLKVTLAVT  377 (678)
T ss_pred             hhccceeEEEEeccCCCC-c--ccceEEEeccHHHHHHHHHhcCccCCCceEEEeccEEeeeeccc
Confidence            999999999999988776 3  467799999999999999876     34 679999999998743

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

Probab=99.97  E-value=9.1e-30  Score=237.09  Aligned_cols=243  Identities=19%  Similarity=0.351  Sum_probs=195.3

Q ss_pred             ceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecCceEEE
Q 016936           33 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV  111 (380)
Q Consensus        33 ~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g~~i~v  111 (380)
                      ..|||+   +++|+..|++.|+.+|+++..      ..+.+.   .+.|||||.|.++++|++|| ++|...+.|++|+|
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~------rvc~d~---tslgy~yvnf~~~~da~~A~~~~n~~~~~~~~~ri   69 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSI------RVCRDA---TSLGYAYVNFQQPADAERALDTMNFDVLKGKPIRI   69 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeE------EEeecC---CccceEEEecCCHHHHHHHHHHcCCcccCCcEEEe
Confidence            368998   899999999999999996541      122333   28899999999999999999 89999999999999


Q ss_pred             ecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCC
Q 016936          112 RRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTG  191 (380)
Q Consensus       112 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~  191 (380)
                      +|+...              +                    ..|||.||+.+++..+|++.|+.||.|.+|++..+. .|
T Consensus        70 m~s~rd--------------~--------------------~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~-~g  114 (369)
T KOG0123|consen   70 MWSQRD--------------P--------------------SLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDE-NG  114 (369)
T ss_pred             ehhccC--------------C--------------------ceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcC-CC
Confidence            995321              1                    239999999999999999999999999999999995 35


Q ss_pred             CCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccCCCCChhHHHHHHHHHHHHHHHHHHHhhhcCccccCCCCC
Q 016936          192 NSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMS  271 (380)
Q Consensus       192 ~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  271 (380)
                       ++|| ||+|.+++.|++|+..+||..+.+.+|.|.....+.....+... ..                           
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 99999999999999999999999999999988655333222211 00                           


Q ss_pred             ccCCccceEEEEeccCCcccCCChHHHHHHHHHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHH
Q 016936          272 LFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKN  351 (380)
Q Consensus       272 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~  351 (380)
                         ..-+.+++.....+.++           ..|.+.|+.||.|.++.++++....  ++|+|  ||.|.++++|..|++
T Consensus       165 ---~~~t~v~vk~~~~~~~~-----------~~l~~~f~~~g~i~s~~v~~~~~g~--~~~~g--fv~f~~~e~a~~av~  226 (369)
T KOG0123|consen  165 ---KRFTNVYVKNLEEDSTD-----------EELKDLFSAYGSITSVAVMRDSIGK--SKGFG--FVNFENPEDAKKAVE  226 (369)
T ss_pred             ---hhhhhhheeccccccch-----------HHHHHhhcccCcceEEEEeecCCCC--CCCcc--ceeecChhHHHHHHH
Confidence               11122222222222221           5899999999999999999877433  45555  999999999999999


Q ss_pred             HHcCcccCCeEEEEEeccc
Q 016936          352 ALSGRKFGGNTVNAFYYPE  370 (380)
Q Consensus       352 ~l~g~~i~gr~l~v~~~~~  370 (380)
                      .|||..+++..+.|.-+..
T Consensus       227 ~l~~~~~~~~~~~V~~aqk  245 (369)
T KOG0123|consen  227 TLNGKIFGDKELYVGRAQK  245 (369)
T ss_pred             hccCCcCCccceeeccccc
Confidence            9999999999999987765

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.97  E-value=6.6e-30  Score=236.90  Aligned_cols=171  Identities=19%  Similarity=0.308  Sum_probs=144.6

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecC
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  106 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g  106 (380)
                      .....++|||+|||+++|+++|+++|+.||.|...      .++.+..+.+++|||||+|.+.++|++|+ .|++..+.+
T Consensus       103 ~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v------~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~g  176 (346)
T TIGR01659       103 TNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTC------RIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRN  176 (346)
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEE------EEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCC
Confidence            44578899999999999999999999999984321      11112223457799999999999999999 799999999


Q ss_pred             ceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEee
Q 016936          107 VAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVK  186 (380)
Q Consensus       107 ~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~  186 (380)
                      ++|+|.++.....                             ....++|||+|||..+++++|+++|++||.|..|++++
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            9999998643210                             01125899999999999999999999999999999999


Q ss_pred             CCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCC--eEEEEEEcccCC
Q 016936          187 DRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD--KTLTVRRATASS  233 (380)
Q Consensus       187 ~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g--~~i~v~~~~~~~  233 (380)
                      ++.+++++|||||+|.+.++|++|++.||+..+.+  ++|+|.++....
T Consensus       228 d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~a~~~~  276 (346)
T TIGR01659       228 DKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAEEHG  276 (346)
T ss_pred             cCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCccc
Confidence            98899999999999999999999999999998865  789999987653

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=8.3e-29  Score=230.65  Aligned_cols=287  Identities=21%  Similarity=0.352  Sum_probs=217.9

Q ss_pred             CCCCCCCCccccchhhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec----CCCcEEEEEeC
Q 016936           13 LGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN----HEKKFAFVEMR   88 (380)
Q Consensus        13 ~~~~~~~~~~~~~~~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~----~~~g~afV~f~   88 (380)
                      +..+..+|+..|..+++...  |||+||+++++.++|+++|+.||.            |+++++-    -++|| ||.|.
T Consensus        59 ~~~~~~~~~rim~s~rd~~~--~~i~nl~~~~~~~~~~d~f~~~g~------------ilS~kv~~~~~g~kg~-FV~f~  123 (369)
T KOG0123|consen   59 FDVLKGKPIRIMWSQRDPSL--VFIKNLDESIDNKSLYDTFSEFGN------------ILSCKVATDENGSKGY-FVQFE  123 (369)
T ss_pred             CcccCCcEEEeehhccCCce--eeecCCCcccCcHHHHHHHHhhcC------------eeEEEEEEcCCCceee-EEEeC
Confidence            34556677776665544444  999999999999999999999999            5555542    37899 99999


Q ss_pred             CHHHHHHHH-HcCCceecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHH
Q 016936           89 TVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTET  167 (380)
Q Consensus        89 ~~~~a~~ai-~l~~~~i~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~  167 (380)
                      +.++|.+|+ .+||+.+.+++|.|......+........                     ....-..+++.+++.+.+.+
T Consensus       124 ~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~er~~~~~~---------------------~~~~~t~v~vk~~~~~~~~~  182 (369)
T KOG0123|consen  124 SEESAKKAIEKLNGMLLNGKKIYVGLFERKEEREAPLGE---------------------YKKRFTNVYVKNLEEDSTDE  182 (369)
T ss_pred             CHHHHHHHHHHhcCcccCCCeeEEeeccchhhhcccccc---------------------hhhhhhhhheeccccccchH
Confidence            999999999 89999999999999876655433221111                     01122479999999999999


Q ss_pred             HHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccCCCCChhHHHHHHHHH
Q 016936          168 QIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQA  247 (380)
Q Consensus       168 ~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~  247 (380)
                      .|.+.|..+|.|..+.++.+. .+.++||+||.|.+.+.|..|+..+++..+.+..+.|..+..     ..++.......
T Consensus       183 ~l~~~f~~~g~i~s~~v~~~~-~g~~~~~gfv~f~~~e~a~~av~~l~~~~~~~~~~~V~~aqk-----k~e~~~~l~~~  256 (369)
T KOG0123|consen  183 ELKDLFSAYGSITSVAVMRDS-IGKSKGFGFVNFENPEDAKKAVETLNGKIFGDKELYVGRAQK-----KSEREAELKRK  256 (369)
T ss_pred             HHHHhhcccCcceEEEEeecC-CCCCCCccceeecChhHHHHHHHhccCCcCCccceeeccccc-----chhhHHHHhhh
Confidence            999999999999999999985 577999999999999999999999999999999999998853     33333333332


Q ss_pred             HHHHHHHHHHhhhcCccccCCCCCccCCccceEEEEeccCCcccCCChHHHHHHHHHHHHhhcccCCeEEEEecCCCCCC
Q 016936          248 QQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNG  327 (380)
Q Consensus       248 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~~f~~~G~I~~v~i~~~~~~~  327 (380)
                      ......++..                 ......+.+.|   .+....       .+.|++.|+.||+|.++.++.+... 
T Consensus       257 ~~~~~~~~~~-----------------~~~~~nl~vkn---ld~~~~-------~e~L~~~f~~~GeI~s~kv~~~~~g-  308 (369)
T KOG0123|consen  257 FEQEFAKRSV-----------------SLQGANLYVKN---LDETLS-------DEKLRKIFSSFGEITSAKVMVDENG-  308 (369)
T ss_pred             hHhhhhhccc-----------------ccccccccccc---Cccccc-------hhHHHHHHhcccceeeEEEEeccCC-
Confidence            2222222110                 11122233333   111111       1589999999999999999887642 


Q ss_pred             CCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEeccccc
Q 016936          328 GETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  372 (380)
Q Consensus       328 ~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~~~  372 (380)
                         +..|++||+|++.++|.+|+..+||+.++++.|.|.++....
T Consensus       309 ---~skG~gfV~fs~~eeA~~A~~~~n~~~i~~k~l~vav~qr~~  350 (369)
T KOG0123|consen  309 ---KSKGFGFVEFSSPEEAKKAMTEMNGRLIGGKPLYVAVAQRKE  350 (369)
T ss_pred             ---CccceEEEEcCCHHHHHHHHHhhChhhhcCCchhhhHHhhhc
Confidence               334666999999999999999999999999999999887543

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.95  E-value=5.1e-27  Score=217.69  Aligned_cols=172  Identities=23%  Similarity=0.307  Sum_probs=143.5

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEE
Q 016936          148 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  227 (380)
Q Consensus       148 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~  227 (380)
                      .....++|||+|||+++++++|+++|+.||.|..|+|++++.+++++|||||+|.++++|++|++.|++..+.+++|+|.
T Consensus       103 ~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~  182 (346)
T TIGR01659       103 TNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVS  182 (346)
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeee
Confidence            34556899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EcccCCCCChhHHHHHHHHHHHHHHHHHHHhhhcCccccCCCCCccCCccceEEEEeccCCcccCCChHHHHHHHHHHHH
Q 016936          228 RATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMRE  307 (380)
Q Consensus       228 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~  307 (380)
                      ++.+...                                        ......+.+.|+.          +..++++|++
T Consensus       183 ~a~p~~~----------------------------------------~~~~~~lfV~nLp----------~~vtee~L~~  212 (346)
T TIGR01659       183 YARPGGE----------------------------------------SIKDTNLYVTNLP----------RTITDDQLDT  212 (346)
T ss_pred             ccccccc----------------------------------------ccccceeEEeCCC----------CcccHHHHHH
Confidence            8753210                                        1111234444421          1223379999


Q ss_pred             hhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCC--eEEEEEeccccc
Q 016936          308 ECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGG--NTVNAFYYPEDK  372 (380)
Q Consensus       308 ~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~g--r~l~v~~~~~~~  372 (380)
                      +|++||.|+.+.++++..++. +  .|+|||+|.+.++|++|++.||+..+.|  +.|+|.++.+..
T Consensus       213 ~F~~fG~V~~v~i~~d~~tg~-~--kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~a~~~~  276 (346)
T TIGR01659       213 IFGKYGQIVQKNILRDKLTGT-P--RGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAEEHG  276 (346)
T ss_pred             HHHhcCCEEEEEEeecCCCCc-c--ceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCccc
Confidence            999999999999998776554 3  3677999999999999999999999866  799999998754

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

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.95  E-value=1e-26  Score=220.11  Aligned_cols=192  Identities=22%  Similarity=0.349  Sum_probs=145.0

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe------cCCCcEEEEEeCCHHHHHHHH-HcCC
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-ALDG  101 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~------~~~~g~afV~f~~~~~a~~ai-~l~~  101 (380)
                      ....++|||+|||..+++++|+++|++||.+            ..+.+      ..++|||||+|.+.++|+.|+ .|++
T Consensus        86 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i------------~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g  153 (352)
T TIGR01661        86 SIKGANLYVSGLPKTMTQHELESIFSPFGQI------------ITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNG  153 (352)
T ss_pred             ccccceEEECCccccCCHHHHHHHHhccCCE------------EEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCC
Confidence            3456789999999999999999999999984            33332      346899999999999999999 8999


Q ss_pred             ceecC--ceEEEecCCCCCccccccCCC--------CCCCCCcc------------------------------------
Q 016936          102 IIFEG--VAVRVRRPTDYNPTLAAALGP--------GQPSPNLN------------------------------------  135 (380)
Q Consensus       102 ~~i~g--~~i~v~~~~~~~~~~~~~~~~--------~~~~~~~~------------------------------------  135 (380)
                      ..+.|  .+|.+.++.............        ........                                    
T Consensus       154 ~~~~g~~~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  233 (352)
T TIGR01661       154 TTPSGCTEPITVKFANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQH  233 (352)
T ss_pred             CccCCCceeEEEEECCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhhhhhhhc
Confidence            98887  678888765432111000000        00000000                                    


Q ss_pred             -----------------cc--cccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceE
Q 016936          136 -----------------LA--AVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGY  196 (380)
Q Consensus       136 -----------------~~--~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~  196 (380)
                                       ..  ................+|||+|||+++++++|+++|++||.|.++++++++.++.++||
T Consensus       234 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~  313 (352)
T TIGR01661       234 AVAQQHAAQRASPPATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGY  313 (352)
T ss_pred             ccccccccccCCCccccccccccccCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccce
Confidence                             00  00000001111233457999999999999999999999999999999999889999999


Q ss_pred             EEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccC
Q 016936          197 GFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  232 (380)
Q Consensus       197 afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~  232 (380)
                      |||+|.+.++|.+|++.|||..+.|++|+|.|+..+
T Consensus       314 aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~~~  349 (352)
T TIGR01661       314 GFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTNK  349 (352)
T ss_pred             EEEEECCHHHHHHHHHHhCCCEECCeEEEEEEccCC
Confidence            999999999999999999999999999999998765

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

>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=7.2e-27  Score=198.30  Aligned_cols=185  Identities=18%  Similarity=0.343  Sum_probs=154.9

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecCc
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  107 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g~  107 (380)
                      ....-.|||+.|..+++.++|++.|..||.|+++      .+|.+..+.++|||+||.|.+.++|+.|| .|+|.=|.+|
T Consensus        59 ~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~a------kvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R  132 (321)
T KOG0148|consen   59 SNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDA------KVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRR  132 (321)
T ss_pred             cccceeEEehhcchhcchHHHHHHhccccccccc------eEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccc
Confidence            3445679999999999999999999999999775      46888899999999999999999999999 8999999999


Q ss_pred             eEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeC
Q 016936          108 AVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKD  187 (380)
Q Consensus       108 ~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~  187 (380)
                      .|+-.|+..+........        +.....=     ...+...++|||+|++..+++++|++.|++||+|.+|++.++
T Consensus       133 ~IRTNWATRKp~e~n~~~--------ltfdeV~-----NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~  199 (321)
T KOG0148|consen  133 TIRTNWATRKPSEMNGKP--------LTFDEVY-----NQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD  199 (321)
T ss_pred             eeeccccccCccccCCCC--------ccHHHHh-----ccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc
Confidence            999999988763322110        1111000     001233469999999999999999999999999999999887


Q ss_pred             CCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccCCCCChh
Q 016936          188 RDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKT  238 (380)
Q Consensus       188 ~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~~~~~~~  238 (380)
                            +|||||.|.+.|.|.+||-.+|+.++.|..++|.|.+.......+
T Consensus       200 ------qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCsWGKe~~~~~~~  244 (321)
T KOG0148|consen  200 ------QGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGKEGDDGINN  244 (321)
T ss_pred             ------cceEEEEecchhhHHHHHHHhcCceeCceEEEEeccccCCCCCCc
Confidence                  479999999999999999999999999999999998876554443

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

Probab=99.95  E-value=1.5e-26  Score=220.17  Aligned_cols=289  Identities=18%  Similarity=0.236  Sum_probs=209.8

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecC
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  106 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g  106 (380)
                      ..+..+.|.|+|||..+..++|...|.+||.            |..+-+.+.--.|+|.|.++.+|.+|+ .+....+..
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            6788899999999999999999999999998            555544544445999999999999999 799999999


Q ss_pred             ceEEEecCCCCCcccc---ccC-----C-----CCCCCCCcccccc---c----CCCC-CCCCCCCCCEEEEcCCCCCCC
Q 016936          107 VAVRVRRPTDYNPTLA---AAL-----G-----PGQPSPNLNLAAV---G----LASG-AIGGAEGPDRVFVGGLPYYFT  165 (380)
Q Consensus       107 ~~i~v~~~~~~~~~~~---~~~-----~-----~~~~~~~~~~~~~---~----~~~~-~~~~~~~~~~l~V~nlp~~~t  165 (380)
                      .++.+.|+..--....   ...     .     +.......+-...   .    .+.- .........+|||+||+++++
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            9999988643222200   000     0     0000000000000   0    0000 001122223499999999999


Q ss_pred             HHHHHHHHHhcCCeeEEEEeeCCCC---CCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccCCCCChhHHHH
Q 016936          166 ETQIKELLESFGTLHGFDLVKDRDT---GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQES  242 (380)
Q Consensus       166 ~~~l~~~F~~~G~i~~v~l~~~~~~---~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~  242 (380)
                      .+++..+|+..|.|..+.|...++.   -.+.|||||+|.+.++|+.|+..|+|..+.|+.|.|+++.........  . 
T Consensus       529 ~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~~k~~~~~g--K-  605 (725)
T KOG0110|consen  529 LEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISENKPASTVG--K-  605 (725)
T ss_pred             hhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEeccCccccccc--c-
Confidence            9999999999999999988765431   135699999999999999999999999999999999998611100000  0 


Q ss_pred             HHHHHHHHHHHHHHHhhhcCccccCCCCCccCCccceEEEEeccCCcccCCChHHHHHHHHHHHHhhcccCCeEEEEecC
Q 016936          243 ILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPR  322 (380)
Q Consensus       243 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~~f~~~G~I~~v~i~~  322 (380)
                                                  .. .....         ....++.|.++.++..+++.+|+.||.|.+|.|++
T Consensus       606 ----------------------------~~-~~kk~---------~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPK  647 (725)
T KOG0110|consen  606 ----------------------------KK-SKKKK---------GTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPK  647 (725)
T ss_pred             ----------------------------cc-ccccc---------cceeeeeccchHHHHHHHHHHHhcccceeeeccch
Confidence                                        00 00110         12234556778888899999999999999999988


Q ss_pred             CCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEeccccc
Q 016936          323 PDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  372 (380)
Q Consensus       323 ~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~~~  372 (380)
                      .- ..  ..++|+|||+|-++.+|.+|+++|.+.++-||+|.++|+..+.
T Consensus       648 K~-~k--~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~~d~  694 (725)
T KOG0110|consen  648 KI-GK--GAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAKSDN  694 (725)
T ss_pred             hh-cc--hhhccceeeeccCcHHHHHHHHhhcccceechhhheehhccch
Confidence            62 22  3345667999999999999999999999999999999998865

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

Probab=99.94  E-value=9.9e-26  Score=219.62  Aligned_cols=176  Identities=20%  Similarity=0.370  Sum_probs=140.2

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEccc
Q 016936          152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  231 (380)
Q Consensus       152 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~  231 (380)
                      .++|||+|||+.+++++|+++|++||.|.+|+++.++.+++++|||||+|.+.++|++|++.|||..+.|+.|+|.+...
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            36999999999999999999999999999999999988999999999999999999999999999999999999986432


Q ss_pred             CCCCChhHHHHHHHHHHHHHHHHHHHhhhcCccccCCCCCccCCccceEEEEecc-CCcccCCChHHHHHHHHHHHHhhc
Q 016936          232 SSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEA-ITADALADDEEYEEILEDMREECG  310 (380)
Q Consensus       232 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~-~~~~~~~~~~~~~~~~~~L~~~f~  310 (380)
                      ...... ...                            ...........+.+.|. .+.++           ++|+++|+
T Consensus       187 ~p~a~~-~~~----------------------------~~~~~~~~~~rLfVgnLp~~vte-----------edLk~lFs  226 (612)
T TIGR01645       187 MPQAQP-IID----------------------------MVQEEAKKFNRIYVASVHPDLSE-----------TDIKSVFE  226 (612)
T ss_pred             cccccc-ccc----------------------------cccccccccceEEeecCCCCCCH-----------HHHHHHHh
Confidence            111000 000                            00000112234555542 22222           69999999


Q ss_pred             ccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEeccc
Q 016936          311 KYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPE  370 (380)
Q Consensus       311 ~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~  370 (380)
                      +||.|.++.+.++..++. ++  |||||+|.+.++|.+|++.|||..++|+.|+|.++..
T Consensus       227 ~FG~I~svrl~~D~~tgk-sK--GfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi~  283 (612)
T TIGR01645       227 AFGEIVKCQLARAPTGRG-HK--GYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVT  283 (612)
T ss_pred             hcCCeeEEEEEecCCCCC-cC--CeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecCC
Confidence            999999999998775443 44  5669999999999999999999999999999998764

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

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

Probab=99.93  E-value=6.1e-24  Score=196.35  Aligned_cols=190  Identities=26%  Similarity=0.373  Sum_probs=147.2

Q ss_pred             cceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCC-----CcEEEEEeCCHHHHHHHH-HcCCceec
Q 016936           32 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE-----KKFAFVEMRTVEEASNAM-ALDGIIFE  105 (380)
Q Consensus        32 ~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~-----~g~afV~f~~~~~a~~ai-~l~~~~i~  105 (380)
                      -=+|-|+|||+.+.+.||..+|++||.            |..+.++..     +|||||.|....+|.+|+ .+|+..|.
T Consensus       117 k~rLIIRNLPf~~k~~dLk~vFs~~G~------------V~Ei~IP~k~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~  184 (678)
T KOG0127|consen  117 KWRLIIRNLPFKCKKPDLKNVFSNFGK------------VVEIVIPRKKDGKLCGFAFVQFKEKKDAEKALEFFNGNKID  184 (678)
T ss_pred             cceEEeecCCcccCcHHHHHHHhhcce------------EEEEEcccCCCCCccceEEEEEeeHHHHHHHHHhccCceec
Confidence            557999999999999999999999998            777877642     499999999999999999 79999999


Q ss_pred             CceEEEecCCCCCcccccc----------------CC-CCCC---------------CC--Ccccc-------------c
Q 016936          106 GVAVRVRRPTDYNPTLAAA----------------LG-PGQP---------------SP--NLNLA-------------A  138 (380)
Q Consensus       106 g~~i~v~~~~~~~~~~~~~----------------~~-~~~~---------------~~--~~~~~-------------~  138 (380)
                      |++|-|.|+-.++.-...+                .. +...               ..  +.+..             .
T Consensus       185 gR~VAVDWAV~Kd~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed~e~d~edeEe~D~~se~~ee~~~~Eee~~~  264 (678)
T KOG0127|consen  185 GRPVAVDWAVDKDTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEEDGEEDSEDEEETDGNSEAFEEGEESEEEEDD  264 (678)
T ss_pred             CceeEEeeecccccccccchhhhhhhhhccchhhhcccccccccccchhcccccccccccccccchhhhccccccccccc
Confidence            9999999987665433211                00 0000               00  00000             0


Q ss_pred             c--cCCCC------------CCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcCh
Q 016936          139 V--GLASG------------AIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP  204 (380)
Q Consensus       139 ~--~~~~~------------~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~  204 (380)
                      +  ..+++            .........+|||+|||+++++++|..+|++||.|..+.++.+++++.++|+|||.|.+.
T Consensus       265 vDd~e~S~~~~~~k~~q~k~~~en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~  344 (678)
T KOG0127|consen  265 VDDEESSGKKESDKKAQNKTTRENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQ  344 (678)
T ss_pred             cccccccccCcccchhccccccccccccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccH
Confidence            0  00000            001112237999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHHh-----CC-CeeCCeEEEEEEcccCC
Q 016936          205 AVTDIACAAL-----NG-LKMGDKTLTVRRATASS  233 (380)
Q Consensus       205 ~~A~~Ai~~l-----~g-~~~~g~~i~v~~~~~~~  233 (380)
                      ..|+.||.+-     .| ..+.||.|.|..+..+.
T Consensus       345 ~~~~~ci~~Aspa~e~g~~ll~GR~Lkv~~Av~Rk  379 (678)
T KOG0127|consen  345 IAAQNCIEAASPASEDGSVLLDGRLLKVTLAVTRK  379 (678)
T ss_pred             HHHHHHHHhcCccCCCceEEEeccEEeeeeccchH
Confidence            9999999976     23 67899999999986653

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

Probab=99.91  E-value=2.1e-23  Score=204.22  Aligned_cols=178  Identities=21%  Similarity=0.302  Sum_probs=141.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      ..++|||+|||..+++++|+++|++||.|..|+++.++.++.++|||||+|.+.++|.+|+. |+|..+.|++|.|.++.
T Consensus        88 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~~~  166 (457)
T TIGR01622        88 DDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQSSQ  166 (457)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEeecc
Confidence            45799999999999999999999999999999999998899999999999999999999997 79999999999998753


Q ss_pred             cCCCCChhHHHHHHHHHHHHHHHHHHHhhhcCccccCCCCCccCCccceEEEEeccCCcccCCChHHHHHHHHHHHHhhc
Q 016936          231 ASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECG  310 (380)
Q Consensus       231 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~~f~  310 (380)
                      .......                 ...     ....+      .......+.+.|+...          .++++|+++|+
T Consensus       167 ~~~~~~~-----------------~~~-----~~~~~------~~p~~~~l~v~nl~~~----------~te~~l~~~f~  208 (457)
T TIGR01622       167 AEKNRAA-----------------KAA-----THQPG------DIPNFLKLYVGNLHFN----------ITEQELRQIFE  208 (457)
T ss_pred             hhhhhhh-----------------hcc-----cccCC------CCCCCCEEEEcCCCCC----------CCHHHHHHHHH
Confidence            2211000                 000     00000      0112456666664321          12269999999


Q ss_pred             ccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEeccc
Q 016936          311 KYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPE  370 (380)
Q Consensus       311 ~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~  370 (380)
                      +||.|..|.+..+..++.   ..|+|||+|.+.++|.+|++.|||..|.|+.|+|.|+.+
T Consensus       209 ~~G~i~~v~~~~d~~~g~---~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~  265 (457)
T TIGR01622       209 PFGDIEDVQLHRDPETGR---SKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQD  265 (457)
T ss_pred             hcCCeEEEEEEEcCCCCc---cceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccC
Confidence            999999999998775533   346779999999999999999999999999999999764

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

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

Probab=99.91  E-value=6.6e-24  Score=170.42  Aligned_cols=165  Identities=28%  Similarity=0.461  Sum_probs=143.7

Q ss_pred             ccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecC------CCcEEEEEeCCHHHHHHHH-HcCCce
Q 016936           31 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH------EKKFAFVEMRTVEEASNAM-ALDGII  103 (380)
Q Consensus        31 ~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~------~~g~afV~f~~~~~a~~ai-~l~~~~  103 (380)
                      ...||||+||+..++++-|+++|-+.|+            |+++.+++      .+||||++|.+.|+|.=|+ -++...
T Consensus         8 qd~tiyvgnld~kvs~~~l~EL~iqagp------------Vv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~Vk   75 (203)
T KOG0131|consen    8 QDATLYVGNLDEKVSEELLYELFIQAGP------------VVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVK   75 (203)
T ss_pred             CCceEEEecCCHHHHHHHHHHHHHhcCc------------eeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHH
Confidence            4579999999999999999999999998            77777654      5799999999999999999 688888


Q ss_pred             ecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeE-E
Q 016936          104 FEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHG-F  182 (380)
Q Consensus       104 i~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~-v  182 (380)
                      +.|++|+|..++..+.+                            .....++||+||.+.+++..|++.|+.||.+.. -
T Consensus        76 LYgrpIrv~kas~~~~n----------------------------l~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P  127 (203)
T KOG0131|consen   76 LYGRPIRVNKASAHQKN----------------------------LDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPP  127 (203)
T ss_pred             hcCceeEEEeccccccc----------------------------ccccccccccccCcchhHHHHHHHHHhccccccCC
Confidence            99999999886632211                            111258999999999999999999999999754 5


Q ss_pred             EEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccCCCC
Q 016936          183 DLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQ  235 (380)
Q Consensus       183 ~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~~~~  235 (380)
                      ++++++++|.++|||||.|.+.+.+.+|+..++|+.+..+++.|.++..+...
T Consensus       128 ~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~ya~k~~~k  180 (203)
T KOG0131|consen  128 KIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVSYAFKKDTK  180 (203)
T ss_pred             cccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEEEEEecCCC
Confidence            88999989999999999999999999999999999999999999998765443

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

Probab=99.91  E-value=9.5e-24  Score=190.09  Aligned_cols=171  Identities=23%  Similarity=0.351  Sum_probs=135.8

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCC-CeeCC--eEEEEEEc
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNG-LKMGD--KTLTVRRA  229 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g-~~~~g--~~i~v~~~  229 (380)
                      -++||+.+|..|+|.||+.+|++||.|.+|.+++|+.++.++|||||.|.++++|.+|+.+|+. +.+.|  .+|.|+++
T Consensus        35 vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqvk~A  114 (510)
T KOG0144|consen   35 VKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQVKYA  114 (510)
T ss_pred             hhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceeeccc
Confidence            5799999999999999999999999999999999999999999999999999999999999876 45554  56788777


Q ss_pred             ccCCCCChhHHHHHHHHHHHHHHHHHHHhhhcCccccCCCCCccCCccceEEEEeccCCcccCCChHHHHHHHHHHHHhh
Q 016936          230 TASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREEC  309 (380)
Q Consensus       230 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~~f  309 (380)
                      ......-                                      ....+.           ++.-.....++.+++++|
T Consensus       115 d~E~er~--------------------------------------~~e~KL-----------Fvg~lsK~~te~evr~iF  145 (510)
T KOG0144|consen  115 DGERERI--------------------------------------VEERKL-----------FVGMLSKQCTENEVREIF  145 (510)
T ss_pred             chhhhcc--------------------------------------ccchhh-----------hhhhccccccHHHHHHHH
Confidence            4321110                                      000000           111111223346999999


Q ss_pred             cccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcc-cCC--eEEEEEeccccccccc
Q 016936          310 GKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRK-FGG--NTVNAFYYPEDKYFNK  376 (380)
Q Consensus       310 ~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~-i~g--r~l~v~~~~~~~~~~~  376 (380)
                      ++||.|++|.|.++...    .++|||||+|.+.+.|..|++.|||.+ +.|  .+|.|-|++.++-..+
T Consensus       146 s~fG~Ied~~ilrd~~~----~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkFADtqkdk~~  211 (510)
T KOG0144|consen  146 SRFGHIEDCYILRDPDG----LSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKFADTQKDKDG  211 (510)
T ss_pred             HhhCccchhhheecccc----cccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEecccCCCchH
Confidence            99999999999998753    345899999999999999999999985 666  6899999998775543

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

Probab=99.90  E-value=1.6e-22  Score=177.70  Aligned_cols=213  Identities=19%  Similarity=0.333  Sum_probs=163.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCee--------EEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCC
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLH--------GFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD  221 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~--------~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g  221 (380)
                      .....|||.|||.++|.+++.++|++||.|.        .|+|.++. .|.-+|-|++.|...+++..|+..|++..++|
T Consensus       132 ~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~-~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg  210 (382)
T KOG1548|consen  132 KVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDN-QGKLKGDALCCYIKRESVELAIKILDEDELRG  210 (382)
T ss_pred             ccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecC-CCCccCceEEEeecccHHHHHHHHhCcccccC
Confidence            3446799999999999999999999999985        48999985 59999999999999999999999999999999


Q ss_pred             eEEEEEEcccCCCCChhHHHHHHHHHHHHHHHHHHHhhhcCccccCCCCCccCCccceEEEEeccCCcccCCChHH-HHH
Q 016936          222 KTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEE-YEE  300 (380)
Q Consensus       222 ~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~-~~~  300 (380)
                      +.|+|+.|.-....................+++.+.+..-++.  +...........+++++.|++++.++..+.. ..+
T Consensus       211 ~~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~--pd~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~d  288 (382)
T KOG1548|consen  211 KKLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWR--PDRDDPSKARADRTVILKNMFTPEDFEKNPDLLND  288 (382)
T ss_pred             cEEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccC--CCccccccccCCcEEEeeecCCHHHhccCHHHHHH
Confidence            9999998865432221111110101111112222211111111  1112222356678999999999999988844 788


Q ss_pred             HHHHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEeccccc
Q 016936          301 ILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  372 (380)
Q Consensus       301 ~~~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~~~  372 (380)
                      +.++|++.|.+||.|.+|.+...++.       |++-|.|.+.++|..|++.|+||+|+||.|..+......
T Consensus       289 lkedl~eec~K~G~v~~vvv~d~hPd-------GvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~DG~t  353 (382)
T KOG1548|consen  289 LKEDLTEECEKFGQVRKVVVYDRHPD-------GVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWDGKT  353 (382)
T ss_pred             HHHHHHHHHHHhCCcceEEEeccCCC-------ceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeCCcc
Confidence            99999999999999999999877664       588999999999999999999999999999999877644

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

Probab=99.90  E-value=2.8e-22  Score=169.46  Aligned_cols=199  Identities=23%  Similarity=0.368  Sum_probs=152.3

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceec
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE  105 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~  105 (380)
                      .+.-..-.|||.+||+.+|.+||+..|++||.|.-..      ++.+-.++-++|.+||.|+..++|+.|| .|||..=-
T Consensus       122 s~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSR------iL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~  195 (360)
T KOG0145|consen  122 SDSIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSR------ILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPS  195 (360)
T ss_pred             hhhhcccceEEecCCccchHHHHHHHHHHhhhhhhhh------hhhhcccceecceeEEEecchhHHHHHHHhccCCCCC
Confidence            3445566799999999999999999999999985432      2333345678999999999999999999 79998866


Q ss_pred             C--ceEEEecCCCCCcccccc-------------CCCCCCC----------------CCccccccc-----CCCCCCCCC
Q 016936          106 G--VAVRVRRPTDYNPTLAAA-------------LGPGQPS----------------PNLNLAAVG-----LASGAIGGA  149 (380)
Q Consensus       106 g--~~i~v~~~~~~~~~~~~~-------------~~~~~~~----------------~~~~~~~~~-----~~~~~~~~~  149 (380)
                      |  .+|.|..+..........             .++..-+                ........+     ..-..++..
T Consensus       196 g~tepItVKFannPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r~r~~~~~~~~~~~~rfsP~~~d~m~~l~~~~lp~~~  275 (360)
T KOG0145|consen  196 GCTEPITVKFANNPSQKTNQALLSQLYQSPARRYGGPMHHQAQRFRLDNLLNPHAAQARFSPMTIDGMSGLAGVNLPGGP  275 (360)
T ss_pred             CCCCCeEEEecCCcccccchhhhHHhhcCccccCCCcccchhhhhccccccchhhhhccCCCccccccceeeeeccCCCC
Confidence            6  679998765433221100             0100000                000000000     111234455


Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      ....+|||-||.+++++.-|+.+|.+||.|..|++++|..+++.+|||||.+.+-++|..||..|||..++++.+.|.+.
T Consensus       276 ~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFK  355 (360)
T KOG0145|consen  276 GGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFK  355 (360)
T ss_pred             CCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEe
Confidence            66789999999999999999999999999999999999989999999999999999999999999999999999999986


Q ss_pred             cc
Q 016936          230 TA  231 (380)
Q Consensus       230 ~~  231 (380)
                      ..
T Consensus       356 tn  357 (360)
T KOG0145|consen  356 TN  357 (360)
T ss_pred             cC
Confidence            53

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

Probab=99.90  E-value=1.8e-22  Score=196.61  Aligned_cols=161  Identities=24%  Similarity=0.327  Sum_probs=132.3

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe-------cCCCcEEEEEeCCHHHHHHHH-HcCC
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-------NHEKKFAFVEMRTVEEASNAM-ALDG  101 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~-------~~~~g~afV~f~~~~~a~~ai-~l~~  101 (380)
                      ...++|||+|||..+++++|.+.|++++..           ++++.+       .+++|||||+|.+.++|..|+ .++.
T Consensus       136 ~~~~rLFVgNLP~~~TeeeL~eeFskv~eg-----------vv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~  204 (578)
T TIGR01648       136 VDNCRLFVGGIPKNKKREEILEEFSKVTEG-----------VVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMP  204 (578)
T ss_pred             ccCceeEeecCCcchhhHHHHHHhhcccCC-----------ceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhc
Confidence            457899999999999999999999998641           222222       356899999999999999999 6653


Q ss_pred             --ceecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhc--C
Q 016936          102 --IIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESF--G  177 (380)
Q Consensus       102 --~~i~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~--G  177 (380)
                        ..+.|+.|.|.|+........                        ......++|||+|||..+++++|+++|++|  |
T Consensus       205 gki~l~Gr~I~VdwA~p~~~~d~------------------------~~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G  260 (578)
T TIGR01648       205 GRIQLWGHVIAVDWAEPEEEVDE------------------------DVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPG  260 (578)
T ss_pred             cceEecCceEEEEeecccccccc------------------------cccccccEEEEeCCCCCCCHHHHHHHHHhcCCC
Confidence              458899999999765321100                        001223689999999999999999999999  9


Q ss_pred             CeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccCC
Q 016936          178 TLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASS  233 (380)
Q Consensus       178 ~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~~  233 (380)
                      .|.+|.+++        +||||+|.+.++|++|++.||+..|.|+.|+|.++.+..
T Consensus       261 ~I~rV~~~r--------gfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~Akp~~  308 (578)
T TIGR01648       261 KVERVKKIR--------DYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKPVD  308 (578)
T ss_pred             ceEEEEeec--------CeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEccCCC
Confidence            999997754        499999999999999999999999999999999997753

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.

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

Probab=99.89  E-value=2.9e-22  Score=198.94  Aligned_cols=194  Identities=20%  Similarity=0.243  Sum_probs=138.9

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecCce
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  108 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g~~  108 (380)
                      ...++|||+|||..+++++|+++|+.||.|...      .++.+...+.++|||||+|.+.++|..|+ .|++..|.|++
T Consensus       293 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~------~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~  366 (509)
T TIGR01642       293 DSKDRIYIGNLPLYLGEDQIKELLESFGDLKAF------NLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNK  366 (509)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEE------EEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeE
Confidence            456899999999999999999999999985321      11122223557899999999999999999 79999999999


Q ss_pred             EEEecCCCCCccccccCCCCCCCCCcccccccCCCCC-CCCCCCCCEEEEcCCCCCC----------CHHHHHHHHHhcC
Q 016936          109 VRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGA-IGGAEGPDRVFVGGLPYYF----------TETQIKELLESFG  177 (380)
Q Consensus       109 i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~l~V~nlp~~~----------t~~~l~~~F~~~G  177 (380)
                      |.|.++................ + ......+..... ..+....+.|+|.|+....          ..++|+++|++||
T Consensus       367 l~v~~a~~~~~~~~~~~~~~~~-~-~~~~~~~~~~~~~~~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G  444 (509)
T TIGR01642       367 LHVQRACVGANQATIDTSNGMA-P-VTLLAKALSQSILQIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYG  444 (509)
T ss_pred             EEEEECccCCCCCCcccccccc-c-cccccccchhhhccccCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcC
Confidence            9999876433221111000000 0 000000000000 0112345789999996421          1367899999999


Q ss_pred             CeeEEEEeeC---CCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEccc
Q 016936          178 TLHGFDLVKD---RDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  231 (380)
Q Consensus       178 ~i~~v~l~~~---~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~  231 (380)
                      .|..|.|++.   ..++.+.|+|||+|.+.++|++|+..|||..|.|+.|.|.+...
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            9999999874   22356689999999999999999999999999999999998753

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

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

Probab=99.89  E-value=4.9e-22  Score=179.96  Aligned_cols=165  Identities=22%  Similarity=0.322  Sum_probs=139.6

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec-------CCCcEEEEEeCCHHHHHHHH-H-c
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN-------HEKKFAFVEMRTVEEASNAM-A-L   99 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~-------~~~g~afV~f~~~~~a~~ai-~-l   99 (380)
                      +...|+|||+|||+..++++|.+.|++.+.           -|+++.+.       +++|||||+|.+...|.-|- + +
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            578899999999999999999999999965           37777764       46899999999999988888 4 4


Q ss_pred             CC-ceecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCC
Q 016936          100 DG-IIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGT  178 (380)
Q Consensus       100 ~~-~~i~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~  178 (380)
                      ++ ..+-|+.+.|.|+........                        ...+.-+.|||+||+..+|++.|+++|..||.
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            44 458899999999876432110                        01233468999999999999999999999999


Q ss_pred             eeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccCCCCC
Q 016936          179 LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQS  236 (380)
Q Consensus       179 i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~~~~~  236 (380)
                      |++|+.++|        ||||.|.++++|.+||+.+||++|.|..|.|..|++....+
T Consensus       286 veRVkk~rD--------YaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP~~k~k  335 (506)
T KOG0117|consen  286 VERVKKPRD--------YAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKPVDKKK  335 (506)
T ss_pred             eEEeecccc--------eeEEeecchHHHHHHHHHhcCceecCceEEEEecCChhhhc
Confidence            999998876        99999999999999999999999999999999998765443

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

Probab=99.87  E-value=1.3e-21  Score=157.27  Aligned_cols=172  Identities=22%  Similarity=0.341  Sum_probs=137.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      .+..+|||+||+..++++.|+++|-+.|+|..+++++|+.++..+||||++|.++|+|+.|++-||...+.|++|+|..+
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            34469999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ccCCCCChhHHHHHHHHHHHHHHHHHHHhhhcCccccCCCCCccCCccceEEEEeccCCcccCCChHHHHHHHHHHHHhh
Q 016936          230 TASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREEC  309 (380)
Q Consensus       230 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~~f  309 (380)
                      ......                                       ....--+.+.|   ++..+|.       .-|...|
T Consensus        87 s~~~~n---------------------------------------l~vganlfvgN---Ld~~vDe-------~~L~dtF  117 (203)
T KOG0131|consen   87 SAHQKN---------------------------------------LDVGANLFVGN---LDPEVDE-------KLLYDTF  117 (203)
T ss_pred             cccccc---------------------------------------ccccccccccc---cCcchhH-------HHHHHHH
Confidence            621000                                       00001112222   2212221       4788999


Q ss_pred             cccCCeEE-EEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEecccccc
Q 016936          310 GKYGTLVN-VVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKY  373 (380)
Q Consensus       310 ~~~G~I~~-v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~~~~  373 (380)
                      +.||.+.+ -++++++.++. ++|  ++||.|++.+.+.+|+..|||..+..++++|+|+-.+..
T Consensus       118 safG~l~~~P~i~rd~~tg~-~~~--~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~ya~k~~~  179 (203)
T KOG0131|consen  118 SAFGVLISPPKIMRDPDTGN-PKG--FGFINYASFEASDAAIGSMNGQYLCNRPITVSYAFKKDT  179 (203)
T ss_pred             HhccccccCCcccccccCCC-CCC--CeEEechhHHHHHHHHHHhccchhcCCceEEEEEEecCC
Confidence            99999877 35666665443 454  559999999999999999999999999999999977543

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

Probab=99.86  E-value=2.2e-21  Score=173.72  Aligned_cols=309  Identities=15%  Similarity=0.182  Sum_probs=194.7

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCC--ceec
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDG--IIFE  105 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~--~~i~  105 (380)
                      ..+++.|+++|||.+++|.||.+++.+||.            |..+...+.+..||++|.+.++|...+ ....  -.++
T Consensus        25 ~~pSkV~HlRnlp~e~tE~elI~Lg~pFG~------------vtn~~~lkGknQAflem~d~~sAvtmv~~y~~~~p~lr   92 (492)
T KOG1190|consen   25 AEPSKVVHLRNLPWEVTEEELISLGLPFGK------------VTNLLMLKGKNQAFLEMADEESAVTMVNYYTSVTPVLR   92 (492)
T ss_pred             cCCcceeEeccCCccccHHHHHHhcccccc------------eeeeeeeccchhhhhhhcchhhhhheeecccccCcccc
Confidence            357899999999999999999999999998            777777888899999999999999866 3333  3488


Q ss_pred             CceEEEecCCCCCccccccCC------C---CCCCCCc--ccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHH
Q 016936          106 GVAVRVRRPTDYNPTLAAALG------P---GQPSPNL--NLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLE  174 (380)
Q Consensus       106 g~~i~v~~~~~~~~~~~~~~~------~---~~~~~~~--~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~  174 (380)
                      |++|.|+++.-..........      .   .......  ........-+...+.+.--+++|.++-+.++.+.|..+|+
T Consensus        93 ~~~~yiq~sn~~~lkt~s~p~q~r~~~vy~~~s~~q~~~~~~s~~~~~~G~~~~~n~vLr~iie~m~ypVslDVLHqvFS  172 (492)
T KOG1190|consen   93 GQPIYIQYSNHSELKTDSQPNQIRGQAVYQAVSSVQEIVLPLSASAVVVGNEDGPNPVLRTIIENMFYPVSLDVLHQVFS  172 (492)
T ss_pred             CcceeehhhhHHHHhccCchhhhhhhhHHhhhhcccccccccccccccccccCCCceeEEEEeccceeeeEHHHHHHHHh
Confidence            999999875332211100000      0   0000000  0000001111222333446789999999999999999999


Q ss_pred             hcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCee--CCeEEEEEEcccCCC-CC-hh----HHHHHHHH
Q 016936          175 SFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM--GDKTLTVRRATASSG-QS-KT----EQESILAQ  246 (380)
Q Consensus       175 ~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~--~g~~i~v~~~~~~~~-~~-~~----~~~~~~~~  246 (380)
                      +||.|..+.-..    ....-.|+|+|.+.+.|+.|...|+|..+  +.|.+++.++....- .+ ..    +..+...+
T Consensus       173 ~fG~VlKIiTF~----Knn~FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~Sklt~LnvKynndkSRDyTnp~LP  248 (492)
T KOG1190|consen  173 KFGFVLKIITFT----KNNGFQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFSKLTDLNVKYNNDKSRDYTNPDLP  248 (492)
T ss_pred             hcceeEEEEEEe----cccchhhhhhccchhhHHHHHHhccCCcccCceeEEEeehhhcccceeeccccccccccCCCCC
Confidence            999998774432    22233599999999999999999999876  446677777544320 00 00    00000000


Q ss_pred             HH-HHHHHHHHHhhh-------cCc--cccCC-----CC-CccCC-ccceEEEEeccCCcccCCChHHHHHHHHHHHHhh
Q 016936          247 AQ-QHIAIQKMALQT-------SGM--NTLGG-----GM-SLFGE-TLAKVLCLTEAITADALADDEEYEEILEDMREEC  309 (380)
Q Consensus       247 ~~-~~~~~~~~~~~~-------~~~--~~~~~-----~~-~~~~~-~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~~f  309 (380)
                      .. .+..++......       +|.  ..+.+     .. ..... ....++.++| .+.        +..+.+.|..+|
T Consensus       249 ~gd~~p~l~~~~~aa~~~~~~~~g~p~aip~~~~~a~~a~~~~~~~~~n~vllvsn-ln~--------~~VT~d~LftlF  319 (492)
T KOG1190|consen  249 VGDGQPSLDQLMAAAFGSVPAVHGAPLAIPSGAAGANAADGKIESPSANVVLLVSN-LNE--------EAVTPDVLFTLF  319 (492)
T ss_pred             CCccccccchhhhccccccccccCCcccCCccchhhcccccccccCCCceEEEEec-Cch--------hccchhHHHHHH
Confidence            00 000000000000       000  00000     00 00000 1123333333 222        223336899999


Q ss_pred             cccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEeccc
Q 016936          310 GKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPE  370 (380)
Q Consensus       310 ~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~  370 (380)
                      +-||.|.+|+|+.++++        -|.|.|.+...|+-|+..|+|.++.|++|+|.|..-
T Consensus       320 gvYGdVqRVkil~nkkd--------~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH  372 (492)
T KOG1190|consen  320 GVYGDVQRVKILYNKKD--------NALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKH  372 (492)
T ss_pred             hhhcceEEEEeeecCCc--------ceeeeecchhHHHHHHHHhhcceecCceEEEeeccC
Confidence            99999999999987753        679999999999999999999999999999999754

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

Probab=99.85  E-value=4.4e-21  Score=183.10  Aligned_cols=168  Identities=23%  Similarity=0.439  Sum_probs=141.7

Q ss_pred             ceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCC---------CcEEEEEeCCHHHHHHHH-HcCCc
Q 016936           33 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE---------KKFAFVEMRTVEEASNAM-ALDGI  102 (380)
Q Consensus        33 ~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~---------~g~afV~f~~~~~a~~ai-~l~~~  102 (380)
                      ++|||+||+.++|.+++..+|+..|.            |+++.+.+.         .|||||+|.+.++|+.|+ .|+|+
T Consensus       516 t~lfvkNlnf~Tt~e~l~~~F~k~G~------------VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgt  583 (725)
T KOG0110|consen  516 TKLFVKNLNFDTTLEDLEDLFSKQGT------------VLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGT  583 (725)
T ss_pred             hhhhhhcCCcccchhHHHHHHHhcCe------------EEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCc
Confidence            34999999999999999999999988            777766543         399999999999999999 79999


Q ss_pred             eecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEE
Q 016936          103 IFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGF  182 (380)
Q Consensus       103 ~i~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v  182 (380)
                      .|.|+.|.|..+..+...   +.+ .....                -.....|+|+|+|+.++..+++.+|..||.+..|
T Consensus       584 vldGH~l~lk~S~~k~~~---~~g-K~~~~----------------kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksv  643 (725)
T KOG0110|consen  584 VLDGHKLELKISENKPAS---TVG-KKKSK----------------KKKGTKILVRNIPFEATKREVRKLFTAFGQLKSV  643 (725)
T ss_pred             eecCceEEEEeccCcccc---ccc-ccccc----------------ccccceeeeeccchHHHHHHHHHHHhcccceeee
Confidence            999999999986622111   111 00000                1113689999999999999999999999999999


Q ss_pred             EEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccC
Q 016936          183 DLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  232 (380)
Q Consensus       183 ~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~  232 (380)
                      +++.-...+.++|||||.|.++.+|.+|+..|.+..+.||++.++|+...
T Consensus       644 RlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~~d  693 (725)
T KOG0110|consen  644 RLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAKSD  693 (725)
T ss_pred             ccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehhccc
Confidence            99987566788999999999999999999999999999999999999754

>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=7.8e-21  Score=163.31  Aligned_cols=148  Identities=22%  Similarity=0.407  Sum_probs=130.0

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccC
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  232 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~  232 (380)
                      ..+||+|||..+++.+|+.+|++||.|.+|+|+++        ||||..++...|+.|+..|+|..|.|..|.|+-++.+
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            47999999999999999999999999999999876        9999999999999999999999999999999987654


Q ss_pred             CCCChhHHHHHHHHHHHHHHHHHHHhhhcCccccCCCCCccCCccceEEEEeccCCcccCCChHHHHHHHHHHHHhhccc
Q 016936          233 SGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKY  312 (380)
Q Consensus       233 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~~f~~~  312 (380)
                                                                +..++.+.+.|+......          .+|+..|++|
T Consensus        75 ------------------------------------------sk~stkl~vgNis~tctn----------~ElRa~fe~y  102 (346)
T KOG0109|consen   75 ------------------------------------------SKASTKLHVGNISPTCTN----------QELRAKFEKY  102 (346)
T ss_pred             ------------------------------------------CCCccccccCCCCccccC----------HHHhhhhccc
Confidence                                                      334445555554333221          5899999999


Q ss_pred             CCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEecccc
Q 016936          313 GTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  371 (380)
Q Consensus       313 G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~~  371 (380)
                      |+|..|.|.++           ++||.|+-.++|..|+..|+|+.|.|++++|+..+..
T Consensus       103 gpviecdivkd-----------y~fvh~d~~eda~~air~l~~~~~~gk~m~vq~stsr  150 (346)
T KOG0109|consen  103 GPVIECDIVKD-----------YAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTSR  150 (346)
T ss_pred             CCceeeeeecc-----------eeEEEEeeccchHHHHhcccccccccceeeeeeeccc
Confidence            99999999873           7799999999999999999999999999999998764

>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=6.5e-21  Score=163.80  Aligned_cols=149  Identities=24%  Similarity=0.437  Sum_probs=133.9

Q ss_pred             ceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecCceEEE
Q 016936           33 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV  111 (380)
Q Consensus        33 ~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g~~i~v  111 (380)
                      -+|||+|||..+++.+|+.+|.+||+            |+.+.+.  |.||||-..+...|+-|| .||+-.|+|..|.|
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            36899999999999999999999998            6666655  567899999999999999 69999999999999


Q ss_pred             ecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCC
Q 016936          112 RRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTG  191 (380)
Q Consensus       112 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~  191 (380)
                      +-++++++                               .+.+|+|+|+.+.++.++|+..|.+||+|.+|+++++    
T Consensus        69 eaSksKsk-------------------------------~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd----  113 (346)
T KOG0109|consen   69 EASKSKSK-------------------------------ASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD----  113 (346)
T ss_pred             EeccccCC-------------------------------CccccccCCCCccccCHHHhhhhcccCCceeeeeecc----
Confidence            98766532                               2258999999999999999999999999999999876    


Q ss_pred             CCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccCCC
Q 016936          192 NSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSG  234 (380)
Q Consensus       192 ~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~~~  234 (380)
                          |+||.|...++|..|+..|++.+|.|++|+|+.+..+..
T Consensus       114 ----y~fvh~d~~eda~~air~l~~~~~~gk~m~vq~stsrlr  152 (346)
T KOG0109|consen  114 ----YAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLR  152 (346)
T ss_pred             ----eeEEEEeeccchHHHHhcccccccccceeeeeeeccccc
Confidence                999999999999999999999999999999999877643

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

Probab=99.83  E-value=2.7e-20  Score=164.50  Aligned_cols=173  Identities=21%  Similarity=0.442  Sum_probs=142.8

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccC
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  232 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~  232 (380)
                      .+|||+.+.+.+.++.|+..|..||+|.++.+.-|+.+++++|||||+|+-+|.|+.|++.|||..++||.|+|.+.+. 
T Consensus       114 cRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPsN-  192 (544)
T KOG0124|consen  114 CRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSN-  192 (544)
T ss_pred             HheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCCC-
Confidence            5899999999999999999999999999999999999999999999999999999999999999999999999985321 


Q ss_pred             CCCChhHHHHHHHHHHHHHHHHHHHhhhcCccccCCCCCccCCccceEEEEeccCCcccCCChHHHHHHHHHHHHhhccc
Q 016936          233 SGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKY  312 (380)
Q Consensus       233 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~~f~~~  312 (380)
                      ..+-.+--+.....+                           ....++++-+-..++.+           +||+.+|+-|
T Consensus       193 mpQAQpiID~vqeeA---------------------------k~fnRiYVaSvHpDLSe-----------~DiKSVFEAF  234 (544)
T KOG0124|consen  193 MPQAQPIIDMVQEEA---------------------------KKFNRIYVASVHPDLSE-----------TDIKSVFEAF  234 (544)
T ss_pred             CcccchHHHHHHHHH---------------------------HhhheEEeeecCCCccH-----------HHHHHHHHhh
Confidence            111111111111111                           23446676666666655           6999999999


Q ss_pred             CCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEe
Q 016936          313 GTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFY  367 (380)
Q Consensus       313 G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~  367 (380)
                      |.|.+|.+.+.. +++..||+|  ||+|.+..+-..|+..||-..++|.-|+|--
T Consensus       235 G~I~~C~LAr~p-t~~~HkGyG--fiEy~n~qs~~eAiasMNlFDLGGQyLRVGk  286 (544)
T KOG0124|consen  235 GEIVKCQLARAP-TGRGHKGYG--FIEYNNLQSQSEAIASMNLFDLGGQYLRVGK  286 (544)
T ss_pred             cceeeEEeeccC-CCCCcccee--eEEeccccchHHHhhhcchhhcccceEeccc
Confidence            999999999877 555566666  9999999999999999999999999999853

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

Probab=99.83  E-value=4.8e-20  Score=156.54  Aligned_cols=81  Identities=28%  Similarity=0.492  Sum_probs=72.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCC-ee--CCeEEEEE
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGL-KM--GDKTLTVR  227 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~-~~--~g~~i~v~  227 (380)
                      ..++|||+.|.+.-.|+|++.+|..||.|++|.+.+.+ .|.++|||||.|.+..+|+.||..|+|. .+  ....+.|+
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~-dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK   96 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGP-DGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVK   96 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCC-CCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEE
Confidence            34799999999999999999999999999999999997 5999999999999999999999999985 34  44678898


Q ss_pred             EcccC
Q 016936          228 RATAS  232 (380)
Q Consensus       228 ~~~~~  232 (380)
                      ++...
T Consensus        97 ~ADTd  101 (371)
T KOG0146|consen   97 FADTD  101 (371)
T ss_pred             eccch
Confidence            88654

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

Probab=99.83  E-value=3.8e-19  Score=159.48  Aligned_cols=300  Identities=17%  Similarity=0.158  Sum_probs=198.3

Q ss_pred             ccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcE-EEEEeCCHHHHHHHH-HcCCceecC--
Q 016936           31 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKF-AFVEMRTVEEASNAM-ALDGIIFEG--  106 (380)
Q Consensus        31 ~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~-afV~f~~~~~a~~ai-~l~~~~i~g--  106 (380)
                      .--++.|.|+-+.++-+-|...|++||.+           ...+++.++.+| |+|.|.+.+.|+.|- .|+|+.|..  
T Consensus       149 ~vLr~iie~m~ypVslDVLHqvFS~fG~V-----------lKIiTF~Knn~FQALvQy~d~~sAq~AK~aLdGqnIyngc  217 (492)
T KOG1190|consen  149 PVLRTIIENMFYPVSLDVLHQVFSKFGFV-----------LKIITFTKNNGFQALVQYTDAVSAQAAKLALDGQNIYNGC  217 (492)
T ss_pred             eeEEEEeccceeeeEHHHHHHHHhhccee-----------EEEEEEecccchhhhhhccchhhHHHHHHhccCCcccCce
Confidence            44567899999999999999999999984           445556677776 999999999999999 899998765  


Q ss_pred             ceEEEecCCCCC------cccccc-----CCCCCCCCCccc--c------------cccCCC---------CCCCCCCCC
Q 016936          107 VAVRVRRPTDYN------PTLAAA-----LGPGQPSPNLNL--A------------AVGLAS---------GAIGGAEGP  152 (380)
Q Consensus       107 ~~i~v~~~~~~~------~~~~~~-----~~~~~~~~~~~~--~------------~~~~~~---------~~~~~~~~~  152 (380)
                      ..|+|.++....      ..+.++     .+....++.+..  .            ..+.++         +........
T Consensus       218 CtLrId~Sklt~LnvKynndkSRDyTnp~LP~gd~~p~l~~~~~aa~~~~~~~~g~p~aip~~~~~a~~a~~~~~~~~~n  297 (492)
T KOG1190|consen  218 CTLRIDFSKLTDLNVKYNNDKSRDYTNPDLPVGDGQPSLDQLMAAAFGSVPAVHGAPLAIPSGAAGANAADGKIESPSAN  297 (492)
T ss_pred             eEEEeehhhcccceeeccccccccccCCCCCCCccccccchhhhccccccccccCCcccCCccchhhcccccccccCCCc
Confidence            567777543211      111111     111101111000  0            000000         000111124


Q ss_pred             CEEEEcCC-CCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEccc
Q 016936          153 DRVFVGGL-PYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  231 (380)
Q Consensus       153 ~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~  231 (380)
                      ..|.|.|| +..+|.+.|..+|..||.|.+|+|+..+.     .-|+|++.+..+|+.|+..|+|..+.|++|+|.+++.
T Consensus       298 ~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkk-----d~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH  372 (492)
T KOG1190|consen  298 VVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKK-----DNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKH  372 (492)
T ss_pred             eEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCC-----cceeeeecchhHHHHHHHHhhcceecCceEEEeeccC
Confidence            56888888 67799999999999999999999998742     3699999999999999999999999999999999876


Q ss_pred             CCCCChhH-HHH-HHHHHHHHHHHHHHHhhhcCccccCCCCCccCCccceEEEEeccCCcccCCChHHHHHHHHHHHHhh
Q 016936          232 SSGQSKTE-QES-ILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREEC  309 (380)
Q Consensus       232 ~~~~~~~~-~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~~f  309 (380)
                      ..-+...+ +.. -.........+.       ....+++......-.++..+.++|+..-          .++++|+++|
T Consensus       373 ~~vqlp~egq~d~glT~dy~~spLh-------rfkkpgsKN~~ni~PpsatlHlsnip~s----------vsee~lk~~f  435 (492)
T KOG1190|consen  373 TNVQLPREGQEDQGLTKDYGNSPLH-------RFKKPGSKNYQNIFPPSATLHLSNIPPS----------VSEEDLKNLF  435 (492)
T ss_pred             ccccCCCCCCccccccccCCCCchh-------hccCcccccccccCCchhheeeccCCcc----------cchhHHHHhh
Confidence            65433221 100 000000000000       0011222222222345556667764322          1237999999


Q ss_pred             cccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCe-EEEEEeccc
Q 016936          310 GKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGN-TVNAFYYPE  370 (380)
Q Consensus       310 ~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr-~l~v~~~~~  370 (380)
                      ..-|...+....-...       .-.|.+.+.++++|..|+..||.+.++.. .|||+|...
T Consensus       436 ~~~g~~vkafkff~kd-------~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvSFSks  490 (492)
T KOG1190|consen  436 QEPGGQVKAFKFFQKD-------RKMALPQLESVEEAIQALIDLHNHYLGENHHLRVSFSKS  490 (492)
T ss_pred             hcCCceEEeeeecCCC-------cceeecccCChhHhhhhccccccccCCCCceEEEEeecc
Confidence            9999887766544321       12789999999999999999999999875 999999753

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

Probab=99.81  E-value=3.4e-18  Score=154.55  Aligned_cols=189  Identities=21%  Similarity=0.290  Sum_probs=137.9

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe-----cCCCcEEEEEeCCHHHHHHHH-HcCC
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-----NHEKKFAFVEMRTVEEASNAM-ALDG  101 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~-----~~~~g~afV~f~~~~~a~~ai-~l~~  101 (380)
                      .....|.+||+|||+++.++||+++|++..-           .|.-+.+     .+.+|||.|+|.++|.+++|+ .||.
T Consensus        40 ~~~r~R~vfItNIpyd~rWqdLKdLvrekvG-----------ev~yveLl~D~~GK~rGcavVEFk~~E~~qKa~E~lnk  108 (608)
T KOG4212|consen   40 VAARDRSVFITNIPYDYRWQDLKDLVREKVG-----------EVEYVELLFDESGKARGCAVVEFKDPENVQKALEKLNK  108 (608)
T ss_pred             cccccceEEEecCcchhhhHhHHHHHHHhcC-----------ceEeeeeecccCCCcCCceEEEeeCHHHHHHHHHHhhh
Confidence            4566778999999999999999999998732           2555554     467899999999999999999 7999


Q ss_pred             ceecCceEEEecCCCCCcccccc---------------------------------CCCCCC-----CCCccccccc---
Q 016936          102 IIFEGVAVRVRRPTDYNPTLAAA---------------------------------LGPGQP-----SPNLNLAAVG---  140 (380)
Q Consensus       102 ~~i~g~~i~v~~~~~~~~~~~~~---------------------------------~~~~~~-----~~~~~~~~~~---  140 (380)
                      ..+.|++|.|+...+.+...-..                                 -+.+..     +...+.....   
T Consensus       109 ~~~~GR~l~vKEd~d~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~  188 (608)
T KOG4212|consen  109 YEVNGRELVVKEDHDEQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDY  188 (608)
T ss_pred             ccccCceEEEeccCchhhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCcccccccc
Confidence            99999999998654422211000                                 000000     0000000000   


Q ss_pred             ------------CCCCCC-C--CCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChh
Q 016936          141 ------------LASGAI-G--GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPA  205 (380)
Q Consensus       141 ------------~~~~~~-~--~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~  205 (380)
                                  .+-..+ .  .+.-..++||.||.+.+..+.|++.|.--|.++.+.+..++. |.++|+|.++|.++-
T Consensus       189 ~~~~~~~lfgl~~~Flr~~h~f~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idKe-G~s~G~~vi~y~hpv  267 (608)
T KOG4212|consen  189 NNSSNYNLFGLSASFLRSLHIFSPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDKE-GNSRGFAVIEYDHPV  267 (608)
T ss_pred             ccchhhhcccchhhhhhhccCCCCCccceeeeeccccccchHHHHHHhccceeeeeeceeeccc-cccCCeeEEEecchH
Confidence                        000000 0  112225799999999999999999999999999999999985 899999999999999


Q ss_pred             HHHHHHHHhCCCeeCCeEEEEEE
Q 016936          206 VTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       206 ~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      .|-.||.++++.-+..+++.++.
T Consensus       268 eavqaIsml~~~g~~~~~~~~Rl  290 (608)
T KOG4212|consen  268 EAVQAISMLDRQGLFDRRMTVRL  290 (608)
T ss_pred             HHHHHHHhhccCCCccccceeec
Confidence            99999999998777777776665

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

Probab=99.78  E-value=1.7e-17  Score=152.81  Aligned_cols=174  Identities=21%  Similarity=0.273  Sum_probs=133.9

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHHHcCCceecCc
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGV  107 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai~l~~~~i~g~  107 (380)
                      .-....-|.+++||+.+|++||.+||+.++.-         ..++.....+..|-|||+|.+.+++++|++++...+..+
T Consensus         6 e~~~~~~vr~rGLPwsat~~ei~~Ff~~~~I~---------~~~~~r~~Gr~sGeA~Ve~~seedv~~AlkkdR~~mg~R   76 (510)
T KOG4211|consen    6 EGSTAFEVRLRGLPWSATEKEILDFFSNCGIE---------NLEIPRRNGRPSGEAYVEFTSEEDVEKALKKDRESMGHR   76 (510)
T ss_pred             CCCcceEEEecCCCccccHHHHHHHHhcCcee---------EEEEeccCCCcCcceEEEeechHHHHHHHHhhHHHhCCc
Confidence            44566789999999999999999999999631         112222335667999999999999999999999999999


Q ss_pred             eEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeE-EEEee
Q 016936          108 AVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHG-FDLVK  186 (380)
Q Consensus       108 ~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~-v~l~~  186 (380)
                      -|.|-.+...+.......                  .....+.....|-+++||+.++++||.++|+..-.+.. +.++.
T Consensus        77 YIEVf~~~~~e~d~~~~~------------------~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~  138 (510)
T KOG4211|consen   77 YIEVFTAGGAEADWVMRP------------------GGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPM  138 (510)
T ss_pred             eEEEEccCCccccccccC------------------CCCCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeec
Confidence            999987654432211100                  00011123358999999999999999999997655544 66677


Q ss_pred             CCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          187 DRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       187 ~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      ++ .+++.|-|||+|++.+.|++|+.. |...++.|-|+|..+.
T Consensus       139 d~-rgR~tGEAfVqF~sqe~ae~Al~r-hre~iGhRYIEvF~Ss  180 (510)
T KOG4211|consen  139 DQ-RGRPTGEAFVQFESQESAEIALGR-HRENIGHRYIEVFRSS  180 (510)
T ss_pred             cC-CCCcccceEEEecCHHHHHHHHHH-HHHhhccceEEeehhH
Confidence            75 588999999999999999999997 6788899999998754

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

Probab=99.77  E-value=5.2e-19  Score=159.42  Aligned_cols=175  Identities=22%  Similarity=0.384  Sum_probs=144.5

Q ss_pred             ccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHHHcCCceecCceEE
Q 016936           31 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVR  110 (380)
Q Consensus        31 ~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai~l~~~~i~g~~i~  110 (380)
                      +.++|||++|+++++++.|+++|.+||.+..+.      ++.+....+++||+||+|.+++.+..++....+.|.|+.|.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~------vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~~~h~~dgr~ve   78 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCV------VMRDPSTGRSRGFGFVTFATPEGVDAVLNARTHKLDGRSVE   78 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEE------EeccCCCCCcccccceecCCCcchheeecccccccCCcccc
Confidence            889999999999999999999999999853311      11111234578999999999999999998888889999999


Q ss_pred             EecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCC
Q 016936          111 VRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDT  190 (380)
Q Consensus       111 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~  190 (380)
                      +..+.........                       ......+.|||++||.++++++++++|.+||.|..+.++.|+.+
T Consensus        79 ~k~av~r~~~~~~-----------------------~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~  135 (311)
T KOG4205|consen   79 PKRAVSREDQTKV-----------------------GRHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTT  135 (311)
T ss_pred             ceeccCccccccc-----------------------ccccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccc
Confidence            9876543221100                       00113468999999999999999999999999999999999999


Q ss_pred             CCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccCCCC
Q 016936          191 GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQ  235 (380)
Q Consensus       191 ~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~~~~  235 (380)
                      .+++||+||.|.+++.+.+++.. ..+.|.++.+.|..|.++...
T Consensus       136 ~~~rgFgfv~~~~e~sVdkv~~~-~f~~~~gk~vevkrA~pk~~~  179 (311)
T KOG4205|consen  136 SRPRGFGFVTFDSEDSVDKVTLQ-KFHDFNGKKVEVKRAIPKEVM  179 (311)
T ss_pred             cccccceeeEeccccccceeccc-ceeeecCceeeEeeccchhhc
Confidence            99999999999999999999984 789999999999999876433

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

Probab=99.77  E-value=2.2e-17  Score=146.58  Aligned_cols=285  Identities=18%  Similarity=0.161  Sum_probs=192.9

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH---HcCCceec
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM---ALDGIIFE  105 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai---~l~~~~i~  105 (380)
                      ...+-.|.|++|-..++|.||.+-++.||+            |.-+...+.+..|.|+|.+.+.|..|+   +-+..++.
T Consensus        28 ~~~spvvhvr~l~~~v~eadl~eal~~fG~------------i~yvt~~P~~r~alvefedi~~akn~Vnfaa~n~i~i~   95 (494)
T KOG1456|consen   28 PNPSPVVHVRGLHQGVVEADLVEALSNFGP------------IAYVTCMPHKRQALVEFEDIEGAKNCVNFAADNQIYIA   95 (494)
T ss_pred             CCCCceEEEeccccccchhHHHHHHhcCCc------------eEEEEeccccceeeeeeccccchhhheehhccCccccc
Confidence            455678999999999999999999999998            666777788899999999999999999   25557788


Q ss_pred             CceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEe
Q 016936          106 GVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLV  185 (380)
Q Consensus       106 g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~  185 (380)
                      |..-.+.++.+...++..   +....                 ...---+-|-|--+.+|.+.|+.+.-..|.|.+|.|.
T Consensus        96 gq~Al~NyStsq~i~R~g---~es~~-----------------pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIf  155 (494)
T KOG1456|consen   96 GQQALFNYSTSQCIERPG---DESAT-----------------PNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIF  155 (494)
T ss_pred             CchhhcccchhhhhccCC---CCCCC-----------------CCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEE
Confidence            888888776554333211   01111                 1111123455656778999999999999999999987


Q ss_pred             eCCCCCCCceEEEEEEcChhHHHHHHHHhCCCee--CCeEEEEEEcccCC-----CCChhHHHHHHHH------HHHHHH
Q 016936          186 KDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM--GDKTLTVRRATASS-----GQSKTEQESILAQ------AQQHIA  252 (380)
Q Consensus       186 ~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~--~g~~i~v~~~~~~~-----~~~~~~~~~~~~~------~~~~~~  252 (380)
                      +.  +|.   .|.|+|.+.+.|++|.+.|||..|  +.+.|+|+++++..     ..+..+.-.....      ......
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            65  333   799999999999999999999877  56789999998764     0111111000000      000000


Q ss_pred             HHHH-------HhhhcC-c--------cccCCC--------------CCcc----CCccceEEEEecc-CCcccCCChHH
Q 016936          253 IQKM-------ALQTSG-M--------NTLGGG--------------MSLF----GETLAKVLCLTEA-ITADALADDEE  297 (380)
Q Consensus       253 ~~~~-------~~~~~~-~--------~~~~~~--------------~~~~----~~~~~~~~~l~~~-~~~~~~~~~~~  297 (380)
                      .++.       ...+.| -        ..++..              .+.+    +...-.++.|... .+.        
T Consensus       231 r~~~p~~~~~~pss~~G~h~~y~sg~~~~p~~~~P~r~~~~~~~~~g~a~p~g~~~g~VmMVyGLdh~k~N~--------  302 (494)
T KOG1456|consen  231 RQRQPAPLGYHPSSRGGGHSGYYSGDRHGPPHPPPSRYRDGYRDGRGYASPGGGAPGCVMMVYGLDHGKMNC--------  302 (494)
T ss_pred             cccCCCccCCChhhcCCCCCCCcccccCCCCCCCCCCCccccccCCCCCCCCCCCCCcEEEEEeccccccch--------
Confidence            0000       000011 0        001000              0000    1111223333321 122        


Q ss_pred             HHHHHHHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEecccc
Q 016936          298 YEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  371 (380)
Q Consensus       298 ~~~~~~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~~  371 (380)
                           +.|.++|..||.|++|+.++..+        |.|.|++-+....++|+..||+-.+-|.+|.|....-.
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                 48999999999999999998654        57799999999999999999999999999999876543

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

Probab=99.76  E-value=2.7e-18  Score=145.93  Aligned_cols=81  Identities=28%  Similarity=0.525  Sum_probs=76.7

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccC
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  232 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~  232 (380)
                      .+|||-.||......+|..+|-.||.|.+.++..|+.++++++|+||.|.++.+|+.||..|||.+|+=++++|....++
T Consensus       286 CNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQLKRPk  365 (371)
T KOG0146|consen  286 CNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQLKRPK  365 (371)
T ss_pred             ceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhhhcCcc
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999999877655


Q ss_pred             C
Q 016936          233 S  233 (380)
Q Consensus       233 ~  233 (380)
                      +
T Consensus       366 d  366 (371)
T KOG0146|consen  366 D  366 (371)
T ss_pred             c
Confidence            3

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

Probab=99.74  E-value=8.5e-17  Score=134.87  Aligned_cols=185  Identities=21%  Similarity=0.299  Sum_probs=141.3

Q ss_pred             cccceEEEcCCCCcCcHHHHHH----HHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCcee
Q 016936           30 RHARRVYVGGLPPLANEQAIAT----FFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIF  104 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~----~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i  104 (380)
                      .+..||||.||...+..++|+.    +|++||.|+.         |..+...+.+|.|||.|.+.+.|..|+ .|+|..+
T Consensus         7 ~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ild---------I~a~kt~KmRGQA~VvFk~~~~As~A~r~l~gfpF   77 (221)
T KOG4206|consen    7 NPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILD---------ISAFKTPKMRGQAFVVFKETEAASAALRALQGFPF   77 (221)
T ss_pred             CCCceEeehhccccccHHHHHHHHHHHHHhhCCeEE---------EEecCCCCccCceEEEecChhHHHHHHHHhcCCcc
Confidence            3455999999999999999998    9999998543         555667788999999999999999999 8999999


Q ss_pred             cCceEEEecCCCCCccccccCCC---CCCC---CCcc----------------cccccCCCCCCCCCCCCCEEEEcCCCC
Q 016936          105 EGVAVRVRRPTDYNPTLAAALGP---GQPS---PNLN----------------LAAVGLASGAIGGAEGPDRVFVGGLPY  162 (380)
Q Consensus       105 ~g~~i~v~~~~~~~~~~~~~~~~---~~~~---~~~~----------------~~~~~~~~~~~~~~~~~~~l~V~nlp~  162 (380)
                      .|++++|.++...........+.   ..+.   ....                ........ ..........+++.|||.
T Consensus        78 ygK~mriqyA~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~-~~~~~ppn~ilf~~niP~  156 (221)
T KOG4206|consen   78 YGKPMRIQYAKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPF-LAQMAPPNNILFLTNIPS  156 (221)
T ss_pred             cCchhheecccCccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCc-cccCCCCceEEEEecCCc
Confidence            99999999987766544332111   0000   0000                00000000 012234456899999999


Q ss_pred             CCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeC-CeEEEEEEc
Q 016936          163 YFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG-DKTLTVRRA  229 (380)
Q Consensus       163 ~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~-g~~i~v~~~  229 (380)
                      .++.+.+..+|.+|..-.+++++...     .+.|||+|.+...|..|...+.+..+. ...|.+.++
T Consensus       157 es~~e~l~~lf~qf~g~keir~i~~~-----~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~a  219 (221)
T KOG4206|consen  157 ESESEMLSDLFEQFPGFKEIRLIPPR-----SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITFA  219 (221)
T ss_pred             chhHHHHHHHHhhCcccceeEeccCC-----CceeEEecchhhhhHHHhhhhccceeccCceEEeccc
Confidence            99999999999999999999997652     468999999999999999999988775 777777765

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

Probab=99.72  E-value=3.6e-16  Score=126.12  Aligned_cols=174  Identities=26%  Similarity=0.366  Sum_probs=128.4

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCC---CcEEEEEeCCHHHHHHHH-HcCCcee
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE---KKFAFVEMRTVEEASNAM-ALDGIIF  104 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~---~g~afV~f~~~~~a~~ai-~l~~~~i  104 (380)
                      .+.+|+|||+|||.++-+.||.++|-+||.            |.++.+...   -.||||+|.++.+|+.|| ..++-.+
T Consensus         3 gr~~~~iyvGNLP~diRekeieDlFyKyg~------------i~~ieLK~r~g~ppfafVeFEd~RDAeDAiygRdGYdy   70 (241)
T KOG0105|consen    3 GRNSRRIYVGNLPGDIREKEIEDLFYKYGR------------IREIELKNRPGPPPFAFVEFEDPRDAEDAIYGRDGYDY   70 (241)
T ss_pred             CcccceEEecCCCcchhhccHHHHHhhhcc------------eEEEEeccCCCCCCeeEEEecCccchhhhhhccccccc
Confidence            356899999999999999999999999998            555655432   469999999999999999 7999999


Q ss_pred             cCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCC---CCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeE
Q 016936          105 EGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAI---GGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHG  181 (380)
Q Consensus       105 ~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~  181 (380)
                      .|..|+|+.+.....+-.     .....+.. ...+......   ....+..+|.|.+||...+++||+++...-|.|..
T Consensus        71 dg~rLRVEfprggr~s~~-----~~G~y~gg-grgGgg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCf  144 (241)
T KOG0105|consen   71 DGCRLRVEFPRGGRSSSD-----RRGSYSGG-GRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCF  144 (241)
T ss_pred             CcceEEEEeccCCCcccc-----cccccCCC-CCCCCCCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeee
Confidence            999999998765432100     00000000 0000000010   11123358999999999999999999999999988


Q ss_pred             EEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCee--CCeEEEEE
Q 016936          182 FDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM--GDKTLTVR  227 (380)
Q Consensus       182 v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~--~g~~i~v~  227 (380)
                      ..+.+|       |.+.|+|...|+-+.|+.+|+...+  .|....+.
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            888776       3789999999999999999987655  34444333

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

Probab=99.70  E-value=2.4e-16  Score=128.40  Aligned_cols=86  Identities=22%  Similarity=0.536  Sum_probs=80.1

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      ....++|||+|||+.+++++|+++|++||.|..|+++.++.+++++|||||+|.+.++|++|++.|++..+.|+.|+|.+
T Consensus        31 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~  110 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNP  110 (144)
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            34457999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             cccCCC
Q 016936          229 ATASSG  234 (380)
Q Consensus       229 ~~~~~~  234 (380)
                      +..+..
T Consensus       111 a~~~~~  116 (144)
T PLN03134        111 ANDRPS  116 (144)
T ss_pred             CCcCCC
Confidence            876543

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

Probab=99.70  E-value=2.7e-16  Score=131.83  Aligned_cols=195  Identities=17%  Similarity=0.271  Sum_probs=137.4

Q ss_pred             CEEEEcCCCCCCCHHHHHH----HHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          153 DRVFVGGLPYYFTETQIKE----LLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~----~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      .+|||.||+..+..++|+.    +|++||.|..|...+   +.+.+|.|||.|.+.+.|-.|+..|+|..+.|..|++.+
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    999999998887764   477899999999999999999999999999999999999


Q ss_pred             cccCCCCChhHHHHHH--HHHHHHHHHHHHHhh---------hcCccccCCCCCccCCccceEEEEeccCCcccCCChHH
Q 016936          229 ATASSGQSKTEQESIL--AQAQQHIAIQKMALQ---------TSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEE  297 (380)
Q Consensus       229 ~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~---------~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~  297 (380)
                      |..+.......+....  ...............         ...++.+.... .....+..++.+.|+....       
T Consensus        87 A~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~-~~~~ppn~ilf~~niP~es-------  158 (221)
T KOG4206|consen   87 AKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFL-AQMAPPNNILFLTNIPSES-------  158 (221)
T ss_pred             ccCccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCcc-ccCCCCceEEEEecCCcch-------
Confidence            9877543322111000  000000000000000         00011111111 2223445555555544332       


Q ss_pred             HHHHHHHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccC-CeEEEEEecc
Q 016936          298 YEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFG-GNTVNAFYYP  369 (380)
Q Consensus       298 ~~~~~~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~-gr~l~v~~~~  369 (380)
                         ..+.|..+|++|.....+.++...+        +.|||+|.+...|..|.+.|.|..|. ...+.+.|+.
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 ---ESEMLSDLFEQFPGFKEIRLIPPRS--------GIAFVEFLSDRQASAAQQALQGFKITKKNTMQITFAK  220 (221)
T ss_pred             ---hHHHHHHHHhhCcccceeEeccCCC--------ceeEEecchhhhhHHHhhhhccceeccCceEEecccC
Confidence               2357788899999999999887553        58899999999999999999999998 8999998875

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

Probab=99.68  E-value=6.3e-16  Score=137.82  Aligned_cols=293  Identities=19%  Similarity=0.223  Sum_probs=190.1

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe-cCCCcEEEEEeCCHHHHHHHHHcCCceecCce
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-NHEKKFAFVEMRTVEEASNAMALDGIIFEGVA  108 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~-~~~~g~afV~f~~~~~a~~ai~l~~~~i~g~~  108 (380)
                      .+...|..++||+..+..+|..||.-.-...++       ..+.... +.+.|+|.|.|.+.|.-.-|++.+.+.+.++.
T Consensus        58 ~~~vvvRaRglpwq~Sd~~ia~ff~gl~ia~gg-------~aKOG~~qgrRnge~lvrf~d~e~RdlalkRhkhh~g~ry  130 (508)
T KOG1365|consen   58 DDNVVVRARGLPWQSSDQDIARFFKGLNIANGG-------RALCLNAQGRRNGEALVRFVDPEGRDLALKRHKHHMGTRY  130 (508)
T ss_pred             CcceEEEecCCCCCcccCCHHHHHhhhhccccc-------eeeeehhhhccccceEEEecCchhhhhhhHhhhhhccCCc
Confidence            344567889999999999999999876443222       2333332 45668999999999999999999999999999


Q ss_pred             EEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCC-CC--CCCEEEEcCCCCCCCHHHHHHHHHhc----CCeeE
Q 016936          109 VRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGG-AE--GPDRVFVGGLPYYFTETQIKELLESF----GTLHG  181 (380)
Q Consensus       109 i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~--~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~  181 (380)
                      |.|..+.......-.                +.++..... ..  .--.|.+++||+++++.|+.++|.+-    |..+.
T Consensus       131 ievYka~ge~f~~ia----------------gg~s~e~~~flsk~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~eg  194 (508)
T KOG1365|consen  131 IEVYKATGEEFLKIA----------------GGTSNEAAPFLSKENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEG  194 (508)
T ss_pred             eeeeccCchhheEec----------------CCccccCCCCCCcccceEEEecCCCCCcchHHHHHhcCCCCcccCCccc
Confidence            999865443221100                111111111 11  11357889999999999999999742    24556


Q ss_pred             EEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccCCCCChhHHHHHHHHHHHHHHHHHHHhhhc
Q 016936          182 FDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTS  261 (380)
Q Consensus       182 v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  261 (380)
                      +.++..+ +|+..|-|||.|..+++|+.|+.+ |...++.|-|++-++...      +.....+..    ....+.....
T Consensus       195 vLFV~rp-dgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYIElFRSTaa------Evqqvlnr~----~s~pLi~~~~  262 (508)
T KOG1365|consen  195 VLFVTRP-DGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYIELFRSTAA------EVQQVLNRE----VSEPLIPGLT  262 (508)
T ss_pred             eEEEECC-CCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHHHHHHHhHH------HHHHHHHhh----ccccccCCCC
Confidence            7777776 599999999999999999999997 555666666666543210      000000000    0000000000


Q ss_pred             CccccCCCCC-ccCCccceEEEEeccCCcccCCChHHHHHHHHHHHHhhcccCCeEE---EEecCCCCCCCCCCCccEEE
Q 016936          262 GMNTLGGGMS-LFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVN---VVIPRPDQNGGETPGVGKVF  337 (380)
Q Consensus       262 ~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~~f~~~G~I~~---v~i~~~~~~~~~~~g~g~af  337 (380)
                      ..-.++.... .+....+.|+.|..          .+|.++.+||..+|..|-.-.+   |.+..+. +|+.   .|-||
T Consensus       263 sp~~p~~p~~~~p~~~~kdcvRLRG----------LPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~-qGrP---SGeAF  328 (508)
T KOG1365|consen  263 SPLLPGGPARLVPPTRSKDCVRLRG----------LPYEATVEDILDFLGDFATDIRFQGVHMVLNG-QGRP---SGEAF  328 (508)
T ss_pred             CCCCCCCccccCCCCCCCCeeEecC----------CChhhhHHHHHHHHHHHhhhcccceeEEEEcC-CCCc---Chhhh
Confidence            0011111111 11233366777666          4677788999999998864322   5554443 4443   37889


Q ss_pred             EEeechhhHHHHHHHHcCcccCCeEEEEEecccc
Q 016936          338 LEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  371 (380)
Q Consensus       338 V~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~~  371 (380)
                      |+|.+.++|..|.+.-|.....+|-|.|--...+
T Consensus       329 Iqm~nae~a~aaaqk~hk~~mk~RYiEvfp~S~e  362 (508)
T KOG1365|consen  329 IQMRNAERARAAAQKCHKKLMKSRYIEVFPCSVE  362 (508)
T ss_pred             hhhhhhHHHHHHHHHHHHhhcccceEEEeeccHH
Confidence            9999999999999999988888999988766543

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

Probab=99.67  E-value=2.1e-16  Score=147.46  Aligned_cols=178  Identities=19%  Similarity=0.314  Sum_probs=139.2

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccC
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  232 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~  232 (380)
                      +++|+-.++...++.+|.++|+.+|.|..|+++.|+.+++++|.|||+|.+.++...|+. |.|..+.|.+|.|......
T Consensus       180 Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aia-LsGqrllg~pv~vq~sEae  258 (549)
T KOG0147|consen  180 RTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIA-LSGQRLLGVPVIVQLSEAE  258 (549)
T ss_pred             HHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhh-hcCCcccCceeEecccHHH
Confidence            688888899899999999999999999999999999999999999999999999999996 8999999999999875321


Q ss_pred             CCCChhHHHHHHHHHHHHHHHHHHHhhhcCccccCCCCCccCCccceEEEEec-cCCcccCCChHHHHHHHHHHHHhhcc
Q 016936          233 SGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTE-AITADALADDEEYEEILEDMREECGK  311 (380)
Q Consensus       233 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~-~~~~~~~~~~~~~~~~~~~L~~~f~~  311 (380)
                      ...                 .+    ..+.+-.++   ....+...  +.+.| .++.++           .+|+..|++
T Consensus       259 knr-----------------~a----~~s~a~~~k---~~~~p~~r--l~vgnLHfNite-----------~~lr~ifep  301 (549)
T KOG0147|consen  259 KNR-----------------AA----NASPALQGK---GFTGPMRR--LYVGNLHFNITE-----------DMLRGIFEP  301 (549)
T ss_pred             HHH-----------------HH----hcccccccc---ccccchhh--hhhcccccCchH-----------HHHhhhccC
Confidence            000                 00    000000000   00001111  22232 344443           699999999


Q ss_pred             cCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEecccc
Q 016936          312 YGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  371 (380)
Q Consensus       312 ~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~~  371 (380)
                      ||.|+.|.+..+.++|. ++|+|  ||+|.+.++|++|++.|||..+.||.|+|.-.++.
T Consensus       302 fg~Ie~v~l~~d~~tG~-skgfG--fi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r  358 (549)
T KOG0147|consen  302 FGKIENVQLTKDSETGR-SKGFG--FITFVNKEDARKALEQLNGFELAGRLIKVSVVTER  358 (549)
T ss_pred             cccceeeeecccccccc-ccCcc--eEEEecHHHHHHHHHHhccceecCceEEEEEeeee
Confidence            99999999999987776 67766  99999999999999999999999999999988763

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

Probab=99.65  E-value=5.9e-16  Score=139.69  Aligned_cols=172  Identities=22%  Similarity=0.404  Sum_probs=140.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      ...++||++|++.++++.|+++|++||.|..|.+++++.+++++||+||+|.+++....++.. ..+.+.|+.|.+..+.
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            446999999999999999999999999999999999999999999999999999999999885 5789999999999998


Q ss_pred             cCCCCChhHHHHHHHHHHHHHHHHHHHhhhcCccccCCCCCccCCccceEEEEec-cCCcccCCChHHHHHHHHHHHHhh
Q 016936          231 ASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTE-AITADALADDEEYEEILEDMREEC  309 (380)
Q Consensus       231 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~-~~~~~~~~~~~~~~~~~~~L~~~f  309 (380)
                      ++..+....+                                  ...++.+.+.. ..+..+           +++++.|
T Consensus        84 ~r~~~~~~~~----------------------------------~~~tkkiFvGG~~~~~~e-----------~~~r~yf  118 (311)
T KOG4205|consen   84 SREDQTKVGR----------------------------------HLRTKKIFVGGLPPDTTE-----------EDFKDYF  118 (311)
T ss_pred             Cccccccccc----------------------------------ccceeEEEecCcCCCCch-----------HHHhhhh
Confidence            7755533211                                  11233343333 223322           6999999


Q ss_pred             cccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEeccccc
Q 016936          310 GKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  372 (380)
Q Consensus       310 ~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~~~  372 (380)
                      .+||.|..+.++.+....+ .+|+|  ||.|.+++...+++. .+-+.|.|+.+.|--|..+.
T Consensus       119 e~~g~v~~~~~~~d~~~~~-~rgFg--fv~~~~e~sVdkv~~-~~f~~~~gk~vevkrA~pk~  177 (311)
T KOG4205|consen  119 EQFGKVADVVIMYDKTTSR-PRGFG--FVTFDSEDSVDKVTL-QKFHDFNGKKVEVKRAIPKE  177 (311)
T ss_pred             hccceeEeeEEeecccccc-cccce--eeEeccccccceecc-cceeeecCceeeEeeccchh
Confidence            9999999999988876554 55555  999999999999988 58889999999998887744

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

Probab=99.61  E-value=3.4e-14  Score=118.18  Aligned_cols=179  Identities=21%  Similarity=0.298  Sum_probs=124.0

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCC----CcEEEEEeCCHHHHHHHH-HcCCc
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE----KKFAFVEMRTVEEASNAM-ALDGI  102 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~----~g~afV~f~~~~~a~~ai-~l~~~  102 (380)
                      +.-.-|||||.+||-++...+|+.+|++|-...+         .....+.+.    +-+|||.|.+..+|..|+ +|||+
T Consensus        30 ~~~~VRTLFVSGLP~DvKpREiynLFR~f~GYEg---------slLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGv  100 (284)
T KOG1457|consen   30 EPGAVRTLFVSGLPNDVKPREIYNLFRRFHGYEG---------SLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGV  100 (284)
T ss_pred             cccccceeeeccCCcccCHHHHHHHhccCCCccc---------eeeeeccCCCccccceEEEEecchHHHHHHHHHhcCe
Confidence            3455899999999999999999999999843211         222222222    369999999999999999 89999


Q ss_pred             eec---CceEEEecCCCCCccccccCCC-CCCCCCccccc----------------------------------------
Q 016936          103 IFE---GVAVRVRRPTDYNPTLAAALGP-GQPSPNLNLAA----------------------------------------  138 (380)
Q Consensus       103 ~i~---g~~i~v~~~~~~~~~~~~~~~~-~~~~~~~~~~~----------------------------------------  138 (380)
                      .|.   +..|+|+.++...+......+. ..+++......                                        
T Consensus       101 rFDpE~~stLhiElAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~~qhd~~l~~p~~l~~~~~a~al~~~~~t~~  180 (284)
T KOG1457|consen  101 RFDPETGSTLHIELAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSADDQHDEGLSDPDELQEPGNADALKENDTTKS  180 (284)
T ss_pred             eeccccCceeEeeehhcCcccccCCCCCCCCCCccccccccChhhcccchhhccccccCccccCCccccccCCCccccch
Confidence            885   5789998776544433221111 00000000000                                        


Q ss_pred             ----------------ccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEc
Q 016936          139 ----------------VGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQ  202 (380)
Q Consensus       139 ----------------~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~  202 (380)
                                      ...++....++....+|||.||...+++++|+.+|+.|..-..++|...    .....||++|+
T Consensus       181 ~~l~a~~~~~P~a~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~----~g~~vaf~~~~  256 (284)
T KOG1457|consen  181 EALSAPDSKAPSANAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRAR----GGMPVAFADFE  256 (284)
T ss_pred             hhhhhhhhcCCcccchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecC----CCcceEeecHH
Confidence                            0011112234555679999999999999999999999987666666432    22357999999


Q ss_pred             ChhHHHHHHHHhCCCee
Q 016936          203 DPAVTDIACAALNGLKM  219 (380)
Q Consensus       203 ~~~~A~~Ai~~l~g~~~  219 (380)
                      ..+.|..||..|+|..+
T Consensus       257 ~~~~at~am~~lqg~~~  273 (284)
T KOG1457|consen  257 EIEQATDAMNHLQGNLL  273 (284)
T ss_pred             HHHHHHHHHHHhhccee
Confidence            99999999999988665

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

Probab=99.61  E-value=6.2e-14  Score=113.29  Aligned_cols=181  Identities=18%  Similarity=0.292  Sum_probs=124.6

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEccc
Q 016936          152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  231 (380)
Q Consensus       152 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~  231 (380)
                      .++|||+|||.++.+.+|.++|-+||.|..|.|...   -..-+||||+|+++-+|+.||..-+|..+.|+.|+|+++..
T Consensus         6 ~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r---~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprg   82 (241)
T KOG0105|consen    6 SRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNR---PGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRG   82 (241)
T ss_pred             cceEEecCCCcchhhccHHHHHhhhcceEEEEeccC---CCCCCeeEEEecCccchhhhhhcccccccCcceEEEEeccC
Confidence            479999999999999999999999999999988543   23456999999999999999999999999999999999765


Q ss_pred             CCCCChhHHHHHHHHHHHHHHHHHHHhhhcCcc--ccCCCCC-ccCCccceEEEEeccCCcccCCChHHHHHHHHHHHHh
Q 016936          232 SSGQSKTEQESILAQAQQHIAIQKMALQTSGMN--TLGGGMS-LFGETLAKVLCLTEAITADALADDEEYEEILEDMREE  308 (380)
Q Consensus       232 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~~  308 (380)
                      -.......                 ....++..  .++++.. .+.-....-++++....--.      |    +||+++
T Consensus        83 gr~s~~~~-----------------G~y~gggrgGgg~gg~rgppsrrSe~RVvVsGLp~SgS------W----QDLKDH  135 (241)
T KOG0105|consen   83 GRSSSDRR-----------------GSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGS------W----QDLKDH  135 (241)
T ss_pred             CCcccccc-----------------cccCCCCCCCCCCCcccCCcccccceeEEEecCCCCCc------h----HHHHHH
Confidence            42111100                 00000000  1111111 11122223333443222111      1    599999


Q ss_pred             hcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccC--CeEEEEEeccccc
Q 016936          309 CGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFG--GNTVNAFYYPEDK  372 (380)
Q Consensus       309 f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~--gr~l~v~~~~~~~  372 (380)
                      +.+-|.|....+.++.          +..|+|...++.+.|+.+|....+.  |.+..+....++.
T Consensus       136 mReaGdvCfadv~rDg----------~GvV~~~r~eDMkYAvr~ld~~~~~seGe~~yirv~~~~~  191 (241)
T KOG0105|consen  136 MREAGDVCFADVQRDG----------VGVVEYLRKEDMKYAVRKLDDQKFRSEGETAYIRVRGDEN  191 (241)
T ss_pred             HHhhCCeeeeeeeccc----------ceeeeeeehhhHHHHHHhhccccccCcCcEeeEEecccCC
Confidence            9999999999987752          4499999999999999999887764  4444444444433

>PF00076 RRM_1: RNA recognition motif

Probab=99.58  E-value=1.3e-14  Score=103.45  Aligned_cols=70  Identities=27%  Similarity=0.644  Sum_probs=67.0

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEE
Q 016936          155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  225 (380)
Q Consensus       155 l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~  225 (380)
                      |||+|||.++++++|+++|++||.|..+.+..+ .++..+|+|||+|.+.++|++|++.++|..+.|++|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            799999999999999999999999999999987 4789999999999999999999999999999999986

(a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....

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

Probab=99.57  E-value=1e-13  Score=122.54  Aligned_cols=199  Identities=18%  Similarity=0.161  Sum_probs=136.5

Q ss_pred             cchhhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEE---ecCCCcEEEEEeCCHHHHHHHH-Hc
Q 016936           24 MTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVY---INHEKKFAFVEMRTVEEASNAM-AL   99 (380)
Q Consensus        24 ~~~~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~---~~~~~g~afV~f~~~~~a~~ai-~l   99 (380)
                      +......-...|||.|||.++|-+++.++|+.||.|.....-+.  +-+.+.   -++-||-|++.|...+++..|+ -|
T Consensus       126 ~~~~~~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~e--pk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~il  203 (382)
T KOG1548|consen  126 WFNPEPKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGE--PKVKLYRDNQGKLKGDALCCYIKRESVELAIKIL  203 (382)
T ss_pred             ccCcccccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCC--eeEEEEecCCCCccCceEEEeecccHHHHHHHHh
Confidence            33334555667999999999999999999999999754322111  111111   1345799999999999999999 79


Q ss_pred             CCceecCceEEEecCCCCCccc-cccCCC---CCCCC------CcccccccCCCCCCCCCCCCCEEEEcCC--C--CCCC
Q 016936          100 DGIIFEGVAVRVRRPTDYNPTL-AAALGP---GQPSP------NLNLAAVGLASGAIGGAEGPDRVFVGGL--P--YYFT  165 (380)
Q Consensus       100 ~~~~i~g~~i~v~~~~~~~~~~-~~~~~~---~~~~~------~~~~~~~~~~~~~~~~~~~~~~l~V~nl--p--~~~t  165 (380)
                      ++..++|++|+|..+.-..+.. ......   ..+..      ...+.+...- ....-....++|.++|+  |  ...+
T Consensus       204 De~~~rg~~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~-~~~sk~r~~~tVi~kn~Ftp~~~~~~  282 (382)
T KOG1548|consen  204 DEDELRGKKLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDR-DDPSKARADRTVILKNMFTPEDFEKN  282 (382)
T ss_pred             CcccccCcEEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCc-cccccccCCcEEEeeecCCHHHhccC
Confidence            9999999999999774322211 111000   00000      0001111111 12233455689999998  2  2233


Q ss_pred             -------HHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          166 -------ETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       166 -------~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                             .++|++-.++||.|..|.+.-.    .+.|.+.|.|.+.+.|..||+.|+|+.|.||.|.....
T Consensus       283 ~~l~~dlkedl~eec~K~G~v~~vvv~d~----hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~  349 (382)
T KOG1548|consen  283 PDLLNDLKEDLTEECEKFGQVRKVVVYDR----HPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIW  349 (382)
T ss_pred             HHHHHHHHHHHHHHHHHhCCcceEEEecc----CCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEe
Confidence                   2467778889999999988644    35678999999999999999999999999999998864

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

Probab=99.56  E-value=3.7e-14  Score=128.64  Aligned_cols=202  Identities=18%  Similarity=0.292  Sum_probs=134.1

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHH-hcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEE
Q 016936          148 GAEGPDRVFVGGLPYYFTETQIKELLE-SFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  226 (380)
Q Consensus       148 ~~~~~~~l~V~nlp~~~t~~~l~~~F~-~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v  226 (380)
                      .+...+.+||+|+|+++.+.+|+++|+ +.|.|+.|.|+.|. .|+++|||.|+|+++|.+++|++.||.+.+.||+|.|
T Consensus        40 ~~~r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~-~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~v  118 (608)
T KOG4212|consen   40 VAARDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDE-SGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVV  118 (608)
T ss_pred             cccccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeeccc-CCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEE
Confidence            344556799999999999999999999 69999999999995 7999999999999999999999999999999999999


Q ss_pred             EEcccCCCCChhHHHHHHHHHHHHHHHHHHHh-----------hhcCccccC--CC----CCcc----------------
Q 016936          227 RRATASSGQSKTEQESILAQAQQHIAIQKMAL-----------QTSGMNTLG--GG----MSLF----------------  273 (380)
Q Consensus       227 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~~~~~--~~----~~~~----------------  273 (380)
                      +-.....      ++.+..       .-+...           .+.+.+..+  .+    ....                
T Consensus       119 KEd~d~q------~~~~~~-------~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~  185 (608)
T KOG4212|consen  119 KEDHDEQ------RDQYGR-------IVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMS  185 (608)
T ss_pred             eccCchh------hhhhhh-------eeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCccccc
Confidence            8654311      000000       000000           000000000  00    0000                


Q ss_pred             ----CCccceEEEE-----------eccCCcccCCChHHHHHHHHHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEE
Q 016936          274 ----GETLAKVLCL-----------TEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFL  338 (380)
Q Consensus       274 ----~~~~~~~~~l-----------~~~~~~~~~~~~~~~~~~~~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV  338 (380)
                          ....-..+.+           ..+.....++-+..|..-..+|.+.|.--|.|+.+.+-.++..  .++  |++.+
T Consensus       186 ~~~~~~~~~~lfgl~~~Flr~~h~f~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idKeG--~s~--G~~vi  261 (608)
T KOG4212|consen  186 NDYNNSSNYNLFGLSASFLRSLHIFSPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDKEG--NSR--GFAVI  261 (608)
T ss_pred             cccccchhhhcccchhhhhhhccCCCCCccceeeeeccccccchHHHHHHhccceeeeeeceeecccc--ccC--CeeEE
Confidence                0000000000           0111111222233333334699999999999999998776643  244  57799


Q ss_pred             EeechhhHHHHHHHHcCcccCCeEEEEEe
Q 016936          339 EYYDAVGCATAKNALSGRKFGGNTVNAFY  367 (380)
Q Consensus       339 ~f~~~~~A~~A~~~l~g~~i~gr~l~v~~  367 (380)
                      +|+++-+|.+|+..|++.-+..++..+.+
T Consensus       262 ~y~hpveavqaIsml~~~g~~~~~~~~Rl  290 (608)
T KOG4212|consen  262 EYDHPVEAVQAISMLDRQGLFDRRMTVRL  290 (608)
T ss_pred             EecchHHHHHHHHhhccCCCccccceeec
Confidence            99999999999999998777778777766

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

Probab=99.53  E-value=1.7e-14  Score=122.40  Aligned_cols=164  Identities=21%  Similarity=0.299  Sum_probs=127.4

Q ss_pred             ceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecCceEEE
Q 016936           33 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV  111 (380)
Q Consensus        33 ~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g~~i~v  111 (380)
                      .+|||++||+.+.+.||..||..||.+            .++.  .-.||+||+|.+..+|.-|+ .+++..+.|-.+-+
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~------------~d~~--mk~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vv   67 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKI------------PDAD--MKNGFGFVEFEDPRDADDAVHDLDGKELCGERLVV   67 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhcccc------------ccce--eecccceeccCchhhhhcccchhcCceecceeeee
Confidence            579999999999999999999999984            3332  34578899999999999999 89999999977888


Q ss_pred             ecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCC
Q 016936          112 RRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTG  191 (380)
Q Consensus       112 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~  191 (380)
                      .|+...+.......+.    ...     +....-..+......+.+.+++..+.+.+|.++|+.+|.+....+       
T Consensus        68 e~~r~~~~~~g~~~~g----~r~-----~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~-------  131 (216)
T KOG0106|consen   68 EHARGKRRGRGRPRGG----DRR-----SDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA-------  131 (216)
T ss_pred             ecccccccccCCCCCC----Ccc-----chhhccCCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhh-------
Confidence            8877644332110000    000     001111122445578999999999999999999999999955544       


Q ss_pred             CCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEE
Q 016936          192 NSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  227 (380)
Q Consensus       192 ~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~  227 (380)
                       ..+++||+|.+.++|.+|+..+++..+.++.|.+.
T Consensus       132 -~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~  166 (216)
T KOG0106|consen  132 -RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVE  166 (216)
T ss_pred             -hccccceeehhhhhhhhcchhccchhhcCceeeec
Confidence             23589999999999999999999999999999994

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

Probab=99.53  E-value=8.6e-14  Score=117.53  Aligned_cols=82  Identities=29%  Similarity=0.441  Sum_probs=78.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      ...+|-|.||+.++++++|.++|.+||.|.++.+.+|+.+|.++|||||.|.++++|.+||+.|||.-+..-.|+|+|+.
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            44689999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             cC
Q 016936          231 AS  232 (380)
Q Consensus       231 ~~  232 (380)
                      ++
T Consensus       268 P~  269 (270)
T KOG0122|consen  268 PS  269 (270)
T ss_pred             CC
Confidence            64

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

Probab=99.52  E-value=6e-14  Score=123.13  Aligned_cols=88  Identities=27%  Similarity=0.564  Sum_probs=80.3

Q ss_pred             CCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeE
Q 016936          144 GAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKT  223 (380)
Q Consensus       144 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~  223 (380)
                      ..+.....+++|+|.|||+...+.||+.+|.+||.|.+|.|+.+  ...+||||||.|++.++|++|-++|||..+.||+
T Consensus        88 t~s~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfN--ERGSKGFGFVTmen~~dadRARa~LHgt~VEGRk  165 (376)
T KOG0125|consen   88 TNSSSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFN--ERGSKGFGFVTMENPADADRARAELHGTVVEGRK  165 (376)
T ss_pred             CcCCCCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEec--cCCCCccceEEecChhhHHHHHHHhhcceeeceE
Confidence            34455677899999999999999999999999999999999987  3568999999999999999999999999999999


Q ss_pred             EEEEEcccCC
Q 016936          224 LTVRRATASS  233 (380)
Q Consensus       224 i~v~~~~~~~  233 (380)
                      |+|+.+..+.
T Consensus       166 IEVn~ATarV  175 (376)
T KOG0125|consen  166 IEVNNATARV  175 (376)
T ss_pred             EEEeccchhh
Confidence            9999988764

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

Probab=99.52  E-value=6.4e-14  Score=114.16  Aligned_cols=85  Identities=19%  Similarity=0.380  Sum_probs=69.1

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceec
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE  105 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~  105 (380)
                      .....+++|||+|||+++++++|+++|++||.|...      .++.+....+++|||||+|.+.++|+.|+ .+++..|.
T Consensus        29 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v------~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~  102 (144)
T PLN03134         29 SLRLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDA------KVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELN  102 (144)
T ss_pred             cccCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEE------EEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEEC
Confidence            455678899999999999999999999999984321      01111123457899999999999999999 79999999


Q ss_pred             CceEEEecCCCC
Q 016936          106 GVAVRVRRPTDY  117 (380)
Q Consensus       106 g~~i~v~~~~~~  117 (380)
                      |++|+|.++...
T Consensus       103 Gr~l~V~~a~~~  114 (144)
T PLN03134        103 GRHIRVNPANDR  114 (144)
T ss_pred             CEEEEEEeCCcC
Confidence            999999997654

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.50  E-value=1.3e-13  Score=98.47  Aligned_cols=70  Identities=27%  Similarity=0.580  Sum_probs=65.0

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEE
Q 016936          155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  225 (380)
Q Consensus       155 l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~  225 (380)
                      |||+|||+.+++++|+++|+.||.|..+++..+++ ++.+|+|||+|.+.++|.+|++.+++..+.|+.|+
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 89999999999999999999999999999999885

k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....

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

Probab=99.47  E-value=1e-13  Score=116.74  Aligned_cols=78  Identities=27%  Similarity=0.571  Sum_probs=72.9

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEccc
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  231 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~  231 (380)
                      ++|||++|+|.++.++|+++|++||.|.+..++.|+.+|+++|||||.|.+.++|.+|++.- .-.|+||+..|+.+..
T Consensus        13 TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp-~piIdGR~aNcnlA~l   90 (247)
T KOG0149|consen   13 TKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDP-NPIIDGRKANCNLASL   90 (247)
T ss_pred             EEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCC-CCcccccccccchhhh
Confidence            58999999999999999999999999999999999999999999999999999999999863 4688999999998765

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

Probab=99.45  E-value=1.3e-12  Score=108.91  Aligned_cols=203  Identities=16%  Similarity=0.184  Sum_probs=121.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEee-CCCCCCCceEEEEEEcChhHHHHHHHHhCCCee---CCeEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVK-DRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM---GDKTL  224 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~-~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~---~g~~i  224 (380)
                      ...-++|||.+||-++...+|+.+|+.|-.-+.+.|-. ++...-.+.+|||.|.+..+|..|+.+|||..|   .+..+
T Consensus        31 ~~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stL  110 (284)
T KOG1457|consen   31 PGAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTL  110 (284)
T ss_pred             ccccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCcee
Confidence            44568999999999999999999999987777665533 333334567999999999999999999999988   47889


Q ss_pred             EEEEcccCCCCChhHHHH------HHH------HHHHHHHHHHHHhhhcCccccCCCCCccCCccceEE-----------
Q 016936          225 TVRRATASSGQSKTEQES------ILA------QAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVL-----------  281 (380)
Q Consensus       225 ~v~~~~~~~~~~~~~~~~------~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------  281 (380)
                      +++.++.+...+++....      ...      ...+...++-..........+-.+.......+....           
T Consensus       111 hiElAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~~qhd~~l~~p~~l~~~~~a~al~~~~~t~~~~l~a~~~~~  190 (284)
T KOG1457|consen  111 HIELAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSADDQHDEGLSDPDELQEPGNADALKENDTTKSEALSAPDSKA  190 (284)
T ss_pred             EeeehhcCcccccCCCCCCCCCCccccccccChhhcccchhhccccccCccccCCccccccCCCccccchhhhhhhhhcC
Confidence            999988765443322111      000      000000000000000000000000000000000000           


Q ss_pred             -----EE-------eccCC-cccCCChHHHHHHHHHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHH
Q 016936          282 -----CL-------TEAIT-ADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCAT  348 (380)
Q Consensus       282 -----~l-------~~~~~-~~~~~~~~~~~~~~~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~  348 (380)
                           .+       ...-. -+-++-|.-.+.+++.|+.+|+.|......+|-..  .     |+-+||++|.+.+.|..
T Consensus       191 P~a~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~--~-----g~~vaf~~~~~~~~at~  263 (284)
T KOG1457|consen  191 PSANAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRAR--G-----GMPVAFADFEEIEQATD  263 (284)
T ss_pred             CcccchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecC--C-----CcceEeecHHHHHHHHH
Confidence                 00       00000 00011122223355799999999999988888442  2     34589999999999999


Q ss_pred             HHHHHcCccc
Q 016936          349 AKNALSGRKF  358 (380)
Q Consensus       349 A~~~l~g~~i  358 (380)
                      |+..|+|..+
T Consensus       264 am~~lqg~~~  273 (284)
T KOG1457|consen  264 AMNHLQGNLL  273 (284)
T ss_pred             HHHHhhccee
Confidence            9999999876

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

Probab=99.45  E-value=2.8e-13  Score=102.99  Aligned_cols=79  Identities=25%  Similarity=0.405  Sum_probs=75.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      .+.+|||+||++.+++++|+++|+.+|.|..|.+=.|+.+..+.|||||+|.+.++|+.|+..++|..+..++|++.|.
T Consensus        35 ~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D  113 (153)
T KOG0121|consen   35 KSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWD  113 (153)
T ss_pred             hcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeecc
Confidence            3469999999999999999999999999999999888888899999999999999999999999999999999999985

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

Probab=99.45  E-value=3.8e-12  Score=117.84  Aligned_cols=171  Identities=16%  Similarity=0.234  Sum_probs=124.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      ...-|-+++|||.+|++||+++|+.++ |+.+.+.+.  +|+..|-|||+|.+.+++++|+++ +...+..|-|+|-.+.
T Consensus         9 ~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r~--~Gr~sGeA~Ve~~seedv~~Alkk-dR~~mg~RYIEVf~~~   84 (510)
T KOG4211|consen    9 TAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPRR--NGRPSGEAYVEFTSEEDVEKALKK-DRESMGHRYIEVFTAG   84 (510)
T ss_pred             cceEEEecCCCccccHHHHHHHHhcCc-eeEEEEecc--CCCcCcceEEEeechHHHHHHHHh-hHHHhCCceEEEEccC
Confidence            346799999999999999999999865 666777765  799999999999999999999995 8899999999998875


Q ss_pred             cCCCCChhHHHHHHHHHHHHHHHHHHHhhhcCccccCCCCCccCCccceEEEEec-cCCcccCCChHHHHHHHHHHHHhh
Q 016936          231 ASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTE-AITADALADDEEYEEILEDMREEC  309 (380)
Q Consensus       231 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~-~~~~~~~~~~~~~~~~~~~L~~~f  309 (380)
                      .....-.                   +.          ........+.-++.|.. ++.++           ++||.++|
T Consensus        85 ~~e~d~~-------------------~~----------~~g~~s~~~d~vVRLRGLPfsct-----------e~dI~~FF  124 (510)
T KOG4211|consen   85 GAEADWV-------------------MR----------PGGPNSSANDGVVRLRGLPFSCT-----------EEDIVEFF  124 (510)
T ss_pred             Ccccccc-------------------cc----------CCCCCCCCCCceEEecCCCccCc-----------HHHHHHHh
Confidence            4321000                   00          00000112444566665 33443           47999999


Q ss_pred             cccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEecc
Q 016936          310 GKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYP  369 (380)
Q Consensus       310 ~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~  369 (380)
                      +.---|....++...+.++   -.|-|||+|++.+.|++|+.. |...|+.|-|.|--+.
T Consensus       125 aGL~Iv~~gi~l~~d~rgR---~tGEAfVqF~sqe~ae~Al~r-hre~iGhRYIEvF~Ss  180 (510)
T KOG4211|consen  125 AGLEIVPDGILLPMDQRGR---PTGEAFVQFESQESAEIALGR-HRENIGHRYIEVFRSS  180 (510)
T ss_pred             cCCcccccceeeeccCCCC---cccceEEEecCHHHHHHHHHH-HHHhhccceEEeehhH
Confidence            9876666644344443443   347889999999999999996 8888999988886554

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

Probab=99.43  E-value=4.5e-13  Score=113.82  Aligned_cols=168  Identities=21%  Similarity=0.375  Sum_probs=120.6

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccC
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  232 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~  232 (380)
                      ..+||++||+.+.+.+|..+|..||.+..+.+..        ||+||+|.+.-+|..|+..++++.|.|-.+.|.++...
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~--------gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~   73 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMKN--------GFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGK   73 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceeec--------ccceeccCchhhhhcccchhcCceecceeeeeeccccc
Confidence            3799999999999999999999999999887743        48999999999999999999999999999888887643


Q ss_pred             CCCC-hhHHHHHHHHHHHHHHHHHHHhhhcCccccC-CCCCccCCccceEEEEeccCCcccCCChHHHHHHHHHHHHhhc
Q 016936          233 SGQS-KTEQESILAQAQQHIAIQKMALQTSGMNTLG-GGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECG  310 (380)
Q Consensus       233 ~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~~f~  310 (380)
                      .... .+.                     +| .-.+ ......+......+++.+.          .......+|.+.|+
T Consensus        74 ~~~~g~~~---------------------~g-~r~~~~~~~~~p~~s~~r~~~~~~----------~~r~~~qdl~d~~~  121 (216)
T KOG0106|consen   74 RRGRGRPR---------------------GG-DRRSDSRRYRPPSRTHFRLIVRNL----------SLRVSWQDLKDHFR  121 (216)
T ss_pred             ccccCCCC---------------------CC-CccchhhccCCcccccceeeeccc----------hhhhhHHHHhhhhc
Confidence            1110 000                     00 0000 0000001111222233331          11222269999999


Q ss_pred             ccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEecccc
Q 016936          311 KYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  371 (380)
Q Consensus       311 ~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~~  371 (380)
                      ++|.+....+..           +.+||+|.+.++|.+|+..|+|..+.+++|.+.+...+
T Consensus       122 ~~g~~~~~~~~~-----------~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~~~~d  171 (216)
T KOG0106|consen  122 PAGEVTYVDARR-----------NFAFVEFSEQEDAKRALEKLDGKKLNGRRISVEKNSRD  171 (216)
T ss_pred             ccCCCchhhhhc-----------cccceeehhhhhhhhcchhccchhhcCceeeecccCcc
Confidence            999996655522           36699999999999999999999999999999655543

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

Probab=99.43  E-value=1.2e-10  Score=104.24  Aligned_cols=300  Identities=15%  Similarity=0.124  Sum_probs=181.9

Q ss_pred             EcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCc-EEEEEeCCHHHHHHHH-HcCCceecC--ceEEEe
Q 016936           37 VGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-FAFVEMRTVEEASNAM-ALDGIIFEG--VAVRVR  112 (380)
Q Consensus        37 V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g-~afV~f~~~~~a~~ai-~l~~~~i~g--~~i~v~  112 (380)
                      |-|=-+.+|-+-|+......|.            |..+.+.+..| .|.|+|++.+.|++|- .|||..|.-  ..|+|+
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            4455566899999999999988            66666655555 6999999999999999 899988753  678888


Q ss_pred             cCCCCCcccc---------------ccCCCCC------CC-CC-----ccccc--ccCCC--------------------
Q 016936          113 RPTDYNPTLA---------------AALGPGQ------PS-PN-----LNLAA--VGLAS--------------------  143 (380)
Q Consensus       113 ~~~~~~~~~~---------------~~~~~~~------~~-~~-----~~~~~--~~~~~--------------------  143 (380)
                      +++....+.-               ...++..      .. ..     .++..  .+..+                    
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            7654332210               0000000      00 00     00000  00000                    


Q ss_pred             ----CCCCCCCCCCEEEEcCCCCC-CCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCe
Q 016936          144 ----GAIGGAEGPDRVFVGGLPYY-FTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLK  218 (380)
Q Consensus       144 ----~~~~~~~~~~~l~V~nlp~~-~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~  218 (380)
                          ..+.+.....-++|-+|... .+-+.|.++|-.||.|++|++++-+     .|.|+|++.+....++|+..||+..
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                11123344467889999654 5667899999999999999999875     3689999999999999999999999


Q ss_pred             eCCeEEEEEEcccCCCCChhHH-HHHHHHHHHHHHHHHHHhhhcCccccCCCCCccCCccceEEEEeccCCcccCCChHH
Q 016936          219 MGDKTLTVRRATASSGQSKTEQ-ESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEE  297 (380)
Q Consensus       219 ~~g~~i~v~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~  297 (380)
                      +.|.+|.|..++...-.+-..- -.......+.....+-    .....+....-..-..+++++..=|   ....     
T Consensus       350 lfG~kl~v~~SkQ~~v~~~~pflLpDgSpSfKdys~SkN----nRFssp~qAsKNrIq~Ps~vLHffN---aP~~-----  417 (494)
T KOG1456|consen  350 LFGGKLNVCVSKQNFVSPVQPFLLPDGSPSFKDYSGSKN----NRFSSPEQASKNRIQPPSNVLHFFN---APLG-----  417 (494)
T ss_pred             cccceEEEeeccccccccCCceecCCCCcchhhcccccc----cccCChhHhhcccccCCcceeEEec---CCCc-----
Confidence            9999999998765431111000 0000000000000000    0000000000001134455554433   1111     


Q ss_pred             HHHHHHHHHHhhcccCC-eEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCC------eEEEEEeccc
Q 016936          298 YEEILEDMREECGKYGT-LVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGG------NTVNAFYYPE  370 (380)
Q Consensus       298 ~~~~~~~L~~~f~~~G~-I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~g------r~l~v~~~~~  370 (380)
                        .+++.|..+|..-+. -.+++++..+ +.+.+  .|  .++|.+.++|..|+..+|.+.|.+      -.|++.|++.
T Consensus       418 --vtEe~l~~i~nek~v~~~svkvFp~k-serSs--sG--llEfe~~s~Aveal~~~NH~pi~~p~gs~PfilKlcfsts  490 (494)
T KOG1456|consen  418 --VTEEQLIGICNEKDVPPTSVKVFPLK-SERSS--SG--LLEFENKSDAVEALMKLNHYPIEGPNGSFPFILKLCFSTS  490 (494)
T ss_pred             --cCHHHHHHHhhhcCCCcceEEeeccc-ccccc--cc--eeeeehHHHHHHHHHHhccccccCCCCCCCeeeeeeeccc
Confidence              122577777765442 4566666544 33322  24  999999999999999999999877      4677777766


Q ss_pred             cc
Q 016936          371 DK  372 (380)
Q Consensus       371 ~~  372 (380)
                      ..
T Consensus       491 ~~  492 (494)
T KOG1456|consen  491 KH  492 (494)
T ss_pred             cc
Confidence            54

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

Probab=99.43  E-value=4e-13  Score=110.62  Aligned_cols=85  Identities=24%  Similarity=0.425  Sum_probs=80.1

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      .++...|.|-||.+.++.++|+.+|++||.|..|.|++|+-+++++|||||.|....+|+.|+++|+|..+.|+.|+|++
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            45667999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cccCC
Q 016936          229 ATASS  233 (380)
Q Consensus       229 ~~~~~  233 (380)
                      |....
T Consensus        90 arygr   94 (256)
T KOG4207|consen   90 ARYGR   94 (256)
T ss_pred             hhcCC
Confidence            86543

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.43  E-value=9.7e-13  Score=114.75  Aligned_cols=75  Identities=21%  Similarity=0.352  Sum_probs=69.9

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEccc
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  231 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~  231 (380)
                      ++|||+|||+.+++++|+++|+.||.|.+|.|+.++   .++|||||+|.++++|+.|+. |+|..|.|+.|+|.++..
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 RTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSEN---ERSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAED   79 (260)
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecC---CCCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccC
Confidence            699999999999999999999999999999998874   357899999999999999996 899999999999999764

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.41  E-value=8e-13  Score=115.26  Aligned_cols=77  Identities=25%  Similarity=0.356  Sum_probs=68.5

Q ss_pred             ccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecC---CCcEEEEEeCCHHHHHHHHHcCCceecCc
Q 016936           31 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH---EKKFAFVEMRTVEEASNAMALDGIIFEGV  107 (380)
Q Consensus        31 ~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~---~~g~afV~f~~~~~a~~ai~l~~~~i~g~  107 (380)
                      ..++|||+|||+.+++++|+++|+.||.            |.++.+..   .+|||||+|.++++|..|+.|+|..|.|+
T Consensus         3 ~~rtVfVgNLs~~tTE~dLrefFS~~G~------------I~~V~I~~d~~~~GfAFVtF~d~eaAe~AllLnG~~l~gr   70 (260)
T PLN03120          3 QVRTVKVSNVSLKATERDIKEFFSFSGD------------IEYVEMQSENERSQIAYVTFKDPQGAETALLLSGATIVDQ   70 (260)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCC------------eEEEEEeecCCCCCEEEEEeCcHHHHHHHHHhcCCeeCCc
Confidence            3689999999999999999999999998            56666543   46999999999999999999999999999


Q ss_pred             eEEEecCCCCCc
Q 016936          108 AVRVRRPTDYNP  119 (380)
Q Consensus       108 ~i~v~~~~~~~~  119 (380)
                      .|+|.++.++..
T Consensus        71 ~V~Vt~a~~~~~   82 (260)
T PLN03120         71 SVTITPAEDYQL   82 (260)
T ss_pred             eEEEEeccCCCC
Confidence            999999877653

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

Probab=99.41  E-value=6.9e-12  Score=91.84  Aligned_cols=80  Identities=23%  Similarity=0.453  Sum_probs=72.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      +...+.|||+|||+++|.++..++|.+||+|..+++=..   ...+|.|||.|++..+|.+|++.|+|..+.++.+.|-+
T Consensus        15 pevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~---k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vly   91 (124)
T KOG0114|consen   15 PEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNT---KETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLY   91 (124)
T ss_pred             hhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCc---cCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEe
Confidence            445578999999999999999999999999999998543   55789999999999999999999999999999999998


Q ss_pred             ccc
Q 016936          229 ATA  231 (380)
Q Consensus       229 ~~~  231 (380)
                      -.+
T Consensus        92 yq~   94 (124)
T KOG0114|consen   92 YQP   94 (124)
T ss_pred             cCH
Confidence            643

>PF00076 RRM_1: RNA recognition motif

Probab=99.39  E-value=7.3e-13  Score=94.36  Aligned_cols=64  Identities=36%  Similarity=0.658  Sum_probs=56.6

Q ss_pred             EEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec-----CCCcEEEEEeCCHHHHHHHH-HcCCceecCce
Q 016936           35 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN-----HEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  108 (380)
Q Consensus        35 v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~-----~~~g~afV~f~~~~~a~~ai-~l~~~~i~g~~  108 (380)
                      |||+|||+++++++|+++|++||.            +..+.+.     +.+++|||+|.+.++|.+|+ .+++..+.|++
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~------------i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~   68 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGK------------IESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKINGRK   68 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTST------------EEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhh------------cccccccccccccccceEEEEEcCHHHHHHHHHHcCCCEECccC
Confidence            799999999999999999999998            4444433     34799999999999999999 69999999999


Q ss_pred             EE
Q 016936          109 VR  110 (380)
Q Consensus       109 i~  110 (380)
                      |+
T Consensus        69 ir   70 (70)
T PF00076_consen   69 IR   70 (70)
T ss_dssp             EE
T ss_pred             cC
Confidence            86

(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 ....

>PF13893 RRM_5: RNA recognition motif

Probab=99.39  E-value=1.8e-12  Score=88.03  Aligned_cols=56  Identities=23%  Similarity=0.438  Sum_probs=50.6

Q ss_pred             HHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEec
Q 016936          305 MREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYY  368 (380)
Q Consensus       305 L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~  368 (380)
                      |+++|++||+|.++.+.+..        .++|||+|.+.++|.+|++.|||..++|++|+|+|+
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            67899999999999998765        158899999999999999999999999999999986

(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 ....

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

Probab=99.37  E-value=6.2e-13  Score=118.92  Aligned_cols=191  Identities=21%  Similarity=0.219  Sum_probs=135.0

Q ss_pred             cceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec--CCCcEEEEEeCCHHHHHHHHHcCCceecCceE
Q 016936           32 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN--HEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  109 (380)
Q Consensus        32 ~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~--~~~g~afV~f~~~~~a~~ai~l~~~~i~g~~i  109 (380)
                      .-.|.+++||.++++.|+.+||..-..+.++     ++-|+-++-.  +-.|-|||.|..+++|+.|+..|...+..|-|
T Consensus       161 qvivRmRGLPfdat~~dVv~FF~~~cpv~~g-----~egvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~khrq~iGqRYI  235 (508)
T KOG1365|consen  161 QVIVRMRGLPFDATALDVVEFFGPPCPVTGG-----TEGVLFVTRPDGRPTGDAFVLFACEEDAQFALRKHRQNIGQRYI  235 (508)
T ss_pred             ceEEEecCCCCCcchHHHHHhcCCCCcccCC-----ccceEEEECCCCCcccceEEEecCHHHHHHHHHHHHHHHhHHHH
Confidence            3468899999999999999999855554322     3346666543  34589999999999999999888888888888


Q ss_pred             EEecCCCCCc--cccccCC-CCCCCCCccccccc-CCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCC-eeE--E
Q 016936          110 RVRRPTDYNP--TLAAALG-PGQPSPNLNLAAVG-LASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGT-LHG--F  182 (380)
Q Consensus       110 ~v~~~~~~~~--~~~~~~~-~~~~~~~~~~~~~~-~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~-i~~--v  182 (380)
                      .+.++...+.  ..+.... +-.+..  ...... ....-.-......+|.+++||+..+.++|.++|..|-. |..  |
T Consensus       236 ElFRSTaaEvqqvlnr~~s~pLi~~~--~sp~~p~~p~~~~p~~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gV  313 (508)
T KOG1365|consen  236 ELFRSTAAEVQQVLNREVSEPLIPGL--TSPLLPGGPARLVPPTRSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGV  313 (508)
T ss_pred             HHHHHhHHHHHHHHHhhccccccCCC--CCCCCCCCccccCCCCCCCCeeEecCCChhhhHHHHHHHHHHHhhhccccee
Confidence            8766543211  1111100 000000  000000 01111112333568999999999999999999999876 443  7


Q ss_pred             EEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          183 DLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       183 ~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      +++.+. .|+..|-|||+|.+.+.|..|+.+.+.+...+|.|+|-.++
T Consensus       314 Hmv~N~-qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp~S  360 (508)
T KOG1365|consen  314 HMVLNG-QGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFPCS  360 (508)
T ss_pred             EEEEcC-CCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEeecc
Confidence            787774 69999999999999999999999988777789999998864

>smart00362 RRM_2 RNA recognition motif

Probab=99.37  E-value=4.9e-12  Score=90.01  Aligned_cols=72  Identities=39%  Similarity=0.691  Sum_probs=67.2

Q ss_pred             EEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEE
Q 016936          154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  227 (380)
Q Consensus       154 ~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~  227 (380)
                      +|+|+|||..++.++|+++|++||.+..+.+..++  +.++|+|||+|.+.++|++|+..+++..+.|+.+.|+
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            48999999999999999999999999999998875  7788999999999999999999999999999998873

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

Probab=99.36  E-value=1.4e-12  Score=99.18  Aligned_cols=77  Identities=25%  Similarity=0.414  Sum_probs=67.2

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec------CCCcEEEEEeCCHHHHHHHH-Hc
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN------HEKKFAFVEMRTVEEASNAM-AL   99 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~------~~~g~afV~f~~~~~a~~ai-~l   99 (380)
                      .+.+.+|||||+||+.-++|++|+++|+++|.|            ..+.++      .-.|||||+|-+.++|+.|+ -+
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            356899999999999999999999999999985            334333      23599999999999999999 79


Q ss_pred             CCceecCceEEEecCC
Q 016936          100 DGIIFEGVAVRVRRPT  115 (380)
Q Consensus       100 ~~~~i~g~~i~v~~~~  115 (380)
                      ++..+..++|++.|.-
T Consensus        99 sgtrLddr~ir~D~D~  114 (153)
T KOG0121|consen   99 SGTRLDDRPIRIDWDA  114 (153)
T ss_pred             ccCcccccceeeeccc
Confidence            9999999999999843

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

Probab=99.34  E-value=1.9e-13  Score=110.25  Aligned_cols=80  Identities=34%  Similarity=0.674  Sum_probs=76.4

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccC
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  232 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~  232 (380)
                      .-|||+|||+.+|+.||.-+|++||.|..|.|++|+.+|+++||||+.|++--+...|+..|||..+.||.|+|......
T Consensus        36 A~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv~~Y  115 (219)
T KOG0126|consen   36 AYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHVSNY  115 (219)
T ss_pred             eEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeecccc
Confidence            47999999999999999999999999999999999999999999999999999999999999999999999999986543

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

Probab=99.34  E-value=8.5e-12  Score=118.43  Aligned_cols=191  Identities=16%  Similarity=0.240  Sum_probs=135.5

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecCc
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  107 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g~  107 (380)
                      .-..++++|++||...++.++.+.+..||.+..      ...+.+..++-++||||.+|.++.....|+ .|||+.+.++
T Consensus       286 ~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~------f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~  359 (500)
T KOG0120|consen  286 PDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKA------FRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDK  359 (500)
T ss_pred             ccccchhhhccCcCccCHHHHHHHHHhcccchh------heeecccccccccceeeeeeeCCcchhhhhcccchhhhcCc
Confidence            455678999999999999999999999999754      445666666678999999999999999999 7999999999


Q ss_pred             eEEEecCCCCCccccccCCCCCCCCCcccccccCCCC-CCCCCCCCCEEEEcCC--CCCCCH--------HHHHHHHHhc
Q 016936          108 AVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASG-AIGGAEGPDRVFVGGL--PYYFTE--------TQIKELLESF  176 (380)
Q Consensus       108 ~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~l~V~nl--p~~~t~--------~~l~~~F~~~  176 (380)
                      ++.++.+.............+.      ....+.... ........+.+.+.|+  |..+..        ++++..+.+|
T Consensus       360 ~lvvq~A~~g~~~~~~~~~~~~------~~~~~i~~~~~q~~g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~  433 (500)
T KOG0120|consen  360 KLVVQRAIVGASNANVNFNISQ------SQVPGIPLLMTQMAGIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKF  433 (500)
T ss_pred             eeEeehhhccchhccccCCccc------cccccchhhhcccCCCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHhccc
Confidence            9999987654332211111000      001111111 0111122234445554  222111        3556677789


Q ss_pred             CCeeEEEEeeC-C--CCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEccc
Q 016936          177 GTLHGFDLVKD-R--DTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  231 (380)
Q Consensus       177 G~i~~v~l~~~-~--~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~  231 (380)
                      |.|..|.+++. .  ...-..|..||+|.+.+++++|++.|+|..|.++.+...+...
T Consensus       434 g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYyde  491 (500)
T KOG0120|consen  434 GAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYDE  491 (500)
T ss_pred             CceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecCH
Confidence            99999999876 2  2234667899999999999999999999999999999998643

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

Probab=99.33  E-value=4.8e-12  Score=101.79  Aligned_cols=76  Identities=21%  Similarity=0.430  Sum_probs=69.1

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEccc
Q 016936          152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  231 (380)
Q Consensus       152 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~  231 (380)
                      .++|||+||+..+++.||..+|..||.|..|-+-+.     +.|||||+|+++-+|+.|+..|+|..|.|..|+|+.+.-
T Consensus        10 ~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn-----PPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G   84 (195)
T KOG0107|consen   10 NTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN-----PPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTG   84 (195)
T ss_pred             CceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec-----CCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecC
Confidence            369999999999999999999999999998877554     468999999999999999999999999999999998754


Q ss_pred             C
Q 016936          232 S  232 (380)
Q Consensus       232 ~  232 (380)
                      .
T Consensus        85 ~   85 (195)
T KOG0107|consen   85 R   85 (195)
T ss_pred             C
Confidence            3

>smart00360 RRM RNA recognition motif

Probab=99.33  E-value=8.5e-12  Score=88.40  Aligned_cols=71  Identities=38%  Similarity=0.700  Sum_probs=66.4

Q ss_pred             EcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEE
Q 016936          157 VGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  227 (380)
Q Consensus       157 V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~  227 (380)
                      |+|||..+++++|+++|++||.|..+.+..++.++.++|+|||+|.+.++|..|+..+++..+.|+.+.|+
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            57899999999999999999999999999887678999999999999999999999999999999998873

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

Probab=99.32  E-value=5.2e-12  Score=111.13  Aligned_cols=88  Identities=18%  Similarity=0.238  Sum_probs=72.1

Q ss_pred             CccceEEEEeccCCcccCCChHHHHHHHHHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHc
Q 016936          275 ETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALS  354 (380)
Q Consensus       275 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~  354 (380)
                      ....+.+.++|+...--.          .||+.+|.+||.|.+|.|+.+++.   +||+|  ||.|++++||.+|-++||
T Consensus        93 ~~~pkRLhVSNIPFrFRd----------pDL~aMF~kfG~VldVEIIfNERG---SKGFG--FVTmen~~dadRARa~LH  157 (376)
T KOG0125|consen   93 KDTPKRLHVSNIPFRFRD----------PDLRAMFEKFGKVLDVEIIFNERG---SKGFG--FVTMENPADADRARAELH  157 (376)
T ss_pred             CCCCceeEeecCCccccC----------ccHHHHHHhhCceeeEEEEeccCC---CCccc--eEEecChhhHHHHHHHhh
Confidence            444566777775432111          499999999999999999997654   77777  999999999999999999


Q ss_pred             CcccCCeEEEEEecccccccccc
Q 016936          355 GRKFGGNTVNAFYYPEDKYFNKD  377 (380)
Q Consensus       355 g~~i~gr~l~v~~~~~~~~~~~~  377 (380)
                      |.++.||+|.|.-++...+.+++
T Consensus       158 gt~VEGRkIEVn~ATarV~n~K~  180 (376)
T KOG0125|consen  158 GTVVEGRKIEVNNATARVHNKKK  180 (376)
T ss_pred             cceeeceEEEEeccchhhccCCc
Confidence            99999999999999987665543

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

Probab=99.32  E-value=7.3e-12  Score=108.87  Aligned_cols=79  Identities=28%  Similarity=0.519  Sum_probs=75.6

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       152 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      -+||||.-|++++++.+|+..|+.||.|..|+|+.++.+|+++|||||+|+++-+-.+|.+..+|..|.|+.|.|.+-.
T Consensus       101 y~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDvER  179 (335)
T KOG0113|consen  101 YKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDVER  179 (335)
T ss_pred             cceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEecc
Confidence            3699999999999999999999999999999999999999999999999999999999999999999999999998743

>PLN03213 repressor of silencing 3; Provisional

Probab=99.32  E-value=7.2e-12  Score=115.65  Aligned_cols=76  Identities=17%  Similarity=0.357  Sum_probs=70.9

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcCh--hHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP--AVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~--~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      -+|||+||++.+++++|...|..||.|..|.|++.  +|  +|||||+|.+.  .++.+||..|||..+.|+.|+|..|+
T Consensus        11 MRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRE--TG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAK   86 (759)
T PLN03213         11 VRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRT--KG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAK   86 (759)
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecc--cC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeecc
Confidence            58999999999999999999999999999999954  66  89999999988  78999999999999999999999986


Q ss_pred             cC
Q 016936          231 AS  232 (380)
Q Consensus       231 ~~  232 (380)
                      +.
T Consensus        87 P~   88 (759)
T PLN03213         87 EH   88 (759)
T ss_pred             HH
Confidence            53

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.32  E-value=6.9e-12  Score=107.63  Aligned_cols=78  Identities=23%  Similarity=0.258  Sum_probs=68.8

Q ss_pred             ccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecC---CCcEEEEEeCCHHHHHHHHHcCCceecCc
Q 016936           31 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH---EKKFAFVEMRTVEEASNAMALDGIIFEGV  107 (380)
Q Consensus        31 ~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~---~~g~afV~f~~~~~a~~ai~l~~~~i~g~  107 (380)
                      ...+|||+||++.+|++||++||+.||.            |.++.+..   .+++|||+|.++++|..|+.|+|..|.++
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~------------I~~V~I~~D~et~gfAfVtF~d~~aaetAllLnGa~l~d~   71 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGA------------IEHVEIIRSGEYACTAYVTFKDAYALETAVLLSGATIVDQ   71 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCC------------eEEEEEecCCCcceEEEEEECCHHHHHHHHhcCCCeeCCc
Confidence            4579999999999999999999999998            55565543   45899999999999999999999999999


Q ss_pred             eEEEecCCCCCcc
Q 016936          108 AVRVRRPTDYNPT  120 (380)
Q Consensus       108 ~i~v~~~~~~~~~  120 (380)
                      +|.|.+...++..
T Consensus        72 ~I~It~~~~y~~~   84 (243)
T PLN03121         72 RVCITRWGQYEDE   84 (243)
T ss_pred             eEEEEeCcccccC
Confidence            9999987776653

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.32  E-value=1.3e-11  Score=105.94  Aligned_cols=74  Identities=16%  Similarity=0.298  Sum_probs=68.9

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      .+|||+||++.+|+++|+++|+.||.|..|+|.++   +..+++|||+|.++++|+.|+. |+|..|.+++|.|....
T Consensus         6 ~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D---~et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~~   79 (243)
T PLN03121          6 YTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRS---GEYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRWG   79 (243)
T ss_pred             eEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecC---CCcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeCc
Confidence            69999999999999999999999999999999987   4556899999999999999996 89999999999999854

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

Probab=99.31  E-value=4.2e-12  Score=97.47  Aligned_cols=84  Identities=26%  Similarity=0.370  Sum_probs=78.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      .....|||.++...+++++|.+.|..||+|..+.|-.|+.+|-.+|||+|+|.+.++|+.|+..+||..+.|..|.|.|+
T Consensus        70 VEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~  149 (170)
T KOG0130|consen   70 VEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWC  149 (170)
T ss_pred             eeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEE
Confidence            34468999999999999999999999999999999999889999999999999999999999999999999999999998


Q ss_pred             ccCC
Q 016936          230 TASS  233 (380)
Q Consensus       230 ~~~~  233 (380)
                      ..+.
T Consensus       150 Fv~g  153 (170)
T KOG0130|consen  150 FVKG  153 (170)
T ss_pred             EecC
Confidence            7653

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

Probab=99.30  E-value=4.4e-11  Score=114.66  Aligned_cols=195  Identities=12%  Similarity=0.058  Sum_probs=142.5

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCC-CcEEEEEeCCHHHHHHHHHcCCceecCc
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE-KKFAFVEMRTVEEASNAMALDGIIFEGV  107 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~-~g~afV~f~~~~~a~~ai~l~~~~i~g~  107 (380)
                      ..+.+.+-+++++...++.|+++||-..-.       ..+. +.......+ .|-++|+|....++++|+..+.+.+..+
T Consensus       308 v~d~~y~~~~gm~fn~~~nd~rkfF~g~~~-------~~~~-l~~~~v~~~~tG~~~v~f~~~~~~q~A~~rn~~~~~~R  379 (944)
T KOG4307|consen  308 VSDKYYNNYKGMEFNNDFNDGRKFFPGRNA-------QSTD-LSENRVAPPQTGRKTVMFTPQAPFQNAFTRNPSDDVNR  379 (944)
T ss_pred             cchhheeeecccccccccchhhhhcCcccc-------cccc-hhhhhcCCCcCCceEEEecCcchHHHHHhcCchhhhhc
Confidence            477899999999999999999999875421       1111 222223333 6999999999999999999999999999


Q ss_pred             eEEEecCCCCCccccccCCCCCCCCCc-------cccc---ccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcC
Q 016936          108 AVRVRRPTDYNPTLAAALGPGQPSPNL-------NLAA---VGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFG  177 (380)
Q Consensus       108 ~i~v~~~~~~~~~~~~~~~~~~~~~~~-------~~~~---~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G  177 (380)
                      .+++..+.+.+...+.......+....       .-..   .+..............|||..||..+++.++.+.|+.--
T Consensus       380 ~~q~~P~g~~~~~~a~~~~~~~~~~~~~~~hg~p~~~pr~~~~~gq~vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~  459 (944)
T KOG4307|consen  380 PFQTGPPGNLGRNGAPPFQAGVPPPVIQNNHGRPIAPPRAMVRPGQNVPFPGGAGGALYVFQLPVMTPIVPPVNKFMGAA  459 (944)
T ss_pred             ceeecCCCccccccCccccccCCCCcccccCCCCCCCcccccCCCCCCCCCCCccceEEeccCCccccccchhhhhhhhh
Confidence            999998887776654332222111000       0000   011111223344557999999999999999999999877


Q ss_pred             CeeE-EEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccC
Q 016936          178 TLHG-FDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  232 (380)
Q Consensus       178 ~i~~-v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~  232 (380)
                      .|+. |.|.+.+ +++-++.|||.|.+++.+.+|...-+.++++.+.|+|......
T Consensus       460 ~Ved~I~lt~~P-~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si~~~  514 (944)
T KOG4307|consen  460 AVEDFIELTRLP-TDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSIADY  514 (944)
T ss_pred             hhhheeEeccCC-cccccchhhheeccccccchhhhcccccccCceEEEeechhhH
Confidence            7766 8887776 6888999999999999999998866667888899999876544

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

Probab=99.30  E-value=2.5e-11  Score=110.51  Aligned_cols=80  Identities=35%  Similarity=0.710  Sum_probs=76.5

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEccc
Q 016936          152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  231 (380)
Q Consensus       152 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~  231 (380)
                      ..+|||+|||..+++++|+++|..||.|..+.+..++.++.++|+|||.|.+.++|..|+..+++..+.|+.|.|.++..
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            47999999999999999999999999999999999987899999999999999999999999999999999999999653

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

Probab=99.28  E-value=2.7e-12  Score=106.69  Aligned_cols=83  Identities=20%  Similarity=0.402  Sum_probs=79.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      ..++|||++|...+++.-|...|-+||.|..+.++.|-.+++++|||||+|.-.|+|..||..||+.++.||.|+|.++.
T Consensus         9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~Ak   88 (298)
T KOG0111|consen    9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAK   88 (298)
T ss_pred             cceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecC
Confidence            34799999999999999999999999999999999998899999999999999999999999999999999999999998


Q ss_pred             cCC
Q 016936          231 ASS  233 (380)
Q Consensus       231 ~~~  233 (380)
                      +..
T Consensus        89 P~k   91 (298)
T KOG0111|consen   89 PEK   91 (298)
T ss_pred             Ccc
Confidence            864

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

Probab=99.27  E-value=9.2e-11  Score=106.79  Aligned_cols=145  Identities=25%  Similarity=0.342  Sum_probs=102.3

Q ss_pred             cceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecCceEE
Q 016936           32 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVR  110 (380)
Q Consensus        32 ~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g~~i~  110 (380)
                      .++|||+|||.++++++|.++|.+||.+...      ....+......+|+|||+|.+.++|..|+ .+++..|.|++|+
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~------~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~  188 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRV------RLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLR  188 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEE------EeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeE
Confidence            6999999999999999999999999985321      01111124567899999999999999999 7999999999999


Q ss_pred             EecCCC-CCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC
Q 016936          111 VRRPTD-YNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDR  188 (380)
Q Consensus       111 v~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~  188 (380)
                      |.+... .........     . ......................+++.+++..++..++..+|..+|.+....+....
T Consensus       189 v~~~~~~~~~~~~~~~-----~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  261 (306)
T COG0724         189 VQKAQPASQPRSELSN-----N-LDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSK  261 (306)
T ss_pred             eecccccccccccccc-----c-cchhhhccccccccccccccceeeccccccccchhHHHHhccccccceeeeccCCC
Confidence            998643 111000000     0 00000000112222334455789999999999999999999999999766665543

>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=99.26  E-value=6.5e-11  Score=84.59  Aligned_cols=74  Identities=36%  Similarity=0.673  Sum_probs=68.4

Q ss_pred             EEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       154 ~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      +|+|+|||..+++++|+++|+.||.|..+.+..++. +.++|+|||+|.+.++|..|+..+++..+.|+.+.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~-~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKD-TKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCC-CCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            489999999999999999999999999999998764 47789999999999999999999999999999998864

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).

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.26  E-value=9e-12  Score=88.81  Aligned_cols=64  Identities=36%  Similarity=0.637  Sum_probs=54.4

Q ss_pred             EEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCC-----CcEEEEEeCCHHHHHHHH-HcCCceecCce
Q 016936           35 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE-----KKFAFVEMRTVEEASNAM-ALDGIIFEGVA  108 (380)
Q Consensus        35 v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~-----~g~afV~f~~~~~a~~ai-~l~~~~i~g~~  108 (380)
                      |||+|||+.+++++|+++|+.+|.            |..+.+..+     +++|||+|.+.++|.+|+ ..++..++|+.
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~------------v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~   68 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGP------------VEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEIDGRK   68 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSB------------EEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCC------------cceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEECCEE
Confidence            799999999999999999999986            666665544     699999999999999999 67779999998


Q ss_pred             EE
Q 016936          109 VR  110 (380)
Q Consensus       109 i~  110 (380)
                      |+
T Consensus        69 l~   70 (70)
T PF14259_consen   69 LR   70 (70)
T ss_dssp             EE
T ss_pred             cC
Confidence            75

k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....

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

Probab=99.24  E-value=3e-11  Score=88.57  Aligned_cols=75  Identities=20%  Similarity=0.255  Sum_probs=67.5

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecC---CCcEEEEEeCCHHHHHHHH-HcCCce
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH---EKKFAFVEMRTVEEASNAM-ALDGII  103 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~---~~g~afV~f~~~~~a~~ai-~l~~~~  103 (380)
                      +..-.+.|||+|||.++|.++++++|.+||+            |.+++++-   .+|.|||.|.+..+|.+|+ .|+|-.
T Consensus        14 ppevnriLyirNLp~~ITseemydlFGkyg~------------IrQIRiG~~k~TrGTAFVVYedi~dAk~A~dhlsg~n   81 (124)
T KOG0114|consen   14 PPEVNRILYIRNLPFKITSEEMYDLFGKYGT------------IRQIRIGNTKETRGTAFVVYEDIFDAKKACDHLSGYN   81 (124)
T ss_pred             ChhhheeEEEecCCccccHHHHHHHhhcccc------------eEEEEecCccCcCceEEEEehHhhhHHHHHHHhcccc
Confidence            4556789999999999999999999999998            77788764   5799999999999999999 899999


Q ss_pred             ecCceEEEecC
Q 016936          104 FEGVAVRVRRP  114 (380)
Q Consensus       104 i~g~~i~v~~~  114 (380)
                      +.++.+.|-+.
T Consensus        82 ~~~ryl~vlyy   92 (124)
T KOG0114|consen   82 VDNRYLVVLYY   92 (124)
T ss_pred             cCCceEEEEec
Confidence            99999999763

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

Probab=99.24  E-value=2.2e-11  Score=115.11  Aligned_cols=80  Identities=36%  Similarity=0.684  Sum_probs=77.5

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccC
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  232 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~  232 (380)
                      +.|||+|+|+++++++|.++|+..|.|..+++..|+.+|+.+||||++|.+.++|.+|++.|||.++.|++|+|.|+...
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~   98 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNR   98 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeeccccc
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999998654

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

Probab=99.24  E-value=8.2e-12  Score=105.31  Aligned_cols=83  Identities=18%  Similarity=0.313  Sum_probs=71.1

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHHHcCCceecCc
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGV  107 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai~l~~~~i~g~  107 (380)
                      -+..-++|||+||++++..++|+++|.+||.|++..      .|.+..++++|||+||.|.+.++|.+|++-.+-.|.||
T Consensus         8 ~DT~~TKifVggL~w~T~~~~l~~yFeqfGeI~eav------vitd~~t~rskGyGfVTf~d~~aa~rAc~dp~piIdGR   81 (247)
T KOG0149|consen    8 GDTTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAV------VITDKNTGRSKGYGFVTFRDAEAATRACKDPNPIIDGR   81 (247)
T ss_pred             CCceEEEEEEcCcccccchHHHHHHHHHhCceEEEE------EEeccCCccccceeeEEeecHHHHHHHhcCCCCccccc
Confidence            345668999999999999999999999999986642      34555578899999999999999999998888889999


Q ss_pred             eEEEecCCC
Q 016936          108 AVRVRRPTD  116 (380)
Q Consensus       108 ~i~v~~~~~  116 (380)
                      +-.+..+..
T Consensus        82 ~aNcnlA~l   90 (247)
T KOG0149|consen   82 KANCNLASL   90 (247)
T ss_pred             ccccchhhh
Confidence            988887654

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

Probab=99.24  E-value=1.8e-11  Score=98.45  Aligned_cols=74  Identities=31%  Similarity=0.452  Sum_probs=64.3

Q ss_pred             ccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec-CCCcEEEEEeCCHHHHHHHH-HcCCceecCce
Q 016936           31 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN-HEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  108 (380)
Q Consensus        31 ~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~-~~~g~afV~f~~~~~a~~ai-~l~~~~i~g~~  108 (380)
                      -.++|||+||+..+++.||...|..||+|            .++-+- .--|||||+|.++.||+.|+ .|+|..|.|..
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~l------------rsvWvArnPPGfAFVEFed~RDA~DAvr~LDG~~~cG~r   76 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPL------------RSVWVARNPPGFAFVEFEDPRDAEDAVRYLDGKDICGSR   76 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcc------------eeEEEeecCCCceEEeccCcccHHHHHhhcCCccccCce
Confidence            37899999999999999999999999984            333332 34699999999999999999 89999999999


Q ss_pred             EEEecCCC
Q 016936          109 VRVRRPTD  116 (380)
Q Consensus       109 i~v~~~~~  116 (380)
                      |+|+.+..
T Consensus        77 ~rVE~S~G   84 (195)
T KOG0107|consen   77 IRVELSTG   84 (195)
T ss_pred             EEEEeecC
Confidence            99987543

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

Probab=99.24  E-value=1.6e-11  Score=103.90  Aligned_cols=82  Identities=20%  Similarity=0.252  Sum_probs=70.1

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecCce
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  108 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g~~  108 (380)
                      .+.++|.|.||+.+++|.||.++|..||.|...+      ...+-.++.++|||||.|.+.++|++|| .|+|.-+..-.
T Consensus       187 ~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvy------lardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LI  260 (270)
T KOG0122|consen  187 DDEATVRVTNLSEDMREDDLEELFRPFGPITRVY------LARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLI  260 (270)
T ss_pred             CccceeEEecCccccChhHHHHHhhccCccceeE------EEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEE
Confidence            3788899999999999999999999999964421      1233346788999999999999999999 79999999999


Q ss_pred             EEEecCCCC
Q 016936          109 VRVRRPTDY  117 (380)
Q Consensus       109 i~v~~~~~~  117 (380)
                      |+|+|+.++
T Consensus       261 LrvEwskP~  269 (270)
T KOG0122|consen  261 LRVEWSKPS  269 (270)
T ss_pred             EEEEecCCC
Confidence            999997653

>PF13893 RRM_5: RNA recognition motif

Probab=99.20  E-value=9.5e-11  Score=79.49  Aligned_cols=56  Identities=23%  Similarity=0.486  Sum_probs=50.6

Q ss_pred             HHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          169 IKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       169 l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      |+++|++||.|..+.+....     +++|||+|.+.++|++|++.|||..+.|++|+|.++
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            68899999999999997653     579999999999999999999999999999999985

(a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....

>smart00361 RRM_1 RNA recognition motif

Probab=99.19  E-value=1.2e-10  Score=82.83  Aligned_cols=61  Identities=15%  Similarity=0.289  Sum_probs=54.6

Q ss_pred             HHHHHHHHH----hcCCeeEEE-EeeCCCC--CCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEE
Q 016936          166 ETQIKELLE----SFGTLHGFD-LVKDRDT--GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  226 (380)
Q Consensus       166 ~~~l~~~F~----~~G~i~~v~-l~~~~~~--~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v  226 (380)
                      +++|+++|+    +||.|.++. +..++.+  +.++|+|||.|.+.++|.+|+..|||..+.|+.|.+
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            567888888    999999985 6666556  889999999999999999999999999999999986

>smart00362 RRM_2 RNA recognition motif

Probab=99.18  E-value=1.3e-10  Score=82.44  Aligned_cols=66  Identities=38%  Similarity=0.655  Sum_probs=58.3

Q ss_pred             eEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCC----CcEEEEEeCCHHHHHHHH-HcCCceecCce
Q 016936           34 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE----KKFAFVEMRTVEEASNAM-ALDGIIFEGVA  108 (380)
Q Consensus        34 ~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~----~g~afV~f~~~~~a~~ai-~l~~~~i~g~~  108 (380)
                      +|+|+|||..+++++|+++|++||.            +..+.+...    +|+|||+|.+.++|..|+ .+++..+.|++
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            555555443    599999999999999999 79999999999


Q ss_pred             EEE
Q 016936          109 VRV  111 (380)
Q Consensus       109 i~v  111 (380)
                      |+|
T Consensus        69 i~v   71 (72)
T smart00362       69 LRV   71 (72)
T ss_pred             Eee
Confidence            887

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

Probab=99.16  E-value=4.2e-10  Score=105.20  Aligned_cols=172  Identities=24%  Similarity=0.281  Sum_probs=115.0

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCc---EEEEEeCCHHHHHHHH-H-cCCc
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK---FAFVEMRTVEEASNAM-A-LDGI  102 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g---~afV~f~~~~~a~~ai-~-l~~~  102 (380)
                      ..+-+++|||++||++++|+.|...|.+||.+.-.+   |+ ..........+|   |+|+.|+++.+++.-+ + ..+ 
T Consensus       255 ~~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~VdW---P~-k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~~-  329 (520)
T KOG0129|consen  255 SPRYSRKVFVGGLPWDITEAQINASFGQFGSVKVDW---PG-KANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSEG-  329 (520)
T ss_pred             ccccccceeecCCCccccHHHHHhhcccccceEeec---CC-CccccccCCCCCcccEEEEEecchHHHHHHHHHHhhc-
Confidence            457789999999999999999999999999863211   00 011111123456   9999999999988877 2 221 


Q ss_pred             eecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHH-hcCCeeE
Q 016936          103 IFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLE-SFGTLHG  181 (380)
Q Consensus       103 ~i~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~-~~G~i~~  181 (380)
                       -.+--+.|.-+..+.+..       +. .-+...............+..+||||++||.-++.++|-.+|+ -||.|..
T Consensus       330 -~~~~yf~vss~~~k~k~V-------QI-rPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~y  400 (520)
T KOG0129|consen  330 -EGNYYFKVSSPTIKDKEV-------QI-RPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLY  400 (520)
T ss_pred             -ccceEEEEecCcccccce-------eE-EeeEeccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEE
Confidence             111112222111111000       00 0000001111112333455668999999999999999999999 6999999


Q ss_pred             EEEeeCCCCCCCceEEEEEEcChhHHHHHHHH
Q 016936          182 FDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA  213 (380)
Q Consensus       182 v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~  213 (380)
                      +-|=.|+..+-++|.|-|.|.+..+-.+||.+
T Consensus       401 aGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  401 VGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             EEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            99988877788999999999999999999986

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

Probab=99.15  E-value=2.5e-11  Score=100.09  Aligned_cols=74  Identities=24%  Similarity=0.403  Sum_probs=64.0

Q ss_pred             CChHHHHHHHHHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEecc
Q 016936          293 ADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYP  369 (380)
Q Consensus       293 ~~~~~~~~~~~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~  369 (380)
                      ++|+.|.++-++|+.+|++||.|-+|.|+.+..+.. ++  |||||.|....+|+.|+++|+|..++|+.|+|+++-
T Consensus        18 VdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~-sR--gFaFVrf~~k~daedA~damDG~~ldgRelrVq~ar   91 (256)
T KOG4207|consen   18 VDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQ-SR--GFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMAR   91 (256)
T ss_pred             ecceeccCCHHHHHHHHHHhCcccceeccccccccc-cc--ceeEEEeeecchHHHHHHhhcceeeccceeeehhhh
Confidence            344556666689999999999999999999886554 55  566999999999999999999999999999999874

>smart00361 RRM_1 RNA recognition motif

Probab=99.11  E-value=1.7e-10  Score=82.00  Aligned_cols=61  Identities=26%  Similarity=0.394  Sum_probs=47.1

Q ss_pred             HHHHhhc----ccCCeEEEE-ecCCCCC-CCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEE
Q 016936          304 DMREECG----KYGTLVNVV-IPRPDQN-GGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAF  366 (380)
Q Consensus       304 ~L~~~f~----~~G~I~~v~-i~~~~~~-~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~  366 (380)
                      +|+++|+    +||.|.++. +..++.+ ...++  |++||+|.+.++|.+|+..|||+.+.||.|+++
T Consensus         4 ~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~r--G~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~~   70 (70)
T smart00361        4 DFEREFSEEEEYFGEVGKINKIYIDNVGYENHKR--GNVYITFERSEDAARAIVDLNGRYFDGRTVKAE   70 (70)
T ss_pred             hHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCc--EEEEEEECCHHHHHHHHHHhCCCEECCEEEEeC
Confidence            5555555    999999995 4443333 12244  567999999999999999999999999999874

>PLN03213 repressor of silencing 3; Provisional

Probab=99.10  E-value=2.5e-10  Score=105.67  Aligned_cols=77  Identities=19%  Similarity=0.375  Sum_probs=66.1

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec--CCCcEEEEEeCCH--HHHHHHH-HcCCce
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN--HEKKFAFVEMRTV--EEASNAM-ALDGII  103 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~--~~~g~afV~f~~~--~~a~~ai-~l~~~~  103 (380)
                      ....-+|||+||+++++++||...|.+||.            |.++.+.  ..+|||||+|.+.  .++.+|| .|+|..
T Consensus         7 ~~~gMRIYVGNLSydVTEDDLravFSeFGs------------VkdVEIpRETGRGFAFVEMssdddaEeeKAISaLNGAE   74 (759)
T PLN03213          7 GGGGVRLHVGGLGESVGRDDLLKIFSPMGT------------VDAVEFVRTKGRSFAYIDFSPSSTNSLTKLFSTYNGCV   74 (759)
T ss_pred             CCcceEEEEeCCCCCCCHHHHHHHHHhcCC------------eeEEEEecccCCceEEEEecCCcHHHHHHHHHHhcCCe
Confidence            445678999999999999999999999998            4545443  3489999999987  7899999 899999


Q ss_pred             ecCceEEEecCCCC
Q 016936          104 FEGVAVRVRRPTDY  117 (380)
Q Consensus       104 i~g~~i~v~~~~~~  117 (380)
                      |+|+.|+|..+...
T Consensus        75 WKGR~LKVNKAKP~   88 (759)
T PLN03213         75 WKGGRLRLEKAKEH   88 (759)
T ss_pred             ecCceeEEeeccHH
Confidence            99999999977643

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

Probab=99.07  E-value=6e-12  Score=101.68  Aligned_cols=88  Identities=27%  Similarity=0.391  Sum_probs=75.9

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceec
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE  105 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~  105 (380)
                      +.=.++--|||+|||+++||.||.-.|++||.+++.+      .|.+-.+++++||||+.|.+-.+...|+ .+||..|.
T Consensus        30 ~~YkdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdin------LiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~  103 (219)
T KOG0126|consen   30 QEYKDSAYIYIGGLPYELTEGDILCVFSQYGEIVDIN------LIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKIL  103 (219)
T ss_pred             hhcccceEEEECCCcccccCCcEEEEeeccCceEEEE------EEecCCCCcccceEEEEecCccceEEEEeccCCceec
Confidence            3446777899999999999999999999999976532      3555567899999999999999999999 89999999


Q ss_pred             CceEEEecCCCCCcc
Q 016936          106 GVAVRVRRPTDYNPT  120 (380)
Q Consensus       106 g~~i~v~~~~~~~~~  120 (380)
                      |+.|+|.+-..|...
T Consensus       104 gRtirVDHv~~Yk~p  118 (219)
T KOG0126|consen  104 GRTIRVDHVSNYKKP  118 (219)
T ss_pred             ceeEEeeecccccCC
Confidence            999999987776554

>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=99.06  E-value=1e-09  Score=78.25  Aligned_cols=68  Identities=38%  Similarity=0.589  Sum_probs=59.5

Q ss_pred             eEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecC-----CCcEEEEEeCCHHHHHHHH-HcCCceecCc
Q 016936           34 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH-----EKKFAFVEMRTVEEASNAM-ALDGIIFEGV  107 (380)
Q Consensus        34 ~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~-----~~g~afV~f~~~~~a~~ai-~l~~~~i~g~  107 (380)
                      +|+|+|||+.+++++|+++|+++|.            +..+.+..     .+++|||+|.+.++|..|+ .+++..+.|+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~------------i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~   68 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGK------------VESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELGGR   68 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCC------------EEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeECCe
Confidence            5899999999999999999999987            55555443     3799999999999999999 7999999999


Q ss_pred             eEEEec
Q 016936          108 AVRVRR  113 (380)
Q Consensus       108 ~i~v~~  113 (380)
                      ++.|.+
T Consensus        69 ~~~v~~   74 (74)
T cd00590          69 PLRVEF   74 (74)
T ss_pred             EEEEeC
Confidence            998864

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).

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

Probab=99.01  E-value=1.3e-09  Score=95.14  Aligned_cols=79  Identities=19%  Similarity=0.213  Sum_probs=70.3

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecCc
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  107 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g~  107 (380)
                      .-+.|||||.-|+++++|.+|+..|+.||.|....      .|.+..+++++|||||+|.+..+...|. ..+|..|.|+
T Consensus        98 gDPy~TLFv~RLnydT~EskLrreF~~YG~Ikrir------lV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgr  171 (335)
T KOG0113|consen   98 GDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIR------LVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGR  171 (335)
T ss_pred             CCccceeeeeeccccccHHHHHHHHHhcCcceeEE------EeeecccCCccceEEEEeccHHHHHHHHHhccCceecCc
Confidence            36789999999999999999999999999986532      3555567899999999999999999999 7999999999


Q ss_pred             eEEEec
Q 016936          108 AVRVRR  113 (380)
Q Consensus       108 ~i~v~~  113 (380)
                      .|-|..
T Consensus       172 ri~VDv  177 (335)
T KOG0113|consen  172 RILVDV  177 (335)
T ss_pred             EEEEEe
Confidence            999976

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

Probab=99.00  E-value=4.6e-10  Score=86.37  Aligned_cols=85  Identities=25%  Similarity=0.225  Sum_probs=70.0

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceec
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE  105 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~  105 (380)
                      +.+.+.=.|||+++...++|+||.+.|..||.|.+..      .-++.+++-.||||+|+|.+.++|++|+ .+|+..+.
T Consensus        67 qrSVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNih------LNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll  140 (170)
T KOG0130|consen   67 QRSVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIH------LNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELL  140 (170)
T ss_pred             ccceeeEEEEEeccCcchhHHHHHHHHhhccccccee------eccccccccccceeeeehHhHHHHHHHHHhccchhhh
Confidence            3445556799999999999999999999999965432      1234445566899999999999999999 89999999


Q ss_pred             CceEEEecCCCC
Q 016936          106 GVAVRVRRPTDY  117 (380)
Q Consensus       106 g~~i~v~~~~~~  117 (380)
                      |.+|.|.|...+
T Consensus       141 ~q~v~VDw~Fv~  152 (170)
T KOG0130|consen  141 GQNVSVDWCFVK  152 (170)
T ss_pred             CCceeEEEEEec
Confidence            999999996543

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

Probab=98.99  E-value=2.5e-10  Score=95.05  Aligned_cols=81  Identities=26%  Similarity=0.432  Sum_probs=71.3

Q ss_pred             chhhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe------cCCCcEEEEEeCCHHHHHHHH-
Q 016936           25 TQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-   97 (380)
Q Consensus        25 ~~~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~------~~~~g~afV~f~~~~~a~~ai-   97 (380)
                      .++....-|+|||++|..+++|.-|...|-.||.            |.++.+      .+++|||||+|...|||..|| 
T Consensus         3 ~~~~a~~KrtlYVGGladeVtekvLhaAFIPFGD------------I~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiD   70 (298)
T KOG0111|consen    3 QQQMANQKRTLYVGGLADEVTEKVLHAAFIPFGD------------IKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAID   70 (298)
T ss_pred             cccccccceeEEeccchHHHHHHHHHhccccccc------------hhhcccccchhcccccceeEEEeeccchhHHHhh
Confidence            3455667899999999999999999999999998            555555      467999999999999999999 


Q ss_pred             HcCCceecCceEEEecCCCC
Q 016936           98 ALDGIIFEGVAVRVRRPTDY  117 (380)
Q Consensus        98 ~l~~~~i~g~~i~v~~~~~~  117 (380)
                      .+|...+.|+.|+|.++.+-
T Consensus        71 NMnesEL~GrtirVN~AkP~   90 (298)
T KOG0111|consen   71 NMNESELFGRTIRVNLAKPE   90 (298)
T ss_pred             cCchhhhcceeEEEeecCCc
Confidence            89999999999999987653

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

Probab=98.95  E-value=1.4e-10  Score=96.54  Aligned_cols=150  Identities=22%  Similarity=0.273  Sum_probs=121.7

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCC----cEEEEEeCCHHHHHHHH-HcCCc
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEK----KFAFVEMRTVEEASNAM-ALDGI  102 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~----g~afV~f~~~~~a~~ai-~l~~~  102 (380)
                      +....+||||.|+...++|+-|.++|-+-|+            |+.+.+.+.+    .||||.|.++-++.-|+ -+||.
T Consensus         5 aae~drtl~v~n~~~~v~eelL~ElfiqaGP------------V~kv~ip~~~d~~~kFa~v~f~~E~sv~~a~~L~ng~   72 (267)
T KOG4454|consen    5 AAEMDRTLLVQNMYSGVSEELLSELFIQAGP------------VYKVGIPSGQDQEQKFAYVFFPNENSVQLAGQLENGD   72 (267)
T ss_pred             CcchhhHHHHHhhhhhhhHHHHHHHhhccCc------------eEEEeCCCCccCCCceeeeecccccchhhhhhhcccc
Confidence            4456799999999999999999999999987            7777776542    49999999999999999 58999


Q ss_pred             eecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEE
Q 016936          103 IFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGF  182 (380)
Q Consensus       103 ~i~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v  182 (380)
                      .+.+.+++++.-...+..                                 -     |...++.+.+...|+.-|++..+
T Consensus        73 ~l~~~e~q~~~r~G~sha---------------------------------p-----ld~r~~~ei~~~v~s~a~p~~~~  114 (267)
T KOG4454|consen   73 DLEEDEEQRTLRCGNSHA---------------------------------P-----LDERVTEEILYEVFSQAGPIEGV  114 (267)
T ss_pred             hhccchhhcccccCCCcc---------------------------------h-----hhhhcchhhheeeecccCCCCCc
Confidence            999999999752211000                                 0     33456888899999999999999


Q ss_pred             EEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          183 DLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       183 ~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      ++..+. +|+++.++|+.+....+...++..+.+....-+++.+.-
T Consensus       115 R~~~~~-d~rnrn~~~~~~qr~~~~P~~~~~y~~l~~~~~~~~~gg  159 (267)
T KOG4454|consen  115 RIPTDN-DGRNRNFGFVTYQRLCAVPFALDLYQGLELFQKKVTIGG  159 (267)
T ss_pred             cccccc-cCCccCccchhhhhhhcCcHHhhhhcccCcCCCCccccc
Confidence            998885 489999999999999999999998888777666665543

>smart00360 RRM RNA recognition motif

Probab=98.94  E-value=3.5e-09  Score=74.71  Aligned_cols=64  Identities=36%  Similarity=0.629  Sum_probs=54.8

Q ss_pred             EcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec------CCCcEEEEEeCCHHHHHHHH-HcCCceecCceE
Q 016936           37 VGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN------HEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  109 (380)
Q Consensus        37 V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~------~~~g~afV~f~~~~~a~~ai-~l~~~~i~g~~i  109 (380)
                      |+|||..+++++|+++|++||.            +..+.+.      .++|+|||+|.+.++|..|+ .+++..+.|++|
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~------------v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~   68 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGK------------IESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPL   68 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCC------------EeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEE
Confidence            5799999999999999999997            4444433      23689999999999999999 799999999998


Q ss_pred             EEe
Q 016936          110 RVR  112 (380)
Q Consensus       110 ~v~  112 (380)
                      +|.
T Consensus        69 ~v~   71 (71)
T smart00360       69 KVK   71 (71)
T ss_pred             EeC
Confidence            873

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

Probab=98.94  E-value=2.7e-09  Score=88.57  Aligned_cols=81  Identities=31%  Similarity=0.534  Sum_probs=75.1

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhc-CCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          152 PDRVFVGGLPYYFTETQIKELLESF-GTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       152 ~~~l~V~nlp~~~t~~~l~~~F~~~-G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      ..-+|+..+|..+.+.++..+|++| |.+..+++.+++.+|.++|||||+|.+++.|+-|.+.||...+.++.|.|.+..
T Consensus        49 ~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~vmp  128 (214)
T KOG4208|consen   49 EGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHVMP  128 (214)
T ss_pred             ccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEEeC
Confidence            3579999999999999999999998 778899999999999999999999999999999999999999999999999875


Q ss_pred             cC
Q 016936          231 AS  232 (380)
Q Consensus       231 ~~  232 (380)
                      +.
T Consensus       129 pe  130 (214)
T KOG4208|consen  129 PE  130 (214)
T ss_pred             ch
Confidence            43

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

Probab=98.93  E-value=2.3e-09  Score=95.42  Aligned_cols=81  Identities=23%  Similarity=0.370  Sum_probs=73.0

Q ss_pred             cchhhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-H-cCC
Q 016936           24 MTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-A-LDG  101 (380)
Q Consensus        24 ~~~~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~-l~~  101 (380)
                      +...++...++|||++|-..++|.||+++|-+||.            |.++.+...++||||+|.+.++|++|. + ++.
T Consensus       220 lepPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGe------------irsi~~~~~~~CAFv~ftTR~aAE~Aae~~~n~  287 (377)
T KOG0153|consen  220 LEPPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGE------------IRSIRILPRKGCAFVTFTTREAAEKAAEKSFNK  287 (377)
T ss_pred             cCCCcccceeEEEecccccchhHHHHHHHHhhcCC------------eeeEEeecccccceeeehhhHHHHHHHHhhcce
Confidence            33456788999999999989999999999999998            888888899999999999999999999 4 777


Q ss_pred             ceecCceEEEecCCC
Q 016936          102 IIFEGVAVRVRRPTD  116 (380)
Q Consensus       102 ~~i~g~~i~v~~~~~  116 (380)
                      ..|.|+.|.|.|...
T Consensus       288 lvI~G~Rl~i~Wg~~  302 (377)
T KOG0153|consen  288 LVINGFRLKIKWGRP  302 (377)
T ss_pred             eeecceEEEEEeCCC
Confidence            779999999999776

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

Probab=98.92  E-value=1.7e-09  Score=102.36  Aligned_cols=81  Identities=27%  Similarity=0.415  Sum_probs=71.8

Q ss_pred             ceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecCceEEE
Q 016936           33 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV  111 (380)
Q Consensus        33 ~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g~~i~v  111 (380)
                      +.|||+|||+++++++|.+.|+..|.|..      ...+.+...++.+||||++|.+.++|..|+ .||+..+.|++|+|
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 SSVFVGNIPYEGSEEQLLSIFSGVGPVLS------FRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRV   92 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccce------eeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEe
Confidence            99999999999999999999999999654      234556666788999999999999999999 79999999999999


Q ss_pred             ecCCCCCc
Q 016936          112 RRPTDYNP  119 (380)
Q Consensus       112 ~~~~~~~~  119 (380)
                      .|+.....
T Consensus        93 ~~~~~~~~  100 (435)
T KOG0108|consen   93 NYASNRKN  100 (435)
T ss_pred             ecccccch
Confidence            99876554

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

Probab=98.85  E-value=5.5e-09  Score=101.88  Aligned_cols=79  Identities=19%  Similarity=0.397  Sum_probs=73.6

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceec
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE  105 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~  105 (380)
                      ....-+|||||++|+..+++.||.++|..||.            |.++.++..++||||...+..+|.+|+ +|++..+.
T Consensus       416 ~isV~SrTLwvG~i~k~v~e~dL~~~feefGe------------iqSi~li~~R~cAfI~M~~RqdA~kalqkl~n~kv~  483 (894)
T KOG0132|consen  416 HISVCSRTLWVGGIPKNVTEQDLANLFEEFGE------------IQSIILIPPRGCAFIKMVRRQDAEKALQKLSNVKVA  483 (894)
T ss_pred             ceeEeeeeeeeccccchhhHHHHHHHHHhccc------------ceeEeeccCCceeEEEEeehhHHHHHHHHHhccccc
Confidence            45677899999999999999999999999998            888999999999999999999999999 89999999


Q ss_pred             CceEEEecCCCC
Q 016936          106 GVAVRVRRPTDY  117 (380)
Q Consensus       106 g~~i~v~~~~~~  117 (380)
                      ++.|+|.|+-.+
T Consensus       484 ~k~Iki~Wa~g~  495 (894)
T KOG0132|consen  484 DKTIKIAWAVGK  495 (894)
T ss_pred             ceeeEEeeeccC
Confidence            999999997654

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

Probab=98.84  E-value=2.6e-09  Score=92.84  Aligned_cols=97  Identities=30%  Similarity=0.517  Sum_probs=80.1

Q ss_pred             CccceEEEEeccCCcccCCChHHHHHHHHHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHc
Q 016936          275 ETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALS  354 (380)
Q Consensus       275 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~  354 (380)
                      .++++++.+.|++...+..++.+     .++++.|++||.|.+|.|+-.+..... . ---.||+|..+++|.+|+-.||
T Consensus       278 ~~ptkvlllrnmVg~gevd~ele-----de~keEceKyg~V~~viifeip~~p~d-e-avRiFveF~r~e~aiKA~Vdln  350 (378)
T KOG1996|consen  278 KCPTKVLLLRNMVGAGEVDEELE-----DETKEECEKYGKVGNVIIFEIPSQPED-E-AVRIFVEFERVESAIKAVVDLN  350 (378)
T ss_pred             hcchHHHHhhhhcCcccccHHHH-----HHHHHHHHhhcceeeEEEEecCCCccc-h-hheeeeeeccHHHHHHHHHhcC
Confidence            67888999999998877655443     588999999999999998876432211 0 1136999999999999999999


Q ss_pred             CcccCCeEEEEEeccccccccccC
Q 016936          355 GRKFGGNTVNAFYYPEDKYFNKDY  378 (380)
Q Consensus       355 g~~i~gr~l~v~~~~~~~~~~~~~  378 (380)
                      |++|+||.++..|++.++|.+.++
T Consensus       351 GRyFGGr~v~A~Fyn~ekfs~~el  374 (378)
T KOG1996|consen  351 GRYFGGRVVSACFYNLEKFSNLEL  374 (378)
T ss_pred             CceecceeeeheeccHHhhhhhhh
Confidence            999999999999999999998765

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.80  E-value=4.7e-09  Score=94.93  Aligned_cols=177  Identities=18%  Similarity=0.223  Sum_probs=134.6

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEE-EEecCCCcEEEEEeCCHHHHHHHHHcCCc-eecCc
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVN-VYINHEKKFAFVEMRTVEEASNAMALDGI-IFEGV  107 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~-~~~~~~~g~afV~f~~~~~a~~ai~l~~~-~i~g~  107 (380)
                      ...++.|++++...+.+.+...++..+|......       ... -....++|++++.|...+.+..|+.+.+. ...++
T Consensus        86 ~~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~-------~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~  158 (285)
T KOG4210|consen   86 GSSSTFFVGELSENIEESEDDNFSSEAGLRVDAR-------SSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGN  158 (285)
T ss_pred             cccccccccccccchhhccccccchhhcCcccch-------hhhhccccccccceeeccccHHHHHHHHHhhhccccccc
Confidence            4689999999999999999999999999743211       111 12345789999999999999999977775 34444


Q ss_pred             eEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEE-EcCCCCCCCHHHHHHHHHhcCCeeEEEEee
Q 016936          108 AVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVF-VGGLPYYFTETQIKELLESFGTLHGFDLVK  186 (380)
Q Consensus       108 ~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~-V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~  186 (380)
                      .+...........            ..+       ...........++| +.+++..+++++|+.+|..+|.|..++++.
T Consensus       159 ~~~~dl~~~~~~~------------~~n-------~~~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~  219 (285)
T KOG4210|consen  159 KGEKDLNTRRGLR------------PKN-------KLSRLSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPT  219 (285)
T ss_pred             cccCccccccccc------------ccc-------hhcccccCccccceeecccccccchHHHhhhccCcCcceeeccCC
Confidence            4444332221100            000       00011123335666 999999999999999999999999999999


Q ss_pred             CCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccCC
Q 016936          187 DRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASS  233 (380)
Q Consensus       187 ~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~~  233 (380)
                      ++.++..+|+|+|.|.....+.+++.. ....+.++.+.+....++.
T Consensus       220 ~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~  265 (285)
T KOG4210|consen  220 DEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEEDEPRP  265 (285)
T ss_pred             CCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccCCCCc
Confidence            999999999999999999999999987 8889999999999887654

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

Probab=98.80  E-value=2.1e-08  Score=89.43  Aligned_cols=75  Identities=17%  Similarity=0.380  Sum_probs=67.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHh-CCCeeCCeEEEEEEc
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL-NGLKMGDKTLTVRRA  229 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l-~g~~~~g~~i~v~~~  229 (380)
                      .-++|||++|-..+++.+|+++|-+||.|..+++...      ++||||+|.+.+.|+.|.++. +-..+.|++|.|.|+
T Consensus       227 ~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~------~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg  300 (377)
T KOG0153|consen  227 SIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR------KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWG  300 (377)
T ss_pred             ceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc------cccceeeehhhHHHHHHHHhhcceeeecceEEEEEeC
Confidence            3479999999889999999999999999999999776      359999999999999999984 445779999999999


Q ss_pred             cc
Q 016936          230 TA  231 (380)
Q Consensus       230 ~~  231 (380)
                      .+
T Consensus       301 ~~  302 (377)
T KOG0153|consen  301 RP  302 (377)
T ss_pred             CC
Confidence            77

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

Probab=98.80  E-value=5.5e-10  Score=109.96  Aligned_cols=151  Identities=23%  Similarity=0.282  Sum_probs=124.1

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeE-EEEecCCCcEEEEEeCCHHHHHHHHHcCCceecC
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVV-NVYINHEKKFAFVEMRTVEEASNAMALDGIIFEG  106 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~-~~~~~~~~g~afV~f~~~~~a~~ai~l~~~~i~g  106 (380)
                      ..++.+++||+||++.+.+.||...|..+|.+...      . +. -+....-+|+|||+|..++++.+|+.+....+.|
T Consensus       663 ~~R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~v------q-i~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~g  735 (881)
T KOG0128|consen  663 EIRDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVV------Q-IVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFG  735 (881)
T ss_pred             HHHHHHHHHHhhcchhhcCchhhhhcCccchhhhH------H-HHHHhhccccccceeeEeecCCchhhhhhhhhhhhhh
Confidence            34788999999999999999999999999885310      0 11 1111234799999999999999999776666665


Q ss_pred             ceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEee
Q 016936          107 VAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVK  186 (380)
Q Consensus       107 ~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~  186 (380)
                           .                                        ..++|.|.|+..|.++++.+++++|.+..++++.
T Consensus       736 -----K----------------------------------------~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt  770 (881)
T KOG0128|consen  736 -----K----------------------------------------ISVAISGPPFQGTKEELKSLASKTGNVTSLRLVT  770 (881)
T ss_pred             -----h----------------------------------------hhhheeCCCCCCchHHHHhhccccCCccccchhh
Confidence                 1                                        2789999999999999999999999999998877


Q ss_pred             CCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEccc
Q 016936          187 DRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  231 (380)
Q Consensus       187 ~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~  231 (380)
                      .+ .|.++|-|+|.|.++.+|.++....+...+.-+.+.|..+.+
T Consensus       771 ~r-~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  771 VR-AGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             hh-ccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCC
Confidence            76 599999999999999999999998887777777777776544

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

Probab=98.78  E-value=7e-09  Score=102.75  Aligned_cols=164  Identities=20%  Similarity=0.345  Sum_probs=131.0

Q ss_pred             chhhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe---cCCCcEEEEEeCCHHHHHHHH-HcC
Q 016936           25 TQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI---NHEKKFAFVEMRTVEEASNAM-ALD  100 (380)
Q Consensus        25 ~~~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~---~~~~g~afV~f~~~~~a~~ai-~l~  100 (380)
                      ...+....+|||++||+..+++.+|+-.|..+|.+..          +++..   +...-||||.|.+...+-.|. .+.
T Consensus       365 ~~DD~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~----------VDiKtP~~~~esa~~f~~~~n~dmtp~ak~e~s  434 (975)
T KOG0112|consen  365 KLDDFRATRTLFLGNLDSKLTESEIRPAFDESGKVEE----------VDIKTPHIKTESAYAFVSLLNTDMTPSAKFEES  434 (975)
T ss_pred             cccchhhhhhhhhcCcccchhhhhhhhhhhhhccccc----------cccccCCCCcccchhhhhhhccccCcccchhhc
Confidence            3346688999999999999999999999999998432          22332   334579999999999999999 888


Q ss_pred             CceecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCee
Q 016936          101 GIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLH  180 (380)
Q Consensus       101 ~~~i~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~  180 (380)
                      +..|....+++.....+                               ....+.+++++|+.++....+...|..||+|.
T Consensus       435 ~~~I~~g~~r~glG~~k-------------------------------st~ttr~~sgglg~w~p~~~l~r~fd~fGpir  483 (975)
T KOG0112|consen  435 GPLIGNGTHRIGLGQPK-------------------------------STPTTRLQSGGLGPWSPVSRLNREFDRFGPIR  483 (975)
T ss_pred             CCccccCcccccccccc-------------------------------cccceeeccCCCCCCChHHHHHHHhhccCcce
Confidence            88887766666552110                               12336899999999999999999999999999


Q ss_pred             EEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCC--eEEEEEEcccCCCC
Q 016936          181 GFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD--KTLTVRRATASSGQ  235 (380)
Q Consensus       181 ~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g--~~i~v~~~~~~~~~  235 (380)
                      .|.+-.    |  ..||+|+|++...|+.|+..+.|..+++  +.++|.++.+....
T Consensus       484 ~Idy~h----g--q~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdla~~~~~~  534 (975)
T KOG0112|consen  484 IIDYRH----G--QPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDLASPPGAT  534 (975)
T ss_pred             eeeccc----C--CcceeeecccCccchhhHHHHhcCcCCCCCcccccccccCCCCC
Confidence            887733    2  3499999999999999999999999976  56888888765444

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

Probab=98.76  E-value=3.5e-08  Score=95.15  Aligned_cols=196  Identities=9%  Similarity=0.016  Sum_probs=123.1

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccC
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  232 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~  232 (380)
                      ..+-++++++.+...|++++|-.. .+..+.|..+...+.-.|-++|.|....++++|+.. +...+-.|.+.+..+...
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            345678889999999999998632 244556666554344478899999999999999986 667777888888776544


Q ss_pred             CCCChhHHHHHHHHHHHHHHHHHHHhhhc--------CccccCCCCCccCCccceEEEEeccCCcccCCChHHHHHHHHH
Q 016936          233 SGQSKTEQESILAQAQQHIAIQKMALQTS--------GMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILED  304 (380)
Q Consensus       233 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~  304 (380)
                      ..........-.-.        .......        +...++...+ .+...+.|+.+....-....          .+
T Consensus       390 ~~~~a~~~~~~~~~--------~~~~~~hg~p~~~pr~~~~~gq~vp-~P~~ag~~lyv~~lP~~t~~----------~~  450 (944)
T KOG4307|consen  390 GRNGAPPFQAGVPP--------PVIQNNHGRPIAPPRAMVRPGQNVP-FPGGAGGALYVFQLPVMTPI----------VP  450 (944)
T ss_pred             ccccCccccccCCC--------CcccccCCCCCCCcccccCCCCCCC-CCCCccceEEeccCCccccc----------cc
Confidence            32221111000000        0000000        0001111111 12344566666653322222          37


Q ss_pred             HHHhhcccCCeEE-EEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEecccccc
Q 016936          305 MREECGKYGTLVN-VVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKY  373 (380)
Q Consensus       305 L~~~f~~~G~I~~-v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~~~~  373 (380)
                      +.+.|..--.|++ |.|.+ ..++..   .+.|||.|..++++.+|...-+-.+++.|.|+|.-+.++..
T Consensus       451 ~v~~f~~~~~Ved~I~lt~-~P~~~~---~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si~~~~m  516 (944)
T KOG4307|consen  451 PVNKFMGAAAVEDFIELTR-LPTDLL---RPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSIADYAM  516 (944)
T ss_pred             hhhhhhhhhhhhheeEecc-CCcccc---cchhhheeccccccchhhhcccccccCceEEEeechhhHHH
Confidence            8899988888888 55544 334332   35679999999999999998888899999999998887543

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

Probab=98.71  E-value=9.5e-08  Score=90.24  Aligned_cols=85  Identities=19%  Similarity=0.360  Sum_probs=75.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      +...++|||.+|...+-..+|+++|++||.|...+++.+..+-..++|+||.+.+.++|.+||..|+..+|.|+.|.|..
T Consensus       402 s~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEk  481 (940)
T KOG4661|consen  402 STLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEK  481 (940)
T ss_pred             cccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeee
Confidence            44558999999999999999999999999999988888755556788999999999999999999999999999999998


Q ss_pred             cccCC
Q 016936          229 ATASS  233 (380)
Q Consensus       229 ~~~~~  233 (380)
                      ++...
T Consensus       482 aKNEp  486 (940)
T KOG4661|consen  482 AKNEP  486 (940)
T ss_pred             cccCc
Confidence            76543

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

Probab=98.69  E-value=9.9e-10  Score=108.19  Aligned_cols=241  Identities=15%  Similarity=0.135  Sum_probs=175.3

Q ss_pred             hhcccceEEEcCCCCcCcHH-HHHHHHHHHHHhccCCCCCCCCeeEEEEecC------CCcEEEEEeCCHHHHHHHHHcC
Q 016936           28 ATRHARRVYVGGLPPLANEQ-AIATFFSQVMTAIGGNSAGPGDAVVNVYINH------EKKFAFVEMRTVEEASNAMALD  100 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~-~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~------~~g~afV~f~~~~~a~~ai~l~  100 (380)
                      .....+...+.++.+..... ..+..|..+|.            +..++..+      ...++++.++...+++.|....
T Consensus       567 ~~~~~~e~~s~~v~p~~~~ke~~~~~~k~~~~------------vekv~~p~~g~k~h~q~~~~~~~s~~~~~esat~pa  634 (881)
T KOG0128|consen  567 APLERREKESTNVYPEQQKKEIQRRQFKGEGN------------VEKVNGPKRGFKAHEQPQQQKVQSKHGSAESATVPA  634 (881)
T ss_pred             hhhhhhhhcccCCCcchhhHHhhHHHhhcccc------------cccccCccccccccccchhhhhhccccchhhccccc
Confidence            45566778888998887666 56788888877            55555544      1238999999999999999888


Q ss_pred             CceecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCee
Q 016936          101 GIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLH  180 (380)
Q Consensus       101 ~~~i~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~  180 (380)
                      +..+.++.+.+..+...........     .++.              .....++|++||+....+.+|...|..+|.+.
T Consensus       635 ~~~~a~~~~av~~ad~~~~~~~~kv-----s~n~--------------~R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e  695 (881)
T KOG0128|consen  635 GGALANRSAAVGLADAEEKEENFKV-----SPNE--------------IRDLIKIFVSNLSPKMSEEDLSERFSPSGTIE  695 (881)
T ss_pred             ccccCCccccCCCCCchhhhhccCc-----CchH--------------HHHHHHHHHhhcchhhcCchhhhhcCccchhh
Confidence            8788888888876544432211110     0000              01113789999999999999999999999988


Q ss_pred             EEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccCCCCChhHHHHHHHHHHHHHHHHHHHhhh
Q 016936          181 GFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQT  260 (380)
Q Consensus       181 ~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  260 (380)
                      .+++....+.++.+|.|++.|..++++.+|+...+++.++...+.++-.                               
T Consensus       696 ~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~gK~~v~i~g~-------------------------------  744 (881)
T KOG0128|consen  696 VVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFGKISVAISGP-------------------------------  744 (881)
T ss_pred             hHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhhhhhhheeCC-------------------------------
Confidence            7766544557899999999999999999999976555544222222211                               


Q ss_pred             cCccccCCCCCccCCccceEEEEeccCCcccCCChHHHHHHHHHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEe
Q 016936          261 SGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEY  340 (380)
Q Consensus       261 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f  340 (380)
                                               .+..           |.+.|+.+|.++|++.+..++... .|.   -.|.|||.|
T Consensus       745 -------------------------pf~g-----------t~e~~k~l~~~~gn~~~~~~vt~r-~gk---pkg~a~v~y  784 (881)
T KOG0128|consen  745 -------------------------PFQG-----------TKEELKSLASKTGNVTSLRLVTVR-AGK---PKGKARVDY  784 (881)
T ss_pred             -------------------------CCCC-----------chHHHHhhccccCCccccchhhhh-ccc---cccceeccC
Confidence                                     1111           225899999999999999876544 433   346789999


Q ss_pred             echhhHHHHHHHHcCcccCCeEEEEEeccc
Q 016936          341 YDAVGCATAKNALSGRKFGGNTVNAFYYPE  370 (380)
Q Consensus       341 ~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~  370 (380)
                      .++.+|.++...+.+..++-+.+.|...++
T Consensus       785 ~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  785 NTEADASRKVASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             CCcchhhhhcccchhhhhhhcCccccccCC
Confidence            999999999999999998888888877433

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

Probab=98.69  E-value=8.9e-08  Score=83.58  Aligned_cols=86  Identities=23%  Similarity=0.396  Sum_probs=77.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      ...+.+|+|.|||+.++.+||+++|..||.+..+-+..++ .|++.|+|-|.|...++|.+|++.+++..+.|+.|.+..
T Consensus        80 ~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~  158 (243)
T KOG0533|consen   80 ETRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEI  158 (243)
T ss_pred             CCCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEE
Confidence            3444789999999999999999999999999999999996 699999999999999999999999999999999999998


Q ss_pred             cccCCCC
Q 016936          229 ATASSGQ  235 (380)
Q Consensus       229 ~~~~~~~  235 (380)
                      .......
T Consensus       159 i~~~~~~  165 (243)
T KOG0533|consen  159 ISSPSQS  165 (243)
T ss_pred             ecCcccc
Confidence            7665444

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

Probab=98.68  E-value=4.3e-08  Score=87.52  Aligned_cols=81  Identities=20%  Similarity=0.413  Sum_probs=76.7

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEccc
Q 016936          152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  231 (380)
Q Consensus       152 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~  231 (380)
                      .+-|||=-|.+.++.++|.-+|+.||.|.+|.+++|..+|.+-.||||+|.+.++.++|.-+|+...|..++|+|.++..
T Consensus       239 eNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDFSQS  318 (479)
T KOG0415|consen  239 ENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDFSQS  318 (479)
T ss_pred             cceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeehhhh
Confidence            36799999999999999999999999999999999998999999999999999999999999999999999999999765


Q ss_pred             C
Q 016936          232 S  232 (380)
Q Consensus       232 ~  232 (380)
                      -
T Consensus       319 V  319 (479)
T KOG0415|consen  319 V  319 (479)
T ss_pred             h
Confidence            4

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

Probab=98.67  E-value=5.1e-08  Score=83.41  Aligned_cols=132  Identities=22%  Similarity=0.360  Sum_probs=104.9

Q ss_pred             cCCCcEEEEEeCCHHHHHHHH-HcCCceecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEE
Q 016936           77 NHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRV  155 (380)
Q Consensus        77 ~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  155 (380)
                      .+-.+++|+.|.....-.++- .-++.++...+|++-........           ...+|            .....+|
T Consensus       137 ~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a~gtswedP-----------sl~ew------------~~~DfRI  193 (290)
T KOG0226|consen  137 QPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLAAGTSWEDP-----------SLAEW------------DEDDFRI  193 (290)
T ss_pred             CccCcccccCcchhhhhhhhccccccccccCcceeeccccccCCc-----------ccccC------------cccccee
Confidence            445689999998777777766 56667777777776543322111           01112            2223699


Q ss_pred             EEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEccc
Q 016936          156 FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  231 (380)
Q Consensus       156 ~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~  231 (380)
                      |++.|.-.++.+.|-..|.+|-.-...++++++.+|+++||+||.|.+..++.+|+..++|++++.++|.++....
T Consensus       194 fcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS~w  269 (290)
T KOG0226|consen  194 FCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKSEW  269 (290)
T ss_pred             ecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhhhH
Confidence            9999999999999999999999988889999999999999999999999999999999999999999999986543

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

Probab=98.67  E-value=5.5e-08  Score=95.09  Aligned_cols=78  Identities=26%  Similarity=0.457  Sum_probs=71.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      ...++||||++|+..+++.||.++|+.||.|.+|.+..      ++|||||.+.+..+|.+|+.+|+...+.++.|+|.|
T Consensus       418 sV~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~------~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~W  491 (894)
T KOG0132|consen  418 SVCSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIP------PRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAW  491 (894)
T ss_pred             eEeeeeeeeccccchhhHHHHHHHHHhcccceeEeecc------CCceeEEEEeehhHHHHHHHHHhcccccceeeEEee
Confidence            34558999999999999999999999999999998854      468999999999999999999999999999999999


Q ss_pred             cccC
Q 016936          229 ATAS  232 (380)
Q Consensus       229 ~~~~  232 (380)
                      +.-.
T Consensus       492 a~g~  495 (894)
T KOG0132|consen  492 AVGK  495 (894)
T ss_pred             eccC
Confidence            8654

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

Probab=98.66  E-value=2.4e-08  Score=99.09  Aligned_cols=160  Identities=15%  Similarity=0.238  Sum_probs=122.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      ...+++||++||+..+++.+|+..|..+|.|.+|.|-.-+ -+...-||||.|.+..++-.|...+.+..|....+++.+
T Consensus       369 ~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~-~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~gl  447 (975)
T KOG0112|consen  369 FRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPH-IKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGL  447 (975)
T ss_pred             hhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCC-CCcccchhhhhhhccccCcccchhhcCCccccCcccccc
Confidence            4455899999999999999999999999999999885543 344455899999999999999999988887666666655


Q ss_pred             cccCCCCChhHHHHHHHHHHHHHHHHHHHhhhcCccccCCCCCccCCccceEEEEeccCCcccCCChHHHHHHHHHHHHh
Q 016936          229 ATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREE  308 (380)
Q Consensus       229 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~~  308 (380)
                      ....                                          ..+++-+...........          ..|..+
T Consensus       448 G~~k------------------------------------------st~ttr~~sgglg~w~p~----------~~l~r~  475 (975)
T KOG0112|consen  448 GQPK------------------------------------------STPTTRLQSGGLGPWSPV----------SRLNRE  475 (975)
T ss_pred             cccc------------------------------------------cccceeeccCCCCCCChH----------HHHHHH
Confidence            4321                                          112222222222111111          478899


Q ss_pred             hcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCC--eEEEEEeccc
Q 016936          309 CGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGG--NTVNAFYYPE  370 (380)
Q Consensus       309 f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~g--r~l~v~~~~~  370 (380)
                      |..||.|..|.+....         -+|||.|.+...|+.|+..|-|..|+|  ++++|.|+.+
T Consensus       476 fd~fGpir~Idy~hgq---------~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdla~~  530 (975)
T KOG0112|consen  476 FDRFGPIRIIDYRHGQ---------PYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDLASP  530 (975)
T ss_pred             hhccCcceeeecccCC---------cceeeecccCccchhhHHHHhcCcCCCCCcccccccccC
Confidence            9999999997774322         389999999999999999999999988  8899999976

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

Probab=98.61  E-value=2.1e-08  Score=85.68  Aligned_cols=167  Identities=14%  Similarity=0.181  Sum_probs=116.7

Q ss_pred             EEEEcCCCCCCCHHH---HHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          154 RVFVGGLPYYFTETQ---IKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       154 ~l~V~nlp~~~t~~~---l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      ..++.++-..+..+-   +...|+.+..+....++++. -+.-.+++|+.|.....-.++...-+++.++.+.+++..+.
T Consensus        98 ~p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~~-p~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a~gt  176 (290)
T KOG0226|consen   98 RPFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRDR-PQPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLAAGT  176 (290)
T ss_pred             cccccccccccCCCCCCcchhhhccchhhhhhhhhhcC-CCccCcccccCcchhhhhhhhccccccccccCcceeecccc
Confidence            344555533333332   36677777777777787774 47778899999999988888887777788887776665443


Q ss_pred             cCCCCChhHHHHHHHHHHHHHHHHHHHhhhcCccccCCCCCccCCccceEEEEeccCCcccCCChHHHHHHHHHHHHhhc
Q 016936          231 ASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECG  310 (380)
Q Consensus       231 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~~f~  310 (380)
                      .-..-.-.                              .+ ........|-.+.|.++.             +.|...|.
T Consensus       177 swedPsl~------------------------------ew-~~~DfRIfcgdlgNevnd-------------~vl~raf~  212 (290)
T KOG0226|consen  177 SWEDPSLA------------------------------EW-DEDDFRIFCGDLGNEVND-------------DVLARAFK  212 (290)
T ss_pred             ccCCcccc------------------------------cC-ccccceeecccccccccH-------------HHHHHHHH
Confidence            21100000                              00 000122233345554444             48889999


Q ss_pred             ccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEec
Q 016936          311 KYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYY  368 (380)
Q Consensus       311 ~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~  368 (380)
                      +|-.....++++++.++. ++|+|  ||.|.++.|+.+|+..|+|..++.|.|++.-.
T Consensus       213 Kfpsf~~akviRdkRTgK-Skgyg--fVSf~~pad~~rAmrem~gkyVgsrpiklRkS  267 (290)
T KOG0226|consen  213 KFPSFQKAKVIRDKRTGK-SKGYG--FVSFRDPADYVRAMREMNGKYVGSRPIKLRKS  267 (290)
T ss_pred             hccchhhccccccccccc-cccce--eeeecCHHHHHHHHHhhcccccccchhHhhhh
Confidence            999999999999998876 67766  99999999999999999999999999987543

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

Probab=98.59  E-value=8.9e-08  Score=79.66  Aligned_cols=66  Identities=14%  Similarity=0.303  Sum_probs=59.0

Q ss_pred             HHHHHhhccc-CCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEecccc
Q 016936          303 EDMREECGKY-GTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  371 (380)
Q Consensus       303 ~~L~~~f~~~-G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~~  371 (380)
                      ..+...|.+| |.|..+.+.++..+|. ++|  ||||+|.+++.|.-|-+.||++-++++.|.|.+.+++
T Consensus        64 ~~~~~~~~q~~g~v~r~rlsRnkrTGN-SKg--YAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~vmppe  130 (214)
T KOG4208|consen   64 TEILNYFRQFGGTVTRFRLSRNKRTGN-SKG--YAFVEFESEEVAKIAAETMNNYLLMEHLLECHVMPPE  130 (214)
T ss_pred             HHHhhhhhhcCCeeEEEEeecccccCC-cCc--eEEEEeccHHHHHHHHHHhhhhhhhhheeeeEEeCch
Confidence            4788888888 7888888889888887 554  5599999999999999999999999999999999998

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

Probab=98.50  E-value=2.5e-07  Score=87.69  Aligned_cols=188  Identities=14%  Similarity=0.107  Sum_probs=112.7

Q ss_pred             CCCCccccchhhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEE-ecCCCcEEEEEeCCHHHHHH
Q 016936           17 PLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVY-INHEKKFAFVEMRTVEEASN   95 (380)
Q Consensus        17 ~~~~~~~~~~~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~-~~~~~g~afV~f~~~~~a~~   95 (380)
                      |.++.+.++...+...++|+|-|||..+++++|...|+.||.|.+            ++ +....|..||+|-+..+|+.
T Consensus        60 ~~p~~~~np~~~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~------------ir~t~~~~~~~~v~FyDvR~A~~  127 (549)
T KOG4660|consen   60 NKPLRPDNPSEKDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIRE------------IRETPNKRGIVFVEFYDVRDAER  127 (549)
T ss_pred             CCCCCcCCCCcccCccceEEEEecCCcCCHHHHHHHHHhhcchhh------------hhcccccCceEEEEEeehHhHHH
Confidence            344444566566788999999999999999999999999999543            33 34567999999999999999


Q ss_pred             HH-HcCCceecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHH
Q 016936           96 AM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLE  174 (380)
Q Consensus        96 ai-~l~~~~i~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~  174 (380)
                      |+ +|++..+.|+.|+ ...........     .....-++-......+...++-.. ..+++ .|++..+..-+...+.
T Consensus       128 Alk~l~~~~~~~~~~k-~~~~~~~~~~~-----~~~~~~~~~~~~p~a~s~pgg~~~-~~~~g-~l~P~~s~~~~~~~~~  199 (549)
T KOG4660|consen  128 ALKALNRREIAGKRIK-RPGGARRAMGL-----QSGTSFLNHFGSPLANSPPGGWPR-GQLFG-MLSPTRSSILLEHISS  199 (549)
T ss_pred             HHHHHHHHHhhhhhhc-CCCcccccchh-----cccchhhhhccchhhcCCCCCCcC-Cccee-eeccchhhhhhhcchh
Confidence            99 8999999998888 21111111100     000000000000111111222221 22332 2777766655566666


Q ss_pred             hcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEccc
Q 016936          175 SFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  231 (380)
Q Consensus       175 ~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~  231 (380)
                      -+|.+.. +..     +.-.-.-|+.|.+..++..+.... |+.+.+....+.+...
T Consensus       200 ~~~~~~~-~~~-----~~~~hq~~~~~~~~~s~a~~~~~~-G~~~s~~~~v~t~S~~  249 (549)
T KOG4660|consen  200 VDGSSPG-RET-----PLLNHQRFVEFADNRSYAFSEPRG-GFLISNSSGVITFSGP  249 (549)
T ss_pred             ccCcccc-ccc-----cchhhhhhhhhccccchhhcccCC-ceecCCCCceEEecCC
Confidence            7777654 321     111114567777777775555432 5666666655555433

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

Probab=98.47  E-value=3.1e-07  Score=82.12  Aligned_cols=81  Identities=15%  Similarity=0.325  Sum_probs=70.0

Q ss_pred             CccceEEEEeccCCcccCCChHHHHHHHHHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHc
Q 016936          275 ETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALS  354 (380)
Q Consensus       275 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~  354 (380)
                      +.+...++-.|+++.++            ||.-+|+.||+|.+|.++++.++|..   .-+|||+|.+.++..+|.-+|+
T Consensus       238 PeNVLFVCKLNPVTtDe------------DLeiIFSrFG~i~sceVIRD~ktgds---LqyaFiEFen~escE~AyFKMd  302 (479)
T KOG0415|consen  238 PENVLFVCKLNPVTTDE------------DLEIIFSRFGKIVSCEVIRDRKTGDS---LQYAFIEFENKESCEQAYFKMD  302 (479)
T ss_pred             CcceEEEEecCCccccc------------chhhHHhhcccceeeeEEecccccch---hheeeeeecchhhHHHHHhhhc
Confidence            44555556667777774            99999999999999999999988863   3478999999999999999999


Q ss_pred             CcccCCeEEEEEeccc
Q 016936          355 GRKFGGNTVNAFYYPE  370 (380)
Q Consensus       355 g~~i~gr~l~v~~~~~  370 (380)
                      +-.|+.|+|+|.|...
T Consensus       303 NvLIDDrRIHVDFSQS  318 (479)
T KOG0415|consen  303 NVLIDDRRIHVDFSQS  318 (479)
T ss_pred             ceeeccceEEeehhhh
Confidence            9999999999999876

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

Probab=98.45  E-value=5.1e-06  Score=78.34  Aligned_cols=182  Identities=18%  Similarity=0.184  Sum_probs=114.3

Q ss_pred             CCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCC---CCCCce---EEEEEEcChhHHHHHHHHhCCCe
Q 016936          145 AIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRD---TGNSKG---YGFCVYQDPAVTDIACAALNGLK  218 (380)
Q Consensus       145 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~---~~~~~g---~afV~f~~~~~A~~Ai~~l~g~~  218 (380)
                      ......-++.|||++||+++++++|...|..||.+. +.++....   .--++|   |+|+.|+++.+.+.-+.++.-  
T Consensus       252 ~~~~~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~--  328 (520)
T KOG0129|consen  252 GYRSPRYSRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSE--  328 (520)
T ss_pred             CCCccccccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhh--
Confidence            334455568999999999999999999999999973 55653211   113556   999999999999888887542  


Q ss_pred             eCCeEEEEEEcccCC----CCChhHHHHHHHHHHHHHHHHHHHhhhcCccccCCCCCccCCccceEEEEeccCCcccCCC
Q 016936          219 MGDKTLTVRRATASS----GQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALAD  294 (380)
Q Consensus       219 ~~g~~i~v~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  294 (380)
                       ....+.+....+..    .+.+++.-..                     ............+.+++.+.....+-    
T Consensus       329 -~~~~~yf~vss~~~k~k~VQIrPW~laD---------------------s~fv~d~sq~lDprrTVFVGgvprpl----  382 (520)
T KOG0129|consen  329 -GEGNYYFKVSSPTIKDKEVQIRPWVLAD---------------------SDFVLDHNQPIDPRRTVFVGGLPRPL----  382 (520)
T ss_pred             -cccceEEEEecCcccccceeEEeeEecc---------------------chhhhccCcccCccceEEecCCCCcc----
Confidence             33333333322221    1112221100                     00111122235666777665532221    


Q ss_pred             hHHHHHHHHHHHHhhc-ccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHH----HcCcccCCeEEEE
Q 016936          295 DEEYEEILEDMREECG-KYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNA----LSGRKFGGNTVNA  365 (380)
Q Consensus       295 ~~~~~~~~~~L~~~f~-~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~----l~g~~i~gr~l~v  365 (380)
                            +.++|..+|+ -||.|..+.|..+++-.- .+|-|  -|.|.+-..-.+||.+    |+...|.. +|.|
T Consensus       383 ------~A~eLA~imd~lyGgV~yaGIDtD~k~KY-PkGaG--RVtFsnqqsYi~AIsarFvql~h~d~~K-RVEI  448 (520)
T KOG0129|consen  383 ------TAEELAMIMEDLFGGVLYVGIDTDPKLKY-PKGAG--RVTFSNQQAYIKAISARFVQLDHTDIDK-RVEI  448 (520)
T ss_pred             ------hHHHHHHHHHHhcCceEEEEeccCcccCC-CCCcc--eeeecccHHHHHHHhhheEEEeccccce-eeee
Confidence                  1158888888 899999999999864433 56666  9999999999999873    34444444 4443

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

Probab=98.43  E-value=3.6e-07  Score=86.39  Aligned_cols=83  Identities=22%  Similarity=0.398  Sum_probs=70.8

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecC
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  106 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g  106 (380)
                      .....|.|||.+|+..+--.||+.+|++||.+++.+      .|+..+..-.+.|+||...+.++|.+|| .||.+.|+|
T Consensus       401 rs~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAK------VVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHG  474 (940)
T KOG4661|consen  401 RSTLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAK------VVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHG  474 (940)
T ss_pred             ccccccceeeeccccchhhhHHHHHHHHhcceecee------eeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcc
Confidence            356678899999999999999999999999988754      3444445555779999999999999999 799999999


Q ss_pred             ceEEEecCCC
Q 016936          107 VAVRVRRPTD  116 (380)
Q Consensus       107 ~~i~v~~~~~  116 (380)
                      +.|.|..+++
T Consensus       475 rmISVEkaKN  484 (940)
T KOG4661|consen  475 RMISVEKAKN  484 (940)
T ss_pred             eeeeeeeccc
Confidence            9999987653

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

Probab=98.40  E-value=1.7e-07  Score=78.44  Aligned_cols=79  Identities=15%  Similarity=0.209  Sum_probs=71.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      +...++|||.|+-..++++-|.++|-+-|+|..+.|..+++ +..+ ||||.|.++.....|++.+||..+.+..+.+.+
T Consensus         6 ae~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d-~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~   83 (267)
T KOG4454|consen    6 AEMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQD-QEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTL   83 (267)
T ss_pred             cchhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCcc-CCCc-eeeeecccccchhhhhhhcccchhccchhhccc
Confidence            34458999999999999999999999999999999998874 5566 999999999999999999999999999999887


Q ss_pred             c
Q 016936          229 A  229 (380)
Q Consensus       229 ~  229 (380)
                      -
T Consensus        84 r   84 (267)
T KOG4454|consen   84 R   84 (267)
T ss_pred             c
Confidence            5

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=98.39  E-value=1e-06  Score=83.24  Aligned_cols=80  Identities=23%  Similarity=0.404  Sum_probs=67.9

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEccc
Q 016936          152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  231 (380)
Q Consensus       152 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~  231 (380)
                      ..+|||+|||.+++.++|.+.|..||.|....|....-.+...+||||+|.+.+.++.|+++ +...++++++.|+-...
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            34599999999999999999999999999887766432244448999999999999999997 68899999999997655


Q ss_pred             C
Q 016936          232 S  232 (380)
Q Consensus       232 ~  232 (380)
                      .
T Consensus       367 ~  367 (419)
T KOG0116|consen  367 G  367 (419)
T ss_pred             c
Confidence            3

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.36  E-value=3.7e-07  Score=82.70  Aligned_cols=179  Identities=15%  Similarity=0.142  Sum_probs=130.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      ...+.|++++.....+.+...++..+|......+........++|++.+.|...+.+..|+.........++.+......
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            45689999999998888889999999988877777766678999999999999999999999644456666666555443


Q ss_pred             cCCCCChhHHHHHHHHHHHHHHHHHHHhhhcCccccCCCCCccCCccceEEEEec-cCCcccCCChHHHHHHHHHHHHhh
Q 016936          231 ASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTE-AITADALADDEEYEEILEDMREEC  309 (380)
Q Consensus       231 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~-~~~~~~~~~~~~~~~~~~~L~~~f  309 (380)
                      ...........                             ........+.+.+.+ .++.           ++++|..+|
T Consensus       167 ~~~~~~~n~~~-----------------------------~~~~~~s~~~~~~~~~~f~~-----------~~d~~~~~~  206 (285)
T KOG4210|consen  167 RRGLRPKNKLS-----------------------------RLSSGPSDTIFFVGELDFSL-----------TRDDLKEHF  206 (285)
T ss_pred             cccccccchhc-----------------------------ccccCccccceeeccccccc-----------chHHHhhhc
Confidence            33211100000                             000022223332222 2222           236888999


Q ss_pred             cccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEecccccc
Q 016936          310 GKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKY  373 (380)
Q Consensus       310 ~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~~~~  373 (380)
                      ..+|.|..+.++....++. .+  |+|||+|.+...+..|+.. ....+.++.+++.+......
T Consensus       207 ~~~~~i~~~r~~~~~~s~~-~k--g~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~  266 (285)
T KOG4210|consen  207 VSSGEITSVRLPTDEESGD-SK--GFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEEDEPRPK  266 (285)
T ss_pred             cCcCcceeeccCCCCCccc-hh--hhhhhhhhhchhHHHHhhc-ccCcccCcccccccCCCCcc
Confidence            9999999999999887765 44  5559999999999999998 99999999999999887643

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=98.35  E-value=3.6e-08  Score=89.86  Aligned_cols=155  Identities=19%  Similarity=0.304  Sum_probs=113.3

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCC-eeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCC-eeCCeEEEEEEcc
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGT-LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGL-KMGDKTLTVRRAT  230 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~-i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~-~~~g~~i~v~~~~  230 (380)
                      ..+|++||....+..++..+|...-- ...-.++       ..||+||.+.+...|.+|++.++|+ ++.|.++.+....
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~-------k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv   74 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV-------KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSV   74 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceee-------ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchh
Confidence            36899999999999999999986421 1111222       2369999999999999999999985 8899999998875


Q ss_pred             cCCCCChhHHHHHHHHHHHHHHHHHHHhhhcCccccCCCCCccCCccceEEEEeccCCcccCCChHHHHHHHHHHHHhhc
Q 016936          231 ASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECG  310 (380)
Q Consensus       231 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~~f~  310 (380)
                      ++..+.+.                                          +.+.|+...      ..|    +-|..+..
T Consensus        75 ~kkqrsrk------------------------------------------~Qirnippq------l~w----evld~Ll~  102 (584)
T KOG2193|consen   75 PKKQRSRK------------------------------------------IQIRNIPPQ------LQW----EVLDSLLA  102 (584)
T ss_pred             hHHHHhhh------------------------------------------hhHhcCCHH------HHH----HHHHHHHh
Confidence            43111110                                          011111110      111    46778899


Q ss_pred             ccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEeccccc
Q 016936          311 KYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  372 (380)
Q Consensus       311 ~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~~~  372 (380)
                      .||+++.|.........      ...-|.|.+.+.++.|+..|+|..++...+++.|.|++.
T Consensus       103 qyg~ve~~eqvnt~~et------avvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~YiPdeq  158 (584)
T KOG2193|consen  103 QYGTVENCEQVNTDSET------AVVNVTYSAQQQHRQAIHKLNGPQLENQHLKVGYIPDEQ  158 (584)
T ss_pred             ccCCHhHhhhhccchHH------HHHHHHHHHHHHHHHHHHhhcchHhhhhhhhcccCchhh
Confidence            99999999874432221      345689999999999999999999999999999999854

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.34  E-value=5.9e-06  Score=61.80  Aligned_cols=78  Identities=23%  Similarity=0.337  Sum_probs=66.5

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHh--cCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeC----CeEEEE
Q 016936          153 DRVFVGGLPYYFTETQIKELLES--FGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG----DKTLTV  226 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~--~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~----g~~i~v  226 (380)
                      ++|.|+|+|-..+.++|.+++..  .|...-+-++.|..++.+.|||||-|.+++.|.+..+.++|..+.    .+...|
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            58999999999999999998885  355666778888778899999999999999999999999998774    455677


Q ss_pred             EEcc
Q 016936          227 RRAT  230 (380)
Q Consensus       227 ~~~~  230 (380)
                      .+|.
T Consensus        82 ~yAr   85 (97)
T PF04059_consen   82 SYAR   85 (97)
T ss_pred             ehhH
Confidence            7764

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

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

Probab=98.31  E-value=7e-07  Score=84.72  Aligned_cols=68  Identities=18%  Similarity=0.308  Sum_probs=63.0

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEE
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  225 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~  225 (380)
                      ++|+|-|||..++.++|+.+|+.||.|..++..+.     .+|..||+|.+.-+|++|++.|++.++.|++|.
T Consensus        76 ~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~-----~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   76 GTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPN-----KRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             ceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccc-----cCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            69999999999999999999999999999776444     467899999999999999999999999999998

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.30  E-value=1e-06  Score=77.13  Aligned_cols=81  Identities=22%  Similarity=0.409  Sum_probs=75.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      ..+.+||+|+.+.++.+++..+|+.||.|..+.++.++..+.++|||||+|.+.+.++.++. |++..+.|+.+.|.+..
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            34689999999999999999999999999999999999888999999999999999999999 89999999999999865


Q ss_pred             cC
Q 016936          231 AS  232 (380)
Q Consensus       231 ~~  232 (380)
                      .+
T Consensus       179 ~~  180 (231)
T KOG4209|consen  179 TN  180 (231)
T ss_pred             ee
Confidence            54

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=98.27  E-value=7e-08  Score=88.07  Aligned_cols=152  Identities=19%  Similarity=0.309  Sum_probs=119.8

Q ss_pred             ceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCc-eecCceEE
Q 016936           33 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGI-IFEGVAVR  110 (380)
Q Consensus        33 ~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~-~i~g~~i~  110 (380)
                      .++|++||.+.++.+||...|..--.            -.+-.+..-.||+||.+.+...|.+|+ .+++. .+.|+.+.
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            46899999999999999999987621            122223345699999999999999999 68774 48899999


Q ss_pred             EecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEee-CCC
Q 016936          111 VRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVK-DRD  189 (380)
Q Consensus       111 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~-~~~  189 (380)
                      +...-.++..                               ++.+-|+|+|....++.+..+..+||.++.|.... ++.
T Consensus        70 ~~~sv~kkqr-------------------------------srk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~e  118 (584)
T KOG2193|consen   70 VEHSVPKKQR-------------------------------SRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSE  118 (584)
T ss_pred             ccchhhHHHH-------------------------------hhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchH
Confidence            9875443221                               25799999999999999999999999999886532 322


Q ss_pred             CCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEccc
Q 016936          190 TGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  231 (380)
Q Consensus       190 ~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~  231 (380)
                      +-    ..=|+|.+.++++.|+..++|.++....+.+.+..+
T Consensus       119 ta----vvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~YiPd  156 (584)
T KOG2193|consen  119 TA----VVNVTYSAQQQHRQAIHKLNGPQLENQHLKVGYIPD  156 (584)
T ss_pred             HH----HHHHHHHHHHHHHHHHHhhcchHhhhhhhhcccCch
Confidence            11    122589999999999999999999999999988543

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=98.26  E-value=5.8e-07  Score=81.47  Aligned_cols=180  Identities=15%  Similarity=0.071  Sum_probs=120.9

Q ss_pred             ceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHHHcCCceecCceEEEe
Q 016936           33 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVR  112 (380)
Q Consensus        33 ~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai~l~~~~i~g~~i~v~  112 (380)
                      ..|.|.||.+.+|.++++.+|...|.|-....++.   +-++.++.....|||.|.+...+..|--|.++.+-++-|.|.
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~---~~d~~~pv~sRtcyVkf~d~~sv~vaQhLtntvfvdraliv~   84 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPN---VDDSKIPVISRTCYVKFLDSQSVTVAQHLTNTVFVDRALIVR   84 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCC---CCCccCcceeeeEEEeccCCcceeHHhhhccceeeeeeEEEE
Confidence            47999999999999999999999999877766665   444555556789999999999999998888888777666555


Q ss_pred             cC-CCCCcccc-------ccCCCCCCCCCcccc------ccc-CCCC------------CCCCCCCCCEEEEcCCCCCCC
Q 016936          113 RP-TDYNPTLA-------AALGPGQPSPNLNLA------AVG-LASG------------AIGGAEGPDRVFVGGLPYYFT  165 (380)
Q Consensus       113 ~~-~~~~~~~~-------~~~~~~~~~~~~~~~------~~~-~~~~------------~~~~~~~~~~l~V~nlp~~~t  165 (380)
                      +. ..-.....       .+..+....++.-+.      ..+ ....            +..-....++++|.+|+..|.
T Consensus        85 p~~~~~~p~r~af~~l~~~navprll~pdg~Lp~~~~lt~~nh~p~ailktP~Lp~~~~A~kleeirRt~~v~sl~~~~~  164 (479)
T KOG4676|consen   85 PYGDEVIPDRFAFVELADQNAVPRLLPPDGVLPGDRPLTKINHSPNAILKTPELPPQAAAKKLEEIRRTREVQSLISAAI  164 (479)
T ss_pred             ecCCCCCccHHHHHhcCcccccccccCCCCccCCCCccccccCCccceecCCCCChHhhhhhhHHHHhhhhhhcchhhhc
Confidence            32 22211110       001110000000000      000 0000            001112237899999999999


Q ss_pred             HHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeC
Q 016936          166 ETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG  220 (380)
Q Consensus       166 ~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~  220 (380)
                      ..++.+.|..+|.|...++-.    +....+|-+.|....+...|+.. +|..+.
T Consensus       165 l~e~~e~f~r~Gev~ya~~as----k~~s~~c~~sf~~qts~~halr~-~gre~k  214 (479)
T KOG4676|consen  165 LPESGESFERKGEVSYAHTAS----KSRSSSCSHSFRKQTSSKHALRS-HGRERK  214 (479)
T ss_pred             chhhhhhhhhcchhhhhhhhc----cCCCcchhhhHhhhhhHHHHHHh-cchhhh
Confidence            999999999999998777643    33344677999998888888885 666654

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=98.23  E-value=2.5e-06  Score=80.64  Aligned_cols=79  Identities=22%  Similarity=0.338  Sum_probs=64.2

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe--cCCCcEEEEEeCCHHHHHHHHHcCCcee
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI--NHEKKFAFVEMRTVEEASNAMALDGIIF  104 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~--~~~~g~afV~f~~~~~a~~ai~l~~~~i  104 (380)
                      .+.+...+|||+|||.++++++|+++|.+||.|...        =..++.  .+...||||+|.+.+++..||..+...+
T Consensus       283 ~~~~~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~--------~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~Asp~~i  354 (419)
T KOG0116|consen  283 EPRADGLGIFVKNLPPDATPAELEEVFKQFGPIKEG--------GIQVRSPGGKNPCFGFVEFENAAAVQNAIEASPLEI  354 (419)
T ss_pred             ceeecccceEeecCCCCCCHHHHHHHHhhccccccc--------ceEEeccCCCcCceEEEEEeecchhhhhhhcCcccc
Confidence            345666779999999999999999999999997643        122222  2333899999999999999998888889


Q ss_pred             cCceEEEec
Q 016936          105 EGVAVRVRR  113 (380)
Q Consensus       105 ~g~~i~v~~  113 (380)
                      .++++.|+.
T Consensus       355 g~~kl~Vee  363 (419)
T KOG0116|consen  355 GGRKLNVEE  363 (419)
T ss_pred             CCeeEEEEe
Confidence            999999975

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=98.16  E-value=9.5e-07  Score=76.11  Aligned_cols=74  Identities=22%  Similarity=0.347  Sum_probs=62.2

Q ss_pred             HHHHHHHHHHhhc-ccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEecccccccc
Q 016936          298 YEEILEDMREECG-KYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFN  375 (380)
Q Consensus       298 ~~~~~~~L~~~f~-~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~~~~~~  375 (380)
                      +.+.-+++..+|+ +||.|+.+.+..+-....    .|-+||.|...++|.+|++.|||++|.|++|.+++.+...|..
T Consensus        78 ~defyEd~f~E~~~kygEiee~~Vc~Nl~~hl----~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pvT~~re  152 (260)
T KOG2202|consen   78 EDEFYEDVFTELEDKYGEIEELNVCDNLGDHL----VGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPVTDFRE  152 (260)
T ss_pred             HHHHHHHHHHHHHHHhhhhhhhhhhcccchhh----hhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCcCchhh
Confidence            4455578888888 999999998877654332    4778999999999999999999999999999999999876643

>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=98.15  E-value=2.2e-05  Score=55.90  Aligned_cols=72  Identities=24%  Similarity=0.294  Sum_probs=50.9

Q ss_pred             ceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecCceEEE
Q 016936           33 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV  111 (380)
Q Consensus        33 ~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g~~i~v  111 (380)
                      ..|+|.|||.+.+...|+.-+++...--|+       .|..+    ..+.|+|.|.+.+.|.+|. .|+|..+.|++|.|
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGG-------kVl~v----~~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v   71 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGG-------KVLSV----SGGTAILRFPNQEFAERAQKRMEGEDVFGNKISV   71 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT---------EEE------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCC-------EEEEE----eCCEEEEEeCCHHHHHHHHHhhcccccccceEEE
Confidence            468999999999999999888876553333       27776    4688999999999999999 89999999999999


Q ss_pred             ecCC
Q 016936          112 RRPT  115 (380)
Q Consensus       112 ~~~~  115 (380)
                      .+..
T Consensus        72 ~~~~   75 (90)
T PF11608_consen   72 SFSP   75 (90)
T ss_dssp             ESS-
T ss_pred             EEcC
Confidence            8753

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.14  E-value=5.6e-06  Score=80.58  Aligned_cols=81  Identities=17%  Similarity=0.315  Sum_probs=70.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeC---CCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEE
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKD---RDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  227 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~---~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~  227 (380)
                      ..+++||+||++.++++.|...|..||+|..++++--   -...+.+.||||-|.+..+|++|++.|+|..+.++.+++.
T Consensus       173 ~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K~g  252 (877)
T KOG0151|consen  173 QTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMKLG  252 (877)
T ss_pred             cccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeeeec
Confidence            3478999999999999999999999999998877542   1234566799999999999999999999999999999999


Q ss_pred             Eccc
Q 016936          228 RATA  231 (380)
Q Consensus       228 ~~~~  231 (380)
                      |+..
T Consensus       253 Wgk~  256 (877)
T KOG0151|consen  253 WGKA  256 (877)
T ss_pred             cccc
Confidence            9854

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.11  E-value=2e-06  Score=75.34  Aligned_cols=81  Identities=27%  Similarity=0.306  Sum_probs=69.6

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHHHcCCceecC
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEG  106 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai~l~~~~i~g  106 (380)
                      +...+.+.|||+|+...+|.+++..+|+.||.+..      +++..+-...+.+|||||+|.+.+.+++++.|++..|.|
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            67889999999999999999999999999998643      222333334567899999999999999999999999999


Q ss_pred             ceEEEec
Q 016936          107 VAVRVRR  113 (380)
Q Consensus       107 ~~i~v~~  113 (380)
                      +.+.+.+
T Consensus       170 ~~i~vt~  176 (231)
T KOG4209|consen  170 PAIEVTL  176 (231)
T ss_pred             ccceeee
Confidence            9999986

>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=98.07  E-value=2.3e-05  Score=55.81  Aligned_cols=64  Identities=19%  Similarity=0.409  Sum_probs=45.3

Q ss_pred             HHHHHHHHHHHHhhcccC-CeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEeccccc
Q 016936          296 EEYEEILEDMREECGKYG-TLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  372 (380)
Q Consensus       296 ~~~~~~~~~L~~~f~~~G-~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~~~  372 (380)
                      .+...+...|++++.-+| .|.+|.       +      +.|+|.|.+.+.|.+|...|+|..+-|++|.|+|.+...
T Consensus        14 ~d~~~I~~RL~qLsdNCGGkVl~v~-------~------~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~~~~r   78 (90)
T PF11608_consen   14 KDPSSIKNRLRQLSDNCGGKVLSVS-------G------GTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFSPKNR   78 (90)
T ss_dssp             S-HHHHHHHHHHHHHTTT--EEE---------T------T-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS--S-
T ss_pred             CCHHHHHHHHHHHhhccCCEEEEEe-------C------CEEEEEeCCHHHHHHHHHhhcccccccceEEEEEcCCcc
Confidence            345667789999999886 566552       1      478999999999999999999999999999999997754

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

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

Probab=98.06  E-value=1.9e-05  Score=69.07  Aligned_cols=81  Identities=16%  Similarity=0.226  Sum_probs=65.4

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe---cCCCcEEEEEeCCHHHHHHHH-HcCCce
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI---NHEKKFAFVEMRTVEEASNAM-ALDGII  103 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~---~~~~g~afV~f~~~~~a~~ai-~l~~~~  103 (380)
                      .+..+.+|+|.|||+.++++||+++|..||.+.          -..+..   +.+.|+|-|.|...+||..|+ .+++..
T Consensus        79 ~~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~----------r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~  148 (243)
T KOG0533|consen   79 NETRSTKVNVSNLPYGVIDADLKELFAEFGELK----------RVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVA  148 (243)
T ss_pred             cCCCcceeeeecCCcCcchHHHHHHHHHhccce----------EEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcc
Confidence            344557899999999999999999999998531          223332   356799999999999999999 899999


Q ss_pred             ecCceEEEecCCCCC
Q 016936          104 FEGVAVRVRRPTDYN  118 (380)
Q Consensus       104 i~g~~i~v~~~~~~~  118 (380)
                      +.|+++++.......
T Consensus       149 ldG~~mk~~~i~~~~  163 (243)
T KOG0533|consen  149 LDGRPMKIEIISSPS  163 (243)
T ss_pred             cCCceeeeEEecCcc
Confidence            999999887654433

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.04  E-value=1.8e-05  Score=59.26  Aligned_cols=79  Identities=11%  Similarity=0.180  Sum_probs=57.8

Q ss_pred             ceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecC----c
Q 016936           33 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG----V  107 (380)
Q Consensus        33 ~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g----~  107 (380)
                      +||+|+|||-..|.++|.+.+.....  +..++  .=.-.+.....+.|||||.|.++++|.+.. ..+|..|..    +
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~--g~yDF--~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~K   77 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFK--GKYDF--FYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKK   77 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhcc--CcceE--EEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCc
Confidence            68999999999999999999998632  11000  000112223346799999999999999999 899988863    6


Q ss_pred             eEEEecCC
Q 016936          108 AVRVRRPT  115 (380)
Q Consensus       108 ~i~v~~~~  115 (380)
                      .+.|.+|.
T Consensus        78 vc~i~yAr   85 (97)
T PF04059_consen   78 VCEISYAR   85 (97)
T ss_pred             EEEEehhH
Confidence            67887764

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=97.97  E-value=1.1e-05  Score=78.68  Aligned_cols=78  Identities=23%  Similarity=0.366  Sum_probs=66.1

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe--c-------CCCcEEEEEeCCHHHHHHHH-H
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI--N-------HEKKFAFVEMRTVEEASNAM-A   98 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~--~-------~~~g~afV~f~~~~~a~~ai-~   98 (380)
                      +...+.|||+||++.++++.|...|.+||+|            ..+++  .       ..+.|+||.|.+..||++|+ .
T Consensus       171 DP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPl------------asvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~  238 (877)
T KOG0151|consen  171 DPQTTNLYVGNLNPSVDENFLLRTFGRFGPL------------ASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKE  238 (877)
T ss_pred             CCcccceeeecCCccccHHHHHHHhcccCcc------------cceeeecccchhhhccccccceeeehhhhhHHHHHHH
Confidence            3455779999999999999999999999984            44443  2       23579999999999999999 8


Q ss_pred             cCCceecCceEEEecCCCCC
Q 016936           99 LDGIIFEGVAVRVRRPTDYN  118 (380)
Q Consensus        99 l~~~~i~g~~i~v~~~~~~~  118 (380)
                      |+|+.+.+.++++.|...-.
T Consensus       239 lqg~iv~~~e~K~gWgk~V~  258 (877)
T KOG0151|consen  239 LQGIIVMEYEMKLGWGKAVP  258 (877)
T ss_pred             hcceeeeeeeeeeccccccc
Confidence            99999999999999975543

>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=97.77  E-value=5.3e-05  Score=58.01  Aligned_cols=69  Identities=23%  Similarity=0.347  Sum_probs=44.5

Q ss_pred             EEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCC-----CeeCCeEEEEEE
Q 016936          154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNG-----LKMGDKTLTVRR  228 (380)
Q Consensus       154 ~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g-----~~~~g~~i~v~~  228 (380)
                      .|.|.+++..++.++|++.|+.||.|..|.+.++.      ..|+|.|.+++.|++|+..+..     ..+.+..+.++.
T Consensus         3 il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~------~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~v   76 (105)
T PF08777_consen    3 ILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGD------TEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLEV   76 (105)
T ss_dssp             EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE-
T ss_pred             EEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCC------CEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEEE
Confidence            68899999999999999999999999999997653      2699999999999999998743     355666665554

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=97.73  E-value=4.1e-05  Score=69.30  Aligned_cols=85  Identities=22%  Similarity=0.379  Sum_probs=76.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCee--------EEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeC
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLH--------GFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG  220 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~--------~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~  220 (380)
                      .....+|||.++|..+++++|.++|.++|.|.        .+.+.+++.+++++|-|.|.|.+...|+.|+.-++++.+.
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            34446899999999999999999999999985        3677888889999999999999999999999999999999


Q ss_pred             CeEEEEEEcccCC
Q 016936          221 DKTLTVRRATASS  233 (380)
Q Consensus       221 g~~i~v~~~~~~~  233 (380)
                      +..|.|..+..+.
T Consensus       143 gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  143 GNTIKVSLAERRT  155 (351)
T ss_pred             CCCchhhhhhhcc
Confidence            9999999887654

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.69  E-value=9.6e-05  Score=66.06  Aligned_cols=65  Identities=20%  Similarity=0.369  Sum_probs=52.0

Q ss_pred             HHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEeccc
Q 016936          306 REECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPE  370 (380)
Q Consensus       306 ~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~  370 (380)
                      .++|++||.|..|.+-+.-.+.....+..-+||.|.+.+||.+||+..+|..++||.|++.|-+-
T Consensus       138 ~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr~lkatYGTT  202 (480)
T COG5175         138 HEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGRVLKATYGTT  202 (480)
T ss_pred             hhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCceEeeecCch
Confidence            48899999999999876543222222222249999999999999999999999999999999764

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=97.59  E-value=0.00022  Score=47.18  Aligned_cols=52  Identities=17%  Similarity=0.290  Sum_probs=42.7

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHH
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC  211 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai  211 (380)
                      +.|-|.+.+.. ..+.+..+|..||+|..+.+...      ..+.+|.|.++.+|++|+
T Consensus         2 ~wI~V~Gf~~~-~~~~vl~~F~~fGeI~~~~~~~~------~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPD-LAEEVLEHFASFGEIVDIYVPES------TNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECch-HHHHHHHHHHhcCCEEEEEcCCC------CcEEEEEECCHHHHHhhC
Confidence            57899999877 45667779999999999887522      338999999999999985

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=97.59  E-value=0.00019  Score=47.51  Aligned_cols=53  Identities=17%  Similarity=0.501  Sum_probs=44.8

Q ss_pred             cceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH
Q 016936           32 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM   97 (380)
Q Consensus        32 ~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai   97 (380)
                      ++.|-|.|.|++.. +++..+|.+||.            |............||.|.++.+|++|+
T Consensus         1 ~~wI~V~Gf~~~~~-~~vl~~F~~fGe------------I~~~~~~~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    1 STWISVSGFPPDLA-EEVLEHFASFGE------------IVDIYVPESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             CcEEEEEeECchHH-HHHHHHHHhcCC------------EEEEEcCCCCcEEEEEECCHHHHHhhC
Confidence            36789999997766 455569999998            788888888899999999999999985

>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=97.45  E-value=0.0002  Score=54.81  Aligned_cols=68  Identities=24%  Similarity=0.285  Sum_probs=43.1

Q ss_pred             ceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-Hc--C---CceecC
Q 016936           33 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-AL--D---GIIFEG  106 (380)
Q Consensus        33 ~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l--~---~~~i~g  106 (380)
                      +.|+|.+++..++-++|++.|++||.            |.-|.+......|||.|.+.++|++|+ .+  .   +..+.+
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~------------V~yVD~~~G~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~   69 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGE------------VAYVDFSRGDTEGYVRFKTPEAAQKALEKLKEANDGKLKIKG   69 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--------------EEEEE--TT-SEEEEEESS---HHHHHHHHHHTTTS-B-TTS
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCC------------cceEEecCCCCEEEEEECCcchHHHHHHHHHhccCCceEEcC
Confidence            57899999999999999999999987            777777788889999999999999999 42  2   345666


Q ss_pred             ceEEEe
Q 016936          107 VAVRVR  112 (380)
Q Consensus       107 ~~i~v~  112 (380)
                      ..+.+.
T Consensus        70 ~~~~~~   75 (105)
T PF08777_consen   70 KEVTLE   75 (105)
T ss_dssp             SSEEEE
T ss_pred             ceEEEE
Confidence            666655

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=97.44  E-value=0.00075  Score=61.75  Aligned_cols=204  Identities=12%  Similarity=0.113  Sum_probs=114.9

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCC---CCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDT---GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       152 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~---~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      ...|-|.||.+.++.++++.+|.-.|.|..+.|+...+.   ....-.|||.|.+...+..|... -...+-++.|.|.+
T Consensus         7 ~~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQhL-tntvfvdraliv~p   85 (479)
T KOG4676|consen    7 LGVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQHL-TNTVFVDRALIVRP   85 (479)
T ss_pred             CceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhhh-ccceeeeeeEEEEe
Confidence            348999999999999999999999999999998774321   12334799999999999988874 45566667776665


Q ss_pred             cccCCCCChhHHHHHHHHHHHHHHHHHHHhhhcCccccCCCCCcc--CCccceEEEEeccCCcc------------cCCC
Q 016936          229 ATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLF--GETLAKVLCLTEAITAD------------ALAD  294 (380)
Q Consensus       229 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~------------~~~~  294 (380)
                      +-...   .+..... .........+.+.  .++.-+++ ..++.  ...+..++.-. .+++.            ..+.
T Consensus        86 ~~~~~---~p~r~af-~~l~~~navprll--~pdg~Lp~-~~~lt~~nh~p~ailktP-~Lp~~~~A~kleeirRt~~v~  157 (479)
T KOG4676|consen   86 YGDEV---IPDRFAF-VELADQNAVPRLL--PPDGVLPG-DRPLTKINHSPNAILKTP-ELPPQAAAKKLEEIRRTREVQ  157 (479)
T ss_pred             cCCCC---CccHHHH-HhcCccccccccc--CCCCccCC-CCccccccCCccceecCC-CCChHhhhhhhHHHHhhhhhh
Confidence            43221   1111100 0000000000000  00000000 00110  01111111111 01100            0112


Q ss_pred             hHHHHHHHHHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEeccccc
Q 016936          295 DEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  372 (380)
Q Consensus       295 ~~~~~~~~~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~~~  372 (380)
                      +.....+..++.+.|..+|.|.+....-.....       ++-|+|..-.....|+. ++|+.+.-...+...+.+++
T Consensus       158 sl~~~~~l~e~~e~f~r~Gev~ya~~ask~~s~-------~c~~sf~~qts~~halr-~~gre~k~qhsr~ai~kP~k  227 (479)
T KOG4676|consen  158 SLISAAILPESGESFERKGEVSYAHTASKSRSS-------SCSHSFRKQTSSKHALR-SHGRERKRQHSRRAIIKPHK  227 (479)
T ss_pred             cchhhhcchhhhhhhhhcchhhhhhhhccCCCc-------chhhhHhhhhhHHHHHH-hcchhhhhhhhhhhhcCccc
Confidence            333344557888999999999987775544322       34589998888888888 58887775555554444433

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=97.39  E-value=0.00046  Score=59.75  Aligned_cols=100  Identities=21%  Similarity=0.257  Sum_probs=81.3

Q ss_pred             HHHHHH-HcCCceecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHH
Q 016936           92 EASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIK  170 (380)
Q Consensus        92 ~a~~ai-~l~~~~i~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~  170 (380)
                      -|+.|- +|.++...++.++|.++..                                    ..|||.||+..++.+.+.
T Consensus         6 ~ae~ak~eLd~~~~~~~~lr~rfa~~------------------------------------a~l~V~nl~~~~sndll~   49 (275)
T KOG0115|consen    6 LAEIAKRELDGRFPKGRSLRVRFAMH------------------------------------AELYVVNLMQGASNDLLE   49 (275)
T ss_pred             HHHHHHHhcCCCCCCCCceEEEeecc------------------------------------ceEEEEecchhhhhHHHH
Confidence            355666 7999999999999998554                                    389999999999999999


Q ss_pred             HHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhC--C--CeeCCeEEEEEE
Q 016936          171 ELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN--G--LKMGDKTLTVRR  228 (380)
Q Consensus       171 ~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~--g--~~~~g~~i~v~~  228 (380)
                      ..|+.||+|..-.+..| +.++..+-++|.|...-.|.+|...+.  +  ....+++.-|.+
T Consensus        50 ~~f~~fg~~e~av~~vD-~r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~~~~~~~~p~~VeP  110 (275)
T KOG0115|consen   50 QAFRRFGPIERAVAKVD-DRGKPTREGIVEFAKKPNARKAARRCREGGFGGTTGGRPVGVEP  110 (275)
T ss_pred             HhhhhcCccchheeeec-ccccccccchhhhhcchhHHHHHHHhccCccccCCCCCccCCCh
Confidence            99999999988766666 468888999999999999999999874  2  233455555554

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.32  E-value=0.00059  Score=61.16  Aligned_cols=80  Identities=15%  Similarity=0.296  Sum_probs=62.9

Q ss_pred             CEEEEcCCCCCCCHHH----H--HHHHHhcCCeeEEEEeeCC-CCCCCceE--EEEEEcChhHHHHHHHHhCCCeeCCeE
Q 016936          153 DRVFVGGLPYYFTETQ----I--KELLESFGTLHGFDLVKDR-DTGNSKGY--GFCVYQDPAVTDIACAALNGLKMGDKT  223 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~----l--~~~F~~~G~i~~v~l~~~~-~~~~~~g~--afV~f~~~~~A~~Ai~~l~g~~~~g~~  223 (380)
                      .-+||-+||+.+..++    |  .++|.+||.|..+.+-+.- ......+.  .+|.|.+.++|.+||+..+|..++|+.
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            5799999988777665    2  4799999999998875542 11122222  389999999999999999999999999


Q ss_pred             EEEEEcccC
Q 016936          224 LTVRRATAS  232 (380)
Q Consensus       224 i~v~~~~~~  232 (380)
                      |+..+...+
T Consensus       195 lkatYGTTK  203 (480)
T COG5175         195 LKATYGTTK  203 (480)
T ss_pred             EeeecCchH
Confidence            999986554

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=97.26  E-value=0.0015  Score=62.63  Aligned_cols=88  Identities=20%  Similarity=0.357  Sum_probs=66.5

Q ss_pred             CccceEEEEeccCCcccCCChHHHHHHHHHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHc
Q 016936          275 ETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALS  354 (380)
Q Consensus       275 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~  354 (380)
                      ..-..|+++.+..-..    ..-....+.-|..+|+++|+|+.+.++.++.+|    +.|++|++|.+..+|+.|++.||
T Consensus        55 eg~D~vVvv~g~PvV~----~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~gg----tkG~lf~E~~~~~~A~~aVK~l~  126 (698)
T KOG2314|consen   55 EGFDSVVVVDGAPVVG----PARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGG----TKGYLFVEYASMRDAKKAVKSLN  126 (698)
T ss_pred             CCcceEEEECCCcccC----hhHHHHHHHHHHHHHHhhccccceeeccCccCC----eeeEEEEEecChhhHHHHHHhcc
Confidence            4556677776643322    222445556788999999999999999888766    35888999999999999999999


Q ss_pred             CcccCC-eEEEEEeccc
Q 016936          355 GRKFGG-NTVNAFYYPE  370 (380)
Q Consensus       355 g~~i~g-r~l~v~~~~~  370 (380)
                      |+.+.. ++..|....+
T Consensus       127 G~~ldknHtf~v~~f~d  143 (698)
T KOG2314|consen  127 GKRLDKNHTFFVRLFKD  143 (698)
T ss_pred             cceecccceEEeehhhh
Confidence            999865 6666655443

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []

Probab=97.25  E-value=0.0011  Score=49.97  Aligned_cols=72  Identities=22%  Similarity=0.304  Sum_probs=52.4

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEE------------EecCCCcEEEEEeCCHHHHHHHH
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNV------------YINHEKKFAFVEMRTVEEASNAM   97 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~------------~~~~~~g~afV~f~~~~~a~~ai   97 (380)
                      ...+-|.|=+.|+. ....|.++|++||.|           +...            ..........|.|+++.+|.+||
T Consensus         4 ~~~~wVtVFGfp~~-~~~~Vl~~F~~~G~I-----------le~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL   71 (100)
T PF05172_consen    4 DSETWVTVFGFPPS-ASNQVLRHFSSFGTI-----------LEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRAL   71 (100)
T ss_dssp             GGCCEEEEE---GG-GHHHHHHHHHCCS-E-----------ECEEGGG----------E-CCTTEEEEEESSHHHHHHHH
T ss_pred             cCCeEEEEEccCHH-HHHHHHHHHHhcceE-----------EEeecccccccccccccCCCCCCEEEEECCCHHHHHHHH
Confidence            45667889999977 667889999999985           2232            34556789999999999999999


Q ss_pred             HcCCceecCceE-EEec
Q 016936           98 ALDGIIFEGVAV-RVRR  113 (380)
Q Consensus        98 ~l~~~~i~g~~i-~v~~  113 (380)
                      ..||..+.|.-+ =|.+
T Consensus        72 ~~NG~i~~g~~mvGV~~   88 (100)
T PF05172_consen   72 QKNGTIFSGSLMVGVKP   88 (100)
T ss_dssp             TTTTEEETTCEEEEEEE
T ss_pred             HhCCeEEcCcEEEEEEE
Confidence            999999998654 4544

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.

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=97.22  E-value=0.00037  Score=63.24  Aligned_cols=90  Identities=19%  Similarity=0.138  Sum_probs=72.4

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCC--CCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceec
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSA--GPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE  105 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~--~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~  105 (380)
                      ....-+|||-+||..+++.+|.++|.++|.|.--+.-  +...+.++.++.+.|+-|.|.|.+...|+.|+ -+++..+.
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            5677789999999999999999999999987533222  12222334556678899999999999999999 79999999


Q ss_pred             CceEEEecCCCCC
Q 016936          106 GVAVRVRRPTDYN  118 (380)
Q Consensus       106 g~~i~v~~~~~~~  118 (380)
                      +.+|+|-.+...+
T Consensus       143 gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  143 GNTIKVSLAERRT  155 (351)
T ss_pred             CCCchhhhhhhcc
Confidence            9999998766554

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=97.22  E-value=0.0029  Score=50.70  Aligned_cols=60  Identities=18%  Similarity=0.386  Sum_probs=48.0

Q ss_pred             HHHHHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEecccc
Q 016936          300 EILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  371 (380)
Q Consensus       300 ~~~~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~~  371 (380)
                      .....|.+.|..||.+.-+++..           +.-+|.|.+-+.|.+|+. |+|..++|+.|+|...+++
T Consensus        48 ~l~~~ll~~~~~~GevvLvRfv~-----------~~mwVTF~dg~sALaals-~dg~~v~g~~l~i~LKtpd  107 (146)
T PF08952_consen   48 NLMDELLQKFAQYGEVVLVRFVG-----------DTMWVTFRDGQSALAALS-LDGIQVNGRTLKIRLKTPD  107 (146)
T ss_dssp             HHHHHHHHHHHCCS-ECEEEEET-----------TCEEEEESSCHHHHHHHH-GCCSEETTEEEEEEE----
T ss_pred             HHHHHHHHHHHhCCceEEEEEeC-----------CeEEEEECccHHHHHHHc-cCCcEECCEEEEEEeCCcc
Confidence            34568999999999999887764           245999999999999998 7999999999999998764

; PDB: 1UFW_A 2DNR_A.

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=97.21  E-value=0.00032  Score=63.10  Aligned_cols=77  Identities=25%  Similarity=0.389  Sum_probs=67.5

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCC--eeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGT--LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~--i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      -.+||+||-|.+|.+||.+.....|-  +.++++..++.+|+++|||+|...+.....+.|+.|-.+++.|..=.|...
T Consensus        81 ~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~~~  159 (498)
T KOG4849|consen   81 YCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVLSY  159 (498)
T ss_pred             EEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeeecc
Confidence            46999999999999999999988774  778899999889999999999999999999999999888998876555443

>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=97.07  E-value=0.002  Score=48.56  Aligned_cols=75  Identities=20%  Similarity=0.283  Sum_probs=51.5

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEE-EeeCC------CCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEE
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFD-LVKDR------DTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  225 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~-l~~~~------~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~  225 (380)
                      +.|.|=+.|.. ....|..+|++||.|.+.. +.++.      ..-.....--|+|.++.+|.+|+.. ||..+.|..|-
T Consensus         7 ~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~-NG~i~~g~~mv   84 (100)
T PF05172_consen    7 TWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQK-NGTIFSGSLMV   84 (100)
T ss_dssp             CEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTT-TTEEETTCEEE
T ss_pred             eEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHh-CCeEEcCcEEE
Confidence            57899999988 7788999999999997764 11100      0011234788999999999999996 99999887664


Q ss_pred             -EEEc
Q 016936          226 -VRRA  229 (380)
Q Consensus       226 -v~~~  229 (380)
                       |.++
T Consensus        85 GV~~~   89 (100)
T PF05172_consen   85 GVKPC   89 (100)
T ss_dssp             EEEE-
T ss_pred             EEEEc
Confidence             5565

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.

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=97.03  E-value=0.00046  Score=59.69  Aligned_cols=71  Identities=21%  Similarity=0.443  Sum_probs=60.8

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCC--------CCCce----EEEEEEcChhHHHHHHHHhCCCeeC
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDT--------GNSKG----YGFCVYQDPAVTDIACAALNGLKMG  220 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~--------~~~~g----~afV~f~~~~~A~~Ai~~l~g~~~~  220 (380)
                      .-||+++||+.....-|+++|+.||.|.+|.|.....+        |.+..    -|+|+|.+--.|.++.+.||+..|+
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            57999999999999999999999999999988775444        22222    3889999999999999999999998


Q ss_pred             CeE
Q 016936          221 DKT  223 (380)
Q Consensus       221 g~~  223 (380)
                      |++
T Consensus       155 gkk  157 (278)
T KOG3152|consen  155 GKK  157 (278)
T ss_pred             CCC
Confidence            875

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=96.83  E-value=0.0054  Score=58.94  Aligned_cols=77  Identities=25%  Similarity=0.349  Sum_probs=62.8

Q ss_pred             CCCEEEEcCCCCCCCH------HHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeC-CeE
Q 016936          151 GPDRVFVGGLPYYFTE------TQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG-DKT  223 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~------~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~-g~~  223 (380)
                      -...|+|.|+|---..      .-|.++|+++|.+....++.+.. |..+|+.|++|.+..+|+.|++.|||+.+. .+.
T Consensus        57 ~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~-ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHt  135 (698)
T KOG2314|consen   57 FDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEE-GGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHT  135 (698)
T ss_pred             cceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCcc-CCeeeEEEEEecChhhHHHHHHhcccceecccce
Confidence            3368999999865332      24678999999999999998865 669999999999999999999999999885 456


Q ss_pred             EEEEE
Q 016936          224 LTVRR  228 (380)
Q Consensus       224 i~v~~  228 (380)
                      ..|..
T Consensus       136 f~v~~  140 (698)
T KOG2314|consen  136 FFVRL  140 (698)
T ss_pred             EEeeh
Confidence            66654

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=96.77  E-value=0.0035  Score=58.25  Aligned_cols=68  Identities=15%  Similarity=0.287  Sum_probs=55.8

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeC---CCC--CC--------CceEEEEEEcChhHHHHHHHHhCCCe
Q 016936          152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKD---RDT--GN--------SKGYGFCVYQDPAVTDIACAALNGLK  218 (380)
Q Consensus       152 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~---~~~--~~--------~~g~afV~f~~~~~A~~Ai~~l~g~~  218 (380)
                      .++|.+.|||.+-..+.|.++|+.+|.|..|+|..=   +.+  +.        .+-||+|+|...+.|.+|.+.++...
T Consensus       231 srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~~e~  310 (484)
T KOG1855|consen  231 SRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLNPEQ  310 (484)
T ss_pred             cceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhchhh
Confidence            479999999999999999999999999999998653   222  22        24579999999999999999886543


Q ss_pred             e
Q 016936          219 M  219 (380)
Q Consensus       219 ~  219 (380)
                      -
T Consensus       311 ~  311 (484)
T KOG1855|consen  311 N  311 (484)
T ss_pred             h
Confidence            3

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

Probab=96.66  E-value=0.0061  Score=53.87  Aligned_cols=64  Identities=16%  Similarity=0.153  Sum_probs=52.6

Q ss_pred             HHHHHHHHhcCCeeEEEEeeCCCCCCC-ceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          167 TQIKELLESFGTLHGFDLVKDRDTGNS-KGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       167 ~~l~~~F~~~G~i~~v~l~~~~~~~~~-~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      +++.+.+++||.|..|.|..++..-.. .---||+|.+.++|.+|+-.|||.+|+|+.++..+..
T Consensus       301 de~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn  365 (378)
T KOG1996|consen  301 DETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYN  365 (378)
T ss_pred             HHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheecc
Confidence            578889999999999988877432111 1137999999999999999999999999999988754

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=96.64  E-value=0.0084  Score=42.94  Aligned_cols=54  Identities=19%  Similarity=0.372  Sum_probs=42.5

Q ss_pred             EEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhC
Q 016936          154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN  215 (380)
Q Consensus       154 ~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~  215 (380)
                      .||--.+|..|...||.++|+.||.| .|.++.+-       -|||.+.+.+.|..|+..++
T Consensus        10 HVFhltFPkeWK~~DI~qlFspfG~I-~VsWi~dT-------SAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen   10 HVFHLTFPKEWKTSDIYQLFSPFGQI-YVSWINDT-------SAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             CEEEEE--TT--HHHHHHHCCCCCCE-EEEEECTT-------EEEEEECCCHHHHHHHHHHT
T ss_pred             eEEEEeCchHhhhhhHHHHhccCCcE-EEEEEcCC-------cEEEEeecHHHHHHHHHHhc
Confidence            56655599999999999999999998 47777652       69999999999999999875

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=96.30  E-value=0.0036  Score=58.14  Aligned_cols=63  Identities=24%  Similarity=0.296  Sum_probs=52.2

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCC-------------------CcEEEEEe
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE-------------------KKFAFVEM   87 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~-------------------~g~afV~f   87 (380)
                      .++.++|+|.+.|||.+-..+.|.++|+.+|.            |..++|.+-                   +-||+|+|
T Consensus       226 ~eel~srtivaenLP~Dh~~enl~kiFg~~G~------------IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEy  293 (484)
T KOG1855|consen  226 EEELPSRTIVAENLPLDHSYENLSKIFGTVGS------------IKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEY  293 (484)
T ss_pred             ccccccceEEEecCCcchHHHHHHHHhhcccc------------eeeeeecCCCCCCcccccCCccchhhhhhhhhhhhh
Confidence            34568999999999999999999999999998            555555432                   46999999


Q ss_pred             CCHHHHHHHHHcCC
Q 016936           88 RTVEEASNAMALDG  101 (380)
Q Consensus        88 ~~~~~a~~ai~l~~  101 (380)
                      ...+.|.+|.++.+
T Consensus       294 e~~~~A~KA~e~~~  307 (484)
T KOG1855|consen  294 EEVEAARKARELLN  307 (484)
T ss_pred             hhhHHHHHHHHhhc
Confidence            99999999996543

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=96.27  E-value=0.024  Score=45.49  Aligned_cols=56  Identities=20%  Similarity=0.367  Sum_probs=44.9

Q ss_pred             HHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccC
Q 016936          168 QIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  232 (380)
Q Consensus       168 ~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~  232 (380)
                      +|.+.|..||.+.=+++..+        .-+|.|.+-.+|-+|+. ++|.++.|+.|.|+..++.
T Consensus        52 ~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals-~dg~~v~g~~l~i~LKtpd  107 (146)
T PF08952_consen   52 ELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALS-LDGIQVNGRTLKIRLKTPD  107 (146)
T ss_dssp             HHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHH-GCCSEETTEEEEEEE----
T ss_pred             HHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHc-cCCcEECCEEEEEEeCCcc
Confidence            77888999998877777654        47899999999999999 6999999999999986543

; PDB: 1UFW_A 2DNR_A.

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=96.20  E-value=0.016  Score=49.08  Aligned_cols=62  Identities=15%  Similarity=0.311  Sum_probs=47.6

Q ss_pred             HHHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHc--CcccCCeEEEEEeccccc
Q 016936          302 LEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALS--GRKFGGNTVNAFYYPEDK  372 (380)
Q Consensus       302 ~~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~--g~~i~gr~l~v~~~~~~~  372 (380)
                      +..|+++|..|+.+.....++.         ++-+.|.|.+.++|.+|.+.|+  +..++|..+++.|+....
T Consensus         9 ~~~l~~l~~~~~~~~~~~~L~s---------FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~~   72 (184)
T PF04847_consen    9 LAELEELFSTYDPPVQFSPLKS---------FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPTP   72 (184)
T ss_dssp             HHHHHHHHHTT-SS-EEEEETT---------TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----SS
T ss_pred             HHHHHHHHHhcCCceEEEEcCC---------CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccccc
Confidence            3689999999999998888763         4578999999999999999999  999999999999996543

Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=96.12  E-value=0.04  Score=37.42  Aligned_cols=54  Identities=19%  Similarity=0.309  Sum_probs=44.4

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhc---CCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHh
Q 016936          153 DRVFVGGLPYYFTETQIKELLESF---GTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL  214 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~---G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l  214 (380)
                      ..|.|.|+. ..+.++|+.+|..|   .....+.++.|.       -|=|.|.+.+.|.+|+.+|
T Consensus         6 eavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    6 EAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             ceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            589999985 47899999999998   235578898774       3779999999999999764

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=96.00  E-value=0.004  Score=54.03  Aligned_cols=66  Identities=21%  Similarity=0.315  Sum_probs=53.4

Q ss_pred             ccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecC--------------C--C--cEEEEEeCCHHH
Q 016936           31 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH--------------E--K--KFAFVEMRTVEE   92 (380)
Q Consensus        31 ~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~--------------~--~--g~afV~f~~~~~   92 (380)
                      ..-.||+++||+.+...-|+++|++||.|            -.+.+-+              +  .  .-|+|+|.+...
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeV------------GRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~Krv  140 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEV------------GRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRV  140 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhcccc------------ceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHH
Confidence            55789999999999999999999999984            3333321              1  1  238999999999


Q ss_pred             HHHHH-HcCCceecCce
Q 016936           93 ASNAM-ALDGIIFEGVA  108 (380)
Q Consensus        93 a~~ai-~l~~~~i~g~~  108 (380)
                      |..+. .||+..|.|++
T Consensus       141 AK~iAe~Lnn~~Iggkk  157 (278)
T KOG3152|consen  141 AKRIAELLNNTPIGGKK  157 (278)
T ss_pred             HHHHHHHhCCCccCCCC
Confidence            99988 79999999965

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=95.96  E-value=0.045  Score=37.17  Aligned_cols=56  Identities=16%  Similarity=0.249  Sum_probs=41.9

Q ss_pred             ccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH
Q 016936           31 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM   97 (380)
Q Consensus        31 ~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai   97 (380)
                      ...+|+|+|+. +++.+||+.+|..|...         .....+.+..+. .|=|.|.+.+.|.+||
T Consensus         4 rpeavhirGvd-~lsT~dI~~y~~~y~~~---------~~~~~IEWIdDt-ScNvvf~d~~~A~~AL   59 (62)
T PF10309_consen    4 RPEAVHIRGVD-ELSTDDIKAYFSEYFDE---------EGPFRIEWIDDT-SCNVVFKDEETAARAL   59 (62)
T ss_pred             eeceEEEEcCC-CCCHHHHHHHHHHhccc---------CCCceEEEecCC-cEEEEECCHHHHHHHH
Confidence            45689999995 89999999999999221         113455655443 3667799999999999

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=95.94  E-value=0.0045  Score=53.87  Aligned_cols=65  Identities=11%  Similarity=0.225  Sum_probs=52.1

Q ss_pred             HHHHHHHH-hcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccC
Q 016936          167 TQIKELLE-SFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  232 (380)
Q Consensus       167 ~~l~~~F~-~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~  232 (380)
                      ++|...|+ +||.|+++.+-.+. ...-.|-++|.|..+++|++|++.||+..+.|++|.+.+....
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl-~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pvT  148 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNL-GDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPVT  148 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhccc-chhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCcC
Confidence            45555566 89999988665542 2345677999999999999999999999999999999986543

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=95.57  E-value=0.011  Score=55.73  Aligned_cols=80  Identities=16%  Similarity=0.167  Sum_probs=68.7

Q ss_pred             chhhhcccceEEEcCCCCcC-cHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHHHcCCce
Q 016936           25 TQQATRHARRVYVGGLPPLA-NEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGII  103 (380)
Q Consensus        25 ~~~~~~~~~~v~V~nLp~~~-t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai~l~~~~  103 (380)
                      +-....+.|.+.+.-.|..+ +..+|..+|.+||.            |.++.+..+.-.|.|.|.+..+|-+|...++..
T Consensus       365 ~g~~~~dhs~l~lek~~~glnt~a~ln~hfA~fG~------------i~n~qv~~~~~~a~vTF~t~aeag~a~~s~~av  432 (526)
T KOG2135|consen  365 PGHAVVDHSPLALEKSPFGLNTIADLNPHFAQFGE------------IENIQVDYSSLHAVVTFKTRAEAGEAYASHGAV  432 (526)
T ss_pred             CcchhcccchhhhhccCCCCchHhhhhhhhhhcCc------------cccccccCchhhheeeeeccccccchhccccce
Confidence            33566788888888888887 78999999999998            666666666677999999999999999999999


Q ss_pred             ecCceEEEecCCC
Q 016936          104 FEGVAVRVRRPTD  116 (380)
Q Consensus       104 i~g~~i~v~~~~~  116 (380)
                      |.++.|+|.|...
T Consensus       433 lnnr~iKl~whnp  445 (526)
T KOG2135|consen  433 LNNRFIKLFWHNP  445 (526)
T ss_pred             ecCceeEEEEecC
Confidence            9999999999665

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=94.85  E-value=0.017  Score=54.45  Aligned_cols=60  Identities=10%  Similarity=0.269  Sum_probs=51.7

Q ss_pred             HHHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEecccc
Q 016936          302 LEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  371 (380)
Q Consensus       302 ~~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~~  371 (380)
                      .++|...|.+||.|+.|.+.....         -|.|.|.+..+|-+|.. .++..|++|.|+|.|....
T Consensus       387 ~a~ln~hfA~fG~i~n~qv~~~~~---------~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~whnps  446 (526)
T KOG2135|consen  387 IADLNPHFAQFGEIENIQVDYSSL---------HAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWHNPS  446 (526)
T ss_pred             HhhhhhhhhhcCccccccccCchh---------hheeeeeccccccchhc-cccceecCceeEEEEecCC
Confidence            469999999999999999965422         34999999999988887 4999999999999998773

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=94.84  E-value=0.02  Score=55.45  Aligned_cols=78  Identities=13%  Similarity=0.149  Sum_probs=63.4

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceec-
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE-  105 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~-  105 (380)
                      .-..+..|+|.||-.-.|.-+|+.++.+-|.+           |...-+-+-|..|||.|.+.++|.... +|||..|- 
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            55778899999999999999999999987764           555544456788999999999999999 89998773 


Q ss_pred             --CceEEEecCCC
Q 016936          106 --GVAVRVRRPTD  116 (380)
Q Consensus       106 --g~~i~v~~~~~  116 (380)
                        .+.|.+.+...
T Consensus       509 sNPK~L~adf~~~  521 (718)
T KOG2416|consen  509 SNPKHLIADFVRA  521 (718)
T ss_pred             CCCceeEeeecch
Confidence              36677776543

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=94.66  E-value=0.016  Score=52.62  Aligned_cols=62  Identities=16%  Similarity=0.270  Sum_probs=50.0

Q ss_pred             HhhcccCCeEEEEecCCC--CCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEeccc
Q 016936          307 EECGKYGTLVNVVIPRPD--QNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPE  370 (380)
Q Consensus       307 ~~f~~~G~I~~v~i~~~~--~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~  370 (380)
                      +.|.+||.|..|.+.++.  ..+....  .-+||.|...++|..||+..+|..+.|+.|+++|.+-
T Consensus        99 eyfgqygki~ki~~~~~~S~~s~~~~~--~s~yITy~~~eda~rci~~v~g~~~dg~~lka~~gtt  162 (327)
T KOG2068|consen   99 EYFGQYGKINKIVKNKDPSSSSSSGGT--CSVYITYEEEEDADRCIDDVDGFVDDGRALKASLGTT  162 (327)
T ss_pred             ccccccccceEEeecCCcccccCCCCC--CcccccccchHhhhhHHHHhhhHHhhhhhhHHhhCCC
Confidence            679999999999998865  2221111  1269999999999999999999999999998888654

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=94.44  E-value=0.14  Score=49.42  Aligned_cols=68  Identities=12%  Similarity=0.152  Sum_probs=55.6

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHh--cCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCC--CeeCCeEEEEE
Q 016936          153 DRVFVGGLPYYFTETQIKELLES--FGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNG--LKMGDKTLTVR  227 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~--~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g--~~~~g~~i~v~  227 (380)
                      +.|.|+-||..+..++++.+|+.  +-.+.+|.+-.+.       -.||.|++..+|+.|...|..  ++|.|++|..+
T Consensus       176 cIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~-------nWyITfesd~DAQqAykylreevk~fqgKpImAR  247 (684)
T KOG2591|consen  176 CIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND-------NWYITFESDTDAQQAYKYLREEVKTFQGKPIMAR  247 (684)
T ss_pred             eEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC-------ceEEEeecchhHHHHHHHHHHHHHhhcCcchhhh
Confidence            46888999999999999999994  7788899886552       389999999999999998753  56777776443

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=94.38  E-value=0.12  Score=45.24  Aligned_cols=95  Identities=18%  Similarity=0.215  Sum_probs=66.4

Q ss_pred             hhHHHHHHHHhCCCeeCCeEEEEEEcccCCCCChhHHHHHHHHHHHHHHHHHHHhhhcCccccCCCCCccCCccceEEEE
Q 016936          204 PAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCL  283 (380)
Q Consensus       204 ~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  283 (380)
                      ..-|..|...|++....++.++|.++..                                               ..+.+
T Consensus         4 rt~ae~ak~eLd~~~~~~~~lr~rfa~~-----------------------------------------------a~l~V   36 (275)
T KOG0115|consen    4 RTLAEIAKRELDGRFPKGRSLRVRFAMH-----------------------------------------------AELYV   36 (275)
T ss_pred             ccHHHHHHHhcCCCCCCCCceEEEeecc-----------------------------------------------ceEEE
Confidence            3457778888999999999999999841                                               22222


Q ss_pred             eccCCcccCCChHHHHHHHHHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccC
Q 016936          284 TEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFG  359 (380)
Q Consensus       284 ~~~~~~~~~~~~~~~~~~~~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~  359 (380)
                      .|..   ..+       ..+.|.+.|+.||.|....+..+...    ++.+-.+|+|...-.|.+|+...+-.-|.
T Consensus        37 ~nl~---~~~-------sndll~~~f~~fg~~e~av~~vD~r~----k~t~eg~v~~~~k~~a~~a~rr~~~~g~~   98 (275)
T KOG0115|consen   37 VNLM---QGA-------SNDLLEQAFRRFGPIERAVAKVDDRG----KPTREGIVEFAKKPNARKAARRCREGGFG   98 (275)
T ss_pred             Eecc---hhh-------hhHHHHHhhhhcCccchheeeecccc----cccccchhhhhcchhHHHHHHHhccCccc
Confidence            2211   111       11578899999999999777665532    22344599999999999999988544443

>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=94.18  E-value=0.66  Score=35.71  Aligned_cols=65  Identities=12%  Similarity=0.181  Sum_probs=47.0

Q ss_pred             EEEEcCCCCCCCHHHHHHHHHhcC-CeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeC
Q 016936          154 RVFVGGLPYYFTETQIKELLESFG-TLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG  220 (380)
Q Consensus       154 ~l~V~nlp~~~t~~~l~~~F~~~G-~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~  220 (380)
                      .+.+...|..++.++|..+.+.+- .|..++++++.  ..++-.+++.|.+.+.|......+||+.+.
T Consensus        15 ~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~--~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fn   80 (110)
T PF07576_consen   15 LCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDG--TPNRYMVLIKFRDQESADEFYEEFNGKPFN   80 (110)
T ss_pred             EEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCC--CCceEEEEEEECCHHHHHHHHHHhCCCccC
Confidence            344444455555566665555544 47788998873  335556999999999999999999998874

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=94.08  E-value=0.19  Score=39.98  Aligned_cols=70  Identities=14%  Similarity=0.188  Sum_probs=52.0

Q ss_pred             CEEEEcCCCCCC----CHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          153 DRVFVGGLPYYF----TETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       153 ~~l~V~nlp~~~----t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      .+|.|+=|....    +...+..-++.||+|.+|.+.-.       ..|.|.|.+..+|-+|+.+++. ...|..+.|.|
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            477776554443    33455566778999999977432       2699999999999999999764 66788888888


Q ss_pred             cc
Q 016936          229 AT  230 (380)
Q Consensus       229 ~~  230 (380)
                      -.
T Consensus       159 qq  160 (166)
T PF15023_consen  159 QQ  160 (166)
T ss_pred             cc
Confidence            53

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=94.07  E-value=0.21  Score=44.64  Aligned_cols=73  Identities=18%  Similarity=0.195  Sum_probs=57.0

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeE-EEEEEcc
Q 016936          152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKT-LTVRRAT  230 (380)
Q Consensus       152 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~-i~v~~~~  230 (380)
                      ...|.|-++|.. .-.-|..+|++||.|.......   +|   .+-.|.|.+.-+|++|+.+ +|+.|+|.. |=|..+.
T Consensus       197 D~WVTVfGFppg-~~s~vL~~F~~cG~Vvkhv~~~---ng---NwMhirYssr~~A~KALsk-ng~ii~g~vmiGVkpCt  268 (350)
T KOG4285|consen  197 DTWVTVFGFPPG-QVSIVLNLFSRCGEVVKHVTPS---NG---NWMHIRYSSRTHAQKALSK-NGTIIDGDVMIGVKPCT  268 (350)
T ss_pred             cceEEEeccCcc-chhHHHHHHHhhCeeeeeecCC---CC---ceEEEEecchhHHHHhhhh-cCeeeccceEEeeeecC
Confidence            467888898876 5567889999999998776542   23   3889999999999999996 999998765 4566665


Q ss_pred             cC
Q 016936          231 AS  232 (380)
Q Consensus       231 ~~  232 (380)
                      ++
T Consensus       269 Dk  270 (350)
T KOG4285|consen  269 DK  270 (350)
T ss_pred             CH
Confidence            44

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=93.90  E-value=0.099  Score=50.92  Aligned_cols=75  Identities=24%  Similarity=0.273  Sum_probs=59.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHh-cCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCee---CCeEEE
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLES-FGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM---GDKTLT  225 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~-~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~---~g~~i~  225 (380)
                      ..++.|+|.||-.-+|.-+|+.++.. .|.|...  +.|+    -+..|||.|.+.++|.....+|||...   +.+.|.
T Consensus       442 ~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~--WmDk----IKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~  515 (718)
T KOG2416|consen  442 EPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF--WMDK----IKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLI  515 (718)
T ss_pred             CccceEeeecccccchHHHHHHHHhhccCchHHH--HHHH----hhcceeEecccHHHHHHHHHHHhccccCCCCCceeE
Confidence            34468999999998999999999994 5666665  3343    245799999999999999999999766   567788


Q ss_pred             EEEcc
Q 016936          226 VRRAT  230 (380)
Q Consensus       226 v~~~~  230 (380)
                      +.|..
T Consensus       516 adf~~  520 (718)
T KOG2416|consen  516 ADFVR  520 (718)
T ss_pred             eeecc
Confidence            87764

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=93.75  E-value=0.41  Score=42.92  Aligned_cols=69  Identities=22%  Similarity=0.337  Sum_probs=54.3

Q ss_pred             cceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHHHcCCceecCce-EE
Q 016936           32 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVA-VR  110 (380)
Q Consensus        32 ~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai~l~~~~i~g~~-i~  110 (380)
                      ..=|-|=++|+.. -.-|..+|.+||.            |++......-.+-+|.|.+..+|.+||..+|+.|.|.. |=
T Consensus       197 D~WVTVfGFppg~-~s~vL~~F~~cG~------------Vvkhv~~~ngNwMhirYssr~~A~KALskng~ii~g~vmiG  263 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQ-VSIVLNLFSRCGE------------VVKHVTPSNGNWMHIRYSSRTHAQKALSKNGTIIDGDVMIG  263 (350)
T ss_pred             cceEEEeccCccc-hhHHHHHHHhhCe------------eeeeecCCCCceEEEEecchhHHHHhhhhcCeeeccceEEe
Confidence            4557777887654 4677889999998            66666665567999999999999999999999999854 44


Q ss_pred             Eec
Q 016936          111 VRR  113 (380)
Q Consensus       111 v~~  113 (380)
                      |..
T Consensus       264 Vkp  266 (350)
T KOG4285|consen  264 VKP  266 (350)
T ss_pred             eee
Confidence            443

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=92.94  E-value=0.47  Score=40.21  Aligned_cols=62  Identities=19%  Similarity=0.263  Sum_probs=45.7

Q ss_pred             CHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhC--CCeeCCeEEEEEEcccC
Q 016936          165 TETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN--GLKMGDKTLTVRRATAS  232 (380)
Q Consensus       165 t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~--g~~~~g~~i~v~~~~~~  232 (380)
                      ..+.|+++|..|+.+..+..++.  -    +-..|.|.+.+.|.+|...|+  +..+.|..++|.++...
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s--F----rRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~   71 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS--F----RRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPT   71 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT--T----TEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----S
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC--C----CEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcccc
Confidence            45789999999999887777654  1    248899999999999999999  89999999999998543

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.

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=92.70  E-value=0.048  Score=49.56  Aligned_cols=80  Identities=18%  Similarity=0.330  Sum_probs=61.9

Q ss_pred             CEEEEcCCCCCCCHHHHH---HHHHhcCCeeEEEEeeCCC--CCC-CceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEE
Q 016936          153 DRVFVGGLPYYFTETQIK---ELLESFGTLHGFDLVKDRD--TGN-SKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  226 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~---~~F~~~G~i~~v~l~~~~~--~~~-~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v  226 (380)
                      +-+||-+|+.....+.+.   ++|.+||.|..+.+.+++.  .+. ...-++|.|...++|..||...+|..+.|+.++.
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lka  157 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALKA  157 (327)
T ss_pred             hhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhHH
Confidence            468999998887766654   5899999999998887652  111 1113899999999999999999999999988777


Q ss_pred             EEcccC
Q 016936          227 RRATAS  232 (380)
Q Consensus       227 ~~~~~~  232 (380)
                      .+...+
T Consensus       158 ~~gttk  163 (327)
T KOG2068|consen  158 SLGTTK  163 (327)
T ss_pred             hhCCCc
Confidence            665544

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=92.41  E-value=0.17  Score=42.67  Aligned_cols=79  Identities=15%  Similarity=0.110  Sum_probs=50.4

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHh-cCCe---eEEEEeeCCC-CC-CCceEEEEEEcChhHHHHHHHHhCCCeeCC-----
Q 016936          153 DRVFVGGLPYYFTETQIKELLES-FGTL---HGFDLVKDRD-TG-NSKGYGFCVYQDPAVTDIACAALNGLKMGD-----  221 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~-~G~i---~~v~l~~~~~-~~-~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g-----  221 (380)
                      ..|.|++||+.+|++++.+.++. ++.-   ..+.-..... .. ..-.-|+|.|.+.+++......++|+.|.+     
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            58999999999999999997776 6655   2333112211 11 123459999999999999999999977732     


Q ss_pred             eEEEEEEccc
Q 016936          222 KTLTVRRATA  231 (380)
Q Consensus       222 ~~i~v~~~~~  231 (380)
                      .+-.|++|..
T Consensus        88 ~~~~VE~Apy   97 (176)
T PF03467_consen   88 YPAVVEFAPY   97 (176)
T ss_dssp             EEEEEEE-SS
T ss_pred             cceeEEEcch
Confidence            3456666543

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.

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=92.40  E-value=0.17  Score=46.00  Aligned_cols=73  Identities=15%  Similarity=0.168  Sum_probs=56.4

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEE------ecCCCcEEEEEeCCHHHHHHHH-HcCCc
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVY------INHEKKFAFVEMRTVEEASNAM-ALDGI  102 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~------~~~~~g~afV~f~~~~~a~~ai-~l~~~  102 (380)
                      -..-.+||+||-+-+|.+||.+.+...|.-.          +.+++      .+.+||||+|..-+.....+.+ -|..+
T Consensus        78 Grk~~~YvGNL~W~TTD~DL~~A~~S~G~~~----------~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k  147 (498)
T KOG4849|consen   78 GRKYCCYVGNLLWYTTDADLLKALQSTGLAQ----------FADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTK  147 (498)
T ss_pred             CceEEEEecceeEEeccHHHHHHHHhhhHHH----------HhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccc
Confidence            3344589999999999999999999888631          33333      3467999999999999888888 57778


Q ss_pred             eecCceEEEe
Q 016936          103 IFEGVAVRVR  112 (380)
Q Consensus       103 ~i~g~~i~v~  112 (380)
                      .|+|..-.|.
T Consensus       148 ~iHGQ~P~V~  157 (498)
T KOG4849|consen  148 TIHGQSPTVL  157 (498)
T ss_pred             eecCCCCeee
Confidence            8998654443

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=92.37  E-value=1.1  Score=32.37  Aligned_cols=41  Identities=15%  Similarity=0.202  Sum_probs=35.3

Q ss_pred             HHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHc
Q 016936          303 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALS  354 (380)
Q Consensus       303 ~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~  354 (380)
                      .||.++|+.||.|.-.-|..           ..|||...+.+.|..|+..+.
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            59999999999998777733           277999999999999998875

; 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.

>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=91.97  E-value=0.075  Score=44.83  Aligned_cols=69  Identities=16%  Similarity=0.229  Sum_probs=42.2

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHH-HHHhccCCCCCCCCeeEEEE--ecC------CCcEEEEEeCCHHHHHHHH-H
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQ-VMTAIGGNSAGPGDAVVNVY--INH------EKKFAFVEMRTVEEASNAM-A   98 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~-~G~i~~~~~~~~~~~i~~~~--~~~------~~g~afV~f~~~~~a~~ai-~   98 (380)
                      .....+|.|++||+.+|++++.+.++. ++....         -..+.  ...      .-.-|||.|.+.+++.... .
T Consensus         4 ~~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~---------w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~   74 (176)
T PF03467_consen    4 EKEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWD---------WYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDR   74 (176)
T ss_dssp             -----EEEEEEE-TTS-HHHHCCCCSS--SSE------------EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHH
T ss_pred             cccCceEEEeCCCCCCCHHHHHHHhhhhcccccc---------eEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHh
Confidence            345669999999999999999886665 322100         12222  111      1246999999999999988 7


Q ss_pred             cCCceecC
Q 016936           99 LDGIIFEG  106 (380)
Q Consensus        99 l~~~~i~g  106 (380)
                      ++|..+.+
T Consensus        75 ~~g~~F~D   82 (176)
T PF03467_consen   75 FDGHVFVD   82 (176)
T ss_dssp             CTTEEEE-
T ss_pred             cCCcEEEC
Confidence            99988755

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes

Probab=91.38  E-value=0.38  Score=33.21  Aligned_cols=51  Identities=22%  Similarity=0.297  Sum_probs=40.7

Q ss_pred             HHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEE
Q 016936          303 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNA  365 (380)
Q Consensus       303 ~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v  365 (380)
                      +|++..+.+|+... |   ....+       |+ ||.|.+..+|+++....+|+.+.+.++..
T Consensus        15 ~d~K~~Lr~y~~~~-I---~~d~t-------Gf-YIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   15 EDFKKRLRKYRWDR-I---RDDRT-------GF-YIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             HHHHHHHhcCCcce-E---EecCC-------EE-EEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            68999999998765 2   22223       44 99999999999999999999988877654

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins []

Probab=90.84  E-value=1.5  Score=31.03  Aligned_cols=59  Identities=24%  Similarity=0.318  Sum_probs=36.9

Q ss_pred             CCCCHHHHHHHHHhcCCe-----eEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          162 YYFTETQIKELLESFGTL-----HGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       162 ~~~t~~~l~~~F~~~G~i-----~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      ..++..+|..++...+.|     -.+++...        |+||+.... .|..++..|++..+.|+++.|+.|
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            457889999999976554     46777543        899988766 699999999999999999999864

; PDB: 2G0C_A 3MOJ_B.

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=90.81  E-value=1.3  Score=42.08  Aligned_cols=68  Identities=18%  Similarity=0.292  Sum_probs=58.1

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcC-CeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCC
Q 016936          152 PDRVFVGGLPYYFTETQIKELLESFG-TLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD  221 (380)
Q Consensus       152 ~~~l~V~nlp~~~t~~~l~~~F~~~G-~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g  221 (380)
                      .+.|+|-.+|...+..||..+...+- .|..++++++..  -++-..+|.|.+.++|......+||+.|..
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            57999999999999999999999765 488999999732  234458999999999999999999998843

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=90.62  E-value=1.1  Score=35.68  Aligned_cols=71  Identities=14%  Similarity=0.133  Sum_probs=51.2

Q ss_pred             hcccceEEEcCCCCcC----cHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCce
Q 016936           29 TRHARRVYVGGLPPLA----NEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGII  103 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~----t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~  103 (380)
                      +.+..||.|+=|...+    +-+.+-..++.||+            |.++.. -++..|.|.|.+..+|=+|+ +++. .
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGp------------I~SVT~-cGrqsavVvF~d~~SAC~Av~Af~s-~  148 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGP------------IQSVTL-CGRQSAVVVFKDITSACKAVSAFQS-R  148 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhcCC------------cceeee-cCCceEEEEehhhHHHHHHHHhhcC-C
Confidence            5677889998777666    33445556666766            566554 37788999999999999999 5554 5


Q ss_pred             ecCceEEEec
Q 016936          104 FEGVAVRVRR  113 (380)
Q Consensus       104 i~g~~i~v~~  113 (380)
                      .-|..++..|
T Consensus       149 ~pgtm~qCsW  158 (166)
T PF15023_consen  149 APGTMFQCSW  158 (166)
T ss_pred             CCCceEEeec
Confidence            5667777766

>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=90.12  E-value=6.8  Score=35.33  Aligned_cols=184  Identities=9%  Similarity=0.079  Sum_probs=104.1

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-------CCCCCceEEEEEEcChhHHHHHHH----HhC--
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDR-------DTGNSKGYGFCVYQDPAVTDIACA----ALN--  215 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~-------~~~~~~g~afV~f~~~~~A~~Ai~----~l~--  215 (380)
                      ....|.|...|+...++...+...|-+||+|++|.++.+.       +........++.|-+.+.+-....    .|.  
T Consensus        12 ~YrTRSLLfeNv~~sidLh~Fl~~fv~~~pIESiYL~~~~~~~~d~~~~d~~~~SilLSFlsr~~CLdFYNnvLQrLsEf   91 (309)
T PF10567_consen   12 EYRTRSLLFENVNNSIDLHSFLTKFVKFGPIESIYLIKSNDKPSDDYNDDKNNQSILLSFLSREICLDFYNNVLQRLSEF   91 (309)
T ss_pred             cceeHHHHHhhccccccHHHHHHHhhccCceeEEEEecCCCcccccccccccceEEEEeeechHHHHHHHHHHHHHHHHH
Confidence            4455789999999999999999999999999999998764       112334568889998887644332    222  


Q ss_pred             CCeeCCeEEEEEEcccCCCCChh-HHHHHHHHHHHHHHHHHHHhhhcCccccCCCCCccCCccceEEEEeccCCcccCCC
Q 016936          216 GLKMGDKTLTVRRATASSGQSKT-EQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALAD  294 (380)
Q Consensus       216 g~~~~g~~i~v~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  294 (380)
                      ...+....+.+.+..-+...... ..+....   +......+.            ........++++.+.-.....   .
T Consensus        92 K~~L~S~~L~lsFV~l~y~~~~~~~~~~~~~---~~~~~~~L~------------~~i~~~gATRSl~IeF~~~~~---~  153 (309)
T PF10567_consen   92 KTKLKSESLTLSFVSLNYQKKTDPNDEEADF---SDYLVASLQ------------YNIINRGATRSLAIEFKDPVD---K  153 (309)
T ss_pred             HHhcCCcceeEEEEEEeccccccccccccch---hhHHhhhhh------------heeecCCcceEEEEEecCccc---h
Confidence            24667788888876643222111 0000000   000000000            011124556666554321111   1


Q ss_pred             hHHHHHHHHHHHHhhccc---CCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHc
Q 016936          295 DEEYEEILEDMREECGKY---GTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALS  354 (380)
Q Consensus       295 ~~~~~~~~~~L~~~f~~~---G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~  354 (380)
                      +.   .+...|.-+...-   -.+++|.++...+... .=|..+|.+.|-+...|...++-|.
T Consensus       154 ~d---l~~~kL~fL~~~~n~RYVlEsIDlVna~~~~~-~Fp~~YaILtFlnIsMAiEV~dYlk  212 (309)
T PF10567_consen  154 DD---LIEKKLPFLKNSNNKRYVLESIDLVNADEPSK-HFPKNYAILTFLNISMAIEVLDYLK  212 (309)
T ss_pred             hH---HHHHhhhhhccCCCceEEEEEEEEeccCcccc-cCCcceEEEeehhHHhHHHHHHHHH
Confidence            11   1223342222221   3577777776433211 1123478999999999999998776

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.

>PF07292 NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909 This entry represents a domain of approximately 90 residues that is tandemly repeated within interferon-induced 35 kDa protein (IFP 35) and the homologous N-myc-interactor (Nmi)

Probab=89.83  E-value=0.47  Score=34.78  Aligned_cols=70  Identities=20%  Similarity=0.236  Sum_probs=44.1

Q ss_pred             EEEEeCCHHHHHHHHHc--CCceecCceEEEe--cCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEc
Q 016936           83 AFVEMRTVEEASNAMAL--DGIIFEGVAVRVR--RPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVG  158 (380)
Q Consensus        83 afV~f~~~~~a~~ai~l--~~~~i~g~~i~v~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~  158 (380)
                      |+|.|.+..-|++.+.+  +...+.+..+.|.  +..........-                      ...-++++|.|.
T Consensus         1 AlITF~e~~VA~~i~~~~~~~v~l~~~~~~V~v~P~~~~~~~k~qv----------------------~~~vs~rtVlvs   58 (88)
T PF07292_consen    1 ALITFEEEGVAQRILKKKKHPVPLEDCCVRVKVSPVTLGHLQKFQV----------------------FSGVSKRTVLVS   58 (88)
T ss_pred             CEEEeCcHHHHHHHHhCCEEEEEECCEEEEEEEEeEecCCceEEEE----------------------EEcccCCEEEEe
Confidence            68999999999998853  3344666554443  322211110000                      002334799999


Q ss_pred             CCCCCCCHHHHHHHHH
Q 016936          159 GLPYYFTETQIKELLE  174 (380)
Q Consensus       159 nlp~~~t~~~l~~~F~  174 (380)
                      |||...++++|++..+
T Consensus        59 gip~~l~ee~l~D~Le   74 (88)
T PF07292_consen   59 GIPDVLDEEELRDKLE   74 (88)
T ss_pred             CCCCCCChhhheeeEE
Confidence            9999999999877654

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=87.95  E-value=0.43  Score=47.33  Aligned_cols=71  Identities=17%  Similarity=0.160  Sum_probs=57.4

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceec
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE  105 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~  105 (380)
                      ++-.+.-+|||+|+...+..+-++.....+|.            |.++..   --|+|..|.....+..|+ .++...+.
T Consensus        35 ~~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~------------v~s~kr---~~fgf~~f~~~~~~~ra~r~~t~~~~~   99 (668)
T KOG2253|consen   35 QPLPPRDTVFVGNISYLVSQEFWKSILAKSGF------------VPSWKR---DKFGFCEFLKHIGDLRASRLLTELNID   99 (668)
T ss_pred             cCCCCCceeEecchhhhhhHHHHHHHHhhCCc------------chhhhh---hhhcccchhhHHHHHHHHHHhcccCCC
Confidence            45567789999999999999999999999987            344332   229999999999999999 67778888


Q ss_pred             CceEEEe
Q 016936          106 GVAVRVR  112 (380)
Q Consensus       106 g~~i~v~  112 (380)
                      |.++.+.
T Consensus       100 ~~kl~~~  106 (668)
T KOG2253|consen  100 DQKLIEN  106 (668)
T ss_pred             cchhhcc
Confidence            8776664

>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=87.15  E-value=1.8  Score=30.69  Aligned_cols=53  Identities=19%  Similarity=0.129  Sum_probs=31.1

Q ss_pred             HHHHhhcccC-----CeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEec
Q 016936          304 DMREECGKYG-----TLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYY  368 (380)
Q Consensus       304 ~L~~~f~~~G-----~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~  368 (380)
                      +|..++..-+     .|-.|.+...           ++||+-. .+.|..+++.|++..+.|++|+|+.|
T Consensus        17 ~iv~~i~~~~gi~~~~IG~I~I~~~-----------~S~vev~-~~~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   17 DIVGAICNEAGIPGRDIGRIDIFDN-----------FSFVEVP-EEVAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             HHHHHHHTCTTB-GGGEEEEEE-SS------------EEEEE--TT-HHHHHHHHTT--SSS----EEE-
T ss_pred             HHHHHHHhccCCCHHhEEEEEEeee-----------EEEEEEC-HHHHHHHHHHhcCCCCCCeeEEEEEC
Confidence            5555555443     4667777542           6688866 56899999999999999999999864

; PDB: 2G0C_A 3MOJ_B.

>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=85.53  E-value=3.2  Score=28.66  Aligned_cols=54  Identities=11%  Similarity=0.140  Sum_probs=41.2

Q ss_pred             cCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecCceEEE
Q 016936           43 LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV  111 (380)
Q Consensus        43 ~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g~~i~v  111 (380)
                      .++-+|++..++.|+-             ..+.  .++-=-||.|.+.++|++|. .-+++.+.+..+.+
T Consensus        11 ~~~v~d~K~~Lr~y~~-------------~~I~--~d~tGfYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRW-------------DRIR--DDRTGFYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCCc-------------ceEE--ecCCEEEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            5788999999999963             3332  23333589999999999999 78888888877655

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=84.94  E-value=6.9  Score=30.13  Aligned_cols=62  Identities=11%  Similarity=0.176  Sum_probs=44.6

Q ss_pred             HHHHhhccc-CCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCC---eEEEEEeccc
Q 016936          304 DMREECGKY-GTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGG---NTVNAFYYPE  370 (380)
Q Consensus       304 ~L~~~f~~~-G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~g---r~l~v~~~~~  370 (380)
                      +|..+.+.+ ..|..+++.++....+     =.+.++|.+.++|..=....||+.|..   ...+|-|...
T Consensus        29 ~l~~f~~~~~~~i~~~riird~~pnr-----ymVLikF~~~~~Ad~Fy~~fNGk~FnslEpE~ChvvfV~~   94 (110)
T PF07576_consen   29 FLLFFGAPFREDIEHIRIIRDGTPNR-----YMVLIKFRDQESADEFYEEFNGKPFNSLEPETCHVVFVKS   94 (110)
T ss_pred             HHHHhhhcccccEEEEEEeeCCCCce-----EEEEEEECCHHHHHHHHHHhCCCccCCCCCceeEEEEEEE
Confidence            565555555 4677888888654332     247999999999999999999998754   5566655544

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=84.27  E-value=0.78  Score=46.85  Aligned_cols=74  Identities=14%  Similarity=0.174  Sum_probs=59.3

Q ss_pred             EEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCee--CCeEEEEEEccc
Q 016936          154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM--GDKTLTVRRATA  231 (380)
Q Consensus       154 ~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~--~g~~i~v~~~~~  231 (380)
                      +.++.|.+-..+---|..+|++||.+.+...+++-+      .|.|.|.+.+.|..|.++++|+++  -|-+.+|.+++.
T Consensus       300 ~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~N------~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~  373 (1007)
T KOG4574|consen  300 KQSLENNAVNLTSSSLATLCSDYGSVASAWTLRDLN------MALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKT  373 (1007)
T ss_pred             hhhhhcccccchHHHHHHHHHhhcchhhheeccccc------chhhhhHHHHHHHHhhhhhcCCcccccCCceeEEeccc
Confidence            344555555666678899999999999988877743      799999999999999999999866  677788888766


Q ss_pred             CC
Q 016936          232 SS  233 (380)
Q Consensus       232 ~~  233 (380)
                      -.
T Consensus       374 ~~  375 (1007)
T KOG4574|consen  374 LP  375 (1007)
T ss_pred             cc
Confidence            44

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=83.28  E-value=1.3  Score=45.43  Aligned_cols=70  Identities=23%  Similarity=0.252  Sum_probs=58.1

Q ss_pred             eEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCcee--cCceEE
Q 016936           34 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIF--EGVAVR  110 (380)
Q Consensus        34 ~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i--~g~~i~  110 (380)
                      +.++.|.+-..+...|..+|++||.            +.+..+.++...|.|+|.+.+.|..|+ +++|+.+  -|.+.+
T Consensus       300 ~~~~~nn~v~~tSssL~~l~s~yg~------------v~s~wtlr~~N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~  367 (1007)
T KOG4574|consen  300 KQSLENNAVNLTSSSLATLCSDYGS------------VASAWTLRDLNMALVSFSSVESAILALDALQGKEVSVTGAPSR  367 (1007)
T ss_pred             hhhhhcccccchHHHHHHHHHhhcc------------hhhheecccccchhhhhHHHHHHHHhhhhhcCCcccccCCcee
Confidence            3455577778899999999999998            677777778889999999999999999 8999774  567788


Q ss_pred             EecCC
Q 016936          111 VRRPT  115 (380)
Q Consensus       111 v~~~~  115 (380)
                      |..++
T Consensus       368 V~~ak  372 (1007)
T KOG4574|consen  368 VSFAK  372 (1007)
T ss_pred             EEecc
Confidence            87654

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	380
2yh0_A	198	Solution Structure Of The Closed Conformation Of Hu		2e-44
2g4b_A	172	Structure Of U2af65 Variant With Polyuridine Tract		1e-42
3vaf_A	174	Structure Of U2af65 Variant With Bru3 Dna Length =		2e-42
2u2f_A	85	Solution Structure Of The Second Rna-Binding Domain		3e-20
1u2f_A	90	Solution Structure Of The First Rna-Binding Domain		4e-19
2hzc_A	87	Crystal Structure Of The N-terminal Rrm Of The U2af		8e-17
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		2e-12
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		4e-10
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		8e-10
4fxw_A	106	Structure Of Phosphorylated Sf1 Complex With U2af65		9e-10
3v4m_A	105	Crystal Structure Of A Rna Binding Domain Of A U2 S		9e-10
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
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		1e-09
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		3e-09
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		3e-09
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		7e-06
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		5e-09
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		8e-09
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		2e-08
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		3e-08
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		1e-07
2ki2_A	90	Solution Structure Of Ss-Dna Binding Protein 12rnp2		3e-07
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		6e-07
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		6e-07
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		7e-07
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		2e-06
2x1a_A	97	Structure Of Rna15 Rrm With Rna Bound (G) Length =		2e-06
2khc_A	118	Bruno Rrm3+ Length = 118		2e-06
2dgv_A	92	Solution Structure Of The Rna Binding Domain In Het		4e-06
2dh9_A	89	Solution Structure Of The C-Terminal Rna Binding Do		4e-06
2cpz_A	115	Solution Structure Of Rna Binding Domain 3 In Cug T		7e-06
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		7e-06
2x1f_A	96	Structure Of Rna15 Rrm With Bound Rna (Gu) Length =		7e-06
2km8_B	84	Interdomain Rrm Packing Contributes To Rna Recognit		8e-06
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		9e-06
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		1e-05
4fxv_A	99	Crystal Structure Of An Elav-Like Protein 1 (Elavl1		1e-05
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		2e-05
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		2e-05
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		2e-05
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		2e-05
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		3e-05
3vf0_B	285	Raver1 In Complex With Metavinculin L954 Deletion M		4e-05
3h2u_B	283	Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Comple		4e-05
3smz_A	284	Human Raver1 Rrm1-3 Domains (Residues 39-320) Lengt		4e-05
2xs2_A	102	Crystal Structure Of The Rrm Domain Of Mouse Delete		4e-05
3dxb_A	222	Structure Of The Uhm Domain Of Puf60 Fused To Thior		4e-05
2dgs_A	99	Solution Structure Of The Second Rna Binding Domain		5e-05
2xs5_A	87	Crystal Structure Of The Rrm Domain Of Mouse Delete		6e-05
1x5t_A	96	Solution Structure Of The Second Rrm Domain In Spli		6e-05
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		1e-04
2xsf_A	89	Crystal Structure Of The Rrm Domain Of Mouse Delete		1e-04
3sde_B	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		2e-04
3ue2_A	118	Crystal Structure Of A Rna Binding Domain Of Poly-U		2e-04
2dny_A	119	Solution Structure Of The Third Rna Binding Domain		4e-04
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		5e-04
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		7e-04
2dgp_A	106	Solution Structure Of The N-Terminal Rna Binding Do		8e-04
2cqg_A	103	Solution Structure Of The Rna Binding Domain Of Tar		8e-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 = 94/199 (47%), Positives = 129/199 (64%), Gaps = 10/199 (5%)
Query: 32  ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 91
           ARR+YVG +P    E+A+  FF+  M  +GG +  PG+ V+ V IN +K FAF+E R+V+
Sbjct: 4   ARRLYVGNIPFGITEEAMMDFFNAQMR-LGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 62
Query: 92  EASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEG 151
           E + AMA DGIIF+G ++++RRP DY P       PG  S N ++   G+ S  +   + 
Sbjct: 63  ETTQAMAFDGIIFQGQSLKIRRPHDYQPL------PGM-SENPSVYVPGVVSTVV--PDS 113
Query: 152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 211
             ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG SKGY FC Y D  VTD A 
Sbjct: 114 AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 173
Query: 212 AALNGLKMGDKTLTVRRAT 230
           A LNG+++GDK L V+RA+
Sbjct: 174 AGLNGMQLGDKKLLVQRAS 192

>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract Length = 172

Iteration: 1
 Score =  170 bits (430), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 91/199 (45%), Positives = 121/199 (60%), Gaps = 30/199 (15%)
Query: 32  ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 91
           ARR+YVG +P    E+A+  FF+  M  +GG +  PG+ V+ V IN +K FAF+E R+V+
Sbjct: 4   ARRLYVGNIPFGITEEAMMDFFNAQMR-LGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 62
Query: 92  EASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEG 151
           E + AMA DGIIF+G ++++RRP DY           QP P                  G
Sbjct: 63  ETTQAMAFDGIIFQGQSLKIRRPHDY-----------QPLP------------------G 93
Query: 152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 211
             ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG SKGY FC Y D  VTD A 
Sbjct: 94  AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 153
Query: 212 AALNGLKMGDKTLTVRRAT 230
           A LNG+++GDK L V+RA+
Sbjct: 154 AGLNGMQLGDKKLLVQRAS 172

>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna Length = 174

Iteration: 1
 Score =  169 bits (429), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 91/199 (45%), Positives = 121/199 (60%), Gaps = 30/199 (15%)
Query: 32  ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 91
           ARR+YVG +P    E+A+  FF+  M  +GG +  PG+ V+ V IN +K FAF+E R+V+
Sbjct: 6   ARRLYVGNIPFGITEEAMMDFFNAQMR-LGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 64
Query: 92  EASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEG 151
           E + AMA DGIIF+G ++++RRP DY           QP P                  G
Sbjct: 65  ETTQAMAFDGIIFQGQSLKIRRPHDY-----------QPLP------------------G 95
Query: 152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 211
             ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG SKGY FC Y D  VTD A 
Sbjct: 96  AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 155
Query: 212 AALNGLKMGDKTLTVRRAT 230
           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 = 95.9 bits (237), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 45/77 (58%), Positives = 56/77 (72%)
Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG SKGY FC Y D  VTD A A 
Sbjct: 3   KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62
Query: 214 LNGLKMGDKTLTVRRAT 230
           LNG+++GDK L V+RA+
Sbjct: 63  LNGMQLGDKKLLVQRAS 79

>pdb|1U2F|A Chain A, Solution Structure Of The First Rna-Binding Domain Of Hu2af65 Length = 90

Iteration: 1
 Score = 92.4 bits (228), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 43/88 (48%), Positives = 62/88 (70%), Gaps = 1/88 (1%)
Query: 32  ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 91
           ARR+YVG +P    E+A+  FF+  M  +GG +  PG+ V+ V IN +K FAF+E R+V+
Sbjct: 1   ARRLYVGNIPFGITEEAMMDFFNAQMR-LGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 59
Query: 92  EASNAMALDGIIFEGVAVRVRRPTDYNP 119
           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 = 8e-17,   Method: Compositional matrix adjust.
 Identities = 40/83 (48%), Positives = 59/83 (71%), Gaps = 1/83 (1%)
Query: 32  ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 91
           ARR+YVG +P    E+A+  FF+  M  +GG +  PG+ V+ V IN +K FAF+E R+V+
Sbjct: 6   ARRLYVGNIPFGITEEAMMDFFNAQMR-LGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 64
Query: 92  EASNAMALDGIIFEGVAVRVRRP 114
           E + AMA DGIIF+G ++++RRP
Sbjct: 65  ETTQAMAFDGIIFQGQSLKIRRP 87

>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage Stimulation Factor 64 Kda Subunit Length = 104

Iteration: 1
 Score = 69.7 bits (169), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 38/88 (43%), Positives = 50/88 (56%), Gaps = 2/88 (2%)
Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           VFVG +PY  TE Q+K++    G +  F LV DR+TG  KGYGFC YQD      A   L
Sbjct: 11  VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 215 NGLKMGDKTLTVRRATASSGQSKTEQES 242
           NG +   + L V    A+S ++K E +S
Sbjct: 71  NGREFSGRALRV--DNAASEKNKEELKS 96

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 62.4 bits (150), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 34/79 (43%), Positives = 42/79 (53%)
Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           + V  LP   T+ + K L  S G +    LV+D+ TG S GYGF  Y DP   D A   L
Sbjct: 7   LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 215 NGLKMGDKTLTVRRATASS 233
           NGLK+  KT+ V  A  SS
Sbjct: 67  NGLKLQTKTIKVSYARPSS 85

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 61.2 bits (147), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 29/83 (34%), Positives = 44/83 (53%)
Query: 148 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 207
           G+ GP R++VG L +  TE  ++ + E FG +    L+ D +TG SKGYGF  + D    
Sbjct: 22  GSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECA 81
Query: 208 DIACAALNGLKMGDKTLTVRRAT 230
             A   LNG ++  + + V   T
Sbjct: 82  KKALEQLNGFELAGRPMKVGHVT 104

>pdb|4FXW|A Chain A, Structure Of Phosphorylated Sf1 Complex With U2af65-uhm Domain Length = 106

Iteration: 1
 Score = 61.2 bits (147), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 28/70 (40%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 309 CGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYY 368
           C KYG + ++ IPRP  +G E PG GK+F+E+     C  A   L+GRKF    V   Y 
Sbjct: 37  CSKYGLVKSIEIPRP-VDGVEVPGCGKIFVEFTSVFDCQKAXQGLTGRKFANRVVVTKYC 95
Query: 369 PEDKYFNKDY 378
             D Y  +D+
Sbjct: 96  DPDSYHRRDF 105

>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 = 9e-10,   Method: Composition-based stats.
 Identities = 28/70 (40%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 309 CGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYY 368
           C KYG + ++ IPRP  +G E PG GK+F+E+     C  A   L+GRKF    V   Y 
Sbjct: 36  CSKYGLVKSIEIPRP-VDGVEVPGCGKIFVEFTSVFDCQKAXQGLTGRKFANRVVVTKYC 94
Query: 369 PEDKYFNKDY 378
             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: 309 CGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYY 368
           C KYG + ++ IPRP  +G E PG GK+F+E+     C  A   L+GRKF    V   Y 
Sbjct: 35  CSKYGLVKSIEIPRP-VDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYC 93
Query: 369 PEDKYFNKDY 378
             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: 309 CGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYY 368
           C KYG + ++ IPRP  +G E PG GK+F+E+     C  A   L+GRKF    V   Y 
Sbjct: 35  CSKYGLVKSIEIPRP-VDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYC 93
Query: 369 PEDKYFNKDY 378
             D Y  +D+
Sbjct: 94  DPDSYHRRDF 103

>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1) Of Hu Antigen C (Huc) Length = 89

Iteration: 1
 Score = 60.8 bits (146), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 34/80 (42%), Positives = 42/80 (52%)
Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           + V  LP   T+ + K L  S G +    LV+D+ TG S GYGF  Y DP   D A   L
Sbjct: 7   LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 215 NGLKMGDKTLTVRRATASSG 234
           NGLK+  KT+ V  A  SS 
Sbjct: 67  NGLKLQTKTIKVSYARPSSA 86

>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna- Binding Region Containing Protein 1 Length = 116

Iteration: 1
 Score = 59.3 bits (142), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 27/69 (39%), Positives = 40/69 (57%)
Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           ++FVGGLPY+ T+  +++  E FG +    ++ DR TG S+GYGF    D A  + AC  
Sbjct: 19  KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 214 LNGLKMGDK 222
            N +  G K
Sbjct: 79  PNPIIDGRK 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 = 3e-09,   Method: Compositional matrix adjust.
 Identities = 43/159 (27%), Positives = 74/159 (46%), Gaps = 20/159 (12%)
Query: 73  NVYINHEKKFAFVEMRTVEEASNAMA-LDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPS 131
           +V + H K FAFVE    E A  A+  ++ ++  G  ++V RP++           GQ  
Sbjct: 64  SVTMKH-KGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNI----------GQAQ 112
Query: 132 PNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTG 191
           P ++  A          A   +R++V  +    ++  IK + E+FG +    L +D  TG
Sbjct: 113 PIIDQLA--------EEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTG 164
Query: 192 NSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT 230
             KGYGF  Y+    +  A +++N   +G + L V +A 
Sbjct: 165 KHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAV 203

>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To Ssdna From A Portion Of Fuse Length = 216

Iteration: 1
 Score = 48.5 bits (114), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 22/77 (28%), Positives = 37/77 (48%)
Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           RV+VG + Y   E  I++    FG +   D+  D  T   KG+ F  Y+ P    +A   
Sbjct: 30  RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 89
Query: 214 LNGLKMGDKTLTVRRAT 230
           +N + +G + + V R +
Sbjct: 90  MNSVMLGGRNIKVGRPS 106

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 58.9 bits (141), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 53/202 (26%), Positives = 88/202 (43%), Gaps = 33/202 (16%)
Query: 34  RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVV----NVYINHEKKFAFVEMRT 89
           RVYVG +     E  I   F+           GP  ++     +V + H K FAFVE   
Sbjct: 15  RVYVGSIYYELGEDTIRQAFAPF---------GPIKSIDMSWDSVTMKH-KGFAFVEYEV 64
Query: 90  VEEASNAMA-LDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGG 148
            E A  A+  ++ ++  G  ++V RP++           GQ  P ++  A          
Sbjct: 65  PEAAQLALEQMNSVMLGGRNIKVGRPSNI----------GQAQPIIDQLA--------EE 106
Query: 149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 208
           A   +R++V  +    ++  IK + E+FG +    L +D  TG  KGYGF  Y+    + 
Sbjct: 107 ARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQ 166
Query: 209 IACAALNGLKMGDKTLTVRRAT 230
            A +++N   +G + L V +A 
Sbjct: 167 DAVSSMNLFDLGGQYLRVGKAV 188

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 58.2 bits (139), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 31/79 (39%), Positives = 42/79 (53%)
Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           + V  LP   T+ + + L  S G +    LV+D+ TG S GYGF  Y DP   + A   L
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 215 NGLKMGDKTLTVRRATASS 233
           NGL++  KT+ V  A  SS
Sbjct: 65  NGLRLQTKTIKVSYARPSS 83

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 57.0 bits (136), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 29/83 (34%), Positives = 43/83 (51%)
Query: 148 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 207
           G+ G   ++VG L +  TE  ++ + E FG +    L+KD DTG SKGYGF  + D    
Sbjct: 1   GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60
Query: 208 DIACAALNGLKMGDKTLTVRRAT 230
             A   LNG ++  + + V   T
Sbjct: 61  RRALEQLNGFELAGRPMRVGHVT 83

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 56.2 bits (134), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 29/83 (34%), Positives = 45/83 (54%), Gaps = 2/83 (2%)
Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           + V  +P    E Q+++L E +G +    +V DR+T  S+GYGF  +Q  +    A A L
Sbjct: 45  LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
Query: 215 NGLKMGDKTLTVRRATASSGQSK 237
           NG  + +K L V  A A+SG  +
Sbjct: 105 NGFNILNKRLKV--ALAASGHQR 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 = 54.3 bits (129), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 51/200 (25%), Positives = 82/200 (41%), Gaps = 29/200 (14%)
Query: 34  RVYVGGLPPLANEQAIATFFSQV--MTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 91
           RVYVG +     E  I   F+    + +I        D   +      K FAFVE    E
Sbjct: 14  RVYVGSIYYELGEDTIRQAFAPFGPIKSI--------DXSWDSVTXKHKGFAFVEYEVPE 65
Query: 92  EASNAMA-LDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAE 150
            A  A+   + +   G  ++V RP++           GQ  P ++  A          A 
Sbjct: 66  AAQLALEQXNSVXLGGRNIKVGRPSNI----------GQAQPIIDQLA--------EEAR 107
Query: 151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA 210
             +R++V  +    ++  IK + E+FG +    L +D  TG  KGYGF  Y+    +  A
Sbjct: 108 AFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDA 167
Query: 211 CAALNGLKMGDKTLTVRRAT 230
            ++ N   +G + L V +A 
Sbjct: 168 VSSXNLFDLGGQYLRVGKAV 187

>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 = 52.8 bits (125), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 27/75 (36%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           ++VG L Y  T  Q+KEL   FG +    L+ DR+T   KG+GF   Q+ +V++ A A L
Sbjct: 4   IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSE-AIAKL 62
Query: 215 NGLKMGDKTLTVRRA 229
           +      +T+ V  A
Sbjct: 63  DNTDFMGRTIRVTEA 77

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 52.0 bits (123), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 28/83 (33%), Positives = 42/83 (50%)
Query: 151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA 210
           G   + V  LP   T+ +++ L  S G +    L++D+  G+S GYGF  Y      + A
Sbjct: 1   GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 211 CAALNGLKMGDKTLTVRRATASS 233
              LNGL++  KT+ V  A  SS
Sbjct: 61  INTLNGLRLQSKTIKVSYARPSS 83

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 52.0 bits (123), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 28/83 (33%), Positives = 42/83 (50%)
Query: 151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA 210
           G   + V  LP   T+ +++ L  S G +    L++D+  G+S GYGF  Y      + A
Sbjct: 1   GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 211 CAALNGLKMGDKTLTVRRATASS 233
              LNGL++  KT+ V  A  SS
Sbjct: 61  INTLNGLRLQSKTIKVSYARPSS 83

>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 = 7e-07,   Method: Compositional matrix adjust.
 Identities = 29/84 (34%), Positives = 43/84 (51%), Gaps = 2/84 (2%)
Query: 151 GPDR--VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 208
           GP R  + V  LP   T+ +++ L  S G +    L++D+  G+S GYGF  Y      +
Sbjct: 1   GPGRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAE 60
Query: 209 IACAALNGLKMGDKTLTVRRATAS 232
            A   LNGL++  KT+ V  A  S
Sbjct: 61  RAINTLNGLRLQSKTIKVSYARPS 84

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/80 (30%), Positives = 45/80 (56%)
Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           ++FVGGL +   E  ++++   +G +    +VKDR+T  S+G+GF  +++      A  A
Sbjct: 14  KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 214 LNGLKMGDKTLTVRRATASS 233
           +NG  +  + + V +A  SS
Sbjct: 74  MNGKSVDGRQIRVDQAGKSS 93

>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G) Length = 97

Iteration: 1
 Score = 50.1 bits (118), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 28/75 (37%), Positives = 42/75 (56%), Gaps = 1/75 (1%)
Query: 151 GPDRV-FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 209
           GP RV ++G +PY  TE QI +L  + G +    ++ D  TG SKGY F  ++D   +  
Sbjct: 1   GPSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSAS 60
Query: 210 ACAALNGLKMGDKTL 224
           A   LNG ++G + L
Sbjct: 61  AVRNLNGYQLGSRFL 75

>pdb|2KHC|A Chain A, Bruno Rrm3+ Length = 118

Iteration: 1
 Score = 50.1 bits (118), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 26/80 (32%), Positives = 42/80 (52%), Gaps = 2/80 (2%)
Query: 150 EGPD--RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 207
           EGP+   +F+  LP  FT+T +      FG +    +  D+ T  SK +GF  + +P   
Sbjct: 36  EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSA 95
Query: 208 DIACAALNGLKMGDKTLTVR 227
            +A  A+NG ++G K L V+
Sbjct: 96  QVAIKAMNGFQVGTKRLKVQ 115

>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein M Length = 92

Iteration: 1
 Score = 49.3 bits (116), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 28/89 (31%), Positives = 46/89 (51%), Gaps = 2/89 (2%)
Query: 148 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 207
           G+ G  ++FV  LP+ FT   +K+     G +   D+    + G SKG G   ++ P V 
Sbjct: 4   GSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADI--KMENGKSKGCGVVKFESPEVA 61
Query: 208 DIACAALNGLKMGDKTLTVRRATASSGQS 236
           + AC  +NG+K+  + + VR    +SG S
Sbjct: 62  ERACRMMNGMKLSGREIDVRIDRNASGPS 90

>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein M Length = 89

Iteration: 1
 Score = 48.9 bits (115), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 28/89 (31%), Positives = 45/89 (50%), Gaps = 2/89 (2%)
Query: 148 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 207
           G+ G   +FV  LP+ FT   +K+     G +   D+    + G SKG G   ++ P V 
Sbjct: 1   GSSGSSGIFVRNLPFDFTWKMLKDKFNECGHVLYADI--KMENGKSKGCGVVKFESPEVA 58
Query: 208 DIACAALNGLKMGDKTLTVRRATASSGQS 236
           + AC  +NG+K+  + + VR    +SG S
Sbjct: 59  ERACRMMNGMKLSGREIDVRIDRNASGPS 87

>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet Repeat Rna-Binding Protein 1 Length = 115

Iteration: 1
 Score = 48.5 bits (114), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 29/94 (30%), Positives = 47/94 (50%), Gaps = 6/94 (6%)
Query: 140 GLASGAIGGA----EGPD--RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNS 193
           GL   +IG A    EGP+   +F+  LP  F +  + ++   FG +    +  D+ T  S
Sbjct: 7   GLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLS 66
Query: 194 KGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR 227
           K +GF  Y +P     A  ++NG ++G K L V+
Sbjct: 67  KCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQ 100

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 48.5 bits (114), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 26/85 (30%), Positives = 44/85 (51%), Gaps = 2/85 (2%)
Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           ++F+GGL +  TE  ++E    +GT+    ++KD  TG S+G+GF  ++ P+  D     
Sbjct: 5   KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 214 LNGLKMGDKTLTVRRATASSGQSKT 238
            + L    K +  +RA     Q KT
Sbjct: 65  QHIL--DGKVIDPKRAIPRDEQDKT 87

>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu) Length = 96

Iteration: 1
 Score = 48.5 bits (114), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 41/74 (55%), Gaps = 1/74 (1%)
Query: 152 PDRV-FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA 210
           P RV ++G +PY  TE QI +L  + G +    ++ D  TG SKGY F  ++D   +  A
Sbjct: 1   PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60
Query: 211 CAALNGLKMGDKTL 224
              LNG ++G + L
Sbjct: 61  VRNLNGYQLGSRFL 74

>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In The Rna15, Hrp1, Anchor Rna 3' Processing Ternary Complex Length = 84

Iteration: 1
 Score = 48.1 bits (113), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 41/74 (55%), Gaps = 1/74 (1%)
Query: 152 PDRV-FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA 210
           P RV ++G +PY  TE QI +L  + G +    ++ D  TG SKGY F  ++D   +  A
Sbjct: 3   PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 62
Query: 211 CAALNGLKMGDKTL 224
              LNG ++G + L
Sbjct: 63  VRNLNGYQLGSRFL 76

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 47.8 bits (112), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 28/88 (31%), Positives = 45/88 (51%), Gaps = 1/88 (1%)
Query: 149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 208
           A+ P ++F+GGL     E  +K +    G +    L+KDR T  S+G+ F  +++PA   
Sbjct: 4   ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAK 62
Query: 209 IACAALNGLKMGDKTLTVRRATASSGQS 236
            A   +NG  +  K + V +A   S QS
Sbjct: 63  NAAKDMNGKSLHGKAIKVEQAKKPSFQS 90

>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 = 47.4 bits (111), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 42/184 (22%), Positives = 73/184 (39%), Gaps = 45/184 (24%)
Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK--FAFVEMRTV 90
           R++++GGL     ++++ + F Q  T          D VV    N ++   F FV   TV
Sbjct: 15  RKLFIGGLSFETTDESLRSHFEQWGTLT--------DCVVMRDPNTKRSRGFGFVTYATV 66
Query: 91  EEASNAM-----ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQ-PSPNLNLAAVGLASG 144
           EE   AM      +DG + E             P  A +    Q P  +L +        
Sbjct: 67  EEVDAAMNARPHKVDGRVVE-------------PKRAVSREDSQRPGAHLTVK------- 106
Query: 145 AIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP 204
                    ++FVGG+     E  +++  E +G +   +++ DR +G  +G+ F  + D 
Sbjct: 107 ---------KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH 157
Query: 205 AVTD 208
              D
Sbjct: 158 DSVD 161

>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 = 1e-05,   Method: Composition-based stats.
 Identities = 26/78 (33%), Positives = 40/78 (51%)
Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           + V  LP   T+ +++ L  S G +    L++D+  G+S GYGF  Y      + A   L
Sbjct: 22  LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 81
Query: 215 NGLKMGDKTLTVRRATAS 232
           NGL++  KT+ V  A  S
Sbjct: 82  NGLRLQSKTIKVSYARPS 99

>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 = 47.0 bits (110), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 42/184 (22%), Positives = 73/184 (39%), Gaps = 45/184 (24%)
Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK--FAFVEMRTV 90
           R++++GGL     ++++ + F Q  T          D VV    N ++   F FV   TV
Sbjct: 13  RKLFIGGLSFETTDESLRSHFEQWGTLT--------DCVVMRDPNTKRSRGFGFVTYATV 64
Query: 91  EEASNAM-----ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQ-PSPNLNLAAVGLASG 144
           EE   AM      +DG + E             P  A +    Q P  +L +        
Sbjct: 65  EEVDAAMNARPHKVDGRVVE-------------PKRAVSREDSQRPGAHLTVK------- 104
Query: 145 AIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP 204
                    ++FVGG+     E  +++  E +G +   +++ DR +G  +G+ F  + D 
Sbjct: 105 ---------KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH 155
Query: 205 AVTD 208
              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 = 47.0 bits (110), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 42/184 (22%), Positives = 73/184 (39%), Gaps = 45/184 (24%)
Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK--FAFVEMRTV 90
           R++++GGL     ++++ + F Q  T          D VV    N ++   F FV   TV
Sbjct: 14  RKLFIGGLSFETTDESLRSHFEQWGTLT--------DCVVMRDPNTKRSRGFGFVTYATV 65
Query: 91  EEASNAM-----ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQ-PSPNLNLAAVGLASG 144
           EE   AM      +DG + E             P  A +    Q P  +L +        
Sbjct: 66  EEVDAAMNARPHKVDGRVVE-------------PKRAVSREDSQRPGAHLTVK------- 105
Query: 145 AIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP 204
                    ++FVGG+     E  +++  E +G +   +++ DR +G  +G+ F  + D 
Sbjct: 106 ---------KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH 156
Query: 205 AVTD 208
              D
Sbjct: 157 DSVD 160

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 42/184 (22%), Positives = 73/184 (39%), Gaps = 45/184 (24%)
Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK--FAFVEMRTV 90
           R++++GGL     ++++ + F Q  T          D VV    N ++   F FV   TV
Sbjct: 7   RKLFIGGLSFETTDESLRSHFEQWGTLT--------DCVVMRDPNTKRSRGFGFVTYATV 58
Query: 91  EEASNAM-----ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQ-PSPNLNLAAVGLASG 144
           EE   AM      +DG + E             P  A +    Q P  +L +        
Sbjct: 59  EEVDAAMNARPHKVDGRVVE-------------PKRAVSREDSQRPGAHLTVK------- 98
Query: 145 AIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP 204
                    ++FVGG+     E  +++  E +G +   +++ DR +G  +G+ F  + D 
Sbjct: 99  ---------KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH 149
Query: 205 AVTD 208
              D
Sbjct: 150 DSVD 153

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 42/184 (22%), Positives = 73/184 (39%), Gaps = 45/184 (24%)
Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK--FAFVEMRTV 90
           R++++GGL     ++++ + F Q  T          D VV    N ++   F FV   TV
Sbjct: 14  RKLFIGGLSFETTDESLRSHFEQWGTLT--------DCVVMRDPNTKRSRGFGFVTYATV 65
Query: 91  EEASNAM-----ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQ-PSPNLNLAAVGLASG 144
           EE   AM      +DG + E             P  A +    Q P  +L +        
Sbjct: 66  EEVDAAMNARPHKVDGRVVE-------------PKRAVSREDSQRPGAHLTVK------- 105
Query: 145 AIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP 204
                    ++FVGG+     E  +++  E +G +   +++ DR +G  +G+ F  + D 
Sbjct: 106 ---------KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH 156
Query: 205 AVTD 208
              D
Sbjct: 157 DSVD 160

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 46.2 bits (108), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 42/184 (22%), Positives = 73/184 (39%), Gaps = 45/184 (24%)
Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK--FAFVEMRTV 90
           R++++GGL     ++++ + F Q  T          D VV    N ++   F FV   TV
Sbjct: 12  RKLFIGGLSFETTDESLRSHFEQWGTLT--------DCVVMRDPNTKRSRGFGFVTYATV 63
Query: 91  EEASNAM-----ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQ-PSPNLNLAAVGLASG 144
           EE   AM      +DG + E             P  A +    Q P  +L +        
Sbjct: 64  EEVDAAMNARPHKVDGRVVE-------------PKRAVSREDSQRPGAHLTVK------- 103
Query: 145 AIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP 204
                    ++FVGG+     E  +++  E +G +   +++ DR +G  +G+ F  + D 
Sbjct: 104 ---------KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH 154
Query: 205 AVTD 208
              D
Sbjct: 155 DSVD 158

>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant Length = 285

Iteration: 1
 Score = 45.8 bits (107), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 29/75 (38%), Positives = 36/75 (48%)
Query: 157 VGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNG 216
           V  LP   T+ Q +EL+  FG+L    LV    TG SKGYGF  Y        A + L G
Sbjct: 100 VANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLG 159
Query: 217 LKMGDKTLTVRRATA 231
             +G +TL V    A
Sbjct: 160 KPLGPRTLYVHWTDA 174

>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With Human Vinculin Tail Domain Vt Length = 283

Iteration: 1
 Score = 45.8 bits (107), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 29/75 (38%), Positives = 36/75 (48%)
Query: 157 VGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNG 216
           V  LP   T+ Q +EL+  FG+L    LV    TG SKGYGF  Y        A + L G
Sbjct: 98  VANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLG 157
Query: 217 LKMGDKTLTVRRATA 231
             +G +TL V    A
Sbjct: 158 KPLGPRTLYVHWTDA 172

>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320) Length = 284

Iteration: 1
 Score = 45.8 bits (107), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 29/75 (38%), Positives = 36/75 (48%)
Query: 157 VGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNG 216
           V  LP   T+ Q +EL+  FG+L    LV    TG SKGYGF  Y        A + L G
Sbjct: 100 VANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLG 159
Query: 217 LKMGDKTLTVRRATA 231
             +G +TL V    A
Sbjct: 160 KPLGPRTLYVHWTDA 174

>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 = 45.8 bits (107), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 28/74 (37%), Positives = 40/74 (54%), Gaps = 6/74 (8%)
Query: 152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC-VYQDPAVTDIA 210
           P+ VFVGG+     ET+I+     +G++    ++ DR TG SKGYGF   Y D  V  I 
Sbjct: 9   PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIV 67
Query: 211 CAALN----GLKMG 220
            + +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 = 45.8 bits (107), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 28/74 (37%), Positives = 40/74 (54%), Gaps = 3/74 (4%)
Query: 309 CGKYGTLVNVVIPRPDQNGGETPG--VGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAF 366
           CGK+G  VN VI   ++ G E     + K+F+E+  A     A  AL+GR F G  V A 
Sbjct: 150 CGKFGA-VNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAE 208
Query: 367 YYPEDKYFNKDYSA 380
            Y ++++ N D SA
Sbjct: 209 VYDQERFDNSDLSA 222

>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In Daz- Associated Protein 1 Length = 99

Iteration: 1
 Score = 45.4 bits (106), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 26/87 (29%), Positives = 44/87 (50%), Gaps = 3/87 (3%)
Query: 153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA 212
           +++FVGG+P+   ET+++E  + FG +    ++ D +    +G+GF  ++D    D A  
Sbjct: 11  NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN 70
Query: 213 ALNGLKMGDKTLTVR---RATASSGQS 236
                 MG K    R   R + SSG S
Sbjct: 71  MHFHDIMGKKVEVKRAEPRDSKSSGPS 97

>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 = 45.4 bits (106), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 28/74 (37%), Positives = 40/74 (54%), Gaps = 6/74 (8%)
Query: 152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC-VYQDPAVTDIA 210
           P+ VFVGG+     ET+I+     +G++    ++ DR TG SKGYGF   Y D  V  I 
Sbjct: 9   PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIV 67
Query: 211 CAALN----GLKMG 220
            + +N     LK+G
Sbjct: 68  ESQINFHGKKLKLG 81

>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 = 6e-05,   Method: Composition-based stats.
 Identities = 27/83 (32%), Positives = 43/83 (51%), Gaps = 1/83 (1%)
Query: 148 GAEGPDRVFVGGLPYYFTETQIKELLESFGT-LHGFDLVKDRDTGNSKGYGFCVYQDPAV 206
           G+ G   +F+G L     E  + +   +FG  L    +++D DTGNSKGY F  +     
Sbjct: 1   GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA 60
Query: 207 TDIACAALNGLKMGDKTLTVRRA 229
           +D A  A+NG  + ++ +TV  A
Sbjct: 61  SDAAIEAMNGQYLCNRPITVSYA 83

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 26/77 (33%), Positives = 38/77 (49%), Gaps = 6/77 (7%)
Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           R+FVG LP   TE   K L E +G      + +DR      G+GF   +   + +IA A 
Sbjct: 24  RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR------GFGFIRLESRTLAEIAKAE 77
Query: 214 LNGLKMGDKTLTVRRAT 230
           L+G  +  + L +R AT
Sbjct: 78  LDGTILKSRPLRIRFAT 94

>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like Length = 89

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 28/74 (37%), Positives = 40/74 (54%), Gaps = 6/74 (8%)
Query: 152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC-VYQDPAVTDIA 210
           P+ VFVGG+     ET+I+     +G++    ++ DR TG SKGYGF   Y D  V  I 
Sbjct: 10  PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIV 68
Query: 211 CAALN----GLKMG 220
            + +N     LK+G
Sbjct: 69  ESQINFHGKKLKLG 82

>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/81 (32%), Positives = 41/81 (50%), Gaps = 6/81 (7%)
Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           R+FVG LP   TE ++++L E +G      + KD      KG+GF   +   + +IA   
Sbjct: 24  RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVE 77
Query: 214 LNGLKMGDKTLTVRRATASSG 234
           L+ + +  K L VR A  S+ 
Sbjct: 78  LDNMPLRGKQLRVRFACHSAS 98

>pdb|3UE2|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U Binding Splicing Factor 60kda (Puf60) From Homo Sapiens At 1.23 A Resolution Length = 118

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 28/74 (37%), Positives = 40/74 (54%), Gaps = 3/74 (4%)
Query: 309 CGKYGTLVNVVIPRPDQNGGETPG--VGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAF 366
           CGK+G  VN VI   ++ G E     + K+F+E+  A     A  AL+GR F G  V A 
Sbjct: 46  CGKFGA-VNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAE 104
Query: 367 YYPEDKYFNKDYSA 380
            Y ++++ N D SA
Sbjct: 105 VYDQERFDNSDLSA 118

>pdb|2DNY|A Chain A, Solution Structure Of The Third Rna Binding Domain Of Fbp- Interacting Repressor, Siahbp1 Length = 119

Iteration: 1
 Score = 42.4 bits (98), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 28/74 (37%), Positives = 40/74 (54%), Gaps = 3/74 (4%)
Query: 309 CGKYGTLVNVVIPRPDQNGGETPG--VGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAF 366
           CGK+G  VN VI   ++ G E     + K+F+E+  A     A  AL+GR F G  V A 
Sbjct: 41  CGKFGA-VNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAE 99
Query: 367 YYPEDKYFNKDYSA 380
            Y ++++ N D SA
Sbjct: 100 VYDQERFDNSDLSA 113

>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 = 42.0 bits (97), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 29/88 (32%), Positives = 39/88 (44%)
Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           VFVG L    T   IK     FG +    +VKD  TG SKGYGF  + +    + A   +
Sbjct: 18  VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 215 NGLKMGDKTLTVRRATASSGQSKTEQES 242
            G  +G + +    AT      K+  ES
Sbjct: 78  GGQWLGGRQIRTNWATRKPPAPKSTYES 105

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 41.6 bits (96), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 29/86 (33%), Positives = 39/86 (45%), Gaps = 4/86 (4%)
Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           VFVG L    T   IK     FG +    +VKD  TG SKGYGF  + +    + A   +
Sbjct: 18  VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 215 NGLKMGDKTL----TVRRATASSGQS 236
            G  +G + +      R+  A SG S
Sbjct: 78  GGQWLGGRQIRTNWATRKPPAPSGPS 103

>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Bruno-Like 4 Rna-Binding Protein Length = 106

Iteration: 1
 Score = 41.6 bits (96), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 18/48 (37%), Positives = 27/48 (56%)
Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 201
           ++F+G +P    E  +K L E FG ++   ++KDR TG  KG  F  Y
Sbjct: 15  KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTY 62

>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna- Binding Protein-43 Length = 103

Iteration: 1
 Score = 41.2 bits (95), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 21/62 (33%), Positives = 33/62 (53%)
Query: 142 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 201
           +SG     +    + V GLP+  TE  +KE   +FG +    + KD  TG+SKG+GF  +
Sbjct: 5   SSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRF 64
Query: 202 QD 203
            +
Sbjct: 65  TE 66

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	380
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	6e-74
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	4e-19
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	3e-64
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	1e-14
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	3e-06
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	8e-35
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-21
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	2e-32
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	7e-12
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	6e-32
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	3e-31
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	1e-30
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-29
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-18
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	3e-06
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-28
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-07
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	8e-28
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-21
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-07
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	2e-26
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	3e-25
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	3e-24
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	1e-10
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	6e-24
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	7e-24
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	5e-14
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-23
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-14
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-23
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-18
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-04
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	7e-23
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	7e-19
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-22
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	3e-14
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	4e-21
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	5e-10
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	1e-20
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	5e-09
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-19
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	7e-15
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-19
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	7e-07
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	2e-19
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	5e-15
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	4e-04
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	3e-19
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	2e-07
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	4e-19
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	2e-06
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	9e-19
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	2e-07
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	9e-19
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	5e-08
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	1e-18
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	1e-09
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	6e-04
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	1e-18
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	1e-08
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	1e-18
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	3e-09
1x4e_A	85	RNA binding motif, single-stranded interacting pro	2e-18
1x4e_A	85	RNA binding motif, single-stranded interacting pro	1e-08
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	4e-18
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	1e-09
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	4e-18
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	6e-09
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	5e-18
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	8e-11
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	7e-18
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	3e-08
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	8e-18
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	2e-09
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	4e-04
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	1e-17
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	4e-08
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	2e-17
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	8e-08
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	2e-17
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	1e-09
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	3e-17
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	2e-09
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	3e-17
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	4e-05
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	4e-17
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	6e-07
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	6e-17
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	6e-09
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	9e-17
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	2e-07
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	9e-17
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	2e-07
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	9e-17
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	5e-07
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-16
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-06
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	2e-16
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	9e-07
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	2e-16
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	2e-16
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	1e-05
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-16
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-08
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	2e-16
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	5e-10
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	2e-16
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	6e-10
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-16
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	8e-09
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	3e-16
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	6e-09
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	5e-04
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	3e-16
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	8e-09
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	4e-16
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	3e-06
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	4e-16
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	6e-06
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	4e-16
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	6e-04
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	9e-16
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	2e-08
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	8e-04
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	1e-15
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	8e-09
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	1e-15
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	2e-08
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	1e-15
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	6e-06
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	1e-15
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	5e-04
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	2e-15
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	4e-08
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	2e-15
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	1e-07
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	2e-15
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	1e-05
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	2e-15
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	2e-05
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	2e-15
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	2e-15
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	1e-05
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	3e-15
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	1e-07
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	6e-06
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	3e-15
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	1e-07
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	3e-15
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	1e-08
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	8e-04
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	3e-15
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	6e-08
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	3e-15
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	2e-12
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	4e-15
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	2e-07
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	4e-15
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	1e-11
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	4e-15
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	4e-04
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	5e-15
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	5e-15
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	8e-09
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	5e-15
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	4e-06
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	5e-15
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	1e-05
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	8e-15
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	2e-09
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	1e-14
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	9e-05
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	1e-14
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	8e-08
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	1e-14
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	2e-06
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-14
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	2e-07
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	2e-06
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	1e-14
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	1e-10
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-04
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	2e-14
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	7e-08
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	3e-14
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	2e-08
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	3e-14
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	2e-11
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	3e-14
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	5e-14
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	6e-14
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	3e-05
2div_A	99	TRNA selenocysteine associated protein; structural	7e-14
2div_A	99	TRNA selenocysteine associated protein; structural	1e-05
2dis_A	109	Unnamed protein product; structural genomics, RRM	1e-13
2dis_A	109	Unnamed protein product; structural genomics, RRM	1e-07
2dis_A	109	Unnamed protein product; structural genomics, RRM	4e-04
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	1e-13
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	1e-09
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	1e-13
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	1e-13
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	1e-13
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-13
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	6e-09
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	6e-06
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	2e-13
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	2e-09
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	2e-13
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	2e-13
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	2e-06
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	4e-13
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	1e-05
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-13
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-10
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	7e-13
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	8e-13
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	1e-12
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	2e-07
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	2e-12
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	4e-09
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	2e-12
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	1e-10
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	2e-12
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	9e-12
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	2e-12
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	1e-09
1x5o_A	114	RNA binding motif, single-stranded interacting pro	4e-12
1x5o_A	114	RNA binding motif, single-stranded interacting pro	2e-05
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	4e-12
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	4e-06
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	5e-12
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	3e-05
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	6e-12
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	4e-11
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	8e-12
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	2e-09
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	1e-11
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	1e-08
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	1e-11
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	9e-09
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	1e-11
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	8e-07
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	1e-05
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	1e-11
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	5e-10
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	2e-11
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	8e-08
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	2e-11
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	3e-10
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	2e-11
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	6e-10
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	4e-11
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	5e-10
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	5e-11
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	1e-05
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	5e-11
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	3e-09
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	6e-11
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	2e-07
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	7e-11
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	1e-07
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	1e-10
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	3e-05
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	1e-10
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	3e-10
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	1e-10
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	6e-10
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	1e-10
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	4e-10
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	3e-10
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	5e-08
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	8e-10
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	2e-05
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	2e-09
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	4e-04
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	2e-09
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	3e-09
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	3e-09
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	9e-08
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	5e-09
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	9e-05
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	1e-04
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	6e-09
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	2e-06
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	7e-09
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	2e-08
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	8e-09
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	6e-08
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	8e-09
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	7e-08
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	1e-08
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	6e-07
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	1e-08
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	2e-07
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	1e-08
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	4e-07
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	2e-08
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	4e-07
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-08
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	6e-06
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-04
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	3e-08
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	1e-07
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	4e-08
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	4e-08
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	5e-08
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	6e-08
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	2e-07
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	7e-08
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	3e-07
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	7e-08
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	6e-07
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	1e-07
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	4e-07
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	1e-07
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	2e-05
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	1e-07
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	2e-07
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	1e-07
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-05
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	9e-05
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	2e-07
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	4e-07
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	2e-07
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	7e-07
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	2e-07
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	3e-07
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	2e-07
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	3e-07
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	3e-07
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	3e-05
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	5e-07
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	5e-07
1x5p_A	97	Negative elongation factor E; structure genomics,	5e-07
1x5p_A	97	Negative elongation factor E; structure genomics,	1e-06
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	1e-06
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	1e-06
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	7e-04
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	2e-06
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	2e-05
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	4e-06
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-05
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	1e-05
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	7e-04
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	7e-05

>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 =  227 bits (581), Expect = 6e-74
 Identities = 91/205 (44%), Positives = 126/205 (61%), Gaps = 10/205 (4%)

Query: 32  ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 91
           ARR+YVG +P    E+A+  FF+  M  +GG +  PG+ V+ V IN +K FAF+E R+V+
Sbjct: 4   ARRLYVGNIPFGITEEAMMDFFNAQMR-LGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 62

Query: 92  EASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEG 151
           E + AMA DGIIF+G ++++RRP DY P    +  P    P +    V          + 
Sbjct: 63  ETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVV---------PDS 113

Query: 152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 211
             ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG SKGY FC Y D  VTD A 
Sbjct: 114 AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 173

Query: 212 AALNGLKMGDKTLTVRRATASSGQS 236
           A LNG+++GDK L V+RA+  +  +
Sbjct: 174 AGLNGMQLGDKKLLVQRASVGAKNA 198

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 83.5 bits (207), Expect = 4e-19
 Identities = 36/216 (16%), Positives = 70/216 (32%), Gaps = 41/216 (18%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHG-----FDLVKDRDTGNSKGYGFCVYQDPAVTD 208
           R++VG +P+  TE  + +   +   L G      + V        K + F  ++    T 
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 209 IACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLG- 267
            A A  +G+    ++L +RR              +      ++      +     + L  
Sbjct: 66  QAMA-FDGIIFQGQSLKIRRP-----HDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFI 119

Query: 268 GGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNG 327
           GG+  +         L +                 + ++E    +G L    + + D   
Sbjct: 120 GGLPNY---------LND-----------------DQVKELLTSFGPLKAFNLVK-DSAT 152

Query: 328 GETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTV 363
           G + G    F EY D      A   L+G + G   +
Sbjct: 153 GLSKGYA--FCEYVDINVTDQAIAGLNGMQLGDKKL 186

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score =  201 bits (513), Expect = 3e-64
 Identities = 89/199 (44%), Positives = 119/199 (59%), Gaps = 30/199 (15%)

Query: 32  ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 91
           ARR+YVG +P    E+A+  FF+  M  +GG +  PG+ V+ V IN +K FAF+E R+V+
Sbjct: 4   ARRLYVGNIPFGITEEAMMDFFNAQM-RLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 62

Query: 92  EASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEG 151
           E + AMA DGIIF+G ++++RRP DY P                               G
Sbjct: 63  ETTQAMAFDGIIFQGQSLKIRRPHDYQPL-----------------------------PG 93

Query: 152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 211
             ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG SKGY FC Y D  VTD A 
Sbjct: 94  AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 153

Query: 212 AALNGLKMGDKTLTVRRAT 230
           A LNG+++GDK L V+RA+
Sbjct: 154 AGLNGMQLGDKKLLVQRAS 172

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 70.0 bits (172), Expect = 1e-14
 Identities = 18/90 (20%), Positives = 34/90 (37%), Gaps = 6/90 (6%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHG-----FDLVKDRDTGNSKGYGFCVYQDPAVTD 208
           R++VG +P+  TE  + +   +   L G      + V        K + F  ++    T 
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 209 IACAALNGLKMGDKTLTVRRATASSGQSKT 238
            A  A +G+    ++L +RR          
Sbjct: 66  QAM-AFDGIIFQGQSLKIRRPHDYQPLPGA 94

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 46.1 bits (110), Expect = 3e-06
 Identities = 19/100 (19%), Positives = 37/100 (37%), Gaps = 25/100 (25%)

Query: 26  QQATRHARRVYVGGLPPLANEQAIATFFSQ--------VMT-AIGGNSAGPGDAVVNVYI 76
            Q    A ++++GGLP   N+  +    +         ++  +  G S G          
Sbjct: 88  YQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKG---------- 137

Query: 77  NHEKKFAFVEMRTVEEASNAMA-LDGIIFEGVAVRVRRPT 115
                +AF E   +     A+A L+G+      + V+R +
Sbjct: 138 -----YAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS 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 =  128 bits (324), Expect = 8e-35
 Identities = 59/348 (16%), Positives = 97/348 (27%), Gaps = 102/348 (29%)

Query: 20  PVQVM---TQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI 76
            ++     T++  R+ R++ + GLP     Q +    S                +   ++
Sbjct: 7   EIRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSD----YE---------LKYCFV 53

Query: 77  NHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLN 135
           +  K  AFV +   E+A  A+ A          + V+                       
Sbjct: 54  DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTDA----------------- 96

Query: 136 LAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKG 195
                              + V  LP   T+ Q +EL+  FG+L    LV    TG SKG
Sbjct: 97  ------------------LLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKG 138

Query: 196 YGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQK 255
           YGF  Y        A + L G  +G +TL V         +     ++L      +    
Sbjct: 139 YGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWT-----DAGQLTPALLHSRCLCVD--- 190

Query: 256 MALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTL 315
                                      L          D +        +        + 
Sbjct: 191 --------R------------------LPPGFN-----DVDA-------LCRALSAVHSP 212

Query: 316 VNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTV 363
               +    Q+G    G     LEY  A     A+    G   GG+ +
Sbjct: 213 TFCQLAC-GQDGQLK-GFA--VLEYETAEMAEEAQQQADGLSLGGSHL 256

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 91.6 bits (228), Expect = 3e-21
 Identities = 42/235 (17%), Positives = 63/235 (26%), Gaps = 44/235 (18%)

Query: 20  PVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVY---I 76
            + V  Q        + V  LPP   +Q                  G  +    VY    
Sbjct: 86  ELSVQLQP---TDALLCVANLPPSLTQQQFEELVRP---------FGSLERCFLVYSERT 133

Query: 77  NHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLN 135
              K + F E    + A+ A   L G       + V                GQ +P L 
Sbjct: 134 GQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTD-----------AGQLTPALL 182

Query: 136 LAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQ-IKELLESFGTLHGFDLVKDRDTGNSK 194
            +                 + V  LP  F +   +   L +  +     L      G  K
Sbjct: 183 HSR---------------CLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACG-QDGQLK 226

Query: 195 GYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQ 249
           G+    Y+   + + A    +GL +G   L V                I AQA  
Sbjct: 227 GFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPGRSMLAALIAAQATA 281

>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 =  115 bits (291), Expect = 2e-32
 Identities = 39/85 (45%), Positives = 56/85 (65%), Gaps = 1/85 (1%)

Query: 30  RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRT 89
             ARR+YVG +P    E+A+  FF+  M   G     PG+ V+ V IN +K FAF+E R+
Sbjct: 4   GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLT-QAPGNPVLAVQINQDKNFAFLEFRS 62

Query: 90  VEEASNAMALDGIIFEGVAVRVRRP 114
           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 = 60.1 bits (146), Expect = 7e-12
 Identities = 17/80 (21%), Positives = 33/80 (41%), Gaps = 6/80 (7%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHG-----FDLVKDRDTGNSKGYGFCVYQDPAVTD 208
           R++VG +P+  TE  + +   +   L G      + V        K + F  ++    T 
Sbjct: 8   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67

Query: 209 IACAALNGLKMGDKTLTVRR 228
               A +G+    ++L +RR
Sbjct: 68  -QAMAFDGIIFQGQSLKIRR 86

>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 (290), Expect = 6e-32
 Identities = 46/105 (43%), Positives = 62/105 (59%), Gaps = 1/105 (0%)

Query: 274 GETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGV 333
           G    +VLCL   +  + L DDEEYEEI+ED+R+EC KYG + ++ IPRP  +G E PG 
Sbjct: 1   GGHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRP-VDGVEVPGC 59

Query: 334 GKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 378
           GK+F+E+     C  A   L+GRKF    V   Y   D Y  +D+
Sbjct: 60  GKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHRRDF 104

>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 =  114 bits (286), Expect = 3e-31
 Identities = 33/136 (24%), Positives = 61/136 (44%), Gaps = 22/136 (16%)

Query: 246 QAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDM 305
            + +H+ +QK+  +                  + V+ L   +        +  +++  ++
Sbjct: 4   SSARHMVMQKLLRKQE----------------STVMVLRNMVDPK-----DIDDDLEGEV 42

Query: 306 REECGKYGTLVNVVIPRPDQNGGET-PGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVN 364
            EECGK+G +  V+I +  Q   E    + K+F+E+  A     A  AL+GR F G  V 
Sbjct: 43  TEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVV 102

Query: 365 AFYYPEDKYFNKDYSA 380
           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 =  112 bits (281), Expect = 1e-30
 Identities = 24/98 (24%), Positives = 40/98 (40%), Gaps = 7/98 (7%)

Query: 279 KVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFL 338
           +   L+         +     EI +D+ EEC K+G ++++ + +           G V++
Sbjct: 8   QCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKN-------SAQGNVYV 60

Query: 339 EYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNK 376
           +         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 =  112 bits (282), Expect = 2e-29
 Identities = 48/212 (22%), Positives = 83/212 (39%), Gaps = 37/212 (17%)

Query: 26  QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHE 79
           Q A     RVYVG +     E  I   F+           GP   + ++ +         
Sbjct: 22  QGALAIMSRVYVGSIYYELGEDTIRQAFAP---------FGP---IKSIDMSWDSVTMKH 69

Query: 80  KKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAA 138
           K FAFVE    E A  A+  ++ ++  G  ++V RP++            + +       
Sbjct: 70  KGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARA----- 124

Query: 139 VGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGF 198
                         +R++V  +    ++  IK + E+FG +    L +D  TG  KGYGF
Sbjct: 125 -------------FNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGF 171

Query: 199 CVYQDPAVTDIACAALNGLKMGDKTLTVRRAT 230
             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 = 82.0 bits (203), Expect = 2e-18
 Identities = 40/216 (18%), Positives = 77/216 (35%), Gaps = 46/216 (21%)

Query: 147 GGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAV 206
           G      RV+VG + Y   E  I++    FG +   D+  D  T   KG+ F  Y+ P  
Sbjct: 23  GALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEA 82

Query: 207 TDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTL 266
             +A   +N + +G + + V R       +  + + I+ Q  +         +    N +
Sbjct: 83  AQLALEQMNSVMLGGRNIKVGRP-----SNIGQAQPIIDQLAE---------EARAFNRI 128

Query: 267 --GGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPD 324
                             + + ++ D +             +     +G + +  + R D
Sbjct: 129 YVAS--------------VHQDLSDDDI-------------KSVFEAFGKIKSATLAR-D 160

Query: 325 QNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGG 360
              G+  G G  F+EY  A     A ++++    GG
Sbjct: 161 PTTGKHKGYG--FIEYEKAQSSQDAVSSMNLFDLGG 194

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 46.5 bits (111), Expect = 3e-06
 Identities = 18/119 (15%), Positives = 37/119 (31%), Gaps = 25/119 (21%)

Query: 20  PVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQ--------VMT-AIGGNSAGPGDA 70
           P+     +  R   R+YV  +    ++  I + F          +      G   G    
Sbjct: 113 PIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKG---- 168

Query: 71  VVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPG 128
                      + 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 =  109 bits (274), Expect = 1e-28
 Identities = 27/210 (12%), Positives = 67/210 (31%), Gaps = 55/210 (26%)

Query: 29  TRHARRVYVGGLPPLANEQAIATFFSQ--------VMTAIGGNSAGPGDAVVNVYINHEK 80
           +     +++G L P  +   +    S+        V+    G +               +
Sbjct: 10  STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTN---------------R 54

Query: 81  KFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVG 140
           KF +V+  + E+   A+ L G+   G  +++ +P              +   +       
Sbjct: 55  KFGYVDFESAEDLEKALELTGLKVFGNEIKLEKP--------------KGRDSKK----- 95

Query: 141 LASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCV 200
                         +    L +  TE ++KE+ E        ++      G SKG  +  
Sbjct: 96  --------VRAARTLLAKNLSFNITEDELKEVFEDAL-----EIRLVSQDGKSKGIAYIE 142

Query: 201 YQDPAVTDIACAALNGLKMGDKTLTVRRAT 230
           ++  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 = 50.3 bits (121), Expect = 1e-07
 Identities = 15/93 (16%), Positives = 29/93 (31%), Gaps = 20/93 (21%)

Query: 26  QQATRHARRVYVGGLPPLANEQAIATFFSQ----VMTAIGGNSAGPGDAVVNVYINHEKK 81
            +  R AR +    L     E  +   F       + +  G S G               
Sbjct: 93  SKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKG--------------- 137

Query: 82  FAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRR 113
            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 =  110 bits (276), Expect = 8e-28
 Identities = 44/335 (13%), Positives = 94/335 (28%), Gaps = 101/335 (30%)

Query: 35  VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE----KKFAFVEMRTV 90
           V V  LP   N+  +  +F            GP   +++V +        +FA +E    
Sbjct: 44  VLVKNLPKSYNQNKVYKYFKH---------CGP---IIHVDVADSLKKNFRFARIEFARY 91

Query: 91  EEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAE 150
           + A  A+     +     + V   T+                                  
Sbjct: 92  DGALAAITKTHKVVGQNEIIVSHLTECT-------------------------------- 119

Query: 151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA 210
               +++   P  +T+  I++LL+    +     +       S+ + +            
Sbjct: 120 ----LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYC 175

Query: 211 CAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGM 270
              LNGLK+   TL  + +       +T+  ++                         G 
Sbjct: 176 VEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLE------------------------GR 211

Query: 271 SLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGET 330
            +       +  L+  +       DE        +RE    +G++  + IP   +     
Sbjct: 212 EIM------IRNLSTELL------DE------NLLRESFEGFGSIEKINIPAGQKEHSFN 253

Query: 331 PGVGKVFLEYYDAVGCATAKNALS--GRKFGGNTV 363
                 F+ + +     +A+ AL       G   +
Sbjct: 254 NCCA--FMVFENK---DSAERALQMNRSLLGNREI 283

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 92.4 bits (230), Expect = 2e-21
 Identities = 28/206 (13%), Positives = 67/206 (32%), Gaps = 42/206 (20%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK---FAFVEMRT 89
             +++   PP   ++ I      +               + +          FA++++ +
Sbjct: 118 CTLWMTNFPPSYTQRNIRDLLQDI---------NVVALSIRLPSLRFNTSRRFAYIDVTS 168

Query: 90  VEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGG 148
            E+A   +  L+G+  EG  +  +     NP   +            +            
Sbjct: 169 KEDARYCVEKLNGLKIEGYTLVTKV---SNPLEKSKRTDSATLEGREI------------ 213

Query: 149 AEGPDRVFVGGLPYYFT-ETQIKELLESFGTLHGFDLVKDRD-TGNSKGYGFCVYQDPAV 206
                   +  L      E  ++E  E FG++   ++   +     +    F V+++   
Sbjct: 214 -------MIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENK-- 264

Query: 207 TDIACAA--LNGLKMGDKTLTVRRAT 230
            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 = 51.1 bits (123), Expect = 2e-07
 Identities = 14/103 (13%), Positives = 30/103 (29%), Gaps = 26/103 (25%)

Query: 25  TQQATRHARRVYVGGLPP-LANEQAIATFFSQ--------VMTAIGGNSAGPGDAVVNVY 75
           T  AT   R + +  L   L +E  +   F          +      +            
Sbjct: 203 TDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEH------------ 250

Query: 76  INHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRV----RRP 114
            +     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 =  100 bits (251), Expect = 2e-26
 Identities = 32/107 (29%), Positives = 47/107 (43%), Gaps = 7/107 (6%)

Query: 273 FGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPG 332
            G+   KV+ L   + A      E  E++  + +EEC KYG +   VI      G     
Sbjct: 3   MGKCPTKVVLLRNMVGAG-----EVDEDLEVETKEECEKYGKVGKCVIFEIP--GAPDDE 55

Query: 333 VGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDYS 379
             ++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 =  102 bits (256), Expect = 3e-25
 Identities = 38/259 (14%), Positives = 71/259 (27%), Gaps = 58/259 (22%)

Query: 17  PLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI 76
            +       ++      R++VG LP    E+     F +          G       V+I
Sbjct: 7   DIKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFER---------YGE---PSEVFI 54

Query: 77  NHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLN 135
           N ++ F F+ + +   A  A   LDG I +   +R+R                     L 
Sbjct: 55  NRDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRF--------------ATHGAAL- 99

Query: 136 LAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKG 195
                                V  L    +   +++    FG +    +V D D G + G
Sbjct: 100 --------------------TVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATG 138

Query: 196 YGFCVYQDPAVTDIACAALNG----LKMGDKTLTVRRATASSGQSKTEQESILAQAQQHI 251
            GF  +        A          L    + + V        +   +++ +  +  Q  
Sbjct: 139 KGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPM-----EQFDDEDGLPEKLMQKT 193

Query: 252 AIQKMALQTSGMNTLGGGM 270
                  +        G  
Sbjct: 194 QQYHKEREQPPRFAQPGTF 212

>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 = 94.6 bits (236), Expect = 3e-24
 Identities = 26/89 (29%), Positives = 44/89 (49%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
            V++G +PY  TE QI +L  + G +    ++ D  TG SKGY F  ++D   +  A   
Sbjct: 4   VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63

Query: 214 LNGLKMGDKTLTVRRATASSGQSKTEQES 242
           LNG ++G + L    ++ S     + +  
Sbjct: 64  LNGYQLGSRFLKCGYSSNSDISGVSLEHH 92

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 56.9 bits (138), Expect = 1e-10
 Identities = 21/94 (22%), Positives = 43/94 (45%), Gaps = 19/94 (20%)

Query: 32  ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFV 85
           +R VY+G +P    E+ I    S V         GP   V+N+ +  + +      +AF+
Sbjct: 2   SRVVYLGSIPYDQTEEQILDLCSNV---------GP---VINLKMMFDPQTGRSKGYAFI 49

Query: 86  EMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYN 118
           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 = 94.4 bits (235), Expect = 6e-24
 Identities = 22/104 (21%), Positives = 37/104 (35%), Gaps = 9/104 (8%)

Query: 279 KVLCLTEAIT-ADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVF 337
           +V+ +       D   D     EI ED+R EC K+G +  +++     +G          
Sbjct: 16  RVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDG-------VAS 68

Query: 338 LEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNK-DYSA 380
           + + D          L GR FGG  + A  +     +     S 
Sbjct: 69  VSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTTDYQSGPSSG 112

>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 = 96.6 bits (241), Expect = 7e-24
 Identities = 42/209 (20%), Positives = 70/209 (33%), Gaps = 48/209 (22%)

Query: 31  HARRVYVGGLPPLANEQAIATFFSQ--------VMT-AIGGNSAGPGDAVVNVYINHEKK 81
             R++++GGL     ++++ + F Q        VM       S G               
Sbjct: 12  QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRG--------------- 56

Query: 82  FAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGL 141
           F FV   TVEE   AM       +G  V  +R         A        P         
Sbjct: 57  FGFVTYATVEEVDAAMNARPHKVDGRVVEPKR---------AVSREDSQRP--------- 98

Query: 142 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 201
                G      ++FVGG+     E  +++  E +G +   +++ DR +G  +G+ F  +
Sbjct: 99  -----GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153

Query: 202 QDPAVTDIACAALNGLKMGDKTLTVRRAT 230
            D    D          +      VR+A 
Sbjct: 154 DDHDSVDKIVIQ-KYHTVNGHNCEVRKAL 181

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 69.2 bits (170), Expect = 5e-14
 Identities = 38/195 (19%), Positives = 74/195 (37%), Gaps = 46/195 (23%)

Query: 150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 209
           E   ++F+GGL +  T+  ++   E +GTL    +++D +T  S+G+GF  Y      D 
Sbjct: 11  EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 70

Query: 210 ACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGG 269
           A  A    K+  + +  +RA +     +            H+ ++K+         +GG 
Sbjct: 71  AMNA-RPHKVDGRVVEPKRAVSREDSQRPG---------AHLTVKKI--------FVGG- 111

Query: 270 MSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGE 329
                        + E                   +R+   +YG +  + I   D+  G+
Sbjct: 112 -------------IKEDTEEH-------------HLRDYFEQYGKIEVIEIMT-DRGSGK 144

Query: 330 TPGVGKVFLEYYDAV 344
             G   V  + +D+V
Sbjct: 145 KRGFAFVTFDDHDSV 159

>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 = 94.9 bits (237), Expect = 1e-23
 Identities = 40/204 (19%), Positives = 72/204 (35%), Gaps = 45/204 (22%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-----FAFVEM 87
           R +YVG L     E  +  +F            GP   + N+ I  +K      +AFVE 
Sbjct: 1   RVLYVGNLDKAITEDILKQYFQV---------GGP---IANIKIMIDKNNKNVNYAFVEY 48

Query: 88  RTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAI 146
               +A+ A+  L+G   E   V++                   S   +           
Sbjct: 49  HQSHDANIALQTLNGKQIENNIVKINWA--------------FQSQQSS----------- 83

Query: 147 GGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAV 206
             ++    +FVG L     +  ++   + F +     ++ D  TG+S+GYGF  +     
Sbjct: 84  --SDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDD 141

Query: 207 TDIACAALNGLKMGDKTLTVRRAT 230
              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 = 68.3 bits (168), Expect = 5e-14
 Identities = 19/89 (21%), Positives = 38/89 (42%), Gaps = 1/89 (1%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           ++VG L    TE  +K+  +  G +    ++ D+    +  Y F  Y      +IA   L
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTL 61

Query: 215 NGLKMGDKTLTVRRATASSGQSKTEQESI 243
           NG ++ +  + +  A  S   S  +  ++
Sbjct: 62  NGKQIENNIVKINWAFQSQQSSSDDTFNL 90

>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 = 1e-23
 Identities = 35/204 (17%), Positives = 71/204 (34%), Gaps = 50/204 (24%)

Query: 35  VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMR 88
           + V  LP    ++   + F            G    + +  +           + FV   
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGS---------IGE---IESCKLVRDKITGQSLGYGFVNYI 52

Query: 89  TVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIG 147
             ++A  A+  L+G+  +   ++V                 +PS                
Sbjct: 53  DPKDAEKAINTLNGLRLQTKTIKVSYA--------------RPS---------------S 83

Query: 148 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 207
            +     ++V GLP   T+ ++++L   +G +    ++ D+ TG S+G GF  +      
Sbjct: 84  ASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEA 143

Query: 208 DIACAALNG--LKMGDKTLTVRRA 229
           + 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 = 80.7 bits (200), Expect = 2e-18
 Identities = 31/84 (36%), Positives = 43/84 (51%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           + V  LP   T+ + + L  S G +    LV+D+ TG S GYGF  Y DP   + A   L
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 215 NGLKMGDKTLTVRRATASSGQSKT 238
           NGL++  KT+ V  A  SS   + 
Sbjct: 65  NGLRLQTKTIKVSYARPSSASIRD 88

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 41.0 bits (97), Expect = 1e-04
 Identities = 20/108 (18%), Positives = 36/108 (33%), Gaps = 30/108 (27%)

Query: 20  PVQVMTQQATR---HARRVYVGGLPPLANEQAIATFFSQ--------VMT-AIGGNSAGP 67
            ++V   + +        +YV GLP    ++ +   FSQ        ++   + G S G 
Sbjct: 73  TIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRG- 131

Query: 68  GDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV--AVRVR 112
                           F+      EA  A+  L+G    G    + V+
Sbjct: 132 --------------VGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVK 165

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 93.0 bits (232), Expect = 7e-23
 Identities = 40/204 (19%), Positives = 74/204 (36%), Gaps = 50/204 (24%)

Query: 35  VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMR 88
           + V  LP    ++ +   F            GP   +    I       +   +AFV+  
Sbjct: 6   LIVNYLPQDMTDRELYALFRA---------IGP---INTCRIMRDYKTGYSYGYAFVDFT 53

Query: 89  TVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIG 147
           +  ++  A+  L+GI      ++V            A   G+   + NL           
Sbjct: 54  SEMDSQRAIKVLNGITVRNKRLKVSY----------ARPGGESIKDTNL----------- 92

Query: 148 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 207
                   +V  LP   T+ Q+  +   +G++   ++++D+ TG  +G  F  Y      
Sbjct: 93  --------YVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 144

Query: 208 DIACAALNG--LKMGDKTLTVRRA 229
             A +ALN    + G + L+VR A
Sbjct: 145 QEAISALNNVIPEGGSQPLSVRLA 168

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 82.2 bits (204), Expect = 7e-19
 Identities = 46/208 (22%), Positives = 70/208 (33%), Gaps = 53/208 (25%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           + V  LP   T+ ++  L  + G ++   +++D  TG S GY F  +     +  A   L
Sbjct: 6   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65

Query: 215 NGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFG 274
           NG+ + +K L V  A       K                                 +L+ 
Sbjct: 66  NGITVRNKRLKVSYARPGGESIK-------------------------------DTNLY- 93

Query: 275 ETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVG 334
                V  L   IT D L                 GKYG++V   I R D+  G   GV 
Sbjct: 94  -----VTNLPRTITDDQL-------------DTIFGKYGSIVQKNILR-DKLTGRPRGVA 134

Query: 335 KVFLEYYDAVGCATAKNALSGRKFGGNT 362
             F+ Y        A +AL+     G +
Sbjct: 135 --FVRYNKREEAQEAISALNNVIPEGGS 160

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 91.8 bits (229), Expect = 2e-22
 Identities = 36/204 (17%), Positives = 68/204 (33%), Gaps = 49/204 (24%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFVE 86
            ++++GGL     E  +  +F +          G    V ++ I  +        F F+ 
Sbjct: 4   CKMFIGGLNWDTTEDNLREYFGK---------YGT---VTDLKIMKDPATGRSRGFGFLS 51

Query: 87  MRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAI 146
                     +    I+ +G  +  +R             P                   
Sbjct: 52  FEKPSSVDEVVKTQHIL-DGKVIDPKRAI-----------PRDEQDK------------- 86

Query: 147 GGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAV 206
                  ++FVGG+       + +E    +GT+    L+ D+DTG S+G+GF  Y     
Sbjct: 87  -----TGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADA 141

Query: 207 TDIACAALNGLKMGDKTLTVRRAT 230
            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 = 69.1 bits (170), Expect = 3e-14
 Identities = 25/85 (29%), Positives = 44/85 (51%), Gaps = 2/85 (2%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           ++F+GGL +  TE  ++E    +GT+    ++KD  TG S+G+GF  ++ P+  D     
Sbjct: 5   KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64

Query: 214 LNGLKMGDKTLTVRRATASSGQSKT 238
            +   +  K +  +RA     Q KT
Sbjct: 65  QH--ILDGKVIDPKRAIPRDEQDKT 87

>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 = 86.2 bits (214), Expect = 4e-21
 Identities = 34/76 (44%), Positives = 42/76 (55%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
            VFVG +PY  TE Q+K++    G +  F LV DR+TG  KGYGFC YQD      A   
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 214 LNGLKMGDKTLTVRRA 229
           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 = 55.3 bits (134), Expect = 5e-10
 Identities = 33/109 (30%), Positives = 50/109 (45%), Gaps = 20/109 (18%)

Query: 30  RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FA 83
           R  R V+VG +P  A E+ +   FS+V         GP   VV+  + ++++      + 
Sbjct: 6   RSLRSVFVGNIPYEATEEQLKDIFSEV---------GP---VVSFRLVYDRETGKPKGYG 53

Query: 84  FVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDY-NPTLAAALGPGQP 130
           F E +  E A +AM  L+G  F G A+RV       N     +LG G P
Sbjct: 54  FCEYQDQETALSAMRNLNGREFSGRALRVDNAASEKNKEELKSLGTGAP 102

>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 = 84.6 bits (210), Expect = 1e-20
 Identities = 21/90 (23%), Positives = 38/90 (42%), Gaps = 2/90 (2%)

Query: 142 ASGAIGGAEGPD--RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC 199
            S  + G   P    V+V  LP+  T   +  +   +G +    ++KD+DT  SKG  F 
Sbjct: 4   GSSGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFI 63

Query: 200 VYQDPAVTDIACAALNGLKMGDKTLTVRRA 229
           ++ 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 = 52.2 bits (126), Expect = 5e-09
 Identities = 19/88 (21%), Positives = 28/88 (31%), Gaps = 19/88 (21%)

Query: 31  HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAF 84
               VYV  LP       +   FS+            G  VV V I  +K        AF
Sbjct: 15  SKSTVYVSNLPFSLTNNDLYRIFSKY-----------GK-VVKVTIMKDKDTRKSKGVAF 62

Query: 85  VEMRTVEEASNAM-ALDGIIFEGVAVRV 111
           +     + A N   A++     G  ++ 
Sbjct: 63  ILFLDKDSAQNCTRAINNKQLFGRVIKA 90

>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 = 1e-19
 Identities = 39/210 (18%), Positives = 71/210 (33%), Gaps = 50/210 (23%)

Query: 32  ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK--------FA 83
           A +++VG +P   +E+ +   F Q          G    V  + +  ++           
Sbjct: 3   AIKMFVGQVPRTWSEKDLRELFEQ---------YGA---VYEINVLRDRSQNPPQSKGCC 50

Query: 84  FVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLA 142
           FV   T + A  A  AL  +                  L     P Q  P         A
Sbjct: 51  FVTFYTRKAALEAQNALHNMK----------------VLPGMHHPIQMKP---------A 85

Query: 143 SGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQ 202
                 A    ++F+G +    TE  I+ +  SFG +    +++    G S+G  F  + 
Sbjct: 86  DSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRG-PDGLSRGCAFVTFT 144

Query: 203 DPAVTDIACAALNG---LKMGDKTLTVRRA 229
             A+   A  A++    ++     + V+ A
Sbjct: 145 TRAMAQTAIKAMHQAQTMEGCSSPMVVKFA 174

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 71.1 bits (175), Expect = 7e-15
 Identities = 20/93 (21%), Positives = 41/93 (44%), Gaps = 2/93 (2%)

Query: 151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGN--SKGYGFCVYQDPAVTD 208
              ++FVG +P  ++E  ++EL E +G ++  ++++DR      SKG  F  +       
Sbjct: 2   DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61

Query: 209 IACAALNGLKMGDKTLTVRRATASSGQSKTEQE 241
            A  AL+ +K+        +   +  +     E
Sbjct: 62  EAQNALHNMKVLPGMHHPIQMKPADSEKNNAVE 94

>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 = 81.5 bits (202), Expect = 2e-19
 Identities = 28/95 (29%), Positives = 51/95 (53%)

Query: 142 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 201
           +SG+ G A    ++FVGGL +   E  ++++   +G +    +VKDR+T  S+G+GF  +
Sbjct: 2   SSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTF 61

Query: 202 QDPAVTDIACAALNGLKMGDKTLTVRRATASSGQS 236
           ++      A  A+NG  +  + + V +A  SS   
Sbjct: 62  ENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDNR 96

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 46.1 bits (110), Expect = 7e-07
 Identities = 24/85 (28%), Positives = 40/85 (47%), Gaps = 17/85 (20%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAV-VNVYINHE----KKFAFVEM 87
            +++VGGL    NEQ++   FS+            G    V V  + E    + F FV  
Sbjct: 13  GKLFVGGLSFDTNEQSLEQVFSKY-----------GQISEVVVVKDRETQRSRGFGFVTF 61

Query: 88  RTVEEASNAM-ALDGIIFEGVAVRV 111
             +++A +AM A++G   +G  +RV
Sbjct: 62  ENIDDAKDAMMAMNGKSVDGRQIRV 86

>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 = 84.6 bits (210), Expect = 2e-19
 Identities = 42/217 (19%), Positives = 79/217 (36%), Gaps = 49/217 (22%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFVE 86
             +YVG L P   E  +   FS          AGP   ++++ +  +        +A+V 
Sbjct: 16  ASLYVGDLHPDVTEAMLYEKFSP---------AGP---ILSIRVCRDMITRRSLGYAYVN 63

Query: 87  MRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGA 145
            +   +A  A+  ++  + +G  VR+                 Q  P+L           
Sbjct: 64  FQQPADAERALDTMNFDVIKGKPVRIMWS--------------QRDPSLR---------- 99

Query: 146 IGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPA 205
                G   +F+  L        + +   +FG +    +V   D   SKGYGF  ++   
Sbjct: 100 ---KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVV--CDENGSKGYGFVHFETQE 154

Query: 206 VTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQES 242
             + A   +NG+ + D+ + V R   S  + + E  +
Sbjct: 155 AAERAIEKMNGMLLNDRKVFVGRFK-SRKEREAELGA 190

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 72.3 bits (178), Expect = 5e-15
 Identities = 20/89 (22%), Positives = 36/89 (40%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           ++VG L    TE  + E     G +    + +D  T  S GY +  +Q PA  + A   +
Sbjct: 18  LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 77

Query: 215 NGLKMGDKTLTVRRATASSGQSKTEQESI 243
           N   +  K + +  +       K+   +I
Sbjct: 78  NFDVIKGKPVRIMWSQRDPSLRKSGVGNI 106

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 40.3 bits (95), Expect = 4e-04
 Identities = 21/106 (19%), Positives = 38/106 (35%), Gaps = 30/106 (28%)

Query: 20  PVQVMTQQATRHARR-----VYVGGLPPLANEQAIATFFSQ--------VMTAIGGNSAG 66
           PV++M  Q     R+     +++  L    + +A+   FS         V+    G+   
Sbjct: 86  PVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS--- 142

Query: 67  PGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV 111
                        K + FV   T E A  A+  ++G++     V V
Sbjct: 143 -------------KGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV 175

>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 = 80.7 bits (200), Expect = 3e-19
 Identities = 29/83 (34%), Positives = 43/83 (51%)

Query: 148 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 207
           G+ G   ++VG L +  TE  ++ + E FG +    L+KD DTG SKGYGF  + D    
Sbjct: 1   GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60

Query: 208 DIACAALNGLKMGDKTLTVRRAT 230
             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 = 47.9 bits (115), Expect = 2e-07
 Identities = 18/87 (20%), Positives = 29/87 (33%), Gaps = 19/87 (21%)

Query: 32  ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFV 85
           +  +YVG L     E  +   F              G  + N+ +         K + F+
Sbjct: 5   SSGLYVGSLHFNITEDMLRGIFEPF-----------GK-IDNIVLMKDSDTGRSKGYGFI 52

Query: 86  EMRTVEEASNAM-ALDGIIFEGVAVRV 111
                E A  A+  L+G    G  +RV
Sbjct: 53  TFSDSECARRALEQLNGFELAGRPMRV 79

>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 = 81.7 bits (202), Expect = 4e-19
 Identities = 29/114 (25%), Positives = 44/114 (38%), Gaps = 2/114 (1%)

Query: 122 AAALGPGQPSPNLNLAAVGLASGAIGGAEGPD--RVFVGGLPYYFTETQIKELLESFGTL 179
               G       L               E      + V  +P    E Q+++L E +G +
Sbjct: 10  YDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPI 69

Query: 180 HGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASS 233
               +V DR+T  S+GYGF  +Q  +    A A LNG  + +K L V  A +  
Sbjct: 70  ESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGH 123

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score = 45.5 bits (108), Expect = 2e-06
 Identities = 24/137 (17%), Positives = 43/137 (31%), Gaps = 23/137 (16%)

Query: 2   AQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIG 61
            Q        Q     + P Q          R + V  +P   +E  +   F +     G
Sbjct: 14  GQTAQLQQLQQQQQQHIPPTQ--MNPEPDVLRNLMVNYIPTTVDEVQLRQLFER----YG 67

Query: 62  GNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVR-- 112
                    + +V I         + + FV+ ++   A  A+  L+G       ++V   
Sbjct: 68  --------PIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA 119

Query: 113 RPTDYNPTLAAALGPGQ 129
                 P +A A+G G 
Sbjct: 120 ASGHQRPGIAGAVGDGN 136

>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 = 80.0 bits (198), Expect = 9e-19
 Identities = 32/103 (31%), Positives = 51/103 (49%)

Query: 128 GQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKD 187
           G    + +  A  +A+    G+ GP R++VG L +  TE  ++ + E FG +    L+ D
Sbjct: 2   GHHHHHHSHMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMD 61

Query: 188 RDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT 230
            +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 = 48.1 bits (115), Expect = 2e-07
 Identities = 18/99 (18%), Positives = 33/99 (33%), Gaps = 19/99 (19%)

Query: 20  PVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI--- 76
            +    Q+ +    R+YVG L     E  +   F            G    + ++ +   
Sbjct: 14  AMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPF---------GR---IESIQLMMD 61

Query: 77  ---NHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV 111
                 K + F+     E A  A+  L+G    G  ++V
Sbjct: 62  SETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKV 100

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 79.5 bits (197), Expect = 9e-19
 Identities = 28/90 (31%), Positives = 46/90 (51%), Gaps = 2/90 (2%)

Query: 147 GGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAV 206
            G+ G  ++FV  LP+ FT   +K+     G +   D+    + G SKG G   ++ P V
Sbjct: 3   SGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADI--KMENGKSKGCGVVKFESPEV 60

Query: 207 TDIACAALNGLKMGDKTLTVRRATASSGQS 236
            + AC  +NG+K+  + + VR    +SG S
Sbjct: 61  AERACRMMNGMKLSGREIDVRIDRNASGPS 90

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 49.1 bits (118), Expect = 5e-08
 Identities = 18/86 (20%), Positives = 33/86 (38%), Gaps = 17/86 (19%)

Query: 32  ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE----KKFAFVEM 87
           A +++V  LP     + +   F++      G+       V+   I  E    K    V+ 
Sbjct: 8   ACQIFVRNLPFDFTWKMLKDKFNEC-----GH-------VLYADIKMENGKSKGCGVVKF 55

Query: 88  RTVEEASNAM-ALDGIIFEGVAVRVR 112
            + E A  A   ++G+   G  + VR
Sbjct: 56  ESPEVAERACRMMNGMKLSGREIDVR 81

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 80.0 bits (198), Expect = 1e-18
 Identities = 23/77 (29%), Positives = 34/77 (44%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
            +FV  +     E +I+E    +G +    L  DR TG SKGY    Y+       A  A
Sbjct: 28  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 87

Query: 214 LNGLKMGDKTLTVRRAT 230
           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 = 54.2 bits (131), Expect = 1e-09
 Identities = 20/92 (21%), Positives = 37/92 (40%), Gaps = 19/92 (20%)

Query: 27  QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK----- 81
           Q +     ++V  +   A E  I   F            G    + N+++N +++     
Sbjct: 21  QRSVEGWILFVTSIHEEAQEDEIQEKFCDY---------GE---IKNIHLNLDRRTGFSK 68

Query: 82  -FAFVEMRTVEEASNAM-ALDGIIFEGVAVRV 111
            +A VE  T ++A  A  AL+G    G  ++V
Sbjct: 69  GYALVEYETHKQALAAKEALNGAEIMGQTIQV 100

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 38.0 bits (89), Expect = 6e-04
 Identities = 18/73 (24%), Positives = 33/73 (45%), Gaps = 6/73 (8%)

Query: 303 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNT 362
           ++++E+   YG + N+ +   D+  G + G     +EY        AK AL+G +  G T
Sbjct: 41  DEIQEKFCDYGEIKNIHLNL-DRRTGFSKGYA--LVEYETHKQALAAKEALNGAEIMGQT 97

Query: 363 --VN-AFYYPEDK 372
             V+  F     +
Sbjct: 98  IQVDWCFVKGPKR 110

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 79.2 bits (196), Expect = 1e-18
 Identities = 18/78 (23%), Positives = 42/78 (53%), Gaps = 1/78 (1%)

Query: 152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 211
             ++F+ GLP+  T+ +++E+ ++ GT+    LV +R  G  KG  +  Y++ +    A 
Sbjct: 17  KHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAV 75

Query: 212 AALNGLKMGDKTLTVRRA 229
             ++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 = 51.1 bits (123), Expect = 1e-08
 Identities = 15/85 (17%), Positives = 33/85 (38%), Gaps = 18/85 (21%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-----NHEKKFAFVEM 87
            ++++ GLP    ++ +                G    V ++ +        K  A+VE 
Sbjct: 18  HKLFISGLPFSCTKEELEEICKAH---------GT---VKDLRLVTNRAGKPKGLAYVEY 65

Query: 88  RTVEEASNAM-ALDGIIFEGVAVRV 111
               +AS A+  +DG+  +   ++V
Sbjct: 66  ENESQASQAVMKMDGMTIKENIIKV 90

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 79.2 bits (196), Expect = 1e-18
 Identities = 25/90 (27%), Positives = 35/90 (38%), Gaps = 6/90 (6%)

Query: 147 GGAEGPDR------VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCV 200
           G   GP R      +FV G+    TE  I +    +G +    L  DR TG  KGY    
Sbjct: 12  GDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVE 71

Query: 201 YQDPAVTDIACAALNGLKMGDKTLTVRRAT 230
           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 = 53.4 bits (129), Expect = 3e-09
 Identities = 23/100 (23%), Positives = 42/100 (42%), Gaps = 24/100 (24%)

Query: 27  QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK----- 81
           Q +     ++V G+   A E+ I   F++            G+ + N+++N +++     
Sbjct: 18  QRSVEGWILFVTGVHEEATEEDIHDKFAEY-----------GE-IKNIHLNLDRRTGYLK 65

Query: 82  -FAFVEMRTVEEASNAM-ALDGIIFEGVAVRV-----RRP 114
            +  VE  T +EA  AM  L+G    G  + V     R P
Sbjct: 66  GYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGP 105

>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 = 78.3 bits (194), Expect = 2e-18
 Identities = 18/84 (21%), Positives = 36/84 (42%)

Query: 148 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 207
           G+ G   +++ GL    T+  + +L + +G +     + D+ T   KGYGF  +  P+  
Sbjct: 1   GSSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAA 60

Query: 208 DIACAALNGLKMGDKTLTVRRATA 231
             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 = 50.6 bits (122), Expect = 1e-08
 Identities = 15/90 (16%), Positives = 28/90 (31%), Gaps = 17/90 (18%)

Query: 31  HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAV-VNVYINHE----KKFAFV 85
            +  +Y+ GL P   +Q +                  G  V     ++      K + FV
Sbjct: 4   GSSGLYIRGLQPGTTDQDLVKLCQPY-----------GKIVSTKAILDKTTNKCKGYGFV 52

Query: 86  EMRTVEEASNAM-ALDGIIFEGVAVRVRRP 114
           +  +   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 = 77.7 bits (192), Expect = 4e-18
 Identities = 26/95 (27%), Positives = 41/95 (43%), Gaps = 1/95 (1%)

Query: 137 AAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGY 196
            + G +       E    VFVG L     E  + EL    G L    + KDR+ G  K +
Sbjct: 1   GSSGSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSF 59

Query: 197 GFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA 231
           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 = 53.8 bits (130), Expect = 1e-09
 Identities = 27/98 (27%), Positives = 36/98 (36%), Gaps = 18/98 (18%)

Query: 24  MTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-----NH 78
           M        R V+VG L     E+ +   F Q         AGP   +  V I       
Sbjct: 8   MFPAQEEADRTVFVGNLEARVREEILYELFLQ---------AGP---LTKVTICKDREGK 55

Query: 79  EKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPT 115
            K F FV  +  E  S A+  L+GI   G  + V  P+
Sbjct: 56  PKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGPS 93

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 79.1 bits (195), Expect = 4e-18
 Identities = 22/105 (20%), Positives = 39/105 (37%), Gaps = 4/105 (3%)

Query: 129 QPSPNLNLAAVGLASGAIGGAEGPD----RVFVGGLPYYFTETQIKELLESFGTLHGFDL 184
               N     V   SG  GG+ G       ++VGGL     +  +      FG +    +
Sbjct: 36  YTCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQI 95

Query: 185 VKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA 229
             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 = 53.2 bits (128), Expect = 6e-09
 Identities = 20/92 (21%), Positives = 36/92 (39%), Gaps = 19/92 (20%)

Query: 27  QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEK 80
            +    R +YVGGL    +++ +   F            G    + ++ I         +
Sbjct: 58  GSATTKRVLYVGGLAEEVDDKVLHAAFIP---------FGD---ITDIQIPLDYETEKHR 105

Query: 81  KFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV 111
            FAFVE    E+A+ A+  ++     G  +RV
Sbjct: 106 GFAFVEFELAEDAAAAIDNMNESELFGRTIRV 137

>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 = 77.7 bits (192), Expect = 5e-18
 Identities = 20/86 (23%), Positives = 32/86 (37%), Gaps = 8/86 (9%)

Query: 153 DRVFVGGLPYYFTETQIKELLESFGTL--------HGFDLVKDRDTGNSKGYGFCVYQDP 204
           + +FV GL    T   + +  +  G +           +L  DR+TG  KG     + DP
Sbjct: 14  NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 73

Query: 205 AVTDIACAALNGLKMGDKTLTVRRAT 230
                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 = 57.3 bits (139), Expect = 8e-11
 Identities = 22/98 (22%), Positives = 37/98 (37%), Gaps = 13/98 (13%)

Query: 26  QQATRHARRVYVGGLPPLANEQAIATFFSQ---VMTAIGGNSAGPGDAVVNVYINHE--- 79
             +      ++V GL      +++A +F Q   + T         G  ++N+Y + E   
Sbjct: 7   HHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKT-----GQPMINLYTDRETGK 61

Query: 80  -KKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPT 115
            K  A V       A  A+   DG  F G  ++V   T
Sbjct: 62  LKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFAT 99

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 79.2 bits (195), Expect = 7e-18
 Identities = 26/114 (22%), Positives = 43/114 (37%), Gaps = 2/114 (1%)

Query: 129 QPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFD--LVK 186
           +PSP  N     +     G       V+VG   ++ T+ Q+ +++ S G     +    +
Sbjct: 32  EPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAE 91

Query: 187 DRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQ 240
           +R  G SKGY   V             L G  +  + + VR AT  +      Q
Sbjct: 92  NRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLSQFEAQ 145

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 51.5 bits (123), Expect = 3e-08
 Identities = 24/123 (19%), Positives = 36/123 (29%), Gaps = 18/123 (14%)

Query: 19  MPVQVMTQQATRHAR-RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAV-VNVYI 76
            P  + T    R+ R  VYVG       +Q +                G  D V +    
Sbjct: 41  TPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRS---------IGVYDVVELKFAE 91

Query: 77  NHE----KKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVR--RPTDYNPTLAAALGPGQ 129
           N      K +A V + +       +  L G +  G  V VR     + +   A A     
Sbjct: 92  NRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLSQFEAQARKREC 151

Query: 130 PSP 132
              
Sbjct: 152 VRV 154

>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 = 79.1 bits (195), Expect = 8e-18
 Identities = 23/73 (31%), Positives = 34/73 (46%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
            +FV  +     E +I+E    +G +    L  DR TG SKGY    Y+       A  A
Sbjct: 74  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 133

Query: 214 LNGLKMGDKTLTV 226
           LNG ++  +T+ V
Sbjct: 134 LNGAEIMGQTIQV 146

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A Length = 165

 Score = 54.8 bits (132), Expect = 2e-09
 Identities = 21/105 (20%), Positives = 39/105 (37%), Gaps = 24/105 (22%)

Query: 27  QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK----- 81
           Q +     ++V  +   A E  I   F            G    + N+++N +++     
Sbjct: 67  QRSVEGWILFVTSIHEEAQEDEIQEKFCDY---------GE---IKNIHLNLDRRTGFSK 114

Query: 82  -FAFVEMRTVEEASNAM-ALDGIIFEGVAVRV-----RRPTDYNP 119
            +A VE  T ++A  A  AL+G    G  ++V     + P     
Sbjct: 115 GYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKRVKK 159

>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 = 39.8 bits (93), Expect = 4e-04
 Identities = 18/73 (24%), Positives = 33/73 (45%), Gaps = 6/73 (8%)

Query: 303 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNT 362
           ++++E+   YG + N+ +   D+  G + G     +EY        AK AL+G +  G T
Sbjct: 87  DEIQEKFCDYGEIKNIHLNL-DRRTGFSKGYA--LVEYETHKQALAAKEALNGAEIMGQT 143

Query: 363 --VN-AFYYPEDK 372
             V+  F     +
Sbjct: 144 IQVDWCFVKGPKR 156

>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 = 76.5 bits (189), Expect = 1e-17
 Identities = 22/93 (23%), Positives = 45/93 (48%), Gaps = 3/93 (3%)

Query: 142 ASGAIGGAEGPD---RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGF 198
           +SG+ G    PD    + V GL  Y TE  ++E+   +G +    +V D+ +  S+G+ F
Sbjct: 2   SSGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAF 61

Query: 199 CVYQDPAVTDIACAALNGLKMGDKTLTVRRATA 231
             +++      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 = 49.5 bits (119), Expect = 4e-08
 Identities = 21/86 (24%), Positives = 37/86 (43%), Gaps = 19/86 (22%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFVE 86
             + V GL     E+ +   FS+          GP   + +V I ++++      FAFV 
Sbjct: 16  CCLGVFGLSLYTTERDLREVFSK---------YGP---IADVSIVYDQQSRRSRGFAFVY 63

Query: 87  MRTVEEASNAM-ALDGIIFEGVAVRV 111
              V++A  A    +G+  +G  +RV
Sbjct: 64  FENVDDAKEAKERANGMELDGRRIRV 89

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 76.1 bits (188), Expect = 2e-17
 Identities = 19/89 (21%), Positives = 37/89 (41%)

Query: 142 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 201
           +SG+ G A     ++VGGL     +  +      FG +    +  D +T   +G+ F  +
Sbjct: 2   SSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 61

Query: 202 QDPAVTDIACAALNGLKMGDKTLTVRRAT 230
           +       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 = 48.8 bits (117), Expect = 8e-08
 Identities = 20/94 (21%), Positives = 37/94 (39%), Gaps = 19/94 (20%)

Query: 25  TQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK--- 81
           +       R +YVGGL    +++ +   F            G    + ++ I  + +   
Sbjct: 5   SSGMATTKRVLYVGGLAEEVDDKVLHAAFIP---------FGD---ITDIQIPLDYETEK 52

Query: 82  ---FAFVEMRTVEEASNAM-ALDGIIFEGVAVRV 111
              FAFVE    E+A+ A+  ++     G  +RV
Sbjct: 53  HRGFAFVEFELAEDAAAAIDNMNESELFGRTIRV 86

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 76.1 bits (188), Expect = 2e-17
 Identities = 28/98 (28%), Positives = 44/98 (44%)

Query: 142 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 201
           +SG I        V+VGGL    +E  + EL    G +    + KDR TG  +GYGF  +
Sbjct: 5   SSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEF 64

Query: 202 QDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTE 239
                 D A   ++ +K+  K + V +A+A +      
Sbjct: 65  LSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKNLSGP 102

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 54.2 bits (131), Expect = 1e-09
 Identities = 26/86 (30%), Positives = 38/86 (44%), Gaps = 19/86 (22%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFVE 86
             VYVGGL    +E  +   F Q         AGP   VVN ++  ++       + FVE
Sbjct: 16  ATVYVGGLDEKVSEPLLWELFLQ---------AGP---VVNTHMPKDRVTGQHQGYGFVE 63

Query: 87  MRTVEEASNAM-ALDGIIFEGVAVRV 111
             + E+A  A+  +D I   G  +RV
Sbjct: 64  FLSEEDADYAIKIMDMIKLYGKPIRV 89

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D* Length = 126

 Score = 76.3 bits (188), Expect = 3e-17
 Identities = 25/90 (27%), Positives = 35/90 (38%), Gaps = 6/90 (6%)

Query: 147 GGAEGPDR------VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCV 200
           G   GP R      +FV G+    TE  I +    +G +    L  DR TG  KGY    
Sbjct: 11  GDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVE 70

Query: 201 YQDPAVTDIACAALNGLKMGDKTLTVRRAT 230
           Y+       A   LNG  +  + ++V    
Sbjct: 71  YETYKEAQAAMEGLNGQDLMGQPISVDWCF 100

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D* Length = 126

 Score = 54.3 bits (131), Expect = 2e-09
 Identities = 23/107 (21%), Positives = 43/107 (40%), Gaps = 19/107 (17%)

Query: 34  RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFVEM 87
            ++V G+   A E+ I   F++            G+ + N+++N +++      +  VE 
Sbjct: 24  ILFVTGVHEEATEEDIHDKFAEY-----------GE-IKNIHLNLDRRTGYLKGYTLVEY 71

Query: 88  RTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPN 133
            T +EA  AM  L+G    G  + V       P      G  + S +
Sbjct: 72  ETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPPKGKRRGGRRRSRS 118

>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 = 75.8 bits (187), Expect = 3e-17
 Identities = 27/93 (29%), Positives = 44/93 (47%), Gaps = 5/93 (5%)

Query: 143 SGAIGGAEGPD--RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCV 200
           S    G +  D  ++F+G +P    E  +K L E FG ++   ++KDR TG  KG  F  
Sbjct: 2   SSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLT 61

Query: 201 YQDPAVTDIACAALNGLKM---GDKTLTVRRAT 230
           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 = 41.5 bits (98), Expect = 4e-05
 Identities = 15/98 (15%), Positives = 33/98 (33%), Gaps = 22/98 (22%)

Query: 25  TQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NH 78
           +      A ++++G +P   +E+ +   F +      G        +  + +        
Sbjct: 6   SGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEF-----GK-------IYELTVLKDRFTGM 53

Query: 79  EKKFAFVEMRTVEEASNAM-ALDG---IIFEGVAVRVR 112
            K  AF+     E A  A  AL     +      ++V+
Sbjct: 54  HKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQVK 91

>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 = 74.9 bits (185), Expect = 4e-17
 Identities = 27/76 (35%), Positives = 41/76 (53%), Gaps = 1/76 (1%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
            ++VG L Y  T  Q+KEL   FG +    L+ DR+T   KG+GF   Q+ +V++ A A 
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSE-AIAK 61

Query: 214 LNGLKMGDKTLTVRRA 229
           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 = 46.0 bits (110), Expect = 6e-07
 Identities = 27/87 (31%), Positives = 38/87 (43%), Gaps = 20/87 (22%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFVE 86
           R +YVG L   A  + +   FSQ            G  V NV + ++++      F FVE
Sbjct: 2   RNIYVGNLVYSATSEQVKELFSQF-----------GK-VFNVKLIYDRETKKPKGFGFVE 49

Query: 87  MRTVEEASNAM-ALDGIIFEGVAVRVR 112
           M+  E  S A+  LD   F G  +RV 
Sbjct: 50  MQE-ESVSEAIAKLDNTDFMGRTIRVT 75

>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 = 74.1 bits (183), Expect = 6e-17
 Identities = 15/76 (19%), Positives = 31/76 (40%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
            ++VGGL     +  +      FG +    +  D +T   +G+ F  ++       A   
Sbjct: 9   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 68

Query: 214 LNGLKMGDKTLTVRRA 229
           +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 = 51.8 bits (125), Expect = 6e-09
 Identities = 20/86 (23%), Positives = 36/86 (41%), Gaps = 19/86 (22%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFVE 86
           R +YVGGL    +++ +   F            G    + ++ I  + +      FAFVE
Sbjct: 8   RVLYVGGLAEEVDDKVLHAAFIP---------FGD---ITDIQIPLDYETEKHRGFAFVE 55

Query: 87  MRTVEEASNAM-ALDGIIFEGVAVRV 111
               E+A+ A+  ++     G  +RV
Sbjct: 56  FELAEDAAAAIDNMNESELFGRTIRV 81

>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 = 74.2 bits (183), Expect = 9e-17
 Identities = 27/92 (29%), Positives = 39/92 (42%), Gaps = 3/92 (3%)

Query: 142 ASGAIGGAEGPD---RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGF 198
           +SG+ G     D    + V  L     ET ++EL   FG++    L KD+ TG SKG+ F
Sbjct: 2   SSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAF 61

Query: 199 CVYQDPAVTDIACAALNGLKMGDKTLTVRRAT 230
             +        A A ++G       L V  A 
Sbjct: 62  ISFHRREDAARAIAGVSGFGYDHLILNVEWAK 93

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 48.0 bits (115), Expect = 2e-07
 Identities = 17/97 (17%), Positives = 36/97 (37%), Gaps = 22/97 (22%)

Query: 34  RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFVEM 87
            + V  L     E  +   F       G        ++  +Y+  +K       FAF+  
Sbjct: 17  TIRVTNLSEDTRETDLQELFRP----FG--------SISRIYLAKDKTTGQSKGFAFISF 64

Query: 88  RTVEEASNAM-ALDGIIFEGVAVRV---RRPTDYNPT 120
              E+A+ A+  + G  ++ + + V   +  T+  P+
Sbjct: 65  HRREDAARAIAGVSGFGYDHLILNVEWAKPSTNSGPS 101

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score = 74.7 bits (184), Expect = 9e-17
 Identities = 28/94 (29%), Positives = 46/94 (48%), Gaps = 1/94 (1%)

Query: 149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 208
           A+ P ++F+GGL     E  +K +    G +    L+KDR T  S+G+ F  +++PA   
Sbjct: 4   ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAK 62

Query: 209 IACAALNGLKMGDKTLTVRRATASSGQSKTEQES 242
            A   +NG  +  K + V +A   S QS   +  
Sbjct: 63  NAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRP 96

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score = 48.5 bits (116), Expect = 2e-07
 Identities = 21/109 (19%), Positives = 38/109 (34%), Gaps = 24/109 (22%)

Query: 34  RVYVGGLPPLANEQAIATFFSQ--------VMTAIGGNSAGPGDAVVNVYINHEKKFAFV 85
           ++++GGL    NE+ +   F +        ++      S G               FAF+
Sbjct: 9   KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRG---------------FAFI 53

Query: 86  EMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPN 133
                 +A NA   ++G    G A++V +    +        P   S N
Sbjct: 54  TFENPADAKNAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSRN 102

>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 = 74.3 bits (183), Expect = 9e-17
 Identities = 26/106 (24%), Positives = 39/106 (36%), Gaps = 6/106 (5%)

Query: 142 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 201
           +SG          VF+  L +   E  + E+L+ FG L    +V   DT +SKG  F  +
Sbjct: 5   SSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQF 64

Query: 202 QDPAVTDIACAALN------GLKMGDKTLTVRRATASSGQSKTEQE 241
                     AA +      GLK+  + L V  A      +     
Sbjct: 65  MTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAASGPSS 110

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 47.0 bits (112), Expect = 5e-07
 Identities = 18/96 (18%), Positives = 32/96 (33%), Gaps = 25/96 (26%)

Query: 29  TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKF 82
               + V++  L   + E+A+     Q          G    +  V +       H K  
Sbjct: 12  VTEGKTVFIRNLSFDSEEEALGEVLQQF---------GD---LKYVRVVLHPDTEHSKGC 59

Query: 83  AFVEMRTVEEASNAMA-------LDGIIFEGVAVRV 111
           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 = 73.3 bits (181), Expect = 1e-16
 Identities = 17/77 (22%), Positives = 33/77 (42%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
            +FVG L     +  ++   + F +     ++ D  TG+S+GYGF  +        A  +
Sbjct: 3   NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62

Query: 214 LNGLKMGDKTLTVRRAT 230
           + 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 = 44.0 bits (105), Expect = 3e-06
 Identities = 18/88 (20%), Positives = 33/88 (37%), Gaps = 25/88 (28%)

Query: 34  RVYVGGLPPLANEQAIATFFSQ--------VMT-AIGGNSAGPGDAVVNVYINHEKKFAF 84
            ++VG L    +++ +   F          VM     G+S G               + F
Sbjct: 3   NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRG---------------YGF 47

Query: 85  VEMRTVEEASNAM-ALDGIIFEGVAVRV 111
           V   + ++A NAM ++ G    G  +R+
Sbjct: 48  VSFTSQDDAQNAMDSMQGQDLNGRPLRI 75

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 73.1 bits (180), Expect = 2e-16
 Identities = 16/90 (17%), Positives = 36/90 (40%)

Query: 142 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 201
           +SG+  G  GP  + V  +P+  +  +I +    +  + G   +K  + G   G     +
Sbjct: 5   SSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAF 64

Query: 202 QDPAVTDIACAALNGLKMGDKTLTVRRATA 231
           +       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 = 45.8 bits (109), Expect = 9e-07
 Identities = 15/86 (17%), Positives = 28/86 (32%), Gaps = 13/86 (15%)

Query: 34  RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK---FAFVEMRTV 90
            + V  +P   +   I  FF                  V +  N +      A V   + 
Sbjct: 17  VIKVQNMPFTVSIDEILDFFYGY---------QVIPGSVCLKYNEKGMPTGEAMVAFESR 67

Query: 91  EEASNAMA-LDGIIFEGVAVRVRRPT 115
           +EA+ A+  L+        V++  P+
Sbjct: 68  DEATAAVIDLNDRPIGSRKVKLSGPS 93

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 73.9 bits (182), Expect = 2e-16
 Identities = 33/113 (29%), Positives = 51/113 (45%), Gaps = 1/113 (0%)

Query: 117 YNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESF 176
              + +A       S  L+ AA   A   I G EG   +F+  LP  FT+T +      F
Sbjct: 6   QFGSASALSTSPLASVALSAAAAAAAGKQIEGPEGC-NLFIYHLPQEFTDTDLASTFLPF 64

Query: 177 GTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA 229
           G +    +  D+ T  SK +GF  + +P    +A  A+NG ++G K L V+  
Sbjct: 65  GNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLK 117

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 73.1 bits (180), Expect = 2e-16
 Identities = 21/85 (24%), Positives = 35/85 (41%), Gaps = 3/85 (3%)

Query: 148 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGN---SKGYGFCVYQDP 204
           G+ G   +F+  L +  TE  +K +    G +    + K ++      S G+GF  Y+ P
Sbjct: 1   GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60

Query: 205 AVTDIACAALNGLKMGDKTLTVRRA 229
                A   L G  +    L VR +
Sbjct: 61  EQAQKALKQLQGHTVDGHKLEVRIS 85

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 42.6 bits (101), Expect = 1e-05
 Identities = 16/89 (17%), Positives = 28/89 (31%), Gaps = 20/89 (22%)

Query: 34  RVYVGGLPPLANEQAIATFFSQ--------VMTAIGGNSAGPGDAVVNVYINHEKKFAFV 85
            +++  L     E+ +   FS+        +                         F FV
Sbjct: 7   GLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVL-----------LSMGFGFV 55

Query: 86  EMRTVEEASNAM-ALDGIIFEGVAVRVRR 113
           E +  E+A  A+  L G   +G  + VR 
Sbjct: 56  EYKKPEQAQKALKQLQGHTVDGHKLEVRI 84

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 73.0 bits (180), Expect = 2e-16
 Identities = 23/84 (27%), Positives = 37/84 (44%)

Query: 148 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 207
           G+ G  R+FV  L Y  +E  +++L  ++G L       D  T   KG+ F  +  P   
Sbjct: 4   GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHA 63

Query: 208 DIACAALNGLKMGDKTLTVRRATA 231
             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 = 50.7 bits (122), Expect = 2e-08
 Identities = 21/85 (24%), Positives = 34/85 (40%), Gaps = 19/85 (22%)

Query: 34  RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEM 87
           R++V  L   ++E+ +   FS           GP   +  ++          K FAFV  
Sbjct: 10  RLFVRNLSYTSSEEDLEKLFSAY---------GP---LSELHYPIDSLTKKPKGFAFVTF 57

Query: 88  RTVEEASNAM-ALDGIIFEGVAVRV 111
              E A  A   +DG +F+G  + V
Sbjct: 58  MFPEHAVKAYAEVDGQVFQGRMLHV 82

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 73.6 bits (181), Expect = 2e-16
 Identities = 20/87 (22%), Positives = 32/87 (36%), Gaps = 8/87 (9%)

Query: 152 PDRVFVGGLPYYFTETQIKELLESFGTL--------HGFDLVKDRDTGNSKGYGFCVYQD 203
            + +FV GL    T   + +  +  G +           +L  DR+TG  KG     + D
Sbjct: 7   NNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDD 66

Query: 204 PAVTDIACAALNGLKMGDKTLTVRRAT 230
           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 = 55.5 bits (134), Expect = 5e-10
 Identities = 26/104 (25%), Positives = 42/104 (40%), Gaps = 14/104 (13%)

Query: 26  QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIG--GNSAGPGDAVVNVYINHE---- 79
           +Q       ++V GL      +++A +F Q    IG    +   G  ++N+Y + E    
Sbjct: 1   EQDNSDNNTIFVQGLGENVTIESVADYFKQ----IGIIKTNKKTGQPMINLYTDRETGKL 56

Query: 80  KKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV---RRPTDYNP 119
           K  A V       A  A+   DG  F G  ++V    R  D+N 
Sbjct: 57  KGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNR 100

>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 = 73.2 bits (180), Expect = 2e-16
 Identities = 22/101 (21%), Positives = 35/101 (34%), Gaps = 14/101 (13%)

Query: 144 GAIGGAEGPDR------VFVGGLPYYFTETQIKELLESFGTL--------HGFDLVKDRD 189
           G+ G +  PD       ++V GL    T   + +  +  G +            +  D++
Sbjct: 1   GSSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKE 60

Query: 190 TGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT 230
           TG  KG     Y+DP     A    +G       L V  A 
Sbjct: 61  TGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLAR 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 = 55.5 bits (134), Expect = 6e-10
 Identities = 21/86 (24%), Positives = 35/86 (40%), Gaps = 7/86 (8%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE----KKFAFVEMR 88
             +YV GL        +A FF Q    +   +   G  ++++Y++ E    K  A V   
Sbjct: 16  SAIYVQGLNDSVTLDDLADFFKQC--GVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYE 73

Query: 89  TVEEASNAM-ALDGIIFEGVAVRVRR 113
               A  A+   DG  F+G  ++V  
Sbjct: 74  DPPTAKAAVEWFDGKDFQGSKLKVSL 99

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 73.1 bits (180), Expect = 3e-16
 Identities = 23/109 (21%), Positives = 44/109 (40%), Gaps = 6/109 (5%)

Query: 142 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 201
           +SGA+        VFV  L Y     ++KE+    G +   D+++D+D G S+G G   +
Sbjct: 5   SSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD-GKSRGIGTVTF 63

Query: 202 QDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQH 250
           +       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 = 51.9 bits (125), Expect = 8e-09
 Identities = 20/118 (16%), Positives = 31/118 (26%), Gaps = 26/118 (22%)

Query: 27  QATRHARRVYVGGLPPLANEQAIATFFSQ--------VMTAIGGNSAGPGDAVVNVYINH 78
           QA R    V+V  L      + +   FS         ++    G S G            
Sbjct: 10  QAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRG------------ 57

Query: 79  EKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVR--RPTDYNPTLAAALGPGQPSPN 133
                 V      EA  A+   +G +     + V+                P Q  P+
Sbjct: 58  ---IGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERALPKGDFFPPERPQQSGPS 112

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 73.2 bits (180), Expect = 3e-16
 Identities = 11/83 (13%), Positives = 25/83 (30%)

Query: 147 GGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAV 206
           GG      V    L     ET +K++   +G +   +++    T    G    ++     
Sbjct: 1   GGQIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRG 60

Query: 207 TDIACAALNGLKMGDKTLTVRRA 229
                  L+   +    +  +  
Sbjct: 61  AKETVKNLHLTSVMGNIIHAQLD 83

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 52.4 bits (126), Expect = 6e-09
 Identities = 12/93 (12%), Positives = 20/93 (21%), Gaps = 19/93 (20%)

Query: 31  HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAF 84
             + V    L     E  +     +          G    V  V I    +       A 
Sbjct: 5   PLKEVTFARLNDNVRETFLKDMCRKY---------GE---VEEVEILLHPRTRKHLGLAR 52

Query: 85  VEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTD 116
           V   +   A   +  L      G  +  +    
Sbjct: 53  VLFTSTRGAKETVKNLHLTSVMGNIIHAQLDIK 85

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 38.5 bits (90), Expect = 5e-04
 Identities = 14/76 (18%), Positives = 26/76 (34%), Gaps = 3/76 (3%)

Query: 303 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNT 362
             +++ C KYG +  V I        +  G+    + +    G       L      GN 
Sbjct: 21  TFLKDMCRKYGEVEEVEILL-HPRTRKHLGLA--RVLFTSTRGAKETVKNLHLTSVMGNI 77

Query: 363 VNAFYYPEDKYFNKDY 378
           ++A    + +   K Y
Sbjct: 78  IHAQLDIKGQQRMKYY 93

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129

 Score = 73.6 bits (181), Expect = 3e-16
 Identities = 17/81 (20%), Positives = 38/81 (46%)

Query: 150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 209
           +    + V GL  Y TE  ++E+   +G +    +V D+ +  S+G+ F  +++      
Sbjct: 44  DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 103

Query: 210 ACAALNGLKMGDKTLTVRRAT 230
           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 = 52.4 bits (126), Expect = 8e-09
 Identities = 23/94 (24%), Positives = 40/94 (42%), Gaps = 24/94 (25%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFVE 86
             + V GL     E+ +   FS+          GP   + +V I ++++      FAFV 
Sbjct: 47  CCLGVFGLSLYTTERDLREVFSKY---------GP---IADVSIVYDQQSRRSRGFAFVY 94

Query: 87  MRTVEEASNAM-ALDGIIFEGVAVRV-----RRP 114
              V++A  A    +G+  +G  +RV     +RP
Sbjct: 95  FENVDDAKEAKERANGMELDGRRIRVDFSITKRP 128

>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 = 72.3 bits (178), Expect = 4e-16
 Identities = 20/94 (21%), Positives = 38/94 (40%), Gaps = 1/94 (1%)

Query: 142 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 201
           +SGA  G  GP  + V  +P+  +  +I +    +  + G   +K  + G   G     +
Sbjct: 5   SSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAF 64

Query: 202 QDPAVTDIACAALNGLKMGDKTLTVRRAT-ASSG 234
           +       A   LN   +G + + +   +  SSG
Sbjct: 65  ESRDEATAAVIDLNDRPIGSRKVKLVLGSGPSSG 98

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 44.6 bits (106), Expect = 3e-06
 Identities = 14/83 (16%), Positives = 26/83 (31%), Gaps = 13/83 (15%)

Query: 35  VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK---FAFVEMRTVE 91
           + V  +P   +   I  FF                  V +  N +      A V   + +
Sbjct: 18  IKVQNMPFTVSIDEILDFFYGY---------QVIPGSVCLKYNEKGMPTGEAMVAFESRD 68

Query: 92  EASNAMA-LDGIIFEGVAVRVRR 113
           EA+ A+  L+        V++  
Sbjct: 69  EATAAVIDLNDRPIGSRKVKLVL 91

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 74.5 bits (183), Expect = 4e-16
 Identities = 35/162 (21%), Positives = 57/162 (35%), Gaps = 18/162 (11%)

Query: 97  MALDGIIFE---------GVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIG 147
           M+LD II           G   R  RP              +P P  +     L     G
Sbjct: 21  MSLDDIIKLNRNQRRVNRGGGPRRNRPAIARGGRNRPAPYSRPKPLPDKWQHDLFDSGCG 80

Query: 148 GAEGPD---RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP 204
           G EG +   ++ V  L +  ++  I+EL   FGTL    +  DR +G S G     ++  
Sbjct: 81  GGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERR 139

Query: 205 AVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQ 246
           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 = 45.2 bits (107), Expect = 6e-06
 Identities = 12/85 (14%), Positives = 30/85 (35%), Gaps = 18/85 (21%)

Query: 34  RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-----FAFVEMR 88
           ++ V  L    ++  I   F++          G    +    +++++       A V   
Sbjct: 90  KLLVSNLDFGVSDADIQELFAEF---------GT---LKKAAVDYDRSGRSLGTADVHFE 137

Query: 89  TVEEASNAMA-LDGIIFEGVAVRVR 112
              +A  AM    G+  +G  + ++
Sbjct: 138 RRADALKAMKQYKGVPLDGRPMDIQ 162

>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 = 78.4 bits (192), Expect = 4e-16
 Identities = 17/83 (20%), Positives = 35/83 (42%), Gaps = 1/83 (1%)

Query: 152 PDRV-FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA 210
             +  FV  + Y  TE++++   E +G +    +V  + +G  +GY F  Y+       A
Sbjct: 101 AFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSA 160

Query: 211 CAALNGLKMGDKTLTVRRATASS 233
               +G K+  + + V      +
Sbjct: 161 YKHADGKKIDGRRVLVDVERGRT 183

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 40.6 bits (94), Expect = 6e-04
 Identities = 15/95 (15%), Positives = 31/95 (32%), Gaps = 19/95 (20%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFVE 86
           + ++V  +     E  +   F            GP   +  +++ + K+      +AF+E
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVY---------GP---IKRIHMVYSKRSGKPRGYAFIE 150

Query: 87  MRTVEEASNAMA-LDGIIFEGVAVRVRRPTDYNPT 120
                +  +A    DG   +G  V V         
Sbjct: 151 YEHERDMHSAYKHADGKKIDGRRVLVDVERGRTVK 185

>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 = 71.5 bits (176), Expect = 9e-16
 Identities = 18/91 (19%), Positives = 40/91 (43%)

Query: 140 GLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC 199
           G +  +    +G   + V  L Y  +   ++ + E +G +    + ++  T   +G+ F 
Sbjct: 1   GSSGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFV 60

Query: 200 VYQDPAVTDIACAALNGLKMGDKTLTVRRAT 230
            + 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 = 50.7 bits (122), Expect = 2e-08
 Identities = 22/98 (22%), Positives = 34/98 (34%), Gaps = 24/98 (24%)

Query: 34  RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI--NHE----KKFAFVEM 87
            + V  L    +  ++   F +          G    V +VYI         + FAFV  
Sbjct: 15  TLKVDNLTYRTSPDSLRRVFEK---------YGR---VGDVYIPREPHTKAPRGFAFVRF 62

Query: 88  RTVEEASNAM-ALDGIIFEGVAVRV-----RRPTDYNP 119
               +A +A  A+DG   +G  +RV      R     P
Sbjct: 63  HDRRDAQDAEAAMDGAELDGRELRVQVARYGRRDLSGP 100

>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 = 37.6 bits (88), Expect = 8e-04
 Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 3/61 (4%)

Query: 303 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNT 362
           + +R    KYG + +V IPR + +     G    F+ ++D      A+ A+ G +  G  
Sbjct: 28  DSLRRVFEKYGRVGDVYIPR-EPHTKAPRGFA--FVRFHDRRDAQDAEAAMDGAELDGRE 84

Query: 363 V 363
           +
Sbjct: 85  L 85

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 72.1 bits (177), Expect = 1e-15
 Identities = 20/84 (23%), Positives = 38/84 (45%)

Query: 147 GGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAV 206
              EG   + V  L Y  +   ++ + E +G +    + +DR T  S+G+ F  + D   
Sbjct: 42  PDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRD 101

Query: 207 TDIACAALNGLKMGDKTLTVRRAT 230
            + 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 = 52.8 bits (127), Expect = 8e-09
 Identities = 24/97 (24%), Positives = 37/97 (38%), Gaps = 24/97 (24%)

Query: 32  ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI--NHE----KKFAFV 85
              + V  L    +   +   F +          G    V +VYI  +      + FAFV
Sbjct: 47  MTSLKVDNLTYRTSPDTLRRVFEKY---------GR---VGDVYIPRDRYTKESRGFAFV 94

Query: 86  EMRTVEEASNAM-ALDGIIFEGVAVRV-----RRPTD 116
                 +A +AM A+DG + +G  +RV      RP D
Sbjct: 95  RFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPD 131

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score = 72.5 bits (178), Expect = 1e-15
 Identities = 20/74 (27%), Positives = 34/74 (45%)

Query: 153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA 212
             ++VG L +Y TE QI EL    G +    +  D+    + G+ F  Y   A  + A  
Sbjct: 40  CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 99

Query: 213 ALNGLKMGDKTLTV 226
            +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 = 52.1 bits (125), Expect = 2e-08
 Identities = 21/93 (22%), Positives = 39/93 (41%), Gaps = 19/93 (20%)

Query: 26  QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI--NHEKK-- 81
           ++  + +  +YVG L     E+ I   FS+         +G    +  + +  +  KK  
Sbjct: 33  EKLLKKSCTLYVGNLSFYTTEEQIYELFSK---------SGD---IKKIIMGLDKMKKTA 80

Query: 82  --FAFVEMRTVEEASNAM-ALDGIIFEGVAVRV 111
             F FVE  +  +A NAM  ++G   +   +R 
Sbjct: 81  CGFCFVEYYSRADAENAMRYINGTRLDDRIIRT 113

>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 = 71.2 bits (175), Expect = 1e-15
 Identities = 31/101 (30%), Positives = 42/101 (41%)

Query: 142 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 201
           +SG          VFVG L    T   IK     FG +    +VKD  TG SKGYGF  +
Sbjct: 5   SSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSF 64

Query: 202 QDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQES 242
            +    + A   + G  +G + +    AT      K+  ES
Sbjct: 65  FNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYES 105

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score = 43.9 bits (104), Expect = 6e-06
 Identities = 24/112 (21%), Positives = 35/112 (31%), Gaps = 29/112 (25%)

Query: 34  RVYVGGLPPLANEQAIATFFSQ--------VMT-AIGGNSAGPGDAVVNVYINHEKKFAF 84
            V+VG L P    + I   F+         V+     G S G               + F
Sbjct: 17  HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKG---------------YGF 61

Query: 85  VEMRTVEEASNAM-ALDGIIFEGVAVRV----RRPTDYNPTLAAALGPGQPS 131
           V      +A NA+  + G    G  +R     R+P     T  +      PS
Sbjct: 62  VSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYESNTKQSGPS 113

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score = 71.2 bits (175), Expect = 1e-15
 Identities = 31/117 (26%), Positives = 53/117 (45%), Gaps = 6/117 (5%)

Query: 131 SPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDT 190
           S  L   ++G A     G EG   +F+  LP  F +  + ++   FG +    +  D+ T
Sbjct: 5   SSGLTQQSIGAAGSQKEGPEGA-NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQT 63

Query: 191 GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQA 247
             SK +GF  Y +P     A  ++NG ++G K L V+       +SK + +S  +  
Sbjct: 64  NLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK-----RSKNDSKSGPSSG 115

>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 = 38.5 bits (90), Expect = 5e-04
 Identities = 14/97 (14%), Positives = 29/97 (29%), Gaps = 27/97 (27%)

Query: 35  VYVGGLPPLANEQAIATFFSQ--------VMT-AIGGNSAGPGDAVVNVYINHEKKFAFV 85
           +++  LP    +Q +   F          V        S                 F FV
Sbjct: 28  LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKC---------------FGFV 72

Query: 86  EMRTVEEASNAM-ALDGIIFEG--VAVRVRRPTDYNP 119
                  A  A+ +++G       + V+++R  + + 
Sbjct: 73  SYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSK 109

>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 = 70.3 bits (173), Expect = 2e-15
 Identities = 14/79 (17%), Positives = 31/79 (39%), Gaps = 2/79 (2%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFD--LVKDRDTGNSKGYGFCVYQDPAVTDIAC 211
            +++G L ++ T+  + E + S G     +    ++R  G SKG+        A +    
Sbjct: 3   ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62

Query: 212 AALNGLKMGDKTLTVRRAT 230
             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 = 49.5 bits (119), Expect = 4e-08
 Identities = 14/94 (14%), Positives = 29/94 (30%), Gaps = 17/94 (18%)

Query: 34  RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAV-VNVYINHE----KKFAFVEMR 88
            +Y+G L     ++ +      +         G  D + +  + N      K FA V + 
Sbjct: 3   ALYIGNLTWWTTDEDLTEAVHSL---------GVNDILEIKFFENRANGQSKGFALVGVG 53

Query: 89  TVEEASNAM-ALDGIIFEGVAVRVR--RPTDYNP 119
           +   +   M  L      G    V      +++ 
Sbjct: 54  SEASSKKLMDLLPKRELHGQNPVVTPSNKLEHHH 87

>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 = 70.3 bits (173), Expect = 2e-15
 Identities = 19/84 (22%), Positives = 40/84 (47%), Gaps = 1/84 (1%)

Query: 149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDR-DTGNSKGYGFCVYQDPAVT 207
           +  P +V +G L    T+  I E+  ++G +   D+  +R     SKGY +  +++P   
Sbjct: 1   SMKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEA 60

Query: 208 DIACAALNGLKMGDKTLTVRRATA 231
           + 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 = 47.9 bits (115), Expect = 1e-07
 Identities = 17/86 (19%), Positives = 32/86 (37%), Gaps = 20/86 (23%)

Query: 34  RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-------NHEKKFAFVE 86
           +V++G L     +  I   FS      G         +  + +       +  K +A+VE
Sbjct: 6   KVHIGRLTRNVTKDHIMEIFST----YG--------KIKMIDMPVERMHPHLSKGYAYVE 53

Query: 87  MRTVEEASNAM-ALDGIIFEGVAVRV 111
               +EA  A+  +DG   +G  +  
Sbjct: 54  FENPDEAEKALKHMDGGQIDGQEITA 79

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 70.7 bits (174), Expect = 2e-15
 Identities = 26/103 (25%), Positives = 42/103 (40%), Gaps = 8/103 (7%)

Query: 147 GGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAV 206
            G   P+ VFVGG+     ET+I+     +G++    ++ DR TG SKGYGF  + +   
Sbjct: 4   EGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVD 62

Query: 207 TDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQ 249
                   + +    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 = 43.0 bits (102), Expect = 1e-05
 Identities = 17/88 (19%), Positives = 31/88 (35%), Gaps = 24/88 (27%)

Query: 34  RVYVGGLPPLANEQAIATFFSQ--------VMTAIGGNSAGPGDAVVNVYINHEKKFAFV 85
            V+VGG+    +E  I +FF++        ++T   G S G               + FV
Sbjct: 11  TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKG---------------YGFV 55

Query: 86  EMRTVEEASNAMALDGIIFEGVAVRVRR 113
                 +    +    I F G  +++  
Sbjct: 56  SFYNDVDVQKIVE-SQINFHGKKLKLGP 82

>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 = 71.2 bits (175), Expect = 2e-15
 Identities = 22/105 (20%), Positives = 40/105 (38%), Gaps = 6/105 (5%)

Query: 142 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 201
             G   G E   ++ V  L +  ++  I+EL   FGTL    +  DR +G S G     +
Sbjct: 25  GCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHF 83

Query: 202 QDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQ 246
           +  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 = 43.1 bits (102), Expect = 2e-05
 Identities = 15/87 (17%), Positives = 26/87 (29%), Gaps = 24/87 (27%)

Query: 34  RVYVGGLPPLANEQAIATFFSQ--------VMTAIGGNSAGPGDAVVNVYINHEKKFAFV 85
           ++ V  L    ++  I   F++        V     G S G                A V
Sbjct: 37  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLG---------------TADV 81

Query: 86  EMRTVEEASNAM-ALDGIIFEGVAVRV 111
                 +A  AM    G+  +G  + +
Sbjct: 82  HFERRADALKAMKQYKGVPLDGRPMDI 108

>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 = 2e-15
 Identities = 18/76 (23%), Positives = 31/76 (40%), Gaps = 5/76 (6%)

Query: 295 DEEYEEILEDM-REECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNAL 353
            E Y+E  E++  E   KYG +  + +            VG V++++        A   L
Sbjct: 33  QEHYDEFFEEVFTEMEEKYGEVEEMNVCDN----LGDHLVGNVYVKFRREEDAEKAVIDL 88

Query: 354 SGRKFGGNTVNAFYYP 369
           + R F G  ++A   P
Sbjct: 89  NNRWFNGQPIHAELSP 104

>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 = 70.8 bits (174), Expect = 2e-15
 Identities = 20/89 (22%), Positives = 33/89 (37%), Gaps = 8/89 (8%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
            +++  L    TE  +  L   F    G  +     TG  +G  F  + +  +   A   
Sbjct: 27  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 86

Query: 214 LNGLKMGDKTLTV--------RRATASSG 234
           +NG K+  K L +        R +  SSG
Sbjct: 87  VNGYKLYGKILVIEFGKNKKQRSSGPSSG 115

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 43.0 bits (102), Expect = 1e-05
 Identities = 12/83 (14%), Positives = 28/83 (33%), Gaps = 13/83 (15%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK---FAFVEMRT 89
           + +Y+  L P   E+ + + F++                   +     +    AF+    
Sbjct: 26  KVLYLKNLSPRVTERDLVSLFARF---------QEKKGPPIQFRMMTGRMRGQAFITFPN 76

Query: 90  VEEASNAM-ALDGIIFEGVAVRV 111
            E A  A+  ++G    G  + +
Sbjct: 77  KEIAWQALHLVNGYKLYGKILVI 99

>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 = 70.5 bits (173), Expect = 3e-15
 Identities = 18/98 (18%), Positives = 40/98 (40%), Gaps = 3/98 (3%)

Query: 153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA 212
             +++  LPY  T  ++ ++   +G +    +     T  ++G  + VY+D      A  
Sbjct: 9   RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNAVD 65

Query: 213 ALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQH 250
            L+G  + ++ L V    A+    K + +    Q +  
Sbjct: 66  HLSGFNVSNRYLVVLYYNANRAFQKMDTKKKEEQLKLL 103

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 48.9 bits (117), Expect = 1e-07
 Identities = 15/83 (18%), Positives = 30/83 (36%), Gaps = 16/83 (19%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK---FAFVEMRT 89
           R +Y+  LP     + +   F +          GP   +  + + +  +    A+V    
Sbjct: 9   RILYIRNLPYKITAEEMYDIFGKY---------GP---IRQIRVGNTPETRGTAYVVYED 56

Query: 90  VEEASNAM-ALDGIIFEGVAVRV 111
           + +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 = 43.9 bits (104), Expect = 6e-06
 Identities = 19/74 (25%), Positives = 30/74 (40%), Gaps = 6/74 (8%)

Query: 303 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNT 362
           E+M +  GKYG +  + +        ET G    ++ Y D      A + LSG       
Sbjct: 23  EEMYDIFGKYGPIRQIRVGNT----PETRGTA--YVVYEDIFDAKNAVDHLSGFNVSNRY 76

Query: 363 VNAFYYPEDKYFNK 376
           +   YY  ++ F K
Sbjct: 77  LVVLYYNANRAFQK 90

>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 = 70.0 bits (172), Expect = 3e-15
 Identities = 23/97 (23%), Positives = 46/97 (47%), Gaps = 2/97 (2%)

Query: 142 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 201
           +SG       P R+ V  +P+ F +  ++++   FG +   +++ +     SKG+GF  +
Sbjct: 5   SSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTF 62

Query: 202 QDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKT 238
           ++ A  D A   L+G  +  + + V  ATA    +  
Sbjct: 63  ENSADADRAREKLHGTVVEGRKIEVNNATARVMTNSG 99

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 48.8 bits (117), Expect = 1e-07
 Identities = 19/84 (22%), Positives = 31/84 (36%), Gaps = 17/84 (20%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI----NHEKKFAFVEMR 88
           +R++V  +P    +  +   F Q          G    +++V I       K F FV   
Sbjct: 16  KRLHVSNIPFRFRDPDLRQMFGQ---------FGK---ILDVEIIFNERGSKGFGFVTFE 63

Query: 89  TVEEASNAM-ALDGIIFEGVAVRV 111
              +A  A   L G + EG  + V
Sbjct: 64  NSADADRAREKLHGTVVEGRKIEV 87

>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 = 71.8 bits (176), Expect = 3e-15
 Identities = 20/82 (24%), Positives = 38/82 (46%)

Query: 149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 208
            EG   + V  L Y  +   ++ + E +G +    + +DR T  S+G+ F  + D    +
Sbjct: 67  VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAE 126

Query: 209 IACAALNGLKMGDKTLTVRRAT 230
            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 = 52.9 bits (127), Expect = 1e-08
 Identities = 24/99 (24%), Positives = 39/99 (39%), Gaps = 24/99 (24%)

Query: 34  RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI--NHE----KKFAFVEM 87
            + V  L    +   +   F +          G    V +VYI  +      + FAFV  
Sbjct: 72  SLKVDNLTYRTSPDTLRRVFEK---------YGR---VGDVYIPRDRYTKESRGFAFVRF 119

Query: 88  RTVEEASNAM-ALDGIIFEGVAVRV-----RRPTDYNPT 120
               +A +AM A+DG + +G  +RV      RP D + +
Sbjct: 120 HDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPDSHHS 158

>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 = 38.7 bits (90), Expect = 8e-04
 Identities = 17/61 (27%), Positives = 29/61 (47%), Gaps = 3/61 (4%)

Query: 303 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNT 362
           + +R    KYG + +V IPR D+   E+ G    F+ ++D      A +A+ G    G  
Sbjct: 85  DTLRRVFEKYGRVGDVYIPR-DRYTKESRGFA--FVRFHDKRDAEDAMDAMDGAVLDGRE 141

Query: 363 V 363
           +
Sbjct: 142 L 142

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 70.0 bits (172), Expect = 3e-15
 Identities = 17/89 (19%), Positives = 32/89 (35%), Gaps = 4/89 (4%)

Query: 142 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 201
           +SG    +     + +  L Y  TE  ++E+ E    +     V     G SKGY F  +
Sbjct: 5   SSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFI----KVPQNQNGKSKGYAFIEF 60

Query: 202 QDPAVTDIACAALNGLKMGDKTLTVRRAT 230
                   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 = 49.2 bits (118), Expect = 6e-08
 Identities = 18/86 (20%), Positives = 34/86 (39%), Gaps = 21/86 (24%)

Query: 32  ARRVYVGGLPPLANEQAIATFFSQ-----VMTAIGGNSAGPGDAVVNVYINHEKKFAFVE 86
           ++ + +  L   A E+ +   F +     V     G S G               +AF+E
Sbjct: 15  SKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKG---------------YAFIE 59

Query: 87  MRTVEEASNAM-ALDGIIFEGVAVRV 111
             + E+A  A+ + +    EG A+R+
Sbjct: 60  FASFEDAKEALNSCNKREIEGRAIRL 85

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 69.5 bits (171), Expect = 3e-15
 Identities = 16/83 (19%), Positives = 37/83 (44%), Gaps = 2/83 (2%)

Query: 148 GAEGPDR-VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAV 206
           G E   R ++VG + Y  T  +++      G+++   ++ D+ +G+ KG+ +  + D   
Sbjct: 1   GMEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKES 60

Query: 207 TDIACAALNGLKMGDKTLTVRRA 229
              +  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 = 61.8 bits (151), Expect = 2e-12
 Identities = 23/88 (26%), Positives = 34/88 (38%), Gaps = 18/88 (20%)

Query: 32  ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFV 85
           AR +YVG +   A  + +   F              G  V  V I       H K FA++
Sbjct: 6   ARSIYVGNVDYGATAEELEAHFHGC-----------GS-VNRVTILCDKFSGHPKGFAYI 53

Query: 86  EMRTVEEASNAMALDGIIFEGVAVRVRR 113
           E    E    ++ALD  +F G  ++V  
Sbjct: 54  EFSDKESVRTSLALDESLFRGRQIKVIP 81

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 69.6 bits (171), Expect = 4e-15
 Identities = 13/88 (14%), Positives = 31/88 (35%), Gaps = 5/88 (5%)

Query: 149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 208
                 +    L +  TE ++KE+ E        ++      G SKG  +  ++  A  +
Sbjct: 13  VRAARTLLAKNLSFNITEDELKEVFEDAL-----EIRLVSQDGKSKGIAYIEFKSEADAE 67

Query: 209 IACAALNGLKMGDKTLTVRRATASSGQS 236
                  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 = 47.6 bits (114), Expect = 2e-07
 Identities = 14/88 (15%), Positives = 28/88 (31%), Gaps = 12/88 (13%)

Query: 25  TQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAF 84
           T +  R AR +    L     E  +   F               +  +       K  A+
Sbjct: 9   TSKKVRAARTLLAKNLSFNITEDELKEVFEDA-----------LEIRLVSQDGKSKGIAY 57

Query: 85  VEMRTVEEASNAM-ALDGIIFEGVAVRV 111
           +E ++  +A   +    G   +G +V +
Sbjct: 58  IEFKSEADAEKNLEEKQGAEIDGRSVSL 85

>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 = 70.5 bits (173), Expect = 4e-15
 Identities = 17/76 (22%), Positives = 36/76 (47%), Gaps = 1/76 (1%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
            V+VG + Y  T   ++    S G+++   ++ D+ +G+ KGY +  + +    D A  A
Sbjct: 38  SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAA-VA 96

Query: 214 LNGLKMGDKTLTVRRA 229
           ++      +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 = 60.5 bits (147), Expect = 1e-11
 Identities = 20/94 (21%), Positives = 35/94 (37%), Gaps = 18/94 (19%)

Query: 26  QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHE 79
           ++     R VYVG +   +  Q +   FS           G    +  + I       H 
Sbjct: 30  EKKEIDKRSVYVGNVDYGSTAQDLEAHFSSC---------GS---INRITILCDKFSGHP 77

Query: 80  KKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRR 113
           K +A++E         A+A+D  +F G  ++V  
Sbjct: 78  KGYAYIEFAERNSVDAAVAMDETVFRGRTIKVLP 111

>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 = 4e-15
 Identities = 30/93 (32%), Positives = 46/93 (49%), Gaps = 4/93 (4%)

Query: 142 ASGAIGGAEGPDR---VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGF 198
            S  + G++       +FVGGLPY+ T+  +++  E FG +    ++ DR TG S+GYGF
Sbjct: 4   GSSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGF 63

Query: 199 CVYQDPAVTDIACAALNGLKMGDKTLTVRRATA 231
               D A  + AC   N +  G +   V  A  
Sbjct: 64  VTMADRAAAERACKDPNPIIDG-RKANVNLAYL 95

>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 = 38.8 bits (91), Expect = 4e-04
 Identities = 19/92 (20%), Positives = 29/92 (31%), Gaps = 24/92 (26%)

Query: 31  HARRVYVGGLPPLANEQAIATFFSQ--------VMT-AIGGNSAGPGDAVVNVYINHEKK 81
              +++VGGLP    + ++  +F          V+T    G S G               
Sbjct: 16  TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRG--------------- 60

Query: 82  FAFVEMRTVEEASNAMALDGIIFEGVAVRVRR 113
           + FV M     A  A      I +G    V  
Sbjct: 61  YGFVTMADRAAAERACKDPNPIIDGRKANVNL 92

>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 = 69.6 bits (171), Expect = 5e-15
 Identities = 26/104 (25%), Positives = 45/104 (43%), Gaps = 10/104 (9%)

Query: 142 ASGAIGGAEGPDR---VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGF 198
           +SG+ G      +   + V GLP+  TE  +KE   +FG +    + KD  TG+SKG+GF
Sbjct: 2   SSGSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGF 61

Query: 199 CVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQES 242
             + +        +  +   +  +    +        SK  Q+S
Sbjct: 62  VRFTEYETQVKVMSQRH--MIDGRWCDCKLP-----NSKQSQDS 98

>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 = 69.2 bits (170), Expect = 5e-15
 Identities = 21/94 (22%), Positives = 37/94 (39%), Gaps = 11/94 (11%)

Query: 148 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 207
           G+ G +++++G L    T   +++L           L          GY F  Y D    
Sbjct: 4   GSSGMNKLYIGNLSPAVTADDLRQLFGDRK------LPLAGQVLLKSGYAFVDYPDQNWA 57

Query: 208 DIACAALNG-LKMGDKTLTVRRATA----SSGQS 236
             A   L+G +++  K + V  + +    SSG S
Sbjct: 58  IRAIETLSGKVELHGKIMEVDYSVSKKLRSSGPS 91

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 51.5 bits (124), Expect = 8e-09
 Identities = 14/82 (17%), Positives = 26/82 (31%), Gaps = 14/82 (17%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 92
            ++Y+G L P      +   F                  +   +  +  +AFV+      
Sbjct: 9   NKLYIGNLSPAVTADDLRQLFGD----RKL--------PLAGQVLLKSGYAFVDYPDQNW 56

Query: 93  ASNAM-ALDGII-FEGVAVRVR 112
           A  A+  L G +   G  + V 
Sbjct: 57  AIRAIETLSGKVELHGKIMEVD 78

>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 = 68.7 bits (169), Expect = 5e-15
 Identities = 27/84 (32%), Positives = 36/84 (42%), Gaps = 1/84 (1%)

Query: 148 GAEGPD-RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAV 206
           G  G    VFVG L    T   I      FG +    +VKD  TG SKGYGF  + +   
Sbjct: 1   GPLGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWD 60

Query: 207 TDIACAALNGLKMGDKTLTVRRAT 230
            + 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 = 43.7 bits (104), Expect = 4e-06
 Identities = 23/95 (24%), Positives = 32/95 (33%), Gaps = 29/95 (30%)

Query: 34  RVYVGGLPPLANEQAIATFFSQ--------VMT-AIGGNSAGPGDAVVNVYINHEKKFAF 84
            V+VG L P     AIA  F+         V+     G S G               + F
Sbjct: 8   HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKG---------------YGF 52

Query: 85  VEMRTVEEASNAM-ALDGIIFEGVAVRV----RRP 114
           V      +A NA+  + G    G  +R     R+P
Sbjct: 53  VSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKP 87

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 69.6 bits (171), Expect = 5e-15
 Identities = 22/90 (24%), Positives = 39/90 (43%), Gaps = 1/90 (1%)

Query: 142 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 201
             G   G E   ++ V  L +  ++  I+EL   FGTL    +  DR +G S G     +
Sbjct: 19  GFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHF 77

Query: 202 QDPAVTDIACAALNGLKMGDKTLTVRRATA 231
           +  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 = 42.7 bits (101), Expect = 1e-05
 Identities = 15/88 (17%), Positives = 28/88 (31%), Gaps = 24/88 (27%)

Query: 34  RVYVGGLPPLANEQAIATFFSQ--------VMTAIGGNSAGPGDAVVNVYINHEKKFAFV 85
           ++ V  L    ++  I   F++        V     G S G                A V
Sbjct: 31  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLG---------------TADV 75

Query: 86  EMRTVEEASNAM-ALDGIIFEGVAVRVR 112
                 +A  AM   +G+  +G  + ++
Sbjct: 76  HFERKADALKAMKQYNGVPLDGRPMNIQ 103

>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 = 68.8 bits (169), Expect = 8e-15
 Identities = 25/96 (26%), Positives = 39/96 (40%), Gaps = 2/96 (2%)

Query: 142 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 201
           +SG +     P  ++VG L    TE  I +L    G      ++ +  +     Y F  +
Sbjct: 5   SSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEF 62

Query: 202 QDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSK 237
            +      A AA+NG K+  K + V  AT  S Q  
Sbjct: 63  YEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQKS 98

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 53.8 bits (130), Expect = 2e-09
 Identities = 23/91 (25%), Positives = 34/91 (37%), Gaps = 17/91 (18%)

Query: 26  QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK---- 81
            +     R +YVG L     E  I   FSQ          GP     +  +  E      
Sbjct: 9   MEDDGQPRTLYVGNLSRDVTEVLILQLFSQ---------IGP---CKSCKMITEHTSNDP 56

Query: 82  FAFVEMRTVEEASNAM-ALDGIIFEGVAVRV 111
           + FVE     +A+ A+ A++G    G  V+V
Sbjct: 57  YCFVEFYEHRDAAAALAAMNGRKILGKEVKV 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 = 68.8 bits (169), Expect = 1e-14
 Identities = 24/103 (23%), Positives = 44/103 (42%), Gaps = 7/103 (6%)

Query: 148 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 207
           G  G   +F+  L        + +   +FG +    +V   D   SKGYGF  ++     
Sbjct: 1   GPLGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVV--CDENGSKGYGFVHFETQEAA 58

Query: 208 DIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQH 250
           + 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 = 9e-05
 Identities = 21/143 (14%), Positives = 38/143 (26%), Gaps = 46/143 (32%)

Query: 35  VYVGGLPPLANEQAIATFFSQ--------VMTAIGGNSAGPGDAVVNVYINHEKKFAFVE 86
           +++  L    + +A+   FS         V+    G+                K + FV 
Sbjct: 8   IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS----------------KGYGFVH 51

Query: 87  MRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGA 145
             T E A  A+  ++G++     V V R        A      +   N            
Sbjct: 52  FETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTN------------ 99

Query: 146 IGGAEGPDRVFVGGLPYYFTETQ 168
                    V++       T   
Sbjct: 100 ---------VYIKNFGPGSTRAA 113

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 68.5 bits (168), Expect = 1e-14
 Identities = 21/84 (25%), Positives = 42/84 (50%), Gaps = 2/84 (2%)

Query: 148 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 207
               P R+ V  +P+ F +  ++++   FG +   +++ +     SKG+GF  +++ A  
Sbjct: 25  NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADA 82

Query: 208 DIACAALNGLKMGDKTLTVRRATA 231
           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 = 49.2 bits (118), Expect = 8e-08
 Identities = 20/93 (21%), Positives = 33/93 (35%), Gaps = 17/93 (18%)

Query: 24  MTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI----NHE 79
           M  +     +R++V  +P    +  +   F Q          G    +++V I       
Sbjct: 21  MNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQ---------FGK---ILDVEIIFNERGS 68

Query: 80  KKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV 111
           K F FV      +A  A   L G + EG  + V
Sbjct: 69  KGFGFVTFENSADADRAREKLHGTVVEGRKIEV 101

>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 = 68.4 bits (168), Expect = 1e-14
 Identities = 22/84 (26%), Positives = 43/84 (51%), Gaps = 1/84 (1%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           ++FVGG+P+   ET+++E  + FG +    ++ D +    +G+GF  ++D    D A   
Sbjct: 12  KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71

Query: 214 LNGLKMGDKTLTVRRATASSGQSK 237
            +   +  K + V+RA     +S 
Sbjct: 72  -HFHDIMGKKVEVKRAEPRDSKSS 94

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 44.9 bits (107), Expect = 2e-06
 Identities = 18/87 (20%), Positives = 33/87 (37%), Gaps = 18/87 (20%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI--NHEKK----FAFVE 86
            +++VGG+P    E  +  +F +      G        V  V +  + EK+    F F+ 
Sbjct: 11  NKIFVGGIPHNCGETELREYFKKF-----GV-------VTEVVMIYDAEKQRPRGFGFIT 58

Query: 87  MRTVEEASNAMALDGIIFEGVAVRVRR 113
               +    A+ +      G  V V+R
Sbjct: 59  FEDEQSVDQAVNMHFHDIMGKKVEVKR 85

>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 = 70.7 bits (173), Expect = 1e-14
 Identities = 35/196 (17%), Positives = 57/196 (29%), Gaps = 25/196 (12%)

Query: 35  VYVGGLPPLA-NEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-FAFVEMRTVEE 92
           + V  L P     Q++   F        G+       V  V I   KK  A V+M    +
Sbjct: 6   LLVSNLNPERVTPQSLFILFGVY-----GD-------VQRVKILFNKKENALVQMADGNQ 53

Query: 93  ASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPS------PNLNLAAVGLASGA 145
           A  AM  L+G    G  +R+      N  L       Q          L+      +   
Sbjct: 54  AQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNF 113

Query: 146 IGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPA 205
                    + +  +P   +E  +K L  S G +        +D    +           
Sbjct: 114 QNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD----RKMALIQMGSVE 169

Query: 206 VTDIACAALNGLKMGD 221
               A   L+   +G+
Sbjct: 170 EAVQALIDLHNHDLGE 185

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 50.3 bits (120), Expect = 2e-07
 Identities = 27/212 (12%), Positives = 52/212 (24%), Gaps = 36/212 (16%)

Query: 155 VFVGGL-PYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           + V  L P   T   +  L   +G +    ++ +      K        D     +A + 
Sbjct: 6   LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMADGNQAQLAMSH 60

Query: 214 LNGLKMGDKTLTVRRATASSGQSKTEQESILAQA----QQHIAIQKMALQTSGMNTLGGG 269
           LNG K+  K + +  +   + Q   E +             +   K     +  N     
Sbjct: 61  LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPS 120

Query: 270 MSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGE 329
            +L    +   +                     ED++      G +V             
Sbjct: 121 ATLHLSNIPPSVS-------------------EEDLKVLFSSNGGVVKGFKFFQKDRKM- 160

Query: 330 TPGVGKVFLEYYDAVGCATAKNALSGRKFGGN 361
                   ++         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 = 47.2 bits (112), Expect = 2e-06
 Identities = 18/81 (22%), Positives = 34/81 (41%), Gaps = 12/81 (14%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 92
             +++  +PP  +E+ +   FS             G      +   ++K A ++M +VEE
Sbjct: 121 ATLHLSNIPPSVSEEDLKVLFSSN----------GGVVKGFKFFQKDRKMALIQMGSVEE 170

Query: 93  ASNAM-ALDGI-IFEGVAVRV 111
           A  A+  L    + E   +RV
Sbjct: 171 AVQALIDLHNHDLGENHHLRV 191

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 70.9 bits (173), Expect = 1e-14
 Identities = 30/204 (14%), Positives = 48/204 (23%), Gaps = 25/204 (12%)

Query: 35  VYVGGLPP-LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-FAFVEMRTVEE 92
           + V GL     N   +   F        GN       V  V     K   A VEM     
Sbjct: 7   LMVYGLDQSKMNCDRVFNVFCLY-----GN-------VEKVKFMKSKPGAAMVEMADGYA 54

Query: 93  ASNAM-ALDGIIFEGVAVRVR---------RPTDYNPTLAAALGPGQPSPNLNLAAVGLA 142
              A+  L+     G  + V            +      + +      S N   +    A
Sbjct: 55  VDRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQA 114

Query: 143 SGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQ 202
           +           +     P   TE    E+ +  G      +            G   + 
Sbjct: 115 AKNRIQHPSN-VLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWD 173

Query: 203 DPAVTDIACAALNGLKMGDKTLTV 226
             +        LN  +M +     
Sbjct: 174 SKSDALETLGFLNHYQMKNPNGPY 197

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 59.3 bits (143), Expect = 1e-10
 Identities = 28/222 (12%), Positives = 52/222 (23%), Gaps = 23/222 (10%)

Query: 148 GAEGPDRVFVGGL-PYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAV 206
           GA+ P  + V GL        ++  +   +G +     +K +      G       D   
Sbjct: 1   GADSP-VLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYA 54

Query: 207 TDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTL 266
            D A   LN   M  + + V  +   +                    +    + S     
Sbjct: 55  VDRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQA 114

Query: 267 GGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQN 326
                     +         +T              E+  E C + G      + +    
Sbjct: 115 AKNRIQHPSNVLHFFNAPLEVTE-------------ENFFEICDELGVKRPTSV-KVFSG 160

Query: 327 GGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYY 368
             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 = 41.2 bits (96), Expect = 2e-04
 Identities = 9/88 (10%), Positives = 23/88 (26%), Gaps = 7/88 (7%)

Query: 20  PVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE 79
           P Q    +    +  ++    P    E+       ++          P    V    +  
Sbjct: 111 PEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDEL------GVKRPTSVKVFSGKSER 164

Query: 80  KKFAFVEMRTVEEASNAMA-LDGIIFEG 106
                +E  +  +A   +  L+    + 
Sbjct: 165 SSSGLLEWDSKSDALETLGFLNHYQMKN 192

>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 = 67.3 bits (165), Expect = 2e-14
 Identities = 26/92 (28%), Positives = 40/92 (43%), Gaps = 6/92 (6%)

Query: 142 ASGAIGGAEGPD---RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGF 198
           +SG+ G          +FV GL    TE  +KE    F       +V DR+TG+SKG+GF
Sbjct: 2   SSGSSGPNARSQPSKTLFVKGLSEDTTEETLKES---FDGSVRARIVTDRETGSSKGFGF 58

Query: 199 CVYQDPAVTDIACAALNGLKMGDKTLTVRRAT 230
             +        A  A+   ++    +T+  A 
Sbjct: 59  VDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAK 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 = 49.2 bits (118), Expect = 7e-08
 Identities = 18/93 (19%), Positives = 35/93 (37%), Gaps = 22/93 (23%)

Query: 26  QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAI------GGNSAGPGDAVVNVYINHE 79
              ++ ++ ++V GL     E+ +   F   + A        G+S G             
Sbjct: 9   NARSQPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKG------------- 55

Query: 80  KKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV 111
             F FV+  + E+A  A  A++    +G  V +
Sbjct: 56  --FGFVDFNSEEDAKAAKEAMEDGEIDGNKVTL 86

>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 = 70.5 bits (172), Expect = 3e-14
 Identities = 19/138 (13%), Positives = 41/138 (29%), Gaps = 2/138 (1%)

Query: 115 TDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLE 174
               P     +    P+   ++      +           +++G L ++ T+  + E + 
Sbjct: 31  NGDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVH 90

Query: 175 SFGTLHGFD--LVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS 232
           S G     +    ++R  G SKG+        A +      L   ++  +   V      
Sbjct: 91  SLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQ 150

Query: 233 SGQSKTEQESILAQAQQH 250
                  Q     Q+ Q 
Sbjct: 151 FLSQFEMQSRKTTQSGQM 168

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Length = 229

 Score = 53.2 bits (127), Expect = 2e-08
 Identities = 23/170 (13%), Positives = 38/170 (22%), Gaps = 17/170 (10%)

Query: 2   AQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIG 61
              M     T            +    T     +Y+G L     ++ +            
Sbjct: 38  RDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHS------ 91

Query: 62  GNSAGPGDAV-VNVYINHE----KKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVR--R 113
               G  D + +  + N      K FA V + +   +   M  L      G    V    
Sbjct: 92  ---LGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVN 148

Query: 114 PTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYY 163
               +     +    Q          G   G+   A        G  P  
Sbjct: 149 KQFLSQFEMQSRKTTQSGQMSGEGKAGPPGGSSRAAFPQGGRGRGRFPGA 198

>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 = 67.7 bits (166), Expect = 3e-14
 Identities = 14/77 (18%), Positives = 32/77 (41%), Gaps = 1/77 (1%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           VF   L        +++   + G +    ++ DR++  SKG  +  + +     +A   L
Sbjct: 28  VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GL 86

Query: 215 NGLKMGDKTLTVRRATA 231
            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 = 60.0 bits (146), Expect = 2e-11
 Identities = 23/94 (24%), Positives = 33/94 (35%), Gaps = 18/94 (19%)

Query: 26  QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHE 79
               R AR V+   L      + +  FFS V         G    V +V I         
Sbjct: 19  SPEERDARTVFCMQLAARIRPRDLEDFFSAV---------GK---VRDVRIISDRNSRRS 66

Query: 80  KKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRR 113
           K  A+VE   ++    A+ L G    GV + V+ 
Sbjct: 67  KGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQA 100

>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 = 67.3 bits (165), Expect = 3e-14
 Identities = 23/84 (27%), Positives = 42/84 (50%), Gaps = 1/84 (1%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           ++F+GGL +  T+  ++E    FG +    +++D  T  S+G+GF  + D A  D   A 
Sbjct: 27  KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 86

Query: 214 LNGLKMGDKTLTVRRATASSGQSK 237
            +  ++  KT+  + A     Q K
Sbjct: 87  -SRHELDSKTIDPKVAFPRRAQPK 109

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 65.6 bits (161), Expect = 5e-14
 Identities = 19/76 (25%), Positives = 38/76 (50%), Gaps = 1/76 (1%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           ++FVGGL    T   +K   E FG +    L+ D+ T   +G+GF  ++   + +  C  
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 214 LNGLKMGDKTLTVRRA 229
            +  ++ +K +  ++A
Sbjct: 61  -HFHEINNKMVECKKA 75

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 66.1 bits (162), Expect = 6e-14
 Identities = 27/84 (32%), Positives = 43/84 (51%), Gaps = 1/84 (1%)

Query: 148 GAEGPDRVFVGGLPYYFTETQIKELLESFGT-LHGFDLVKDRDTGNSKGYGFCVYQDPAV 206
           G+ G   +F+G L     E  + +   +FG  L    +++D DTGNSKGY F  +     
Sbjct: 1   GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA 60

Query: 207 TDIACAALNGLKMGDKTLTVRRAT 230
           +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 = 41.4 bits (98), Expect = 3e-05
 Identities = 14/79 (17%), Positives = 32/79 (40%), Gaps = 6/79 (7%)

Query: 34  RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEA 93
            +++G L P  +E+ +   FS       G        + +    + K +AF+   + + +
Sbjct: 7   GIFIGNLDPEIDEKLLYDTFSAF-----GVILQTPKIMRDPDTGNSKGYAFINFASFDAS 61

Query: 94  SNAM-ALDGIIFEGVAVRV 111
             A+ A++G       + V
Sbjct: 62  DAAIEAMNGQYLCNRPITV 80

>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 = 66.2 bits (162), Expect = 7e-14
 Identities = 21/85 (24%), Positives = 36/85 (42%), Gaps = 1/85 (1%)

Query: 144 GAIGGAEGPDRVFVGGLPYYFTETQIKELLESFG-TLHGFDLVKDRDTGNSKGYGFCVYQ 202
           G+ G +     +++G L  Y  E  I     + G T+    ++++R TG   GY F  + 
Sbjct: 1   GSSGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFA 60

Query: 203 DPAVTDIACAALNGLKMGDKTLTVR 227
           D A  +     +NG  +   T   R
Sbjct: 61  DLATAEKCLHKINGKPLPGATPAKR 85

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 42.7 bits (101), Expect = 1e-05
 Identities = 18/88 (20%), Positives = 33/88 (37%), Gaps = 18/88 (20%)

Query: 32  ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFV 85
           A  +++G L P  +E  I+  F+ +           G+ V++V I           + FV
Sbjct: 9   AASLWMGDLEPYMDENFISRAFATM-----------GETVMSVKIIRNRLTGIPAGYCFV 57

Query: 86  EMRTVEEASNAM-ALDGIIFEGVAVRVR 112
           E   +  A   +  ++G    G     R
Sbjct: 58  EFADLATAEKCLHKINGKPLPGATPAKR 85

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 66.0 bits (161), Expect = 1e-13
 Identities = 15/82 (18%), Positives = 31/82 (37%), Gaps = 4/82 (4%)

Query: 153 DRVFVGGLPYYFTETQIKELLESFGT-LHGFDLVKD-RDTGNSKGYGFCVYQDPAVTDIA 210
            R+F+GG+P      +I E +      +    +     D   ++G+ F  Y+      +A
Sbjct: 9   CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 68

Query: 211 CAALN--GLKMGDKTLTVRRAT 230
              L    +++    + V  A 
Sbjct: 69  RRKLMPGRIQLWGHQIAVDWAE 90

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 49.0 bits (117), Expect = 1e-07
 Identities = 18/91 (19%), Positives = 35/91 (38%), Gaps = 21/91 (23%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-------NHEKKFAFV 85
            R+++GG+P +   + I    ++V            + V++V +          + FAFV
Sbjct: 9   CRLFIGGIPKMKKREEILEEIAKV-----------TEGVLDVIVYASAADKMKNRGFAFV 57

Query: 86  EMRTVEEASNA---MALDGIIFEGVAVRVRR 113
           E  +   A+ A   +    I   G  + V  
Sbjct: 58  EYESHRAAAMARRKLMPGRIQLWGHQIAVDW 88

>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 = 38.6 bits (90), Expect = 4e-04
 Identities = 14/64 (21%), Positives = 26/64 (40%), Gaps = 5/64 (7%)

Query: 303 EDMREECGKYGTLV-NVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKF--G 359
           E++ EE  K    V +V++     +  +  G    F+EY      A A+  L   +    
Sbjct: 23  EEILEEIAKVTEGVLDVIVYASAADKMKNRGFA--FVEYESHRAAAMARRKLMPGRIQLW 80

Query: 360 GNTV 363
           G+ +
Sbjct: 81  GHQI 84

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 65.8 bits (161), Expect = 1e-13
 Identities = 21/81 (25%), Positives = 36/81 (44%), Gaps = 2/81 (2%)

Query: 150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 209
           E P   +VG LP+   +  I  + +         LV+D+DT   KG+ +  + +      
Sbjct: 13  EPPYTAYVGNLPFNTVQGDIDAIFKDLSIR-SVRLVRDKDTDKFKGFCYVEFDEVDSLKE 71

Query: 210 ACAALNGLKMGDKTLTVRRAT 230
           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 = 54.2 bits (131), Expect = 1e-09
 Identities = 18/85 (21%), Positives = 30/85 (35%), Gaps = 19/85 (22%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFVE 86
              YVG LP    +  I   F  +              + +V +  +K       F +VE
Sbjct: 16  YTAYVGNLPFNTVQGDIDAIFKDLS-------------IRSVRLVRDKDTDKFKGFCYVE 62

Query: 87  MRTVEEASNAMALDGIIFEGVAVRV 111
              V+    A+  DG +    ++RV
Sbjct: 63  FDEVDSLKEALTYDGALLGDRSLRV 87

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 65.7 bits (161), Expect = 1e-13
 Identities = 22/101 (21%), Positives = 43/101 (42%), Gaps = 4/101 (3%)

Query: 140 GLASGAIGGAEGPDR---VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGY 196
           G +  +     G D    +FVGGL +  T+  ++     +G +    ++KD+ T  S+G+
Sbjct: 1   GSSGSSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGF 60

Query: 197 GFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSK 237
           GF  ++DP       A+     +  + +  +  T    Q  
Sbjct: 61  GFVKFKDPNCVGTVLAS-RPHTLDGRNIDPKPCTPRGMQPS 100

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 64.8 bits (159), Expect = 1e-13
 Identities = 21/76 (27%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           ++F+GGL +  T+  ++E    FG +    +++D  T  S+G+GF  + D A  D   A 
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 214 LNGLKMGDKTLTVRRA 229
            +  ++  KT+  + A
Sbjct: 62  -SRHELDSKTIDPKVA 76

>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 = 64.9 bits (159), Expect = 1e-13
 Identities = 19/88 (21%), Positives = 44/88 (50%), Gaps = 4/88 (4%)

Query: 145 AIGGAEGPD---RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 201
            I  ++  +   ++FVGGL +  ++  +K+    FG +    +  D +TG S+G+GF ++
Sbjct: 1   GINASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILF 60

Query: 202 QDPAVTDIACAALNGLKMGDKTLTVRRA 229
           +D A  +         ++  + +  ++A
Sbjct: 61  KDAASVEKVLDQKEH-RLDGRVIDPKKA 87

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 68.5 bits (167), Expect = 1e-13
 Identities = 34/196 (17%), Positives = 58/196 (29%), Gaps = 25/196 (12%)

Query: 35  VYVGGLPPLA-NEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-FAFVEMRTVEE 92
           + V  L P     Q++   F        G+       V  V I   KK  A V+M    +
Sbjct: 37  LLVSNLNPERVTPQSLFILFGVY-----GD-------VQRVKILFNKKENALVQMADGNQ 84

Query: 93  ASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQP------SPNLNLAAVGLASGA 145
           A  AM  L+G    G  +R+      N  L       Q       +  L+      +   
Sbjct: 85  AQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNF 144

Query: 146 IGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPA 205
                    + +  +P   +E  +K L  S G +    +   +     +           
Sbjct: 145 QNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGV----VKGFKFFQKDRKMALIQMGSVE 200

Query: 206 VTDIACAALNGLKMGD 221
               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 = 6e-09
 Identities = 29/244 (11%), Positives = 62/244 (25%), Gaps = 43/244 (17%)

Query: 130 PSPNLNLAAVGLASGAIGGAEGPDR-------VFVGGL-PYYFTETQIKELLESFGTLHG 181
              + + + +      +G    P         + V  L P   T   +  L   +G +  
Sbjct: 5   HHHHHHSSGLVPRGSHMGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQR 64

Query: 182 FDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQE 241
             ++ +      K        D     +A + LNG K+  K + +  +   + Q   E +
Sbjct: 65  VKILFN-----KKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQ 119

Query: 242 SILAQAQ----QHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEE 297
                 +      +   K     +  N      +L    +   +                
Sbjct: 120 EDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVS--------------- 164

Query: 298 YEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRK 357
                ED++      G +V        ++           ++         A   L    
Sbjct: 165 ----EEDLKVLFSSNGGVVKGFK-FFQKDR------KMALIQMGSVEEAVQALIDLHNHD 213

Query: 358 FGGN 361
            G N
Sbjct: 214 LGEN 217

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 45.8 bits (108), Expect = 6e-06
 Identities = 20/94 (21%), Positives = 37/94 (39%), Gaps = 12/94 (12%)

Query: 20  PVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE 79
           P     Q     +  +++  +PP  +E+ +   FS             G      +   +
Sbjct: 139 PGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSN----------GGVVKGFKFFQKD 188

Query: 80  KKFAFVEMRTVEEASNAM-ALDGI-IFEGVAVRV 111
           +K A ++M +VEEA  A+  L    + E   +RV
Sbjct: 189 RKMALIQMGSVEEAVQALIDLHNHDLGENHHLRV 222

>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 = 64.7 bits (158), Expect = 2e-13
 Identities = 14/86 (16%), Positives = 27/86 (31%), Gaps = 7/86 (8%)

Query: 148 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 207
           G+ G   + V  LP      ++ +LL+ +        +K      +K   F    +    
Sbjct: 1   GSSGSSGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQA 53

Query: 208 DIACAALNGLKMGDKTLTVRRATASS 233
             A    +      K L V+     +
Sbjct: 54  QNAIQMFHQYSFRGKDLIVQLQPTDA 79

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 53.2 bits (128), Expect = 2e-09
 Identities = 24/105 (22%), Positives = 38/105 (36%), Gaps = 21/105 (20%)

Query: 29  TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMR 88
           +  +  + V  LP  +N Q +                     +   Y++  K+ AFV + 
Sbjct: 2   SSGSSGILVKNLPQDSNCQEVHDLLKDY-------------DLKYCYVDRNKRTAFVTLL 48

Query: 89  TVEEASNAM-ALDGIIFEGVAVRVRR-PTDYNPTLAAALGPGQPS 131
             E+A NA+       F G  + V+  PTD      A L  G  S
Sbjct: 49  NGEQAQNAIQMFHQYSFRGKDLIVQLQPTD------ALLCSGPSS 87

>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 = 64.1 bits (157), Expect = 2e-13
 Identities = 16/80 (20%), Positives = 30/80 (37%), Gaps = 9/80 (11%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           ++FVGGL     E +I+E    FG +   +L  D  T   +G+ F  +++          
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 214 ----LNGLKMGDKTLTVRRA 229
               +           ++ A
Sbjct: 61  KYHNVGL-----SKCEIKVA 75

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 65.0 bits (159), Expect = 2e-13
 Identities = 22/92 (23%), Positives = 41/92 (44%), Gaps = 2/92 (2%)

Query: 142 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRD-TGNSKGYGFCV 200
           +SG +   +   ++ V  +P+   + +I+EL  +FG L    L K    TG  +G+GF  
Sbjct: 5   SSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVD 64

Query: 201 YQDPAVTDIACAAL-NGLKMGDKTLTVRRATA 231
           +        A  AL +   +  + L +  A +
Sbjct: 65  FITKQDAKKAFNALCHSTHLYGRRLVLEWADS 96

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 45.0 bits (107), Expect = 2e-06
 Identities = 16/88 (18%), Positives = 29/88 (32%), Gaps = 21/88 (23%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-------NHEKKFAFV 85
            ++ V  +P  AN++ I   FS           G    +  V +          + F FV
Sbjct: 16  SKILVRNIPFQANQREIRELFSTF---------GE---LKTVRLPKKMTGTGAHRGFGFV 63

Query: 86  EMRTVEEASNAMA--LDGIIFEGVAVRV 111
           +  T ++A  A           G  + +
Sbjct: 64  DFITKQDAKKAFNALCHSTHLYGRRLVL 91

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 64.0 bits (156), Expect = 4e-13
 Identities = 17/91 (18%), Positives = 30/91 (32%), Gaps = 8/91 (8%)

Query: 148 GAEGPDR-VFVGGLPYY------FTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCV 200
           G  G D+ + V G P          +  +  L    G +   +   D  TG +KG+ F  
Sbjct: 1   GPLGSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVE 60

Query: 201 YQDPAVTDIACAALNGLKMGDK-TLTVRRAT 230
                       + +G ++  K  L +    
Sbjct: 61  CGSMNDAKKIIKSFHGKRLDLKHRLFLYTMK 91

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 42.8 bits (101), Expect = 1e-05
 Identities = 14/88 (15%), Positives = 30/88 (34%), Gaps = 7/88 (7%)

Query: 293 ADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNA 352
               +   + + +     K G +VN+  P  D+  G+T G    F+E            +
Sbjct: 17  IPSAKVPVLKKALTSLFSKAGKVVNMEFPI-DEATGKTKGFL--FVECGSMNDAKKIIKS 73

Query: 353 LSGRKFGGN---TVNAFYYPEDKYFNKD 377
             G++        +       ++Y + D
Sbjct: 74  FHGKRLDLKHRLFLYTM-KDVERYNSDD 100

>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 = 5e-13
 Identities = 23/107 (21%), Positives = 41/107 (38%), Gaps = 16/107 (14%)

Query: 9   GATQLGAFPLM---PVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSA 65
           G+  +G  P +    V  + + A       Y+G +P  A E  +   F            
Sbjct: 1   GSQTIGLPPQVNPQAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNF--------- 51

Query: 66  GPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV 111
             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 = 2e-10
 Identities = 15/73 (20%), Positives = 27/73 (36%), Gaps = 6/73 (8%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
             ++G +P++ TE  +  L ++FG +  F    +      KG  F  Y       +   A
Sbjct: 29  TAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE------KGCCFIKYDTHEQAAVCIVA 82

Query: 214 LNGLKMGDKTLTV 226
           L       + L  
Sbjct: 83  LANFPFQGRNLRT 95

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 63.8 bits (156), Expect = 7e-13
 Identities = 22/78 (28%), Positives = 40/78 (51%), Gaps = 1/78 (1%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           ++F+GGL +  TE  ++   E +G L    +++D  +  S+G+GF  +   A  D A AA
Sbjct: 29  KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA 88

Query: 214 LNGLKMGDKTLTVRRATA 231
                +  + +  +RA A
Sbjct: 89  -RPHSIDGRVVEPKRAVA 105

>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 = 66.4 bits (162), Expect = 8e-13
 Identities = 30/87 (34%), Positives = 49/87 (56%), Gaps = 2/87 (2%)

Query: 296 EEYEEILE-DMREECGKYGTLVNVVIPRPDQNGGE-TPGVGKVFLEYYDAVGCATAKNAL 353
           ++ ++ LE ++ EECGK+G +  V+I +  Q   E    + K+F+E+  A     A  AL
Sbjct: 136 KDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQAL 195

Query: 354 SGRKFGGNTVNAFYYPEDKYFNKDYSA 380
           +GR F G  V A  Y ++++ N D SA
Sbjct: 196 NGRWFAGRKVVAEVYDQERFDNSDLSA 222

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 62.7 bits (153), Expect = 1e-12
 Identities = 17/86 (19%), Positives = 33/86 (38%), Gaps = 6/86 (6%)

Query: 153 DRVFVGGLPYYFTETQIKELLESFGTLHGFD--LVKDRDTGNSKGYGFCVYQDPAVTDIA 210
           D + +  +  +     I   L  + +L   +  L+KD+ T  ++G+ F            
Sbjct: 10  DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQL 69

Query: 211 CAALNG----LKMGDKTLTVRRATAS 232
              L      LK+  KT+ V  A ++
Sbjct: 70  LQILQSLHPPLKIDGKTIGVDFAKSA 95

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 47.7 bits (114), Expect = 2e-07
 Identities = 17/99 (17%), Positives = 32/99 (32%), Gaps = 21/99 (21%)

Query: 24  MTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------N 77
           M      H   + +  + P     +I T  S                V N+ +       
Sbjct: 1   MGHHHHHHMDTIILRNIAPHTVVDSIMTALSPY---------ASLA-VNNIRLIKDKQTQ 50

Query: 78  HEKKFAFVEMRTVEEASNAM-ALDG----IIFEGVAVRV 111
             + FAFV++ +  +AS  +  L      +  +G  + V
Sbjct: 51  QNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGV 89

>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 = 61.8 bits (151), Expect = 2e-12
 Identities = 24/90 (26%), Positives = 40/90 (44%), Gaps = 8/90 (8%)

Query: 148 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 207
           G+ G  ++F+G LP   TE +I+ L E +G +   D++        K YGF   +D    
Sbjct: 4   GSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAA 55

Query: 208 DIACAALNGLKMGDKTLTVRRATASSGQSK 237
           + A   L+  K+    + V  +   S  S 
Sbjct: 56  EDAIRNLHHYKLHGVNINVEASKNKSKASS 85

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 52.2 bits (126), Expect = 4e-09
 Identities = 21/80 (26%), Positives = 32/80 (40%), Gaps = 15/80 (18%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 92
            ++++G LP  A EQ I + F Q          G    V+   I   K + FV +     
Sbjct: 9   VKLFIGNLPREATEQEIRSLFEQY---------GK---VLECDI--IKNYGFVHIEDKTA 54

Query: 93  ASNAM-ALDGIIFEGVAVRV 111
           A +A+  L      GV + V
Sbjct: 55  AEDAIRNLHHYKLHGVNINV 74

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 61.9 bits (151), Expect = 2e-12
 Identities = 15/83 (18%), Positives = 34/83 (40%), Gaps = 2/83 (2%)

Query: 149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 208
           +  P  +F+G L    +  ++K  +      +    V D  TG ++ +G+  ++     +
Sbjct: 14  STTPFNLFIGNLNPNKSVAELKVAISELFAKNDL-AVVDVRTGTNRKFGYVDFESAEDLE 72

Query: 209 IACAALNGLKMGDKTLTVRRATA 231
            A   L GLK+    + + +   
Sbjct: 73  KA-LELTGLKVFGNEIKLEKPKG 94

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 56.5 bits (137), Expect = 1e-10
 Identities = 16/85 (18%), Positives = 34/85 (40%), Gaps = 13/85 (15%)

Query: 34  RVYVGGLPPLANEQAIATFFSQ---VMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTV 90
            +++G L P  +   +    S+                  VV+V     +KF +V+  + 
Sbjct: 19  NLFIGNLNPNKSVAELKVAISELFAKNDLA----------VVDVRTGTNRKFGYVDFESA 68

Query: 91  EEASNAMALDGIIFEGVAVRVRRPT 115
           E+   A+ L G+   G  +++ +P 
Sbjct: 69  EDLEKALELTGLKVFGNEIKLEKPK 93

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 61.9 bits (151), Expect = 2e-12
 Identities = 23/92 (25%), Positives = 37/92 (40%), Gaps = 13/92 (14%)

Query: 26  QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFV 85
           ++      R++VG LPP   E+ +   F +     G            V+I+ +K F F+
Sbjct: 9   EKTFTQRSRLFVGNLPPDITEEEMRKLFEK----YG--------KAGEVFIHKDKGFGFI 56

Query: 86  EMRTVEEASNAM-ALDGIIFEGVAVRVRRPTD 116
            + 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 = 60.0 bits (146), Expect = 9e-12
 Identities = 30/95 (31%), Positives = 48/95 (50%), Gaps = 9/95 (9%)

Query: 142 ASGAIGGAEGPD---RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGF 198
           +SG+ GG +      R+FVG LP   TE ++++L E +G      + KD      KG+GF
Sbjct: 2   SSGSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGF 55

Query: 199 CVYQDPAVTDIACAALNGLKMGDKTLTVRRATASS 233
              +   + +IA   L+ + +  K L VR A  S+
Sbjct: 56  IRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA 90

>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 = 62.0 bits (151), Expect = 2e-12
 Identities = 22/106 (20%), Positives = 38/106 (35%), Gaps = 13/106 (12%)

Query: 142 ASGAIGGAEGPD----------RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTG 191
           +SG+ G + G            R++VG LP       I+++   +G +   DL   R   
Sbjct: 2   SSGSSGMSGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR--- 58

Query: 192 NSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSK 237
               + F  ++DP   + A    +G       L V    +  G   
Sbjct: 59  GGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGTGS 104

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 54.6 bits (132), Expect = 1e-09
 Identities = 26/101 (25%), Positives = 42/101 (41%), Gaps = 21/101 (20%)

Query: 28  ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK---FAF 84
           A  +  R+YVG LPP    + I   F +          G    + ++ + + +    FAF
Sbjct: 18  AGNNDCRIYVGNLPPDIRTKDIEDVFYK---------YGA---IRDIDLKNRRGGPPFAF 65

Query: 85  VEMRTVEEASNAM-ALDGIIFEGVAVRV-----RRPTDYNP 119
           VE     +A +A+   DG  ++G  +RV      R T   P
Sbjct: 66  VEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGTGSGP 106

>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 = 61.5 bits (150), Expect = 4e-12
 Identities = 15/80 (18%), Positives = 33/80 (41%), Gaps = 1/80 (1%)

Query: 150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 209
           + P  +++  LP    E +++ +L+ FG +    +++D  +G S+G GF   +     + 
Sbjct: 23  QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEA 81

Query: 210 ACAALNGLKMGDKTLTVRRA 229
                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 = 42.2 bits (100), Expect = 2e-05
 Identities = 14/97 (14%), Positives = 27/97 (27%), Gaps = 24/97 (24%)

Query: 24  MTQQATRHARRVYVGGLPPLANEQAIATFFSQ--------VMTAIGGNSAGPGDAVVNVY 75
           M +Q  +    +Y+  LP   +EQ +              ++    G S G         
Sbjct: 17  MAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRG--------- 67

Query: 76  INHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV 111
                   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 = 61.1 bits (149), Expect = 4e-12
 Identities = 23/91 (25%), Positives = 40/91 (43%), Gaps = 4/91 (4%)

Query: 142 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 201
           +SG+        ++FVG L    +E  +  L + FG +    +++  D G+SKG  F  +
Sbjct: 5   SSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPD-GSSKGCAFVKF 63

Query: 202 QDPAVTDIACAALNG---LKMGDKTLTVRRA 229
                   A  AL+G   +     +L V+ A
Sbjct: 64  SSHTEAQAAIHALHGSQTMPGASSSLVVKFA 94

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 44.2 bits (105), Expect = 4e-06
 Identities = 20/84 (23%), Positives = 31/84 (36%), Gaps = 25/84 (29%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQ--------VMTAIGGNSAGPGDAVVNVYINHEKKFAF 84
           R+++VG L    +E+ +   F          V+    G+S G                AF
Sbjct: 16  RKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKG---------------CAF 60

Query: 85  VEMRTVEEASNAM-ALDG-IIFEG 106
           V+  +  EA  A+ AL G     G
Sbjct: 61  VKFSSHTEAQAAIHALHGSQTMPG 84

>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 = 61.1 bits (149), Expect = 5e-12
 Identities = 22/89 (24%), Positives = 39/89 (43%), Gaps = 10/89 (11%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
            ++V  L     + ++++    FGT+    ++   + G SKG+GF  +  P     A   
Sbjct: 17  NLYVKNLDDGIDDERLRKAFSPFGTITSAKVM--MEGGRSKGFGFVCFSSPEEATKAVTE 74

Query: 214 LNGLKMGDKTLTV--------RRATASSG 234
           +NG  +  K L V        R++  SSG
Sbjct: 75  MNGRIVATKPLYVALAQRKEERQSGPSSG 103

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 41.8 bits (99), Expect = 3e-05
 Identities = 21/87 (24%), Positives = 32/87 (36%), Gaps = 25/87 (28%)

Query: 34  RVYVGGLPPLANEQAIATFFSQ--------VMTAIGGNSAGPGDAVVNVYINHEKKFAFV 85
            +YV  L    +++ +   FS         VM   GG S G               F FV
Sbjct: 17  NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKG---------------FGFV 60

Query: 86  EMRTVEEASNAM-ALDGIIFEGVAVRV 111
              + 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 = 60.4 bits (147), Expect = 6e-12
 Identities = 21/89 (23%), Positives = 34/89 (38%), Gaps = 13/89 (14%)

Query: 26  QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEK-KFAF 84
              +   R V+V G P   +   ++ +F            GP   V +V ++ +K  FA 
Sbjct: 2   SSGSSGLRSVFVSGFPRGVDSAQLSEYFLA---------FGP---VASVVMDKDKGVFAI 49

Query: 85  VEMRTVEEASNAMALDGIIFEGVAVRVRR 113
           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 = 58.1 bits (141), Expect = 4e-11
 Identities = 22/93 (23%), Positives = 33/93 (35%), Gaps = 6/93 (6%)

Query: 145 AIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP 204
              G+ G   VFV G P      Q+ E   +FG +    +V D+D G    +      D 
Sbjct: 1   GSSGSSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVA--SVVMDKDKG---VFAIVEMGDV 55

Query: 205 AVTDIACAALNGLKMGDKTLTVRRATASSGQSK 237
              +    + +   +G   L VR       QS 
Sbjct: 56  GAREAVL-SQSQHSLGGHRLRVRPREQKEFQSP 87

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 60.6 bits (147), Expect = 8e-12
 Identities = 17/93 (18%), Positives = 28/93 (30%), Gaps = 12/93 (12%)

Query: 28  ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEM 87
                 R+ +  LP   + Q +     +                 +V          +E 
Sbjct: 24  LPAKRYRITMKNLPEGCSWQDLKDLARE---------NSLETTFSSVNTRDFDGTGALEF 74

Query: 88  RTVEEASNAMA-LDGIIFEGVAVRVRRPTDYNP 119
            + E    A+  L+ I F G  + V R  D NP
Sbjct: 75  PSEEILVEALERLNNIEFRGSVITVER--DDNP 105

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 53.7 bits (129), Expect = 2e-09
 Identities = 15/77 (19%), Positives = 27/77 (35%), Gaps = 3/77 (3%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           R+ +  LP   +   +K+L         F      +T +  G G   +    +   A   
Sbjct: 30  RITMKNLPEGCSWQDLKDLARENSLETTFS---SVNTRDFDGTGALEFPSEEILVEALER 86

Query: 214 LNGLKMGDKTLTVRRAT 230
           LN ++     +TV R  
Sbjct: 87  LNNIEFRGSVITVERDD 103

>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 = 60.0 bits (146), Expect = 1e-11
 Identities = 21/95 (22%), Positives = 42/95 (44%), Gaps = 13/95 (13%)

Query: 19  MPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH 78
           +  + +  Q++     VY GG+     +Q +   FS      G         ++ + +  
Sbjct: 12  LRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSP----FG--------QIMEIRVFP 59

Query: 79  EKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVR 112
           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 = 14/84 (16%), Positives = 29/84 (34%), Gaps = 6/84 (7%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
            V+ GG+    T+  +++    FG +    +  +      KGY F  +        A  +
Sbjct: 27  TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVS 80

Query: 214 LNGLKMGDKTLTVRRATASSGQSK 237
           +NG  +    +       S   + 
Sbjct: 81  VNGTTIEGHVVKCYWGKESPDMTS 104

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 59.8 bits (145), Expect = 1e-11
 Identities = 15/85 (17%), Positives = 31/85 (36%), Gaps = 3/85 (3%)

Query: 142 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 201
           +SG++   +   ++ +  +P +     +  LL  +G +   + V               Y
Sbjct: 5   SSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET---AVVNVTY 61

Query: 202 QDPAVTDIACAALNGLKMGDKTLTV 226
                   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 = 51.3 bits (123), Expect = 9e-09
 Identities = 15/89 (16%), Positives = 33/89 (37%), Gaps = 10/89 (11%)

Query: 29  TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMR 88
            +  R++ +  +PP    + + +   Q          G  ++   V  + E     V   
Sbjct: 12  RQRIRKLQIRNIPPHLQWEVLDSLLVQ---------YGVVESCEQVNTDSETAVVNVTYS 62

Query: 89  TVEEASNAM-ALDGIIFEGVAVRVRRPTD 116
           + ++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 = 59.7 bits (145), Expect = 1e-11
 Identities = 22/90 (24%), Positives = 35/90 (38%), Gaps = 10/90 (11%)

Query: 149 AEGPDR-VFVGGLPYYFTE------TQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 201
           A+G D  + V  +P    +        I ++   FG +   +     + G +KGY F  Y
Sbjct: 11  ADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKIT--NDFYPEEDGKTKGYIFLEY 68

Query: 202 QDPAVTDIACAALNGLKMGDK-TLTVRRAT 230
             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 = 46.3 bits (110), Expect = 8e-07
 Identities = 19/77 (24%), Positives = 27/77 (35%), Gaps = 8/77 (10%)

Query: 293 ADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNA 352
              +  E++   + +   K+G + N   P  D   G+T G    FLEY        A   
Sbjct: 26  VGPDRLEKLKNVIHKIFSKFGKITNDFYPEED---GKTKGYI--FLEYASPAHAVDAVKN 80

Query: 353 LSGRKFGGN---TVNAF 366
             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 = 42.8 bits (101), Expect = 1e-05
 Identities = 19/97 (19%), Positives = 34/97 (35%), Gaps = 24/97 (24%)

Query: 33  RRVYVGGLPPLANEQ------AIATFFSQVMTAIGGNSAGPGDAVVNVYINHE----KKF 82
             + V  +P +  ++       I   FS+          G    + N +   E    K +
Sbjct: 16  SVIVVDNVPQVGPDRLEKLKNVIHKIFSKF---------GK---ITNDFYPEEDGKTKGY 63

Query: 83  AFVEMRTVEEASNAM-ALDGIIFEG-VAVRVRRPTDY 117
            F+E  +   A +A+   DG   +     RV   TD+
Sbjct: 64  IFLEYASPAHAVDAVKNADGYKLDKQHTFRVNLFTDF 100

>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 = 59.6 bits (145), Expect = 1e-11
 Identities = 22/82 (26%), Positives = 37/82 (45%), Gaps = 3/82 (3%)

Query: 150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKD-RDTGNSKGYGFCVYQDPAVTD 208
             P   F+G LPY  TE  IKE            L ++  +    KG+G+  ++D   + 
Sbjct: 13  SPPYTAFLGNLPYDVTEESIKEFFRGLNISA-VRLPREPSNPERLKGFGYAEFEDLD-SL 70

Query: 209 IACAALNGLKMGDKTLTVRRAT 230
           ++  +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 = 55.3 bits (134), Expect = 5e-10
 Identities = 15/87 (17%), Positives = 30/87 (34%), Gaps = 20/87 (22%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-------FAFV 85
              ++G LP    E++I  FF  +              +  V +  E         F + 
Sbjct: 16  YTAFLGNLPYDVTEESIKEFFRGL-------------NISAVRLPREPSNPERLKGFGYA 62

Query: 86  EMRTVEEASNAMALDGIIFEGVAVRVR 112
           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 = 59.1 bits (143), Expect = 2e-11
 Identities = 21/76 (27%), Positives = 30/76 (39%), Gaps = 5/76 (6%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
            V+VG LP     + +K  L   G++              +   F  Y D A    A + 
Sbjct: 21  DVYVGNLPRDARVSDLKRALRELGSV-----PLRLTWQGPRRRAFLHYPDSAAAQQAVSC 75

Query: 214 LNGLKMGDKTLTVRRA 229
           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 = 48.7 bits (116), Expect = 8e-08
 Identities = 17/87 (19%), Positives = 29/87 (33%), Gaps = 12/87 (13%)

Query: 27  QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVE 86
           +    A  VYVG LP  A    +     ++           G   + +     ++ AF+ 
Sbjct: 14  EGAPLAADVYVGNLPRDARVSDLKRALREL-----------GSVPLRLTWQGPRRRAFLH 62

Query: 87  MRTVEEASNAM-ALDGIIFEGVAVRVR 112
                 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 = 58.8 bits (143), Expect = 2e-11
 Identities = 21/82 (25%), Positives = 37/82 (45%), Gaps = 3/82 (3%)

Query: 150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDR-DTGNSKGYGFCVYQDPAVTD 208
             P   F+G LPY  TE  IKE            L ++  +    KG+G+  ++D   + 
Sbjct: 17  SPPYTAFLGNLPYDVTEESIKEFFRGLNIS-AVRLPREPSNPERLKGFGYAEFEDLD-SL 74

Query: 209 IACAALNGLKMGDKTLTVRRAT 230
           ++  +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 = 55.7 bits (135), Expect = 3e-10
 Identities = 15/86 (17%), Positives = 30/86 (34%), Gaps = 20/86 (23%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-------FAFV 85
              ++G LP    E++I  FF  +              +  V +  E         F + 
Sbjct: 20  YTAFLGNLPYDVTEESIKEFFRGL-------------NISAVRLPREPSNPERLKGFGYA 66

Query: 86  EMRTVEEASNAMALDGIIFEGVAVRV 111
           E   ++   +A++L+        +RV
Sbjct: 67  EFEDLDSLLSALSLNEESLGNRRIRV 92

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 58.4 bits (142), Expect = 2e-11
 Identities = 24/93 (25%), Positives = 40/93 (43%), Gaps = 8/93 (8%)

Query: 144 GAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD 203
           G+ G +    ++FVG +    T  +++ L E  G +   D+V        K Y F   + 
Sbjct: 1   GSSGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEK 52

Query: 204 PAVTDIACAALNGLKMGDKTLTVRRATASSGQS 236
            A    A A LNG ++  K + V  +T    +S
Sbjct: 53  EADAKAAIAQLNGKEVKGKRINVELSTKGQKKS 85

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 54.5 bits (132), Expect = 6e-10
 Identities = 17/84 (20%), Positives = 34/84 (40%), Gaps = 15/84 (17%)

Query: 29  TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMR 88
           + +  +++VG +      Q + + F +          G    V+   +   K +AFV M 
Sbjct: 6   SGNTWKIFVGNVSAACTSQELRSLFER---------RGR---VIECDV--VKDYAFVHME 51

Query: 89  TVEEASNAM-ALDGIIFEGVAVRV 111
              +A  A+  L+G   +G  + V
Sbjct: 52  KEADAKAAIAQLNGKEVKGKRINV 75

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 58.5 bits (142), Expect = 4e-11
 Identities = 16/83 (19%), Positives = 35/83 (42%), Gaps = 5/83 (6%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           +V+VG L     + +++     +G L    + ++       G+ F  ++DP   + A   
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRG 56

Query: 214 LNGLKMGDKTLTVRRATASSGQS 236
           L+G  +    + V  +T    +S
Sbjct: 57  LDGKVICGSRVRVELSTGMPRRS 79

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 55.0 bits (133), Expect = 5e-10
 Identities = 26/80 (32%), Positives = 35/80 (43%), Gaps = 14/80 (17%)

Query: 34  RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-FAFVEMRTVEE 92
           +VYVG L   A +  +   FS           GP   +  V+I      FAFVE     +
Sbjct: 2   KVYVGNLGTGAGKGELERAFSY---------YGP---LRTVWIARNPPGFAFVEFEDPRD 49

Query: 93  ASNAM-ALDGIIFEGVAVRV 111
           A +A+  LDG +  G  VRV
Sbjct: 50  AEDAVRGLDGKVICGSRVRV 69

>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 = 57.6 bits (140), Expect = 5e-11
 Identities = 16/90 (17%), Positives = 32/90 (35%), Gaps = 7/90 (7%)

Query: 148 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 207
           G+ G   VFVG      TE +++E    +G +    + K       + + F  + D  + 
Sbjct: 1   GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIA 55

Query: 208 DIACAALNGLKMGDKTLTVRRATASSGQSK 237
              C     L +   ++ +  A      + 
Sbjct: 56  QSLCG--EDLIIKGISVHISNAEPKHNSNS 83

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 42.2 bits (100), Expect = 1e-05
 Identities = 22/89 (24%), Positives = 37/89 (41%), Gaps = 14/89 (15%)

Query: 28  ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-FAFVE 86
            +  +  V+VG       E  +  FFSQ      G+       V++V+I    + FAFV 
Sbjct: 1   GSSGSSGVFVGRCTGDMTEDELREFFSQY-----GD-------VMDVFIPKPFRAFAFVT 48

Query: 87  MRTVEEASNAMALDGIIFEGVAVRVRRPT 115
               + A +    D II +G++V +    
Sbjct: 49  FADDQIAQSLCGEDLII-KGISVHISNAE 76

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 58.2 bits (141), Expect = 5e-11
 Identities = 13/94 (13%), Positives = 28/94 (29%), Gaps = 1/94 (1%)

Query: 143 SGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQ 202
           SG            +  +P+  T+  + + LE          V   + G   G     ++
Sbjct: 6   SGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFK 65

Query: 203 DPAVTDIACAALNGLKMGDKTLTVRRATASSGQS 236
           +      +   L+  K+  +   V   T    + 
Sbjct: 66  NEDDARKS-ERLHRKKLNGREAFVHVVTLEDMRE 98

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 53.2 bits (128), Expect = 3e-09
 Identities = 14/112 (12%), Positives = 33/112 (29%), Gaps = 14/112 (12%)

Query: 27  QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK---FA 83
                    ++  +P    +  +  F   +            +  V+V +++  +    A
Sbjct: 10  DVNSAKVCAHITNIPFSITKMDVLQFLEGI---------PVDENAVHVLVDNNGQGLGQA 60

Query: 84  FVEMRTVEEASNAMALDGIIFEGVAVRVRRPT--DYNPTLAAALGPGQPSPN 133
            V+ +  ++A  +  L      G    V   T  D           G+  P+
Sbjct: 61  LVQFKNEDDARKSERLHRKKLNGREAFVHVVTLEDMREIEKNPPAQGKSGPS 112

>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 = 57.6 bits (140), Expect = 6e-11
 Identities = 18/81 (22%), Positives = 34/81 (41%), Gaps = 13/81 (16%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 92
            R++VGGL P  +  A+A  F +     G        ++  +       FA+++  +++ 
Sbjct: 18  TRLWVGGLGPNTSLAALAREFDR----FG--------SIRTIDHVKGDSFAYIQYESLDA 65

Query: 93  ASNAM-ALDGIIFEGVAVRVR 112
           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 = 47.6 bits (114), Expect = 2e-07
 Identities = 17/74 (22%), Positives = 30/74 (40%), Gaps = 6/74 (8%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           R++VGGL    +   +    + FG++   D VK         + +  Y+       ACA 
Sbjct: 19  RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD------SFAYIQYESLDAAQAACAK 72

Query: 214 LNGLKMGDKTLTVR 227
           + G  +G     +R
Sbjct: 73  MRGFPLGGPDRRLR 86

>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 = 57.3 bits (139), Expect = 7e-11
 Identities = 17/90 (18%), Positives = 35/90 (38%), Gaps = 14/90 (15%)

Query: 25  TQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAF 84
           +    +    +YVGGL     E  +   F Q            G+ +  + +   ++ AF
Sbjct: 5   SSGEDKTITTLYVGGLGDTITETDLRNHFYQ-----------FGE-IRTITVVQRQQCAF 52

Query: 85  VEMRTVEEASNAM--ALDGIIFEGVAVRVR 112
           ++  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 = 1e-07
 Identities = 16/74 (21%), Positives = 31/74 (41%), Gaps = 7/74 (9%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA-CAA 213
           ++VGGL    TET ++     FG +    +V+       +   F  +      ++A   +
Sbjct: 15  LYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKS 68

Query: 214 LNGLKMGDKTLTVR 227
            N L +  + L V+
Sbjct: 69  FNKLIVNGRRLNVK 82

>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 = 56.8 bits (138), Expect = 1e-10
 Identities = 15/99 (15%), Positives = 32/99 (32%), Gaps = 15/99 (15%)

Query: 147 GGAEGPDR---VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD 203
           G          VFVG      T  ++++    +G +    + K       + + F  + D
Sbjct: 3   GSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFAD 57

Query: 204 PAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQES 242
             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 = 41.1 bits (97), Expect = 3e-05
 Identities = 22/89 (24%), Positives = 35/89 (39%), Gaps = 14/89 (15%)

Query: 26  QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-FAF 84
                H  +V+VG        + +  FF Q      G        VV+V+I    + FAF
Sbjct: 5   HHHHHHGSKVFVGRCTEDMTAEELQQFFCQY-----GE-------VVDVFIPKPFRAFAF 52

Query: 85  VEMRTVEEASNAMALDGIIFEGVAVRVRR 113
           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 = 57.1 bits (138), Expect = 1e-10
 Identities = 19/96 (19%), Positives = 32/96 (33%), Gaps = 17/96 (17%)

Query: 27  QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI--NHEKKF-- 82
           +     R VY+ G P  A    I  +             G    V+N+ +     K F  
Sbjct: 6   KNDVKNRSVYIKGFPTDATLDDIKEWLEDK---------GQ---VLNIQMRRTLHKAFKG 53

Query: 83  -AFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDY 117
             FV   ++E A   +   G  ++   + +    DY
Sbjct: 54  SIFVVFDSIESAKKFVETPGQKYKETDLLILFKDDY 89

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 55.9 bits (135), Expect = 3e-10
 Identities = 19/89 (21%), Positives = 32/89 (35%), Gaps = 6/89 (6%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           V++ G P   T   IKE LE  G +    + +       KG  F V+      + A   +
Sbjct: 14  VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSI---ESAKKFV 69

Query: 215 --NGLKMGDKTLTVRRATASSGQSKTEQE 241
              G K  +  L +        +   E++
Sbjct: 70  ETPGQKYKETDLLILFKDDYFAKKNEERK 98

>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 = 56.5 bits (137), Expect = 1e-10
 Identities = 22/85 (25%), Positives = 37/85 (43%), Gaps = 15/85 (17%)

Query: 28  ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEM 87
           + + + +++VG + P    Q +   F +          GP   V+   I   K +AFV M
Sbjct: 6   SGKASTKLHVGNISPTCTNQELRAKFEE---------YGP---VIECDI--VKDYAFVHM 51

Query: 88  RTVEEASNAM-ALDGIIFEGVAVRV 111
              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 = 54.5 bits (132), Expect = 6e-10
 Identities = 15/81 (18%), Positives = 31/81 (38%), Gaps = 8/81 (9%)

Query: 150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 209
           +   ++ VG +    T  +++   E +G +   D+V        K Y F   +       
Sbjct: 8   KASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAVE 59

Query: 210 ACAALNGLKMGDKTLTVRRAT 230
           A   L+  +   K + V+ +T
Sbjct: 60  AIRGLDNTEFQGKRMHVQLST 80

>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 = 58.4 bits (141), Expect = 1e-10
 Identities = 15/76 (19%), Positives = 32/76 (42%), Gaps = 5/76 (6%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           +V+VG L     +T+++     +G L    + ++       G+ F  ++DP     A   
Sbjct: 75  KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRE 129

Query: 214 LNGLKMGDKTLTVRRA 229
           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 = 56.8 bits (137), Expect = 4e-10
 Identities = 25/101 (24%), Positives = 39/101 (38%), Gaps = 14/101 (13%)

Query: 13  LGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVV 72
           +          M + +     +VYVG L    N+  +   F            GP   + 
Sbjct: 54  VTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYY---------GP---LR 101

Query: 73  NVYINHEKK-FAFVEMRTVEEASNAM-ALDGIIFEGVAVRV 111
           +V++      FAFVE     +A++A+  LDG    G  VRV
Sbjct: 102 SVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRV 142

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 56.2 bits (136), Expect = 3e-10
 Identities = 14/76 (18%), Positives = 31/76 (40%), Gaps = 8/76 (10%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           R+FV   P    E+++ E+   FG +    ++         G+ F  +++      A   
Sbjct: 33  RLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESAAKAIEE 84

Query: 214 LNGLKMGDKTLTVRRA 229
           ++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 = 49.6 bits (119), Expect = 5e-08
 Identities = 21/89 (23%), Positives = 30/89 (33%), Gaps = 15/89 (16%)

Query: 26  QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFV 85
           Q+      R++V   P    E  +   F            GP   +  V I     FAFV
Sbjct: 25  QEGELSNTRLFVRPFPLDVQESELNEIFGPF---------GP---MKEVKI--LNGFAFV 70

Query: 86  EMRTVEEASNAM-ALDGIIFEGVAVRVRR 113
           E    E A+ A+  + G  F    + V  
Sbjct: 71  EFEEAESAAKAIEEVHGKSFANQPLEVVY 99

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 53.9 bits (130), Expect = 8e-10
 Identities = 18/79 (22%), Positives = 30/79 (37%), Gaps = 9/79 (11%)

Query: 155 VFVGGLP------YYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 208
           + V  +P          +  I ++   FG +   +     + G +KGY F  Y  PA   
Sbjct: 4   IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKIT--NDFYPEEDGKTKGYIFLEYASPAHAV 61

Query: 209 IACAALNGLKMGDK-TLTV 226
            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: 293 ADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNA 352
              +  E++   + +   K+G + N   P  D   G+T G    FLEY        A   
Sbjct: 12  VGPDRLEKLKNVIHKIFSKFGKITNDFYPEED---GKTKGYI--FLEYASPAHAVDAVKN 66

Query: 353 LSGRKFGGN---TVN 364
             G K        VN
Sbjct: 67  ADGYKLDKQHTFRVN 81

>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 = 54.8 bits (132), Expect = 2e-09
 Identities = 15/85 (17%), Positives = 29/85 (34%), Gaps = 5/85 (5%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDL-----VKDRDTGNSKGYGFCVYQDPAVTD 208
           R++V  L  +  E  +K +   +             ++    G  KG  F    +     
Sbjct: 47  RIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAA 106

Query: 209 IACAALNGLKMGDKTLTVRRATASS 233
            A    NG  +  K + V+ A ++ 
Sbjct: 107 KALKEANGYVLFGKPMVVQFARSAR 131

>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 = 39.4 bits (92), Expect = 4e-04
 Identities = 14/80 (17%), Positives = 30/80 (37%), Gaps = 2/80 (2%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 92
            R+YV  L     E+ +   F + +      +      +  +     K  AF+ +   + 
Sbjct: 46  CRIYVKNLAKHVQEKDLKYIFGRYVD-FSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKA 104

Query: 93  ASNAM-ALDGIIFEGVAVRV 111
           A+ A+   +G +  G  + V
Sbjct: 105 AAKALKEANGYVLFGKPMVV 124

>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 = 53.4 bits (129), Expect = 2e-09
 Identities = 20/80 (25%), Positives = 34/80 (42%), Gaps = 13/80 (16%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 92
           + +YV  L    +E+ I   F+ +          PG       +   + +AFV     E+
Sbjct: 16  KILYVRNLMLSTSEEMIEKEFNNI---------KPG---AVERVKKIRDYAFVHFSNRED 63

Query: 93  ASNAM-ALDGIIFEGVAVRV 111
           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 = 52.7 bits (127), Expect = 3e-09
 Identities = 17/91 (18%), Positives = 30/91 (32%), Gaps = 9/91 (9%)

Query: 142 ASGAIGGAEGPDRV---FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGF 198
           +SG+ G  +    V   +V  L    +E  I++   +                  + Y F
Sbjct: 2   SSGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKP------GAVERVKKIRDYAF 55

Query: 199 CVYQDPAVTDIACAALNGLKMGDKTLTVRRA 229
             + +      A  ALNG  +    + V  A
Sbjct: 56  VHFSNREDAVEAMKALNGKVLDGSPIEVTLA 86

>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 = 53.2 bits (128), Expect = 3e-09
 Identities = 14/98 (14%), Positives = 40/98 (40%), Gaps = 4/98 (4%)

Query: 142 ASGAIGGAEGPDR---VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGF 198
           +SG+ G +        V + GLP+  ++ +I +       +     +     G S G  F
Sbjct: 2   SSGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAF 61

Query: 199 CVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQS 236
             +    + + A    +  ++G + + + +++ +  ++
Sbjct: 62  VQFASQEIAEKAL-KKHKERIGHRYIEIFKSSRAEVRT 98

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 49.0 bits (117), Expect = 9e-08
 Identities = 16/93 (17%), Positives = 35/93 (37%), Gaps = 12/93 (12%)

Query: 26  QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK---F 82
              T +   V + GLP   +++ I  FFS +     G         + + ++ + +    
Sbjct: 9   SPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNG---------MTLPVDFQGRSTGE 59

Query: 83  AFVEMRTVEEASNAMALDGIIFEGVAVRVRRPT 115
           AFV+  + E A  A+           + + + +
Sbjct: 60  AFVQFASQEIAEKALKKHKERIGHRYIEIFKSS 92

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 52.6 bits (126), Expect = 5e-09
 Identities = 16/83 (19%), Positives = 27/83 (32%), Gaps = 6/83 (7%)

Query: 155 VFVGGLPYYFTETQI---KELLESFGTLHGFDLVKDRDTGNSK---GYGFCVYQDPAVTD 208
           VFV GL     + ++    E    FG +H   +        S+      +  Y       
Sbjct: 18  VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77

Query: 209 IACAALNGLKMGDKTLTVRRATA 231
            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 = 40.6 bits (95), Expect = 9e-05
 Identities = 13/69 (18%), Positives = 23/69 (33%)

Query: 299 EEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKF 358
           +  +    E  GK+G +  VVI       G        ++ Y  +     A   ++    
Sbjct: 29  DPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVV 88

Query: 359 GGNTVNAFY 367
            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 = 39.8 bits (93), Expect = 1e-04
 Identities = 16/88 (18%), Positives = 33/88 (37%), Gaps = 21/88 (23%)

Query: 35  VYVGGLPP-LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK---------FAF 84
           V+V GL   LA+ + +     +     G         +  V IN+             A+
Sbjct: 18  VFVVGLSQRLADPEVLKR--PEYFGKFG--------KIHKVVINNSTSYAGSQGPSASAY 67

Query: 85  VEMRTVEEASNAM-ALDGIIFEGVAVRV 111
           V     E+A  A+  ++ ++ +G  ++ 
Sbjct: 68  VTYIRSEDALRAIQCVNNVVVDGRTLKA 95

>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 = 52.1 bits (125), Expect = 6e-09
 Identities = 19/85 (22%), Positives = 27/85 (31%), Gaps = 14/85 (16%)

Query: 30  RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRT 89
           R   RV V GLPP  + Q +     +            GD V    + +      VE   
Sbjct: 13  RSENRVVVSGLPPSGSWQDLKDHMREA-----------GD-VCYADV-YRDGTGVVEFVR 59

Query: 90  VEEASNAMA-LDGIIFEGVAVRVRR 113
            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 = 45.2 bits (107), Expect = 2e-06
 Identities = 15/79 (18%), Positives = 25/79 (31%), Gaps = 7/79 (8%)

Query: 151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA 210
             +RV V GLP   +   +K+ +   G +   D+ +D       G G   +        A
Sbjct: 14  SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYA 66

Query: 211 CAALNGLKMGDKTLTVRRA 229
              L+  K           
Sbjct: 67  VRKLDNTKFRSHEGETAYI 85

>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 = 52.5 bits (126), Expect = 7e-09
 Identities = 16/91 (17%), Positives = 33/91 (36%), Gaps = 1/91 (1%)

Query: 150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 209
           E    V++ GLP+      + +  +    +     +     G + G GF  +++ A    
Sbjct: 23  EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKA 82

Query: 210 ACAALNGLKMGDKTLTVRRATASSGQSKTEQ 240
           A    +   MG++ + V   T      K + 
Sbjct: 83  AL-CRHKQYMGNRFIQVHPITKKGMLEKIDM 112

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 51.4 bits (123), Expect = 2e-08
 Identities = 17/104 (16%), Positives = 31/104 (29%), Gaps = 14/104 (13%)

Query: 35  VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK---FAFVEMRTVE 91
           VY+ GLP  A  + +  FF ++            +  + +      K     FVE R   
Sbjct: 28  VYLKGLPFEAENKHVIDFFKKL---------DIVEDSIYIAYGPNGKATGEGFVEFRNEA 78

Query: 92  EASNAMALDGIIFEGVAVRVRR--PTDYNPTLAAALGPGQPSPN 133
           +   A+           ++V           +       Q  P+
Sbjct: 79  DYKAALCRHKQYMGNRFIQVHPITKKGMLEKIDMIRKRLQSGPS 122

>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 = 52.6 bits (126), Expect = 8e-09
 Identities = 12/78 (15%), Positives = 30/78 (38%), Gaps = 1/78 (1%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           V + GLP+  T+ +I +       +     +     G   G  F  +    + + A    
Sbjct: 45  VRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKAL-GK 103

Query: 215 NGLKMGDKTLTVRRATAS 232
           +  ++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 = 49.9 bits (119), Expect = 6e-08
 Identities = 17/93 (18%), Positives = 33/93 (35%), Gaps = 12/93 (12%)

Query: 26  QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK---F 82
              + +   V + GLP    ++ I  FFS +               + + ++ E K    
Sbjct: 36  SADSANDGFVRLRGLPFGCTKEEIVQFFSGL---------EIVPNGITLPVDPEGKITGE 86

Query: 83  AFVEMRTVEEASNAMALDGIIFEGVAVRVRRPT 115
           AFV+  + E A  A+           + V + +
Sbjct: 87  AFVQFASQELAEKALGKHKERIGHRYIEVFKSS 119

>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 = 1e-08
 Identities = 19/109 (17%), Positives = 35/109 (32%), Gaps = 13/109 (11%)

Query: 142 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 201
            S    G      +FV  L    TE  +++    FG L     +KD        Y F  +
Sbjct: 1   GSSGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHF 52

Query: 202 QDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQH 250
            +      A   +NG  +  + + +  A     +   ++       +Q 
Sbjct: 53  DERDGAVKAMEEMNGKDLEGENIEIVFA-----KPPDQKRKERKAQRQA 96

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A Length = 103

 Score = 46.5 bits (111), Expect = 6e-07
 Identities = 21/105 (20%), Positives = 35/105 (33%), Gaps = 19/105 (18%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 92
           + ++V  L     E+ +   FSQ          G    +  V     K +AF+     + 
Sbjct: 12  KVLFVRNLANTVTEEILEKAFSQF---------GK---LERVKKL--KDYAFIHFDERDG 57

Query: 93  ASNAM-ALDGIIFEGVAVRV---RRPTDYNPTLAAALGPG-QPSP 132
           A  AM  ++G   EG  + +   + P        A       PS 
Sbjct: 58  AVKAMEEMNGKDLEGENIEIVFAKPPDQKRKERKAQRQAASGPSS 102

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 52.5 bits (126), Expect = 1e-08
 Identities = 23/94 (24%), Positives = 32/94 (34%), Gaps = 18/94 (19%)

Query: 25  TQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK--- 81
               +     V++ GLP  A E  I  FFS +               V V+I        
Sbjct: 39  FTVQSTTGHCVHMRGLPYKATENDIYNFFSPL-------------NPVRVHIEIGPDGRV 85

Query: 82  --FAFVEMRTVEEASNAMALDGIIFEGVAVRVRR 113
              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 = 49.1 bits (117), Expect = 2e-07
 Identities = 16/117 (13%), Positives = 32/117 (27%), Gaps = 7/117 (5%)

Query: 126 GPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLV 185
                +    +      S     +     V + GLPY  TE  I         +    + 
Sbjct: 20  HMASMTGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPV-RVHIE 78

Query: 186 KDRDTGNSKGYGFCVYQDPAVTDIACAAL--NGLKMGDKTLTVRRATASSGQSKTEQ 240
              D G   G     +      + A AA+  +   M  + + +   + +   +    
Sbjct: 79  IGPD-GRVTGEADVEFATH---EEAVAAMSKDRANMQHRYIELFLNSTTGASNGAYS 131

>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 = 51.6 bits (124), Expect = 1e-08
 Identities = 18/83 (21%), Positives = 31/83 (37%), Gaps = 9/83 (10%)

Query: 154 RVFVGGLPYYF-TETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA 212
           RVF+G L      ++ ++ +   +G + G  +         KGY F  Y +      A  
Sbjct: 29  RVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVL 80

Query: 213 ALNGLKMGDKTLTVRRATASSGQ 235
             NG  +  +TL +  A      
Sbjct: 81  GENGRVLAGQTLDINMAGEPKPD 103

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110

 Score = 47.4 bits (113), Expect = 4e-07
 Identities = 18/82 (21%), Positives = 32/82 (39%), Gaps = 16/82 (19%)

Query: 33  RRVYVGGLPP-LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 91
            RV++G L   L  +  + T FS+          G    V    ++  K +AFV+     
Sbjct: 28  SRVFIGNLNTALVKKSDVETIFSK---------YGR---VAGCSVH--KGYAFVQYSNER 73

Query: 92  EASNAM-ALDGIIFEGVAVRVR 112
            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 = 51.1 bits (122), Expect = 2e-08
 Identities = 19/106 (17%), Positives = 38/106 (35%), Gaps = 16/106 (15%)

Query: 35  VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-----FAFVEMRT 89
           V + GLP   + + +  F S              D V  V+  + ++      AFVE+ +
Sbjct: 20  VKLRGLPWSCSIEDVQNFLS---------DCTIHDGVAGVHFIYTREGRQSGEAFVELES 70

Query: 90  VEEASNAMALDGIIFEGVAVRVRR--PTDYNPTLAAALGPGQPSPN 133
            ++   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 = 47.2 bits (112), Expect = 4e-07
 Identities = 23/119 (19%), Positives = 46/119 (38%), Gaps = 16/119 (13%)

Query: 142 ASGAIGGAEGPDR-----VFVGGLPYYFTETQIKELLESF---GTLHGFDLVKDRDTGNS 193
           +SG+ G   GP+      V + GLP+  +   ++  L        + G   +  R+ G  
Sbjct: 2   SSGSSGMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQ 60

Query: 194 KGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIA 252
            G  F   +      +A    +   MG + + V ++       +TE + +L  +  + A
Sbjct: 61  SGEAFVELESEDDVKLAL-KKDRESMGHRYIEVFKS------HRTEMDWVLKHSGPNSA 112

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 51.0 bits (122), Expect = 2e-08
 Identities = 16/100 (16%), Positives = 28/100 (28%), Gaps = 10/100 (10%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           +    LP      +I+E    FG+      +               + +P     A   L
Sbjct: 13  ILAKNLPAGTLAAEIQETFSRFGS------LGRVLLPEGGITAIVEFLEPLEARKAFRHL 66

Query: 215 NGLKMGDKTLTVRRA----TASSGQSKTEQESILAQAQQH 250
              K     L +  A      ++ Q K  Q    A+  + 
Sbjct: 67  AYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAEKAES 106

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 44.0 bits (104), Expect = 6e-06
 Identities = 17/87 (19%), Positives = 24/87 (27%), Gaps = 13/87 (14%)

Query: 26  QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFV 85
             + R    +    LP       I   FS+          G    +  V +      A V
Sbjct: 4   GSSGRSKTVILAKNLPAGTLAAEIQETFSR---------FGS---LGRVLLPEGGITAIV 51

Query: 86  EMRTVEEASNAM-ALDGIIFEGVAVRV 111
           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 = 40.2 bits (94), Expect = 1e-04
 Identities = 12/71 (16%), Positives = 28/71 (39%), Gaps = 9/71 (12%)

Query: 303 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNT 362
            +++E   ++G+L  V++P          G     +E+ + +    A   L+  KF    
Sbjct: 25  AEIQETFSRFGSLGRVLLP---------EGGITAIVEFLEPLEARKAFRHLAYSKFHHVP 75

Query: 363 VNAFYYPEDKY 373
           +   + P   +
Sbjct: 76  LYLEWAPIGVF 86

>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 = 50.0 bits (120), Expect = 3e-08
 Identities = 12/81 (14%), Positives = 32/81 (39%), Gaps = 9/81 (11%)

Query: 154 RVFVGGLPY-YFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA 212
           R+F+G LP    ++  +  +   +G +   ++           +GF  + +P     A  
Sbjct: 24  RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAIE 75

Query: 213 ALNGLKMGDKTLTVRRATASS 233
             +      K L +  +++++
Sbjct: 76  XESQEMNFGKKLILEVSSSNA 96

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 48.5 bits (116), Expect = 1e-07
 Identities = 12/81 (14%), Positives = 30/81 (37%), Gaps = 16/81 (19%)

Query: 33  RRVYVGGLPPL-ANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 91
            R+++G LP    +++ +   FS           G    ++ + I     F F++    +
Sbjct: 23  SRLFIGNLPLKNVSKEDLFRIFSPY---------GH---IMQINIK--NAFGFIQFDNPQ 68

Query: 92  EASNAMA-LDGIIFEGVAVRV 111
              +A+      +  G  + +
Sbjct: 69  SVRDAIEXESQEMNFGKKLIL 89

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 50.3 bits (120), Expect = 4e-08
 Identities = 19/109 (17%), Positives = 36/109 (33%), Gaps = 15/109 (13%)

Query: 7   PFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAG 66
                  G  P       ++ A   +R +++  LP    E  + +              G
Sbjct: 6   HHHHHSSGLVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPF---------G 56

Query: 67  PGDAVVNVYINHEKKFAFVEMRTVEEASNAM---ALDGIIFEGVAVRVR 112
               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 = 50.3 bits (120), Expect = 4e-08
 Identities = 20/111 (18%), Positives = 35/111 (31%), Gaps = 11/111 (9%)

Query: 125 LGPGQP--SPNLNLAAVGLASGAIGGAEGPDRV-FVGGLPYYFTETQIKELLESFGTLHG 181
           +G        +  L   G   G    A  P RV  +  LP   TE ++  L   FG +  
Sbjct: 1   MGSSHHHHHHSSGLVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTN 60

Query: 182 FDLVKDRDTGNSKGYGFCVYQDP--AVTDIACAALNGLKMGDKTLTVRRAT 230
             ++K       K   F        A T +         +  + + ++ + 
Sbjct: 61  LLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSN 105

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 50.0 bits (119), Expect = 5e-08
 Identities = 21/71 (29%), Positives = 27/71 (38%), Gaps = 5/71 (7%)

Query: 148 GAEGPDR---VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRD--TGNSKGYGFCVYQ 202
           G+ G      VFVGGLP    E +I      FG L      K         KGY F ++Q
Sbjct: 1   GSSGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQ 60

Query: 203 DPAVTDIACAA 213
           + +       A
Sbjct: 61  EESSVQALIDA 71

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 49.1 bits (118), Expect = 6e-08
 Identities = 12/81 (14%), Positives = 32/81 (39%), Gaps = 9/81 (11%)

Query: 154 RVFVGGLPYY-FTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA 212
           R+F+G LP    ++  +  +   +G +   ++           +GF  + +P     A  
Sbjct: 12  RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAIE 63

Query: 213 ALNGLKMGDKTLTVRRATASS 233
             +      K L +  +++++
Sbjct: 64  CESQEMNFGKKLILEVSSSNA 84

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 48.0 bits (115), Expect = 2e-07
 Identities = 12/80 (15%), Positives = 30/80 (37%), Gaps = 16/80 (20%)

Query: 34  RVYVGGLPPL-ANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 92
           R+++G LP    +++ +   FS           G    ++ + I     F F++    + 
Sbjct: 12  RLFIGNLPLKNVSKEDLFRIFSP---------YGH---IMQINIK--NAFGFIQFDNPQS 57

Query: 93  ASNAM-ALDGIIFEGVAVRV 111
             +A+      +  G  + +
Sbjct: 58  VRDAIECESQEMNFGKKLIL 77

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 49.5 bits (118), Expect = 7e-08
 Identities = 16/86 (18%), Positives = 30/86 (34%), Gaps = 9/86 (10%)

Query: 148 GAEGPDRV-FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP-- 204
           G+  P RV  +  LP   TE ++  L   FG +    ++K       K   F        
Sbjct: 11  GSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEA 64

Query: 205 AVTDIACAALNGLKMGDKTLTVRRAT 230
           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 = 47.5 bits (113), Expect = 3e-07
 Identities = 16/83 (19%), Positives = 30/83 (36%), Gaps = 15/83 (18%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 92
           R +++  LP    E  + +              G    V N+ +   K  AF+EM T E 
Sbjct: 17  RVIHIRKLPIDVTEGEVISLGLPF---------GK---VTNLLMLKGKNQAFIEMNTEEA 64

Query: 93  ASNAMA---LDGIIFEGVAVRVR 112
           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 = 49.4 bits (118), Expect = 7e-08
 Identities = 19/76 (25%), Positives = 31/76 (40%), Gaps = 3/76 (3%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           V V G+P+   E  +++       +    L+KD   G + G G   +  P  T  A    
Sbjct: 19  VSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEAL-KR 75

Query: 215 NGLKMGDKTLTVRRAT 230
           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 = 46.7 bits (111), Expect = 6e-07
 Identities = 20/102 (19%), Positives = 35/102 (34%), Gaps = 18/102 (17%)

Query: 35  VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI--NHEKK---FAFVEMRT 89
           V V G+P  A E  +  FF              G  V  V++  +H  +      V+  +
Sbjct: 19  VSVHGMPFSAMENDVRDFFH-------------GLRVDAVHLLKDHVGRNNGNGLVKFLS 65

Query: 90  VEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPS 131
            ++   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 = 48.6 bits (116), Expect = 1e-07
 Identities = 16/99 (16%), Positives = 28/99 (28%), Gaps = 23/99 (23%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 92
             V+V GL     E  +     +          G    +  V +   K+ A VE   ++ 
Sbjct: 16  PVVHVRGLCESVVEADLVEALEKF---------GT---ICYVMMMPFKRQALVEFENIDS 63

Query: 93  ASNAMA---LDGIIFEGVAVRVR--------RPTDYNPT 120
           A   +       +   G              RP +  P+
Sbjct: 64  AKECVTFAADVPVYIAGQQAFFNYSTSKRITRPGNSGPS 102

>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 = 4e-07
 Identities = 15/75 (20%), Positives = 24/75 (32%), Gaps = 8/75 (10%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP--AVTDIACA 212
           V V GL     E  + E LE FGT      +        K      +++   A   +  A
Sbjct: 18  VHVRGLCESVVEADLVEALEKFGT------ICYVMMMPFKRQALVEFENIDSAKECVTFA 71

Query: 213 ALNGLKMGDKTLTVR 227
           A   + +  +     
Sbjct: 72  ADVPVYIAGQQAFFN 86

>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 = 48.7 bits (116), Expect = 1e-07
 Identities = 19/85 (22%), Positives = 27/85 (31%), Gaps = 14/85 (16%)

Query: 30  RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRT 89
           R   RV V GLPP  + Q +     +            GD V    + +      VE   
Sbjct: 14  RSENRVVVSGLPPSGSWQDLKDHMREA-----------GD-VCYADV-YRDGTGVVEFVR 60

Query: 90  VEEASNAMA-LDGIIFEGVAVRVRR 113
            E+ + A+  LD   F         
Sbjct: 61  KEDMTYAVRKLDNTKFRSHEGETAY 85

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 42.5 bits (100), Expect = 2e-05
 Identities = 15/76 (19%), Positives = 24/76 (31%), Gaps = 7/76 (9%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           RV V GLP   +   +K+ +   G +   D+ +D       G G   +        A   
Sbjct: 18  RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRK 70

Query: 214 LNGLKMGDKTLTVRRA 229
           L+  K           
Sbjct: 71  LDNTKFRSHEGETAYI 86

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 49.1 bits (117), Expect = 1e-07
 Identities = 20/96 (20%), Positives = 34/96 (35%), Gaps = 7/96 (7%)

Query: 22  QVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK 81
           +V    +  +   V + GLP  A  + +  FF Q          G  + ++ V     + 
Sbjct: 13  EVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQH-----CPITGGKEGILFVTYPDGRP 67

Query: 82  --FAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPT 115
              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 = 48.3 bits (115), Expect = 2e-07
 Identities = 18/84 (21%), Positives = 33/84 (39%), Gaps = 10/84 (11%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFD----LVKDRDTGNSKGYGFCVYQDPAVTDIA 210
           V + GLP+  T  ++         + G       V   D G   G  F ++      + A
Sbjct: 26  VRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPD-GRPTGDAFVLFACE---EYA 81

Query: 211 CAAL--NGLKMGDKTLTVRRATAS 232
             AL  +   +G + + + R+TA+
Sbjct: 82  QNALRKHKDLLGKRYIELFRSTAA 105

>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 = 1e-07
 Identities = 15/121 (12%), Positives = 45/121 (37%), Gaps = 7/121 (5%)

Query: 154 RVFVGGLPYYFTETQIKELL----ESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 209
            +++  L     + ++K+ L      FG +     +    +   +G  F ++++ +    
Sbjct: 11  TIYINNLNEKIKKDELKKSLYAIFSQFGQILD---ILVSRSLKMRGQAFVIFKEVSSATN 67

Query: 210 ACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGG 269
           A  ++ G    DK + ++ A   S      + + + + ++    +  + +T        G
Sbjct: 68  ALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQG 127

Query: 270 M 270
            
Sbjct: 128 G 128

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 44.9 bits (105), Expect = 2e-05
 Identities = 17/92 (18%), Positives = 36/92 (39%), Gaps = 12/92 (13%)

Query: 24  MTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-- 81
           M    TR    +Y+  L     +  +      + +  G         ++++ ++   K  
Sbjct: 1   MAVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFG--------QILDILVSRSLKMR 52

Query: 82  -FAFVEMRTVEEASNAM-ALDGIIFEGVAVRV 111
             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 = 42.9 bits (100), Expect = 9e-05
 Identities = 16/75 (21%), Positives = 24/75 (32%), Gaps = 6/75 (8%)

Query: 156 FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN 215
           F+  LP    E  +  L   F       LV  R         F  + +      A  AL 
Sbjct: 211 FLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQ 265

Query: 216 GLKM-GDKTLTVRRA 229
           G K+  +  + +  A
Sbjct: 266 GFKITQNNAMKISFA 280

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 48.2 bits (115), Expect = 2e-07
 Identities = 23/86 (26%), Positives = 32/86 (37%), Gaps = 18/86 (20%)

Query: 35  VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-----FAFVEMRT 89
           V++ GLP  A E  I  FFS +               + V+I           A VE  T
Sbjct: 18  VHMRGLPYRATENDIYNFFSPL-------------NPMRVHIEIGPDGRVTGEADVEFAT 64

Query: 90  VEEASNAMALDGIIFEGVAVRVRRPT 115
            E+A  AMA D    +   V +   +
Sbjct: 65  HEDAVAAMAKDKANMQHRYVELFLNS 90

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 47.0 bits (112), Expect = 4e-07
 Identities = 17/95 (17%), Positives = 30/95 (31%), Gaps = 7/95 (7%)

Query: 143 SGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQ 202
           SG+   +     V + GLPY  TE  I              +    D G   G     + 
Sbjct: 6   SGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPD-GRVTGEADVEFA 63

Query: 203 DPAVTDIACAAL--NGLKMGDKTLTVRRATASSGQ 235
                + A AA+  +   M  + + +   + +   
Sbjct: 64  TH---EDAVAAMAKDKANMQHRYVELFLNSTAGTS 95

>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 = 47.9 bits (114), Expect = 2e-07
 Identities = 16/82 (19%), Positives = 32/82 (39%), Gaps = 9/82 (10%)

Query: 152 PDRV-FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP--AVTD 208
           P RV  +  LP   TET++  L   FG +    ++K       K   F        A+T 
Sbjct: 14  PSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITM 67

Query: 209 IACAALNGLKMGDKTLTVRRAT 230
           +   +     + ++ + ++ + 
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 = 46.4 bits (110), Expect = 7e-07
 Identities = 14/83 (16%), Positives = 27/83 (32%), Gaps = 15/83 (18%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 92
           R +++  LP    E  +                G    V N+ +   K  AF+E+ T E 
Sbjct: 16  RVLHIRKLPGEVTETEVIALGLPF---------GK---VTNILMLKGKNQAFLELATEEA 63

Query: 93  ASNAM---ALDGIIFEGVAVRVR 112
           A   +   +          + ++
Sbjct: 64  AITMVNYYSAVTPHLRNQPIYIQ 86

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 47.3 bits (113), Expect = 2e-07
 Identities = 22/89 (24%), Positives = 35/89 (39%), Gaps = 9/89 (10%)

Query: 148 GAEGPDR--VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPA 205
           G+ G     V + G P+  TE  + E L          +V++   GN  GY F  + +  
Sbjct: 4   GSSGTTCHTVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAH-GNKTGYIFVDFSNE- 60

Query: 206 VTDIACAAL--NGLKMGDKTLTVRRATAS 232
             +    AL  N   MG + + V R  + 
Sbjct: 61  --EEVKQALKCNREYMGGRYIEVFREKSG 87

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 46.9 bits (112), Expect = 3e-07
 Identities = 16/86 (18%), Positives = 26/86 (30%), Gaps = 18/86 (20%)

Query: 35  VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI--NHEKK---FAFVEMRT 89
           V + G P    E+ +  F +                 V + I  N       + FV+   
Sbjct: 13  VKLRGAPFNVTEKNVMEFLA-------------PLKPVAIRIVRNAHGNKTGYIFVDFSN 59

Query: 90  VEEASNAMALDGIIFEGVAVRVRRPT 115
            EE   A+  +     G  + V R  
Sbjct: 60  EEEVKQALKCNREYMGGRYIEVFREK 85

>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 = 47.9 bits (114), Expect = 2e-07
 Identities = 13/90 (14%), Positives = 28/90 (31%), Gaps = 8/90 (8%)

Query: 26  QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK--FA 83
           ++       +   GLP     + +  FFS              + +  +     K+   A
Sbjct: 5   EEEVDDVFLIRAQGLPWSCTMEDVLNFFS------DCRIRNGENGIHFLLNRDGKRRGDA 58

Query: 84  FVEMRTVEEASNAMALDGIIFEGVAVRVRR 113
            +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 = 47.5 bits (113), Expect = 3e-07
 Identities = 14/98 (14%), Positives = 31/98 (31%), Gaps = 11/98 (11%)

Query: 155 VFVGGLPYYFTETQIKELLESF---GTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 211
           +   GLP+  T   +             +G   + +RD G  +G      +       A 
Sbjct: 14  IRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKAL 72

Query: 212 AALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQ 249
              + + MG + + V            + ++++   Q 
Sbjct: 73  -EKHRMYMGQRYVEVYEIN------NEDVDALMKSLQV 103

>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 = 47.2 bits (113), Expect = 3e-07
 Identities = 13/84 (15%), Positives = 34/84 (40%), Gaps = 7/84 (8%)

Query: 154 RVFVGGLPYYFTETQIKELL----ESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 209
            +++  L     + ++K+ L      FG +     +    +   +G  F ++++ +    
Sbjct: 10  TIYINNLNEKIKKDELKKSLHAIFSRFGQILD---ILVSRSLKMRGQAFVIFKEVSSATN 66

Query: 210 ACAALNGLKMGDKTLTVRRATASS 233
           A  ++ G    DK + ++ A   S
Sbjct: 67  ALRSMQGFPFYDKPMRIQYAKTDS 90

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 41.4 bits (98), Expect = 3e-05
 Identities = 17/95 (17%), Positives = 39/95 (41%), Gaps = 23/95 (24%)

Query: 33  RRVYVGGLPPLANE----QAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK---FAFV 85
             +Y+  L     +    +++   FS+          G    ++++ ++   K    AFV
Sbjct: 9   HTIYINNLNEKIKKDELKKSLHAIFSRF---------GQ---ILDILVSRSLKMRGQAFV 56

Query: 86  EMRTVEEASNAM-ALDGIIFEGVAVRV---RRPTD 116
             + V  A+NA+ ++ G  F    +R+   +  +D
Sbjct: 57  IFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSD 91

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 46.7 bits (111), Expect = 5e-07
 Identities = 19/82 (23%), Positives = 29/82 (35%), Gaps = 15/82 (18%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 92
             V++ GL     E  +     +          GP   +  V +  +K+ A VE   V  
Sbjct: 22  PVVHIRGLIDGVVEADLVEALQEF---------GP---ISYVVVMPKKRQALVEFEDVLG 69

Query: 93  ASNAM---ALDGIIFEGVAVRV 111
           A NA+   A + I   G    V
Sbjct: 70  ACNAVNYAADNQIYIAGHPAFV 91

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 46.7 bits (111), Expect = 5e-07
 Identities = 15/74 (20%), Positives = 26/74 (35%), Gaps = 8/74 (10%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP--AVTDIACA 212
           V + GL     E  + E L+ FG +    ++        K      ++D   A   +  A
Sbjct: 24  VHIRGLIDGVVEADLVEALQEFGPISYVVVMP------KKRQALVEFEDVLGACNAVNYA 77

Query: 213 ALNGLKMGDKTLTV 226
           A N + +      V
Sbjct: 78  ADNQIYIAGHPAFV 91

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 46.5 bits (111), Expect = 5e-07
 Identities = 20/87 (22%), Positives = 36/87 (41%), Gaps = 15/87 (17%)

Query: 26  QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFV 85
           ++A R    +YV G         +   FS       GN       ++++ ++  +  AFV
Sbjct: 9   RRAPRKGNTLYVYGED--MTPTLLRGAFSPF-----GN-------IIDLSMDPPRNCAFV 54

Query: 86  EMRTVEEASNAM-ALDGIIFEGVAVRV 111
               +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 = 45.7 bits (109), Expect = 1e-06
 Identities = 22/104 (21%), Positives = 38/104 (36%), Gaps = 16/104 (15%)

Query: 142 ASGAIGGAEGPDR---VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGF 198
           +SG+ G    P +   ++V G     T T ++     FG       + D      +   F
Sbjct: 2   SSGSSGERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGN------IIDLSMDPPRNCAF 53

Query: 199 CVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQES 242
             Y+     D A A LNG ++    L V     +  + +   +S
Sbjct: 54  VTYEKMESADQAVAELNGTQVESVQLKV-----NIARKQPMLDS 92

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 45.7 bits (109), Expect = 1e-06
 Identities = 22/79 (27%), Positives = 36/79 (45%), Gaps = 3/79 (3%)

Query: 154 RVFVGGLPYYFTETQIKEL-LESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA 212
            +FVG L     +  + E  ++ + +  G  +V D+ TG SKGYGF  + D      A  
Sbjct: 11  SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALT 69

Query: 213 ALNG-LKMGDKTLTVRRAT 230
              G + +G K + +  A 
Sbjct: 70  ECQGAVGLGSKPVRLSVAI 88

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 47.5 bits (112), Expect = 1e-06
 Identities = 20/104 (19%), Positives = 34/104 (32%), Gaps = 17/104 (16%)

Query: 19  MPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-- 76
           +P      +     R VY+ G P  A    I  +             G    V+N+ +  
Sbjct: 96  LPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDK---------GQ---VLNIQMRR 143

Query: 77  NHEKKF---AFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDY 117
              K F    FV   ++E A   +   G  ++   + +    DY
Sbjct: 144 TLHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKDDY 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 = 39.4 bits (91), Expect = 7e-04
 Identities = 17/78 (21%), Positives = 25/78 (32%), Gaps = 2/78 (2%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
            V++ G P   T   IKE LE  G +    + +       KG  F V+            
Sbjct: 111 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVET 169

Query: 214 LNGLKMGDKTLTVRRATA 231
             G K  +  L +     
Sbjct: 170 P-GQKYKETDLLILFKDD 186

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 45.3 bits (107), Expect = 2e-06
 Identities = 16/101 (15%), Positives = 34/101 (33%), Gaps = 9/101 (8%)

Query: 154 RVFVGGLPYYFTETQIKELL----ESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 209
            V +  +     + +++ LL     S G +   D+V D  + ++ G  + V+        
Sbjct: 31  VVLITNINPEVPKEKLQALLYALASSQGDI--LDIVVDL-SDDNSGKAYIVFATQESAQA 87

Query: 210 ACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQH 250
              A  G       L +  +      S+  ++  L     H
Sbjct: 88  FVEAFQGYPFQGNPLVITFSETPQ--SQVAEDGSLEHHHHH 126

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 43.0 bits (101), Expect = 2e-05
 Identities = 16/108 (14%), Positives = 34/108 (31%), Gaps = 23/108 (21%)

Query: 20  PVQVMTQQATRHARRVYVGGLPPLANE----QAIATFFSQVMTAIGGNSAGPGDAVVNVY 75
           P    T   T  ++ V +  + P   +      +    S           G    ++++ 
Sbjct: 17  PDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQ---------GD---ILDIV 64

Query: 76  INHEKK---FAFVEMRTVEEASNAM-ALDGIIFEGVAVRV---RRPTD 116
           ++        A++   T E A   + A  G  F+G  + +     P  
Sbjct: 65  VDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQS 112

>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 = 45.0 bits (106), Expect = 4e-06
 Identities = 16/95 (16%), Positives = 31/95 (32%), Gaps = 14/95 (14%)

Query: 24  MTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-- 81
           M          V + GLP   + + +  F S              D    V+  + ++  
Sbjct: 36  MLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDC---------TIHDGAAGVHFIYTREGR 86

Query: 82  ---FAFVEMRTVEEASNAMALDGIIFEGVAVRVRR 113
               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 = 43.1 bits (101), Expect = 2e-05
 Identities = 17/96 (17%), Positives = 34/96 (35%), Gaps = 11/96 (11%)

Query: 155 VFVGGLPYYFTETQIKELLESF---GTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 211
           V + GLP+  +   ++  L          G   +  R+ G   G  F          +A 
Sbjct: 47  VKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMAL 105

Query: 212 AALNGLKMGDKTLTVRRATASSGQSKTEQESILAQA 247
              +   MG + + V ++       +TE + +L  +
Sbjct: 106 -KKDRESMGHRYIEVFKS------HRTEMDWVLKHS 134

>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 = 1e-05
 Identities = 17/67 (25%), Positives = 27/67 (40%), Gaps = 6/67 (8%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           V  GGL    +  Q+  +LE  G +    +  +      K Y F  Y+    +  A   L
Sbjct: 30  VANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTL 83

Query: 215 NGLKMGD 221
           NG ++ D
Sbjct: 84  NGKEVVD 90

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 38.0 bits (88), Expect = 7e-04
 Identities = 14/68 (20%), Positives = 22/68 (32%), Gaps = 13/68 (19%)

Query: 35  VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEAS 94
           V  GGL    +   +                     V  + +   K ++F   RT EE+ 
Sbjct: 30  VANGGLGNGVSRNQLLPVLE------------KCGLVDALLMPPNKPYSFARYRTTEESK 77

Query: 95  NAM-ALDG 101
            A   L+G
Sbjct: 78  RAYVTLNG 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 = 40.7 bits (95), Expect = 7e-05
 Identities = 20/96 (20%), Positives = 34/96 (35%), Gaps = 16/96 (16%)

Query: 26  QQATRHARRVYVGGLP-PLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAF 84
            Q     R +++  LP    ++ A+                 P   + N  +   K  AF
Sbjct: 19  DQKQELGRVIHLSNLPHSGYSDSAVLKLAE------------PYGKIKNYILMRMKSQAF 66

Query: 85  VEMRTVEEASNAM---ALDGIIFEGVAVRVRRPTDY 117
           +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	380
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	99.98
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.98
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.97
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	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
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.97
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.97
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.97
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.97
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.96
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.96
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.96
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.96
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.96
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.96
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.96
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.96
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.96
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.96
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.95
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.95
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.95
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.95
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.95
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.94
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.94
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.94
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.93
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.93
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.93
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.91
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.87
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.86
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.82
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.82
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.82
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.78
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.78
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.78
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.77
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.77
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.76
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.76
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.75
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.75
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.75
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.75
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.75
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.75
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.75
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.75
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.74
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.74
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.74
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.74
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.74
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.74
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.74
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.73
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.73
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.73
2div_A	99	TRNA selenocysteine associated protein; structural	99.73
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.73
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.73
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.73
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.73
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.73
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.72
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.72
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.72
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.72
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.72
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.72
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.72
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.72
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.71
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.71
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.71
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.71
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.71
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.71
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.71
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.71
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.71
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.71
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.71
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.71
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.71
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.71
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.71
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.71
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.7
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.7
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.7
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.7
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.7
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.7
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.7
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.7
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.7
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.7
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.7
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.69
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.69
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.69
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.69
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.69
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.69
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.68
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.68
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.68
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.68
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.68
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.68
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.68
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.68
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.68
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.68
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.68
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.68
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.68
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.67
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.67
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.67
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.67
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.67
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.67
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.67
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.66
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.66
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.66
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.66
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.66
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.66
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.66
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.66
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.65
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.65
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.65
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.65
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.65
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.65
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.65
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.65
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.65
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.65
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.64
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.64
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.64
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.64
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.64
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.64
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.64
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.64
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.64
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.64
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.63
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.63
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.63
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.63
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.63
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.63
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.63
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.63
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.63
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.63
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.63
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.62
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.62
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.62
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.62
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.62
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.62
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.62
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.62
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.62
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.62
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.62
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.62
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.62
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.61
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.61
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.61
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.61
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.61
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.61
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.61
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.61
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.61
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.61
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.61
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.61
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.6
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.6
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.6
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.6
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.6
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.6
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.6
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.6
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.6
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.6
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.59
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.59
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.59
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.59
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.59
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.59
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.59
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.59
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.59
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.59
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.37
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.59
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.59
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.59
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.58
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.58
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.58
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.58
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.58
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.58
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.58
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.58
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.58
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.58
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.58
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.58
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.58
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.58
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.58
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.58
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.58
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.58
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.58
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.57
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.57
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.57
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.57
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.57
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.57
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.57
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.57
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.57
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.57
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.57
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.57
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.57
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.57
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.57
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.57
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.56
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.56
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.56
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.56
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.56
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.56
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.56
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.56
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.56
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.56
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.56
1x5p_A	97	Negative elongation factor E; structure genomics,	99.56
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.55
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.55
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.55
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.55
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.55
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.55
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.55
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.55
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.55
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.55
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.55
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.55
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.54
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.54
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.54
2div_A	99	TRNA selenocysteine associated protein; structural	99.54
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.54
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.54
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.54
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.54
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.54
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.54
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.54
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.54
1x5p_A	97	Negative elongation factor E; structure genomics,	99.54
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.54
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.53
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.53
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.53
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.53
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.53
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.53
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.53
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.53
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.53
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.53
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.52
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.52
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.52
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.52
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.52
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.52
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.52
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.52
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.51
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.51
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.51
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.51
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.51
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.51
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.51
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.5
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.5
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.5
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.5
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.5
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.5
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.5
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.49
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.49
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	99.49
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.48
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.48
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.48
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.48
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.47
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.47
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.47
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.47
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.47
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.46
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.46
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.46
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.46
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.45
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.45
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.45
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.44
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.44
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.44
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.43
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.43
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.43
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.43
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.42
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.42
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.42
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.13
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.41
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.41
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.41
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.4
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.4
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.39
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.39
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.38
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.37
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.37
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.31
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.26
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.2
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.17
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.14
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.12
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.11
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.11
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.92
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.91
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.82
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.73
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.7
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.7
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.53
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.37
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.34
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.84
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.78
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.7
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.44
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.33
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.2
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.18
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.12
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	96.79
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	96.21
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	95.9
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	95.89
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	95.66
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	95.62
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	95.34
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	94.89
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	94.89
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	88.14

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=100.00  E-value=1.7e-42  Score=317.12  Aligned_cols=248  Identities=23%  Similarity=0.327  Sum_probs=215.0

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceec
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE  105 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~  105 (380)
                      .....+++|||+|||+++|+++|+++|++||             |..+.+.+++|||||+|.+.++|.+|+ .+++..+.
T Consensus        17 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G-------------i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~   83 (284)
T 3smz_A           17 RQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-------------LKYCFVDKYKGTAFVTLLNGEQAEAAINAFHQSRLR   83 (284)
T ss_dssp             HHHHCCCEEEEECCCTTCCHHHHHHHTTTSC-------------EEEEEEETTTTEEEEEESSHHHHHHHHHHHTTCEET
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHHcC-------------CEEEEEecCCCEEEEEeCCHHHHHHHHHHcCCCeeC
Confidence            4557889999999999999999999999997             456667899999999999999999999 79999999


Q ss_pred             CceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEe
Q 016936          106 GVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLV  185 (380)
Q Consensus       106 g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~  185 (380)
                      |++|+|.++..                                   ..+|||+|||+.+++++|+++|++||.|..+.++
T Consensus        84 g~~i~v~~~~~-----------------------------------~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~  128 (284)
T 3smz_A           84 ERELSVQLQPT-----------------------------------DALLCVANLPPSLTQQQFEELVRPFGSLERCFLV  128 (284)
T ss_dssp             TEECEEEECCC-----------------------------------SCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEE
T ss_pred             CeEEEEEecCC-----------------------------------CCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEE
Confidence            99999998432                                   2599999999999999999999999999999999


Q ss_pred             eCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccCCCCChhHHHHHHHHHHHHHHHHHHHhhhcCccc
Q 016936          186 KDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNT  265 (380)
Q Consensus       186 ~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  265 (380)
                      .++.+|.++|+|||+|.+.++|.+|+..++|..+.|+.|.|.++.......                             
T Consensus       129 ~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~~~~~~~-----------------------------  179 (284)
T 3smz_A          129 YSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTP-----------------------------  179 (284)
T ss_dssp             ECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCGGGCCT-----------------------------
T ss_pred             eeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCCCCc-----------------------------
Confidence            998889999999999999999999999999999999999999986542211                             


Q ss_pred             cCCCCCccCCccceEEEEeccCCc-ccCCChHHHHHHHHHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechh
Q 016936          266 LGGGMSLFGETLAKVLCLTEAITA-DALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAV  344 (380)
Q Consensus       266 ~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~~~~~~~~~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~  344 (380)
                              ......++.+.|.... ..          +++|+++|++||.|.++.++++. ++   +..|+|||+|.+.+
T Consensus       180 --------~~~~~~~l~v~nlp~~~~~----------~~~l~~~f~~~G~i~~v~i~~~~-~g---~~~g~afV~f~~~~  237 (284)
T 3smz_A          180 --------ALLHSRCLCVDRLPPGFND----------VDALCRALSAVHSPTFCQLACGQ-DG---QLKGFAVLEYETAE  237 (284)
T ss_dssp             --------TTTSCSEEEEECCCTTCCC----------HHHHHHHTCSSSCCSEEEEEECS-SC---CEEEEEEEECSSHH
T ss_pred             --------ccCCccEEEEecCCcccCC----------HHHHHHHhhCCCCeEEEEEEECC-CC---CcccEEEEEeCCHH
Confidence                    1344566777774332 11          16999999999999999998875 33   23577899999999


Q ss_pred             hHHHHHHHHcCcccCCeEEEEEecccccc
Q 016936          345 GCATAKNALSGRKFGGNTVNAFYYPEDKY  373 (380)
Q Consensus       345 ~A~~A~~~l~g~~i~gr~l~v~~~~~~~~  373 (380)
                      +|.+|+..|||..|+|++|+|.|+....-
T Consensus       238 ~A~~A~~~l~g~~~~g~~l~v~~a~~~~~  266 (284)
T 3smz_A          238 MAEEAQQQADGLSLGGSHLRVSFCAPGPP  266 (284)
T ss_dssp             HHHHHHHHHTTCEETTEECEEEECCSSSC
T ss_pred             HHHHHHHHhCCCccCCeEEEEEEecCCCc
Confidence            99999999999999999999999987653

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=100.00  E-value=1.8e-41  Score=311.63  Aligned_cols=248  Identities=16%  Similarity=0.239  Sum_probs=199.7

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecC----CCcEEEEEeCCHHHHHHHHHcCCc
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH----EKKFAFVEMRTVEEASNAMALDGI  102 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~----~~g~afV~f~~~~~a~~ai~l~~~  102 (380)
                      ..+++.++|||+|||+++|+++|+++|++||.            |.++.+..    ++|||||+|.+.++|.+|+.+++.
T Consensus        36 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~------------i~~v~i~~~~~~~~g~afV~f~~~~~A~~A~~~~~~  103 (292)
T 2ghp_A           36 TRNRELTTVLVKNLPKSYNQNKVYKYFKHCGP------------IIHVDVADSLKKNFRFARIEFARYDGALAAITKTHK  103 (292)
T ss_dssp             ------CEEEEEEECTTCCHHHHHHHHGGGSC------------EEEEEEEECTTSSSEEEEEEESSHHHHHHHHTTTTC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------eEEEEEEECCCCCcEEEEEEECCHHHHHHHHHhCCc
Confidence            45688999999999999999999999999997            66666644    579999999999999999999999


Q ss_pred             eecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcC-CeeE
Q 016936          103 IFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFG-TLHG  181 (380)
Q Consensus       103 ~i~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-~i~~  181 (380)
                      .+.|++|.|.++.                                    .++|||+|||..+++++|+++|+.|| .|..
T Consensus       104 ~~~g~~i~v~~~~------------------------------------~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~  147 (292)
T 2ghp_A          104 VVGQNEIIVSHLT------------------------------------ECTLWMTNFPPSYTQRNIRDLLQDINVVALS  147 (292)
T ss_dssp             EETTEECEEEECC------------------------------------SCEEEEECCCTTCCHHHHHHHHHHTTCCCCE
T ss_pred             EeCCcEEEEEECC------------------------------------CCEEEEECCCCCCCHHHHHHHHHHhCCCeEE
Confidence            9999999999842                                    25999999999999999999999999 9999


Q ss_pred             EEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccCCCCChhHHHHHHHHHHHHHHHHHHHhhhc
Q 016936          182 FDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTS  261 (380)
Q Consensus       182 v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  261 (380)
                      |.++.++. +.++|||||+|.+.++|.+|+..|+|..+.|+.|.|.++.+.......                       
T Consensus       148 v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~~~-----------------------  203 (292)
T 2ghp_A          148 IRLPSLRF-NTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRT-----------------------  203 (292)
T ss_dssp             EECC--------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCC-----------------------------
T ss_pred             EEEEeCCC-CCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCcccccc-----------------------
Confidence            99999864 889999999999999999999999999999999999998765322111                       


Q ss_pred             CccccCCCCCccCCccceEEEEeccC-C-cccCCChHHHHHHHHHHHHhhcccCCeEEEEecCCCC-CCCCCCCccEEEE
Q 016936          262 GMNTLGGGMSLFGETLAKVLCLTEAI-T-ADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQ-NGGETPGVGKVFL  338 (380)
Q Consensus       262 ~~~~~~~~~~~~~~~~~~~~~l~~~~-~-~~~~~~~~~~~~~~~~L~~~f~~~G~I~~v~i~~~~~-~~~~~~g~g~afV  338 (380)
                                .....+..++.+.|.. + .++           ++|+++|++||.|.+|.++++.. ++. +  .|+|||
T Consensus       204 ----------~~~~~~~~~l~v~nlp~~~~t~-----------~~l~~~F~~~G~v~~v~i~~~~~~tg~-~--~g~afV  259 (292)
T 2ghp_A          204 ----------DSATLEGREIMIRNLSTELLDE-----------NLLRESFEGFGSIEKINIPAGQKEHSF-N--NCCAFM  259 (292)
T ss_dssp             -------------CCTTTEEEEEEECTTTCCH-----------HHHHHHHGGGSCEEEEECCSCCC---C-C--CEEEEE
T ss_pred             ----------cccCCCCceEEEECCCcccCCH-----------HHHHHHHhccCCeeEEEEEecCCcCCC-C--ceEEEE
Confidence                      0013455667676643 2 222           69999999999999999988764 132 3  467799


Q ss_pred             EeechhhHHHHHHHHcCcccCCeEEEEEecccc
Q 016936          339 EYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  371 (380)
Q Consensus       339 ~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~~  371 (380)
                      +|.+.++|.+|+ .|||..|+|++|+|.|+..+
T Consensus       260 ~F~~~~~A~~A~-~l~g~~~~g~~i~V~~a~~k  291 (292)
T 2ghp_A          260 VFENKDSAERAL-QMNRSLLGNREISVSLADKK  291 (292)
T ss_dssp             EESSHHHHHHHG-GGTTEEETTEEEEEEECCCC
T ss_pred             EeCCHHHHHHHH-HhcCCEECCcEEEEEEecCC
Confidence            999999999999 99999999999999999764

>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=1e-32  Score=232.99  Aligned_cols=171  Identities=51%  Similarity=0.909  Sum_probs=152.4

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHHHcCCceecCceE
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  109 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai~l~~~~i~g~~i  109 (380)
                      +++++|||+|||+++|+++|+++|++||.+.+... .+...|.++.+.+++|||||+|.+.++|.+|+.+++..+.|++|
T Consensus         2 r~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~-~~~~~v~~~~~~~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~i   80 (172)
T 2g4b_A            2 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQ-APGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSL   80 (172)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCS-SSSCSEEEEEEETTTTEEEEEESSHHHHHHHGGGTTCEETTEEC
T ss_pred             CcccEEEEcCCCcccCHHHHHHHHHHHhhhccccc-CCCCceeeeEecCCCCEEEEEeCCHHHHHHHHHhCCcEecCcee
Confidence            46899999999999999999999999988765211 11224899999999999999999999999999999999999999


Q ss_pred             EEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCC
Q 016936          110 RVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRD  189 (380)
Q Consensus       110 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~  189 (380)
                      +|.++..+...                             ...++|||+|||..+++++|+++|++||.|..+.++.++.
T Consensus        81 ~v~~~~~~~~~-----------------------------~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~  131 (172)
T 2g4b_A           81 KIRRPHDYQPL-----------------------------PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSA  131 (172)
T ss_dssp             EEECCSSCCCC-----------------------------TTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTT
T ss_pred             eecCCcccCCC-----------------------------CCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCC
Confidence            99986554211                             1246999999999999999999999999999999999987


Q ss_pred             CCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          190 TGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       190 ~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      +|.++|+|||+|.+.++|.+|++.|||..+.|+.|.|.+|.
T Consensus       132 ~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~As  172 (172)
T 2g4b_A          132 TGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS  172 (172)
T ss_dssp             TCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeCC
Confidence            89999999999999999999999999999999999999873

>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=4e-32  Score=234.69  Aligned_cols=194  Identities=46%  Similarity=0.792  Sum_probs=159.0

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHHHcCCceecCceE
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  109 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai~l~~~~i~g~~i  109 (380)
                      +.+|+|||+|||+++++++|+++|++||.+.+... .+...|.++.+.+++|||||+|.+.++|.+|+.+++..|.|++|
T Consensus         2 ~~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~-~~~~~v~~~~~~~~~g~afV~F~~~~~A~~Al~l~g~~~~g~~i   80 (198)
T 2yh0_A            2 AMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQ-APGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSL   80 (198)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCS-SSSCSEEEEEEETTTTEEEEEESCSHHHHHHGGGTTEEETTEEE
T ss_pred             CceeEEEEcCCCCCCCHHHHHHHHHHHHhhccccc-CCCCceEEeEecCCCCEEEEEeCCHHHHHHHHHhcCCEEcCceE
Confidence            46899999999999999999999999998876321 12235899999999999999999999999999999999999999


Q ss_pred             EEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCC
Q 016936          110 RVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRD  189 (380)
Q Consensus       110 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~  189 (380)
                      +|.++..+.........+....+         ...........++|||+|||..+++++|+++|++||.|..+.+..++.
T Consensus        81 ~v~~~~~~~~~~~~~~~~~~~~~---------~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~  151 (198)
T 2yh0_A           81 KIRRPHDYQPLPGMSENPSVYVP---------GVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSA  151 (198)
T ss_dssp             EEECCCCCCCCCCSSSCSSCCCT---------TSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTT
T ss_pred             EEeCCCCCCCCCCCcCCCcCCCC---------CCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCC
Confidence            99998765432211000000000         001112234568999999999999999999999999999999999987


Q ss_pred             CCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccCC
Q 016936          190 TGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASS  233 (380)
Q Consensus       190 ~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~~  233 (380)
                      ++.++|||||+|.+.++|.+|++.|+|..+.|+.|+|.++.++.
T Consensus       152 ~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  195 (198)
T 2yh0_A          152 TGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA  195 (198)
T ss_dssp             TCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCCC
T ss_pred             CCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            89999999999999999999999999999999999999997754

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.98  E-value=6.3e-32  Score=236.35  Aligned_cols=164  Identities=21%  Similarity=0.392  Sum_probs=140.8

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe------cCCCcEEEEEeCCHHHHHHHH-Hc
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-AL   99 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~------~~~~g~afV~f~~~~~a~~ai-~l   99 (380)
                      .++.+.++|||+|||+++|+++|+++|++||.            |.++.+      ++++|||||+|.+.++|.+|+ .+
T Consensus        10 ~p~~p~~tlfVgnLp~~~te~~L~~~F~~~G~------------I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~   77 (213)
T 4f02_A           10 APSYPMASLYVGDLHPDVTEAMLYEKFSPAGP------------ILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM   77 (213)
T ss_dssp             -----CCEEEEESCCTTCCHHHHHHHHGGGSC------------EEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHH
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhhCC------------EEEEEEecccCCCCccccccceeCCHHHHHHHHHHh
Confidence            44567789999999999999999999999998            555654      345799999999999999999 79


Q ss_pred             CCceecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCe
Q 016936          100 DGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTL  179 (380)
Q Consensus       100 ~~~~i~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i  179 (380)
                      ++..+.|+.|++.++........                           ....+|||+|||+.+++++|+++|++||.|
T Consensus        78 ~~~~~~g~~i~~~~~~~~~~~~~---------------------------~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i  130 (213)
T 4f02_A           78 NFDVIKGKPVRIMWSQRDPSLRK---------------------------SGVGNIFIKNLDKSIDNKALYDTFSAFGNI  130 (213)
T ss_dssp             TTCEETTEECEEEECCCCTHHHH---------------------------HCTTEEEEESCCTTCCHHHHHHHHGGGSCE
T ss_pred             hhhhcCCcccccccccccccccc---------------------------cccccceECCcccccHHHHHHHHHhhcCCe
Confidence            99999999999998655432211                           112589999999999999999999999999


Q ss_pred             eEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEccc
Q 016936          180 HGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  231 (380)
Q Consensus       180 ~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~  231 (380)
                      ..|++++++  +.++|||||+|.+.++|++|++.|||..+.|++|+|.++.+
T Consensus       131 ~~~~i~~d~--~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~  180 (213)
T 4f02_A          131 LSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS  180 (213)
T ss_dssp             EEEEEEEET--TEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             EEEEeeccC--CCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            999999984  56899999999999999999999999999999999999854

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.98  E-value=2.3e-31  Score=223.08  Aligned_cols=159  Identities=23%  Similarity=0.427  Sum_probs=143.0

Q ss_pred             ceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe-----cCCCcEEEEEeCCHHHHHHHH-HcCCceecC
Q 016936           33 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-----NHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  106 (380)
Q Consensus        33 ~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~-----~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g  106 (380)
                      |+|||+|||+++|+++|+++|++||.            |.++.+     ++++|||||+|.+.++|.+|+ .+++..+.|
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            78999999999999999999999997            666665     345699999999999999999 899999999


Q ss_pred             ceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEee
Q 016936          107 VAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVK  186 (380)
Q Consensus       107 ~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~  186 (380)
                      ++|+|.++......                           .....++|||+|||..+++++|+++|++||.|..+.++.
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            99999987554321                           122346899999999999999999999999999999999


Q ss_pred             CCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          187 DRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       187 ~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      ++.++.++|+|||+|.+.++|.+|+..|||..+.|+.|+|.++.
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            98889999999999999999999999999999999999999985

>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=1e-30  Score=221.50  Aligned_cols=167  Identities=17%  Similarity=0.356  Sum_probs=147.5

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHHHcCCceecC
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEG  106 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai~l~~~~i~g  106 (380)
                      ....+.++|||+|||.++++++|+++|++||.+.+.       .+.+...++++|||||+|.+.++|.+|+++++..+.|
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~-------~~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g   80 (175)
T 1fje_B            8 SESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDL-------AVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFG   80 (175)
T ss_dssp             SSCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTC-------CCCEEEEETTTTEEEEEESSHHHHHHHHHGGGEEETT
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceE-------EEEECCCCccccEEEEEECCHHHHHHHHhcCCCEeCC
Confidence            456778999999999999999999999999998752       3778888999999999999999999999999999999


Q ss_pred             ceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEee
Q 016936          107 VAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVK  186 (380)
Q Consensus       107 ~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~  186 (380)
                      ++|+|.++......                           .....++|||+|||..+++++|+++|++||.|..+    
T Consensus        81 ~~l~v~~~~~~~~~---------------------------~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~----  129 (175)
T 1fje_B           81 NEIKLEKPKGRDSK---------------------------KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV----  129 (175)
T ss_dssp             EEEEEECCCCSSCS---------------------------TTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE----
T ss_pred             eEEEEecCCCcccc---------------------------ccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe----
Confidence            99999997654211                           01223699999999999999999999999988666    


Q ss_pred             CCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccC
Q 016936          187 DRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  232 (380)
Q Consensus       187 ~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~  232 (380)
                       ..++.++|+|||+|.+.++|.+|+..|+|..+.|+.|+|.++.++
T Consensus       130 -~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          130 -SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             -CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECSSC
T ss_pred             -cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecCCC
Confidence             347899999999999999999999999999999999999999765

>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=1.3e-30  Score=224.85  Aligned_cols=172  Identities=22%  Similarity=0.417  Sum_probs=143.1

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec------CCCcEEEEEeCCHHHHHHHHHcCC
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN------HEKKFAFVEMRTVEEASNAMALDG  101 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~------~~~g~afV~f~~~~~a~~ai~l~~  101 (380)
                      ...+.++|||+|||+++|+++|+++|++||.            |.++.+.      .++|||||+|.+.++|.+|+..++
T Consensus         9 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~------------i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~   76 (196)
T 1l3k_A            9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGT------------LTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARP   76 (196)
T ss_dssp             CCGGGGEEEEESCCTTCCHHHHHHHHGGGSC------------EEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCC------------EEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhcCC
Confidence            4567899999999999999999999999998            5555543      357899999999999999998899


Q ss_pred             ceecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeE
Q 016936          102 IIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHG  181 (380)
Q Consensus       102 ~~i~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~  181 (380)
                      ..+.|+.|.|.++........                       .......++|||+|||+.+++++|+++|++||.|..
T Consensus        77 ~~~~g~~l~v~~~~~~~~~~~-----------------------~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~  133 (196)
T 1l3k_A           77 HKVDGRVVEPKRAVSREDSQR-----------------------PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEV  133 (196)
T ss_dssp             CEETTEECEEEECCC----------------------------------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEE
T ss_pred             CEECCEEeeeecccCcccccc-----------------------cccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEE
Confidence            999999999998765432210                       011223479999999999999999999999999999


Q ss_pred             EEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccCCCC
Q 016936          182 FDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQ  235 (380)
Q Consensus       182 v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~~~~  235 (380)
                      |.++.++.++.++|||||+|.+.++|.+|+.. ++..+.|+.|.|.++.++...
T Consensus       134 v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a~~k~~~  186 (196)
T 1l3k_A          134 IEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQEM  186 (196)
T ss_dssp             EEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEECC-----
T ss_pred             EEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEecCChhHh
Confidence            99999988899999999999999999999986 899999999999999776443

>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=2.2e-30  Score=217.31  Aligned_cols=158  Identities=22%  Similarity=0.386  Sum_probs=140.0

Q ss_pred             ccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecC------CCcEEEEEeCCHHHHHHHH-HcCCce
Q 016936           31 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH------EKKFAFVEMRTVEEASNAM-ALDGII  103 (380)
Q Consensus        31 ~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~------~~g~afV~f~~~~~a~~ai-~l~~~~  103 (380)
                      .+++|||+|||+++++++|+++|++||.            |.++.+..      ++|||||+|.+.++|.+|+ .+++..
T Consensus         1 s~~~l~v~nlp~~~~~~~l~~~f~~~G~------------i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~   68 (167)
T 1fxl_A            1 SKTNLIVNYLPQNMTQEEFRSLFGSIGE------------IESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLR   68 (167)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSC------------EEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CcceEEEcCCCCCCCHHHHHHHHHhcCC------------eEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCc
Confidence            3689999999999999999999999997            55565543      3499999999999999999 699999


Q ss_pred             ecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEE
Q 016936          104 FEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFD  183 (380)
Q Consensus       104 i~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~  183 (380)
                      +.|++|+|.++......                             ...++|||+|||..+++++|+++|++||.|..++
T Consensus        69 ~~g~~l~v~~~~~~~~~-----------------------------~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~  119 (167)
T 1fxl_A           69 LQTKTIKVSYARPSSAS-----------------------------IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSR  119 (167)
T ss_dssp             ETTEECEEEECCCCCGG-----------------------------GTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEE
T ss_pred             cCCceEEEEecCCCccc-----------------------------CCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEE
Confidence            99999999987643211                             1236899999999999999999999999999999


Q ss_pred             EeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeE--EEEEEc
Q 016936          184 LVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKT--LTVRRA  229 (380)
Q Consensus       184 l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~--i~v~~~  229 (380)
                      ++.++.+|.++|+|||+|.+.++|.+|++.|||..+.|+.  |+|.||
T Consensus       120 i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          120 ILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             EEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             EEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEEeC
Confidence            9999878999999999999999999999999999999965  888775

>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=2.6e-30  Score=217.28  Aligned_cols=158  Identities=21%  Similarity=0.358  Sum_probs=141.6

Q ss_pred             ccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec------CCCcEEEEEeCCHHHHHHHH-HcCCce
Q 016936           31 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN------HEKKFAFVEMRTVEEASNAM-ALDGII  103 (380)
Q Consensus        31 ~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~------~~~g~afV~f~~~~~a~~ai-~l~~~~  103 (380)
                      +.++|||+|||+++++++|+++|++||.            |.++.+.      .++|||||+|.+.++|.+|+ .+++..
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~------------i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~   69 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGP------------INTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGIT   69 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSC------------EEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCC------------eeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCE
Confidence            5789999999999999999999999997            6666543      24689999999999999999 699999


Q ss_pred             ecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEE
Q 016936          104 FEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFD  183 (380)
Q Consensus       104 i~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~  183 (380)
                      +.|++|+|.++.....                             ....++|||+|||..+++++|+++|++||.|..+.
T Consensus        70 ~~g~~l~v~~~~~~~~-----------------------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~  120 (168)
T 1b7f_A           70 VRNKRLKVSYARPGGE-----------------------------SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKN  120 (168)
T ss_dssp             ETTEECEEEECCCCSS-----------------------------TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEE
T ss_pred             eCCcEEEEEecCCCcc-----------------------------cCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEE
Confidence            9999999998764321                             12236999999999999999999999999999999


Q ss_pred             EeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCC--eEEEEEEc
Q 016936          184 LVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD--KTLTVRRA  229 (380)
Q Consensus       184 l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g--~~i~v~~~  229 (380)
                      +++++.++.++|+|||+|.+.++|.+|+..|+|..+.|  ++|+|.+|
T Consensus       121 i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          121 ILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             EEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             EEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEEeC
Confidence            99998789999999999999999999999999999977  99999875

>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=8e-31  Score=229.67  Aligned_cols=178  Identities=26%  Similarity=0.455  Sum_probs=150.3

Q ss_pred             hhhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec------CCCcEEEEEeCCHHHHHHHH-H
Q 016936           26 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN------HEKKFAFVEMRTVEEASNAM-A   98 (380)
Q Consensus        26 ~~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~------~~~g~afV~f~~~~~a~~ai-~   98 (380)
                      .....+.++|||+|||.++++++|+++|++||.            |.++.+.      .++|||||+|.+.++|.+|+ .
T Consensus        22 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~------------i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~   89 (216)
T 2qfj_A           22 QGALAIMSRVYVGSIYYELGEDTIRQAFAPFGP------------IKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ   89 (216)
T ss_dssp             HHHHHHHTEEEEECCCTTCCHHHHHHHHGGGSC------------EEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHH
T ss_pred             CcccCcCCEEEEECCCCCCCHHHHHHHHHhCCC------------EEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHH
Confidence            356778999999999999999999999999997            6666653      46899999999999999999 6


Q ss_pred             cCCceecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCC
Q 016936           99 LDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGT  178 (380)
Q Consensus        99 l~~~~i~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~  178 (380)
                      +++..|.|++|+|.++..........            ..      ........++|||+|||..+++++|+++|++||.
T Consensus        90 l~~~~~~g~~l~v~~~~~~~~~~~~~------------~~------~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~  151 (216)
T 2qfj_A           90 MNSVMLGGRNIKVGRPSNIGQAQPII------------DQ------LAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGK  151 (216)
T ss_dssp             HSSCCCC-CCCEEECCSCCGGGHHHH------------HH------HHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSC
T ss_pred             ccCCeeCCeeEEEecCCCccccchhh------------hh------hhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCC
Confidence            99999999999998876543221100            00      0000123369999999999999999999999999


Q ss_pred             eeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccCC
Q 016936          179 LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASS  233 (380)
Q Consensus       179 i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~~  233 (380)
                      |..++++.++.+++++|||||+|.+.++|.+|+..|||..+.|+.|+|.++.+..
T Consensus       152 v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a~~~~  206 (216)
T 2qfj_A          152 IKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPP  206 (216)
T ss_dssp             EEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEECSSCS
T ss_pred             eeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEecCCC
Confidence            9999999998889999999999999999999999999999999999999987653

>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=4.6e-30  Score=224.51  Aligned_cols=167  Identities=15%  Similarity=0.219  Sum_probs=140.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      ..++|||+|||+++++++|+++|++||.|.+|+|++++.+++++|||||+|.+.++|++|++.+++..+.|+.|++.++.
T Consensus        14 p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~~   93 (213)
T 4f02_A           14 PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   93 (213)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCccccccccc
Confidence            34699999999999999999999999999999999998899999999999999999999999999999999999999875


Q ss_pred             cCCCCChhHHHHHHHHHHHHHHHHHHHhhhcCccccCCCCCccCCccceEEEEeccC-CcccCCChHHHHHHHHHHHHhh
Q 016936          231 ASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAI-TADALADDEEYEEILEDMREEC  309 (380)
Q Consensus       231 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~~~~~~~~~~~~~~~L~~~f  309 (380)
                      .....     .                                 ......+.+.|.. +.+           .++|+++|
T Consensus        94 ~~~~~-----~---------------------------------~~~~~~l~v~nl~~~~t-----------~~~l~~~F  124 (213)
T 4f02_A           94 RDPSL-----R---------------------------------KSGVGNIFIKNLDKSID-----------NKALYDTF  124 (213)
T ss_dssp             CCTHH-----H---------------------------------HHCTTEEEEESCCTTCC-----------HHHHHHHH
T ss_pred             ccccc-----c---------------------------------ccccccceECCcccccH-----------HHHHHHHH
Confidence            43100     0                                 1122345555532 222           26999999


Q ss_pred             cccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEecccc
Q 016936          310 GKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  371 (380)
Q Consensus       310 ~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~~  371 (380)
                      ++||.|.+|.++++...     ..|+|||+|.+.++|.+|++.|||..|+|++|+|.|+...
T Consensus       125 ~~~G~i~~~~i~~d~~~-----~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~~  181 (213)
T 4f02_A          125 SAFGNILSCKVVCDENG-----SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR  181 (213)
T ss_dssp             GGGSCEEEEEEEEETTE-----EEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCH
T ss_pred             hhcCCeEEEEeeccCCC-----CceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            99999999999886522     2477899999999999999999999999999999999764

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.97  E-value=1.7e-30  Score=218.29  Aligned_cols=160  Identities=22%  Similarity=0.493  Sum_probs=141.1

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec------CCCcEEEEEeCCHHHHHHHHHcCCce
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN------HEKKFAFVEMRTVEEASNAMALDGII  103 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~------~~~g~afV~f~~~~~a~~ai~l~~~~  103 (380)
                      +++++|||+|||+++|+++|+++|++||.            |.++.+.      .++|||||+|.+.++|.+|+. ++..
T Consensus         1 k~~~~l~v~nLp~~~t~~~l~~~F~~~G~------------i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~   67 (167)
T 2cjk_A            1 KESCKMFIGGLNWDTTEDNLREYFGKYGT------------VTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK-TQHI   67 (167)
T ss_dssp             CGGGEEEECSCCTTCCHHHHHHHHTTTCC------------EEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHH-SCCE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhCCC------------EEEEEEEECCCCCCccceEEEEEccHHHHHHHHh-cccc
Confidence            46899999999999999999999999997            6666653      457999999999999999996 3578


Q ss_pred             ecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEE
Q 016936          104 FEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFD  183 (380)
Q Consensus       104 i~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~  183 (380)
                      +.|+.|.+.++......                             ...++|||+|||..+++++|+++|++||.|..++
T Consensus        68 ~~g~~i~v~~~~~~~~~-----------------------------~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~  118 (167)
T 2cjk_A           68 LDGKVIDPKRAIPRDEQ-----------------------------DKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQ  118 (167)
T ss_dssp             ETTEECCCEECCCHHHH-----------------------------HHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEE
T ss_pred             cCCeEcccccccchhhc-----------------------------cCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEE
Confidence            99999999876542211                             1125899999999999999999999999999999


Q ss_pred             EeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccC
Q 016936          184 LVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  232 (380)
Q Consensus       184 l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~  232 (380)
                      ++.++.++.++|||||+|.+.++|.+|++ +++..+.|+.|.|.++.++
T Consensus       119 i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A          119 LMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAEPR  166 (167)
T ss_dssp             CCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECCCC
T ss_pred             EEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecCCC
Confidence            99998889999999999999999999998 7999999999999999765

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.97  E-value=7.6e-30  Score=215.82  Aligned_cols=158  Identities=22%  Similarity=0.354  Sum_probs=136.3

Q ss_pred             ccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec--------CCCcEEEEEeCCHHHHHHHH-HcCC
Q 016936           31 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN--------HEKKFAFVEMRTVEEASNAM-ALDG  101 (380)
Q Consensus        31 ~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~--------~~~g~afV~f~~~~~a~~ai-~l~~  101 (380)
                      ++++|||+|||+++|+++|+++|++||.            |.++.+.        +++|||||+|.+.++|.+|+ .+++
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~------------i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~   69 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGA------------VYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHN   69 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSC------------EEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTT
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCC------------EEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcC
Confidence            5789999999999999999999999998            5555442        46799999999999999999 7999


Q ss_pred             ceec---CceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCC
Q 016936          102 IIFE---GVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGT  178 (380)
Q Consensus       102 ~~i~---g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~  178 (380)
                      ..+.   ++++.+.++......                            ....++|||+|||..+++++|+++|++||.
T Consensus        70 ~~~~~~~~~~~~~~~~~~~~~~----------------------------~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~  121 (175)
T 3nmr_A           70 MKVLPGMHHPIQMKPADSEKNN----------------------------AVEDRKLFIGMISKKCTENDIRVMFSSFGQ  121 (175)
T ss_dssp             TCCCTTCSSCCEEEECGGGCCS----------------------------CGGGSEEEEESCCTTCCHHHHHHHHGGGSC
T ss_pred             cEEccCCccceEEccccccccc----------------------------cCCCCeEEEcCCCCcCCHHHHHHHHHhCCC
Confidence            8876   577888775432211                            112368999999999999999999999999


Q ss_pred             eeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeC---CeEEEEEEc
Q 016936          179 LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG---DKTLTVRRA  229 (380)
Q Consensus       179 i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~---g~~i~v~~~  229 (380)
                      |..+++++++ +|.++|||||+|.+.++|.+|+..|||..+.   +++|.|.++
T Consensus       122 i~~v~~~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~~a  174 (175)
T 3nmr_A          122 IEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFA  174 (175)
T ss_dssp             EEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEEEC
T ss_pred             EEEEEEEECC-CCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEEec
Confidence            9999999996 5999999999999999999999999998775   499999987

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.96  E-value=9.6e-29  Score=207.09  Aligned_cols=166  Identities=17%  Similarity=0.275  Sum_probs=141.8

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccC
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  232 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~  232 (380)
                      ++|||+|||.++++++|+++|++||.|..+.++.++ .++++|||||+|.+.++|++|++.++|..+.|+.|.|.++...
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            589999999999999999999999999999999997 4889999999999999999999999999999999999998654


Q ss_pred             CCCChhHHHHHHHHHHHHHHHHHHHhhhcCccccCCCCCccCCccceEEEEeccCCcccCCChHHHHHHHHHHHHhhccc
Q 016936          233 SGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKY  312 (380)
Q Consensus       233 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~~f~~~  312 (380)
                      ...                                      ...+...+.+.|.....          +.++|+++|++|
T Consensus        80 ~~~--------------------------------------~~~~~~~l~v~nl~~~~----------t~~~l~~~f~~~  111 (166)
T 3md3_A           80 QQS--------------------------------------SSDDTFNLFVGDLNVNV----------DDETLRNAFKDF  111 (166)
T ss_dssp             CCC--------------------------------------CCTTCEEEEEESCCTTC----------CHHHHHHHHTTS
T ss_pred             CCC--------------------------------------CCCCCceEEECCCCCCC----------CHHHHHHHHhcc
Confidence            221                                      13455667777643221          126999999999


Q ss_pred             CCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEeccc
Q 016936          313 GTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPE  370 (380)
Q Consensus       313 G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~  370 (380)
                      |.|.++.+..+..++.   ..|+|||+|.+.++|.+|+..|||..++|++|+|.|+.+
T Consensus       112 G~i~~~~i~~~~~~~~---~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  166 (166)
T 3md3_A          112 PSYLSGHVMWDMQTGS---SRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK  166 (166)
T ss_dssp             TTEEEEEEEECTTTCC---EEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCC
T ss_pred             CCeeEEEEEecCCCCC---cceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEecCC
Confidence            9999999998765543   357789999999999999999999999999999999863

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=99.96  E-value=1.1e-28  Score=207.37  Aligned_cols=164  Identities=23%  Similarity=0.325  Sum_probs=141.8

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEccc
Q 016936          152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  231 (380)
Q Consensus       152 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~  231 (380)
                      .++|||+|||.++++++|+++|++||.|..+.+++++.+++++|||||+|.+.++|++|++.+++..+.|+.|.|.++.+
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            47999999999999999999999999999999999987899999999999999999999999999999999999999865


Q ss_pred             CCCCChhHHHHHHHHHHHHHHHHHHHhhhcCccccCCCCCccCCccceEEEEeccCCcccCCChHHHHHHHHHHHHhhcc
Q 016936          232 SSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGK  311 (380)
Q Consensus       232 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~~f~~  311 (380)
                      ...                                        ......+.+.|.....          +.++|+++|++
T Consensus        83 ~~~----------------------------------------~~~~~~l~v~nl~~~~----------t~~~l~~~f~~  112 (168)
T 1b7f_A           83 GGE----------------------------------------SIKDTNLYVTNLPRTI----------TDDQLDTIFGK  112 (168)
T ss_dssp             CSS----------------------------------------TTTTCEEEEESCCTTC----------CHHHHHHHHTS
T ss_pred             Ccc----------------------------------------cCCCCCEEEeCCCCCC----------CHHHHHHhhhc
Confidence            321                                        2234566667643221          12699999999


Q ss_pred             cCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCC--eEEEEEec
Q 016936          312 YGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGG--NTVNAFYY  368 (380)
Q Consensus       312 ~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~g--r~l~v~~~  368 (380)
                      ||.|.++.+.++..++.   ..|+|||+|.+.++|.+|++.|||..+.|  ++|+|.||
T Consensus       113 ~G~i~~~~i~~~~~~~~---~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          113 YGSIVQKNILRDKLTGR---PRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             SSCEEEEEEEECTTTCC---EEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCcEEEEEEEEcCCCCC---cceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEEeC
Confidence            99999999988775543   34678999999999999999999999988  99999986

>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=6.4e-29  Score=215.26  Aligned_cols=185  Identities=15%  Similarity=0.126  Sum_probs=139.8

Q ss_pred             ccceEEEcCCC-CcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecC-CCcEEEEEeCCHHHHHHHH-HcCCceecCc
Q 016936           31 HARRVYVGGLP-PLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH-EKKFAFVEMRTVEEASNAM-ALDGIIFEGV  107 (380)
Q Consensus        31 ~~~~v~V~nLp-~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~-~~g~afV~f~~~~~a~~ai-~l~~~~i~g~  107 (380)
                      +.++|||+||| ..+++++|+++|++||.            |.++++.+ ++|||||+|.+.++|++|+ .|||..+.|+
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~------------v~~v~i~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~   70 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGN------------VEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNNFMFGQ   70 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSC------------EEEEEECTTSTTCEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCC------------eEEEEEecCCCCEEEEEECCHHHHHHHHHHhCCCEECCc
Confidence            57899999999 89999999999999998            77887765 4799999999999999999 7999999999


Q ss_pred             eEEEecCCCCCccccccCCCCCCCCC-cccccc---cCC----CCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCe
Q 016936          108 AVRVRRPTDYNPTLAAALGPGQPSPN-LNLAAV---GLA----SGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTL  179 (380)
Q Consensus       108 ~i~v~~~~~~~~~~~~~~~~~~~~~~-~~~~~~---~~~----~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i  179 (380)
                      +|+|.++................... ......   ...    ..........++|||+|||+.+++++|+++|++||.|
T Consensus        71 ~l~v~~s~~~~~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v  150 (205)
T 3tyt_A           71 KMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVK  150 (205)
T ss_dssp             ECEEEECSCSCCCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHTCC
T ss_pred             eEEEEEccCCccCCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhcCCc
Confidence            99999876543211000000000000 000000   000    0000112335789999999999999999999999999


Q ss_pred             --eEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCe----EEEEEEc
Q 016936          180 --HGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDK----TLTVRRA  229 (380)
Q Consensus       180 --~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~----~i~v~~~  229 (380)
                        ..+++..+.  +.++|+|||+|.+.++|.+|+..|||..+.|+    ++.|+++
T Consensus       151 ~~~~v~~~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          151 RPTSVKVFSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             CCSEEEECSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEEE
T ss_pred             ceEEEEEEcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEEec
Confidence              899998774  56679999999999999999999999999876    5776654

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.96  E-value=2e-28  Score=205.36  Aligned_cols=163  Identities=27%  Similarity=0.429  Sum_probs=139.8

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccC
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  232 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~  232 (380)
                      ++|||+|||+.+++++|+++|+.||.|..+.+++++.+|.++|+|||+|.+.++|++|++.++|..+.|+.|+|.++.+.
T Consensus         3 ~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~   82 (167)
T 1fxl_A            3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPS   82 (167)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             ceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCCC
Confidence            69999999999999999999999999999999999888999999999999999999999999999999999999998643


Q ss_pred             CCCChhHHHHHHHHHHHHHHHHHHHhhhcCccccCCCCCccCCccceEEEEeccCCcccCCChHHHHHHHHHHHHhhccc
Q 016936          233 SGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKY  312 (380)
Q Consensus       233 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~~f~~~  312 (380)
                      ..                                        ......+.+.|.....          +.++|+++|++|
T Consensus        83 ~~----------------------------------------~~~~~~l~v~nl~~~~----------t~~~l~~~f~~~  112 (167)
T 1fxl_A           83 SA----------------------------------------SIRDANLYVSGLPKTM----------TQKELEQLFSQY  112 (167)
T ss_dssp             CG----------------------------------------GGTTCEEEEESCCTTC----------CHHHHHHHHGGG
T ss_pred             cc----------------------------------------cCCCCcEEECCCCCcC----------CHHHHHHHHHhc
Confidence            11                                        2233456666643211          126999999999


Q ss_pred             CCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeE--EEEEec
Q 016936          313 GTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNT--VNAFYY  368 (380)
Q Consensus       313 G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~--l~v~~~  368 (380)
                      |.|.++.+..+..++.   ..|+|||+|.+.++|.+|++.|||..++|+.  |+|.||
T Consensus       113 G~i~~~~i~~~~~~g~---~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          113 GRIITSRILVDQVTGV---SRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             SCEEEEEEEECTTTCC---EEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCEeEEEEEecCCCCC---ccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEEeC
Confidence            9999999988765543   3477899999999999999999999999975  999886

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.96  E-value=6.5e-29  Score=224.00  Aligned_cols=159  Identities=21%  Similarity=0.349  Sum_probs=144.7

Q ss_pred             hhhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCcee
Q 016936           26 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIF  104 (380)
Q Consensus        26 ~~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i  104 (380)
                      +......++|||+|||+++|+++|+++|++||.            |.++.+.+++|||||+|.+.++|.+|+ .+++..+
T Consensus        16 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~------------i~~v~i~~~kg~afV~f~~~~~A~~A~~~l~g~~i   83 (261)
T 3sde_A           16 EKTYTQRCRLFVGNLPTDITEEDFKRLFERYGE------------PSEVFINRDRGFGFIRLESRTLAEIAKAELDGTIL   83 (261)
T ss_dssp             CCSSCGGGEEEEESCCTTCCHHHHHHHTGGGCC------------CSEEEEETTTTEEEEECSSHHHHHHHHHHHTTCEE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCC------------EEEEEEeCCCcEEEEEECCHHHHHHHHHHcCCcEE
Confidence            345677899999999999999999999999997            777888899999999999999999999 6999999


Q ss_pred             cCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEE
Q 016936          105 EGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDL  184 (380)
Q Consensus       105 ~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l  184 (380)
                      .|++|+|.++..                                   ..+|||+|||..+++++|+++|+.||.|..|.+
T Consensus        84 ~g~~l~v~~a~~-----------------------------------~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i  128 (261)
T 3sde_A           84 KSRPLRIRFATH-----------------------------------GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVV  128 (261)
T ss_dssp             TTEECEEEECCC-----------------------------------SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEE
T ss_pred             CCceeEeeeccc-----------------------------------CCcccccCCCCCCCHHHHHHHHHhcCCeEEEEe
Confidence            999999998543                                   258999999999999999999999999999999


Q ss_pred             eeCCCCCCCceEEEEEEcChhHHHHHHHHhC-CCeeC---CeEEEEEEcccC
Q 016936          185 VKDRDTGNSKGYGFCVYQDPAVTDIACAALN-GLKMG---DKTLTVRRATAS  232 (380)
Q Consensus       185 ~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~-g~~~~---g~~i~v~~~~~~  232 (380)
                      +.++ +|.++|||||+|.+.++|.+|+..|+ +..+.   +++|.|.++...
T Consensus       129 ~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~~~~~~  179 (261)
T 3sde_A          129 VVDD-RGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQF  179 (261)
T ss_dssp             EEET-TSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEEECCCE
T ss_pred             eeCC-CCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEeecccc
Confidence            9994 79999999999999999999999995 55554   999999998764

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.96  E-value=2.8e-28  Score=215.52  Aligned_cols=186  Identities=19%  Similarity=0.209  Sum_probs=144.0

Q ss_pred             hcccceEEEcCCCC-cCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCC-CcEEEEEeCCHHHHHHHH-HcCCceec
Q 016936           29 TRHARRVYVGGLPP-LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE-KKFAFVEMRTVEEASNAM-ALDGIIFE  105 (380)
Q Consensus        29 ~~~~~~v~V~nLp~-~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~-~g~afV~f~~~~~a~~ai-~l~~~~i~  105 (380)
                      ..++++|||+|||+ ++++++|+++|++||.            |.++.+..+ +|||||+|.+.++|.+|+ .+++..+.
T Consensus        31 ~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~------------i~~v~i~~~~~g~afV~F~~~~~A~~Ai~~l~g~~~~   98 (229)
T 2adc_A           31 GAGNSVLLVSNLNPERVTPQSLFILFGVYGD------------VQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLH   98 (229)
T ss_dssp             CCCCSEEEEESCCTTTCCHHHHHHHHHHHTC------------EEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCS
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhCCC------------eEEEEEEECCCCEEEEEECCHHHHHHHHHHhCCCeEC
Confidence            45789999999999 9999999999999997            778887665 599999999999999999 69999999


Q ss_pred             CceEEEecCCCCCccccccCCCCCCCCCcccccc---c----CCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcC-
Q 016936          106 GVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAV---G----LASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFG-  177 (380)
Q Consensus       106 g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~----~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-  177 (380)
                      |++|+|.++................. .......   .    ............++|||+|||..+++++|+++|++|| 
T Consensus        99 g~~l~v~~a~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~  177 (229)
T 2adc_A           99 GKPIRITLSKHQNVQLPREGQEDQGL-TKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGG  177 (229)
T ss_dssp             SSBCEEECCSCCCCCCCCSSSSTTTT-EEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSC
T ss_pred             CeEEEEEEecCccccCcccccccccc-ccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCC
Confidence            99999998765432211100000000 0000000   0    0000011123458999999999999999999999999 


Q ss_pred             CeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeC-CeEEEEEEcccC
Q 016936          178 TLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG-DKTLTVRRATAS  232 (380)
Q Consensus       178 ~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~-g~~i~v~~~~~~  232 (380)
                      .|..+++..+     ++|+|||+|.+.++|.+|+..|+|..+. |+.|+|.++.+.
T Consensus       178 ~i~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          178 VVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             CEEEEEECSS-----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             CeeEEEEEEC-----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecCC
Confidence            9999999653     3679999999999999999999999999 999999998753

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.96  E-value=2.2e-28  Score=223.13  Aligned_cols=187  Identities=20%  Similarity=0.322  Sum_probs=142.6

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHH----HHHHHHHHhccCCCCCCCCeeEEEE---ecCCCcEEEEEeCCHHHHHHHH-H
Q 016936           27 QATRHARRVYVGGLPPLANEQAIA----TFFSQVMTAIGGNSAGPGDAVVNVY---INHEKKFAFVEMRTVEEASNAM-A   98 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~----~~f~~~G~i~~~~~~~~~~~i~~~~---~~~~~g~afV~f~~~~~a~~ai-~   98 (380)
                      ....+.++|||+|||+++++++|+    ++|++||.            |.++.   .++++|||||+|.+.++|.+|+ .
T Consensus         4 ~~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~------------i~~v~~~~~~~~~g~afV~f~~~~~a~~A~~~   71 (282)
T 3pgw_A            4 PETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQ------------ILDILVSRSLKMRGQAFVIFKEVSSATNALRS   71 (282)
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCC------------eEEEEEcCCCCcceEEEEEECCHHHHHHHHHH
Confidence            456789999999999999999966    89999998            45555   4567899999999999999999 8


Q ss_pred             cCCceecCceEEEecCCCCCccccccCCCCCCCC----------------Ccccc-------------------------
Q 016936           99 LDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSP----------------NLNLA-------------------------  137 (380)
Q Consensus        99 l~~~~i~g~~i~v~~~~~~~~~~~~~~~~~~~~~----------------~~~~~-------------------------  137 (380)
                      +++..|.|++|+|.++...........+......                .....                         
T Consensus        72 l~g~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  151 (282)
T 3pgw_A           72 MQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAP  151 (282)
T ss_pred             hcCCeeCCcEEEEEEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccc
Confidence            9999999999999987654421100000000000                00000                         


Q ss_pred             --------------------cccCCC---------------------CCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhc
Q 016936          138 --------------------AVGLAS---------------------GAIGGAEGPDRVFVGGLPYYFTETQIKELLESF  176 (380)
Q Consensus       138 --------------------~~~~~~---------------------~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~  176 (380)
                                          ..+...                     .........++|||+|||..+++++|+++|++|
T Consensus       152 ~~~~~~~g~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~  231 (282)
T 3pgw_A          152 RIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQF  231 (282)
T ss_pred             cccccCCCCCCCCCCCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHHHHHHHHhc
Confidence                                000000                     000122345789999999999999999999999


Q ss_pred             CCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeC-CeEEEEEEcc
Q 016936          177 GTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG-DKTLTVRRAT  230 (380)
Q Consensus       177 G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~-g~~i~v~~~~  230 (380)
                      |.|..|+++.++     +|+|||+|.+.++|.+|+..|||..+. |+.|+|.|++
T Consensus       232 G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          232 PGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             CCeEEEEEecCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            999999998653     589999999999999999999999999 9999999974

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.96  E-value=4.8e-28  Score=211.96  Aligned_cols=179  Identities=20%  Similarity=0.348  Sum_probs=143.7

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccC
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  232 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~  232 (380)
                      ++|||+|||.++++++|+++|+.||.|..|++++++.++.++|||||+|.+.++|++|++.|++..+.|+.|.|.++...
T Consensus        29 ~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~~  108 (216)
T 2qfj_A           29 SRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNI  108 (216)
T ss_dssp             TEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCSCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCCCc
Confidence            69999999999999999999999999999999999878999999999999999999999999999999999999987543


Q ss_pred             CCCChhHHHHHHHHHHHHHHHHHHHhhhcCccccCCCCCccCCccceEEEEeccCCcccCCChHHHHHHHHHHHHhhccc
Q 016936          233 SGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKY  312 (380)
Q Consensus       233 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~~f~~~  312 (380)
                      .....     ....      ..   .               ......++.+.|.....          +.++|+++|++|
T Consensus       109 ~~~~~-----~~~~------~~---~---------------~~~~~~~l~v~nlp~~~----------t~~~l~~~f~~~  149 (216)
T 2qfj_A          109 GQAQP-----IIDQ------LA---E---------------EARAFNRIYVASVHQDL----------SDDDIKSVFEAF  149 (216)
T ss_dssp             GGGHH-----HHHH------HH---H---------------HHTTSCEEEEECCCTTC----------CHHHHHHHHTTS
T ss_pred             cccch-----hhhh------hh---c---------------ccCCCcEEEEeCCCCcC----------CHHHHHHHHhcc
Confidence            21110     0000      00   0               03345667777643221          126999999999


Q ss_pred             CCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEecccccc
Q 016936          313 GTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKY  373 (380)
Q Consensus       313 G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~~~~  373 (380)
                      |.|.++.+.++..++.   ..|+|||+|.+.++|.+|+..|||..|+|++|+|.|+.....
T Consensus       150 G~v~~v~i~~~~~~g~---~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a~~~~~  207 (216)
T 2qfj_A          150 GKIKSATLARDPTTGK---HKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPM  207 (216)
T ss_dssp             SCEEEEEEEECTTTCC---EEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEECSSCSS
T ss_pred             CCeeEEEEEecCCCCC---cCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEecCCCC
Confidence            9999999998765543   347889999999999999999999999999999999987543

>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=9.7e-28  Score=206.76  Aligned_cols=175  Identities=19%  Similarity=0.294  Sum_probs=140.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      ...++|||+|||+++++++|+++|+.||.|..|.+++++.++.++|||||+|.+.++|++|++. ++..+.|+.|.|.++
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            3447999999999999999999999999999999999988899999999999999999999986 899999999999998


Q ss_pred             ccCCCCChhHHHHHHHHHHHHHHHHHHHhhhcCccccCCCCCccCCccceEEEEeccCCcccCCChHHHHHHHHHHHHhh
Q 016936          230 TASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREEC  309 (380)
Q Consensus       230 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~~f  309 (380)
                      ........+                                  ........+.+.|.....          +.++|+++|
T Consensus        90 ~~~~~~~~~----------------------------------~~~~~~~~l~V~nLp~~~----------t~~~l~~~F  125 (196)
T 1l3k_A           90 VSREDSQRP----------------------------------GAHLTVKKIFVGGIKEDT----------EEHHLRDYF  125 (196)
T ss_dssp             CC---------------------------------------------CCSEEEEECCTTTC----------CHHHHHHHH
T ss_pred             cCccccccc----------------------------------ccCCCcceEEEeCCCCCC----------CHHHHHHHH
Confidence            654221110                                  012344667777643211          126999999


Q ss_pred             cccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEecccccc
Q 016936          310 GKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKY  373 (380)
Q Consensus       310 ~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~~~~  373 (380)
                      ++||.|.+|.++.+..++.   ..|+|||+|.+.++|.+|+.. +|..|+|+.|.|.|+..+.-
T Consensus       126 ~~~G~i~~v~i~~~~~~g~---~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a~~k~~  185 (196)
T 1l3k_A          126 EQYGKIEVIEIMTDRGSGK---KRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQE  185 (196)
T ss_dssp             TTTSCEEEEEEEECTTTCC---EEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEECC----
T ss_pred             hcCCCeEEEEEeecCCCCC---ccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEecCChhH
Confidence            9999999999998765543   357789999999999999987 89999999999999987543

>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=1.5e-27  Score=201.61  Aligned_cols=165  Identities=19%  Similarity=0.309  Sum_probs=137.1

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCC--CCceEEEEEEcChhHHHHHHHHhCCCeeC---CeEEEE
Q 016936          152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTG--NSKGYGFCVYQDPAVTDIACAALNGLKMG---DKTLTV  226 (380)
Q Consensus       152 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~--~~~g~afV~f~~~~~A~~Ai~~l~g~~~~---g~~i~v  226 (380)
                      .++|||+|||+++++++|+++|++||.|..|++++++.++  +++|||||+|.+.++|++|++.+++..+.   ++.+.+
T Consensus         3 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~~   82 (175)
T 3nmr_A            3 AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQM   82 (175)
T ss_dssp             CEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEE
T ss_pred             ceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceEE
Confidence            3699999999999999999999999999999999998766  89999999999999999999999998775   678888


Q ss_pred             EEcccCCCCChhHHHHHHHHHHHHHHHHHHHhhhcCccccCCCCCccCCccceEEEEeccCCcccCCChHHHHHHHHHHH
Q 016936          227 RRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMR  306 (380)
Q Consensus       227 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~  306 (380)
                      .++......                                       ......+.+.|.....          +.++|+
T Consensus        83 ~~~~~~~~~---------------------------------------~~~~~~l~v~nl~~~~----------t~~~l~  113 (175)
T 3nmr_A           83 KPADSEKNN---------------------------------------AVEDRKLFIGMISKKC----------TENDIR  113 (175)
T ss_dssp             EECGGGCCS---------------------------------------CGGGSEEEEESCCTTC----------CHHHHH
T ss_pred             ccccccccc---------------------------------------cCCCCeEEEcCCCCcC----------CHHHHH
Confidence            877543221                                       3345567777643211          126999


Q ss_pred             HhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccC---CeEEEEEecc
Q 016936          307 EECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFG---GNTVNAFYYP  369 (380)
Q Consensus       307 ~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~---gr~l~v~~~~  369 (380)
                      ++|++||.|.++.++++.. +   +..|+|||+|.+.++|.+|++.|||..+.   |++|+|.|++
T Consensus       114 ~~F~~~G~i~~v~~~~~~~-g---~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~~ad  175 (175)
T 3nmr_A          114 VMFSSFGQIEECRILRGPD-G---LSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFAD  175 (175)
T ss_dssp             HHHGGGSCEEEEEEEECTT-S---CEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEEECC
T ss_pred             HHHHhCCCEEEEEEEECCC-C---CEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEEecC
Confidence            9999999999999988753 3   23577899999999999999999999876   4999999984

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=99.95  E-value=1.4e-27  Score=218.82  Aligned_cols=168  Identities=15%  Similarity=0.352  Sum_probs=140.7

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHH-HhccCCCCCCCCeeEEEEe-----cCCCcEEEEEeCCHHHHHHHH-HcCCc
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVM-TAIGGNSAGPGDAVVNVYI-----NHEKKFAFVEMRTVEEASNAM-ALDGI  102 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G-~i~~~~~~~~~~~i~~~~~-----~~~~g~afV~f~~~~~a~~ai-~l~~~  102 (380)
                      ...++|||+|||+.+++++|+++|++|| .            |..+.+     +.++|||||+|.+.++|.+|+ .+++.
T Consensus       115 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~------------i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~  182 (292)
T 2ghp_A          115 LTECTLWMTNFPPSYTQRNIRDLLQDINVV------------ALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGL  182 (292)
T ss_dssp             CCSCEEEEECCCTTCCHHHHHHHHHHTTCC------------CCEEECC-------CCEEEEECSSHHHHHHHHHHHTTC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCC------------eEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCC
Confidence            3689999999999999999999999999 7            444544     347899999999999999999 69999


Q ss_pred             eecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCC-CCHHHHHHHHHhcCCeeE
Q 016936          103 IFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYY-FTETQIKELLESFGTLHG  181 (380)
Q Consensus       103 ~i~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~-~t~~~l~~~F~~~G~i~~  181 (380)
                      .+.|++|+|.++.........                      .......++|||+|||.. +++++|+++|++||.|..
T Consensus       183 ~~~g~~l~v~~a~~~~~~~~~----------------------~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~  240 (292)
T 2ghp_A          183 KIEGYTLVTKVSNPLEKSKRT----------------------DSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEK  240 (292)
T ss_dssp             EETTEECEEEECCCC-------------------------------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEE
T ss_pred             EeCCcEEEEEECCCCcccccc----------------------cccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeE
Confidence            999999999987654322110                      011234479999999999 999999999999999999


Q ss_pred             EEEeeCCC-CCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccC
Q 016936          182 FDLVKDRD-TGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  232 (380)
Q Consensus       182 v~l~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~  232 (380)
                      |++++++. ++.++|||||+|.+.++|.+|+ .|||..+.|+.|.|.++.++
T Consensus       241 v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V~~a~~k  291 (292)
T 2ghp_A          241 INIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVSLADKK  291 (292)
T ss_dssp             EECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEEEECCCC
T ss_pred             EEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEEEEecCC
Confidence            99999865 4999999999999999999999 99999999999999999764

>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=8.6e-28  Score=207.61  Aligned_cols=184  Identities=19%  Similarity=0.214  Sum_probs=142.0

Q ss_pred             ccceEEEcCCCC-cCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCC-CcEEEEEeCCHHHHHHHH-HcCCceecCc
Q 016936           31 HARRVYVGGLPP-LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE-KKFAFVEMRTVEEASNAM-ALDGIIFEGV  107 (380)
Q Consensus        31 ~~~~v~V~nLp~-~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~-~g~afV~f~~~~~a~~ai-~l~~~~i~g~  107 (380)
                      .+++|||+|||+ ++++++|+++|++||.            |.++.+..+ +|||||+|.+.++|.+|+ .+++..+.|+
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~------------i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~   69 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGD------------VQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGK   69 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCC------------CSEEECSTTCSSCCEEECTTTHHHHHHHHHHTTCCCSSC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCC------------EEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCeecCe
Confidence            468999999999 9999999999999987            677776655 699999999999999999 6999999999


Q ss_pred             eEEEecCCCCCccccccCCCCCCCCCcccccc---c----CCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcC-Ce
Q 016936          108 AVRVRRPTDYNPTLAAALGPGQPSPNLNLAAV---G----LASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFG-TL  179 (380)
Q Consensus       108 ~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~----~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-~i  179 (380)
                      +|+|.++................ ........   .    ............++|||+|||..+++++|+++|++|| .|
T Consensus        70 ~l~v~~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v  148 (198)
T 1qm9_A           70 PIRITLSKHQNVQLPREGQEDQG-LTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVV  148 (198)
T ss_dssp             CCEEEECCCCSCCCSSSSSSSSS-CEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCC
T ss_pred             EEEEEEecCCCcCCCCcCCcccc-ccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCc
Confidence            99999876543221110000000 00000000   0    0000011123368999999999999999999999999 99


Q ss_pred             eEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeC-CeEEEEEEcccC
Q 016936          180 HGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG-DKTLTVRRATAS  232 (380)
Q Consensus       180 ~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~-g~~i~v~~~~~~  232 (380)
                      ..+++..+     .+|+|||+|.+.++|.+|+..|+|..+. |+.|+|.++.+.
T Consensus       149 ~~v~i~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          149 KGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             CEEEESST-----TSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECCC
T ss_pred             eEEEEEeC-----CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeeccc
Confidence            99999664     2689999999999999999999999999 999999998653

>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=3e-27  Score=215.80  Aligned_cols=165  Identities=18%  Similarity=0.231  Sum_probs=144.2

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe------cCCCcEEEEEeCCHHHHHHHH-HcCCc
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-ALDGI  102 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~------~~~~g~afV~f~~~~~a~~ai-~l~~~  102 (380)
                      ...++|||+|||+.+++++|+++|++||.            |..+.+      +.++|||||+|.+.++|.+|+ .+++.
T Consensus        93 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~------------i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~  160 (284)
T 3smz_A           93 PTDALLCVANLPPSLTQQQFEELVRPFGS------------LERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGK  160 (284)
T ss_dssp             CCSCEEEEESCCTTCCHHHHHHHHGGGSC------------EEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHHhcCC------------eeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCC
Confidence            45689999999999999999999999998            454543      235789999999999999999 89999


Q ss_pred             eecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCC-CHHHHHHHHHhcCCeeE
Q 016936          103 IFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYF-TETQIKELLESFGTLHG  181 (380)
Q Consensus       103 ~i~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~-t~~~l~~~F~~~G~i~~  181 (380)
                      .+.|++|.|.++.......                          .....++|||+|||..+ ++++|+++|+.||.|..
T Consensus       161 ~~~g~~i~v~~a~~~~~~~--------------------------~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~  214 (284)
T 3smz_A          161 PLGPRTLYVHWTDAGQLTP--------------------------ALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTF  214 (284)
T ss_dssp             EETTEECEEEECCGGGCCT--------------------------TTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSE
T ss_pred             EeCCcEEEEEECCCCCCCc--------------------------ccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEE
Confidence            9999999999975432110                          11234799999999995 99999999999999999


Q ss_pred             EEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccCC
Q 016936          182 FDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASS  233 (380)
Q Consensus       182 v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~~  233 (380)
                      ++++.++ +|.++|+|||+|.+.++|.+|+..|+|..+.|++|+|.++.++.
T Consensus       215 v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  265 (284)
T 3smz_A          215 CQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGP  265 (284)
T ss_dssp             EEEEECS-SCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCSSS
T ss_pred             EEEEECC-CCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEEecCCC
Confidence            9999986 69999999999999999999999999999999999999997654

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.95  E-value=2.3e-27  Score=199.11  Aligned_cols=162  Identities=20%  Similarity=0.347  Sum_probs=137.2

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccC
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  232 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~  232 (380)
                      ++|||+|||+++++++|+++|++||.|..|++++++.+|+++|||||+|.+.++|++|+..  +..+.|+.|.+.++.+.
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            6999999999999999999999999999999999988899999999999999999999984  67899999999987532


Q ss_pred             CCCChhHHHHHHHHHHHHHHHHHHHhhhcCccccCCCCCccCCccceEEEEeccC-CcccCCChHHHHHHHHHHHHhhcc
Q 016936          233 SGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAI-TADALADDEEYEEILEDMREECGK  311 (380)
Q Consensus       233 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~~~~~~~~~~~~~~~L~~~f~~  311 (380)
                           ..                                   ..+...+.+.|.. +.+           .++|+++|++
T Consensus        82 -----~~-----------------------------------~~~~~~l~V~nlp~~~t-----------~~~l~~~F~~  110 (167)
T 2cjk_A           82 -----DE-----------------------------------QDKTGKIFVGGIGPDVR-----------PKEFEEFFSQ  110 (167)
T ss_dssp             -----HH-----------------------------------HHHCEEEEEEEECTTCC-----------HHHHHHHHHT
T ss_pred             -----hh-----------------------------------ccCCCeEEECCCCCCCC-----------HHHHHHHHHh
Confidence                 10                                   1123456666532 222           2699999999


Q ss_pred             cCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEecccc
Q 016936          312 YGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  371 (380)
Q Consensus       312 ~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~~  371 (380)
                      ||.|.++.+..+..++. +  .|+|||+|.+.++|.+|++ |||..++|++|+|.|+.++
T Consensus       111 ~G~i~~~~i~~~~~~g~-~--~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A          111 WGTIIDAQLMLDKDTGQ-S--RGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAEPR  166 (167)
T ss_dssp             TSCCSEEECCCSSSSST-T--SEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECCCC
T ss_pred             CccEEEEEEEEcCCCCc-c--ceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecCCC
Confidence            99999999998765543 3  4677999999999999998 8999999999999999764

>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=4.1e-26  Score=208.09  Aligned_cols=198  Identities=16%  Similarity=0.229  Sum_probs=138.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHH----HHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEE
Q 016936          151 GPDRVFVGGLPYYFTETQIK----ELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  226 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~----~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v  226 (380)
                      ..++|||+|||+.+++++|+    ++|++||.|..|++.+   +++++|||||+|.+.++|++|++.|||..+.|+.|+|
T Consensus         8 ~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   84 (282)
T 3pgw_A            8 PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   84 (282)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEEEE
Confidence            34799999999999999966    8999999999999876   5889999999999999999999999999999999999


Q ss_pred             EEcccCCCCChhHHHH--------HHHH--HHHHHHHHHHHhhhcC------cccc------------------------
Q 016936          227 RRATASSGQSKTEQES--------ILAQ--AQQHIAIQKMALQTSG------MNTL------------------------  266 (380)
Q Consensus       227 ~~~~~~~~~~~~~~~~--------~~~~--~~~~~~~~~~~~~~~~------~~~~------------------------  266 (380)
                      .++.............        ....  ................      ....                        
T Consensus        85 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~  164 (282)
T 3pgw_A           85 QYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYM  164 (282)
T ss_pred             EEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccCCCCCCCC
Confidence            9986654211100000        0000  0000000000000000      0000                        


Q ss_pred             --------CCC-----------------------CCccCCccceEEEEeccCCcccCCChHHHHHHHHHHHHhhcccCCe
Q 016936          267 --------GGG-----------------------MSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTL  315 (380)
Q Consensus       267 --------~~~-----------------------~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~~f~~~G~I  315 (380)
                              .+.                       .......+.+++.+.|+..          ..+.++|+++|++||.|
T Consensus       165 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~----------~~~~~~l~~~F~~~G~i  234 (282)
T 3pgw_A          165 PPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPE----------ETNELMLSMLFNQFPGF  234 (282)
T ss_pred             CCCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCC----------cCCHHHHHHHHHhcCCe
Confidence                    000                       0001122345666666432          22337999999999999


Q ss_pred             EEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccC-CeEEEEEecc
Q 016936          316 VNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFG-GNTVNAFYYP  369 (380)
Q Consensus       316 ~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~-gr~l~v~~~~  369 (380)
                      .+|.+.++.+        |+|||+|.+.++|.+|++.|||+.|+ |+.|+|+|+.
T Consensus       235 ~~v~~~~~~~--------g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          235 KEVRLVPGRH--------DIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             EEEEEecCCC--------cEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            9999986542        58899999999999999999999999 9999999985

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=99.94  E-value=5.7e-26  Score=191.46  Aligned_cols=157  Identities=20%  Similarity=0.304  Sum_probs=129.6

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhc----C-------CeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCC
Q 016936          153 DRVFVGGLPYYFTETQIKELLESF----G-------TLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD  221 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~----G-------~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g  221 (380)
                      ++|||+|||+++++++|+++|++|    |       .|..+.+.      +++|||||+|.+.++|++|+ .+++..+.|
T Consensus         5 ~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~------~~~g~afV~f~~~~~A~~A~-~~~~~~~~g   77 (172)
T 2g4b_A            5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN------QDKNFAFLEFRSVDETTQAM-AFDGIIFQG   77 (172)
T ss_dssp             GEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEE------TTTTEEEEEESSHHHHHHHG-GGTTCEETT
T ss_pred             cEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEec------CCCCEEEEEeCCHHHHHHHH-HhCCcEecC
Confidence            699999999999999999999999    6       66666553      44789999999999999999 799999999


Q ss_pred             eEEEEEEcccCCCCChhHHHHHHHHHHHHHHHHHHHhhhcCccccCCCCCccCCccceEEEEeccCCcccCCChHHHHHH
Q 016936          222 KTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEI  301 (380)
Q Consensus       222 ~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~  301 (380)
                      +.|.|.++.....                                        ......+.+.|.....          +
T Consensus        78 ~~i~v~~~~~~~~----------------------------------------~~~~~~l~v~nlp~~~----------t  107 (172)
T 2g4b_A           78 QSLKIRRPHDYQP----------------------------------------LPGAHKLFIGGLPNYL----------N  107 (172)
T ss_dssp             EECEEECCSSCCC----------------------------------------CTTTTCEEEECCCTTC----------C
T ss_pred             ceeeecCCcccCC----------------------------------------CCCCCEEEEEcCCCcC----------C
Confidence            9999998754311                                        1224556666633211          1


Q ss_pred             HHHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEecc
Q 016936          302 LEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYP  369 (380)
Q Consensus       302 ~~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~  369 (380)
                      .++|+++|++||.|.++.+.++..++.   ..|+|||+|.+.++|.+|++.|||..|+|++|+|.|+.
T Consensus       108 ~~~l~~~f~~~G~v~~v~i~~~~~~g~---~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~As  172 (172)
T 2g4b_A          108 DDQVKELLTSFGPLKAFNLVKDSATGL---SKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS  172 (172)
T ss_dssp             HHHHHHHHHTTSCEEEEEEEECTTTCS---EEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             HHHHHHHHHhcCCceEEEEEecCCCCC---cceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeCC
Confidence            269999999999999999998765543   34678999999999999999999999999999999974

>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=1.6e-25  Score=193.07  Aligned_cols=181  Identities=18%  Similarity=0.256  Sum_probs=137.5

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcC-----------CeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeC
Q 016936          152 PDRVFVGGLPYYFTETQIKELLESFG-----------TLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG  220 (380)
Q Consensus       152 ~~~l~V~nlp~~~t~~~l~~~F~~~G-----------~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~  220 (380)
                      .++|||+|||+++++++|+++|++||           .|..+.+      ++++|||||+|.+.++|++|+ .|+|..+.
T Consensus         4 ~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~------~~~~g~afV~F~~~~~A~~Al-~l~g~~~~   76 (198)
T 2yh0_A            4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDKNFAFLEFRSVDETTQAM-AFDGIIFQ   76 (198)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE------ETTTTEEEEEESCSHHHHHHG-GGTTEEET
T ss_pred             eeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe------cCCCCEEEEEeCCHHHHHHHH-HhcCCEEc
Confidence            47999999999999999999999994           4544544      456899999999999999999 79999999


Q ss_pred             CeEEEEEEcccCCCCChhHHHHHHHHHHHHHHHHHHHhhhcCccccCCCCCccCCccceEEEEeccCCcccCCChHHHHH
Q 016936          221 DKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEE  300 (380)
Q Consensus       221 g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~  300 (380)
                      |+.|.|.++..........                   .......++ ........+...+.+.|.....          
T Consensus        77 g~~i~v~~~~~~~~~~~~~-------------------~~~~~~~~~-~~~~~~~~~~~~l~v~nl~~~~----------  126 (198)
T 2yh0_A           77 GQSLKIRRPHDYQPLPGMS-------------------ENPSVYVPG-VVSTVVPDSAHKLFIGGLPNYL----------  126 (198)
T ss_dssp             TEEEEEECCCCCCCCCCSS-------------------SCSSCCCTT-SSCCCSSCCCCEEEEECCCTTC----------
T ss_pred             CceEEEeCCCCCCCCCCCc-------------------CCCcCCCCC-CccCCCCCCCCEEEEeCCCCCC----------
Confidence            9999999986653222110                   000001111 1111223556677777743211          


Q ss_pred             HHHHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEeccccc
Q 016936          301 ILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  372 (380)
Q Consensus       301 ~~~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~~~  372 (380)
                      +.++|+++|++||.|.++.+..+..++.   ..|+|||+|.+.++|.+|++.|||..|+|++|+|.|+....
T Consensus       127 ~~~~l~~~f~~~G~v~~~~~~~~~~~~~---~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  195 (198)
T 2yh0_A          127 NDDQVKELLTSFGPLKAFNLVKDSATGL---SKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA  195 (198)
T ss_dssp             CHHHHHHHHHTBSCEEEEEEEECTTTCS---EEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCCC
T ss_pred             CHHHHHHHHHHcCCccEEEEeecCCCCC---cceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            1269999999999999999998765543   34778999999999999999999999999999999997753

>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=1.8e-26  Score=195.19  Aligned_cols=164  Identities=17%  Similarity=0.306  Sum_probs=132.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      ....++|||+|||.++++++|+++|+.||.+..+ ++.+..++.++|||||+|.+.++|++|++ |++..+.|+.|.|.+
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~-~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v~~   87 (175)
T 1fje_B           10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDL-AVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   87 (175)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTC-CCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceE-EEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEEec
Confidence            3445799999999999999999999999987763 33333468899999999999999999995 999999999999999


Q ss_pred             cccCCCCChhHHHHHHHHHHHHHHHHHHHhhhcCccccCCCCCccCCccceEEEEeccC-CcccCCChHHHHHHHHHHHH
Q 016936          229 ATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAI-TADALADDEEYEEILEDMRE  307 (380)
Q Consensus       229 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~~~~~~~~~~~~~~~L~~  307 (380)
                      +......                                      .......+.+.|.. +.++           ++|++
T Consensus        88 ~~~~~~~--------------------------------------~~~~~~~l~v~nlp~~~t~-----------~~l~~  118 (175)
T 1fje_B           88 PKGRDSK--------------------------------------KVRAARTLLAKNLSFNITE-----------DELKE  118 (175)
T ss_dssp             CCCSSCS--------------------------------------TTGGGGEEEEESCCSSCCH-----------HHHHH
T ss_pred             CCCcccc--------------------------------------ccccCCEEEEeCCCCCCCH-----------HHHHH
Confidence            8754221                                      13345667777743 2222           69999


Q ss_pred             hhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEecccc
Q 016936          308 ECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  371 (380)
Q Consensus       308 ~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~~  371 (380)
                      +|++||.|..+   .  .++   +..|+|||+|.+.++|.+|+..|||..|+|++|+|+|+.++
T Consensus       119 ~F~~~g~v~~~---~--~~~---~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          119 VFEDALEIRLV---S--QDG---KSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             HCTTCSEEEEE---C--SSS---SCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECSSC
T ss_pred             HHHhcCeEEEe---c--CCC---CCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecCCC
Confidence            99999999877   1  122   22367799999999999999999999999999999999764

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.93  E-value=2.7e-25  Score=196.32  Aligned_cols=193  Identities=13%  Similarity=0.128  Sum_probs=138.9

Q ss_pred             CCCCEEEEcCCCC-CCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          150 EGPDRVFVGGLPY-YFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       150 ~~~~~l~V~nlp~-~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      ...++|||+|||+ .+++++|+++|++||.|..|++.+++     +|||||+|.+.++|++|++.|++..+.|+.|.|.+
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            3457999999999 99999999999999999999998874     78999999999999999999999999999999999


Q ss_pred             cccCCCCChhHHHHHHHHHHHHHHHHHHHh-hhcCccccCCCCCccCCccceEEEEeccCCcccCCChHHHHHHHHHHHH
Q 016936          229 ATASSGQSKTEQESILAQAQQHIAIQKMAL-QTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMRE  307 (380)
Q Consensus       229 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~  307 (380)
                      +.................      ...... .......+..........+..++.+.|.....          +.++|++
T Consensus       107 a~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~----------t~~~l~~  170 (229)
T 2adc_A          107 SKHQNVQLPREGQEDQGL------TKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSV----------SEEDLKV  170 (229)
T ss_dssp             CSCCCCCCCCSSSSTTTT------EEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTC----------CHHHHHH
T ss_pred             ecCccccCcccccccccc------ccccccCcccccCCccccccccCCCCCCEEEEeCCCccC----------CHHHHHH
Confidence            876532211000000000      000000 00000000000001112345777777743221          1269999


Q ss_pred             hhcccC-CeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccC-CeEEEEEecccc
Q 016936          308 ECGKYG-TLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFG-GNTVNAFYYPED  371 (380)
Q Consensus       308 ~f~~~G-~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~-gr~l~v~~~~~~  371 (380)
                      +|++|| .|.++.+.+..      +  |+|||+|.+.++|.+|++.|||..++ |++|+|.|+...
T Consensus       171 ~f~~~G~~i~~v~i~~~~------~--g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          171 LFSSNGGVVKGFKFFQKD------R--KMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             HHHTTSCCEEEEEECSSS------T--TCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             HHHHcCCCeeEEEEEECC------C--cEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecCC
Confidence            999999 99999996632      2  57799999999999999999999999 999999998753

>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=99.93  E-value=3.6e-25  Score=191.69  Aligned_cols=181  Identities=14%  Similarity=0.099  Sum_probs=128.0

Q ss_pred             CCEEEEcCCC-CCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          152 PDRVFVGGLP-YYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       152 ~~~l~V~nlp-~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      ..+|||+||| +.+++++|+++|++||.|.+|+++++     ++|||||+|.+.++|++|++.|||..+.|++|+|.++.
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            3699999999 89999999999999999999999865     36899999999999999999999999999999999986


Q ss_pred             cCCCCChhHHHHHHHHHHHHHHHHHHHhhhcC--ccccCC---CCCccCCccceEEEEeccC-CcccCCChHHHHHHHHH
Q 016936          231 ASSGQSKTEQESILAQAQQHIAIQKMALQTSG--MNTLGG---GMSLFGETLAKVLCLTEAI-TADALADDEEYEEILED  304 (380)
Q Consensus       231 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~---~~~~~~~~~~~~~~l~~~~-~~~~~~~~~~~~~~~~~  304 (380)
                      .....+....... ..     .. . .....+  .+....   ........+.+.+.+.|.. +.++           ++
T Consensus        79 ~~~~~p~~~~~~~-~~-----~~-~-~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~-----------~~  139 (205)
T 3tyt_A           79 QPAIMPGQSYGLE-DG-----SC-S-YKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTE-----------EN  139 (205)
T ss_dssp             CSCCCCCSCCBCT-TS-----CB-S-EEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCH-----------HH
T ss_pred             CCccCCCcccccc-cC-----Cc-c-ccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCH-----------HH
Confidence            5432111000000 00     00 0 000000  000000   0000012345567777643 2222           69


Q ss_pred             HHHhhcccCCe--EEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCe
Q 016936          305 MREECGKYGTL--VNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGN  361 (380)
Q Consensus       305 L~~~f~~~G~I--~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr  361 (380)
                      |+++|++||.|  .++.++.+. .+  .  .|+|||+|.+.++|.+|+..|||..|.|+
T Consensus       140 L~~~F~~~G~v~~~~v~~~~~~-~~--~--~g~gfV~f~~~~~A~~Ai~~lng~~~~g~  193 (205)
T 3tyt_A          140 FFEICDELGVKRPTSVKVFSGK-SE--R--SSSGLLEWDSKSDALETLGFLNHYQMKNP  193 (205)
T ss_dssp             HHHHHHHHTCCCCSEEEECSCC-SS--S--SEEEEEECSSHHHHHHHHHHHTTCEECCS
T ss_pred             HHHHHHhcCCcceEEEEEEcCC-CC--C--ceEEEEEeCCHHHHHHHHHHhCCCCccCC
Confidence            99999999999  899998764 21  2  26779999999999999999999999998

>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=1.8e-25  Score=192.99  Aligned_cols=187  Identities=13%  Similarity=0.125  Sum_probs=138.2

Q ss_pred             CCEEEEcCCCC-CCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          152 PDRVFVGGLPY-YFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       152 ~~~l~V~nlp~-~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      .++|||+|||. .+++++|+++|++||.|..|++++++     +|||||+|.+.++|++|+..|+|..+.|+.|.|.++.
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~   77 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   77 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECC
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEec
Confidence            36999999999 99999999999999999999998764     6899999999999999999999999999999999987


Q ss_pred             cCCCCChhHHHHHHHHHHHHHHHHHHHhhhc-----CccccCCCCCccCCccceEEEEeccCCcccCCChHHHHHHHHHH
Q 016936          231 ASSGQSKTEQESILAQAQQHIAIQKMALQTS-----GMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDM  305 (380)
Q Consensus       231 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L  305 (380)
                      ..............          ......+     ....++.........+..++.+.|.....          +.++|
T Consensus        78 ~~~~~~~~~~~~~~----------~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~----------~~~~l  137 (198)
T 1qm9_A           78 HQNVQLPREGQEDQ----------GLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSV----------SEEDL  137 (198)
T ss_dssp             CCSCCCSSSSSSSS----------SCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTC----------CHHHH
T ss_pred             CCCcCCCCcCCccc----------cccccccCCchhhccCccccccccCCCCccEEEEeCCCCCC----------CHHHH
Confidence            65322110000000          0000000     00000000111112346777777743221          12699


Q ss_pred             HHhhcccC-CeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccC-CeEEEEEecccc
Q 016936          306 REECGKYG-TLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFG-GNTVNAFYYPED  371 (380)
Q Consensus       306 ~~~f~~~G-~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~-gr~l~v~~~~~~  371 (380)
                      +++|++|| .|.++.+.++.        .|+|||+|.+.++|.+|++.|||..++ |++|+|.|+...
T Consensus       138 ~~~f~~~G~~v~~v~i~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          138 KVLFSSNGGVVKGFKFFQKD--------RKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             HHHHHHTTSCCCEEEESSTT--------SSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECCC
T ss_pred             HHHHHHcCCCceEEEEEeCC--------CcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeeccc
Confidence            99999999 99999997643        257799999999999999999999999 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=99.91  E-value=9.8e-24  Score=190.05  Aligned_cols=157  Identities=24%  Similarity=0.324  Sum_probs=130.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      ...++|||+|||+++|+++|+++|++||.|..|.+.++      +|||||+|.+.++|.+|+..++|..+.|+.|.|.++
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            34469999999999999999999999999999998543      689999999999999999999999999999999997


Q ss_pred             ccCCCCChhHHHHHHHHHHHHHHHHHHHhhhcCccccCCCCCccCCccceEEEEeccCCcccCCChHHHHHHHHHHHHhh
Q 016936          230 TASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREEC  309 (380)
Q Consensus       230 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~~f  309 (380)
                      .+                                              ...+.+.|.....          +.++|+++|
T Consensus        94 ~~----------------------------------------------~~~l~v~nl~~~~----------t~~~l~~~F  117 (261)
T 3sde_A           94 TH----------------------------------------------GAALTVKNLSPVV----------SNELLEQAF  117 (261)
T ss_dssp             CC----------------------------------------------SSEEEEESCCTTC----------CHHHHHHHH
T ss_pred             cc----------------------------------------------CCcccccCCCCCC----------CHHHHHHHH
Confidence            42                                              2346666532211          126999999


Q ss_pred             cccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcC-cccC---CeEEEEEeccccc
Q 016936          310 GKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSG-RKFG---GNTVNAFYYPEDK  372 (380)
Q Consensus       310 ~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g-~~i~---gr~l~v~~~~~~~  372 (380)
                      ++||.|.+|.++.+. ++.   ..|+|||+|.+.++|.+|+..||+ ..+.   ||+|.|.++....
T Consensus       118 ~~~G~i~~v~i~~~~-~g~---~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~~~~~~~  180 (261)
T 3sde_A          118 SQFGPVEKAVVVVDD-RGR---ATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFD  180 (261)
T ss_dssp             GGGSCEEEEEEEEET-TSC---EEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEEECCCEE
T ss_pred             HhcCCeEEEEeeeCC-CCC---cCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEeeccccC
Confidence            999999999998874 432   357789999999999999999954 4554   9999999998754

>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=2.4e-21  Score=160.93  Aligned_cols=140  Identities=17%  Similarity=0.176  Sum_probs=106.0

Q ss_pred             CCCcEEEEEeCCHHHHHHHH-HcCCceecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEE
Q 016936           78 HEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVF  156 (380)
Q Consensus        78 ~~~g~afV~f~~~~~a~~ai-~l~~~~i~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  156 (380)
                      +++|||||+|.+.++|++|+ .+++....+..+.+............    .            .............+||
T Consensus        11 ~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~----~------------~~~~~~~~~~~~~~l~   74 (158)
T 2kn4_A           11 TLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEG----S------------HHHHHHMDVEGMTSLK   74 (158)
T ss_dssp             SCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEEECC----C------------CCSSCCCCCCBCCEEE
T ss_pred             cccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCcccccccccc----c------------cccccccCCCCCCEEE
Confidence            57899999999999999999 66653322223332211110000000    0            0000111123347999


Q ss_pred             EcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccCC
Q 016936          157 VGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASS  233 (380)
Q Consensus       157 V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~~  233 (380)
                      |+|||+.+++++|+++|++||.|..|+++.++.++.++|||||+|.+.++|++|+..|||..+.|+.|+|.++.+..
T Consensus        75 v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  151 (158)
T 2kn4_A           75 VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGR  151 (158)
T ss_dssp             EESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCSS
T ss_pred             EeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCC
Confidence            99999999999999999999999999999998889999999999999999999999999999999999999998754

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A

Probab=99.86  E-value=1.2e-21  Score=150.42  Aligned_cols=103  Identities=43%  Similarity=0.825  Sum_probs=94.3

Q ss_pred             CccceEEEEeccCCcccCCChHHHHHHHHHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHc
Q 016936          275 ETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALS  354 (380)
Q Consensus       275 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~  354 (380)
                      ..++++++|.|++++.++.++.+|.+++++|+++|++||.|.+|.|+++..+. ..++.|+|||+|.+.++|.+|++.||
T Consensus         2 g~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~-~~~~~G~~fV~f~~~~~A~~Ai~~ln   80 (105)
T 3v4m_A            2 GHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGV-EVPGCGKIFVEFTSVFDCQKAMQGLT   80 (105)
T ss_dssp             CSCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTB-CCTTTTEEEEEESSHHHHHHHHHHHT
T ss_pred             CCCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCC-CcCCcEEEEEEECCHHHHHHHHHHhC
Confidence            46899999999999999999999999999999999999999999998876432 13456788999999999999999999


Q ss_pred             CcccCCeEEEEEeccccccccccC
Q 016936          355 GRKFGGNTVNAFYYPEDKYFNKDY  378 (380)
Q Consensus       355 g~~i~gr~l~v~~~~~~~~~~~~~  378 (380)
                      |+.|+||.|+|+|+++++|+.++|
T Consensus        81 G~~f~GR~i~v~~~~~~~f~~~~~  104 (105)
T 3v4m_A           81 GRKFANRVVVTKYCDPDSYHRRDF  104 (105)
T ss_dssp             TCEETTEECEEEEECHHHHHTTCC
T ss_pred             CCEeCCCEEEEEEeCHHHHhhccC
Confidence            999999999999999999999987

>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=99.82  E-value=5.1e-20  Score=151.45  Aligned_cols=136  Identities=15%  Similarity=0.158  Sum_probs=110.1

Q ss_pred             CCCcEEEEEeCCHHHHHHHH-Hc-CCceecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEE
Q 016936           78 HEKKFAFVEMRTVEEASNAM-AL-DGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRV  155 (380)
Q Consensus        78 ~~~g~afV~f~~~~~a~~ai-~l-~~~~i~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  155 (380)
                      +-+|+++|+|.+.++|++|+ ++ ++..+.| +|.+.++............             .............++|
T Consensus        11 ~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~~~-------------~~~~~~~~~~~~~~~l   76 (150)
T 2i2y_A           11 TLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGSHH-------------HHHHMHRDSCPLDCKV   76 (150)
T ss_dssp             SSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSSSS-------------CCCCSCSSSSTTSCEE
T ss_pred             cccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCcccccccccc-------------ccccccccCCCCCCEE
Confidence            56799999999999999999 78 9999999 9999976543211110000             0001111223445799


Q ss_pred             EEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccC
Q 016936          156 FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  232 (380)
Q Consensus       156 ~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~  232 (380)
                      ||+|||+.+++++|+++|++||.|..|+++++     ++|||||+|.+.++|.+|+..|||..+.|++|+|.++.++
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     5789999999999999999999999999999999998764

>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=99.82  E-value=9.7e-20  Score=138.48  Aligned_cols=80  Identities=31%  Similarity=0.542  Sum_probs=77.1

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEccc
Q 016936          152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  231 (380)
Q Consensus       152 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~  231 (380)
                      .++|||+|||+++|+++|+++|++||.|..|++++++.+|+++|||||+|.+.++|++|++.|||..+.|++|+|.++.|
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            36899999999999999999999999999999999988999999999999999999999999999999999999999865

>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=99.82  E-value=1.8e-20  Score=146.49  Aligned_cols=101  Identities=31%  Similarity=0.504  Sum_probs=88.4

Q ss_pred             CccceEEEEeccCCcccCCChHHHHHHHHHHHHhhcccCCeEEEEecCCCCCC-CCCCCccEEEEEeechhhHHHHHHHH
Q 016936          275 ETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNG-GETPGVGKVFLEYYDAVGCATAKNAL  353 (380)
Q Consensus       275 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~~f~~~G~I~~v~i~~~~~~~-~~~~g~g~afV~f~~~~~A~~A~~~l  353 (380)
                      ..+++|++|.|+++++++.++     ++++|+++|++||.|.+|.|+++..+. ...++.|++||+|.+.++|.+|++.|
T Consensus        17 ~~ps~vl~L~Nm~~~~el~dd-----leedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~L   91 (118)
T 3ue2_A           17 KQESTVMVLRNMVDPKDIDDD-----LEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQAL   91 (118)
T ss_dssp             HHSCCEEEEESCSCGGGCCTT-----HHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHH
T ss_pred             CCCCCEEEEECCCCHHHHHHH-----HHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHH
Confidence            447899999999999887654     457999999999999999999876421 12345688899999999999999999


Q ss_pred             cCcccCCeEEEEEeccccccccccCCC
Q 016936          354 SGRKFGGNTVNAFYYPEDKYFNKDYSA  380 (380)
Q Consensus       354 ~g~~i~gr~l~v~~~~~~~~~~~~~~~  380 (380)
                      ||++|+||.|+|+|+++++|..++|++
T Consensus        92 nGr~f~GR~i~v~~~~~~~f~~~~~~~  118 (118)
T 3ue2_A           92 NGRWFAGRKVVAEVYDQERFDNSDLSA  118 (118)
T ss_dssp             TTCEETTEECEEEEECHHHHHTTCCCC
T ss_pred             CCCEECCcEEEEEEcChHhccccccCC
Confidence            999999999999999999999999986

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.78  E-value=3.7e-19  Score=133.12  Aligned_cols=82  Identities=20%  Similarity=0.328  Sum_probs=76.3

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcC-CeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHh-CCCeeCCeEEEEEEcc
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFG-TLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL-NGLKMGDKTLTVRRAT  230 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G-~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l-~g~~~~g~~i~v~~~~  230 (380)
                      ++|||+|||+++|+++|+++|++|| .|.+|++++++.++.++|||||+|.+.++|++|++.+ ++..+.|++|+|.++.
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            6899999999999999999999999 7999999999989999999999999999999999976 4678999999999998


Q ss_pred             cCCC
Q 016936          231 ASSG  234 (380)
Q Consensus       231 ~~~~  234 (380)
                      ++..
T Consensus        82 ~~~~   85 (91)
T 2lxi_A           82 PKPK   85 (91)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            7644

>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=3.3e-19  Score=139.59  Aligned_cols=105  Identities=18%  Similarity=0.237  Sum_probs=66.2

Q ss_pred             ccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec----CCCcEEEEEeCCHHHHHHHH-HcCCceec
Q 016936           31 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN----HEKKFAFVEMRTVEEASNAM-ALDGIIFE  105 (380)
Q Consensus        31 ~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~----~~~g~afV~f~~~~~a~~ai-~l~~~~i~  105 (380)
                      .+.+|||+|||+++++++|+++|++||.            |.++++.    .++|||||+|.+.++|++|+ .|++..|.
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~------------v~~v~i~~d~~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~   71 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGN------------ILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLN   71 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSC------------EEEEEEEEETTEEEEEEEEEESCHHHHHHHHHHHTTCEET
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCC------------EEEEEEeecCCCCCceEEEEECCHHHHHHHHHHcCCCEEC
Confidence            4678999999999999999999999998            5555543    34789999999999999999 79999999


Q ss_pred             CceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHH
Q 016936          106 GVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQ  168 (380)
Q Consensus       106 g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~  168 (380)
                      |++|+|.++..........                     ........+|||+|||+.+|++.
T Consensus        72 g~~i~V~~a~~~~~~~~~~---------------------~~~~~~~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           72 DRKVFVGRFKSRKEREAEL---------------------GARAKEFTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             TEECEEEESSCCCC-------------------------------------------------
T ss_pred             CEEEEEEECCCcccccccc---------------------ccccCCCCceEeCCCCCCccccc
Confidence            9999999876543211100                     00112235799999999998763

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.78  E-value=2e-18  Score=133.72  Aligned_cols=80  Identities=11%  Similarity=0.139  Sum_probs=77.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      ..++|||+|||+.+++++|+++|++||.|.+|++++++.+++++|||||+|.+.++|++|++.|||..+.|+.|+|.++.
T Consensus         5 p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a~   84 (110)
T 3s8s_A            5 PLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDI   84 (110)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            34799999999999999999999999999999999999899999999999999999999999999999999999999985

>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=99.77  E-value=7.4e-19  Score=136.32  Aligned_cols=95  Identities=25%  Similarity=0.419  Sum_probs=87.1

Q ss_pred             CccceEEEEeccCCcccCCChHHHHHHHHHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHc
Q 016936          275 ETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALS  354 (380)
Q Consensus       275 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~  354 (380)
                      +.+++|++|.|+++++++.++.++.++++||+++|++||.|.+|.+.++.     +  .|+|||+|.+.++|.+|++.||
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-----A--QGNVYVKCPSIAAAIAAVNALH   76 (114)
T ss_dssp             CCCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC-----T--TCCEEEECSSHHHHHHHHHHHT
T ss_pred             CCCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC-----C--cEEEEEEECCHHHHHHHHHHhC
Confidence            57899999999999999999999999999999999999999999997754     2  3677999999999999999999


Q ss_pred             CcccCCeEEEEEeccccccccc
Q 016936          355 GRKFGGNTVNAFYYPEDKYFNK  376 (380)
Q Consensus       355 g~~i~gr~l~v~~~~~~~~~~~  376 (380)
                      |++|+||.|+|+|++++.|+++
T Consensus        77 G~~f~GR~i~v~~~~~~~y~~~   98 (114)
T 3s6e_A           77 GRWFAGKMITAAYVPLPTYHNL   98 (114)
T ss_dssp             TCEETTEECEEEEECHHHHHHH
T ss_pred             CCEECCEEEEEEEEcHHHHHHh
Confidence            9999999999999999888653

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.77  E-value=1.1e-18  Score=131.11  Aligned_cols=82  Identities=20%  Similarity=0.320  Sum_probs=75.8

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCC--eeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCC----eeCCeE
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGT--LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGL----KMGDKT  223 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~--i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~----~~~g~~  223 (380)
                      ....+|||+|||+.+|+++|+++|++||.  +..|++++|+.+++++|||||+|.+.++|++|++.||+.    .+.|++
T Consensus         7 ~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~   86 (95)
T 2lkz_A            7 HHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKT   86 (95)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEE
T ss_pred             CccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEE
Confidence            44579999999999999999999999995  678999999989999999999999999999999999986    589999


Q ss_pred             EEEEEccc
Q 016936          224 LTVRRATA  231 (380)
Q Consensus       224 i~v~~~~~  231 (380)
                      |.|.+|+.
T Consensus        87 i~V~~Aks   94 (95)
T 2lkz_A           87 IGVDFAKS   94 (95)
T ss_dssp             EEEEECCC
T ss_pred             EEEEEccC
Confidence            99999864

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.76  E-value=1.7e-18  Score=132.68  Aligned_cols=99  Identities=29%  Similarity=0.453  Sum_probs=84.6

Q ss_pred             CccceEEEEeccCCcccCCChHHHHHHHHHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHc
Q 016936          275 ETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALS  354 (380)
Q Consensus       275 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~  354 (380)
                      ..+++++.+.|+++++++.++     +.++|+++|++||.|.+|.+++++..+.  +..|+|||+|.+.++|.+|++.||
T Consensus         5 ~~~s~~l~l~Nm~~~~~l~dd-----~~~dl~~~f~~~G~V~~v~i~~~~~~~~--~~~G~~FV~f~~~~~A~~Ai~~ln   77 (105)
T 2pe8_A            5 KCPTKVVLLRNMVGAGEVDED-----LEVETKEECEKYGKVGKCVIFEIPGAPD--DEAVRIFLEFERVESAIKAVVDLN   77 (105)
T ss_dssp             GSCCSEEEEESSSCSCCC--------CHHHHHHHGGGGSCEEEEEEEECSSCCT--TTSEEEEEEESSHHHHHHHHHHHT
T ss_pred             CCCCCEEEEEcCCChHHhhHH-----HHHHHHHHHHhcCCEEEEEEecCCCCCC--CCcEEEEEEECCHHHHHHHHHHHC
Confidence            567899999999988776543     4579999999999999999988754332  234677999999999999999999


Q ss_pred             CcccCCeEEEEEeccccccccccCCC
Q 016936          355 GRKFGGNTVNAFYYPEDKYFNKDYSA  380 (380)
Q Consensus       355 g~~i~gr~l~v~~~~~~~~~~~~~~~  380 (380)
                      |+.|+||.|+|.|++++.|..++|++
T Consensus        78 G~~~~Gr~i~v~~a~~~~f~~~~~~~  103 (105)
T 2pe8_A           78 GRYFGGRVVKACFYNLDKFRVLDLAE  103 (105)
T ss_dssp             TCEETTEECEEEECCHHHHHTTCCCC
T ss_pred             CCEECCcEEEEEEcCHHHhhhhhccc
Confidence            99999999999999999999999974

>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=99.76  E-value=5.3e-18  Score=125.75  Aligned_cols=82  Identities=30%  Similarity=0.455  Sum_probs=76.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      ..++|||+|||..+++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|++|++.|++..+.|+.|+|.++.
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            34699999999999999999999999999999999998889999999999999999999999999999999999999986


Q ss_pred             cC
Q 016936          231 AS  232 (380)
Q Consensus       231 ~~  232 (380)
                      ++
T Consensus        85 ~k   86 (87)
T 3bs9_A           85 RK   86 (87)
T ss_dssp             --
T ss_pred             CC
Confidence            54

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=7.7e-18  Score=128.87  Aligned_cols=88  Identities=28%  Similarity=0.536  Sum_probs=81.3

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEE
Q 016936          148 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  227 (380)
Q Consensus       148 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~  227 (380)
                      .....++|||+|||..+++++|+++|++||.|..|+++.++.++.++|||||+|.+.++|++|++.||+..+.|+.|+|.
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            34556899999999999999999999999999999999998889999999999999999999999999999999999999


Q ss_pred             EcccCCCC
Q 016936          228 RATASSGQ  235 (380)
Q Consensus       228 ~~~~~~~~  235 (380)
                      ++.++...
T Consensus        88 ~a~~~~~~   95 (102)
T 1x5s_A           88 QAGKSSDN   95 (102)
T ss_dssp             EEECCCCC
T ss_pred             ECCCCCCC
Confidence            99776433

>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=99.75  E-value=9.7e-18  Score=123.16  Aligned_cols=80  Identities=21%  Similarity=0.408  Sum_probs=77.0

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccC
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  232 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~  232 (380)
                      .+|||+|||..+++++|+++|++||.|..+.+++++.++.++|||||+|.+.++|++|+..|+|..+.|+.|+|.++.++
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            48999999999999999999999999999999999888999999999999999999999999999999999999999765

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A

Probab=99.75  E-value=6.4e-18  Score=132.24  Aligned_cols=80  Identities=23%  Similarity=0.473  Sum_probs=74.8

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEccc
Q 016936          152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  231 (380)
Q Consensus       152 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~  231 (380)
                      ..+|||+|||+.+++++|+++|++||.|..|++++++  +.++|||||+|.+.++|++|++.|++..+.|++|+|.++.+
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  56899999999999999999999999999999999999876


Q ss_pred             CC
Q 016936          232 SS  233 (380)
Q Consensus       232 ~~  233 (380)
                      +.
T Consensus        83 ~~   84 (115)
T 4f25_A           83 RK   84 (115)
T ss_dssp             CC
T ss_pred             cc
Confidence            53

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.75  E-value=1e-17  Score=126.47  Aligned_cols=85  Identities=33%  Similarity=0.644  Sum_probs=79.8

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      ..+++|||+|||..+++++|+++|++||.|..|.++.++.+++++|||||+|.+.++|++|++.||+..+.|+.|+|.++
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            34579999999999999999999999999999999999888999999999999999999999999999999999999999


Q ss_pred             ccCCC
Q 016936          230 TASSG  234 (380)
Q Consensus       230 ~~~~~  234 (380)
                      .++..
T Consensus        83 ~~~~~   87 (95)
T 2dnz_A           83 TERLD   87 (95)
T ss_dssp             SCCCC
T ss_pred             ccccC
Confidence            77643

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.75  E-value=1.6e-17  Score=130.05  Aligned_cols=88  Identities=30%  Similarity=0.437  Sum_probs=81.5

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEE
Q 016936          148 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  227 (380)
Q Consensus       148 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~  227 (380)
                      .....++|||+|||..+++++|+++|++||.|..|+++.++.++.++|||||+|.+.++|++|++.|++..+.|+.|+|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   90 (115)
T 2dgo_A           11 DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTN   90 (115)
T ss_dssp             CSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34556899999999999999999999999999999999998889999999999999999999999999999999999999


Q ss_pred             EcccCCCC
Q 016936          228 RATASSGQ  235 (380)
Q Consensus       228 ~~~~~~~~  235 (380)
                      ++..+...
T Consensus        91 ~a~~~~~~   98 (115)
T 2dgo_A           91 WATRKPPA   98 (115)
T ss_dssp             ESSCCCCC
T ss_pred             EccCCCCC
Confidence            99876443

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=7.4e-18  Score=128.96  Aligned_cols=87  Identities=18%  Similarity=0.306  Sum_probs=80.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      ....++|||+|||..+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|++|++.|++..+.|+.|+|.+
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            44568999999999999999999999999999999999988899999999999999999999999999999999999999


Q ss_pred             cccCCCC
Q 016936          229 ATASSGQ  235 (380)
Q Consensus       229 ~~~~~~~  235 (380)
                      +.+....
T Consensus        89 a~~~~~~   95 (102)
T 2cqb_A           89 AKPMRIK   95 (102)
T ss_dssp             CCCCCCC
T ss_pred             CCCCCCC
Confidence            9876433

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.75  E-value=9.1e-18  Score=126.43  Aligned_cols=82  Identities=23%  Similarity=0.448  Sum_probs=77.4

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      ....++|||+|||..+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|++|++.||+..+.|++|+|.+
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            34557999999999999999999999999999999999988899999999999999999999999999999999999998


Q ss_pred             cc
Q 016936          229 AT  230 (380)
Q Consensus       229 ~~  230 (380)
                      ++
T Consensus        93 ak   94 (94)
T 2e5h_A           93 AI   94 (94)
T ss_dssp             CC
T ss_pred             cC
Confidence            73

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.75  E-value=1.3e-17  Score=126.90  Aligned_cols=85  Identities=26%  Similarity=0.431  Sum_probs=79.8

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      ...++|||+|||..+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|++|++.|++..+.|+.|+|.++
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            34579999999999999999999999999999999999878999999999999999999999999999999999999999


Q ss_pred             ccCCC
Q 016936          230 TASSG  234 (380)
Q Consensus       230 ~~~~~  234 (380)
                      .++..
T Consensus        86 ~~~~~   90 (99)
T 1whw_A           86 TIKKE   90 (99)
T ss_dssp             CCCST
T ss_pred             CCCcc
Confidence            87643

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=1.2e-17  Score=126.05  Aligned_cols=83  Identities=20%  Similarity=0.418  Sum_probs=77.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      ....++|||+|||..+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|++|++.|++..+.|++|+|.+
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            34457999999999999999999999999999999999988899999999999999999999999999999999999999


Q ss_pred             ccc
Q 016936          229 ATA  231 (380)
Q Consensus       229 ~~~  231 (380)
                      +.+
T Consensus        92 a~~   94 (95)
T 2cqc_A           92 PSS   94 (95)
T ss_dssp             CSC
T ss_pred             cCC
Confidence            853

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=1e-17  Score=128.39  Aligned_cols=85  Identities=20%  Similarity=0.382  Sum_probs=79.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      ....++|||+|||..+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|++|++.||+..+.|+.|+|.+
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2dnm_A           10 VDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQV   89 (103)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            34558999999999999999999999999999999999988899999999999999999999999999999999999999


Q ss_pred             cccCC
Q 016936          229 ATASS  233 (380)
Q Consensus       229 ~~~~~  233 (380)
                      +....
T Consensus        90 a~~~~   94 (103)
T 2dnm_A           90 ARYGR   94 (103)
T ss_dssp             CSSCC
T ss_pred             CCcCC
Confidence            97654

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=1.1e-17  Score=128.29  Aligned_cols=86  Identities=29%  Similarity=0.436  Sum_probs=80.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      ....++|||+|||..+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|++|+..|++..+.|+.|+|.+
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            44557999999999999999999999999999999999988899999999999999999999999999999999999999


Q ss_pred             cccCCC
Q 016936          229 ATASSG  234 (380)
Q Consensus       229 ~~~~~~  234 (380)
                      +.++..
T Consensus        92 a~~~~~   97 (103)
T 2cq0_A           92 AKPSTN   97 (103)
T ss_dssp             SSCCCC
T ss_pred             CCCCCC
Confidence            977643

>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=99.74  E-value=1e-17  Score=123.64  Aligned_cols=80  Identities=19%  Similarity=0.341  Sum_probs=76.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      ..++|||+|||..+++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++.|||..+.|+.|+|++++
T Consensus         6 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~ak   85 (85)
T 3mdf_A            6 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   85 (85)
T ss_dssp             CSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            44799999999999999999999999999999999998889999999999999999999999999999999999999873

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=1.3e-17  Score=126.06  Aligned_cols=85  Identities=29%  Similarity=0.518  Sum_probs=79.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEE-EEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGF-DLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v-~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      ..++|||+|||..+++++|+++|++||.|..+ +++.++.++.++|||||+|.+.++|++|+..|++..+.|+.|+|.++
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            44799999999999999999999999999999 99999888999999999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 016936          230 TASSGQ  235 (380)
Q Consensus       230 ~~~~~~  235 (380)
                      .++...
T Consensus        84 ~~~~~~   89 (96)
T 1x5t_A           84 FKKDSK   89 (96)
T ss_dssp             CCCCCC
T ss_pred             cccCCC
Confidence            776433

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=1.9e-17  Score=125.90  Aligned_cols=85  Identities=25%  Similarity=0.537  Sum_probs=79.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      ...++|||+|||..+++++|+++|++||.|..|.++.++.+++++|||||+|.+.++|++|++ +++..+.|+.|+|.++
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            345799999999999999999999999999999999998889999999999999999999999 8999999999999999


Q ss_pred             ccCCCC
Q 016936          230 TASSGQ  235 (380)
Q Consensus       230 ~~~~~~  235 (380)
                      .++...
T Consensus        87 ~~~~~~   92 (99)
T 2dgs_A           87 EPRDSK   92 (99)
T ss_dssp             CCCCCC
T ss_pred             CCCccc
Confidence            876443

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A

Probab=99.74  E-value=1.7e-17  Score=127.93  Aligned_cols=86  Identities=29%  Similarity=0.463  Sum_probs=79.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCee---CCeEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM---GDKTLT  225 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~---~g~~i~  225 (380)
                      ....++|||+|||..+++++|+++|++||.|..|+++.++.+++++|||||+|.+.++|++|++.|++..+   .|+.|+
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            34457999999999999999999999999999999999988899999999999999999999999999987   899999


Q ss_pred             EEEcccCCC
Q 016936          226 VRRATASSG  234 (380)
Q Consensus       226 v~~~~~~~~  234 (380)
                      |.++.....
T Consensus        90 v~~a~~~~~   98 (106)
T 2dgp_A           90 VKPADSESR   98 (106)
T ss_dssp             EEECCCCSC
T ss_pred             EEECCcccc
Confidence            999977643

>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=99.73  E-value=2.3e-17  Score=126.91  Aligned_cols=86  Identities=29%  Similarity=0.436  Sum_probs=80.4

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      ....++|||+|||..+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|++|++.|++..+.|+.|+|.+
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            34558999999999999999999999999999999999988899999999999999999999999999999999999999


Q ss_pred             cccCCC
Q 016936          229 ATASSG  234 (380)
Q Consensus       229 ~~~~~~  234 (380)
                      +.+...
T Consensus        92 a~~~~~   97 (105)
T 1x5u_A           92 ASAHNK   97 (105)
T ss_dssp             TTTTSC
T ss_pred             CCCCCc
Confidence            977643

>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=99.73  E-value=2.9e-18  Score=128.07  Aligned_cols=80  Identities=18%  Similarity=0.342  Sum_probs=72.6

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcC--CeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFG--TLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G--~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      .+|||+|||+++++++|+++|++||  .|.+++++.++.+|+++|||||+|.+.++|++|++.|||..+.|+.|+|.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            4799999999999999999999999  99999999998899999999999999999999999999999999999999987


Q ss_pred             cC
Q 016936          231 AS  232 (380)
Q Consensus       231 ~~  232 (380)
                      +.
T Consensus        82 ~~   83 (90)
T 3p5t_L           82 KL   83 (90)
T ss_dssp             --
T ss_pred             CC
Confidence            65

>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=99.73  E-value=2.2e-17  Score=124.86  Aligned_cols=81  Identities=32%  Similarity=0.556  Sum_probs=77.8

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccC
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  232 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~  232 (380)
                      ++|||+|||..+++++|+++|++||.|..|+++.++.++.++|||||+|.+.++|++|++.|+|..+.|+.|+|.++.++
T Consensus         3 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~   82 (96)
T 2x1f_A            3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSNS   82 (96)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCS
T ss_pred             cEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCCC
Confidence            69999999999999999999999999999999999888999999999999999999999999999999999999999775


Q ss_pred             C
Q 016936          233 S  233 (380)
Q Consensus       233 ~  233 (380)
                      .
T Consensus        83 ~   83 (96)
T 2x1f_A           83 D   83 (96)
T ss_dssp             S
T ss_pred             C
Confidence            4

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=1.5e-17  Score=126.51  Aligned_cols=84  Identities=24%  Similarity=0.396  Sum_probs=79.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCee-EEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeE----
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLH-GFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKT----  223 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~-~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~----  223 (380)
                      ....++|||+|||..+++++|+++|++||.|. .|++++++.++.++|||||+|.+.++|++|++.||+..+.|+.    
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            44558999999999999999999999999999 9999999888999999999999999999999999999999999    


Q ss_pred             EEEEEcccC
Q 016936          224 LTVRRATAS  232 (380)
Q Consensus       224 i~v~~~~~~  232 (380)
                      |+|.++.+.
T Consensus        86 l~v~~a~~~   94 (99)
T 2div_A           86 FKLNYATYS   94 (99)
T ss_dssp             CCEEETTCC
T ss_pred             EEEeecCCC
Confidence            999998764

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.73  E-value=4.1e-17  Score=124.34  Aligned_cols=83  Identities=22%  Similarity=0.542  Sum_probs=78.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      ...++|||+|||..+++++|+++|++||.|..|+++.++ +++++|||||+|.+.++|++|++.|++..+.|+.|+|.++
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            345799999999999999999999999999999999997 7999999999999999999999999999999999999999


Q ss_pred             ccCC
Q 016936          230 TASS  233 (380)
Q Consensus       230 ~~~~  233 (380)
                      .++.
T Consensus        94 ~~~~   97 (100)
T 2do4_A           94 NSGP   97 (100)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            7654

>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=99.73  E-value=3e-17  Score=127.62  Aligned_cols=87  Identities=28%  Similarity=0.410  Sum_probs=80.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhC------CCeeCCe
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN------GLKMGDK  222 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~------g~~~~g~  222 (380)
                      ....++|||+|||+.+++++|+++|++||.|..|+++.++.++.++|||||+|.+.++|++|++.++      +..+.|+
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            3455799999999999999999999999999999999998889999999999999999999999999      9999999


Q ss_pred             EEEEEEcccCCCC
Q 016936          223 TLTVRRATASSGQ  235 (380)
Q Consensus       223 ~i~v~~~~~~~~~  235 (380)
                      .|+|.++.++...
T Consensus        92 ~l~v~~a~~~~~~  104 (111)
T 1x4h_A           92 QLKVDLAVTRDEA  104 (111)
T ss_dssp             EEEEECCCCCCCC
T ss_pred             EEEEEECCCCccC
Confidence            9999999876443

>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=99.73  E-value=2.9e-17  Score=128.55  Aligned_cols=86  Identities=24%  Similarity=0.475  Sum_probs=80.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      ...++|||+|||.++++++|+++|++||.|..|+++.++.+++++|||||+|.+.++|++|++.||+..+.|+.|+|.++
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            34479999999999999999999999999999999999888999999999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 016936          230 TASSGQ  235 (380)
Q Consensus       230 ~~~~~~  235 (380)
                      .++...
T Consensus       103 ~~~~~~  108 (115)
T 2cpz_A          103 RSKNDS  108 (115)
T ss_dssp             CCSCCC
T ss_pred             CCCCcC
Confidence            876543

>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=99.73  E-value=1.9e-17  Score=127.99  Aligned_cols=85  Identities=34%  Similarity=0.711  Sum_probs=79.7

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEE
Q 016936          148 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  227 (380)
Q Consensus       148 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~  227 (380)
                      +...+++|||+|||..+++++|+++|++||.|..|.++.++.+++++|||||+|.+.++|++|++.++|..+.|+.|+|.
T Consensus        22 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~  101 (108)
T 2jrs_A           22 GSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVG  101 (108)
T ss_dssp             SCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34556899999999999999999999999999999999998889999999999999999999999999999999999999


Q ss_pred             EcccC
Q 016936          228 RATAS  232 (380)
Q Consensus       228 ~~~~~  232 (380)
                      ++.++
T Consensus       102 ~a~~k  106 (108)
T 2jrs_A          102 HVTER  106 (108)
T ss_dssp             CSCSS
T ss_pred             EcccC
Confidence            98765

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens}

Probab=99.73  E-value=2.2e-17  Score=124.62  Aligned_cols=80  Identities=31%  Similarity=0.553  Sum_probs=75.8

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      ...++|||+|||+.+++++|+++|++||.|..|+++.++. ++++|||||+|.+.++|++|++.|++..+.|+.|+|.++
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            4457999999999999999999999999999999999975 999999999999999999999999999999999999997


Q ss_pred             c
Q 016936          230 T  230 (380)
Q Consensus       230 ~  230 (380)
                      .
T Consensus        93 ~   93 (95)
T 2ywk_A           93 S   93 (95)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.72  E-value=4.4e-17  Score=125.76  Aligned_cols=87  Identities=23%  Similarity=0.438  Sum_probs=80.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeC-CCCCCCceEEEEEEcChhHHHHHHHHh-CCCeeCCeEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKD-RDTGNSKGYGFCVYQDPAVTDIACAAL-NGLKMGDKTLTV  226 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~-~~~~~~~g~afV~f~~~~~A~~Ai~~l-~g~~~~g~~i~v  226 (380)
                      ....++|||+|||..+++++|+++|++||.|..|+++.+ +.++.++|||||+|.+.++|++|+..| ++..+.|+.|.|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~v   91 (107)
T 2cph_A           12 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL   91 (107)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEEE
Confidence            344579999999999999999999999999999999998 678999999999999999999999999 999999999999


Q ss_pred             EEcccCCCC
Q 016936          227 RRATASSGQ  235 (380)
Q Consensus       227 ~~~~~~~~~  235 (380)
                      .++.++...
T Consensus        92 ~~a~~~~~~  100 (107)
T 2cph_A           92 EWADSEVTV  100 (107)
T ss_dssp             EECCCCCCC
T ss_pred             EeCCCCCCC
Confidence            999876443

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.72  E-value=2.1e-17  Score=125.45  Aligned_cols=84  Identities=24%  Similarity=0.452  Sum_probs=77.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCC---CCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEE
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRD---TGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  227 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~---~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~  227 (380)
                      ..++|||+|||..+++++|+++|++||.|..|.+..++.   ++.++|||||+|.+.++|++|+..|++..+.|+.|+|.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   83 (98)
T 2cpf_A            4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVR   83 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            447999999999999999999999999999999998865   55899999999999999999999999999999999999


Q ss_pred             EcccCCC
Q 016936          228 RATASSG  234 (380)
Q Consensus       228 ~~~~~~~  234 (380)
                      ++.++..
T Consensus        84 ~a~~~~~   90 (98)
T 2cpf_A           84 ISERATK   90 (98)
T ss_dssp             CSSCSSC
T ss_pred             EccCCCC
Confidence            9977643

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.72  E-value=4.8e-18  Score=129.47  Aligned_cols=80  Identities=16%  Similarity=0.268  Sum_probs=76.6

Q ss_pred             CCEEEEcCCCC------CCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCC-eEE
Q 016936          152 PDRVFVGGLPY------YFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD-KTL  224 (380)
Q Consensus       152 ~~~l~V~nlp~------~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g-~~i  224 (380)
                      .++|||+|||.      .+++++|+++|++||.|..|+++.++.+++++|||||+|.+.++|++|++.|||..+.| +.|
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            36999999999      99999999999999999999999998889999999999999999999999999999999 999


Q ss_pred             EEEEccc
Q 016936          225 TVRRATA  231 (380)
Q Consensus       225 ~v~~~~~  231 (380)
                      +|.++.+
T Consensus        86 ~V~~a~~   92 (100)
T 3ns6_A           86 FLYTMKD   92 (100)
T ss_dssp             EEEESHH
T ss_pred             EEEECch
Confidence            9999854

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=2.9e-17  Score=126.35  Aligned_cols=87  Identities=24%  Similarity=0.521  Sum_probs=80.6

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEE
Q 016936          148 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  227 (380)
Q Consensus       148 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~  227 (380)
                      .....++|||+|||+.+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|++|+.. ++..+.|+.|.|.
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~   90 (105)
T 2dh8_A           12 GADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPK   90 (105)
T ss_dssp             CSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEE
Confidence            345568999999999999999999999999999999999988899999999999999999999998 9999999999999


Q ss_pred             EcccCCCC
Q 016936          228 RATASSGQ  235 (380)
Q Consensus       228 ~~~~~~~~  235 (380)
                      ++.++...
T Consensus        91 ~a~~~~~~   98 (105)
T 2dh8_A           91 PCTPRGMQ   98 (105)
T ss_dssp             CSCCSSCC
T ss_pred             EccCCCCC
Confidence            99876544

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A

Probab=99.72  E-value=4.9e-17  Score=120.54  Aligned_cols=79  Identities=24%  Similarity=0.572  Sum_probs=74.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      ...++|||+|||+.+++++|+++|++||.|..|+++.++.+++++|||||+|.+.++|++|++. ++..+.|+.|.|++|
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 EDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQ-KEHRLDGRVIDPKKA   87 (87)
T ss_dssp             SCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHS-SCEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHh-CCCEECCEEEEEEeC
Confidence            4457999999999999999999999999999999999988899999999999999999999975 888999999999875

>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=99.72  E-value=6.6e-17  Score=122.17  Aligned_cols=81  Identities=20%  Similarity=0.256  Sum_probs=74.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHH----HHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEE
Q 016936          150 EGPDRVFVGGLPYYFTETQIK----ELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  225 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~----~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~  225 (380)
                      ....+|||+|||+.+++++|+    ++|++||.|..|+++.++.+   +|||||+|.+.++|++|++.|||..+.|++|+
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            344799999999999999999    99999999999999988654   88999999999999999999999999999999


Q ss_pred             EEEcccCC
Q 016936          226 VRRATASS  233 (380)
Q Consensus       226 v~~~~~~~  233 (380)
                      |.++.+..
T Consensus        84 V~~a~~~~   91 (96)
T 2dgx_A           84 VSLATGAS   91 (96)
T ss_dssp             EEECCCSS
T ss_pred             EEEcCCCC
Confidence            99997653

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A

Probab=99.72  E-value=5.4e-17  Score=120.83  Aligned_cols=79  Identities=16%  Similarity=0.377  Sum_probs=75.9

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccC
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  232 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~  232 (380)
                      ++|||+|||..+++++|+++|++||.|..++++.++.+++++|||||+|.+.++|++|+ .+++..+.|+.|+|.++.+.
T Consensus         7 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~~~   85 (89)
T 3ucg_A            7 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKRTN   85 (89)
T ss_dssp             TEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETTTT
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEccCC
Confidence            69999999999999999999999999999999999888999999999999999999999 89999999999999998764

>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=99.72  E-value=8.5e-17  Score=133.30  Aligned_cols=150  Identities=17%  Similarity=0.145  Sum_probs=102.8

Q ss_pred             EEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccCCCCChhHHHHHHHHHHHHHHHHHHHhhh
Q 016936          181 GFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQT  260 (380)
Q Consensus       181 ~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  260 (380)
                      .+++..+  .+.++|||||+|.+.++|++|+..+++....+..+.+.........                         
T Consensus         2 ~~kl~ln--~~~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~-------------------------   54 (158)
T 2kn4_A            2 QYKLILN--GKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTV-------------------------   54 (158)
T ss_dssp             EEEEEEE--CSSCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEE-------------------------
T ss_pred             cEEEEec--CccccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCccccccc-------------------------
Confidence            3566666  3478999999999999999999887754332233322211100000                         


Q ss_pred             cCccccCCCCCccCCccceEEEEeccC-CcccCCChHHHHHHHHHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEE
Q 016936          261 SGMNTLGGGMSLFGETLAKVLCLTEAI-TADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLE  339 (380)
Q Consensus       261 ~~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~~~~~~~~~~~~~~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~  339 (380)
                        ..................+.+.|.. +.+           .++|+++|++||.|.+|.++.+..++. +  .|+|||+
T Consensus        55 --~~~~~~~~~~~~~~~~~~l~v~nl~~~~~-----------~~~l~~~F~~~G~v~~~~i~~~~~~g~-~--~g~afV~  118 (158)
T 2kn4_A           55 --TEGSHHHHHHMDVEGMTSLKVDNLTYRTS-----------PDTLRRVFEKYGRVGDVYIPRDRYTKE-S--RGFAFVR  118 (158)
T ss_dssp             --ECCCCCSSCCCCCCBCCEEEEESCCTTCC-----------HHHHHHHHHHHSCEEEEECCCCSSCTT-S--CCEEEEE
T ss_pred             --cccccccccccCCCCCCEEEEeCCCCCCC-----------HHHHHHHHHhcCCeEEEEEeecCCCCc-c--ceEEEEE
Confidence              0000000111123445677777643 222           269999999999999999998875554 3  4677999


Q ss_pred             eechhhHHHHHHHHcCcccCCeEEEEEecccccc
Q 016936          340 YYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKY  373 (380)
Q Consensus       340 f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~~~~  373 (380)
                      |.+.++|.+|++.|||..|+|++|+|.|+....-
T Consensus       119 f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  152 (158)
T 2kn4_A          119 FHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRP  152 (158)
T ss_dssp             ESBHHHHHHHHHHSTTEESSSSEEEEEEECCSSC
T ss_pred             ECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCC
Confidence            9999999999999999999999999999987643

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=1.3e-16  Score=122.26  Aligned_cols=85  Identities=27%  Similarity=0.397  Sum_probs=77.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      ....++|||+|||..+++++|+++|++||.|..|+++.++  +.++|||||+|.+.++|++|+..|++..+.|+.|+|.+
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            3455899999999999999999999999999999999985  44789999999999999999999999999999999999


Q ss_pred             cccCCCC
Q 016936          229 ATASSGQ  235 (380)
Q Consensus       229 ~~~~~~~  235 (380)
                      +.+....
T Consensus        90 a~~~~~~   96 (103)
T 2cqi_A           90 ATTPSSQ   96 (103)
T ss_dssp             CCCTTCC
T ss_pred             CCCCccc
Confidence            9876443

>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=99.71  E-value=3.8e-17  Score=136.37  Aligned_cols=141  Identities=20%  Similarity=0.177  Sum_probs=79.6

Q ss_pred             EEeCCHHHHHHHH-HcCCceec--CceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCC
Q 016936           85 VEMRTVEEASNAM-ALDGIIFE--GVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLP  161 (380)
Q Consensus        85 V~f~~~~~a~~ai-~l~~~~i~--g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp  161 (380)
                      .+|.+.++|..|+ .+++....  |+-....+........-.....+.+         ......+......++|||+|||
T Consensus        11 ee~e~~~d~e~~~~~~~~~~~~~kgr~~~~~~~~~~~~~~~~~~~~s~~---------~~~~~~~~~~~~~~~l~V~nLp   81 (165)
T 1rk8_A           11 EEFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDD---------DELEPGPQRSVEGWILFVTSIH   81 (165)
T ss_dssp             ----------------------------------------------------------------CCCCC-CEEEEEESCC
T ss_pred             hhhhccccccccchhhccccccccCCCCCCCccccccccCccccccCCC---------CCCCCCCCCCCCCCEEEEeCCC
Confidence            7899999999999 77775544  5555554422111000000000000         0000011122344789999999


Q ss_pred             CCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccCCC
Q 016936          162 YYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSG  234 (380)
Q Consensus       162 ~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~~~  234 (380)
                      +.+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|.+|+..|||..|.|+.|.|.++.....
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            9999999999999999999999999988999999999999999999999999999999999999999977643

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.71  E-value=5.7e-17  Score=123.28  Aligned_cols=80  Identities=25%  Similarity=0.431  Sum_probs=76.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeE--------EEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCe
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHG--------FDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDK  222 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~--------v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~  222 (380)
                      ..++|||+|||.++++++|+++|++||.|..        ++++.++.+++++|||||+|.+.++|++|++.|+|..+.|+
T Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~g~   91 (99)
T 2la6_A           12 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGN   91 (99)
T ss_dssp             CCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBSSSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCc
Confidence            3479999999999999999999999999999        99999988899999999999999999999999999999999


Q ss_pred             EEEEEEcc
Q 016936          223 TLTVRRAT  230 (380)
Q Consensus       223 ~i~v~~~~  230 (380)
                      .|+|++++
T Consensus        92 ~l~V~~A~   99 (99)
T 2la6_A           92 PIKVSFAT   99 (99)
T ss_dssp             BCEEEECC
T ss_pred             EEEEEecC
Confidence            99999873

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.71  E-value=6.2e-17  Score=124.04  Aligned_cols=85  Identities=25%  Similarity=0.502  Sum_probs=78.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      ....++|||+|||+.+++++|+++|++|| |..|+++.++.+++++|||||+|.+.++|++|+ .|++..+.|+.|+|.+
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            34457999999999999999999999997 999999999888999999999999999999999 7999999999999999


Q ss_pred             cccCCCC
Q 016936          229 ATASSGQ  235 (380)
Q Consensus       229 ~~~~~~~  235 (380)
                      +.++...
T Consensus        90 a~~~~~~   96 (103)
T 2dng_A           90 AEGRKQD   96 (103)
T ss_dssp             CCCCCCC
T ss_pred             ecCCCCC
Confidence            9776433

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A

Probab=99.71  E-value=8.1e-17  Score=123.81  Aligned_cols=85  Identities=24%  Similarity=0.384  Sum_probs=78.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCC---eEEEE
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD---KTLTV  226 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g---~~i~v  226 (380)
                      ...++|||+|||..+++++|+++|++||.|..|+++.++ ++.++|||||+|.+.++|++|++.|++..+.|   +.|+|
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            345799999999999999999999999999999999997 69999999999999999999999999999988   99999


Q ss_pred             EEcccCCCC
Q 016936          227 RRATASSGQ  235 (380)
Q Consensus       227 ~~~~~~~~~  235 (380)
                      .++......
T Consensus        92 ~~a~~~~~~  100 (105)
T 2dnh_A           92 KFADTDKES  100 (105)
T ss_dssp             EESCSSCCC
T ss_pred             EECccCccc
Confidence            999876443

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=4.5e-17  Score=125.50  Aligned_cols=82  Identities=26%  Similarity=0.359  Sum_probs=78.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      ..++|||+|||..+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|++|+..|+|..+.|+.|.|.++.
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            34689999999999999999999999999999999998889999999999999999999999999999999999999987


Q ss_pred             cC
Q 016936          231 AS  232 (380)
Q Consensus       231 ~~  232 (380)
                      ++
T Consensus       102 ~~  103 (106)
T 1p27_B          102 VR  103 (106)
T ss_dssp             ES
T ss_pred             CC
Confidence            65

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.71  E-value=9.1e-18  Score=135.13  Aligned_cols=124  Identities=19%  Similarity=0.302  Sum_probs=80.1

Q ss_pred             cEEEEEeCCHHHHHHHH-HcCCceecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcC
Q 016936           81 KFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGG  159 (380)
Q Consensus        81 g~afV~f~~~~~a~~ai-~l~~~~i~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~n  159 (380)
                      -++|.+|.+...+..|+ .+++....|+.- +.+.              .+               .......++|||+|
T Consensus         5 ~~~~~~~~~~~~~~~a~~~~~g~~~~g~~~-~~~~--------------~~---------------~~~~~~~~~l~V~n   54 (135)
T 2lea_A            5 HHHHHHSSGLVPRGSHMASMTGGQQMGRGS-MSYG--------------RP---------------PPDVEGMTSLKVDN   54 (135)
T ss_dssp             -------------------------------CCSC--------------CS---------------CSSGGGCCCEEEEC
T ss_pred             ccccccccCCCchhhhhhhccCCCCCCCCC-CCcC--------------CC---------------CCCCCCCCEEEEeC
Confidence            46788888888899999 677755444321 1110              00               01122346999999


Q ss_pred             CCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccCCC
Q 016936          160 LPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSG  234 (380)
Q Consensus       160 lp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~~~  234 (380)
                      ||..+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|++|+..|++..+.|+.|+|.++.+...
T Consensus        55 Lp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~~~  129 (135)
T 2lea_A           55 LTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRP  129 (135)
T ss_dssp             CCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCCCC
T ss_pred             CCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            999999999999999999999999999988899999999999999999999999999999999999999976543

>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=99.71  E-value=1.4e-17  Score=125.64  Aligned_cols=82  Identities=16%  Similarity=0.339  Sum_probs=75.4

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      ...+++|||+|||+.+++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++.||+..+.|+.|+|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~   91 (95)
T 2ek1_A           12 KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSG   91 (95)
T ss_dssp             ---CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEe
Confidence            34457999999999999999999999999999998888878899999999999999999999999999999999999998


Q ss_pred             cc
Q 016936          229 AT  230 (380)
Q Consensus       229 ~~  230 (380)
                      +.
T Consensus        92 a~   93 (95)
T 2ek1_A           92 PS   93 (95)
T ss_dssp             CC
T ss_pred             cc
Confidence            75

>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=99.71  E-value=3.3e-17  Score=124.37  Aligned_cols=84  Identities=15%  Similarity=0.322  Sum_probs=77.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      ....++|||+|||+.+++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++.|++..+.|+.|+|.+
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   91 (98)
T 2cqp_A           12 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   91 (98)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEE
Confidence            34457899999999999999999999999999888888878899999999999999999999999999999999999999


Q ss_pred             cccC
Q 016936          229 ATAS  232 (380)
Q Consensus       229 ~~~~  232 (380)
                      +..+
T Consensus        92 a~~~   95 (98)
T 2cqp_A           92 GSGP   95 (98)
T ss_dssp             SSCS
T ss_pred             cCCC
Confidence            8654

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=1.7e-16  Score=121.61  Aligned_cols=85  Identities=25%  Similarity=0.547  Sum_probs=77.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      ....++|||+|||..+++++|+++|++||.|..|+++.++  +.++|||||+|.+.++|++|+..|++..+.|+.|+|.+
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 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN   89 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT--TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecC--CCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4455899999999999999999999999999999999885  34899999999999999999999999999999999999


Q ss_pred             cccCCCC
Q 016936          229 ATASSGQ  235 (380)
Q Consensus       229 ~~~~~~~  235 (380)
                      +.++...
T Consensus        90 a~~~~~~   96 (103)
T 2cq3_A           90 ATARVMT   96 (103)
T ss_dssp             CCSSCCC
T ss_pred             cccCCCC
Confidence            9876443

>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=99.71  E-value=4.5e-17  Score=120.93  Aligned_cols=81  Identities=23%  Similarity=0.491  Sum_probs=75.7

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCC-CceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGN-SKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       152 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~-~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      +++|||+|||..+++++|+++|++||.|..+.++.++.++. ++|||||+|.+.++|++|++.|||..+.|+.|+|.++.
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            46999999999999999999999999999999999876655 89999999999999999999999999999999999986


Q ss_pred             cC
Q 016936          231 AS  232 (380)
Q Consensus       231 ~~  232 (380)
                      +.
T Consensus        84 ~~   85 (88)
T 4a8x_A           84 AP   85 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.71  E-value=6.1e-17  Score=125.64  Aligned_cols=83  Identities=28%  Similarity=0.340  Sum_probs=78.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      ..++|||+|||..+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|++|+..|+|..+.|+.|.|.++.
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            34789999999999999999999999999999999998889999999999999999999999999999999999999987


Q ss_pred             cCC
Q 016936          231 ASS  233 (380)
Q Consensus       231 ~~~  233 (380)
                      ++.
T Consensus       105 ~~~  107 (110)
T 1oo0_B          105 VKG  107 (110)
T ss_dssp             ESS
T ss_pred             cCC
Confidence            653

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=6.5e-17  Score=123.90  Aligned_cols=85  Identities=22%  Similarity=0.400  Sum_probs=78.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      ....++|||+|||+.+++++|+++|++||.|..|+++.+  ++.++|||||+|.+.++|++|++.|++..+.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2d9p_A           12 RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVAL   89 (103)
T ss_dssp             CSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            345579999999999999999999999999999999988  799999999999999999999999999999999999999


Q ss_pred             cccCCCC
Q 016936          229 ATASSGQ  235 (380)
Q Consensus       229 ~~~~~~~  235 (380)
                      +.++...
T Consensus        90 a~~~~~~   96 (103)
T 2d9p_A           90 AQRKEER   96 (103)
T ss_dssp             CSSCCCC
T ss_pred             ecccccC
Confidence            9876443

>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=99.71  E-value=6e-17  Score=124.35  Aligned_cols=84  Identities=27%  Similarity=0.492  Sum_probs=77.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCC-CCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDT-GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~-~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      ...++|||+|||+.+++++|+++|++|| |..|.++.++.+ ++++|||||+|.+.++|++|+ .|++..+.|+.|+|.+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~   90 (104)
T 1wi8_A           13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEEE
Confidence            4457999999999999999999999999 999999999877 899999999999999999999 8999999999999999


Q ss_pred             cccCCCC
Q 016936          229 ATASSGQ  235 (380)
Q Consensus       229 ~~~~~~~  235 (380)
                      +.++...
T Consensus        91 a~~~~~~   97 (104)
T 1wi8_A           91 ADQAQDK   97 (104)
T ss_dssp             CCCCCCC
T ss_pred             ccCCCCC
Confidence            9876543

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.71  E-value=7.4e-17  Score=120.89  Aligned_cols=82  Identities=30%  Similarity=0.589  Sum_probs=76.5

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      ...++|||+|||..+++++|+++|++||.|..+++.++  +++++|||||+|.+.++|++|++.|++..+.|+.|+|.++
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  7899999999999999999999999999999999999998


Q ss_pred             ccCC
Q 016936          230 TASS  233 (380)
Q Consensus       230 ~~~~  233 (380)
                      .+..
T Consensus        84 ~~~~   87 (92)
T 2dgv_A           84 RNAS   87 (92)
T ss_dssp             SCCS
T ss_pred             CCCC
Confidence            7654

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=8.9e-17  Score=125.32  Aligned_cols=85  Identities=21%  Similarity=0.368  Sum_probs=79.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCee--------EEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCC
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLH--------GFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD  221 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~--------~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g  221 (380)
                      ...++|||+|||..+++++|+++|++||.|.        .|+++.++.+++++|||||+|.+.++|++|++.||+..+.|
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            4457999999999999999999999999999        69999998889999999999999999999999999999999


Q ss_pred             eEEEEEEcccCCC
Q 016936          222 KTLTVRRATASSG  234 (380)
Q Consensus       222 ~~i~v~~~~~~~~  234 (380)
                      +.|+|.++..+..
T Consensus        93 ~~l~V~~a~~~~~  105 (113)
T 2cpe_A           93 SKLKVSLARKKPP  105 (113)
T ss_dssp             EECEEECSSCCCC
T ss_pred             CEEEEEECCCCCC
Confidence            9999999877643

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.70  E-value=9.3e-17  Score=126.23  Aligned_cols=82  Identities=28%  Similarity=0.498  Sum_probs=77.4

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEE
Q 016936          148 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  227 (380)
Q Consensus       148 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~  227 (380)
                      .....++|||+|||+++++++|+++|++||.|..|++++++.+++++|||||+|.+.++|++|++.||+..+.|+.|+|+
T Consensus        36 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~  115 (118)
T 2khc_A           36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQ  115 (118)
T ss_dssp             CCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34455899999999999999999999999999999999998889999999999999999999999999999999999999


Q ss_pred             Ec
Q 016936          228 RA  229 (380)
Q Consensus       228 ~~  229 (380)
                      ++
T Consensus       116 ~a  117 (118)
T 2khc_A          116 LK  117 (118)
T ss_dssp             EC
T ss_pred             ec
Confidence            86

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens}

Probab=99.70  E-value=7.7e-17  Score=126.19  Aligned_cols=83  Identities=30%  Similarity=0.572  Sum_probs=78.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      ...++|||+|||..+++++|+++|++||.|..|.+..++ +++++|||||+|.+.++|++|++.|+|..+.|+.|.|.++
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            344799999999999999999999999999999999997 8999999999999999999999999999999999999999


Q ss_pred             ccCC
Q 016936          230 TASS  233 (380)
Q Consensus       230 ~~~~  233 (380)
                      ....
T Consensus        84 ~~~~   87 (116)
T 2fy1_A           84 KKPS   87 (116)
T ss_dssp             CCSS
T ss_pred             CCCC
Confidence            7654

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=1.2e-16  Score=125.24  Aligned_cols=83  Identities=33%  Similarity=0.605  Sum_probs=77.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      ....++|||+|||..+++++|+++|++||.|..|++++++.+++++|||||+|.+.++|++|++.+++ .+.|+.|+|.+
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~~   92 (116)
T 2cqd_A           14 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNL   92 (116)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEEE
Confidence            34458999999999999999999999999999999999988899999999999999999999999998 89999999999


Q ss_pred             cccC
Q 016936          229 ATAS  232 (380)
Q Consensus       229 ~~~~  232 (380)
                      +...
T Consensus        93 a~~~   96 (116)
T 2cqd_A           93 AYLG   96 (116)
T ss_dssp             STTT
T ss_pred             cccC
Confidence            8654

>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=99.70  E-value=1.2e-16  Score=123.40  Aligned_cols=82  Identities=26%  Similarity=0.415  Sum_probs=77.2

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEE
Q 016936          148 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  227 (380)
Q Consensus       148 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~  227 (380)
                      .....++|||+|||+.+++++|+++|++||.|..|.++.++ ++.++|||||+|.+.++|++|++.|++..+.|+.|+|.
T Consensus        25 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~  103 (107)
T 3ulh_A           25 GVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQ  103 (107)
T ss_dssp             CCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            34556799999999999999999999999999999999998 89999999999999999999999999999999999999


Q ss_pred             Ecc
Q 016936          228 RAT  230 (380)
Q Consensus       228 ~~~  230 (380)
                      ++.
T Consensus       104 ~a~  106 (107)
T 3ulh_A          104 LVT  106 (107)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            975

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.70  E-value=7.7e-17  Score=116.76  Aligned_cols=73  Identities=18%  Similarity=0.301  Sum_probs=69.0

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       152 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      +..|||+||++.+++++|+++|.+||+|.++++..      ++|||||+|.++++|.+|++.||+..+.|+.|+|.++.
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            46899999999999999999999999999999854      58999999999999999999999999999999999984

>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=99.70  E-value=1.4e-16  Score=130.87  Aligned_cols=139  Identities=22%  Similarity=0.218  Sum_probs=104.5

Q ss_pred             CCCCceEEEEEEcChhHHHHHHHHh-CCCeeCCeEEEEEEcccCCCCChhHHHHHHHHHHHHHHHHHHHhhhcCccccCC
Q 016936          190 TGNSKGYGFCVYQDPAVTDIACAAL-NGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGG  268 (380)
Q Consensus       190 ~~~~~g~afV~f~~~~~A~~Ai~~l-~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  268 (380)
                      ....+|+++|+|.+.++|++|++.+ +|..+.| .|.+.++........                        .......
T Consensus         9 g~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~------------------------~~~~~~~   63 (150)
T 2i2y_A            9 GKTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTE------------------------GSHHHHH   63 (150)
T ss_dssp             CSSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEEC------------------------SSSSCCC
T ss_pred             cccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCcccccc------------------------ccccccc
Confidence            3567899999999999999999999 9999999 999998754211000                        0000001


Q ss_pred             CCCccCCccceEEEEeccC-CcccCCChHHHHHHHHHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHH
Q 016936          269 GMSLFGETLAKVLCLTEAI-TADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCA  347 (380)
Q Consensus       269 ~~~~~~~~~~~~~~l~~~~-~~~~~~~~~~~~~~~~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~  347 (380)
                      ........+.+.+.+.|.. +.++           ++|+++|++||.|.+|.+++++      +  |+|||+|.+.++|.
T Consensus        64 ~~~~~~~~~~~~l~V~nl~~~~t~-----------~~l~~~F~~~G~i~~v~i~~~~------~--g~afV~f~~~~~a~  124 (150)
T 2i2y_A           64 HMHRDSCPLDCKVYVGNLGNNGNK-----------TELERAFGYYGPLRSVWVARNP------P--GFAFVEFEDPRDAA  124 (150)
T ss_dssp             CSCSSSSTTSCEEEEESCCSCCSC-----------HHHHHHHHHHSCEEEEEECSSS------C--SEEEEEESSHHHHH
T ss_pred             cccccCCCCCCEEEEeCCCCCCCH-----------HHHHHHHHhhCCEEEEEEeeCC------C--cEEEEEECCHHHHH
Confidence            1111224455667777743 3322           6999999999999999998762      2  67899999999999


Q ss_pred             HHHHHHcCcccCCeEEEEEeccccc
Q 016936          348 TAKNALSGRKFGGNTVNAFYYPEDK  372 (380)
Q Consensus       348 ~A~~~l~g~~i~gr~l~v~~~~~~~  372 (380)
                      +|++.|||..|+|++|+|+|+...+
T Consensus       125 ~A~~~l~g~~~~g~~l~v~~a~~~~  149 (150)
T 2i2y_A          125 DAVRELDGRTLCGCRVRVELSNGEK  149 (150)
T ss_dssp             HHHHHHSSSCSSSSCCEEEECCCCC
T ss_pred             HHHHHcCCCEECCeEEEEEEcCCCC
Confidence            9999999999999999999997653

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.70  E-value=2e-16  Score=123.58  Aligned_cols=83  Identities=23%  Similarity=0.372  Sum_probs=77.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      ....++|||+|||..+++++|+++|++||.|..|+++.++ +++++|||||+|.+.++|++|++.|++..+.|+.|+|.+
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            3445799999999999999999999999999999999997 599999999999999999999999999999999999999


Q ss_pred             cccC
Q 016936          229 ATAS  232 (380)
Q Consensus       229 ~~~~  232 (380)
                      +...
T Consensus        91 a~~~   94 (114)
T 2do0_A           91 DERA   94 (114)
T ss_dssp             CSCC
T ss_pred             cccC
Confidence            8654

>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=99.70  E-value=2.2e-16  Score=120.96  Aligned_cols=85  Identities=24%  Similarity=0.393  Sum_probs=78.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      ....++|||+|||+.+++++|+++|++||.|..|+++.++.++.++|||||+|.+.++|++|+.  ++..+.|+.|.|.+
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            4455799999999999999999999999999999999998889999999999999999999998  47899999999999


Q ss_pred             cccCCCC
Q 016936          229 ATASSGQ  235 (380)
Q Consensus       229 ~~~~~~~  235 (380)
                      +.++...
T Consensus        90 a~~~~~~   96 (103)
T 2cqg_A           90 PNSKQSQ   96 (103)
T ss_dssp             CCTTCCC
T ss_pred             cCCCCcC
Confidence            9876543

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=3.1e-17  Score=125.33  Aligned_cols=77  Identities=22%  Similarity=0.266  Sum_probs=73.5

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       152 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      .++|||+|||+++++++|+++|++||.|..|.+++++. ++++|||||+|.+.++|++|+. +++..+.|+.|.|.++.
T Consensus        11 ~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~~   87 (103)
T 1s79_A           11 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   87 (103)
T ss_dssp             GGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEch
Confidence            36999999999999999999999999999999999986 9999999999999999999999 89999999999999864

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A

Probab=99.70  E-value=5.5e-17  Score=129.42  Aligned_cols=84  Identities=20%  Similarity=0.397  Sum_probs=79.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      ....++|||+|||..+++++|+++|++||.|..|+++.++.+++++|||||+|.+.++|++|++.|++..+.|++|.|.+
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            44557999999999999999999999999999999999988899999999999999999999999999999999999999


Q ss_pred             cccC
Q 016936          229 ATAS  232 (380)
Q Consensus       229 ~~~~  232 (380)
                      +.++
T Consensus       123 a~~~  126 (129)
T 2kxn_B          123 SITK  126 (129)
T ss_dssp             CSSS
T ss_pred             ecCC
Confidence            8765

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.70  E-value=2.4e-17  Score=118.55  Aligned_cols=75  Identities=25%  Similarity=0.585  Sum_probs=71.9

Q ss_pred             EEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       154 ~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      +|||+|||+.+++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++ +++..+.|++|+|++|
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            58999999999999999999999999999999998889999999999999999999998 8999999999999875

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.69  E-value=7.9e-17  Score=124.69  Aligned_cols=85  Identities=26%  Similarity=0.437  Sum_probs=77.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      ...++|||+|||..+++++|+++|+.||.|..|++++++.+|+++|||||+|.+.++|++|+..+ +..+.|+.|.|.++
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            44579999999999999999999999999999999999888999999999999999999999975 59999999999999


Q ss_pred             ccCCCC
Q 016936          230 TASSGQ  235 (380)
Q Consensus       230 ~~~~~~  235 (380)
                      .++..+
T Consensus       102 ~~~~~~  107 (109)
T 2rs2_A          102 FPRRAQ  107 (109)
T ss_dssp             CCCCCC
T ss_pred             cCCCCC
Confidence            876544

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.69  E-value=9.3e-17  Score=132.29  Aligned_cols=81  Identities=25%  Similarity=0.430  Sum_probs=76.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcC--CeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFG--TLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G--~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      ..++|||+|||+++++++|+++|++||  .|..|+++.++.+|+++|||||+|.+.++|++|++.|||..+.|+.|.|.+
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  999999999988999999999999999999999999999999999999999


Q ss_pred             ccc
Q 016936          229 ATA  231 (380)
Q Consensus       229 ~~~  231 (380)
                      +.+
T Consensus       134 a~~  136 (156)
T 3n9u_C          134 ATR  136 (156)
T ss_dssp             CCH
T ss_pred             cCC
Confidence            853

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.69  E-value=7.4e-17  Score=123.83  Aligned_cols=84  Identities=26%  Similarity=0.403  Sum_probs=78.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHh-cCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCe-eCCeEEEEEE
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLES-FGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLK-MGDKTLTVRR  228 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~-~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~-~~g~~i~v~~  228 (380)
                      ..++|||+|||+.+++++|+++|++ ||.|..|+++.++ ++.++|||||+|.+.++|.+|++.|++.. +.|+.|+|.+
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~~   86 (104)
T 2dhg_A            8 PEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSV   86 (104)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCCB
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEEE
Confidence            3479999999999999999999999 9999999999998 89999999999999999999999999999 9999999999


Q ss_pred             cccCCCC
Q 016936          229 ATASSGQ  235 (380)
Q Consensus       229 ~~~~~~~  235 (380)
                      +.++...
T Consensus        87 a~~~~~~   93 (104)
T 2dhg_A           87 AIPKASR   93 (104)
T ss_dssp             CCCCCSC
T ss_pred             ccCCCcC
Confidence            8766433

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.69  E-value=1.9e-16  Score=128.29  Aligned_cols=87  Identities=30%  Similarity=0.521  Sum_probs=81.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      ....++|||+|||..+++++|+++|+.||.|..|+++.++.+++++|||||+|.+.++|.+|++.|++..+.|+.|+|.+
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            44558999999999999999999999999999999999988899999999999999999999999999999999999999


Q ss_pred             cccCCCC
Q 016936          229 ATASSGQ  235 (380)
Q Consensus       229 ~~~~~~~  235 (380)
                      +.+....
T Consensus       119 a~~~~~~  125 (139)
T 1u6f_A          119 AASGHQR  125 (139)
T ss_dssp             SSCCCCC
T ss_pred             CCCCCCC
Confidence            9876443

>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=99.69  E-value=6.9e-17  Score=123.98  Aligned_cols=80  Identities=43%  Similarity=0.746  Sum_probs=76.8

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccC
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  232 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~  232 (380)
                      ++|||+|||..+++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|++|++.|+|..+.|+.|+|.++.+.
T Consensus         9 ~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   88 (104)
T 1p1t_A            9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASE   88 (104)
T ss_dssp             SCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTCT
T ss_pred             cEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCCCc
Confidence            69999999999999999999999999999999999888999999999999999999999999999999999999998654

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=3.1e-16  Score=117.22  Aligned_cols=81  Identities=23%  Similarity=0.365  Sum_probs=75.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      ...++|||+|||+.+++++|+++|+.| .|..|+++.+ .+|+++|||||+|.+.++|++|+. +++..+.|+.|.|.++
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            345799999999999999999999999 9999999999 579999999999999999999999 9999999999999998


Q ss_pred             ccCC
Q 016936          230 TASS  233 (380)
Q Consensus       230 ~~~~  233 (380)
                      ..+.
T Consensus        85 ~~~~   88 (91)
T 2dgw_A           85 KSGP   88 (91)
T ss_dssp             SSCC
T ss_pred             CcCC
Confidence            7653

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=1.3e-16  Score=121.22  Aligned_cols=79  Identities=13%  Similarity=0.172  Sum_probs=71.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhC--CCeeCCeEEEEEE
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN--GLKMGDKTLTVRR  228 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~--g~~~~g~~i~v~~  228 (380)
                      ..++|||+|||+++++++|+++|++||.|.+|+++++      +|||||+|.+.++|++|++.++  +..+.|++|+|.+
T Consensus        15 ~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~   88 (105)
T 1sjq_A           15 PSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQF   88 (105)
T ss_dssp             CCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEE
Confidence            3479999999999999999999999999999999865      6899999999999999999886  4789999999999


Q ss_pred             cccCCCC
Q 016936          229 ATASSGQ  235 (380)
Q Consensus       229 ~~~~~~~  235 (380)
                      +..+...
T Consensus        89 A~~~~~~   95 (105)
T 1sjq_A           89 SNHKELK   95 (105)
T ss_dssp             CSSSSCC
T ss_pred             cCCCCCC
Confidence            9876444

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.68  E-value=2.6e-16  Score=127.56  Aligned_cols=83  Identities=20%  Similarity=0.365  Sum_probs=77.4

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEE
Q 016936          147 GGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  226 (380)
Q Consensus       147 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v  226 (380)
                      ......++|||+|||..+++++|+++|++||.|..+++++++.+++++|||||+|.+.++|++|++.|++..+.|+.|+|
T Consensus        58 ~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  137 (140)
T 2ku7_A           58 GSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRV  137 (140)
T ss_dssp             SSCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEE
T ss_pred             CCCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            34556689999999999999999999999999999999999888999999999999999999999999999999999999


Q ss_pred             EEc
Q 016936          227 RRA  229 (380)
Q Consensus       227 ~~~  229 (380)
                      ++|
T Consensus       138 ~~A  140 (140)
T 2ku7_A          138 NLA  140 (140)
T ss_dssp             EC-
T ss_pred             EeC
Confidence            875

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=1.4e-17  Score=122.86  Aligned_cols=80  Identities=21%  Similarity=0.424  Sum_probs=75.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      ..++|||+|||+.+++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|++|++.|||..+.|+.+++.+..
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~~   83 (85)
T 1x4e_A            4 GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGPS   83 (85)
T ss_dssp             CCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCCC
Confidence            45799999999999999999999999999999999998889999999999999999999999999999999999887653

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.68  E-value=1.3e-16  Score=115.53  Aligned_cols=73  Identities=18%  Similarity=0.223  Sum_probs=69.0

Q ss_pred             ccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecCceE
Q 016936           31 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  109 (380)
Q Consensus        31 ~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g~~i  109 (380)
                      .+.-|||+||++++||++|+++|.+||+            |.++.+..++|||||+|.++++|.+|+ .||+..+.|++|
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~------------V~~~~l~~~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I   73 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGP------------LVSFHPYLNQGIALCKYTTREEANKAQMALNNCVLANTTI   73 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSC------------EEEEEEETTTTEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCC------------EEEEEEcCCCcEEEEEECCHHHHHHHHHHhcCCEECCcEE
Confidence            3678999999999999999999999998            888999999999999999999999999 899999999999


Q ss_pred             EEecCC
Q 016936          110 RVRRPT  115 (380)
Q Consensus       110 ~v~~~~  115 (380)
                      +|..+.
T Consensus        74 ~V~~A~   79 (89)
T 2wbr_A           74 FAESPS   79 (89)
T ss_dssp             EEECCC
T ss_pred             EEEECC
Confidence            999874

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=1.6e-16  Score=122.98  Aligned_cols=82  Identities=26%  Similarity=0.585  Sum_probs=75.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      ....++|||+|||..+++++|+++|++||.|..|++..++  +.++|||||+|.+.++|++|++.|+|..+.|+.|+|.+
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            4455899999999999999999999999999999999884  45899999999999999999999999999999999999


Q ss_pred             cccC
Q 016936          229 ATAS  232 (380)
Q Consensus       229 ~~~~  232 (380)
                      +.++
T Consensus       104 a~~~  107 (109)
T 2err_A          104 ATAR  107 (109)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            8764

>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=99.68  E-value=1.3e-16  Score=124.76  Aligned_cols=78  Identities=19%  Similarity=0.398  Sum_probs=72.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      ..++|||+|||..+++++|+++|++||.|..|.++.+   +.++|||||+|.+.++|.+|+..|||..+.|+.|.|.++.
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   83 (115)
T 3lqv_A            7 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYN   83 (115)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEec
Confidence            3479999999999999999999999999999999875   5568999999999999999999999999999999999986


Q ss_pred             c
Q 016936          231 A  231 (380)
Q Consensus       231 ~  231 (380)
                      +
T Consensus        84 ~   84 (115)
T 3lqv_A           84 A   84 (115)
T ss_dssp             H
T ss_pred             C
Confidence            4

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.68  E-value=5.1e-16  Score=123.11  Aligned_cols=85  Identities=21%  Similarity=0.345  Sum_probs=79.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      ....++|||+|||..+++++|+++|++||.|..|++..++ +++++|||||+|.+.++|++|+..|++..+.|+.|+|.+
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            4555799999999999999999999999999999999997 899999999999999999999999999999999999999


Q ss_pred             cccCCC
Q 016936          229 ATASSG  234 (380)
Q Consensus       229 ~~~~~~  234 (380)
                      +.....
T Consensus       111 a~~~~~  116 (124)
T 2kt5_A          111 VASQID  116 (124)
T ss_dssp             ECCTTC
T ss_pred             eCCCCC
Confidence            876543

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.68  E-value=4.8e-17  Score=117.57  Aligned_cols=76  Identities=28%  Similarity=0.494  Sum_probs=72.9

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      ++|||+|||..+++++|+++|++||.|..+.+++++.+++++|+|||+|.+.++|++|++.++ ..+.|+.|+|+++
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            379999999999999999999999999999999998889999999999999999999999998 9999999999986

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.68  E-value=2.4e-16  Score=118.46  Aligned_cols=77  Identities=17%  Similarity=0.161  Sum_probs=69.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCe--eCCeEEEEE
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLK--MGDKTLTVR  227 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~--~~g~~i~v~  227 (380)
                      ..+++|||+|||.++++++|+++|++||.|.+++++++      +|+|||+|.+.++|.+|++.+++..  +.|++|.|.
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            34479999999999999999999999999999999753      6799999999999999999999875  789999999


Q ss_pred             EcccC
Q 016936          228 RATAS  232 (380)
Q Consensus       228 ~~~~~  232 (380)
                      ++..+
T Consensus        93 ~S~~k   97 (100)
T 3r27_A           93 YSTSQ   97 (100)
T ss_dssp             ECSCS
T ss_pred             ecccc
Confidence            98764

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.68  E-value=5.2e-17  Score=130.12  Aligned_cols=84  Identities=21%  Similarity=0.288  Sum_probs=78.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeE--EEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCC----eeCCe
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHG--FDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGL----KMGDK  222 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~--v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~----~~~g~  222 (380)
                      ....++|||+|||+.+++++|+++|++||.|..  |++++++.+|+++|||||+|.+. +|.+|+..|||.    .+.|+
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            345579999999999999999999999999976  99999988999999999999999 999999999999    99999


Q ss_pred             EEEEEEcccCC
Q 016936          223 TLTVRRATASS  233 (380)
Q Consensus       223 ~i~v~~~~~~~  233 (380)
                      .|.|.++.+..
T Consensus        99 ~l~V~~a~~~~  109 (131)
T 2m2b_A           99 TINVEFAKGSK  109 (131)
T ss_dssp             CCCCEECCCSC
T ss_pred             EEEEEECCCCC
Confidence            99999997653

>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=99.68  E-value=1.8e-16  Score=126.06  Aligned_cols=85  Identities=25%  Similarity=0.341  Sum_probs=79.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      ..++|||+|||+.+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|++|++.||+..+.|+.|.|.++.
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            34799999999999999999999999999999999998889999999999999999999999999999999999999998


Q ss_pred             cCCCC
Q 016936          231 ASSGQ  235 (380)
Q Consensus       231 ~~~~~  235 (380)
                      .....
T Consensus       101 ~~~~~  105 (126)
T 3ex7_B          101 VRGPP  105 (126)
T ss_dssp             ESSSC
T ss_pred             CCCCC
Confidence            76544

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=1.4e-16  Score=120.96  Aligned_cols=78  Identities=19%  Similarity=0.223  Sum_probs=70.4

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcC--Cceec
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALD--GIIFE  105 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~--~~~i~  105 (380)
                      ..+.++|||+|||+++|+++|+++|++||.            |.++.+.+++|||||+|.+.++|++|+ .++  +..+.
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~------------V~~v~i~~~kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~   80 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGK------------VTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLR   80 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCC------------EEEEEEETTTTEEEEEESSHHHHHHHHHHHTTSCCEET
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------EEEEEEEcCCCEEEEEECCHHHHHHHHHHhccCCceEC
Confidence            456799999999999999999999999998            888888889999999999999999999 575  47899


Q ss_pred             CceEEEecCCCCC
Q 016936          106 GVAVRVRRPTDYN  118 (380)
Q Consensus       106 g~~i~v~~~~~~~  118 (380)
                      |++|+|.++..+.
T Consensus        81 Gr~l~V~~A~~~~   93 (105)
T 1sjq_A           81 GQPIYIQFSNHKE   93 (105)
T ss_dssp             TEECCBCCCSSSS
T ss_pred             CEEEEEEEcCCCC
Confidence            9999999986654

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=5.1e-16  Score=120.19  Aligned_cols=84  Identities=20%  Similarity=0.411  Sum_probs=75.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      ....++|||+|||..+++++|+++|++||.|..|.+..+   +.++|||||+|.+.++|++|++.||+..+.|+.|+|.+
T Consensus        19 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   95 (109)
T 1x4a_A           19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF   95 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            344579999999999999999999999999999999654   56899999999999999999999999999999999999


Q ss_pred             cccCCCC
Q 016936          229 ATASSGQ  235 (380)
Q Consensus       229 ~~~~~~~  235 (380)
                      +.+....
T Consensus        96 a~~~~~~  102 (109)
T 1x4a_A           96 PRSGRGT  102 (109)
T ss_dssp             CCCCCCC
T ss_pred             cccCCCC
Confidence            9776433

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.67  E-value=8.2e-17  Score=122.87  Aligned_cols=74  Identities=34%  Similarity=0.468  Sum_probs=66.9

Q ss_pred             ceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecC-CCcEEEEEeCCHHHHHHHH-HcCCceecCceEE
Q 016936           33 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH-EKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVR  110 (380)
Q Consensus        33 ~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~-~~g~afV~f~~~~~a~~ai-~l~~~~i~g~~i~  110 (380)
                      ++|||+|||+++++++|+++|++||.            |..+.+.. ++|||||+|.+.++|++|+ .+++..+.|++|+
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            58999999999999999999999997            66666665 4999999999999999999 6999999999999


Q ss_pred             EecCCCCC
Q 016936          111 VRRPTDYN  118 (380)
Q Consensus       111 v~~~~~~~  118 (380)
                      |.++....
T Consensus        69 V~~a~~~~   76 (101)
T 2hvz_A           69 VELSTGMP   76 (101)
T ss_dssp             EEESSSCC
T ss_pred             EEEccCCC
Confidence            99977654

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=1.6e-16  Score=124.04  Aligned_cols=78  Identities=18%  Similarity=0.368  Sum_probs=75.1

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEccc
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  231 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~  231 (380)
                      ++|||+|||..+++++|+++|++||.|..|+++.++.++.++|||||+|.+.++|++|+ .|++..+.|+.|+|.++.+
T Consensus        26 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~  103 (114)
T 2cq4_A           26 RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQA  103 (114)
T ss_dssp             TEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHHH
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEecCC
Confidence            79999999999999999999999999999999999888999999999999999999999 8999999999999999854

>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=99.67  E-value=3.3e-17  Score=122.26  Aligned_cols=79  Identities=33%  Similarity=0.567  Sum_probs=74.0

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccC
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  232 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~  232 (380)
                      ++|||+|||..+++++|+++|++||.|..+.+.+++.+++++|||||+|.+.+ |.+|+..|||..+.|+.|+|.++.+.
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            58999999999999999999999999999999999888999999999999999 99999999999999999999998765

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.67  E-value=1.2e-16  Score=120.09  Aligned_cols=79  Identities=22%  Similarity=0.156  Sum_probs=71.3

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCce--e
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGII--F  104 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~--i  104 (380)
                      ...++++|||+|||.++|+++|+++|++||.            |.++.+.++||+|||+|.+.++|.+|+ .+++..  +
T Consensus        17 ~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~------------V~~v~i~~~kg~AFVef~~~~~A~~Av~~ln~~~~~i   84 (100)
T 3r27_A           17 KTPASPVVHIRGLIDGVVEADLVEALQEFGP------------ISYVVVMPKKRQALVEFEDVLGACNAVNYAADNQIYI   84 (100)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHGGGSC------------EEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCEEE
T ss_pred             cCCCCcEEEEeCCCCCCCHHHHHHHHhccCC------------EEEEEEEcCCCEEEEEECCHHHHHHHHHHhcCCCcee
Confidence            4567899999999999999999999999998            888888889999999999999999999 788764  7


Q ss_pred             cCceEEEecCCCCC
Q 016936          105 EGVAVRVRRPTDYN  118 (380)
Q Consensus       105 ~g~~i~v~~~~~~~  118 (380)
                      .|++|+|.++..++
T Consensus        85 ~Gr~i~V~~S~~k~   98 (100)
T 3r27_A           85 AGHPAFVNYSTSQK   98 (100)
T ss_dssp             TTEEEEEEECSCSC
T ss_pred             CCcEEEEEeccccc
Confidence            89999999977653

>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=99.67  E-value=1.2e-16  Score=121.32  Aligned_cols=77  Identities=19%  Similarity=0.357  Sum_probs=66.7

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe------cCCCcEEEEEeCCHHHHHHHH-Hc
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-AL   99 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~------~~~~g~afV~f~~~~~a~~ai-~l   99 (380)
                      ..-...++|||+|||+++|+++|+++|++||.            |.++.+      +.++|||||+|.+.++|.+|+ .+
T Consensus        14 n~~~~gt~lfV~nLp~~~te~~L~~~F~~~G~------------I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~l   81 (99)
T 4fxv_A           14 NLYFQGTNLIVNYLPQNMTQDELRSLFSSIGE------------VESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL   81 (99)
T ss_dssp             --CCCCSEEEEESCCTTCCHHHHHHHHHTTSC------------EEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHH
T ss_pred             cccCCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------EEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHh
Confidence            34456789999999999999999999999998            555554      345789999999999999999 79


Q ss_pred             CCceecCceEEEecCC
Q 016936          100 DGIIFEGVAVRVRRPT  115 (380)
Q Consensus       100 ~~~~i~g~~i~v~~~~  115 (380)
                      |+..|.|++|+|.|+.
T Consensus        82 ng~~~~gr~l~V~~Ak   97 (99)
T 4fxv_A           82 NGLRLQSKTIKVSYAR   97 (99)
T ss_dssp             TTCEETTEECEEEECC
T ss_pred             CCCEECCEEEEEEEee
Confidence            9999999999999864

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.67  E-value=2e-16  Score=122.87  Aligned_cols=83  Identities=18%  Similarity=0.281  Sum_probs=76.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHH---HHHHhcCCeeEEEEeeCCCCC---CCceEEEEEEcChhHHHHHHHHhCCCeeCCeEE
Q 016936          151 GPDRVFVGGLPYYFTETQIK---ELLESFGTLHGFDLVKDRDTG---NSKGYGFCVYQDPAVTDIACAALNGLKMGDKTL  224 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~---~~F~~~G~i~~v~l~~~~~~~---~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i  224 (380)
                      ..++|||+|||+.+++++|+   ++|++||.|..|.+++++.++   +++|||||+|.+.++|++|++.||+..+.|+.|
T Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~l   93 (111)
T 2cpi_A           14 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   93 (111)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCEEE
Confidence            44799999999999999999   999999999999999886543   566999999999999999999999999999999


Q ss_pred             EEEEcccCC
Q 016936          225 TVRRATASS  233 (380)
Q Consensus       225 ~v~~~~~~~  233 (380)
                      +|.++.++.
T Consensus        94 ~V~~a~~k~  102 (111)
T 2cpi_A           94 KASLGTTKY  102 (111)
T ss_dssp             EEESCCCCS
T ss_pred             EEEeccccc
Confidence            999998764

>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=99.67  E-value=6.3e-16  Score=127.75  Aligned_cols=85  Identities=24%  Similarity=0.372  Sum_probs=79.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      ...++|||+|||..+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++|++.|++..+.|+.|+|.++
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            34579999999999999999999999999999999999888999999999999999999999999999999999999999


Q ss_pred             ccCCC
Q 016936          230 TASSG  234 (380)
Q Consensus       230 ~~~~~  234 (380)
                      .+...
T Consensus       117 ~~~~~  121 (156)
T 1h2v_Z          117 AGFKE  121 (156)
T ss_dssp             SCCCT
T ss_pred             CCCCC
Confidence            87543

>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=99.66  E-value=1.9e-16  Score=123.64  Aligned_cols=81  Identities=12%  Similarity=0.215  Sum_probs=75.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCe-eEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTL-HGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  227 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i-~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~  227 (380)
                      ....++|||+|||+.+++++|+++|+.||.| ..|+++.++ +++++|||||+|.+.++|++|++. ++..+.|+.|.|.
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            3445799999999999999999999999999 899999998 899999999999999999999997 9999999999999


Q ss_pred             Eccc
Q 016936          228 RATA  231 (380)
Q Consensus       228 ~~~~  231 (380)
                      ++..
T Consensus        90 ~a~~   93 (114)
T 2cpy_A           90 VVTL   93 (114)
T ss_dssp             EECH
T ss_pred             ECCH
Confidence            9853

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=2.6e-16  Score=123.30  Aligned_cols=82  Identities=27%  Similarity=0.518  Sum_probs=77.8

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccC
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  232 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~  232 (380)
                      ++|||+|||..+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|++|+.. ++..+.|+.|+|.++.++
T Consensus        28 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a~~~  106 (116)
T 1x4b_A           28 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAVAR  106 (116)
T ss_dssp             TEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECCCC
Confidence            7999999999999999999999999999999999988899999999999999999999998 999999999999999876


Q ss_pred             CCC
Q 016936          233 SGQ  235 (380)
Q Consensus       233 ~~~  235 (380)
                      ...
T Consensus       107 ~~~  109 (116)
T 1x4b_A          107 EES  109 (116)
T ss_dssp             CCC
T ss_pred             ccC
Confidence            543

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=5.8e-16  Score=117.54  Aligned_cols=79  Identities=14%  Similarity=0.140  Sum_probs=70.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHh--CCCeeCCeEEEEE
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL--NGLKMGDKTLTVR  227 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l--~g~~~~g~~i~v~  227 (380)
                      ...++|||+|||+.+++++|+++|++||.|..|.++++      +|||||+|.+.++|.+|++.+  ++..+.|++|.|.
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            34579999999999999999999999999999988764      689999999999999999976  4678999999999


Q ss_pred             EcccCCC
Q 016936          228 RATASSG  234 (380)
Q Consensus       228 ~~~~~~~  234 (380)
                      ++..+..
T Consensus        87 ~a~~~~~   93 (101)
T 2cq1_A           87 YSNHKEL   93 (101)
T ss_dssp             ECSCSSC
T ss_pred             EcCcccC
Confidence            9986643

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.66  E-value=4.2e-16  Score=119.78  Aligned_cols=80  Identities=24%  Similarity=0.344  Sum_probs=73.9

Q ss_pred             CCEEEEcCCCCCC------CHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCe-EE
Q 016936          152 PDRVFVGGLPYYF------TETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDK-TL  224 (380)
Q Consensus       152 ~~~l~V~nlp~~~------t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~-~i  224 (380)
                      .++|||+|||+.+      ++++|+++|++||.|..|.+++  .+|+++|||||+|.+.++|++|+..|||..+.|+ .|
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            4799999999999      7899999999999999999984  4799999999999999999999999999999998 99


Q ss_pred             EEEEcccCC
Q 016936          225 TVRRATASS  233 (380)
Q Consensus       225 ~v~~~~~~~  233 (380)
                      +|.++....
T Consensus        93 ~V~~a~~~~  101 (105)
T 2nlw_A           93 RVNLFTDFD  101 (105)
T ss_dssp             EEECSCCCC
T ss_pred             EEEEcchHh
Confidence            999987543

>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=99.66  E-value=3.9e-16  Score=120.81  Aligned_cols=83  Identities=18%  Similarity=0.312  Sum_probs=76.6

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCC-eeEEEEe-eCCCCCCCceEEEEEEcChhHHHHHHHHhC--CCeeCCeEEEEE
Q 016936          152 PDRVFVGGLPYYFTETQIKELLESFGT-LHGFDLV-KDRDTGNSKGYGFCVYQDPAVTDIACAALN--GLKMGDKTLTVR  227 (380)
Q Consensus       152 ~~~l~V~nlp~~~t~~~l~~~F~~~G~-i~~v~l~-~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~--g~~~~g~~i~v~  227 (380)
                      .++|||+|||..+++++|+++|++||. |..+.++ .++.++.++|||||+|.+.++|.+|+..|+  +..+.|+.|+|.
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~V~   87 (109)
T 2dis_A            8 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVD   87 (109)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEE
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEEEE
Confidence            479999999999999999999999998 9999998 777788999999999999999999999996  589999999999


Q ss_pred             EcccCCC
Q 016936          228 RATASSG  234 (380)
Q Consensus       228 ~~~~~~~  234 (380)
                      ++.++..
T Consensus        88 ~a~~~~~   94 (109)
T 2dis_A           88 WAEPEID   94 (109)
T ss_dssp             ESCSSCS
T ss_pred             EcCCCCC
Confidence            9987643

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens}

Probab=99.66  E-value=8.1e-17  Score=122.63  Aligned_cols=81  Identities=27%  Similarity=0.506  Sum_probs=74.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDR-DTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      ...++|||+|||+.+++++|+++|++|| |..|+++.++ .+|+++|||||+|.+.++|.+|+ .|+|..+.|+.|+|.+
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            3447999999999999999999999999 9999999987 58999999999999999999999 7999999999999999


Q ss_pred             cccC
Q 016936          229 ATAS  232 (380)
Q Consensus       229 ~~~~  232 (380)
                      +.++
T Consensus        95 a~~~   98 (100)
T 2j76_E           95 ADQA   98 (100)
T ss_dssp             CCCS
T ss_pred             ccCC
Confidence            8765

>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=99.66  E-value=2.8e-16  Score=119.96  Aligned_cols=81  Identities=16%  Similarity=0.207  Sum_probs=74.1

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      ....++|||+|||+++++++|+++|++||.+ .|+++.++ +++++|||||+|.+.++|++|++ +|+..+.|+.|+|.+
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            3445799999999999999999999999955 99999997 79999999999999999999996 699999999999998


Q ss_pred             cccC
Q 016936          229 ATAS  232 (380)
Q Consensus       229 ~~~~  232 (380)
                      +...
T Consensus        89 ~~~~   92 (102)
T 1wez_A           89 NSTA   92 (102)
T ss_dssp             ECCC
T ss_pred             CCCC
Confidence            8654

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.66  E-value=3.5e-16  Score=122.83  Aligned_cols=79  Identities=18%  Similarity=0.315  Sum_probs=74.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCC---eeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEE
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGT---LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  226 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~---i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v  226 (380)
                      ...++|||+|||+.+++++|+++|+.||.   |..|+++.++. ++++|||||+|.+.++|++|++ +++..+.|+.|+|
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            34579999999999999999999999999   89999999976 9999999999999999999999 8999999999999


Q ss_pred             EEcc
Q 016936          227 RRAT  230 (380)
Q Consensus       227 ~~~~  230 (380)
                      .++.
T Consensus        93 ~~a~   96 (118)
T 2db1_A           93 FKSH   96 (118)
T ss_dssp             EEEC
T ss_pred             EECC
Confidence            9984

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.65  E-value=4.1e-16  Score=123.68  Aligned_cols=79  Identities=22%  Similarity=0.430  Sum_probs=75.8

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccC
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  232 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~  232 (380)
                      ++|||+|||.++++++|+++|++||.|..|+++.++.++.++|||||+|.+.++|++|+ .|+|..+.|+.|+|.++...
T Consensus        37 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~  115 (124)
T 2jwn_A           37 RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRTN  115 (124)
T ss_dssp             TEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESSCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCCC
Confidence            79999999999999999999999999999999999888999999999999999999999 79999999999999998764

>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=99.65  E-value=1.2e-16  Score=114.95  Aligned_cols=75  Identities=23%  Similarity=0.439  Sum_probs=71.4

Q ss_pred             EEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       154 ~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      +|||+|||..+++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|++|++. ++..+.|+.|.|+++
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-SSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEC
Confidence            589999999999999999999999999999999988899999999999999999999995 899999999999875

>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=99.65  E-value=3.9e-16  Score=119.71  Aligned_cols=81  Identities=16%  Similarity=0.332  Sum_probs=74.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeE-EEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHG-FDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~-v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      ....+|||+|||+.+++++|+++|++||.|.. |+++.+ .+++++|||||+|.+.++|++|+.. ++..+.|+.|+|.+
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~~   90 (104)
T 1wg5_A           13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIFK   90 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEEE
Confidence            44579999999999999999999999999987 888888 5899999999999999999999997 99999999999999


Q ss_pred             cccC
Q 016936          229 ATAS  232 (380)
Q Consensus       229 ~~~~  232 (380)
                      +...
T Consensus        91 ~~~~   94 (104)
T 1wg5_A           91 SSRA   94 (104)
T ss_dssp             ECTT
T ss_pred             CCHH
Confidence            8654

>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=99.65  E-value=1e-16  Score=125.35  Aligned_cols=101  Identities=19%  Similarity=0.232  Sum_probs=85.4

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe---cCCCcEEEEEeCCHHHHHHHH-HcCCcee
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI---NHEKKFAFVEMRTVEEASNAM-ALDGIIF  104 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~---~~~~g~afV~f~~~~~a~~ai-~l~~~~i  104 (380)
                      +...++|||+|||..+++++|+++|++||.            |.++.+   ..++|||||+|.+.++|.+|+ .+|+..+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------v~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~   72 (115)
T 3lqv_A            5 PEVNRILYIRNLPYKITAEEMYDIFGKYGP------------IRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNV   72 (115)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSC------------EEEEEEECSTTTTTCEEEEESSHHHHHHHHHHHTTCBS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------eEEEEEeeCCCCCcEEEEEECCHHHHHHHHHHcCCCEE
Confidence            346789999999999999999999999998            566665   456899999999999999999 6999999


Q ss_pred             cCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCC
Q 016936          105 EGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGT  178 (380)
Q Consensus       105 ~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~  178 (380)
                      .|+.|+|.++......                                     ++++...++++|..+|++||.
T Consensus        73 ~g~~l~v~~a~~~~~~-------------------------------------~~~~~~~~~~~l~~~~~~~g~  109 (115)
T 3lqv_A           73 SNRYLVVLYYNANRAF-------------------------------------QKMDTKKKEEQLKLLKEKYGI  109 (115)
T ss_dssp             SSCBCEEEECCHHHHT-------------------------------------TTSCHHHHHHHHHHHHHHHCC
T ss_pred             CCeEEEEEEecCChhh-------------------------------------hhhhHhHhHHHHHHHHHHhCC
Confidence            9999999986542110                                     455666788999999999985

>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=9.8e-16  Score=118.57  Aligned_cols=91  Identities=22%  Similarity=0.360  Sum_probs=79.4

Q ss_pred             CCCCCccccchhhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHH
Q 016936           16 FPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASN   95 (380)
Q Consensus        16 ~~~~~~~~~~~~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~   95 (380)
                      .+..+...+........++|||+|||..+++++|+++|++||.            |..+.+..++|||||+|.+.++|.+
T Consensus         9 ~~~~~~~~~~~~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~------------i~~v~i~~~~g~afV~f~~~~~a~~   76 (109)
T 1x4g_A            9 TKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQ------------IMEIRVFPEKGYSFVRFSTHESAAH   76 (109)
T ss_dssp             SCSCCHHHHHHHSCSSCCEEEEECCSSCCCHHHHHHHHHHHSC------------EEEEEEETTTTEEEEEESSHHHHHH
T ss_pred             cccCCccccccCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCC------------eEEEEEeCCCCEEEEEECCHHHHHH
Confidence            3334444455566788999999999999999999999999997            8888888889999999999999999


Q ss_pred             HH-HcCCceecCceEEEecCCCCC
Q 016936           96 AM-ALDGIIFEGVAVRVRRPTDYN  118 (380)
Q Consensus        96 ai-~l~~~~i~g~~i~v~~~~~~~  118 (380)
                      |+ .|++..|.|++|+|.|+....
T Consensus        77 A~~~l~g~~~~g~~l~v~~a~~~~  100 (109)
T 1x4g_A           77 AIVSVNGTTIEGHVVKCYWGKESP  100 (109)
T ss_dssp             HHHHHTTCEETTEECEEECCCCCC
T ss_pred             HHHHcCCCEECCcEEEEEecCCCC
Confidence            99 899999999999999977653

>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=99.65  E-value=7.6e-16  Score=117.64  Aligned_cols=79  Identities=16%  Similarity=0.153  Sum_probs=70.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCC--CeeCCeEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNG--LKMGDKTLTV  226 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g--~~~~g~~i~v  226 (380)
                      ....++|||+|||+.+++++|+++|++||.|..|.++++      +|||||+|.+.++|.+|++.|++  ..+.|++|.|
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V   85 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFF   85 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            344579999999999999999999999999999998754      68999999999999999998865  4599999999


Q ss_pred             EEcccCC
Q 016936          227 RRATASS  233 (380)
Q Consensus       227 ~~~~~~~  233 (380)
                      .++..+.
T Consensus        86 ~~a~~~~   92 (104)
T 1wex_A           86 NYSTSKR   92 (104)
T ss_dssp             EECSSSS
T ss_pred             EEccCcc
Confidence            9997654

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.65  E-value=7.8e-16  Score=117.38  Aligned_cols=81  Identities=17%  Similarity=0.308  Sum_probs=73.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      ....++|||+|||..+++++|+++|++||.|   +++.+ .+++++|||||+|.+.++|++|+..|++..+.|+.|+|.+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   87 (101)
T 2fc9_A           12 SGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLEL   87 (101)
T ss_dssp             SCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEE
Confidence            3456899999999999999999999999977   56666 4789999999999999999999999999999999999999


Q ss_pred             cccCC
Q 016936          229 ATASS  233 (380)
Q Consensus       229 ~~~~~  233 (380)
                      +.++.
T Consensus        88 a~~~~   92 (101)
T 2fc9_A           88 QGPRG   92 (101)
T ss_dssp             CSSCC
T ss_pred             cCCCC
Confidence            97764

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.65  E-value=3.2e-16  Score=120.72  Aligned_cols=75  Identities=25%  Similarity=0.381  Sum_probs=71.1

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      .+|||+|||+.+++++|+++|+.| .|..|+|+.++. |+++|||||+|.+.++|++|+ .+|+..+.|+.|+|..+.
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-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPAT   91 (109)
T ss_dssp             HEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECC
T ss_pred             CEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            689999999999999999999999 899999999975 999999999999999999999 589999999999998874

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.65  E-value=2e-16  Score=118.21  Aligned_cols=80  Identities=23%  Similarity=0.206  Sum_probs=64.4

Q ss_pred             cceEEEcCCCCcCcHHHHHHHHHHHH-HhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-Hc-CCceecCce
Q 016936           32 ARRVYVGGLPPLANEQAIATFFSQVM-TAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-AL-DGIIFEGVA  108 (380)
Q Consensus        32 ~~~v~V~nLp~~~t~~~l~~~f~~~G-~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l-~~~~i~g~~  108 (380)
                      +++|||+|||+++|+++|+++|++|| .|...      ..+.+-..+.++|||||+|.+.++|++|+ .+ ++..+.|++
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v------~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~   74 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREV------RLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQK   74 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBC------CSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEE------EEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEE
Confidence            57999999999999999999999999 54321      11222234567899999999999999999 45 456799999


Q ss_pred             EEEecCCCC
Q 016936          109 VRVRRPTDY  117 (380)
Q Consensus       109 i~v~~~~~~  117 (380)
                      |+|.++..+
T Consensus        75 i~V~~a~~~   83 (91)
T 2lxi_A           75 VSMHYSDPK   83 (91)
T ss_dssp             EEEECCCSC
T ss_pred             EEEEEcCCC
Confidence            999997654

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.65  E-value=9.9e-16  Score=114.20  Aligned_cols=78  Identities=28%  Similarity=0.503  Sum_probs=71.5

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      ...++|||+|||..+++++|+++|++||.|..|.+.        +|||||+|.+.++|++|++.|++..+.|+.|+|.++
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            445799999999999999999999999999999987        469999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 016936          230 TASSGQ  235 (380)
Q Consensus       230 ~~~~~~  235 (380)
                      .++...
T Consensus        78 ~~~~~~   83 (90)
T 2dnq_A           78 KNKSKA   83 (90)
T ss_dssp             SCCCCC
T ss_pred             CCCCCC
Confidence            776443

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A

Probab=99.64  E-value=3.5e-16  Score=125.37  Aligned_cols=79  Identities=18%  Similarity=0.286  Sum_probs=74.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCC---eeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEE
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGT---LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  226 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~---i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v  226 (380)
                      ...++|||+|||+++|+++|+++|++||.   |..|+++.++. |+++|||||+|.+.++|++|++ +++..+.|+.|+|
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            44579999999999999999999999999   89999999986 9999999999999999999999 9999999999999


Q ss_pred             EEcc
Q 016936          227 RRAT  230 (380)
Q Consensus       227 ~~~~  230 (380)
                      .++.
T Consensus       120 ~~a~  123 (136)
T 2hgl_A          120 FKSH  123 (136)
T ss_dssp             EECC
T ss_pred             EECC
Confidence            9974

>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=99.64  E-value=1.8e-15  Score=116.83  Aligned_cols=78  Identities=22%  Similarity=0.279  Sum_probs=72.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCC-----eEE
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD-----KTL  224 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g-----~~i  224 (380)
                      ....+|||+|||+++++++|+++|++||.|..|.++.+       |||||+|.+.++|++|++.||+..+.|     +.|
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            44579999999999999999999999999999999865       799999999999999999999999999     999


Q ss_pred             EEEEcccCCC
Q 016936          225 TVRRATASSG  234 (380)
Q Consensus       225 ~v~~~~~~~~  234 (380)
                      +|.++.++..
T Consensus        86 ~V~~a~~~~~   95 (108)
T 1x4c_A           86 RVKVDGPRSP   95 (108)
T ss_dssp             EEEESSCCSC
T ss_pred             EEEeCCCCCC
Confidence            9999987643

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=1e-15  Score=119.46  Aligned_cols=82  Identities=21%  Similarity=0.484  Sum_probs=76.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCee--------CC
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM--------GD  221 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~--------~g  221 (380)
                      ...++|||+|||..+++++|+++|++||.|..|+++.++ ++.++|||||+|.+.++|++|++.|||..+        .+
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            345799999999999999999999999999999999998 899999999999999999999999999999        67


Q ss_pred             eEEEEEEcccC
Q 016936          222 KTLTVRRATAS  232 (380)
Q Consensus       222 ~~i~v~~~~~~  232 (380)
                      ++|.|.++.++
T Consensus       102 ~~l~v~~a~p~  112 (114)
T 1x5o_A          102 EPLLCKFSGPS  112 (114)
T ss_dssp             SCBEEEECCCS
T ss_pred             CceeEEccCCC
Confidence            88999998754

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.64  E-value=7.1e-16  Score=119.07  Aligned_cols=78  Identities=17%  Similarity=0.157  Sum_probs=70.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcC-CeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFG-TLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G-~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      ...+|||+|||+++++++|+++|++|| .|..+.+..    +.++|||||+|.+.++|++|++.|||..+.|+.|+|.++
T Consensus        27 ~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~----~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a  102 (111)
T 2jvr_A           27 KRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNT----RDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERD  102 (111)
T ss_dssp             CCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSS----CSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEc----CCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            346999999999999999999999999 899998853    347899999999999999999999999999999999998


Q ss_pred             ccC
Q 016936          230 TAS  232 (380)
Q Consensus       230 ~~~  232 (380)
                      ...
T Consensus       103 ~~~  105 (111)
T 2jvr_A          103 DNP  105 (111)
T ss_dssp             CC-
T ss_pred             CCC
Confidence            643

>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=119.70  Aligned_cols=76  Identities=22%  Similarity=0.400  Sum_probs=69.9

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecCc
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  107 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g~  107 (380)
                      ....++|||+|||.++++++|+++|++||.            |.++.+.+++|||||+|.+.++|.+|+ .+++..+.|+
T Consensus        24 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~------------i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~   91 (101)
T 2la4_A           24 PPRVTTAYIGNIPHFATEADLIPLFQNFGF------------ILDFKHYPEKGCCFIKYDTHEQAAVCIVALANFPFQGR   91 (101)
T ss_dssp             CSSCCEEEEESCCTTCCHHHHHHHHHTTSC------------CSEEEEETTTTEEEEECSSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCEEEEcCCCcccCHHHHHHHHHhCCC------------EEEEEEecCCCEEEEEECCHHHHHHHHHHhCCCeECCe
Confidence            455789999999999999999999999997            677777899999999999999999999 8999999999


Q ss_pred             eEEEecCCC
Q 016936          108 AVRVRRPTD  116 (380)
Q Consensus       108 ~i~v~~~~~  116 (380)
                      +|+|.|+..
T Consensus        92 ~l~V~~a~~  100 (101)
T 2la4_A           92 NLRTGWGKE  100 (101)
T ss_dssp             ECCCCBCCC
T ss_pred             EEEEEeccC
Confidence            999998754

>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=99.64  E-value=7e-16  Score=116.67  Aligned_cols=87  Identities=13%  Similarity=0.264  Sum_probs=68.4

Q ss_pred             CCCCCccccchhhhcccceEEEcCCCC-cCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHH
Q 016936           16 FPLMPVQVMTQQATRHARRVYVGGLPP-LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEAS   94 (380)
Q Consensus        16 ~~~~~~~~~~~~~~~~~~~v~V~nLp~-~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~   94 (380)
                      .+.+|.+........+.++|||+|||. ++++++|+++|++||.            |.++.+  .+|||||+|.+.++|.
T Consensus         6 ~~~~~~~~~~~~~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~------------v~~v~i--~~g~afV~f~~~~~A~   71 (97)
T 2xnq_A            6 HHHHHSSGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGH------------IMQINI--KNAFGFIQFDNPQSVR   71 (97)
T ss_dssp             -------------CCTTCEEEEESCCSSCCCHHHHHHHHGGGSC------------EEEEEE--CSSEEEEEESSHHHHH
T ss_pred             CCCCCCcccccCCCCCCCEEEEeCCCcccCCHHHHHHHHHhcCC------------EEEEEE--eCCEEEEEECCHHHHH
Confidence            344455555667788999999999998 9999999999999997            677766  4899999999999999


Q ss_pred             HHH-HcCCceecCceEEEecCCC
Q 016936           95 NAM-ALDGIIFEGVAVRVRRPTD  116 (380)
Q Consensus        95 ~ai-~l~~~~i~g~~i~v~~~~~  116 (380)
                      +|+ .+++..+.|++|+|.++..
T Consensus        72 ~Ai~~l~g~~~~g~~l~V~~a~~   94 (97)
T 2xnq_A           72 DAIEXESQEMNFGKKLILEVSSS   94 (97)
T ss_dssp             HHHHHHTTSEETTEECEEEECCC
T ss_pred             HHHHHcCCCEECCEEEEEEecCC
Confidence            999 6999999999999998654

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.64  E-value=1e-15  Score=121.19  Aligned_cols=79  Identities=11%  Similarity=0.219  Sum_probs=71.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHH----HHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEE
Q 016936          151 GPDRVFVGGLPYYFTETQIK----ELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  226 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~----~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v  226 (380)
                      ..++|||+|||+.+++++|+    ++|++||.|..|.+..   +++++|||||+|.+.++|.+|+..|||..+.|++|+|
T Consensus        28 p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V  104 (127)
T 2a3j_A           28 PSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVI  104 (127)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEE
Confidence            34799999999999999865    7999999999988753   5789999999999999999999999999999999999


Q ss_pred             EEcccC
Q 016936          227 RRATAS  232 (380)
Q Consensus       227 ~~~~~~  232 (380)
                      .++..+
T Consensus       105 ~~a~~~  110 (127)
T 2a3j_A          105 TFSETP  110 (127)
T ss_dssp             EECCCC
T ss_pred             EEccCc
Confidence            999754

>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=99.64  E-value=5.5e-16  Score=117.59  Aligned_cols=77  Identities=13%  Similarity=0.088  Sum_probs=69.5

Q ss_pred             CCCEEEEcCCCC-CCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCC--CeeCCeEEEEE
Q 016936          151 GPDRVFVGGLPY-YFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNG--LKMGDKTLTVR  227 (380)
Q Consensus       151 ~~~~l~V~nlp~-~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g--~~~~g~~i~v~  227 (380)
                      ..++|||+|||+ .+++++|+++|++||.|.+|.++++      +|||||+|.+.++|..|++.|++  ..+.|++|+|.
T Consensus        14 p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~   87 (102)
T 1x4d_A           14 TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVH   87 (102)
T ss_dssp             CCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEE
Confidence            457999999999 9999999999999999999999865      47999999999999999999885  46999999999


Q ss_pred             EcccCC
Q 016936          228 RATASS  233 (380)
Q Consensus       228 ~~~~~~  233 (380)
                      ++....
T Consensus        88 ~a~~~~   93 (102)
T 1x4d_A           88 LSQKYK   93 (102)
T ss_dssp             EECCCT
T ss_pred             ECCCCC
Confidence            997543

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.64  E-value=1.8e-16  Score=115.71  Aligned_cols=72  Identities=25%  Similarity=0.405  Sum_probs=67.2

Q ss_pred             CEEEEcCCCCCC------CHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCe-EEE
Q 016936          153 DRVFVGGLPYYF------TETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDK-TLT  225 (380)
Q Consensus       153 ~~l~V~nlp~~~------t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~-~i~  225 (380)
                      ++|||+|||..+      ++++|+++|++||.|..+.+++  .+|+++|||||+|.+.++|++|+..|||..+.|+ +|+
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      7799999999999999999884  4799999999999999999999999999999999 887


Q ss_pred             E
Q 016936          226 V  226 (380)
Q Consensus       226 v  226 (380)
                      |
T Consensus        80 V   80 (81)
T 2krb_A           80 V   80 (81)
T ss_dssp             C
T ss_pred             e
Confidence            6

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=1.4e-15  Score=112.08  Aligned_cols=75  Identities=21%  Similarity=0.403  Sum_probs=69.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHh-CCCeeCCeEEEEEE
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL-NGLKMGDKTLTVRR  228 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l-~g~~~~g~~i~v~~  228 (380)
                      ...++|||+|||..+++++|+++|++||.|..|.+.++      +|||||+|.+.++|++|+..| ++..+.|++|+|++
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            34579999999999999999999999999999999864      689999999999999999998 99999999999998


Q ss_pred             cc
Q 016936          229 AT  230 (380)
Q Consensus       229 ~~  230 (380)
                      ++
T Consensus        84 ak   85 (85)
T 2ytc_A           84 GR   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            73

>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=99.63  E-value=2.4e-16  Score=122.74  Aligned_cols=91  Identities=19%  Similarity=0.178  Sum_probs=73.7

Q ss_pred             CCCCccccchhhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHH
Q 016936           17 PLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNA   96 (380)
Q Consensus        17 ~~~~~~~~~~~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~a   96 (380)
                      ..+-..........++++|||+|||+++++++|+++|++||.            |.++.+.+++|||||+|.+.++|.+|
T Consensus        16 ~~~~~~~~~~~~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~------------V~~v~i~~~kG~AFVeF~~~e~A~~A   83 (119)
T 2ad9_A           16 PRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGK------------VTNLLMLKGKNQAFIEMNTEEAANTM   83 (119)
T ss_dssp             ------CCTTSCSSCCSEEEEESCCTTCCHHHHHHHHTTTSC------------CCEEEEEGGGTEEEEECSCHHHHHHH
T ss_pred             CcccccccccccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------EEEEEEeCCCCEEEEEECCHHHHHHH
Confidence            333344444456677899999999999999999999999998            77777778899999999999999999


Q ss_pred             H-HcC--CceecCceEEEecCCCCCc
Q 016936           97 M-ALD--GIIFEGVAVRVRRPTDYNP  119 (380)
Q Consensus        97 i-~l~--~~~i~g~~i~v~~~~~~~~  119 (380)
                      + .++  +..+.|++|+|.++..+..
T Consensus        84 i~~l~~~~~~l~Gr~l~V~~a~~k~~  109 (119)
T 2ad9_A           84 VNYYTSVTPVLRGQPIYIQFSNHKEL  109 (119)
T ss_dssp             HHHHHHHCCCBTTBCCEEEECSSSSC
T ss_pred             HHHhccCCceECCeEEEEEEccCCCC
Confidence            9 576  4679999999999876543

>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=99.63  E-value=1.2e-15  Score=118.78  Aligned_cols=79  Identities=13%  Similarity=0.172  Sum_probs=71.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhC--CCeeCCeEEEEEE
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN--GLKMGDKTLTVRR  228 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~--g~~~~g~~i~v~~  228 (380)
                      ..++|||+|||+++++++|+++|++||.|..|.++++      +|||||+|.+.++|++|++.++  +..+.|++|+|.+
T Consensus        30 ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~~  103 (119)
T 2ad9_A           30 PSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQF  103 (119)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEEE
Confidence            3479999999999999999999999999999999875      6899999999999999999887  4789999999999


Q ss_pred             cccCCCC
Q 016936          229 ATASSGQ  235 (380)
Q Consensus       229 ~~~~~~~  235 (380)
                      +..+...
T Consensus       104 a~~k~~~  110 (119)
T 2ad9_A          104 SNHKELK  110 (119)
T ss_dssp             CSSSSCC
T ss_pred             ccCCCCC
Confidence            9776433

>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=99.63  E-value=9.3e-16  Score=119.89  Aligned_cols=85  Identities=19%  Similarity=0.266  Sum_probs=71.7

Q ss_pred             cccchhhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe------cCCCcEEEEEeCCHHHHHH
Q 016936           22 QVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASN   95 (380)
Q Consensus        22 ~~~~~~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~------~~~~g~afV~f~~~~~a~~   95 (380)
                      +...+....+.++|||+|||.++++++|+++|++||.|            ..+.+      ..++|||||+|.+.++|++
T Consensus        15 ~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i------------~~v~i~~~~~~g~~~g~afV~f~~~~~a~~   82 (115)
T 2cpz_A           15 AAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNV------------VSAKVFIDKQTNLSKCFGFVSYDNPVSAQA   82 (115)
T ss_dssp             CBSCCCCCSTTCCEEEESCCSSCCHHHHHHHHGGGSCC------------SEEEEEECSSSCSEEEEEEEECSSHHHHHH
T ss_pred             cCccCcCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCe------------EEEEEEECCCCCCcCccEEEEECCHHHHHH
Confidence            34444566788999999999999999999999999984            33433      3446899999999999999


Q ss_pred             HH-HcCCceecCceEEEecCCCCC
Q 016936           96 AM-ALDGIIFEGVAVRVRRPTDYN  118 (380)
Q Consensus        96 ai-~l~~~~i~g~~i~v~~~~~~~  118 (380)
                      |+ .|++..|.|++|+|.++....
T Consensus        83 A~~~l~g~~~~g~~l~V~~a~~~~  106 (115)
T 2cpz_A           83 AIQSMNGFQIGMKRLKVQLKRSKN  106 (115)
T ss_dssp             HHHHHTTCEETTEECEEECCCCSC
T ss_pred             HHHHcCCCEECCEEEEEEEcCCCC
Confidence            99 899999999999999977654

>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=99.63  E-value=1.5e-15  Score=115.29  Aligned_cols=79  Identities=33%  Similarity=0.532  Sum_probs=72.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      ....++|||+|||..+++++|+++|++||.|..|++.++      +|||||+|.+.++|++|++.|++..+.|+.|+|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~   85 (99)
T 2cpj_A           12 FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRF   85 (99)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEE
Confidence            344579999999999999999999999999999999754      67999999999999999999999999999999999


Q ss_pred             cccCC
Q 016936          229 ATASS  233 (380)
Q Consensus       229 ~~~~~  233 (380)
                      +.++.
T Consensus        86 a~~~~   90 (99)
T 2cpj_A           86 ACHSA   90 (99)
T ss_dssp             SSCCS
T ss_pred             cCCCC
Confidence            97754

>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=99.63  E-value=6.5e-16  Score=117.30  Aligned_cols=81  Identities=16%  Similarity=0.136  Sum_probs=71.3

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-Hc--CCce
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-AL--DGII  103 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l--~~~~  103 (380)
                      ....++++|||+|||+++++++|+++|++||.            |.++.+.+++|||||+|.+.++|.+|+ .+  ++..
T Consensus        10 ~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~------------v~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~   77 (101)
T 2cq1_A           10 MDGAPSRVLHIRKLPGEVTETEVIALGLPFGK------------VTNILMLKGKNQAFLELATEEAAITMVNYYSAVTPH   77 (101)
T ss_dssp             CCSSCCSEEEEESCCTTCCHHHHHHTTTTTSC------------EEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------EEEEEEECCCCEEEEEECCHHHHHHHHHHhccCCce
Confidence            34456899999999999999999999999998            778888888999999999999999999 55  5678


Q ss_pred             ecCceEEEecCCCCCc
Q 016936          104 FEGVAVRVRRPTDYNP  119 (380)
Q Consensus       104 i~g~~i~v~~~~~~~~  119 (380)
                      +.|++|+|.++.....
T Consensus        78 ~~Gr~l~V~~a~~~~~   93 (101)
T 2cq1_A           78 LRNQPIYIQYSNHKEL   93 (101)
T ss_dssp             ETTEECEEEECSCSSC
T ss_pred             ECCcEEEEEEcCcccC
Confidence            9999999999876543

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=2.3e-15  Score=112.19  Aligned_cols=77  Identities=29%  Similarity=0.417  Sum_probs=70.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      ...++|||+|||..+++++|+++|++||.|..|++.++        ||||+|.+.++|++|++.|++..+.|+.|+|.++
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            34579999999999999999999999999999999743        9999999999999999999999999999999999


Q ss_pred             ccCCC
Q 016936          230 TASSG  234 (380)
Q Consensus       230 ~~~~~  234 (380)
                      .+...
T Consensus        79 ~~~~~   83 (90)
T 2dnp_A           79 TKGQK   83 (90)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            77643

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.63  E-value=1.1e-15  Score=115.58  Aligned_cols=77  Identities=21%  Similarity=0.347  Sum_probs=70.8

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceec--
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE--  105 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~--  105 (380)
                      ..+.++|||+|||.++++++|+++|++||.            |.++.+..++|||||+|.+.++|++|+ .+|+..+.  
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------v~~v~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~   81 (97)
T 1why_A           14 ANPTTRLWVGGLGPNTSLAALAREFDRFGS------------IRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFPLGGP   81 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSC------------EEEEEECSSSCCEEEEESSHHHHHHHHHHHTTCBCSSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------eeEEEEeCCCCEEEEEECCHHHHHHHHHHHCCCEeCCC
Confidence            456799999999999999999999999997            788888888999999999999999999 69999999  


Q ss_pred             CceEEEecCCCC
Q 016936          106 GVAVRVRRPTDY  117 (380)
Q Consensus       106 g~~i~v~~~~~~  117 (380)
                      |++|+|.++...
T Consensus        82 g~~l~V~~a~~~   93 (97)
T 1why_A           82 DRRLRVDFAKSG   93 (97)
T ss_dssp             SCBCEEEECCCC
T ss_pred             CcEEEEEECCCC
Confidence            999999997654

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=1.8e-15  Score=115.51  Aligned_cols=83  Identities=27%  Similarity=0.393  Sum_probs=74.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      ....++|||+|||..+++++|+++|+.|+   .+.++.++.++.++|||||+|.+.++|++|++.|++..+.|+.|+|.+
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            34457999999999999999999999773   677888877899999999999999999999999999999999999999


Q ss_pred             cccCCC
Q 016936          229 ATASSG  234 (380)
Q Consensus       229 ~~~~~~  234 (380)
                      +.++..
T Consensus        89 a~~~~~   94 (102)
T 2fc8_A           89 AKPKGE   94 (102)
T ss_dssp             CCCCCS
T ss_pred             ecCCCC
Confidence            987643

>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=99.63  E-value=7.1e-16  Score=117.82  Aligned_cols=79  Identities=18%  Similarity=0.157  Sum_probs=69.7

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCC--ceec
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDG--IIFE  105 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~--~~i~  105 (380)
                      ..++++|||+|||+++++++|+++|++||.            |.++.+.+++|||||+|.+.++|.+|+ .+++  ..+.
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~------------V~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~i~   79 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEADLVEALEKFGT------------ICYVMMMPFKRQALVEFENIDSAKECVTFAADVPVYIA   79 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSC------------EEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCBSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCC------------EEEEEEECCCCEEEEEECCHHHHHHHHHHhccCCceEC
Confidence            345799999999999999999999999997            778888888999999999999999999 5765  4599


Q ss_pred             CceEEEecCCCCCc
Q 016936          106 GVAVRVRRPTDYNP  119 (380)
Q Consensus       106 g~~i~v~~~~~~~~  119 (380)
                      |++|+|.++..+..
T Consensus        80 Gr~l~V~~a~~~~~   93 (104)
T 1wex_A           80 GQQAFFNYSTSKRI   93 (104)
T ss_dssp             SSBCEEEECSSSSC
T ss_pred             CEEEEEEEccCccc
Confidence            99999999876543

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.63  E-value=2.4e-15  Score=114.63  Aligned_cols=83  Identities=20%  Similarity=0.421  Sum_probs=74.2

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHHHcCCceecCc
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGV  107 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai~l~~~~i~g~  107 (380)
                      .....++|||+|||.++++++|+++|++||.+...       .+.+...+.++|||||+|.+.++|.+|+++++..|.|+
T Consensus        13 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~-------~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~   85 (101)
T 1fj7_A           13 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDL-------AVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGN   85 (101)
T ss_dssp             TCSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHTC-------CCCEEEEETTTTEEEEEESSHHHHHHHHHGGGCCBTTB
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceE-------EEecCCCCCcCcEEEEEECCHHHHHHHHhcCCcEECCc
Confidence            34567899999999999999999999999998651       36677788999999999999999999999999999999


Q ss_pred             eEEEecCCCC
Q 016936          108 AVRVRRPTDY  117 (380)
Q Consensus       108 ~i~v~~~~~~  117 (380)
                      +|+|.++..+
T Consensus        86 ~l~V~~a~~~   95 (101)
T 1fj7_A           86 EIKLEKPKGR   95 (101)
T ss_dssp             CCEEECCSCC
T ss_pred             EEEEEEcCCC
Confidence            9999997654

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=3.6e-15  Score=111.59  Aligned_cols=77  Identities=21%  Similarity=0.357  Sum_probs=70.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      ...++|||+|||..+++++|+++|++||.|..|.+.++        ||||+|.+.++|++|+..||+..+.|+.|+|.++
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            34479999999999999999999999999999999743        9999999999999999999999999999999999


Q ss_pred             ccCCC
Q 016936          230 TASSG  234 (380)
Q Consensus       230 ~~~~~  234 (380)
                      .++..
T Consensus        80 ~~~~~   84 (92)
T 2dgt_A           80 TSRLR   84 (92)
T ss_dssp             SCCCS
T ss_pred             cCCCC
Confidence            77643

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.62  E-value=1.1e-15  Score=118.27  Aligned_cols=78  Identities=13%  Similarity=0.097  Sum_probs=71.3

Q ss_pred             CEEEEcCC----CCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcC----hhH----HHHHHH--HhCCCe
Q 016936          153 DRVFVGGL----PYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD----PAV----TDIACA--ALNGLK  218 (380)
Q Consensus       153 ~~l~V~nl----p~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~----~~~----A~~Ai~--~l~g~~  218 (380)
                      ..|||+||    |+.+++++|+++|++||.|.+|.++.|+.+|+++|||||+|.+    +++    |.+|+.  .++|..
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    889988  789999


Q ss_pred             eCCeEEEEEEcc
Q 016936          219 MGDKTLTVRRAT  230 (380)
Q Consensus       219 ~~g~~i~v~~~~  230 (380)
                      |.|+.|+|..-.
T Consensus        83 I~Gr~irV~ln~   94 (136)
T 2j8a_A           83 IMGFKFEVILNK   94 (136)
T ss_dssp             ETTEEEEEEECC
T ss_pred             ecCcEEEEEECc
Confidence            999999999754

>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=99.62  E-value=2.8e-16  Score=121.23  Aligned_cols=80  Identities=16%  Similarity=0.270  Sum_probs=74.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCC---eeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGT---LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  225 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~---i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~  225 (380)
                      .....+|||+|||+++++++|+++|+.||.   |..|+++.++. |+++|||||+|.+.++|++|+. +++..+.|+.|+
T Consensus         8 ~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~   85 (107)
T 2lmi_A            8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVE   85 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCC
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEE
Confidence            344579999999999999999999999998   89999999986 9999999999999999999999 899999999999


Q ss_pred             EEEcc
Q 016936          226 VRRAT  230 (380)
Q Consensus       226 v~~~~  230 (380)
                      |.++.
T Consensus        86 V~~a~   90 (107)
T 2lmi_A           86 VYEIN   90 (107)
T ss_dssp             CEECC
T ss_pred             EEECC
Confidence            99985

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A

Probab=99.62  E-value=1.5e-15  Score=112.45  Aligned_cols=85  Identities=46%  Similarity=0.810  Sum_probs=72.3

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHHHcCCceecCce
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVA  108 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai~l~~~~i~g~~  108 (380)
                      +++.++|||+|||+++++++|+++|++||.+.+... .+...|.++.+.+++|||||+|.+.++|.+|+.+++..+.|++
T Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~-~~~~~v~~~~~~~~kg~afV~f~~~~~a~~A~~l~g~~~~g~~   81 (87)
T 2hzc_A            3 LGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQ-APGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQS   81 (87)
T ss_dssp             SGGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCS-SSSCSEEEEEECSSSSEEEEEESSHHHHHHHGGGTTCEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhhhccccc-CCCCcceEEEecCCCcEEEEEcCCHHHHHHHHhcCCCEECCeE
Confidence            467899999999999999999999999965433111 1122489999999999999999999999999999999999999


Q ss_pred             EEEecC
Q 016936          109 VRVRRP  114 (380)
Q Consensus       109 i~v~~~  114 (380)
                      |+|.++
T Consensus        82 l~V~rp   87 (87)
T 2hzc_A           82 LKIRRP   87 (87)
T ss_dssp             CEEECC
T ss_pred             EEEeCC
Confidence            999763

>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=99.62  E-value=3.2e-15  Score=113.07  Aligned_cols=77  Identities=26%  Similarity=0.526  Sum_probs=71.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeC--CeEEEEEE
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG--DKTLTVRR  228 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~--g~~i~v~~  228 (380)
                      ..++|||+|||..+++++|+++|++||.|..|.+..+      +|||||+|.+.++|++|++.||+..+.  |+.|+|.+
T Consensus        16 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~   89 (97)
T 1why_A           16 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDF   89 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEE
Confidence            4479999999999999999999999999999998754      679999999999999999999999999  99999999


Q ss_pred             cccCC
Q 016936          229 ATASS  233 (380)
Q Consensus       229 ~~~~~  233 (380)
                      +.++.
T Consensus        90 a~~~~   94 (97)
T 1why_A           90 AKSGP   94 (97)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            97753

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.62  E-value=1.5e-16  Score=121.40  Aligned_cols=82  Identities=20%  Similarity=0.335  Sum_probs=74.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      ..++|||+|||+.+++++|+++|++||.|.. .++.++.+++++|||||+|.+.++|++|++ |++..+.|+.|+|.++.
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            4579999999999999999999999999888 566665678999999999999999999999 99999999999999997


Q ss_pred             cCCC
Q 016936          231 ASSG  234 (380)
Q Consensus       231 ~~~~  234 (380)
                      ++..
T Consensus        94 ~~~~   97 (101)
T 1fj7_A           94 GRDG   97 (101)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6543

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.62  E-value=4.3e-16  Score=119.93  Aligned_cols=80  Identities=24%  Similarity=0.314  Sum_probs=70.9

Q ss_pred             hhhcccceEEEcCCCCc-CcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcC--Cc
Q 016936           27 QATRHARRVYVGGLPPL-ANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALD--GI  102 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~-~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~--~~  102 (380)
                      ....++++|||+|||++ +++++|+++|++||.            |.++.+.+++|||||+|.+.++|++|+ .++  +.
T Consensus        20 ~~~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~------------V~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~   87 (112)
T 1x4f_A           20 QKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGK------------IKNYILMRMKSQAFIEMETREDAMAMVDHCLKKAL   87 (112)
T ss_dssp             CSSCCCCEEEEESCCCSSCCSHHHHTTTTTTSC------------CSEEEEETTTTEEEEECSSHHHHHHHHHHHHHSCC
T ss_pred             ccCCCCCEEEEeCCCCccCCHHHHHHHHHhcCC------------EEEEEEecCCCEEEEEECCHHHHHHHHHHhccCCc
Confidence            45678999999999998 999999999999998            777888889999999999999999999 665  46


Q ss_pred             eecCceEEEecCCCCC
Q 016936          103 IFEGVAVRVRRPTDYN  118 (380)
Q Consensus       103 ~i~g~~i~v~~~~~~~  118 (380)
                      .|.|++|+|.++..+.
T Consensus        88 ~l~Gr~l~V~~a~~~~  103 (112)
T 1x4f_A           88 WFQGRCVKVDLSEKYK  103 (112)
T ss_dssp             CSSSSCCEEEEECSCS
T ss_pred             eECCEEEEEEECcccc
Confidence            6999999999976543

>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=99.62  E-value=6.8e-16  Score=122.37  Aligned_cols=82  Identities=18%  Similarity=0.309  Sum_probs=74.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      .....+|||+|||+.+++++|+++|+.||.|..+.++.+..+++++|||||+|.+.++|++|+. +|+..+.|+.|.|.+
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~  100 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHP  100 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEE
Confidence            3445799999999999999999999999999886666665689999999999999999999999 999999999999999


Q ss_pred             ccc
Q 016936          229 ATA  231 (380)
Q Consensus       229 ~~~  231 (380)
                      +..
T Consensus       101 a~~  103 (124)
T 1wel_A          101 ITK  103 (124)
T ss_dssp             ECH
T ss_pred             CCH
Confidence            853

>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=99.62  E-value=3.5e-16  Score=118.71  Aligned_cols=78  Identities=22%  Similarity=0.232  Sum_probs=70.4

Q ss_pred             hcccceEEEcCCCC-cCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCC--cee
Q 016936           29 TRHARRVYVGGLPP-LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDG--IIF  104 (380)
Q Consensus        29 ~~~~~~v~V~nLp~-~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~--~~i  104 (380)
                      ..++++|||+|||+ +++++||+++|++||.            |.++.+.+++|||||+|.+.++|..|+ .+++  ..|
T Consensus        12 ~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~------------V~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~   79 (102)
T 1x4d_A           12 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGV------------ISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPALV   79 (102)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSC------------EEEEEECSSSSCEEEEESSHHHHHHHHHHHHHSCCEE
T ss_pred             CCCCCEEEEeCCCCCcCCHHHHHHHHHhcCC------------EEEEEEEcCCCEEEEEECCHHHHHHHHHHHcCCCceE
Confidence            45789999999999 9999999999999998            888888899999999999999999999 6775  459


Q ss_pred             cCceEEEecCCCCC
Q 016936          105 EGVAVRVRRPTDYN  118 (380)
Q Consensus       105 ~g~~i~v~~~~~~~  118 (380)
                      .|++|+|.++..+.
T Consensus        80 ~Gr~l~V~~a~~~~   93 (102)
T 1x4d_A           80 FGKPVRVHLSQKYK   93 (102)
T ss_dssp             TTEECEEEEECCCT
T ss_pred             CCcEEEEEECCCCC
Confidence            99999999987543

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A

Probab=99.62  E-value=4.1e-15  Score=113.77  Aligned_cols=78  Identities=19%  Similarity=0.314  Sum_probs=71.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      ...++|||+|||..+++++|+++|++||.|..|++++        |||||+|.+.++|++|++.|++..+.|+.|.|.++
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            3457999999999999999999999999999999863        49999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 016936          230 TASSGQ  235 (380)
Q Consensus       230 ~~~~~~  235 (380)
                      .+....
T Consensus        81 ~~~~~~   86 (103)
T 2dgu_A           81 KPPDQK   86 (103)
T ss_dssp             CCCCCC
T ss_pred             CCCccc
Confidence            876544

>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=99.62  E-value=3.9e-15  Score=113.87  Aligned_cols=80  Identities=26%  Similarity=0.382  Sum_probs=70.5

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecC----CCcEEEEEeCCHHHHHHHH-HcCC
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH----EKKFAFVEMRTVEEASNAM-ALDG  101 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~----~~g~afV~f~~~~~a~~ai-~l~~  101 (380)
                      ......++|||+|||+.+++++|+++|++||.            |..+.+..    ++|||||+|.+.++|.+|+ .+++
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------i~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g   77 (103)
T 2cqi_A           10 EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGP------------CKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNG   77 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHHHHHSC------------EEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCCCCCEEEEeCCCccCCHHHHHHHHHhcCC------------EeEEEEEecCCCCCCEEEEEECCHHHHHHHHHHhCC
Confidence            34567899999999999999999999999998            66666644    5799999999999999999 6999


Q ss_pred             ceecCceEEEecCCCCC
Q 016936          102 IIFEGVAVRVRRPTDYN  118 (380)
Q Consensus       102 ~~i~g~~i~v~~~~~~~  118 (380)
                      ..|.|++|+|.++....
T Consensus        78 ~~~~g~~l~V~~a~~~~   94 (103)
T 2cqi_A           78 RKILGKEVKVNWATTPS   94 (103)
T ss_dssp             EEETTEEEEEEECCCTT
T ss_pred             CCcCCCeEEEEECCCCc
Confidence            99999999999976643

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.62  E-value=1.9e-15  Score=116.55  Aligned_cols=77  Identities=18%  Similarity=0.446  Sum_probs=71.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      ....++|||+|||..+++++|+++|++||.|..|.+.        +|||||+|.+.++|++|+..|+|..+.|+.|.|.+
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            3455899999999999999999999999999999987        57999999999999999999999999999999999


Q ss_pred             cccCC
Q 016936          229 ATASS  233 (380)
Q Consensus       229 ~~~~~  233 (380)
                      +.+..
T Consensus       100 a~~~~  104 (108)
T 2jvo_A          100 SKLPA  104 (108)
T ss_dssp             CSCCC
T ss_pred             ecCCC
Confidence            87653

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=2.9e-15  Score=115.88  Aligned_cols=78  Identities=18%  Similarity=0.379  Sum_probs=72.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      ..++|||+|||..+++++|+++|++||.|..|++..+      +|||||+|.+.++|++|+..|++..+.|+.|+|.++.
T Consensus        24 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   97 (109)
T 1x4g_A           24 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGK   97 (109)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecC
Confidence            3479999999999999999999999999999999875      6799999999999999999999999999999999998


Q ss_pred             cCCC
Q 016936          231 ASSG  234 (380)
Q Consensus       231 ~~~~  234 (380)
                      ++..
T Consensus        98 ~~~~  101 (109)
T 1x4g_A           98 ESPD  101 (109)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            7643

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C

Probab=99.62  E-value=1e-15  Score=134.31  Aligned_cols=81  Identities=17%  Similarity=0.334  Sum_probs=76.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcC--CeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFG--TLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G--~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      ..++|||+|||+.+++++|+++|++||  .|..|+|++++.+++++|||||+|.+.++|++||+.||+..|.|+.|+|.+
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  999999999988999999999999999999999999999999999999999


Q ss_pred             ccc
Q 016936          229 ATA  231 (380)
Q Consensus       229 ~~~  231 (380)
                      +..
T Consensus       147 a~~  149 (229)
T 3q2s_C          147 VNK  149 (229)
T ss_dssp             CCH
T ss_pred             CCC
Confidence            853

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.61  E-value=1.3e-15  Score=119.74  Aligned_cols=76  Identities=18%  Similarity=0.270  Sum_probs=68.0

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec------CCCcEEEEEeCCHHHHHHHH-Hc
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN------HEKKFAFVEMRTVEEASNAM-AL   99 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~------~~~g~afV~f~~~~~a~~ai-~l   99 (380)
                      ....+.++|||+|||+++++++|+++|++||.            |.++.+.      +++|||||+|.+.++|++|+ .+
T Consensus        35 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l  102 (118)
T 2khc_A           35 IEGPEGCNLFIYHLPQEFTDTDLASTFLPFGN------------VISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM  102 (118)
T ss_dssp             CCCCCSEEEEEECSCTTCCHHHHHHHTTTSCE------------EEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------EEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHc
Confidence            45677899999999999999999999999997            6666654      45799999999999999999 79


Q ss_pred             CCceecCceEEEecC
Q 016936          100 DGIIFEGVAVRVRRP  114 (380)
Q Consensus       100 ~~~~i~g~~i~v~~~  114 (380)
                      |+..|.|++|+|.++
T Consensus       103 ~g~~~~g~~l~V~~a  117 (118)
T 2khc_A          103 NGFQVGTKRLKVQLK  117 (118)
T ss_dssp             CCCEETTEECCEEEC
T ss_pred             CCCEECCEEEEEEec
Confidence            999999999999875

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.61  E-value=4.5e-16  Score=120.40  Aligned_cols=90  Identities=22%  Similarity=0.316  Sum_probs=71.1

Q ss_pred             CCCCCccccchhhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec----CCCcEEEEEeCCHH
Q 016936           16 FPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN----HEKKFAFVEMRTVE   91 (380)
Q Consensus        16 ~~~~~~~~~~~~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~----~~~g~afV~f~~~~   91 (380)
                      .+.++...+........++|||+|||.++++++|+++|++||.            |..+.+.    .++|||||+|.+.+
T Consensus        13 ~~~~~~~S~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~------------i~~v~i~~~~~~~kg~afV~f~~~~   80 (109)
T 2err_A           13 GLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGK------------ILDVEIIFNERGSKGFGFVTFENSA   80 (109)
T ss_dssp             ---------CCSCTTCCCEEEEESCCTTCCHHHHHHHGGGTCC------------CSCEEECCBTTBCTTEEEEECCCSH
T ss_pred             CCCCCCCCCCccCCCCCCEEEEECCCCcCCHHHHHHHHHhcCC------------EEEEEEEECCCCCceEEEEEECCHH
Confidence            3444455566677888999999999999999999999999998            4445543    34899999999999


Q ss_pred             HHHHHH-HcCCceecCceEEEecCCCC
Q 016936           92 EASNAM-ALDGIIFEGVAVRVRRPTDY  117 (380)
Q Consensus        92 ~a~~ai-~l~~~~i~g~~i~v~~~~~~  117 (380)
                      +|++|+ .+++..+.|++|+|.++..+
T Consensus        81 ~A~~Ai~~l~g~~~~g~~l~V~~a~~~  107 (109)
T 2err_A           81 DADRAREKLHGTVVEGRKIEVNNATAR  107 (109)
T ss_dssp             HHHHHHHHHTTCEETTEECEEEECCCS
T ss_pred             HHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            999999 69999999999999997643

>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=99.61  E-value=6e-16  Score=120.99  Aligned_cols=86  Identities=20%  Similarity=0.261  Sum_probs=73.8

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      ...++|||+|||..+++++|+++|++||.|..+.+..+..+++++|||||+|.+.++|++|+..|++..+.|+.|+|.++
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            34579999999999999999999999999954433322236889999999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 016936          230 TASSGQ  235 (380)
Q Consensus       230 ~~~~~~  235 (380)
                      .++...
T Consensus       103 ~~~~~~  108 (115)
T 2cpx_A          103 KNKKQR  108 (115)
T ss_dssp             CCCSCC
T ss_pred             cCCCCC
Confidence            876543

>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=99.61  E-value=1.2e-15  Score=115.47  Aligned_cols=79  Identities=14%  Similarity=0.362  Sum_probs=73.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHH----HHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEE
Q 016936          151 GPDRVFVGGLPYYFTETQIK----ELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  226 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~----~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v  226 (380)
                      ..++|||+|||..+++++|+    ++|++||.|..|.+.+   ++.++|||||+|.+.++|++|+..|+|..+.|+.|+|
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   83 (97)
T 1nu4_A            7 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   83 (97)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEEE
Confidence            34799999999999999999    9999999999998874   4778899999999999999999999999999999999


Q ss_pred             EEcccC
Q 016936          227 RRATAS  232 (380)
Q Consensus       227 ~~~~~~  232 (380)
                      .++.+.
T Consensus        84 ~~a~~~   89 (97)
T 1nu4_A           84 QYAKTD   89 (97)
T ss_dssp             EECSSC
T ss_pred             EEccCC
Confidence            999765

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.61  E-value=1.7e-15  Score=115.43  Aligned_cols=75  Identities=20%  Similarity=0.401  Sum_probs=69.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      ..++|||+|||..+++++|+++|++||.|..+++.      +++|||||+|.+.++|.+|+..|+|..+.|+.|+|.++.
T Consensus        26 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~------~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   99 (101)
T 2la4_A           26 RVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY------PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGK   99 (101)
T ss_dssp             SCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE------TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCC
T ss_pred             CCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe------cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEecc
Confidence            34799999999999999999999999999999987      347899999999999999999999999999999999986


Q ss_pred             c
Q 016936          231 A  231 (380)
Q Consensus       231 ~  231 (380)
                      +
T Consensus       100 ~  100 (101)
T 2la4_A          100 E  100 (101)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.61  E-value=5.7e-15  Score=115.38  Aligned_cols=85  Identities=15%  Similarity=0.260  Sum_probs=71.8

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecC
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  106 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g  106 (380)
                      ...+.++|||+|||.++++++|+++|++||.|...      .........+++|||||+|.+.++|.+|+ .|++..|.|
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~------~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g   94 (115)
T 2cpx_A           21 PGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGP------PIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYG   94 (115)
T ss_dssp             CCSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSS------CCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccce------EEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCC
Confidence            34577999999999999999999999999996431      11334445678899999999999999999 799999999


Q ss_pred             ceEEEecCCCCC
Q 016936          107 VAVRVRRPTDYN  118 (380)
Q Consensus       107 ~~i~v~~~~~~~  118 (380)
                      ++|+|.++....
T Consensus        95 ~~l~v~~a~~~~  106 (115)
T 2cpx_A           95 KILVIEFGKNKK  106 (115)
T ss_dssp             CBCEEEECCCCS
T ss_pred             cEEEEEEccCCC
Confidence            999999987653

>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=99.61  E-value=1e-15  Score=112.76  Aligned_cols=75  Identities=21%  Similarity=0.357  Sum_probs=69.2

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-Hc-CCceec
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-AL-DGIIFE  105 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l-~~~~i~  105 (380)
                      .....++|||+|||.++++++|+++|++||.            |..+.+.+++|||||+|.+.++|.+|+ .+ ++..+.
T Consensus         8 ~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~------------i~~~~~~~~kg~afV~f~~~~~A~~a~~~l~~~~~~~   75 (85)
T 2ytc_A            8 EDKTITTLYVGGLGDTITETDLRNHFYQFGE------------IRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKLIVN   75 (85)
T ss_dssp             SCSSCCCEEEECCTTTSCHHHHHHHHHTTSC------------EEEEEEEGGGTEEEEEESSHHHHHHHHHTTTTTCEET
T ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHHhCCC------------EeEEEEECCCCEEEEEECCHHHHHHHHHHhcCCeeEC
Confidence            3456799999999999999999999999987            788888889999999999999999999 58 999999


Q ss_pred             CceEEEecC
Q 016936          106 GVAVRVRRP  114 (380)
Q Consensus       106 g~~i~v~~~  114 (380)
                      |++|+|.|+
T Consensus        76 g~~l~v~~a   84 (85)
T 2ytc_A           76 GRRLNVKWG   84 (85)
T ss_dssp             TEECCEEEC
T ss_pred             CCEEEEEec
Confidence            999999985

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.61  E-value=6.4e-16  Score=119.92  Aligned_cols=77  Identities=21%  Similarity=0.156  Sum_probs=71.7

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecC
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  106 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g  106 (380)
                      ..+..++|||+|||+++++++|+++|++||.            |..+.+.+++|||||+|.+.++|++|+ .||+..+.|
T Consensus         6 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~------------i~~v~i~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   73 (111)
T 1whx_A            6 SGRSKTVILAKNLPAGTLAAEIQETFSRFGS------------LGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKFHH   73 (111)
T ss_dssp             TSEEEEEEEEESCCTTCCHHHHHHHHHTTSC------------EEEEECCSSSSCEEEEESCHHHHHHHHHHHTTCBSSS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------EEEEEEeCCCCEEEEEeCCHHHHHHHHHHhCCCEECC
Confidence            4567899999999999999999999999997            788888889999999999999999999 799999999


Q ss_pred             ceEEEecCCC
Q 016936          107 VAVRVRRPTD  116 (380)
Q Consensus       107 ~~i~v~~~~~  116 (380)
                      ++|+|.|+..
T Consensus        74 ~~l~V~~a~~   83 (111)
T 1whx_A           74 VPLYLEWAPI   83 (111)
T ss_dssp             SBCEEEEEET
T ss_pred             eEEEEEECCC
Confidence            9999999754

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.61  E-value=1.2e-15  Score=118.02  Aligned_cols=77  Identities=14%  Similarity=0.061  Sum_probs=68.0

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe------cCCCcEEEEEeCCHHHHHHHH-HcCCc
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-ALDGI  102 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~------~~~~g~afV~f~~~~~a~~ai-~l~~~  102 (380)
                      .+.++|||+|||+++++++|+++|++||.            |.++.+      ++++|||||+|.+.++|.+|+ .||+.
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~------------i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~   71 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGE------------VEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLT   71 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSC------------EEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCC------------eeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCC
Confidence            45789999999999999999999999998            555554      456799999999999999999 79999


Q ss_pred             eecCceEEEecCCCCC
Q 016936          103 IFEGVAVRVRRPTDYN  118 (380)
Q Consensus       103 ~i~g~~i~v~~~~~~~  118 (380)
                      .+.|++|+|.++....
T Consensus        72 ~~~gr~i~V~~a~~~~   87 (110)
T 3s8s_A           72 SVMGNIIHAQLDIKGQ   87 (110)
T ss_dssp             EETTEECEEEECSTTH
T ss_pred             EECCeEEEEEECCCCc
Confidence            9999999999876543

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.61  E-value=3.1e-15  Score=113.13  Aligned_cols=78  Identities=28%  Similarity=0.433  Sum_probs=70.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      ...++|||+|||+.+++++|+++|++||.|. +.++.    ++++|||||+|.+.++|++|++.|||..+.|+.|+|.++
T Consensus        17 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~----~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   91 (97)
T 2e5j_A           17 PLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTW----QGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALA   91 (97)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEE----ETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEEC
T ss_pred             CCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEc----CCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            3457999999999999999999999999997 66664    467899999999999999999999999999999999998


Q ss_pred             ccC
Q 016936          230 TAS  232 (380)
Q Consensus       230 ~~~  232 (380)
                      .++
T Consensus        92 ~~~   94 (97)
T 2e5j_A           92 RQQ   94 (97)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            765

>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=99.61  E-value=5e-15  Score=114.53  Aligned_cols=80  Identities=29%  Similarity=0.499  Sum_probs=70.3

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecC---CCcEEEEEeCCHHHHHHHH-HcCCc
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH---EKKFAFVEMRTVEEASNAM-ALDGI  102 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~---~~g~afV~f~~~~~a~~ai-~l~~~  102 (380)
                      ....+.++|||+|||.++++++|+++|++||.            |..+.+..   ++|||||+|.+.++|++|+ .+++.
T Consensus        17 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~------------v~~~~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~   84 (109)
T 1x4a_A           17 PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGA------------IRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGY   84 (109)
T ss_dssp             CCCCCSSEEEEESCCTTCCHHHHHHHHGGGSC------------EEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------eEEEEEEECCCCCcEEEEEECCHHHHHHHHHHcCCC
Confidence            45567899999999999999999999999998            56666543   5789999999999999999 89999


Q ss_pred             eecCceEEEecCCCCC
Q 016936          103 IFEGVAVRVRRPTDYN  118 (380)
Q Consensus       103 ~i~g~~i~v~~~~~~~  118 (380)
                      .|.|++|+|.++....
T Consensus        85 ~~~g~~l~V~~a~~~~  100 (109)
T 1x4a_A           85 DYDGYRLRVEFPRSGR  100 (109)
T ss_dssp             EETTEECEEECCCCCC
T ss_pred             EECCeEEEEEEcccCC
Confidence            9999999999976643

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.61  E-value=1.7e-15  Score=115.56  Aligned_cols=76  Identities=20%  Similarity=0.375  Sum_probs=71.4

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccC
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  232 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~  232 (380)
                      ++|||+|||.++++++|+++|++||.|..|.++.+     ++|||||+|.+.++|++|++.|++..+.|+.|+|.++.+.
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            37999999999999999999999999999999876     6889999999999999999999999999999999999775


Q ss_pred             C
Q 016936          233 S  233 (380)
Q Consensus       233 ~  233 (380)
                      .
T Consensus        76 ~   76 (101)
T 2hvz_A           76 P   76 (101)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.60  E-value=1.2e-15  Score=116.48  Aligned_cols=79  Identities=29%  Similarity=0.586  Sum_probs=74.5

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEccc
Q 016936          152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  231 (380)
Q Consensus       152 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~  231 (380)
                      .++|||+|||..+++++|+++|++||.|..|+++.++ ++.++|||||+|.+.++|++|+.  ++..+.|+.|.|.++..
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            3699999999999999999999999999999999998 89999999999999999999999  89999999999999876


Q ss_pred             CC
Q 016936          232 SS  233 (380)
Q Consensus       232 ~~  233 (380)
                      +.
T Consensus        86 ~~   87 (102)
T 2xs2_A           86 KQ   87 (102)
T ss_dssp             CC
T ss_pred             Cc
Confidence            53

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.60  E-value=1.3e-15  Score=117.45  Aligned_cols=80  Identities=24%  Similarity=0.316  Sum_probs=68.4

Q ss_pred             cchhhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCc
Q 016936           24 MTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGI  102 (380)
Q Consensus        24 ~~~~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~  102 (380)
                      ..+..+...++|||+|||.++++++|+++|++||.            |..+.+.  +|||||+|.+.++|++|+ .+++.
T Consensus        23 ~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~------------i~~v~i~--kg~afV~f~~~~~A~~Ai~~l~g~   88 (108)
T 2jvo_A           23 HRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGP------------MKEVKIL--NGFAFVEFEEAESAAKAIEEVHGK   88 (108)
T ss_dssp             -----CCSCSEEEECSSCTTCCHHHHHHHHTTTSC------------CCEEEEE--TTEEEEECSSHHHHHHHHHHHTTC
T ss_pred             cccCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCC------------EEEEEEE--CCEEEEEECCHHHHHHHHHHcCCC
Confidence            33456788999999999999999999999999998            5555555  899999999999999999 79999


Q ss_pred             eecCceEEEecCCCC
Q 016936          103 IFEGVAVRVRRPTDY  117 (380)
Q Consensus       103 ~i~g~~i~v~~~~~~  117 (380)
                      .+.|++|+|.++...
T Consensus        89 ~~~g~~l~V~~a~~~  103 (108)
T 2jvo_A           89 SFANQPLEVVYSKLP  103 (108)
T ss_dssp             EETTEECEEESCSCC
T ss_pred             EECCeEEEEEEecCC
Confidence            999999999997654

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=2.5e-15  Score=112.68  Aligned_cols=79  Identities=23%  Similarity=0.394  Sum_probs=69.8

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCC-eeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCC-CeeCCeEEEEE
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGT-LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNG-LKMGDKTLTVR  227 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~-i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g-~~~~g~~i~v~  227 (380)
                      ...++|||+|||..+++++|+++|++||. |..+.+.       ++|||||+|.+.++|++|++.||+ ..+.|+.|+|.
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            44579999999999999999999999999 6666653       367999999999999999999999 99999999999


Q ss_pred             EcccCCCC
Q 016936          228 RATASSGQ  235 (380)
Q Consensus       228 ~~~~~~~~  235 (380)
                      ++.++...
T Consensus        79 ~a~~~~~~   86 (93)
T 2cqh_A           79 YSVSKKLR   86 (93)
T ss_dssp             ECCCCCCC
T ss_pred             EccCcccc
Confidence            99876433

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.60  E-value=2.2e-15  Score=116.33  Aligned_cols=78  Identities=18%  Similarity=0.205  Sum_probs=67.4

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHH-HhccCCCCCCCCeeEEEEec--CCCcEEEEEeCCHHHHHHHH-HcCCc
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVM-TAIGGNSAGPGDAVVNVYIN--HEKKFAFVEMRTVEEASNAM-ALDGI  102 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G-~i~~~~~~~~~~~i~~~~~~--~~~g~afV~f~~~~~a~~ai-~l~~~  102 (380)
                      ......++|||+|||+++++++|+++|++|| .            |..+.+.  .++|||||+|.+.++|++|+ .+|+.
T Consensus        23 ~~p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~------------v~~v~i~~~~~rGfaFV~F~~~e~A~~Ai~~lng~   90 (111)
T 2jvr_A           23 KLPAKRYRITMKNLPEGCSWQDLKDLARENSLE------------TTFSSVNTRDFDGTGALEFPSEEILVEALERLNNI   90 (111)
T ss_dssp             --CCCCEEEEEECSSCCCCHHHHHHHHHHHTCC------------CSEEECSSCSSSCCEEEEESSHHHHHHHHHHTTTE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHHhCCe------------eEEEEEEcCCCCCEEEEEECCHHHHHHHHHHcCCC
Confidence            3445678999999999999999999999999 6            4555553  57899999999999999999 79999


Q ss_pred             eecCceEEEecCCC
Q 016936          103 IFEGVAVRVRRPTD  116 (380)
Q Consensus       103 ~i~g~~i~v~~~~~  116 (380)
                      .+.|++|+|.++..
T Consensus        91 ~l~Gr~i~V~~a~~  104 (111)
T 2jvr_A           91 EFRGSVITVERDDN  104 (111)
T ss_dssp             EETTEEEEEEESCC
T ss_pred             EECCeEEEEEECCC
Confidence            99999999998654

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.60  E-value=3.7e-16  Score=117.32  Aligned_cols=80  Identities=20%  Similarity=0.344  Sum_probs=67.2

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEE------ecCCCcEEEEEeCCHHHHHHHH-Hc
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVY------INHEKKFAFVEMRTVEEASNAM-AL   99 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~------~~~~~g~afV~f~~~~~a~~ai-~l   99 (380)
                      .......||||+|||+.+|+++|+++|++||.+.          +.+++      .++++|||||+|.+.++|++|+ .+
T Consensus         4 ~~~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~----------v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~l   73 (95)
T 2lkz_A            4 HHHHHMDTIILRNIAPHTVVDSIMTALSPYASLA----------VNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQIL   73 (95)
T ss_dssp             CSSCCCCEEEEESCCTTCCHHHHHHHSTTTCCCC----------GGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHH
T ss_pred             ccCCccCEEEEeCCCCcCCHHHHHHHHHhhCCcc----------EEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHh
Confidence            4566788999999999999999999999999631          23333      3567899999999999999999 78


Q ss_pred             CCc----eecCceEEEecCCC
Q 016936          100 DGI----IFEGVAVRVRRPTD  116 (380)
Q Consensus       100 ~~~----~i~g~~i~v~~~~~  116 (380)
                      |+.    .+.|++|.|.++.+
T Consensus        74 ng~~~~~~i~Gr~i~V~~Aks   94 (95)
T 2lkz_A           74 QSLHPPLKIDGKTIGVDFAKS   94 (95)
T ss_dssp             HSSSSCEEETTEEEEEEECCC
T ss_pred             cCCCCCceECCEEEEEEEccC
Confidence            886    58999999999764

>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=99.60  E-value=8.3e-16  Score=116.78  Aligned_cols=79  Identities=28%  Similarity=0.476  Sum_probs=72.2

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceec
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE  105 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~  105 (380)
                      ....+.++|||+|||+.+++++|+++|++||.            |..+.+.+++|||||+|.+.++|.+|+ .+++..|.
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------i~~v~~~~~kg~afV~f~~~~~a~~a~~~l~g~~~~   77 (99)
T 2cpj_A           10 KTFTQRSRLFVGNLPPDITEEEMRKLFEKYGK------------AGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLR   77 (99)
T ss_dssp             CCCCCTTEEEEESCCTTCCHHHHHHHTSTTCC------------CSEEEEETTTTEEEEECSSSHHHHHHHHHHTTCCBT
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHHHhhcCC------------eEEEEEecCCCEEEEEECCHHHHHHHHHHhCCCEeC
Confidence            34467799999999999999999999999987            777888889999999999999999999 89999999


Q ss_pred             CceEEEecCCCC
Q 016936          106 GVAVRVRRPTDY  117 (380)
Q Consensus       106 g~~i~v~~~~~~  117 (380)
                      |++|+|.++...
T Consensus        78 g~~l~v~~a~~~   89 (99)
T 2cpj_A           78 GKQLRVRFACHS   89 (99)
T ss_dssp             TBCCEEEESSCC
T ss_pred             CceEEEEEcCCC
Confidence            999999997654

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.60  E-value=3.6e-15  Score=112.76  Aligned_cols=79  Identities=20%  Similarity=0.272  Sum_probs=69.2

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecC
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  106 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g  106 (380)
                      .....++|||+|||+++++++|+++|++||.|.           ..+....++|||||+|.+.++|++|+ .||+..|.|
T Consensus        15 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-----------~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   83 (97)
T 2e5j_A           15 GAPLAADVYVGNLPRDARVSDLKRALRELGSVP-----------LRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGT   83 (97)
T ss_dssp             SSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-----------SEEEEETTTTEEEEECSSHHHHHHHHHHHTTCCSSS
T ss_pred             CCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-----------EEEEcCCCCcEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            345678999999999999999999999999851           23445688999999999999999999 899999999


Q ss_pred             ceEEEecCCCC
Q 016936          107 VAVRVRRPTDY  117 (380)
Q Consensus       107 ~~i~v~~~~~~  117 (380)
                      ++|+|.++...
T Consensus        84 ~~l~V~~a~~~   94 (97)
T 2e5j_A           84 DTLRVALARQQ   94 (97)
T ss_dssp             SCCEEEECCCC
T ss_pred             cEEEEEEcCCC
Confidence            99999997654

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.60  E-value=3.1e-15  Score=113.82  Aligned_cols=79  Identities=19%  Similarity=0.341  Sum_probs=69.2

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec-----CCCcEEEEEeCCHHHHHHHH-HcC
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN-----HEKKFAFVEMRTVEEASNAM-ALD  100 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~-----~~~g~afV~f~~~~~a~~ai-~l~  100 (380)
                      ....+.++|||+|||+++++++|+++|++||.            |..+.+.     +++|||||+|.+.++|.+|+ .++
T Consensus        12 ~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~------------i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~   79 (100)
T 2do4_A           12 STSLEKHKLFISGLPFSCTKEELEEICKAHGT------------VKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMD   79 (100)
T ss_dssp             SSCCCCSCEEEESCCTTCCHHHHHHHHTTTSC------------EEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHT
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhCCC------------eEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhC
Confidence            44567899999999999999999999999997            5556553     34599999999999999999 899


Q ss_pred             CceecCceEEEecCCCC
Q 016936          101 GIIFEGVAVRVRRPTDY  117 (380)
Q Consensus       101 ~~~i~g~~i~v~~~~~~  117 (380)
                      +..+.|++|+|.++...
T Consensus        80 g~~~~g~~l~v~~a~~~   96 (100)
T 2do4_A           80 GMTIKENIIKVAISNSG   96 (100)
T ss_dssp             TEESSSCEEEEEECCCC
T ss_pred             CCEECCEEEEEEECCCC
Confidence            99999999999997654

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A

Probab=99.60  E-value=7.9e-15  Score=110.82  Aligned_cols=74  Identities=16%  Similarity=0.366  Sum_probs=68.9

Q ss_pred             CCCEEEEcCCCC-CCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          151 GPDRVFVGGLPY-YFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       151 ~~~~l~V~nlp~-~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      ..++|||+|||. .+++++|+++|++||.|..+++.        +|||||+|.+.++|++|+..|+|..+.|+.|+|.++
T Consensus        21 ~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   92 (97)
T 2xnq_A           21 MKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVS   92 (97)
T ss_dssp             TTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEEC
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            347999999998 99999999999999999999883        679999999999999999999999999999999998


Q ss_pred             ccC
Q 016936          230 TAS  232 (380)
Q Consensus       230 ~~~  232 (380)
                      ..+
T Consensus        93 ~~~   95 (97)
T 2xnq_A           93 SSN   95 (97)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.60  E-value=3.8e-16  Score=149.73  Aligned_cols=83  Identities=20%  Similarity=0.420  Sum_probs=78.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      ..++|||+|||+.+++++|.++|++||.|..|.|+.++.++.++|||||+|.+.++|.+||..|||..|.|+.|.|.++.
T Consensus       101 ~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a~  180 (437)
T 3pgw_S          101 AFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  180 (437)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            34699999999999999999999999999999999998889999999999999999999999999999999999999997


Q ss_pred             cCC
Q 016936          231 ASS  233 (380)
Q Consensus       231 ~~~  233 (380)
                      ...
T Consensus       181 ~~~  183 (437)
T 3pgw_S          181 GRT  183 (437)
T ss_pred             CCC
Confidence            653

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.59  E-value=3e-15  Score=113.45  Aligned_cols=77  Identities=23%  Similarity=0.362  Sum_probs=67.4

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec---------CCCcEEEEEeCCHHHHHHHH-Hc
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN---------HEKKFAFVEMRTVEEASNAM-AL   99 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~---------~~~g~afV~f~~~~~a~~ai-~l   99 (380)
                      .+.++|||+|||+++++++|+++|++||.            |..+.+.         .++|||||+|.+.++|++|+ .|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~------------i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l   70 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGA------------IKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQL   70 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSC------------EEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------eEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHh
Confidence            46799999999999999999999999998            4444432         45789999999999999999 69


Q ss_pred             CCceecCceEEEecCCCCC
Q 016936          100 DGIIFEGVAVRVRRPTDYN  118 (380)
Q Consensus       100 ~~~~i~g~~i~v~~~~~~~  118 (380)
                      ++..|.|++|+|.++....
T Consensus        71 ~g~~~~g~~l~V~~a~~~~   89 (98)
T 2cpf_A           71 QGHTVDGHKLEVRISERAT   89 (98)
T ss_dssp             TTCEETTEECEEECSSCSS
T ss_pred             CCCeeCCeEEEEEEccCCC
Confidence            9999999999999976643

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.59  E-value=4.5e-15  Score=110.61  Aligned_cols=76  Identities=26%  Similarity=0.449  Sum_probs=68.9

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecCc
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  107 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g~  107 (380)
                      ..+.++|||+|||.++++++|+++|++||.            |..+.+.  +|||||+|.+.++|++|+ .+++..+.|+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------i~~v~~~--~g~afV~f~~~~~A~~A~~~l~g~~~~g~   70 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGK------------VLECDII--KNYGFVHIEDKTAAEDAIRNLHHYKLHGV   70 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSC------------EEEEEEE--TTEEEEEESSHHHHHHHHHHHTTCBCSSC
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCC------------EEEEEEE--CCEEEEEECCHHHHHHHHHHhcCCccCCc
Confidence            456799999999999999999999999997            6667666  799999999999999999 7999999999


Q ss_pred             eEEEecCCCCC
Q 016936          108 AVRVRRPTDYN  118 (380)
Q Consensus       108 ~i~v~~~~~~~  118 (380)
                      +|+|.++....
T Consensus        71 ~l~v~~a~~~~   81 (90)
T 2dnq_A           71 NINVEASKNKS   81 (90)
T ss_dssp             BCEEECSSCCC
T ss_pred             EEEEEECCCCC
Confidence            99999976653

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.59  E-value=6.1e-15  Score=115.20  Aligned_cols=82  Identities=23%  Similarity=0.376  Sum_probs=71.0

Q ss_pred             hhhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecC------CCcEEEEEeCCHHHHHHHH-H
Q 016936           26 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH------EKKFAFVEMRTVEEASNAM-A   98 (380)
Q Consensus        26 ~~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~------~~g~afV~f~~~~~a~~ai-~   98 (380)
                      +....+.++|||+|||..+++++|+++|++||.            |..+.+..      ++|||||+|.+.++|++|+ .
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~   76 (115)
T 2dgo_A            9 KKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGR------------ISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ   76 (115)
T ss_dssp             CCCSTTCEEEEEESCCTTCCHHHHHHHHGGGSC------------EEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHH
T ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCC------------eEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHH
Confidence            345567899999999999999999999999998            55555543      3689999999999999999 7


Q ss_pred             cCCceecCceEEEecCCCCCc
Q 016936           99 LDGIIFEGVAVRVRRPTDYNP  119 (380)
Q Consensus        99 l~~~~i~g~~i~v~~~~~~~~  119 (380)
                      +++..|.|+.|+|.++.....
T Consensus        77 l~g~~~~g~~l~V~~a~~~~~   97 (115)
T 2dgo_A           77 MGGQWLGGRQIRTNWATRKPP   97 (115)
T ss_dssp             TTTCEETTEECEEEESSCCCC
T ss_pred             hCCCEECCEEEEEEEccCCCC
Confidence            999999999999999876543

>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=99.59  E-value=3.4e-15  Score=115.77  Aligned_cols=76  Identities=18%  Similarity=0.145  Sum_probs=70.5

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccC
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  232 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~  232 (380)
                      ++|||+|||+.+++++|+++|++||.|..|.++.      ++|||||+|.+.++|++|+..|||..+.|+.|.|.|+...
T Consensus        11 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~   84 (111)
T 1whx_A           11 TVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             EEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCCC
Confidence            6899999999999999999999999999998864      4679999999999999999999999999999999998765


Q ss_pred             CC
Q 016936          233 SG  234 (380)
Q Consensus       233 ~~  234 (380)
                      ..
T Consensus        85 ~~   86 (111)
T 1whx_A           85 VF   86 (111)
T ss_dssp             TT
T ss_pred             cc
Confidence            43

>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=99.59  E-value=2.2e-15  Score=113.52  Aligned_cols=79  Identities=29%  Similarity=0.441  Sum_probs=68.1

Q ss_pred             hhhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecC-----CCcEEEEEeCCHHHHHHHH-Hc
Q 016936           26 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH-----EKKFAFVEMRTVEEASNAM-AL   99 (380)
Q Consensus        26 ~~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~-----~~g~afV~f~~~~~a~~ai-~l   99 (380)
                      .....+.++|||+|||+.+++++|+++|++||.            |.++.+..     ++|||||+|.+.++|.+|+ .+
T Consensus        10 ~~~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~------------i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l   77 (95)
T 2ywk_A           10 PAQEEADRTVFVGNLEARVREEILYELFLQAGP------------LTKVTICKDREGKPKSFGFVCFKHPESVSYAIALL   77 (95)
T ss_dssp             --CTTGGGEEEEECCCTTCCHHHHHHHHGGGSC------------EEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHH
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCC------------EEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHh
Confidence            345567899999999999999999999999997            56666543     4789999999999999999 69


Q ss_pred             CCceecCceEEEecCCC
Q 016936          100 DGIIFEGVAVRVRRPTD  116 (380)
Q Consensus       100 ~~~~i~g~~i~v~~~~~  116 (380)
                      ++..+.|++|+|.++..
T Consensus        78 ~g~~~~g~~l~V~~a~~   94 (95)
T 2ywk_A           78 NGIRLYGRPINVSGPSS   94 (95)
T ss_dssp             TTCEETTEECEEECCCC
T ss_pred             CCCEECCCEEEEEEcCC
Confidence            99999999999998653

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.59  E-value=1.9e-15  Score=118.97  Aligned_cols=78  Identities=18%  Similarity=0.274  Sum_probs=72.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCe----eEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEE
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTL----HGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  226 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i----~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v  226 (380)
                      ...+|||+|||+++++++|+++|++||.|    ..|+|+.++ +|+++|||||+|.+.++|++|++. ++..+.|+.|+|
T Consensus        22 ~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~-~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~V   99 (123)
T 2dha_A           22 NQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP-DGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIEL   99 (123)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECT-TSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECC-CCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEEE
Confidence            34799999999999999999999999985    689999985 799999999999999999999996 999999999999


Q ss_pred             EEcc
Q 016936          227 RRAT  230 (380)
Q Consensus       227 ~~~~  230 (380)
                      ..+.
T Consensus       100 ~~a~  103 (123)
T 2dha_A          100 FRST  103 (123)
T ss_dssp             EEEC
T ss_pred             EECC
Confidence            9874

>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=99.59  E-value=2.9e-15  Score=109.79  Aligned_cols=74  Identities=18%  Similarity=0.388  Sum_probs=65.5

Q ss_pred             cceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec------CCCcEEEEEeCCHHHHHHHH-HcCCcee
Q 016936           32 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN------HEKKFAFVEMRTVEEASNAM-ALDGIIF  104 (380)
Q Consensus        32 ~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~------~~~g~afV~f~~~~~a~~ai-~l~~~~i  104 (380)
                      +++|||+|||.++++++|+++|++||.            |.++.+.      .++|||||+|.+.++|++|+ .+++..+
T Consensus         1 t~~l~V~nlp~~~t~~~l~~~f~~~G~------------i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~   68 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDETLRNAFKDFPS------------YLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDL   68 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTTSTT------------EEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEE
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCC------------eeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCee
Confidence            468999999999999999999999998            5555543      33799999999999999999 6999999


Q ss_pred             cCceEEEecCCCC
Q 016936          105 EGVAVRVRRPTDY  117 (380)
Q Consensus       105 ~g~~i~v~~~~~~  117 (380)
                      .|++|+|.++..+
T Consensus        69 ~g~~l~v~~a~~~   81 (83)
T 3md1_A           69 NGRPLRINWAAKL   81 (83)
T ss_dssp             TTEECEEEECCCC
T ss_pred             CCcEEEEEecCcC
Confidence            9999999997654

>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=99.59  E-value=1.5e-14  Score=111.62  Aligned_cols=76  Identities=25%  Similarity=0.339  Sum_probs=69.4

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecC--
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG--  106 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g--  106 (380)
                      ...++|||+|||+++++++|+++|++||.            |..+.+..+ |||||+|.+.++|++|| .||+..|.|  
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~------------i~~~~i~~~-g~afV~f~~~~~a~~Ai~~l~g~~~~g~~   79 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGD------------VCYADVYRD-GTGVVEFVRKEDMTYAVRKLDNTKFRSHE   79 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSC------------EEEEEEETT-TEEEEEESSHHHHHHHHHHSSSEEEECTT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------EeEEEEecC-CEEEEEECCHHHHHHHHHHHCcCCccCCc
Confidence            45799999999999999999999999997            777887766 99999999999999999 699999999  


Q ss_pred             ---ceEEEecCCCCC
Q 016936          107 ---VAVRVRRPTDYN  118 (380)
Q Consensus       107 ---~~i~v~~~~~~~  118 (380)
                         ++|+|.++..+.
T Consensus        80 ~~~~~i~V~~a~~~~   94 (108)
T 1x4c_A           80 GETAYIRVKVDGPRS   94 (108)
T ss_dssp             SCEEEEEEEESSCCS
T ss_pred             CcceEEEEEeCCCCC
Confidence               999999987643

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.59  E-value=8.1e-15  Score=111.26  Aligned_cols=80  Identities=25%  Similarity=0.394  Sum_probs=69.8

Q ss_pred             chhhhcccceEEEcCCCCcCcHHHHHHHHHHH--HHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCC
Q 016936           25 TQQATRHARRVYVGGLPPLANEQAIATFFSQV--MTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDG  101 (380)
Q Consensus        25 ~~~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~--G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~  101 (380)
                      .+....+.++|||+|||+.+++++|+++|++|  |.            |..+.+  .+|||||+|.+.++|.+|+ .+++
T Consensus         8 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~------------v~~~~~--~~g~afV~f~~~~~A~~A~~~l~g   73 (99)
T 2cpd_A            8 DEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGA------------VERVKK--IRDYAFVHFSNREDAVEAMKALNG   73 (99)
T ss_dssp             CCSCSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTC------------EEEEEE--CSSEEEEEESSHHHHHHHHHHHSS
T ss_pred             cccccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcc------------eEEEEE--eCCeEEEEeCCHHHHHHHHHHhCC
Confidence            33556678999999999999999999999999  55            666655  4789999999999999999 6999


Q ss_pred             ceecCceEEEecCCCCC
Q 016936          102 IIFEGVAVRVRRPTDYN  118 (380)
Q Consensus       102 ~~i~g~~i~v~~~~~~~  118 (380)
                      ..|.|++|+|.++....
T Consensus        74 ~~~~g~~l~v~~a~~~~   90 (99)
T 2cpd_A           74 KVLDGSPIEVTLAKPVD   90 (99)
T ss_dssp             EEETTEEEEEECCCCCC
T ss_pred             CEeCCcEEEEEECCCCC
Confidence            99999999999976643

>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=99.59  E-value=5.2e-15  Score=113.21  Aligned_cols=80  Identities=24%  Similarity=0.390  Sum_probs=70.8

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecC----CCcEEEEEeCCHHHHHHHH-HcCC
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH----EKKFAFVEMRTVEEASNAM-ALDG  101 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~----~~g~afV~f~~~~~a~~ai-~l~~  101 (380)
                      ....+.++|||+|||+++++++|+++|++||.            |..+.+..    ++|||||+|.+.++|.+|+ .+++
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~------------v~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g   77 (103)
T 2cq3_A           10 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGK------------ILDVEIIFNERGSKGFGFVTFENSADADRAREKLHG   77 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHGGGTSC------------EEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTT
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------eEEEEEEecCCCCcEEEEEEECCHHHHHHHHHHhCC
Confidence            44567899999999999999999999999997            66777654    3899999999999999999 7999


Q ss_pred             ceecCceEEEecCCCCC
Q 016936          102 IIFEGVAVRVRRPTDYN  118 (380)
Q Consensus       102 ~~i~g~~i~v~~~~~~~  118 (380)
                      ..|.|++|+|.++....
T Consensus        78 ~~~~g~~l~v~~a~~~~   94 (103)
T 2cq3_A           78 TVVEGRKIEVNNATARV   94 (103)
T ss_dssp             CEETTEECEEEECCSSC
T ss_pred             CEECCEEEEEEEcccCC
Confidence            99999999999976643

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.37  E-value=1e-16  Score=125.67  Aligned_cols=81  Identities=25%  Similarity=0.422  Sum_probs=76.8

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeE--------EEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeE
Q 016936          152 PDRVFVGGLPYYFTETQIKELLESFGTLHG--------FDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKT  223 (380)
Q Consensus       152 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~--------v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~  223 (380)
                      .++|||+|||..+++++|+++|++||.|..        |.++.++.+++++|||||+|.+.++|++|+..|++..+.|+.
T Consensus         7 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~   86 (116)
T 2lcw_A            7 NNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNP   86 (116)
Confidence            469999999999999999999999999998        899998878999999999999999999999999999999999


Q ss_pred             EEEEEcccC
Q 016936          224 LTVRRATAS  232 (380)
Q Consensus       224 i~v~~~~~~  232 (380)
                      |+|.++.++
T Consensus        87 l~V~~a~~~   95 (116)
T 2lcw_A           87 IKVSFATRR   95 (116)
Confidence            999998765

>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=99.59  E-value=6.3e-15  Score=111.19  Aligned_cols=76  Identities=17%  Similarity=0.167  Sum_probs=68.5

Q ss_pred             cccceEEEcCCCCcCcHHHHH----HHHHHHHHhccCCCCCCCCeeEEEEecCC---CcEEEEEeCCHHHHHHHH-HcCC
Q 016936           30 RHARRVYVGGLPPLANEQAIA----TFFSQVMTAIGGNSAGPGDAVVNVYINHE---KKFAFVEMRTVEEASNAM-ALDG  101 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~----~~f~~~G~i~~~~~~~~~~~i~~~~~~~~---~g~afV~f~~~~~a~~ai-~l~~  101 (380)
                      .+.++|||+|||+++++++|+    ++|++||.            |.++.+..+   +|||||+|.+.++|++|+ .+|+
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~------------v~~v~i~~~~~~rg~afV~f~~~~~A~~Ai~~l~g   74 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGK------------VKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHR   74 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSC------------EEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCc------------EEEEEEEeCCCCCeEEEEEECCHHHHHHHHHHhCC
Confidence            456899999999999999999    99999997            777777644   899999999999999999 7999


Q ss_pred             ceecCceEEEecCCCC
Q 016936          102 IIFEGVAVRVRRPTDY  117 (380)
Q Consensus       102 ~~i~g~~i~v~~~~~~  117 (380)
                      ..+.|++|+|.++...
T Consensus        75 ~~~~gr~l~V~~a~~~   90 (96)
T 2dgx_A           75 YKIGSKKILVSLATGA   90 (96)
T ss_dssp             EEETTEEEEEEECCCS
T ss_pred             CEECCeEEEEEEcCCC
Confidence            9999999999997543

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.59  E-value=3e-15  Score=112.49  Aligned_cols=76  Identities=24%  Similarity=0.293  Sum_probs=67.6

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec------CCCcEEEEEeCCHHHHHHHH-Hc
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN------HEKKFAFVEMRTVEEASNAM-AL   99 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~------~~~g~afV~f~~~~~a~~ai-~l   99 (380)
                      ....+.++|||+|||+++++++|+++|++||.            |..+.+.      .++|||||+|.+.++|.+|+ .+
T Consensus        11 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~------------v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l   78 (94)
T 2e5h_A           11 GLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGK------------VVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI   78 (94)
T ss_dssp             SCCCCTTSEEEESCCTTSCHHHHHHHTTTTSC------------EEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHT
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCC------------eEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHc
Confidence            34457799999999999999999999999997            6666664      35789999999999999999 79


Q ss_pred             CCceecCceEEEecC
Q 016936          100 DGIIFEGVAVRVRRP  114 (380)
Q Consensus       100 ~~~~i~g~~i~v~~~  114 (380)
                      ++..|.|++|+|.++
T Consensus        79 ~g~~~~g~~l~v~~a   93 (94)
T 2e5h_A           79 NNKQLFGRVIKASIA   93 (94)
T ss_dssp             TTEEETTEEEEEEEC
T ss_pred             CCCeeCCcEEEEEec
Confidence            999999999999985

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.59  E-value=3.7e-15  Score=112.22  Aligned_cols=78  Identities=26%  Similarity=0.392  Sum_probs=68.0

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec------CCCcEEEEEeCCHHHHHHHH-Hc
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN------HEKKFAFVEMRTVEEASNAM-AL   99 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~------~~~g~afV~f~~~~~a~~ai-~l   99 (380)
                      ....+.++|||+|||+++++++|+++|++||.            |..+.+.      +++|||||+|.+.++|.+|+ .+
T Consensus        10 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~------------v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l   77 (95)
T 2cqc_A           10 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGP------------IADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA   77 (95)
T ss_dssp             CSCCGGGCEEEESCCSSCCHHHHHHHHHTTSC------------EEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHH
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCC------------eeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHh
Confidence            34556899999999999999999999999997            5555553      45789999999999999999 69


Q ss_pred             CCceecCceEEEecCCC
Q 016936          100 DGIIFEGVAVRVRRPTD  116 (380)
Q Consensus       100 ~~~~i~g~~i~v~~~~~  116 (380)
                      ++..+.|++|+|.++..
T Consensus        78 ~g~~~~g~~l~v~~a~~   94 (95)
T 2cqc_A           78 NGMELDGRRIRVSGPSS   94 (95)
T ss_dssp             TTEEETTEEEEEECCSC
T ss_pred             CCCEECCEEEEEEecCC
Confidence            99999999999998653

>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=99.58  E-value=2.3e-15  Score=118.72  Aligned_cols=80  Identities=19%  Similarity=0.383  Sum_probs=72.4

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCee--EEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLH--GFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  226 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~--~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v  226 (380)
                      .....+|||+|||+.+++++|+++|++| .|.  .|+|+.++. |+++|||||+|.+.++|++|++. ++..+.|+.|+|
T Consensus        39 ~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~~-~~~~l~gR~I~V  115 (126)
T 2hgm_A           39 SANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALGK-HKERIGHRYIEV  115 (126)
T ss_dssp             SSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHTT-TTCCBTTBCCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHHH-CCCEECCEEEEE
Confidence            3455799999999999999999999999 666  899999986 99999999999999999999995 779999999999


Q ss_pred             EEccc
Q 016936          227 RRATA  231 (380)
Q Consensus       227 ~~~~~  231 (380)
                      .++..
T Consensus       116 ~~a~~  120 (126)
T 2hgm_A          116 FKSSQ  120 (126)
T ss_dssp             EEECH
T ss_pred             EECCH
Confidence            98753

>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=99.58  E-value=2.4e-15  Score=111.23  Aligned_cols=76  Identities=25%  Similarity=0.363  Sum_probs=64.8

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec------CCCcEEEEEeCCHHHHHHHH-HcCC
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN------HEKKFAFVEMRTVEEASNAM-ALDG  101 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~------~~~g~afV~f~~~~~a~~ai-~l~~  101 (380)
                      ..+.++|||+|||.++++++|+++|++||.            |.++.+.      .++|||||+|.+.++|++|+ .+++
T Consensus         3 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~------------i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g   70 (87)
T 3bs9_A            3 LGSHFHVFVGDLSPEITTAAIAAAFAPFGR------------ISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGG   70 (87)
T ss_dssp             ---CEEEEEESCCTTCCHHHHHHHHGGGSC------------EEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCceEEEEeCCCCCCCHHHHHHHHHhcCC------------EeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCC
Confidence            346789999999999999999999999998            5555553      24689999999999999999 6999


Q ss_pred             ceecCceEEEecCCC
Q 016936          102 IIFEGVAVRVRRPTD  116 (380)
Q Consensus       102 ~~i~g~~i~v~~~~~  116 (380)
                      ..+.|++|+|.++..
T Consensus        71 ~~~~g~~l~v~~a~~   85 (87)
T 3bs9_A           71 QWLGGRQIRTNWATR   85 (87)
T ss_dssp             CEETTEECEEEEEC-
T ss_pred             CEECCeEEEEEecCC
Confidence            999999999998654

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.58  E-value=5.2e-15  Score=124.49  Aligned_cols=84  Identities=23%  Similarity=0.382  Sum_probs=78.5

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEE
Q 016936          148 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  227 (380)
Q Consensus       148 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~  227 (380)
                      .....++|||+|||+.+++++|+++|++||.|..|.++.++ ++.++|||||+|.+.++|++|++.|++..+.|+.|.|.
T Consensus        84 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~  162 (177)
T 2f3j_A           84 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ  162 (177)
T ss_dssp             SCTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34556799999999999999999999999999999999997 89999999999999999999999999999999999999


Q ss_pred             EcccC
Q 016936          228 RATAS  232 (380)
Q Consensus       228 ~~~~~  232 (380)
                      ++...
T Consensus       163 ~a~~~  167 (177)
T 2f3j_A          163 LVASQ  167 (177)
T ss_dssp             EESSG
T ss_pred             EecCC
Confidence            98654

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.58  E-value=4.2e-15  Score=112.86  Aligned_cols=79  Identities=19%  Similarity=0.402  Sum_probs=70.0

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec------CCCcEEEEEeCCHHHHHHHHHcCC
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN------HEKKFAFVEMRTVEEASNAMALDG  101 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~------~~~g~afV~f~~~~~a~~ai~l~~  101 (380)
                      ...+.++|||+|||..+++++|+++|++||.            |..+.+.      .++|||||+|.+.++|.+|+.+++
T Consensus         6 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~~~   73 (99)
T 2dgs_A            6 SGSKSNKIFVGGIPHNCGETELREYFKKFGV------------VTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMHF   73 (99)
T ss_dssp             CCSSCCEEEEESCCSSCCHHHHHHHHSSSSC------------EEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHHHCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------eEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHHhCC
Confidence            3456799999999999999999999999987            6667664      357999999999999999999999


Q ss_pred             ceecCceEEEecCCCCC
Q 016936          102 IIFEGVAVRVRRPTDYN  118 (380)
Q Consensus       102 ~~i~g~~i~v~~~~~~~  118 (380)
                      ..|.|++|+|.++..+.
T Consensus        74 ~~~~g~~l~V~~a~~~~   90 (99)
T 2dgs_A           74 HDIMGKKVEVKRAEPRD   90 (99)
T ss_dssp             CBSSSCBCEEEECCCCC
T ss_pred             CEECCeEEEEEECCCCc
Confidence            99999999999977653

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.58  E-value=5.8e-15  Score=113.72  Aligned_cols=80  Identities=21%  Similarity=0.330  Sum_probs=70.9

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCC-------CcEEEEEeCCHHHHHHHH-H
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE-------KKFAFVEMRTVEEASNAM-A   98 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~-------~g~afV~f~~~~~a~~ai-~   98 (380)
                      ....+.++|||+|||..+++++|+++|++||.            |..+.+..+       +|||||+|.+.++|.+|+ .
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~   77 (107)
T 2cph_A           10 PKKQTTSKILVRNIPFQANQREIRELFSTFGE------------LKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNA   77 (107)
T ss_dssp             CCSSCCCCEEEESCCTTCCHHHHHHHHHTTSC------------EEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHH
T ss_pred             ccCCCCCEEEEeCCCCcCCHHHHHHHHHccCC------------eEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHH
Confidence            44567899999999999999999999999997            677776544       799999999999999999 7


Q ss_pred             c-CCceecCceEEEecCCCCC
Q 016936           99 L-DGIIFEGVAVRVRRPTDYN  118 (380)
Q Consensus        99 l-~~~~i~g~~i~v~~~~~~~  118 (380)
                      + ++..|.|++|+|.++....
T Consensus        78 l~~~~~~~g~~l~v~~a~~~~   98 (107)
T 2cph_A           78 LCHSTHLYGRRLVLEWADSEV   98 (107)
T ss_dssp             HHTCCBSSSCBCEEEECCCCC
T ss_pred             hccCCeECCCEEEEEeCCCCC
Confidence            8 9999999999999976643

>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=99.58  E-value=4.9e-15  Score=111.79  Aligned_cols=77  Identities=26%  Similarity=0.444  Sum_probs=68.8

Q ss_pred             ccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec------CCCcEEEEEeCCHHHHHHHH-HcCCce
Q 016936           31 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN------HEKKFAFVEMRTVEEASNAM-ALDGII  103 (380)
Q Consensus        31 ~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~------~~~g~afV~f~~~~~a~~ai-~l~~~~  103 (380)
                      ++++|||+|||.++++++|+++|++||.            |.++.+.      .++|||||+|.+.++|.+|+ .+++..
T Consensus         1 P~~~l~V~nLp~~~t~~~l~~~F~~~G~------------i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~   68 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQTEEQILDLCSNVGP------------VINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQ   68 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSC------------EEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCC------------EEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCe
Confidence            4689999999999999999999999997            6677664      34799999999999999999 799999


Q ss_pred             ecCceEEEecCCCCCc
Q 016936          104 FEGVAVRVRRPTDYNP  119 (380)
Q Consensus       104 i~g~~i~v~~~~~~~~  119 (380)
                      +.|++|+|.++.....
T Consensus        69 ~~g~~l~V~~a~~~~~   84 (96)
T 2x1f_A           69 LGSRFLKCGYSSNSDI   84 (96)
T ss_dssp             ETTEECEEEECSCSSG
T ss_pred             ECCeEEEEEEcCCCCC
Confidence            9999999999876543

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.58  E-value=2.5e-15  Score=114.67  Aligned_cols=79  Identities=22%  Similarity=0.331  Sum_probs=69.5

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec-----CCCcEEEEEeCCHHHHHHHHHcCC
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN-----HEKKFAFVEMRTVEEASNAMALDG  101 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~-----~~~g~afV~f~~~~~a~~ai~l~~  101 (380)
                      ..+...++|||+|||+++|+++|+++|++||.            |.++.+.     .++|||||+|.+.++|.+|+.+++
T Consensus         6 ~~~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~------------v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~~~~   73 (103)
T 1s79_A            6 KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQ------------VLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPG   73 (103)
T ss_dssp             SSCSGGGCEEEECCCTTCCHHHHHHHHHTSSC------------EEEEEEECCCTTSCCCEEEEEESSHHHHHHHHTSSC
T ss_pred             cccCCCCEEEEECCCCCCCHHHHHHHHhhcCC------------EEEEEEEECCCCCCccEEEEEECCHHHHHHHHHcCC
Confidence            34566799999999999999999999999998            6666654     468999999999999999999999


Q ss_pred             ceecCceEEEecCCCC
Q 016936          102 IIFEGVAVRVRRPTDY  117 (380)
Q Consensus       102 ~~i~g~~i~v~~~~~~  117 (380)
                      ..+.|++|.|.++.++
T Consensus        74 ~~~~gr~l~V~~~~~~   89 (103)
T 1s79_A           74 QKYKETDLLILFKDDY   89 (103)
T ss_dssp             CCCTTTTCEEEEHHHH
T ss_pred             CEECCEEEEEEEchHH
Confidence            9999999999986553

>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=99.58  E-value=3.2e-15  Score=110.07  Aligned_cols=74  Identities=26%  Similarity=0.458  Sum_probs=66.5

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec------CCCcEEEEEeCCHHHHHHHH-HcCC
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN------HEKKFAFVEMRTVEEASNAM-ALDG  101 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~------~~~g~afV~f~~~~~a~~ai-~l~~  101 (380)
                      ..+.++|||+|||+++++++|+++|++||.            |.++.+.      .++|||||+|.+.++|.+|+ .+++
T Consensus         4 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~------------i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g   71 (85)
T 3mdf_A            4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGD------------ITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNE   71 (85)
T ss_dssp             CCCSSEEEEECCCTTCCHHHHHHHHGGGSC------------EEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhccCC------------EEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCC
Confidence            457899999999999999999999999997            6666653      35799999999999999999 8999


Q ss_pred             ceecCceEEEecC
Q 016936          102 IIFEGVAVRVRRP  114 (380)
Q Consensus       102 ~~i~g~~i~v~~~  114 (380)
                      ..+.|++|+|.++
T Consensus        72 ~~~~g~~l~v~~a   84 (85)
T 3mdf_A           72 SELFGRTIRVNLA   84 (85)
T ss_dssp             CEETTEECEEEEC
T ss_pred             CEECCcEEEEEEc
Confidence            9999999999985

>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=99.58  E-value=8.3e-15  Score=111.17  Aligned_cols=78  Identities=26%  Similarity=0.349  Sum_probs=69.7

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecC------CCcEEEEEeCCHHHHHHHH-HcCC
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH------EKKFAFVEMRTVEEASNAM-ALDG  101 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~------~~g~afV~f~~~~~a~~ai-~l~~  101 (380)
                      ..+.++|||+|||+++++++|+++|++||.            |..+.+..      ++|||||+|.+.++|.+|+ .+++
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g   72 (99)
T 1whw_A            5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGP------------LSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDG   72 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSC------------EEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------EeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCC
Confidence            457899999999999999999999999997            66777643      4699999999999999999 8999


Q ss_pred             ceecCceEEEecCCCCC
Q 016936          102 IIFEGVAVRVRRPTDYN  118 (380)
Q Consensus       102 ~~i~g~~i~v~~~~~~~  118 (380)
                      ..|.|++|+|.++....
T Consensus        73 ~~~~g~~l~V~~a~~~~   89 (99)
T 1whw_A           73 QVFQGRMLHVLPSTIKK   89 (99)
T ss_dssp             EESSSCEEEEEECCCCS
T ss_pred             CEECCcEEEEEEcCCCc
Confidence            99999999999977654

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.58  E-value=4.3e-15  Score=114.86  Aligned_cols=83  Identities=12%  Similarity=0.233  Sum_probs=64.9

Q ss_pred             ccchhhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec------CCCcEEEEEeCCHHHHHHH
Q 016936           23 VMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN------HEKKFAFVEMRTVEEASNA   96 (380)
Q Consensus        23 ~~~~~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~------~~~g~afV~f~~~~~a~~a   96 (380)
                      ........+.++|||+|||.++++++|+++|++||.            |..+.+.      .++|||||+|.+.++|.+|
T Consensus        16 ~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~------------i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~A   83 (109)
T 2rs2_A           16 PRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGE------------VKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV   83 (109)
T ss_dssp             ----------CCEEEESCCTTCCHHHHHHHHTTTSC------------EEEEEECCCTTTCCCTTCEEEEESSHHHHHHH
T ss_pred             ccccccCCCCCEEEEeCCCCCCCHHHHHHHHHccCC------------eEEEEEEECCCCCCcCcEEEEEECCHHHHHHH
Confidence            344466778999999999999999999999999998            6666653      4579999999999999999


Q ss_pred             HHcCCceecCceEEEecCCCC
Q 016936           97 MALDGIIFEGVAVRVRRPTDY  117 (380)
Q Consensus        97 i~l~~~~i~g~~i~v~~~~~~  117 (380)
                      +...+..+.|+.|+|.++..+
T Consensus        84 i~~~~~~l~g~~l~V~~a~~~  104 (109)
T 2rs2_A           84 LAQSRHELDSKTIDPKVAFPR  104 (109)
T ss_dssp             HHSSCEEETTEEEEEEECCCC
T ss_pred             HHHCCCcCCCEEEEEEEccCC
Confidence            966679999999999987654

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3

Probab=99.58  E-value=5.9e-15  Score=112.78  Aligned_cols=88  Identities=23%  Similarity=0.371  Sum_probs=69.1

Q ss_pred             ceEEEEeccCC-cccCC---Ch-----------HHHHHHHHHHHHhh-cccCCeEEEEecCCCCCCCCCCCccEEEEEee
Q 016936          278 AKVLCLTEAIT-ADALA---DD-----------EEYEEILEDMREEC-GKYGTLVNVVIPRPDQNGGETPGVGKVFLEYY  341 (380)
Q Consensus       278 ~~~~~l~~~~~-~~~~~---~~-----------~~~~~~~~~L~~~f-~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~  341 (380)
                      ++++.+.|++. ++...   ++           ..+.++.++|+++| ++||.|.+|.++++.. +   +..|+|||+|.
T Consensus         1 s~~~~l~nm~~~p~~~~~~~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~-~---~~~G~~fV~f~   76 (104)
T 1jmt_A            1 SQTIALLNIYRNPQNSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLG-D---HLVGNVYVKFR   76 (104)
T ss_dssp             CCEEEEEEEEECCC------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSS-S---SSEEEEEEEES
T ss_pred             CcEEEEeeccCCccccccccCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCC-C---CccEEEEEEEC
Confidence            36788888883 44322   22           22456668888888 9999999999988653 2   34577899999


Q ss_pred             chhhHHHHHHHHcCcccCCeEEEEEecc
Q 016936          342 DAVGCATAKNALSGRKFGGNTVNAFYYP  369 (380)
Q Consensus       342 ~~~~A~~A~~~l~g~~i~gr~l~v~~~~  369 (380)
                      +.++|.+|+..|||+.|+||.|+|+|+|
T Consensus        77 ~~~~A~~A~~~lng~~~~Gr~i~v~~sp  104 (104)
T 1jmt_A           77 REEDAEKAVIDLNNRWFNGQPIHAELSP  104 (104)
T ss_dssp             CHHHHHHHHHHHTTCEETTEECCEEECC
T ss_pred             CHHHHHHHHHHHCCCEECCEEEEEEEcC
Confidence            9999999999999999999999999986

>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=99.58  E-value=2.5e-15  Score=117.20  Aligned_cols=80  Identities=28%  Similarity=0.372  Sum_probs=70.9

Q ss_pred             chhhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec------CCCcEEEEEeCCHHHHHHHHH
Q 016936           25 TQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN------HEKKFAFVEMRTVEEASNAMA   98 (380)
Q Consensus        25 ~~~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~------~~~g~afV~f~~~~~a~~ai~   98 (380)
                      ....+...++|||+|||.++++++|+++|++||.            |..+.+.      .++|||||+|.+.++|.+|+.
T Consensus        18 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~   85 (114)
T 2cq4_A           18 LSPEERDARTVFCMQLAARIRPRDLEDFFSAVGK------------VRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG   85 (114)
T ss_dssp             CCTTHHHHTEEEEESCCTTCCHHHHHHHHTTTSC------------EEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH
T ss_pred             cCcccCCCCEEEEeCCCCCCCHHHHHHHHHhCCC------------EeEEEEEecCCCCccCcEEEEEeCcHHHHHHHHH
Confidence            3356778899999999999999999999999997            6666663      467999999999999999999


Q ss_pred             cCCceecCceEEEecCCC
Q 016936           99 LDGIIFEGVAVRVRRPTD  116 (380)
Q Consensus        99 l~~~~i~g~~i~v~~~~~  116 (380)
                      +++..|.|++|+|.++..
T Consensus        86 l~g~~~~g~~l~V~~a~~  103 (114)
T 2cq4_A           86 LTGQRLLGVPIIVQASQA  103 (114)
T ss_dssp             HTTEEETTEEEEEEEHHH
T ss_pred             cCCCEeCCeEEEEEecCC
Confidence            999999999999998644

>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=99.58  E-value=1.1e-14  Score=112.82  Aligned_cols=73  Identities=25%  Similarity=0.493  Sum_probs=68.5

Q ss_pred             CCEEEEcCCCCC-CCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          152 PDRVFVGGLPYY-FTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       152 ~~~l~V~nlp~~-~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      .++|||+|||+. +++++|+++|++||.|..|.+        ++|||||+|.+.++|++|+..|++..+.|+.|+|.++.
T Consensus        27 ~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~   98 (110)
T 1wf1_A           27 NSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAG   98 (110)
T ss_dssp             SSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEESC
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECC
Confidence            479999999999 999999999999999999988        36799999999999999999999999999999999987


Q ss_pred             cC
Q 016936          231 AS  232 (380)
Q Consensus       231 ~~  232 (380)
                      ..
T Consensus        99 ~~  100 (110)
T 1wf1_A           99 EP  100 (110)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.58  E-value=6.1e-15  Score=116.75  Aligned_cols=79  Identities=15%  Similarity=0.267  Sum_probs=68.6

Q ss_pred             hhcccceEEEcCCCCcCcHHHHH----HHHHHHHHhccCCCCCCCCeeEEEEe---cCCCcEEEEEeCCHHHHHHHH-Hc
Q 016936           28 ATRHARRVYVGGLPPLANEQAIA----TFFSQVMTAIGGNSAGPGDAVVNVYI---NHEKKFAFVEMRTVEEASNAM-AL   99 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~----~~f~~~G~i~~~~~~~~~~~i~~~~~---~~~~g~afV~f~~~~~a~~ai-~l   99 (380)
                      ...+.++|||+|||+.+++++|+    ++|++||.            |.++.+   .+++|||||+|.+.++|..|+ .+
T Consensus        25 ~~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~------------I~~v~i~~~~~~rG~aFV~F~~~~~A~~Ai~~l   92 (127)
T 2a3j_A           25 HTEPSQVVLITNINPEVPKEKLQALLYALASSQGD------------ILDIVVDLSDDNSGKAYIVFATQESAQAFVEAF   92 (127)
T ss_dssp             CCSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSC------------EEEEEECCCCSSCCCEEEEESSHHHHHHHHHHS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCC------------eEEEEeccCCCcCCEEEEEECCHHHHHHHHHHH
Confidence            34568999999999999999876    69999998            555554   467899999999999999999 89


Q ss_pred             CCceecCceEEEecCCCCC
Q 016936          100 DGIIFEGVAVRVRRPTDYN  118 (380)
Q Consensus       100 ~~~~i~g~~i~v~~~~~~~  118 (380)
                      ||..|.|++|+|.|+....
T Consensus        93 ng~~l~gr~l~V~~a~~~~  111 (127)
T 2a3j_A           93 QGYPFQGNPLVITFSETPQ  111 (127)
T ss_dssp             TTCCCTTSCCEEEECCCCC
T ss_pred             CCCEeCCCEEEEEEccCcc
Confidence            9999999999999987654

>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=99.58  E-value=3.1e-15  Score=110.70  Aligned_cols=76  Identities=16%  Similarity=0.392  Sum_probs=66.2

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe------cCCCcEEEEEeCCHHHHHHHHHcC
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAMALD  100 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~------~~~~g~afV~f~~~~~a~~ai~l~  100 (380)
                      ..+.+.++|||+|||+++++++|+++|++||.            |..+.+      ++++|||||+|.+.++|.+|++++
T Consensus         6 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~   73 (87)
T 3s7r_A            6 KNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGE------------VVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQK   73 (87)
T ss_dssp             -CCSCTTEEEEECCCTTCCHHHHHHHHTTTSC------------EEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHSS
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCC------------EEEEEEeecCCCCccccEEEEEECCHHHHHHHHHhC
Confidence            45678899999999999999999999999998            555554      334789999999999999999889


Q ss_pred             CceecCceEEEecC
Q 016936          101 GIIFEGVAVRVRRP  114 (380)
Q Consensus       101 ~~~i~g~~i~v~~~  114 (380)
                      +..+.|++|+|.++
T Consensus        74 ~~~~~g~~i~v~~A   87 (87)
T 3s7r_A           74 EHRLDGRVIDPKKA   87 (87)
T ss_dssp             CEEETTEEEEEEEC
T ss_pred             CCEECCEEEEEEeC
Confidence            99999999999864

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.58  E-value=3.4e-15  Score=112.65  Aligned_cols=78  Identities=15%  Similarity=0.307  Sum_probs=71.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      ..++|||+|||..+++++|+++|++||.|..+   .  .++.++|||||+|.+.++|++|+..|+|..+.|+.|+|.++.
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---S--QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTG   89 (96)
T ss_dssp             GGGEEEEESCCSSCCHHHHHHHHCSEEEECCE---E--ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe---C--CCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcC
Confidence            34799999999999999999999999988766   2  368899999999999999999999999999999999999997


Q ss_pred             cCC
Q 016936          231 ASS  233 (380)
Q Consensus       231 ~~~  233 (380)
                      ++.
T Consensus        90 ~~~   92 (96)
T 1fjc_A           90 EKG   92 (96)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            654

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.58  E-value=9e-15  Score=110.33  Aligned_cols=78  Identities=18%  Similarity=0.252  Sum_probs=70.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEE-EEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGF-DLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v-~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      ..++|||+|||+.+++++|+++|++||.|..| .++.++.+    |.|||+|.+.++|++|+..|||..+.|+.|+|.++
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~----~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a   89 (96)
T 2e44_A           14 RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET----AVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYI   89 (96)
T ss_dssp             SCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSS----EEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEEC
T ss_pred             CCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCC----CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            45799999999999999999999999999999 47776543    34999999999999999999999999999999999


Q ss_pred             ccC
Q 016936          230 TAS  232 (380)
Q Consensus       230 ~~~  232 (380)
                      .++
T Consensus        90 ~~~   92 (96)
T 2e44_A           90 PDE   92 (96)
T ss_dssp             CCC
T ss_pred             Ccc
Confidence            776

>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=99.58  E-value=5.1e-15  Score=109.79  Aligned_cols=75  Identities=17%  Similarity=0.241  Sum_probs=69.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      ..++|||+|||+.+++++|+++|++| .|..+++.      +++|||||+|.+.++|++|++.|||..+.|++|+|.++.
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            34799999999999999999999999 99999884      568999999999999999999999999999999999986


Q ss_pred             cC
Q 016936          231 AS  232 (380)
Q Consensus       231 ~~  232 (380)
                      ..
T Consensus        77 ~~   78 (88)
T 1wg1_A           77 TD   78 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.58  E-value=8.2e-15  Score=110.11  Aligned_cols=79  Identities=24%  Similarity=0.393  Sum_probs=69.5

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      ...++|||+|||+.+++++|+++|++||.|..|  +.++.+++   ||||+|.+.++|++|+. |++..+.|+.|.|.++
T Consensus         6 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a   79 (94)
T 2e5g_A            6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPR   79 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEEC
Confidence            344799999999999999999999999999987  44544554   99999999999999999 9999999999999988


Q ss_pred             ccCCC
Q 016936          230 TASSG  234 (380)
Q Consensus       230 ~~~~~  234 (380)
                      ..+..
T Consensus        80 ~~~~~   84 (94)
T 2e5g_A           80 EQKEF   84 (94)
T ss_dssp             CCSCC
T ss_pred             CcCCC
Confidence            76543

>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=99.57  E-value=4.5e-15  Score=115.00  Aligned_cols=76  Identities=21%  Similarity=0.380  Sum_probs=67.9

Q ss_pred             hhcccceEEEcCCCCc-CcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceec
Q 016936           28 ATRHARRVYVGGLPPL-ANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE  105 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~-~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~  105 (380)
                      +....++|||+|||++ +++++|+++|++||.            |..+.+  ++|||||+|.+.++|++|+ .+++..|.
T Consensus        23 ~~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~------------v~~v~i--~~g~afV~f~~~~~A~~A~~~l~g~~~~   88 (110)
T 1wf1_A           23 PKSINSRVFIGNLNTALVKKSDVETIFSKYGR------------VAGCSV--HKGYAFVQYSNERHARAAVLGENGRVLA   88 (110)
T ss_dssp             CTTCSSEEEECSCCCSSCCHHHHHHHHGGGSC------------CSEEEE--ETTEEEEECSSSHHHHHHHHHHTTCEET
T ss_pred             CCCCCcEEEEeCCCcccCCHHHHHHHHHhCCC------------eEEEEE--eCCEEEEEECCHHHHHHHHHHcCCCEEC
Confidence            4455699999999999 999999999999998            555655  7899999999999999999 89999999


Q ss_pred             CceEEEecCCCC
Q 016936          106 GVAVRVRRPTDY  117 (380)
Q Consensus       106 g~~i~v~~~~~~  117 (380)
                      |++|+|.++...
T Consensus        89 g~~l~V~~a~~~  100 (110)
T 1wf1_A           89 GQTLDINMAGEP  100 (110)
T ss_dssp             TEECCEEESCCC
T ss_pred             CeEEEEEECCCC
Confidence            999999997643

>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=99.57  E-value=7.9e-16  Score=123.73  Aligned_cols=81  Identities=16%  Similarity=0.197  Sum_probs=73.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      ...++|||+|||+++++++|+++|++|| |..|+|+.+++ ++++|||||+|.+.++|++|+ .+++..+.|+.|+|..+
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            3457999999999999999999999999 66999999975 999999999999999999999 68999999999999998


Q ss_pred             ccCC
Q 016936          230 TASS  233 (380)
Q Consensus       230 ~~~~  233 (380)
                      ....
T Consensus       121 ~~~~  124 (139)
T 2hgn_A          121 STTG  124 (139)
T ss_dssp             CCSC
T ss_pred             CCCC
Confidence            7653

>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=99.57  E-value=4.2e-15  Score=114.41  Aligned_cols=78  Identities=14%  Similarity=0.224  Sum_probs=69.4

Q ss_pred             CCCCEEEEcCCCCC-CCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhC--CCeeCCeEEEE
Q 016936          150 EGPDRVFVGGLPYY-FTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN--GLKMGDKTLTV  226 (380)
Q Consensus       150 ~~~~~l~V~nlp~~-~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~--g~~~~g~~i~v  226 (380)
                      ...++|||+|||++ +++++|+++|++||.|..|.+.+      ++|||||+|.+.++|++|++.|+  +..+.|++|+|
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 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKV   96 (112)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEE
T ss_pred             CCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            34579999999998 99999999999999999999964      36899999999999999999885  46799999999


Q ss_pred             EEcccCC
Q 016936          227 RRATASS  233 (380)
Q Consensus       227 ~~~~~~~  233 (380)
                      .++..+.
T Consensus        97 ~~a~~~~  103 (112)
T 1x4f_A           97 DLSEKYK  103 (112)
T ss_dssp             EEECSCS
T ss_pred             EECcccc
Confidence            9987653

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.57  E-value=8.2e-15  Score=110.31  Aligned_cols=77  Identities=23%  Similarity=0.361  Sum_probs=68.2

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec------CCCcEEEEEeCCHHHHHHHH-HcCCc
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN------HEKKFAFVEMRTVEEASNAM-ALDGI  102 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~------~~~g~afV~f~~~~~a~~ai-~l~~~  102 (380)
                      .++++|||+|||.++++++|+++|++||.            |..+.+.      +++|||||+|.+.++|.+|+ .+++.
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~------------v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~   70 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGK------------IDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGF   70 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSC------------EEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCC------------EeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCC
Confidence            46799999999999999999999999997            5666653      35789999999999999999 69999


Q ss_pred             eecCceEEEecCCCCC
Q 016936          103 IFEGVAVRVRRPTDYN  118 (380)
Q Consensus       103 ~i~g~~i~v~~~~~~~  118 (380)
                      .|.|++|+|.++..+.
T Consensus        71 ~~~g~~l~V~~a~~~~   86 (95)
T 2dnz_A           71 ELAGRPMRVGHVTERL   86 (95)
T ss_dssp             CSSSSCCEEEESSCCC
T ss_pred             eeCCcEEEEEEccccc
Confidence            9999999999976653

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.57  E-value=1.8e-14  Score=111.92  Aligned_cols=99  Identities=22%  Similarity=0.356  Sum_probs=81.3

Q ss_pred             CCccceEEEEeccCCcccCC-ChHHHHHHHHHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHH
Q 016936          274 GETLAKVLCLTEAITADALA-DDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNA  352 (380)
Q Consensus       274 ~~~~~~~~~l~~~~~~~~~~-~~~~~~~~~~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~  352 (380)
                      .+.+++++.+.|++...++. +..++.+++++|+++|++||.|.+|.+... .    +  .|+|||+|.+.++|.+|++.
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 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR-H----P--DGVASVSFRDPEEADYCIQT   83 (112)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT-C----T--TCEEEEECSCHHHHHHHHHH
T ss_pred             CCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEEecC-C----C--CEEEEEEECCHHHHHHHHHH
Confidence            46789999999998877643 345678899999999999999999977432 2    2  36779999999999999999


Q ss_pred             HcCcccCCeEEEEEeccc-cccccccCC
Q 016936          353 LSGRKFGGNTVNAFYYPE-DKYFNKDYS  379 (380)
Q Consensus       353 l~g~~i~gr~l~v~~~~~-~~~~~~~~~  379 (380)
                      |||+.|+||+|+|.|+.+ ..|..+.-+
T Consensus        84 lng~~~~gr~l~v~~a~~~~~~~~~~~s  111 (112)
T 2dit_A           84 LDGRWFGGRQITAQAWDGTTDYQSGPSS  111 (112)
T ss_dssp             STTCEETTEECEEEECCSCCCSSCCCCC
T ss_pred             cCCCEECCcEEEEEEeCCCCCcccCCCC
Confidence            999999999999999877 455554433

>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=99.57  E-value=5.7e-15  Score=109.46  Aligned_cols=75  Identities=21%  Similarity=0.329  Sum_probs=66.6

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec-------CCCcEEEEEeCCHHHHHHHH-HcCC
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN-------HEKKFAFVEMRTVEEASNAM-ALDG  101 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~-------~~~g~afV~f~~~~~a~~ai-~l~~  101 (380)
                      ..+++|||+|||.++++++|+++|++||.            |.++.+.       +++|||||+|.+.++|.+|+ .+++
T Consensus         2 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g   69 (88)
T 4a8x_A            2 MKPTKVHIGRLTRNVTKDHIMEIFSTYGK------------IKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDG   69 (88)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTTSC------------EEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCC------------EEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCC
Confidence            45789999999999999999999999997            6666652       26899999999999999999 6999


Q ss_pred             ceecCceEEEecCCC
Q 016936          102 IIFEGVAVRVRRPTD  116 (380)
Q Consensus       102 ~~i~g~~i~v~~~~~  116 (380)
                      ..+.|++|+|.++..
T Consensus        70 ~~~~g~~l~v~~a~~   84 (88)
T 4a8x_A           70 GQIDGQEITATAVLA   84 (88)
T ss_dssp             CEETTEECEEEEECC
T ss_pred             CeECCeEEEEEECCC
Confidence            999999999998644

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.57  E-value=6.6e-15  Score=112.39  Aligned_cols=78  Identities=27%  Similarity=0.516  Sum_probs=68.3

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecC------CCcEEEEEeCCHHHHHHHH-HcCC
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH------EKKFAFVEMRTVEEASNAM-ALDG  101 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~------~~g~afV~f~~~~~a~~ai-~l~~  101 (380)
                      ..+.++|||+|||+++++++|+++|++||.            |..+.+..      ++|||||+|.+.++|.+|+ .+++
T Consensus         9 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~------------i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g   76 (102)
T 1x5s_A            9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQ------------ISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNG   76 (102)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHHSC------------CCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTT
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCC------------eEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCC
Confidence            346799999999999999999999999998            55555543      5789999999999999999 8999


Q ss_pred             ceecCceEEEecCCCCC
Q 016936          102 IIFEGVAVRVRRPTDYN  118 (380)
Q Consensus       102 ~~i~g~~i~v~~~~~~~  118 (380)
                      ..|.|++|+|.++....
T Consensus        77 ~~~~g~~l~v~~a~~~~   93 (102)
T 1x5s_A           77 KSVDGRQIRVDQAGKSS   93 (102)
T ss_dssp             CCTTSCCCEEEEEECCC
T ss_pred             CEECCeEEEEEECCCCC
Confidence            99999999999976543

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.57  E-value=1.3e-14  Score=108.09  Aligned_cols=76  Identities=22%  Similarity=0.418  Sum_probs=68.7

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecC
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  106 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g  106 (380)
                      ...+.++|||+|||.++++++|+++|++||.            |..+.+.  ++||||+|.+.++|++|+ .+++..+.|
T Consensus         5 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------v~~~~~~--~~~afV~f~~~~~a~~A~~~l~g~~~~g   70 (90)
T 2dnp_A            5 SSGNTWKIFVGNVSAACTSQELRSLFERRGR------------VIECDVV--KDYAFVHMEKEADAKAAIAQLNGKEVKG   70 (90)
T ss_dssp             SSCCSCCEEEESCCTTCCHHHHHHHHHHHSC------------EEEEEEC--SSCEEEEESCHHHHHHHHHHHTTCEETT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHcCCC------------EEEEEEE--CCEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            4567899999999999999999999999997            7777776  559999999999999999 699999999


Q ss_pred             ceEEEecCCCC
Q 016936          107 VAVRVRRPTDY  117 (380)
Q Consensus       107 ~~i~v~~~~~~  117 (380)
                      ++|+|.++...
T Consensus        71 ~~l~v~~a~~~   81 (90)
T 2dnp_A           71 KRINVELSTKG   81 (90)
T ss_dssp             EECEEEESCCC
T ss_pred             cEEEEEECCCC
Confidence            99999997654

>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=99.57  E-value=4.8e-15  Score=113.79  Aligned_cols=80  Identities=21%  Similarity=0.270  Sum_probs=69.5

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecC-----CCcEEEEEeCCHHHHHHHH-HcC
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH-----EKKFAFVEMRTVEEASNAM-ALD  100 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~-----~~g~afV~f~~~~~a~~ai-~l~  100 (380)
                      ....+.++|||+|||+.+++++|+++|++||.            |..+.+..     ++|||||+|.+.++|.+|+ .|+
T Consensus        10 ~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~------------i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~   77 (105)
T 2dnh_A           10 SRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGV------------IDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALH   77 (105)
T ss_dssp             CSCCCCCEEEEESCCTTCCHHHHHHHHTTTSC------------EEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHS
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------eEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHc
Confidence            44567899999999999999999999999998            55565543     3799999999999999999 799


Q ss_pred             CceecC---ceEEEecCCCCC
Q 016936          101 GIIFEG---VAVRVRRPTDYN  118 (380)
Q Consensus       101 ~~~i~g---~~i~v~~~~~~~  118 (380)
                      +..+.|   ++|+|.++....
T Consensus        78 g~~~~gg~~~~l~V~~a~~~~   98 (105)
T 2dnh_A           78 GSQTMPGASSSLVVKFADTDK   98 (105)
T ss_dssp             SCCCCTTCSSCCEEEESCSSC
T ss_pred             CCccCCCCCccEEEEECccCc
Confidence            999998   999999976543

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A

Probab=99.57  E-value=1.4e-14  Score=118.45  Aligned_cols=78  Identities=23%  Similarity=0.288  Sum_probs=70.7

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCC--eEEEEEEc
Q 016936          152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD--KTLTVRRA  229 (380)
Q Consensus       152 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g--~~i~v~~~  229 (380)
                      ..+|||+||++.+++++|+++|++||.|.+|.+..+    +++|||||+|.+.++|++|++.|||..|.|  +.|+|.++
T Consensus        46 vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k----~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~A  121 (164)
T 1sjr_A           46 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS  121 (164)
T ss_dssp             EEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES----SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEEC
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC----CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEe
Confidence            357999999999999999999999999999998654    257899999999999999999999999965  99999999


Q ss_pred             ccCC
Q 016936          230 TASS  233 (380)
Q Consensus       230 ~~~~  233 (380)
                      .++.
T Consensus       122 k~~~  125 (164)
T 1sjr_A          122 KLTS  125 (164)
T ss_dssp             SSSS
T ss_pred             cCCc
Confidence            8763

>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=99.57  E-value=9.6e-15  Score=114.17  Aligned_cols=78  Identities=23%  Similarity=0.483  Sum_probs=68.2

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec-----CCCcEEEEEeCCHHHHHHHH-HcCCc
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN-----HEKKFAFVEMRTVEEASNAM-ALDGI  102 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~-----~~~g~afV~f~~~~~a~~ai-~l~~~  102 (380)
                      ..+.++|||+|||.++++++|+++|++||.            |.++.+.     .++|||||+|.+.++|++|+ .+++.
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~------------i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~   71 (116)
T 2fy1_A            4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGP------------ISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGK   71 (116)
T ss_dssp             TCSCCEEEEECCTTTCCHHHHHHHHHTSSC------------CSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------EEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCC
Confidence            456799999999999999999999999998            4445543     35699999999999999999 79999


Q ss_pred             eecCceEEEecCCCCC
Q 016936          103 IFEGVAVRVRRPTDYN  118 (380)
Q Consensus       103 ~i~g~~i~v~~~~~~~  118 (380)
                      .|.|++|+|.++....
T Consensus        72 ~~~g~~l~V~~a~~~~   87 (116)
T 2fy1_A           72 SLHGKAIKVEQAKKPS   87 (116)
T ss_dssp             BCSSSBCEEEECCCSS
T ss_pred             EECCEEEEEEECCCCC
Confidence            9999999999976544

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.57  E-value=6.1e-15  Score=111.27  Aligned_cols=75  Identities=16%  Similarity=0.379  Sum_probs=69.5

Q ss_pred             CCCEEEEcCCCC-CCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          151 GPDRVFVGGLPY-YFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       151 ~~~~l~V~nlp~-~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      ..++|||+|||. .+++++|+++|++||.|..|.+.        +|||||+|.+.++|++|+..|++..+.|+.|+|.++
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            347999999998 99999999999999999999984        579999999999999999999999999999999998


Q ss_pred             ccCC
Q 016936          230 TASS  233 (380)
Q Consensus       230 ~~~~  233 (380)
                      ....
T Consensus        81 ~~~~   84 (96)
T 2kvi_A           81 SSNA   84 (96)
T ss_dssp             ECCC
T ss_pred             CcCC
Confidence            7654

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.57  E-value=1.6e-14  Score=113.88  Aligned_cols=79  Identities=22%  Similarity=0.306  Sum_probs=70.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceE-EEEEEcChhHHHHHHHHhCCCeeCC--eEEEE
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGY-GFCVYQDPAVTDIACAALNGLKMGD--KTLTV  226 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~-afV~f~~~~~A~~Ai~~l~g~~~~g--~~i~v  226 (380)
                      +.-.+|||+||++.+++++|+++|++||.|.+|++..+     ++|+ |||+|.+.++|++|++.|||..+.|  +.|+|
T Consensus        26 s~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~-----~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI  100 (130)
T 3zzy_A           26 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRI  100 (130)
T ss_dssp             CSEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE-----TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEE
T ss_pred             CceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC-----CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEE
Confidence            34457999999999999999999999999999988764     2577 9999999999999999999999988  99999


Q ss_pred             EEcccCC
Q 016936          227 RRATASS  233 (380)
Q Consensus       227 ~~~~~~~  233 (380)
                      +++++..
T Consensus       101 ~~ak~~~  107 (130)
T 3zzy_A          101 DFSKLTS  107 (130)
T ss_dssp             EECSCSS
T ss_pred             EecCCCc
Confidence            9997653

>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=99.57  E-value=8.3e-15  Score=112.47  Aligned_cols=80  Identities=30%  Similarity=0.450  Sum_probs=70.0

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec------CCCcEEEEEeCCHHHHHHHH-Hc
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN------HEKKFAFVEMRTVEEASNAM-AL   99 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~------~~~g~afV~f~~~~~a~~ai-~l   99 (380)
                      ......++|||+|||.++++++|+++|++||.            |..+.+.      .++|||||+|.+.++|.+|+ .|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l   77 (105)
T 1x5u_A           10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGP------------VVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM   77 (105)
T ss_dssp             CCCCTTTEEEEECCCTTCCHHHHHHHHHTTSC------------EEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHS
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------eEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHh
Confidence            34567899999999999999999999999997            6666654      35689999999999999999 69


Q ss_pred             CCceecCceEEEecCCCCC
Q 016936          100 DGIIFEGVAVRVRRPTDYN  118 (380)
Q Consensus       100 ~~~~i~g~~i~v~~~~~~~  118 (380)
                      ++..|.|++|+|.++....
T Consensus        78 ~g~~~~g~~l~v~~a~~~~   96 (105)
T 1x5u_A           78 DMIKLYGKPIRVNKASAHN   96 (105)
T ss_dssp             SSCBCSSCBCEEEETTTTS
T ss_pred             CCCeECCeEEEEEECCCCC
Confidence            9999999999999976643

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.57  E-value=5.2e-15  Score=111.61  Aligned_cols=80  Identities=16%  Similarity=0.313  Sum_probs=67.2

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCee-EEE---EecCCCcEEEEEeCCHHHHHHHH-HcCCcee
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAV-VNV---YINHEKKFAFVEMRTVEEASNAM-ALDGIIF  104 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i-~~~---~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i  104 (380)
                      .+.++|||+|||+++++++|+++|++||.|..         + ...   ....++|||||+|.+.++|++|+ .+++..+
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~---------~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~   73 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQ---------TPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYL   73 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSS---------CCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeE---------EEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEE
Confidence            46799999999999999999999999998532         2 111   12345899999999999999999 5999999


Q ss_pred             cCceEEEecCCCCC
Q 016936          105 EGVAVRVRRPTDYN  118 (380)
Q Consensus       105 ~g~~i~v~~~~~~~  118 (380)
                      .|++|+|.++....
T Consensus        74 ~g~~l~v~~a~~~~   87 (96)
T 1x5t_A           74 CNRPITVSYAFKKD   87 (96)
T ss_dssp             TTEECEEEESCCCC
T ss_pred             CCEEEEEEEecccC
Confidence            99999999976653

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.57  E-value=3.8e-15  Score=114.00  Aligned_cols=80  Identities=21%  Similarity=0.285  Sum_probs=70.5

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec----CCCcEEEEEeCCHHHHHHHH-HcCC
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN----HEKKFAFVEMRTVEEASNAM-ALDG  101 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~----~~~g~afV~f~~~~~a~~ai-~l~~  101 (380)
                      ....+.++|||+|||+.+++++|+++|++||.            |..+.+.    .++|||||+|.+.++|.+|+ .+++
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------i~~v~i~~~~g~~~g~afV~f~~~~~A~~A~~~l~g   77 (103)
T 2d9p_A           10 ITRYQVVNLYVKNLDDGIDDERLRKAFSPFGT------------ITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNG   77 (103)
T ss_dssp             CCCSSCCCEEEECCCTTCCHHHHHHTTTTTSC------------EEEEEEEECSSSEEEEEEEEESSHHHHHHHHHHHTT
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------EEEEEEEcCCCCcCEEEEEEECCHHHHHHHHHHhCC
Confidence            44568899999999999999999999999998            5555554    45899999999999999999 6999


Q ss_pred             ceecCceEEEecCCCCC
Q 016936          102 IIFEGVAVRVRRPTDYN  118 (380)
Q Consensus       102 ~~i~g~~i~v~~~~~~~  118 (380)
                      ..|.|++|+|.++..+.
T Consensus        78 ~~~~g~~l~V~~a~~~~   94 (103)
T 2d9p_A           78 RIVATKPLYVALAQRKE   94 (103)
T ss_dssp             CBSSSSBCEEEECSSCC
T ss_pred             CEeCCcEEEEEEecccc
Confidence            99999999999977654

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.56  E-value=1.2e-14  Score=106.23  Aligned_cols=72  Identities=13%  Similarity=0.159  Sum_probs=64.6

Q ss_pred             EEEEcCCCCCCCHHH----HHHHHHhcC-CeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          154 RVFVGGLPYYFTETQ----IKELLESFG-TLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       154 ~l~V~nlp~~~t~~~----l~~~F~~~G-~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      .|||+|||+.+++++    |+++|++|| .|..|       ++   |+|||+|.+.++|++|++.|+|..+.|++|+|.+
T Consensus        11 ~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~~   80 (96)
T 2diu_A           11 LLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFGNRIIVSF   80 (96)
T ss_dssp             EEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEES
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCCceEEEEe
Confidence            399999999999987    558999995 99877       33   8999999999999999999999999999999999


Q ss_pred             cccCCCC
Q 016936          229 ATASSGQ  235 (380)
Q Consensus       229 ~~~~~~~  235 (380)
                      +..+...
T Consensus        81 A~~~sd~   87 (96)
T 2diu_A           81 TPKNREL   87 (96)
T ss_dssp             SCCSCCC
T ss_pred             cCCCcce
Confidence            9877543

>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=99.56  E-value=2.4e-14  Score=109.50  Aligned_cols=75  Identities=21%  Similarity=0.317  Sum_probs=67.7

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecCce
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  108 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g~~  108 (380)
                      .+.++|||+|||+++++++|+++|++||.            |..+.+.  ++||||+|.+.++|.+|+ .|++..|.|++
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~------------i~~v~~~--~~~afV~f~~~~~a~~A~~~l~g~~~~g~~   74 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGK------------LERVKKL--KDYAFIHFDERDGAVKAMEEMNGKDLEGEN   74 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSC------------EEEEEEC--SSCEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------EEEEEEE--CCEEEEEeCCHHHHHHHHHHHCCCccCCCE
Confidence            45799999999999999999999999997            6777665  679999999999999999 69999999999


Q ss_pred             EEEecCCCCC
Q 016936          109 VRVRRPTDYN  118 (380)
Q Consensus       109 i~v~~~~~~~  118 (380)
                      |+|.++....
T Consensus        75 l~v~~a~~~~   84 (103)
T 2dgu_A           75 IEIVFAKPPD   84 (103)
T ss_dssp             EEEEECCCCC
T ss_pred             EEEEEcCCCc
Confidence            9999986654

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.56  E-value=3.4e-14  Score=107.77  Aligned_cols=77  Identities=18%  Similarity=0.276  Sum_probs=70.0

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhc--CCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEE
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESF--GTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  227 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~  227 (380)
                      ...++|||+|||+.+++++|+++|++|  |.|..+.+.        +|||||+|.+.++|++|+..||+..+.|+.|+|.
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            344799999999999999999999999  889988774        4599999999999999999999999999999999


Q ss_pred             EcccCCC
Q 016936          228 RATASSG  234 (380)
Q Consensus       228 ~~~~~~~  234 (380)
                      ++.++..
T Consensus        85 ~a~~~~~   91 (99)
T 2cpd_A           85 LAKPVDK   91 (99)
T ss_dssp             CCCCCCC
T ss_pred             ECCCCCC
Confidence            9987643

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.56  E-value=3.9e-15  Score=113.90  Aligned_cols=79  Identities=24%  Similarity=0.326  Sum_probs=69.6

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec------CCCcEEEEEeCCHHHHHHHH-HcC
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN------HEKKFAFVEMRTVEEASNAM-ALD  100 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~------~~~g~afV~f~~~~~a~~ai-~l~  100 (380)
                      ...+.++|||+|||.++++++|+++|++||.            |..+.+.      .++|||||+|.+.++|++|+ .++
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~------------i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~   76 (103)
T 2dnm_A            9 DVDGMITLKVDNLTYRTSPDSLRRVFEKYGR------------VGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMD   76 (103)
T ss_dssp             CCSCCCEEEEESCCTTCCHHHHHHHHTTTSC------------EEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHS
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhcCC------------EEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcC
Confidence            3456899999999999999999999999987            6667653      35799999999999999999 699


Q ss_pred             CceecCceEEEecCCCCC
Q 016936          101 GIIFEGVAVRVRRPTDYN  118 (380)
Q Consensus       101 ~~~i~g~~i~v~~~~~~~  118 (380)
                      +..|.|++|+|.++....
T Consensus        77 g~~~~g~~l~V~~a~~~~   94 (103)
T 2dnm_A           77 GAELDGRELRVQVARYGR   94 (103)
T ss_dssp             SCCBTTBCCEEEECSSCC
T ss_pred             CCEECCcEEEEEECCcCC
Confidence            999999999999976543

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.56  E-value=5e-15  Score=113.05  Aligned_cols=78  Identities=24%  Similarity=0.440  Sum_probs=68.6

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe------cCCCcEEEEEeCCHHHHHHHH-HcCC
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-ALDG  101 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~------~~~~g~afV~f~~~~~a~~ai-~l~~  101 (380)
                      ..+.++|||+|||+++++++|+++|++||.            |..+.+      .+++|||||+|.+.++|++|+ .+++
T Consensus         9 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~------------i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g   76 (102)
T 2cqb_A            9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGD------------ITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNE   76 (102)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHTTTSC------------CCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhccCC------------EEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCC
Confidence            356899999999999999999999999998            444554      346899999999999999999 7999


Q ss_pred             ceecCceEEEecCCCCC
Q 016936          102 IIFEGVAVRVRRPTDYN  118 (380)
Q Consensus       102 ~~i~g~~i~v~~~~~~~  118 (380)
                      ..|.|++|+|.++....
T Consensus        77 ~~~~g~~l~V~~a~~~~   93 (102)
T 2cqb_A           77 SELFGRTIRVNLAKPMR   93 (102)
T ss_dssp             EEETTEEEEEEECCCCC
T ss_pred             CEECCcEEEEEeCCCCC
Confidence            99999999999977654

>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=99.56  E-value=4.6e-15  Score=110.24  Aligned_cols=76  Identities=29%  Similarity=0.448  Sum_probs=67.2

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec------CCCcEEEEEeCCHHHHHHHHHcCCc
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN------HEKKFAFVEMRTVEEASNAMALDGI  102 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~------~~~g~afV~f~~~~~a~~ai~l~~~  102 (380)
                      +.+.++|||+|||+++++++|+++|++||.            |..+.+.      +++|||||+|.+.++|.+|+.+++.
T Consensus         3 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~g~   70 (89)
T 3ucg_A            3 EADARSIYVGNVDYGATAEELEAHFHGCGS------------VNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALDES   70 (89)
T ss_dssp             HHHHTEEEEESCCTTCCHHHHHHHHGGGCC------------EEEEEEEESCSSSSCCEEEEEEESSTHHHHHHGGGTTC
T ss_pred             CCcCCEEEEeCCCCCCCHHHHHHHHHhCCC------------EEEEEEEecCCCCCcceEEEEEECCHHHHHHHHhcCCC
Confidence            456799999999999999999999999998            5555543      4589999999999999999999999


Q ss_pred             eecCceEEEecCCC
Q 016936          103 IFEGVAVRVRRPTD  116 (380)
Q Consensus       103 ~i~g~~i~v~~~~~  116 (380)
                      .+.|++|+|.++..
T Consensus        71 ~~~g~~l~V~~a~~   84 (89)
T 3ucg_A           71 LFRGRQIKVIPKRT   84 (89)
T ss_dssp             EETTEECEEEETTT
T ss_pred             EECCcEEEEEEccC
Confidence            99999999998654

>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=99.56  E-value=2.4e-14  Score=111.04  Aligned_cols=79  Identities=22%  Similarity=0.340  Sum_probs=69.8

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec------CCCcEEEEEeCCHHHHHHHH-HcC
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN------HEKKFAFVEMRTVEEASNAM-ALD  100 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~------~~~g~afV~f~~~~~a~~ai-~l~  100 (380)
                      ...+.++|||+|||+++++++|+++|++||.            |.++.+.      .++|||||+|.+.++|.+|+ .++
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~------------i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~   78 (111)
T 1x4h_A           11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGD------------LKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAAS   78 (111)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSC------------EEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHC
T ss_pred             cCCCCCEEEEECCCCCCCHHHHHHHHHhcCC------------eEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhc
Confidence            3456799999999999999999999999997            6677664      45899999999999999999 799


Q ss_pred             ------CceecCceEEEecCCCCC
Q 016936          101 ------GIIFEGVAVRVRRPTDYN  118 (380)
Q Consensus       101 ------~~~i~g~~i~v~~~~~~~  118 (380)
                            +..|.|++|+|.++..+.
T Consensus        79 ~~~~~~~~~~~g~~l~v~~a~~~~  102 (111)
T 1x4h_A           79 LEAEGGGLKLDGRQLKVDLAVTRD  102 (111)
T ss_dssp             TTTTTCCEESSSCEEEEECCCCCC
T ss_pred             cccccCCcEEcCEEEEEEECCCCc
Confidence                  999999999999977653

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.56  E-value=3e-14  Score=111.40  Aligned_cols=78  Identities=19%  Similarity=0.324  Sum_probs=68.5

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecC------CCcEEEEEeCCHHHHHHHH-Hc
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH------EKKFAFVEMRTVEEASNAM-AL   99 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~------~~g~afV~f~~~~~a~~ai-~l   99 (380)
                      ..+.+.++|||+|||+++++++|+++|++||.            |.++.+..      ++|||||+|.+.++|++|+ .+
T Consensus        12 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~   79 (116)
T 2cqd_A           12 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGD------------IEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP   79 (116)
T ss_dssp             CCSCSSSEEEEECCCSSCCHHHHHHHHHTTSC------------EEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCS
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCC------------eeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhC
Confidence            45667899999999999999999999999997            66666643      5789999999999999999 67


Q ss_pred             CCceecCceEEEecCCCC
Q 016936          100 DGIIFEGVAVRVRRPTDY  117 (380)
Q Consensus       100 ~~~~i~g~~i~v~~~~~~  117 (380)
                      ++ .|.|++|+|.++...
T Consensus        80 ~~-~~~g~~l~V~~a~~~   96 (116)
T 2cqd_A           80 NP-IIDGRKANVNLAYLG   96 (116)
T ss_dssp             SC-EETTEECEEEESTTT
T ss_pred             CC-cCCCEEEEEEEcccC
Confidence            87 899999999998654

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.56  E-value=1e-14  Score=114.12  Aligned_cols=80  Identities=20%  Similarity=0.422  Sum_probs=69.0

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe------cCCCcEEEEEeCCHHHHHHHHHcC
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAMALD  100 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~------~~~~g~afV~f~~~~~a~~ai~l~  100 (380)
                      ....+.++|||+|||.++++++|+++|++||.            |..+.+      +.++|||||+|.+.++|.+|+..+
T Consensus        22 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~------------i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~   89 (116)
T 1x4b_A           22 REKEQFRKLFIGGLSFETTEESLRNYYEQWGK------------LTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAAR   89 (116)
T ss_dssp             CHHHHHTEEEEECCTTCCCHHHHHHHHTSSCC------------CSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSC
T ss_pred             cccCCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------EEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHhC
Confidence            45667899999999999999999999999998            444444      345799999999999999999669


Q ss_pred             CceecCceEEEecCCCCC
Q 016936          101 GIIFEGVAVRVRRPTDYN  118 (380)
Q Consensus       101 ~~~i~g~~i~v~~~~~~~  118 (380)
                      +..|.|++|+|.++..+.
T Consensus        90 ~~~~~g~~l~V~~a~~~~  107 (116)
T 1x4b_A           90 PHSIDGRVVEPKRAVARE  107 (116)
T ss_dssp             SEEETTEEEEEECCSSCC
T ss_pred             CcEECCEEEEEEECCCCc
Confidence            999999999999976654

>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=99.56  E-value=1.4e-14  Score=111.40  Aligned_cols=80  Identities=18%  Similarity=0.259  Sum_probs=69.1

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec------CCCcEEEEEeCCHHHHHHHH-Hc
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN------HEKKFAFVEMRTVEEASNAM-AL   99 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~------~~~g~afV~f~~~~~a~~ai-~l   99 (380)
                      ..+.+.++|||+|||.++++++|+++|++||.            |..+.+.      +++|||||+|.+.++|.+|+ .+
T Consensus         8 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l   75 (106)
T 2dgp_A            8 MKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGK------------IYELTVLKDRFTGMHKGCAFLTYCERESALKAQSAL   75 (106)
T ss_dssp             CCCTTCEEEEEESCCTTCCHHHHHHHHHHHSC------------CCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHH
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------eeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHh
Confidence            34567899999999999999999999999998            5555553      46799999999999999999 79


Q ss_pred             CCcee---cCceEEEecCCCCC
Q 016936          100 DGIIF---EGVAVRVRRPTDYN  118 (380)
Q Consensus       100 ~~~~i---~g~~i~v~~~~~~~  118 (380)
                      ++..+   .|++|+|.++....
T Consensus        76 ~g~~~~~~~g~~l~v~~a~~~~   97 (106)
T 2dgp_A           76 HEQKTLPGMNRPIQVKPADSES   97 (106)
T ss_dssp             TTTCCCTTCSSCCEEEECCCCS
T ss_pred             cCCcccCCCCceEEEEECCccc
Confidence            99887   88999999976643

>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=99.56  E-value=5.5e-15  Score=114.00  Aligned_cols=79  Identities=22%  Similarity=0.376  Sum_probs=69.1

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec------CCCcEEEEEeCCHHHHHHHH-Hc
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN------HEKKFAFVEMRTVEEASNAM-AL   99 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~------~~~g~afV~f~~~~~a~~ai-~l   99 (380)
                      ....+.++|||+|||..+++++|+++|++||.            |..+.+.      .++|||||+|.+.++|.+|+ .+
T Consensus        21 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~------------i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l   88 (108)
T 2jrs_A           21 KGSAGPMRLYVGSLHFNITEDMLRGIFEPFGR------------IESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL   88 (108)
T ss_dssp             CSCSSCEEEEEECCCSSCCHHHHHHHHTTTSC------------EEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHH
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------eEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHc
Confidence            45677899999999999999999999999998            5555543      34689999999999999999 79


Q ss_pred             CCceecCceEEEecCCCC
Q 016936          100 DGIIFEGVAVRVRRPTDY  117 (380)
Q Consensus       100 ~~~~i~g~~i~v~~~~~~  117 (380)
                      ++..+.|++|+|.++..+
T Consensus        89 ~g~~i~g~~l~V~~a~~k  106 (108)
T 2jrs_A           89 NGFELAGRPMKVGHVTER  106 (108)
T ss_dssp             TTCCSSSSCCEEECSCSS
T ss_pred             CCCEECCEEEEEEEcccC
Confidence            999999999999997654

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.56  E-value=3.9e-14  Score=107.02  Aligned_cols=77  Identities=22%  Similarity=0.338  Sum_probs=69.5

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      ...++|||+|+  .+++++|+++|++||.|..|.+.      +++|||||+|.+.++|++|+..|++..+.|+.|+|.++
T Consensus        13 ~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a   84 (97)
T 1x5p_A           13 RKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA   84 (97)
T ss_dssp             CCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECC
T ss_pred             CCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEC
Confidence            34579999996  89999999999999999999884      45789999999999999999999999999999999999


Q ss_pred             ccCCC
Q 016936          230 TASSG  234 (380)
Q Consensus       230 ~~~~~  234 (380)
                      .++..
T Consensus        85 ~~~~~   89 (97)
T 1x5p_A           85 RKQPM   89 (97)
T ss_dssp             SSCCC
T ss_pred             CCCCC
Confidence            77643

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.55  E-value=5.1e-15  Score=112.40  Aligned_cols=86  Identities=22%  Similarity=0.351  Sum_probs=65.9

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe----cCCCcEEEEEeCCHHHHHHHH-HcCC
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI----NHEKKFAFVEMRTVEEASNAM-ALDG  101 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~----~~~~g~afV~f~~~~~a~~ai-~l~~  101 (380)
                      ......++|||+|||.++++++|+++|++||.|.....  ...++..+..    +.++|||||+|.+.++|.+|+ .+++
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~--~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g   85 (99)
T 2la6_A            8 HSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKK--TGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDG   85 (99)
T ss_dssp             CSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETT--TTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTT
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccc--cccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCC
Confidence            44566799999999999999999999999998421000  0000022222    234799999999999999999 7999


Q ss_pred             ceecCceEEEecC
Q 016936          102 IIFEGVAVRVRRP  114 (380)
Q Consensus       102 ~~i~g~~i~v~~~  114 (380)
                      ..+.|++|+|.++
T Consensus        86 ~~~~g~~l~V~~A   98 (99)
T 2la6_A           86 KEFSGNPIKVSFA   98 (99)
T ss_dssp             CBSSSSBCEEEEC
T ss_pred             CEeCCcEEEEEec
Confidence            9999999999885

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.55  E-value=9e-15  Score=112.26  Aligned_cols=79  Identities=23%  Similarity=0.361  Sum_probs=69.1

Q ss_pred             hhcccceEEEcCCCCcC------cHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec----CCCcEEEEEeCCHHHHHHHH
Q 016936           28 ATRHARRVYVGGLPPLA------NEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN----HEKKFAFVEMRTVEEASNAM   97 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~------t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~----~~~g~afV~f~~~~~a~~ai   97 (380)
                      ....+++|||+|||+.+      ++++|+++|++||.            |.++.+.    +++|||||+|.+.++|.+|+
T Consensus        11 ~~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~------------v~~v~i~~~~g~~~G~afV~f~~~~~A~~Ai   78 (105)
T 2nlw_A           11 ADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGK------------ITNDFYPEEDGKTKGYIFLEYASPAHAVDAV   78 (105)
T ss_dssp             CCSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSC------------EEEEECCCBTTBSCCEEEEEECSSSHHHHHH
T ss_pred             CCCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCC------------EEEEEeeCCCCCeeeEEEEEECCHHHHHHHH
Confidence            44567999999999999      88999999999998            5666654    56899999999999999999


Q ss_pred             -HcCCceecCc-eEEEecCCCCC
Q 016936           98 -ALDGIIFEGV-AVRVRRPTDYN  118 (380)
Q Consensus        98 -~l~~~~i~g~-~i~v~~~~~~~  118 (380)
                       .+||..|.|+ +|+|.++.+..
T Consensus        79 ~~l~g~~~~g~~~l~V~~a~~~~  101 (105)
T 2nlw_A           79 KNADGYKLDKQHTFRVNLFTDFD  101 (105)
T ss_dssp             HHCSSEECSTTCEEEEECSCCCC
T ss_pred             HHhCCcccCCCceEEEEEcchHh
Confidence             7999999998 99999987643

>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=99.55  E-value=1.5e-14  Score=111.37  Aligned_cols=77  Identities=23%  Similarity=0.345  Sum_probs=68.8

Q ss_pred             CCCEEEE--cCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCee-----CCeE
Q 016936          151 GPDRVFV--GGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM-----GDKT  223 (380)
Q Consensus       151 ~~~~l~V--~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~-----~g~~  223 (380)
                      ..++|||  +||++.+++++|+++|++||.|..|.++.+      +|||||+|.+.++|++|++.|||+.+     .|++
T Consensus        24 pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~------rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~   97 (114)
T 2cq2_A           24 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKIT   97 (114)
T ss_dssp             CCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEE
T ss_pred             CCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcE
Confidence            3478999  779999999999999999999999988642      68999999999999999999999988     7899


Q ss_pred             EEEEEcccCC
Q 016936          224 LTVRRATASS  233 (380)
Q Consensus       224 i~v~~~~~~~  233 (380)
                      |.|.++....
T Consensus        98 l~v~~a~~~p  107 (114)
T 2cq2_A           98 LYLNFVEKVQ  107 (114)
T ss_dssp             CEEEEESCCC
T ss_pred             EEEEecccCc
Confidence            9999987544

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens}

Probab=99.55  E-value=1.7e-14  Score=117.24  Aligned_cols=81  Identities=21%  Similarity=0.269  Sum_probs=72.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEE--------EEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCC
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGF--------DLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD  221 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v--------~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g  221 (380)
                      ...++|||+|||+.+++++|+++|++||.|..+        ++.   .+++++|||||+|.+.++|.+|+..|||..+.|
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            344799999999999999999999999998774        222   268899999999999999999999999999999


Q ss_pred             eEEEEEEcccCC
Q 016936          222 KTLTVRRATASS  233 (380)
Q Consensus       222 ~~i~v~~~~~~~  233 (380)
                      +.|.|.++....
T Consensus       120 ~~l~V~~a~~~~  131 (143)
T 3egn_A          120 KPMVVQFARSAR  131 (143)
T ss_dssp             EECEEEECCCSC
T ss_pred             cEEEEEECCCCC
Confidence            999999997653

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.55  E-value=1.4e-14  Score=108.38  Aligned_cols=78  Identities=27%  Similarity=0.441  Sum_probs=69.0

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceec
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE  105 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~  105 (380)
                      ....+.++|||+|||.++++++|+++|++||.            |..+.+.  ++||||+|.+.++|.+|+ .+++..+.
T Consensus         5 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~------------v~~v~~~--~~~afV~f~~~~~a~~A~~~l~g~~~~   70 (92)
T 2dgt_A            5 SSGKASTKLHVGNISPTCTNQELRAKFEEYGP------------VIECDIV--KDYAFVHMERAEDAVEAIRGLDNTEFQ   70 (92)
T ss_dssp             CCCCSSEEEEEESCCSSCCHHHHHHHHHTTSC------------CCEEEEC--SSEEEEEESCHHHHHHHHHHHTTEEET
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------eEEEEEE--CCEEEEEECCHHHHHHHHHHhCCCeeC
Confidence            34567899999999999999999999999997            6666665  559999999999999999 79999999


Q ss_pred             CceEEEecCCCCC
Q 016936          106 GVAVRVRRPTDYN  118 (380)
Q Consensus       106 g~~i~v~~~~~~~  118 (380)
                      |++|+|.++....
T Consensus        71 g~~l~V~~a~~~~   83 (92)
T 2dgt_A           71 GKRMHVQLSTSRL   83 (92)
T ss_dssp             TEEEEEEESSCCC
T ss_pred             CcEEEEEEccCCC
Confidence            9999999976643

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.55  E-value=3.4e-15  Score=113.78  Aligned_cols=81  Identities=20%  Similarity=0.278  Sum_probs=68.6

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecC
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  106 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g  106 (380)
                      .+.+.++|||+|||.++++++|+++|++||.|.          +......+++|||||+|.+.++|++|+ .+++..|.|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~----------~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g   80 (101)
T 2fc9_A           11 WSGESKTLVLSNLSYSATEETLQEVFEKATFIK----------VPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEG   80 (101)
T ss_dssp             CSCCCSEEEEESCCTTCCHHHHHHHCSSCSEEE----------CCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEEE----------EEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCC
Confidence            456789999999999999999999999998741          111134567899999999999999999 699999999


Q ss_pred             ceEEEecCCCCC
Q 016936          107 VAVRVRRPTDYN  118 (380)
Q Consensus       107 ~~i~v~~~~~~~  118 (380)
                      ++|+|.++....
T Consensus        81 ~~l~v~~a~~~~   92 (101)
T 2fc9_A           81 RAIRLELQGPRG   92 (101)
T ss_dssp             EEEEEEECSSCC
T ss_pred             eEEEEEEcCCCC
Confidence            999999976643

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.55  E-value=5.4e-15  Score=110.61  Aligned_cols=77  Identities=21%  Similarity=0.273  Sum_probs=67.5

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec----CCCcEEEEEeCCHHHHHHHH-HcCCce
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN----HEKKFAFVEMRTVEEASNAM-ALDGII  103 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~----~~~g~afV~f~~~~~a~~ai-~l~~~~  103 (380)
                      ..+.++|||+|||.++++++|+++|++||.            |..+.+.    .++|||||+|.+.++|++|+ .+++..
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~------------v~~~~i~~~~g~~~g~afV~f~~~~~a~~a~~~l~g~~   72 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGH------------VLYADIKMENGKSKGCGVVKFESPEVAERACRMMNGMK   72 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSC------------EEEEEEEESSSCEEEEEEEEESSHHHHHHHHHHHTTCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCC------------EEEEEEEccCCCcceEEEEEECCHHHHHHHHHHhCCCE
Confidence            456799999999999999999999999998            4555543    35799999999999999999 699999


Q ss_pred             ecCceEEEecCCCC
Q 016936          104 FEGVAVRVRRPTDY  117 (380)
Q Consensus       104 i~g~~i~v~~~~~~  117 (380)
                      +.|++|+|.++...
T Consensus        73 ~~g~~l~v~~a~~~   86 (92)
T 2dgv_A           73 LSGREIDVRIDRNA   86 (92)
T ss_dssp             BTTBCCCCEECSCC
T ss_pred             ECCcEEEEEEcCCC
Confidence            99999999987654

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.55  E-value=2.3e-14  Score=115.84  Aligned_cols=80  Identities=18%  Similarity=0.299  Sum_probs=69.9

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec------CCCcEEEEEeCCHHHHHHHH-Hc
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN------HEKKFAFVEMRTVEEASNAM-AL   99 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~------~~~g~afV~f~~~~~a~~ai-~l   99 (380)
                      ......++|||+|||.++++++|+++|+.||.            |.++.+.      +++|||||+|.+.++|.+|+ .+
T Consensus        37 ~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~------------i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l  104 (139)
T 1u6f_A           37 PEPDVLRNLMVNYIPTTVDEVQLRQLFERYGP------------IESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL  104 (139)
T ss_dssp             CCTTTTSEEEEESCSTTCCHHHHHHHHHHHSC------------EEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHT
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------eEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHh
Confidence            45677899999999999999999999999998            5555543      34799999999999999999 69


Q ss_pred             CCceecCceEEEecCCCCC
Q 016936          100 DGIIFEGVAVRVRRPTDYN  118 (380)
Q Consensus       100 ~~~~i~g~~i~v~~~~~~~  118 (380)
                      ++..|.|++|+|.++....
T Consensus       105 ~g~~~~g~~l~v~~a~~~~  123 (139)
T 1u6f_A          105 NGFNILNKRLKVALAASGH  123 (139)
T ss_dssp             TTEECSSCEEEEEESSCCC
T ss_pred             CCCEECCeEEEEEECCCCC
Confidence            9999999999999977653

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.55  E-value=1e-14  Score=115.50  Aligned_cols=79  Identities=24%  Similarity=0.419  Sum_probs=69.5

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe------cCCCcEEEEEeCCHHHHHHHHHcC
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAMALD  100 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~------~~~~g~afV~f~~~~~a~~ai~l~  100 (380)
                      ....+.++|||+|||.++++++|+++|++||.            |.++.+      +.++|||||+|.+.++|.+|+.++
T Consensus        31 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~l~   98 (124)
T 2jwn_A           31 KKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGS------------INRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMD   98 (124)
T ss_dssp             HHHHHHTEEEEEEECTTCCHHHHHHHHHTTSC------------EEEEEEEEECTTSSCEEEEEEEESSHHHHHHHHTTT
T ss_pred             cccCCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------EEEEEEEecCCCCCcccEEEEEECCHHHHHHHHhcC
Confidence            55677899999999999999999999999998            455544      345899999999999999999999


Q ss_pred             CceecCceEEEecCCCC
Q 016936          101 GIIFEGVAVRVRRPTDY  117 (380)
Q Consensus       101 ~~~i~g~~i~v~~~~~~  117 (380)
                      +..|.|+.|+|.++...
T Consensus        99 g~~~~g~~l~V~~a~~~  115 (124)
T 2jwn_A           99 ETVFRGRTIKVLPKRTN  115 (124)
T ss_dssp             TCEETTEECEEEESSCC
T ss_pred             CCeECCeEEEEEECCCC
Confidence            99999999999997643

>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=99.55  E-value=2.2e-15  Score=114.59  Aligned_cols=86  Identities=17%  Similarity=0.277  Sum_probs=64.0

Q ss_pred             CCccccchhhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe-------cCCCcEEEEEeCCHH
Q 016936           19 MPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-------NHEKKFAFVEMRTVE   91 (380)
Q Consensus        19 ~~~~~~~~~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~-------~~~~g~afV~f~~~~   91 (380)
                      +|.+..+.......++|||+|||.++++++|+++|++|| |            ..+.+       ++++|||||+|.+.+
T Consensus         6 ~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i------------~~v~i~~~~~~~g~~~g~afV~f~~~~   72 (100)
T 2j76_E            6 HHHHHRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-I------------SAVRLPREPSNPERLKGFGYAEFEDLD   72 (100)
T ss_dssp             --------------CEEEESCCSSCCSSSHHHHHSCSSC-E------------EEEECSCCTTTTCCCCSCEEEEECCHH
T ss_pred             CCCCCCCcCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-C------------eEEEEEecCCcCCccCeEEEEEECCHH
Confidence            333445556778899999999999999999999999997 4            33443       345799999999999


Q ss_pred             HHHHHHHcCCceecCceEEEecCCCC
Q 016936           92 EASNAMALDGIIFEGVAVRVRRPTDY  117 (380)
Q Consensus        92 ~a~~ai~l~~~~i~g~~i~v~~~~~~  117 (380)
                      +|.+|+.+++..|.|+.|+|.++...
T Consensus        73 ~a~~Ai~l~g~~~~g~~l~V~~a~~~   98 (100)
T 2j76_E           73 SLLSALSLNEESLGNRRIRVDVADQA   98 (100)
T ss_dssp             HHHHHHHTTTCCBTTBCCCCEECCCS
T ss_pred             HHHHHHhcCCCEECCeEEEEEeccCC
Confidence            99999999999999999999997654

>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=99.55  E-value=6.4e-15  Score=117.38  Aligned_cols=79  Identities=24%  Similarity=0.328  Sum_probs=69.7

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec------CCCcEEEEEeCCHHHHHHHH-Hc
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN------HEKKFAFVEMRTVEEASNAM-AL   99 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~------~~~g~afV~f~~~~~a~~ai-~l   99 (380)
                      ....+.++|||+|||+++++++|+++|++||.            |..+.+.      +++|||||+|.+.++|++|+ .+
T Consensus        41 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~------------I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~l  108 (129)
T 2kxn_B           41 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGP------------IADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA  108 (129)
T ss_dssp             SCCCCSSCBCEETCTTSCCHHHHHHHHTTTSC------------EEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHH
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------eEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHh
Confidence            34567899999999999999999999999998            5666653      56799999999999999999 69


Q ss_pred             CCceecCceEEEecCCCC
Q 016936          100 DGIIFEGVAVRVRRPTDY  117 (380)
Q Consensus       100 ~~~~i~g~~i~v~~~~~~  117 (380)
                      ++..|.|++|+|.++..+
T Consensus       109 ng~~i~g~~l~V~~a~~~  126 (129)
T 2kxn_B          109 NGMELDGRRIRVDFSITK  126 (129)
T ss_dssp             TTCCSSSSCCEESCCSSS
T ss_pred             CCCEECCEEEEEEEecCC
Confidence            999999999999997654

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.55  E-value=6.7e-15  Score=113.20  Aligned_cols=77  Identities=26%  Similarity=0.309  Sum_probs=67.8

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec------CCCcEEEEEeCCHHHHHHHH-HcC
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN------HEKKFAFVEMRTVEEASNAM-ALD  100 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~------~~~g~afV~f~~~~~a~~ai-~l~  100 (380)
                      ...+.++|||+|||..+++++|+++|++||.            |.++.+.      .++|||||+|.+.++|++|+ .++
T Consensus        19 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~------------i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~   86 (106)
T 1p27_B           19 RSVEGWILFVTGVHEEATEEDIHDKFAEYGE------------IKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLN   86 (106)
T ss_dssp             CBTTBEEEEEECCCTTCCHHHHHHHHGGGSC------------EEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCC------------eEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhc
Confidence            4456799999999999999999999999998            5666553      34799999999999999999 699


Q ss_pred             CceecCceEEEecCCC
Q 016936          101 GIIFEGVAVRVRRPTD  116 (380)
Q Consensus       101 ~~~i~g~~i~v~~~~~  116 (380)
                      +..|.|++|+|.++..
T Consensus        87 g~~~~g~~l~V~~a~~  102 (106)
T 1p27_B           87 GQDLMGQPISVDWCFV  102 (106)
T ss_dssp             TCBSSSSBCEEEESEE
T ss_pred             CCEECCcEEEEEeecC
Confidence            9999999999998654

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.54  E-value=3.8e-14  Score=108.35  Aligned_cols=81  Identities=15%  Similarity=0.093  Sum_probs=71.4

Q ss_pred             CCCEEEEcCCCC-----CCCHHHHHHHHHhcCCeeEEEEeeCCCC-CCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEE
Q 016936          151 GPDRVFVGGLPY-----YFTETQIKELLESFGTLHGFDLVKDRDT-GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTL  224 (380)
Q Consensus       151 ~~~~l~V~nlp~-----~~t~~~l~~~F~~~G~i~~v~l~~~~~~-~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i  224 (380)
                      .+++|+|.|+..     +-++++|+++|++||.|.+|.+++++.+ ++++|+|||+|.+.++|.+|+..|||+.+.|+.|
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            347999999952     2368999999999999999999998653 6899999999999999999999999999999999


Q ss_pred             EEEEccc
Q 016936          225 TVRRATA  231 (380)
Q Consensus       225 ~v~~~~~  231 (380)
                      .|.++..
T Consensus        87 ~v~~a~~   93 (105)
T 2pe8_A           87 KACFYNL   93 (105)
T ss_dssp             EEEECCH
T ss_pred             EEEEcCH
Confidence            9999853

>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=99.54  E-value=4.6e-15  Score=111.26  Aligned_cols=77  Identities=18%  Similarity=0.371  Sum_probs=66.0

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCC-ceecC
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDG-IIFEG  106 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~-~~i~g  106 (380)
                      ....++|||+|||+++++++|+++|++||.++.           .+.+ .++|||||+|.+.++|.+|+ .+|+ ..+.|
T Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~-----------~~~~-~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g   72 (93)
T 2cqh_A            5 SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLA-----------GQVL-LKSGYAFVDYPDQNWAIRAIETLSGKVELHG   72 (93)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCS-----------SCEE-EETTEEEECCSCHHHHHHHHHHHTTTCEETT
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceE-----------EEEE-cCCCEEEEEECCHHHHHHHHHHccCCeeECC
Confidence            346789999999999999999999999998321           1111 36899999999999999999 7999 99999


Q ss_pred             ceEEEecCCCC
Q 016936          107 VAVRVRRPTDY  117 (380)
Q Consensus       107 ~~i~v~~~~~~  117 (380)
                      ++|+|.++...
T Consensus        73 ~~l~v~~a~~~   83 (93)
T 2cqh_A           73 KIMEVDYSVSK   83 (93)
T ss_dssp             EECEEEECCCC
T ss_pred             EEEEEEEccCc
Confidence            99999997654

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.54  E-value=9.8e-15  Score=113.64  Aligned_cols=89  Identities=22%  Similarity=0.248  Sum_probs=70.0

Q ss_pred             hhhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe------cCCCcEEEEEeCCHHHHHHHH-H
Q 016936           26 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-A   98 (380)
Q Consensus        26 ~~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~------~~~~g~afV~f~~~~~a~~ai-~   98 (380)
                      .....+.++|||+|||+++++++|+++|++||.|.......    ...+.+      .+++|||||+|.+.++|.+|+ .
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~----~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~   84 (113)
T 2cpe_A            9 PDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTG----QPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEW   84 (113)
T ss_dssp             CCCCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSC----CBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHH
T ss_pred             cccCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccC----ccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHH
Confidence            35567889999999999999999999999999853100000    002333      345799999999999999999 6


Q ss_pred             cCCceecCceEEEecCCCCC
Q 016936           99 LDGIIFEGVAVRVRRPTDYN  118 (380)
Q Consensus        99 l~~~~i~g~~i~v~~~~~~~  118 (380)
                      |++..|.|++|+|.++..+.
T Consensus        85 l~g~~~~g~~l~V~~a~~~~  104 (113)
T 2cpe_A           85 FDGKDFQGSKLKVSLARKKP  104 (113)
T ss_dssp             HTTCEETTEECEEECSSCCC
T ss_pred             cCCCccCCCEEEEEECCCCC
Confidence            99999999999999977653

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.54  E-value=1e-14  Score=110.63  Aligned_cols=78  Identities=22%  Similarity=0.378  Sum_probs=67.1

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeE-EEEec------CCCcEEEEEeCCHHHHHHHH-Hc
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVV-NVYIN------HEKKFAFVEMRTVEEASNAM-AL   99 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~-~~~~~------~~~g~afV~f~~~~~a~~ai-~l   99 (380)
                      ...++++|||+|||+++++++|+++|++||.|            . ++.+.      .++|||||+|.+.++|++|+ .+
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i------------~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l   72 (99)
T 2div_A            5 SSGMAASLWMGDLEPYMDENFISRAFATMGET------------VMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKI   72 (99)
T ss_dssp             CCSSSSEEEECSCCTTCCHHHHHHHHHHTTCC------------CCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTT
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHHhCCc------------ceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHH
Confidence            34578999999999999999999999999984            3 44443      34699999999999999999 69


Q ss_pred             CCceecCce----EEEecCCCC
Q 016936          100 DGIIFEGVA----VRVRRPTDY  117 (380)
Q Consensus       100 ~~~~i~g~~----i~v~~~~~~  117 (380)
                      |+..+.|+.    |+|.|+...
T Consensus        73 ~g~~~~g~~~~~~l~v~~a~~~   94 (99)
T 2div_A           73 NGKPLPGATPAKRFKLNYATYS   94 (99)
T ss_dssp             TTSEESSCSSCEECCEEETTCC
T ss_pred             cCCccCCCCcceeEEEeecCCC
Confidence            999999999    999987653

>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=99.54  E-value=9.7e-15  Score=110.36  Aligned_cols=77  Identities=21%  Similarity=0.422  Sum_probs=68.6

Q ss_pred             hcccceEEEcCCCCcCcHHHHH----HHHHHHHHhccCCCCCCCCeeEEEEec---CCCcEEEEEeCCHHHHHHHH-HcC
Q 016936           29 TRHARRVYVGGLPPLANEQAIA----TFFSQVMTAIGGNSAGPGDAVVNVYIN---HEKKFAFVEMRTVEEASNAM-ALD  100 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~----~~f~~~G~i~~~~~~~~~~~i~~~~~~---~~~g~afV~f~~~~~a~~ai-~l~  100 (380)
                      ..++++|||+|||.++++++|+    ++|++||.            |..+.+.   +++|||||+|.+.++|.+|+ .++
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~------------i~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~   72 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQ------------ILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQ   72 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSC------------EEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCC------------EEEEEEEcCCCcCcEEEEEeCCHHHHHHHHHHhC
Confidence            4578999999999999999999    99999997            6666654   56899999999999999999 799


Q ss_pred             CceecCceEEEecCCCC
Q 016936          101 GIIFEGVAVRVRRPTDY  117 (380)
Q Consensus       101 ~~~i~g~~i~v~~~~~~  117 (380)
                      +..+.|++|+|.++...
T Consensus        73 g~~~~g~~l~v~~a~~~   89 (97)
T 1nu4_A           73 GFPFYDKPMRIQYAKTD   89 (97)
T ss_dssp             TCEETTEECEEEECSSC
T ss_pred             CCEECCcEEEEEEccCC
Confidence            99999999999997654

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.54  E-value=5.7e-15  Score=112.29  Aligned_cols=75  Identities=23%  Similarity=0.342  Sum_probs=67.0

Q ss_pred             cccceEEEcCCCC------cCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe------cCCCcEEEEEeCCHHHHHHHH
Q 016936           30 RHARRVYVGGLPP------LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM   97 (380)
Q Consensus        30 ~~~~~v~V~nLp~------~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~------~~~~g~afV~f~~~~~a~~ai   97 (380)
                      ...++|||+|||.      ++++++|+++|++||.            |.++.+      ++++|||||+|.+.++|.+|+
T Consensus         4 ~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~------------i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai   71 (100)
T 3ns6_A            4 GSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGK------------VVNMEFPIDEATGKTKGFLFVECGSMNDAKKII   71 (100)
T ss_dssp             CGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSC------------EEEEECCEETTTTEECSEEEEEESSHHHHHHHH
T ss_pred             CcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCC------------EeEEEEEEcCCCCccceEEEEEECCHHHHHHHH
Confidence            4578999999999      9999999999999998            666665      346799999999999999999


Q ss_pred             -HcCCceecC-ceEEEecCCC
Q 016936           98 -ALDGIIFEG-VAVRVRRPTD  116 (380)
Q Consensus        98 -~l~~~~i~g-~~i~v~~~~~  116 (380)
                       .+|+..+.| ++|+|.++.+
T Consensus        72 ~~lng~~~~g~r~l~V~~a~~   92 (100)
T 3ns6_A           72 KSFHGKRLDLKHRLFLYTMKD   92 (100)
T ss_dssp             HHHTTCBSSSSCBCEEEESHH
T ss_pred             HHhCCcccCCCeEEEEEECch
Confidence             799999999 9999998754

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.54  E-value=1.6e-14  Score=112.64  Aligned_cols=75  Identities=28%  Similarity=0.440  Sum_probs=63.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCC---CCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEE
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDT---GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  226 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~---~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v  226 (380)
                      ...++|||+|||+.+++++|+++|++||.|. +.++.++.+   |+++|||||+|.+.++|++|++.++  .+.|+.+.+
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            3457999999999999999999999999999 888887666   7999999999999999999999882  244444444


Q ss_pred             E
Q 016936          227 R  227 (380)
Q Consensus       227 ~  227 (380)
                      .
T Consensus        83 ~   83 (114)
T 2dnl_A           83 V   83 (114)
T ss_dssp             E
T ss_pred             c
Confidence            3

>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=99.54  E-value=7.3e-15  Score=111.27  Aligned_cols=83  Identities=16%  Similarity=0.116  Sum_probs=68.6

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecC
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  106 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g  106 (380)
                      .....++|||+|||+++++++|+++|++||.|...      ..+.+....+++|||||+|.+.++|++|+ .+++..|.|
T Consensus        11 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~------~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g   84 (98)
T 2cqp_A           11 GKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGS------VCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGS   84 (98)
T ss_dssp             CCCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTT------CEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccce------EEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCC
Confidence            34557899999999999999999999999986432      12222223456899999999999999999 899999999


Q ss_pred             ceEEEecCCC
Q 016936          107 VAVRVRRPTD  116 (380)
Q Consensus       107 ~~i~v~~~~~  116 (380)
                      ++|+|.++..
T Consensus        85 ~~l~V~~a~~   94 (98)
T 2cqp_A           85 RKVKLVLGSG   94 (98)
T ss_dssp             EECEEEESSC
T ss_pred             eEEEEEEcCC
Confidence            9999998654

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.54  E-value=1.5e-14  Score=110.73  Aligned_cols=79  Identities=18%  Similarity=0.294  Sum_probs=68.8

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHH-HHHhccCCCCCCCCeeEEEEec-----CCCcEEEEEeCCHHHHHHHH-HcC
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQ-VMTAIGGNSAGPGDAVVNVYIN-----HEKKFAFVEMRTVEEASNAM-ALD  100 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~-~G~i~~~~~~~~~~~i~~~~~~-----~~~g~afV~f~~~~~a~~ai-~l~  100 (380)
                      ...+.++|||+|||+++++++|+++|++ ||.            |..+.+.     .++|||||+|.+.++|.+|+ .++
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~------------v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~   72 (104)
T 2dhg_A            5 SSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPS------------CRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQ   72 (104)
T ss_dssp             CSSCCCCEEEECCCTTCCHHHHHHHHHHHCTT------------EEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTT
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCC------------eEEEEEEECCCCCccceEEEEECCHHHHHHHHHHcc
Confidence            3456799999999999999999999999 998            5555553     35799999999999999999 699


Q ss_pred             Cce-ecCceEEEecCCCCC
Q 016936          101 GII-FEGVAVRVRRPTDYN  118 (380)
Q Consensus       101 ~~~-i~g~~i~v~~~~~~~  118 (380)
                      +.. +.|++|+|.++....
T Consensus        73 g~~~~~g~~l~v~~a~~~~   91 (104)
T 2dhg_A           73 GAVGLGSKPVRLSVAIPKA   91 (104)
T ss_dssp             TCCSSSSSCCCCCBCCCCC
T ss_pred             CCcccCCEeEEEEEccCCC
Confidence            999 999999999976543

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.54  E-value=4.5e-14  Score=110.77  Aligned_cols=75  Identities=19%  Similarity=0.209  Sum_probs=67.7

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceE-EEEEEcChhHHHHHHHHhCCCeeCC--eEEEEEEc
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGY-GFCVYQDPAVTDIACAALNGLKMGD--KTLTVRRA  229 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~-afV~f~~~~~A~~Ai~~l~g~~~~g--~~i~v~~~  229 (380)
                      ..|||+||++.+++++|+++|++||.|.+|++...      .|| |||+|.+.++|..|++.|||..|.|  +.|+|.++
T Consensus        26 l~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~------~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~A   99 (124)
T 2e5i_A           26 LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR------NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYA   99 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES------SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECC
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEe
Confidence            46789999999999999999999999999998652      276 9999999999999999999999987  69999999


Q ss_pred             ccCC
Q 016936          230 TASS  233 (380)
Q Consensus       230 ~~~~  233 (380)
                      .++.
T Consensus       100 k~~~  103 (124)
T 2e5i_A          100 RPTR  103 (124)
T ss_dssp             SCSC
T ss_pred             cCCc
Confidence            7764

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.54  E-value=7.1e-15  Score=112.44  Aligned_cols=80  Identities=18%  Similarity=0.367  Sum_probs=69.6

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec------CCCcEEEEEeCCHHHHHHHH-Hc
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN------HEKKFAFVEMRTVEEASNAM-AL   99 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~------~~~g~afV~f~~~~~a~~ai-~l   99 (380)
                      ....+.++|||+|||+++++++|+++|++||.            |..+.+.      .++|||||+|.+.++|.+|+ .+
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~------------i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l   77 (103)
T 2cq0_A           10 RRADDNATIRVTNLSEDTRETDLQELFRPFGS------------ISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGV   77 (103)
T ss_dssp             CCCSSSEEEEEESCCTTCCHHHHHTTSTTTCC------------EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHT
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCC------------eEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHc
Confidence            44567899999999999999999999999997            5555553      34689999999999999999 69


Q ss_pred             CCceecCceEEEecCCCCC
Q 016936          100 DGIIFEGVAVRVRRPTDYN  118 (380)
Q Consensus       100 ~~~~i~g~~i~v~~~~~~~  118 (380)
                      ++..|.|++|+|.++....
T Consensus        78 ~g~~~~g~~l~v~~a~~~~   96 (103)
T 2cq0_A           78 SGFGYDHLILNVEWAKPST   96 (103)
T ss_dssp             TTCEETTEECEEEESSCCC
T ss_pred             CCCeeCCcEEEEEECCCCC
Confidence            9999999999999976653

>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=99.54  E-value=1.8e-14  Score=110.97  Aligned_cols=77  Identities=18%  Similarity=0.282  Sum_probs=68.9

Q ss_pred             hcccceEEE--cCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCcee-
Q 016936           29 TRHARRVYV--GGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIF-  104 (380)
Q Consensus        29 ~~~~~~v~V--~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i-  104 (380)
                      ..+.++|||  +||+.++++++|+++|++||.            |.++.+..++|||||+|.+.++|++|+ .|||..+ 
T Consensus        22 ~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~------------v~~v~i~~~rgfaFV~f~~~~~A~~Ai~~lnG~~~~   89 (114)
T 2cq2_A           22 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGL------------VDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVV   89 (114)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSC------------EEEEECCTTCSCEEEEESSHHHHHHHHHHTTTCEEE
T ss_pred             CCCCCEEEEECCCCCCCCCHHHHHHHHHhcCC------------eEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEEc
Confidence            456789999  779999999999999999997            788888888999999999999999999 7999988 


Q ss_pred             ----cCceEEEecCCCC
Q 016936          105 ----EGVAVRVRRPTDY  117 (380)
Q Consensus       105 ----~g~~i~v~~~~~~  117 (380)
                          .|++|.|.++...
T Consensus        90 ~~lg~g~~l~v~~a~~~  106 (114)
T 2cq2_A           90 DDLGQKITLYLNFVEKV  106 (114)
T ss_dssp             CTTSCEEECEEEEESCC
T ss_pred             cccCCCcEEEEEecccC
Confidence                6789999886544

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.54  E-value=3.4e-14  Score=107.36  Aligned_cols=76  Identities=24%  Similarity=0.364  Sum_probs=69.5

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecC
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  106 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g  106 (380)
                      ...+.++|||+||  ++++++|+++|++||.            |..+.+.+++|||||+|.+.++|.+|+ .|++..|.|
T Consensus        11 ~~~~~~~l~V~n~--~~t~~~l~~~F~~~G~------------i~~v~i~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g   76 (97)
T 1x5p_A           11 APRKGNTLYVYGE--DMTPTLLRGAFSPFGN------------IIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVES   76 (97)
T ss_dssp             CCCCCSEEEEECS--SCCHHHHHHHHTTTSC------------EEEEEEETTTTEEEEEESSHHHHHHHHHHTTTEEETT
T ss_pred             CCCCCCEEEEcCC--CCCHHHHHHHHhhCCC------------EEEEEecCCCCEEEEEECCHHHHHHHHHHhCCCeECC
Confidence            3456799999996  8999999999999997            788888899999999999999999999 899999999


Q ss_pred             ceEEEecCCCC
Q 016936          107 VAVRVRRPTDY  117 (380)
Q Consensus       107 ~~i~v~~~~~~  117 (380)
                      ++|+|.++...
T Consensus        77 ~~l~v~~a~~~   87 (97)
T 1x5p_A           77 VQLKVNIARKQ   87 (97)
T ss_dssp             EEEEEECCSSC
T ss_pred             eEEEEEECCCC
Confidence            99999997654

>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=99.54  E-value=5.1e-14  Score=108.79  Aligned_cols=79  Identities=24%  Similarity=0.373  Sum_probs=68.0

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec-------CCCcEEEEEeCCHHHHHHHH-HcC
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN-------HEKKFAFVEMRTVEEASNAM-ALD  100 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~-------~~~g~afV~f~~~~~a~~ai-~l~  100 (380)
                      +.+.++|||+|||.++++++|+++|++||..           |.++.+.       .++|||||+|.+.++|.+|+ .++
T Consensus         5 s~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~-----------v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~   73 (109)
T 2dis_A            5 SSGNCRLFIGGIPKMKKREEILEEIAKVTEG-----------VLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLM   73 (109)
T ss_dssp             CCCSEEEEEECCCTTSCHHHHHHHHHHHSTT-----------EEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTT
T ss_pred             ccCCCEEEEeCCCCcCCHHHHHHHHHHhcCC-----------ceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhh
Confidence            3467999999999999999999999999861           5555554       57899999999999999999 686


Q ss_pred             --CceecCceEEEecCCCCC
Q 016936          101 --GIIFEGVAVRVRRPTDYN  118 (380)
Q Consensus       101 --~~~i~g~~i~v~~~~~~~  118 (380)
                        +..+.|++|+|.++....
T Consensus        74 ~g~~~~~g~~l~V~~a~~~~   93 (109)
T 2dis_A           74 PGRIQLWGHQIAVDWAEPEI   93 (109)
T ss_dssp             TCCSCBTTBCCEEEESCSSC
T ss_pred             CCCceecCCeEEEEEcCCCC
Confidence              589999999999987654

>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=99.53  E-value=5.4e-15  Score=109.67  Aligned_cols=75  Identities=23%  Similarity=0.338  Sum_probs=66.9

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecCce
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  108 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g~~  108 (380)
                      +..++|||+|||+++++++|+++|++| .            |..+.+.+++|||||+|.+.++|++|+ .+++..+.|++
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~-~------------v~~~~i~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~   69 (88)
T 1wg1_A            3 SGSSGILVKNLPQDSNCQEVHDLLKDY-D------------LKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKD   69 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSS-C------------CCCEEEEGGGTEEEECCSCHHHHHHHHHHHTTEEETTEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhC-C------------eEEEEEeCCCcEEEEEECCHHHHHHHHHHhCCCeECCcE
Confidence            467899999999999999999999999 6            444555588999999999999999999 79999999999


Q ss_pred             EEEecCCCC
Q 016936          109 VRVRRPTDY  117 (380)
Q Consensus       109 i~v~~~~~~  117 (380)
                      |+|.++...
T Consensus        70 l~V~~a~~~   78 (88)
T 1wg1_A           70 LIVQLQPTD   78 (88)
T ss_dssp             EEEEECCCC
T ss_pred             EEEEEcCCC
Confidence            999997543

>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=99.53  E-value=1.4e-14  Score=112.19  Aligned_cols=78  Identities=26%  Similarity=0.285  Sum_probs=69.0

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecC------CCcEEEEEeCCHHHHHHHH-Hc
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH------EKKFAFVEMRTVEEASNAM-AL   99 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~------~~g~afV~f~~~~~a~~ai-~l   99 (380)
                      ....+.++|||+|||..+++++|+++|++||.            |..+.+..      ++|||||+|.+.++|.+|+ .+
T Consensus        21 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l   88 (110)
T 1oo0_B           21 QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGE------------IKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL   88 (110)
T ss_dssp             CCBTTBEEEEEESCCTTCCHHHHHHHHGGGSC------------EEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHH
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------EEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHc
Confidence            34567899999999999999999999999997            66776643      4799999999999999999 69


Q ss_pred             CCceecCceEEEecCCC
Q 016936          100 DGIIFEGVAVRVRRPTD  116 (380)
Q Consensus       100 ~~~~i~g~~i~v~~~~~  116 (380)
                      ++..|.|++|+|.++..
T Consensus        89 ~g~~~~g~~l~V~~a~~  105 (110)
T 1oo0_B           89 NGAEIMGQTIQVDWCFV  105 (110)
T ss_dssp             TTCEETTEECEEEESEE
T ss_pred             CCCEECCcEEEEEEccc
Confidence            99999999999998654

>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=99.53  E-value=8.6e-15  Score=113.56  Aligned_cols=80  Identities=19%  Similarity=0.304  Sum_probs=69.6

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHH---HHHHHHHHhccCCCCCCCCeeEEEEecC---------CCcEEEEEeCCHHHHH
Q 016936           27 QATRHARRVYVGGLPPLANEQAIA---TFFSQVMTAIGGNSAGPGDAVVNVYINH---------EKKFAFVEMRTVEEAS   94 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~---~~f~~~G~i~~~~~~~~~~~i~~~~~~~---------~~g~afV~f~~~~~a~   94 (380)
                      ......++|||+|||+++++++|+   ++|++||.            |..+.+..         ++|||||+|.+.++|+
T Consensus        10 ~r~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~------------i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~   77 (111)
T 2cpi_A           10 VRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGK------------IHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL   77 (111)
T ss_dssp             CCCCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSC------------EEEEEEECCSSCCSSSCCCEEEEEEESSHHHHH
T ss_pred             ccccCCCEEEEECCCCCCCHHHHHHHHHHhhccCC------------EEEEEEecCCCcCccCCCCeEEEEEECcHHHHH
Confidence            445568899999999999999999   99999998            56666543         3489999999999999


Q ss_pred             HHH-HcCCceecCceEEEecCCCCC
Q 016936           95 NAM-ALDGIIFEGVAVRVRRPTDYN  118 (380)
Q Consensus        95 ~ai-~l~~~~i~g~~i~v~~~~~~~  118 (380)
                      +|+ .||+..|.|++|+|.++..+.
T Consensus        78 ~Ai~~lng~~~~gr~l~V~~a~~k~  102 (111)
T 2cpi_A           78 RAIQCVNNVVVDGRTLKASLGTTKY  102 (111)
T ss_dssp             HHHHHHTTEEETTEEEEEESCCCCS
T ss_pred             HHHHHhCCCEECCEEEEEEeccccc
Confidence            999 799999999999999987654

>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=99.53  E-value=1.5e-14  Score=111.43  Aligned_cols=76  Identities=17%  Similarity=0.248  Sum_probs=67.2

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec-----CCCcEEEEEeCCHHHHHHHH-HcCC
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN-----HEKKFAFVEMRTVEEASNAM-ALDG  101 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~-----~~~g~afV~f~~~~~a~~ai-~l~~  101 (380)
                      .....++|||+|||+.+++++|+++|++||.            |..+.+.     +++|||||+|.+.++|++|+ .|++
T Consensus        25 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g   92 (107)
T 3ulh_A           25 GVETGGKLLVSNLDFGVSDADIQELFAEFGT------------LKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNG   92 (107)
T ss_dssp             CCCCSEEEEEESCCTTCCHHHHHHHHHTTSC------------EEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------eEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCC
Confidence            3466899999999999999999999999998            5555554     45799999999999999999 6999


Q ss_pred             ceecCceEEEecCC
Q 016936          102 IIFEGVAVRVRRPT  115 (380)
Q Consensus       102 ~~i~g~~i~v~~~~  115 (380)
                      ..|.|++|+|.++.
T Consensus        93 ~~~~g~~l~V~~a~  106 (107)
T 3ulh_A           93 VPLDGRPMNIQLVT  106 (107)
T ss_dssp             CEETTEECEEEEEC
T ss_pred             CEeCCcEEEEEEeC
Confidence            99999999999854

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A

Probab=99.53  E-value=2.6e-14  Score=105.62  Aligned_cols=71  Identities=24%  Similarity=0.541  Sum_probs=65.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhc----C-------CeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCee
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESF----G-------TLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM  219 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~----G-------~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~  219 (380)
                      ..++|||+|||+.+++++|+++|++|    |       .|..+.+.++      +|||||+|.+.++|++|+ .||+..+
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~l~g~~~   77 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDGIIF   77 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-hcCCCEE
Confidence            34799999999999999999999999    8       8999988654      689999999999999999 8999999


Q ss_pred             CCeEEEEEE
Q 016936          220 GDKTLTVRR  228 (380)
Q Consensus       220 ~g~~i~v~~  228 (380)
                      .|+.|+|++
T Consensus        78 ~g~~l~V~r   86 (87)
T 2hzc_A           78 QGQSLKIRR   86 (87)
T ss_dssp             TTEECEEEC
T ss_pred             CCeEEEEeC
Confidence            999999974

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.53  E-value=5.3e-15  Score=116.03  Aligned_cols=82  Identities=20%  Similarity=0.229  Sum_probs=68.3

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHH---hccCCCCCCCCeeEEEE--ecCCCcEEEEEeCCHHHHHHHHHcCC
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMT---AIGGNSAGPGDAVVNVY--INHEKKFAFVEMRTVEEASNAMALDG  101 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~---i~~~~~~~~~~~i~~~~--~~~~~g~afV~f~~~~~a~~ai~l~~  101 (380)
                      ....+.++|||+|||+++|+++|+++|++||.   |..         |..+.  .++++|||||+|.+.++|++|+.+++
T Consensus        12 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~---------v~i~~~~~g~~~G~afV~F~~~~~a~~Al~~~g   82 (118)
T 2db1_A           12 PEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAG---------VHFIYTREGRQSGEAFVELESEDDVKLALKKDR   82 (118)
T ss_dssp             SCBCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGG---------EEEEECSSSCEEEEEEEEBSSHHHHHHHGGGTT
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCcee---------EEEEECCCCCCCeEEEEEECCHHHHHHHHhcCC
Confidence            44567899999999999999999999999987   332         22222  24567999999999999999999999


Q ss_pred             ceecCceEEEecCCCC
Q 016936          102 IIFEGVAVRVRRPTDY  117 (380)
Q Consensus       102 ~~i~g~~i~v~~~~~~  117 (380)
                      ..|.|+.|+|.++...
T Consensus        83 ~~~~gr~i~V~~a~~~   98 (118)
T 2db1_A           83 ESMGHRYIEVFKSHRT   98 (118)
T ss_dssp             EEETTEEEEEEEECHH
T ss_pred             CeECCeEEEEEECCHH
Confidence            9999999999986543

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.53  E-value=9e-15  Score=110.32  Aligned_cols=80  Identities=18%  Similarity=0.255  Sum_probs=69.2

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceec
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE  105 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~  105 (380)
                      ....+.++|||+|||..+++++|+++|++||.|..         +  .....++|||||+|.+.++|.+|+ .+++..|.
T Consensus        11 ~~~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~---------~--~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~   79 (96)
T 1fjc_A           11 KKVRAARTLLAKNLSFNITEDELKEVFEDALEIRL---------V--SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEID   79 (96)
T ss_dssp             STTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECC---------E--EETTEEEEEEEEEESSHHHHHHHHHHTTEEEET
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEE---------e--CCCCCcceEEEEEECCHHHHHHHHHHhCCCEEC
Confidence            44567899999999999999999999999988521         2  344567899999999999999999 69999999


Q ss_pred             CceEEEecCCCC
Q 016936          106 GVAVRVRRPTDY  117 (380)
Q Consensus       106 g~~i~v~~~~~~  117 (380)
                      |++|+|.++..+
T Consensus        80 g~~l~v~~a~~~   91 (96)
T 1fjc_A           80 GRSVSLYYTGEK   91 (96)
T ss_dssp             TEEEEEEECSSS
T ss_pred             CeEEEEEEcCCC
Confidence            999999997654

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.53  E-value=2.6e-14  Score=111.37  Aligned_cols=78  Identities=21%  Similarity=0.213  Sum_probs=67.8

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecC-----CCcEEEEEeCCHHHHHHHH-HcCC
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH-----EKKFAFVEMRTVEEASNAM-ALDG  101 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~-----~~g~afV~f~~~~~a~~ai-~l~~  101 (380)
                      .....++|||+|||.++++++|+++|++||.            |..+.+..     ++|||||+|.+.++|++|+ .|++
T Consensus        11 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~------------i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g   78 (114)
T 2do0_A           11 AGRLGSTVFVANLDYKVGWKKLKEVFSMAGV------------VVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNG   78 (114)
T ss_dssp             CCCCCSCEEEESCCTTCCHHHHHHHHTTTSC------------EEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTT
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------eEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCC
Confidence            3456899999999999999999999999997            55555543     3789999999999999999 6999


Q ss_pred             ceecCceEEEecCCCC
Q 016936          102 IIFEGVAVRVRRPTDY  117 (380)
Q Consensus       102 ~~i~g~~i~v~~~~~~  117 (380)
                      ..|.|++|+|.++...
T Consensus        79 ~~~~g~~l~v~~a~~~   94 (114)
T 2do0_A           79 QLLFDRPMHVKMDERA   94 (114)
T ss_dssp             CEETTEECEEEECSCC
T ss_pred             CEeCCCEEEEEEcccC
Confidence            9999999999987543

>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=99.53  E-value=2.8e-14  Score=109.27  Aligned_cols=76  Identities=20%  Similarity=0.340  Sum_probs=66.4

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe-------cCCCcEEEEEeCCHHHHHHHHHcCCc
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-------NHEKKFAFVEMRTVEEASNAMALDGI  102 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~-------~~~~g~afV~f~~~~~a~~ai~l~~~  102 (380)
                      .+.++|||+|||+++++++|+++|++|| |            ..+.+       .+++|||||+|.+.++|++|+.+++.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i------------~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~   79 (104)
T 1wi8_A           13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-I------------SAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEE   79 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-E------------EEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTC
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHCC-c------------eEEEEecCCCCCCCcCeEEEEEECCHHHHHHHHhcCCC
Confidence            4569999999999999999999999997 4            33443       34589999999999999999999999


Q ss_pred             eecCceEEEecCCCCC
Q 016936          103 IFEGVAVRVRRPTDYN  118 (380)
Q Consensus       103 ~i~g~~i~v~~~~~~~  118 (380)
                      .|.|++|+|.++....
T Consensus        80 ~~~g~~l~V~~a~~~~   95 (104)
T 1wi8_A           80 SLGNKRIRVDVADQAQ   95 (104)
T ss_dssp             EETTEECEEEECCCCC
T ss_pred             EeCCcEEEEEEccCCC
Confidence            9999999999976653

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.53  E-value=2.2e-14  Score=118.01  Aligned_cols=75  Identities=23%  Similarity=0.337  Sum_probs=65.2

Q ss_pred             ccceEEEcCCCCcCcHHHHHHHHHHHH--HhccCCCCCCCCeeEEEEe------cCCCcEEEEEeCCHHHHHHHH-HcCC
Q 016936           31 HARRVYVGGLPPLANEQAIATFFSQVM--TAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-ALDG  101 (380)
Q Consensus        31 ~~~~v~V~nLp~~~t~~~l~~~f~~~G--~i~~~~~~~~~~~i~~~~~------~~~~g~afV~f~~~~~a~~ai-~l~~  101 (380)
                      ..++|||+|||+++++++|+++|++||  .            |.++.+      ++++|||||+|.+.++|.+|| .|++
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~------------v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng  121 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYD------------VVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPG  121 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCC------------EEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCcc------------EEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCC
Confidence            568999999999999999999999999  5            555554      345799999999999999999 7899


Q ss_pred             ceecCceEEEecCCCC
Q 016936          102 IIFEGVAVRVRRPTDY  117 (380)
Q Consensus       102 ~~i~g~~i~v~~~~~~  117 (380)
                      ..|.|++|+|.++...
T Consensus       122 ~~~~Gr~l~V~~a~~~  137 (156)
T 3n9u_C          122 KVLNGEKVDVRPATRQ  137 (156)
T ss_dssp             CEETTEECEEEECCHH
T ss_pred             CEECCeEeEEEEcCCC
Confidence            9999999999987653

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.52  E-value=8.8e-15  Score=110.39  Aligned_cols=76  Identities=14%  Similarity=0.305  Sum_probs=66.2

Q ss_pred             hhcccceEEEcCCCC-cCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceec
Q 016936           28 ATRHARRVYVGGLPP-LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE  105 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~-~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~  105 (380)
                      ...+.++|||+|||. .+++++|+++|++||.            |.++.+.  +|||||+|.+.++|.+|+ .+++..+.
T Consensus         6 ~~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~------------v~~v~i~--~g~afV~f~~~~~A~~A~~~l~g~~~~   71 (96)
T 2kvi_A            6 NIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGH------------IMQINIK--NAFGFIQFDNPQSVRDAIECESQEMNF   71 (96)
T ss_dssp             ---CCEEEEEESSTTSCCCHHHHHHHHTTTCC------------CCEEEEE--TTEEEEEESCHHHHHHHHHHHTCSSCB
T ss_pred             cCCCCCEEEEeCCCcccCCHHHHHHHHHhcCC------------EEEEEEe--CCEEEEEECCHHHHHHHHHHcCCCeeC
Confidence            456789999999998 9999999999999998            5556653  899999999999999999 69999999


Q ss_pred             CceEEEecCCCC
Q 016936          106 GVAVRVRRPTDY  117 (380)
Q Consensus       106 g~~i~v~~~~~~  117 (380)
                      |++|+|.++...
T Consensus        72 g~~l~V~~a~~~   83 (96)
T 2kvi_A           72 GKKLILEVSSSN   83 (96)
T ss_dssp             TTTBCEEEEECC
T ss_pred             CcEEEEEEcCcC
Confidence            999999987554

>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=99.52  E-value=4.6e-15  Score=117.53  Aligned_cols=85  Identities=18%  Similarity=0.170  Sum_probs=70.3

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHHHcCCceecC
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEG  106 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai~l~~~~i~g  106 (380)
                      .+....++|||+|||+++++++|+++|++||.|...      ..+.+...++++|||||+|.+.++|.+||.+++..|.|
T Consensus        20 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~------~~~~~~~~g~~~G~afV~F~~~~~a~~Al~~~g~~~~g   93 (124)
T 1wel_A           20 SPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDS------IYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGN   93 (124)
T ss_dssp             SCCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTT------CEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTT
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccce------EEEEECCCCCCCeEEEEEECCHHHHHHHHHhCCCeECC
Confidence            345677999999999999999999999999986431      11222234566899999999999999999999999999


Q ss_pred             ceEEEecCCCC
Q 016936          107 VAVRVRRPTDY  117 (380)
Q Consensus       107 ~~i~v~~~~~~  117 (380)
                      +.|+|.++...
T Consensus        94 r~i~V~~a~~~  104 (124)
T 1wel_A           94 RFIQVHPITKK  104 (124)
T ss_dssp             SCBEEEEECHH
T ss_pred             cEEEEEECCHH
Confidence            99999987543

>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=99.52  E-value=6.4e-15  Score=110.89  Aligned_cols=80  Identities=18%  Similarity=0.170  Sum_probs=65.2

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecCce
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  108 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g~~  108 (380)
                      ...++|||+|||+++++++|+++|++||.|...      ..+.+....+++|||||+|.+.++|++|+ .+|+..|.|++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~------~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~   86 (95)
T 2ek1_A           13 PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGS------VCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRK   86 (95)
T ss_dssp             --CEEEEEECCCTTCCHHHHHHHTTTSCBCTTC------CEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCccce------EEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcE
Confidence            346899999999999999999999999986432      11222223356799999999999999999 69999999999


Q ss_pred             EEEecCC
Q 016936          109 VRVRRPT  115 (380)
Q Consensus       109 i~v~~~~  115 (380)
                      |+|.++.
T Consensus        87 l~v~~a~   93 (95)
T 2ek1_A           87 VKLSGPS   93 (95)
T ss_dssp             CEEECCC
T ss_pred             EEEEecc
Confidence            9999854

>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=99.52  E-value=1.7e-14  Score=110.56  Aligned_cols=78  Identities=22%  Similarity=0.235  Sum_probs=66.7

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEE-EEe-----cCCCcEEEEEeCCHHHHHHHHHcCC
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVN-VYI-----NHEKKFAFVEMRTVEEASNAMALDG  101 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~-~~~-----~~~~g~afV~f~~~~~a~~ai~l~~  101 (380)
                      .....++|||+|||+++++++|+++|++||.            |.. +.+     ++++|||||+|.+.++|++|+..++
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~------------v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~~~   78 (104)
T 1wg5_A           11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEI------------VPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHK   78 (104)
T ss_dssp             SCSCCCEEEEESCCTTCCHHHHHHHTTTCCE------------EEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTTTT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------cceeEEEEECCCCCcceEEEEEECCHHHHHHHHHhCc
Confidence            3456799999999999999999999999987            433 443     4568999999999999999996699


Q ss_pred             ceecCceEEEecCCCC
Q 016936          102 IIFEGVAVRVRRPTDY  117 (380)
Q Consensus       102 ~~i~g~~i~v~~~~~~  117 (380)
                      ..+.|+.|+|.++...
T Consensus        79 ~~~~gr~i~v~~~~~~   94 (104)
T 1wg5_A           79 ERIGHRYIEIFKSSRA   94 (104)
T ss_dssp             CCSSSSCCEEEEECTT
T ss_pred             chhCCcEEEEEECCHH
Confidence            9999999999886544

>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=99.52  E-value=7.8e-15  Score=112.38  Aligned_cols=80  Identities=33%  Similarity=0.487  Sum_probs=68.6

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec------CCCcEEEEEeCCHHHHHHHH-HcC
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN------HEKKFAFVEMRTVEEASNAM-ALD  100 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~------~~~g~afV~f~~~~~a~~ai-~l~  100 (380)
                      .+...++|||+|||..+++++|+++|++||.|            ..+.+.      .++|||||+|.+.++|.+|+ .++
T Consensus         4 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i------------~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~   71 (104)
T 1p1t_A            4 VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPV------------VSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLN   71 (104)
T ss_dssp             SHHHHSCEEEESCCTTSCHHHHHHHHHTTSCC------------SEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSS
T ss_pred             cCCCccEEEEeCCCCcCCHHHHHHHHHhcCCe------------eEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhC
Confidence            34567999999999999999999999999984            334432      34799999999999999999 799


Q ss_pred             CceecCceEEEecCCCCCc
Q 016936          101 GIIFEGVAVRVRRPTDYNP  119 (380)
Q Consensus       101 ~~~i~g~~i~v~~~~~~~~  119 (380)
                      +..+.|++|+|.++.....
T Consensus        72 g~~~~g~~l~v~~a~~~~~   90 (104)
T 1p1t_A           72 GREFSGRALRVDNAASEKN   90 (104)
T ss_dssp             SBSCSSSCBEEEETTCTTH
T ss_pred             CCeeCCcEEEEEeCCCccc
Confidence            9999999999999876543

>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=99.52  E-value=5.4e-14  Score=104.33  Aligned_cols=73  Identities=18%  Similarity=0.347  Sum_probs=62.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCe--eCCeEEEEEE
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLK--MGDKTLTVRR  228 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~--~~g~~i~v~~  228 (380)
                      ...+|||+|||+++++++|+++|++||.|.+|+++++     ++|||||+|.+.++|++    +++..  +.|+.|.|.+
T Consensus        10 ~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~~   80 (89)
T 3d2w_A           10 HGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS----LCGEDLIIKGISVHISN   80 (89)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEEE
Confidence            3469999999999999999999999999999999864     68999999999999983    45554  5699999999


Q ss_pred             cccC
Q 016936          229 ATAS  232 (380)
Q Consensus       229 ~~~~  232 (380)
                      +.++
T Consensus        81 a~~k   84 (89)
T 3d2w_A           81 AEPK   84 (89)
T ss_dssp             CC--
T ss_pred             cCCC
Confidence            8764

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.52  E-value=1.3e-14  Score=105.79  Aligned_cols=68  Identities=22%  Similarity=0.380  Sum_probs=60.8

Q ss_pred             cceEEEcCCCCcC------cHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec----CCCcEEEEEeCCHHHHHHHH-HcC
Q 016936           32 ARRVYVGGLPPLA------NEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN----HEKKFAFVEMRTVEEASNAM-ALD  100 (380)
Q Consensus        32 ~~~v~V~nLp~~~------t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~----~~~g~afV~f~~~~~a~~ai-~l~  100 (380)
                      +++|||+|||..+      ++++|+++|++||.            |.++.+.    +++|||||+|.+.++|.+|+ .+|
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~------------i~~v~i~~~~g~~~g~afV~f~~~~~A~~Ai~~ln   68 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGK------------ITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNAD   68 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCC------------EEEEECCCBTTBCCCEEEEEESSHHHHHHHHTTSS
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCC------------eEEEEecCCCCcEeEEEEEEECCHHHHHHHHHHhc
Confidence            4799999999999      78999999999998            6666654    46899999999999999999 799


Q ss_pred             CceecCc-eEEE
Q 016936          101 GIIFEGV-AVRV  111 (380)
Q Consensus       101 ~~~i~g~-~i~v  111 (380)
                      +..+.|+ +|+|
T Consensus        69 g~~~~g~~~l~V   80 (81)
T 2krb_A           69 GYKLDKQHTFRV   80 (81)
T ss_dssp             SCCCSSSSCCCC
T ss_pred             CcccCCceeEEe
Confidence            9999999 8876

>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=99.52  E-value=7e-15  Score=109.54  Aligned_cols=76  Identities=14%  Similarity=0.178  Sum_probs=60.2

Q ss_pred             ceEEEcCCCCcCcHHHHHHHHHHHH--HhccCCCCCCCCeeEEEE---ecCCCcEEEEEeCCHHHHHHHH-HcCCceecC
Q 016936           33 RRVYVGGLPPLANEQAIATFFSQVM--TAIGGNSAGPGDAVVNVY---INHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  106 (380)
Q Consensus        33 ~~v~V~nLp~~~t~~~l~~~f~~~G--~i~~~~~~~~~~~i~~~~---~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g  106 (380)
                      .+|||+|||+++++++|+++|++||  .|..         +..+.   .++++|||||+|.+.++|++|+ .+++..+.|
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~---------v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~g   72 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILE---------IKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHG   72 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCC---------EEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSS
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEE---------EEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCC
Confidence            5799999999999999999999999  6432         22222   2356799999999999999999 799999999


Q ss_pred             ceEEEecCCCC
Q 016936          107 VAVRVRRPTDY  117 (380)
Q Consensus       107 ~~i~v~~~~~~  117 (380)
                      ++|+|.++...
T Consensus        73 r~i~V~~~~~~   83 (90)
T 3p5t_L           73 QNPVVTPSNKL   83 (90)
T ss_dssp             CCCEECCC---
T ss_pred             EEEEEEECCCC
Confidence            99999986553

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.51  E-value=2.1e-14  Score=107.15  Aligned_cols=77  Identities=19%  Similarity=0.317  Sum_probs=66.3

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe-----cCCCcEEEEEeCCHHHHHHHHHcCCc
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-----NHEKKFAFVEMRTVEEASNAMALDGI  102 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~-----~~~~g~afV~f~~~~~a~~ai~l~~~  102 (380)
                      .....++|||+|||+++++++|+++|++| .|            ..+.+     ++++|||||+|.+.++|.+|+.+++.
T Consensus         6 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i------------~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~~g~   72 (91)
T 2dgw_A            6 SGTTCHTVKLRGAPFNVTEKNVMEFLAPL-KP------------VAIRIVRNAHGNKTGYIFVDFSNEEEVKQALKCNRE   72 (91)
T ss_dssp             CCCCCCEEEEECCCSSCCHHHHHHHHTTS-CC------------SEEEEEECTTSCEEEEEEEECSSHHHHHHHHHSCSE
T ss_pred             CCCCccEEEEECCCCCCCHHHHHHHHhhC-Cc------------eEEEEEECCCCCCceEEEEEECCHHHHHHHHHhCCc
Confidence            34678999999999999999999999999 63            33333     34579999999999999999999999


Q ss_pred             eecCceEEEecCCCC
Q 016936          103 IFEGVAVRVRRPTDY  117 (380)
Q Consensus       103 ~i~g~~i~v~~~~~~  117 (380)
                      .|.|++|+|.++...
T Consensus        73 ~~~gr~i~v~~a~~~   87 (91)
T 2dgw_A           73 YMGGRYIEVFREKSG   87 (91)
T ss_dssp             EETTEEEEEEEESSC
T ss_pred             eeCCcEEEEEECCcC
Confidence            999999999987654

>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=1.4e-14  Score=103.99  Aligned_cols=69  Identities=16%  Similarity=0.352  Sum_probs=61.4

Q ss_pred             eEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe------cCCCcEEEEEeCCHHHHHHHHHcCCceecCc
Q 016936           34 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAMALDGIIFEGV  107 (380)
Q Consensus        34 ~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~------~~~~g~afV~f~~~~~a~~ai~l~~~~i~g~  107 (380)
                      +|||+|||+++++++|+++|++||.|            .++.+      +.++|||||+|.+.++|++|+++++..+.|+
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i------------~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~   68 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKV------------DDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNK   68 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCC------------SEECCCBCSSSTTSCBEEEEECSCHHHHHHHHSSSCCCSSSC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCE------------EEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHCCCCEECCE
Confidence            59999999999999999999999984            44443      3457999999999999999999999999999


Q ss_pred             eEEEecC
Q 016936          108 AVRVRRP  114 (380)
Q Consensus       108 ~i~v~~~  114 (380)
                      +|+|.++
T Consensus        69 ~l~v~~A   75 (75)
T 2mss_A           69 MVECKKA   75 (75)
T ss_dssp             CCEEECC
T ss_pred             EEEEEeC
Confidence            9999874

>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=99.51  E-value=5.4e-14  Score=107.48  Aligned_cols=79  Identities=25%  Similarity=0.395  Sum_probs=67.6

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe------cCCCcEEEEEeCCHHHHHHHHHcC
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAMALD  100 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~------~~~~g~afV~f~~~~~a~~ai~l~  100 (380)
                      ....+.++|||+|||.++++++|+++|++||.            |..+.+      ..++|||||+|.+.++|.+|+. +
T Consensus        10 ~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~------------i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~   76 (103)
T 2cqg_A           10 RAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGE------------VLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS-Q   76 (103)
T ss_dssp             CCCCCCCCEEEESCCSSCCHHHHHHHHGGGSC------------EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH-S
T ss_pred             CccCCCCEEEEEcCCCcCCHHHHHHHHHhcCC------------eEEEEEEecCCCCCccceEEEEECCHHHHHHHHH-c
Confidence            45567899999999999999999999999998            555554      3346899999999999999997 4


Q ss_pred             CceecCceEEEecCCCCC
Q 016936          101 GIIFEGVAVRVRRPTDYN  118 (380)
Q Consensus       101 ~~~i~g~~i~v~~~~~~~  118 (380)
                      +..|.|++|+|.++..+.
T Consensus        77 ~~~~~g~~l~v~~a~~~~   94 (103)
T 2cqg_A           77 RHMIDGRWCDCKLPNSKQ   94 (103)
T ss_dssp             CEEETTEEEEEECCCTTC
T ss_pred             CCeeCCeEEEEEecCCCC
Confidence            778999999999987654

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.51  E-value=2e-14  Score=110.65  Aligned_cols=74  Identities=20%  Similarity=0.260  Sum_probs=64.7

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe-----cCCCcEEEEEeCCHHHHHHHHHcCCcee
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-----NHEKKFAFVEMRTVEEASNAMALDGIIF  104 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~-----~~~~g~afV~f~~~~~a~~ai~l~~~~i  104 (380)
                      .+.++|||+|||++++++||+++|++| .            |.++.+     ++++|||||+|.+.++|.+|+.+++..|
T Consensus        14 ~~~~~v~V~nLp~~~te~dl~~~F~~~-~------------v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~~~~~~   80 (109)
T 2dnn_A           14 PDDLYVSVHGMPFSAMENDVRDFFHGL-R------------VDAVHLLKDHVGRNNGNGLVKFLSPQDTFEALKRNRMLM   80 (109)
T ss_dssp             HHHHEEEEECCCSSCCHHHHHHHTTTS-C------------CCEEEECCCTTCCCCSEEEEECSSHHHHHHHHHTTTEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhccC-C------------eeEEEEEECCCCCCCeEEEEEECCHHHHHHHHhcCCCeE
Confidence            446899999999999999999999999 5            445554     3468999999999999999999999999


Q ss_pred             cCceEEEecCCC
Q 016936          105 EGVAVRVRRPTD  116 (380)
Q Consensus       105 ~g~~i~v~~~~~  116 (380)
                      .|+.|.|..+..
T Consensus        81 ~gr~i~V~~a~~   92 (109)
T 2dnn_A           81 IQRYVEVSPATE   92 (109)
T ss_dssp             TTEEEEEEECCH
T ss_pred             CCeEEEEEECCc
Confidence            999999987654

>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=99.51  E-value=5.2e-15  Score=118.54  Aligned_cols=81  Identities=21%  Similarity=0.244  Sum_probs=68.3

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHH---hccCCCCCCCCeeEEEE--ecCCCcEEEEEeCCHHHHHHHHHcCC
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMT---AIGGNSAGPGDAVVNVY--INHEKKFAFVEMRTVEEASNAMALDG  101 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~---i~~~~~~~~~~~i~~~~--~~~~~g~afV~f~~~~~a~~ai~l~~  101 (380)
                      ....+.++|||+|||+++|+++|+++|++||.   |..         |..+.  .++++|||||+|.+.++|++|+.+++
T Consensus        39 ~~~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~---------v~i~~d~~g~srG~aFV~F~~~e~a~~Al~~~g  109 (136)
T 2hgl_A           39 PEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAG---------VHFIYTREGRQSGEAFVELGSEDDVKMALKKDR  109 (136)
T ss_dssp             SSCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTT---------EEEEECSSSCEEEEEEEECSSHHHHHHHHTTTE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeE---------EEEEECCCCCCCeEEEEEECCHHHHHHHHhcCC
Confidence            45567899999999999999999999999997   322         32222  24568999999999999999999999


Q ss_pred             ceecCceEEEecCCC
Q 016936          102 IIFEGVAVRVRRPTD  116 (380)
Q Consensus       102 ~~i~g~~i~v~~~~~  116 (380)
                      ..|.|++|+|.++..
T Consensus       110 ~~l~gr~i~V~~a~~  124 (136)
T 2hgl_A          110 ESMGHRYIEVFKSHR  124 (136)
T ss_dssp             EESSSSEEEEEECCH
T ss_pred             CEECCEEEEEEECCh
Confidence            999999999998653

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.51  E-value=3.7e-15  Score=109.76  Aligned_cols=75  Identities=19%  Similarity=0.313  Sum_probs=66.0

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec------CCCcEEEEEeCCHHHHHHHH-HcCC
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN------HEKKFAFVEMRTVEEASNAM-ALDG  101 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~------~~~g~afV~f~~~~~a~~ai-~l~~  101 (380)
                      ..+.++|||+|||+++++++|+++|++||.            |..+.+.      .++|||||+|.+.++|.+|+ .+|+
T Consensus         2 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~------------i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g   69 (85)
T 1x4e_A            2 SSGSSGLYIRGLQPGTTDQDLVKLCQPYGK------------IVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKA   69 (85)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHTTSTTTSC------------EEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHH
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCC------------eEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcC
Confidence            356799999999999999999999999997            6666653      34799999999999999999 6999


Q ss_pred             ceecCceEEEecCC
Q 016936          102 IIFEGVAVRVRRPT  115 (380)
Q Consensus       102 ~~i~g~~i~v~~~~  115 (380)
                      ..+.|+.|++.++.
T Consensus        70 ~~~~g~~~~~~~~~   83 (85)
T 1x4e_A           70 SGVQAQMAKQSGPS   83 (85)
T ss_dssp             HTCCEESCCSSCCC
T ss_pred             CeEeeEEEeecCCC
Confidence            99999999988754

>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=99.51  E-value=1.2e-14  Score=104.26  Aligned_cols=69  Identities=20%  Similarity=0.379  Sum_probs=61.0

Q ss_pred             eEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe------cCCCcEEEEEeCCHHHHHHHHHcCCceecCc
Q 016936           34 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAMALDGIIFEGV  107 (380)
Q Consensus        34 ~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~------~~~~g~afV~f~~~~~a~~ai~l~~~~i~g~  107 (380)
                      +|||+|||+++++++|+++|++||.            |.++.+      +.++|||||+|.+.++|.+|+.+++..+.|+
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~------------i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~   68 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGE------------VESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLS   68 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSC------------CSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTTSSCCBTTB
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCC------------eEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHhCCCeECCE
Confidence            6999999999999999999999998            444444      4568999999999999999998799999999


Q ss_pred             eEEEecC
Q 016936          108 AVRVRRP  114 (380)
Q Consensus       108 ~i~v~~~  114 (380)
                      +|+|.++
T Consensus        69 ~l~v~~a   75 (75)
T 1iqt_A           69 KCEIKVA   75 (75)
T ss_dssp             CCCEEEC
T ss_pred             EEEEEEC
Confidence            9999763

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.50  E-value=4.4e-14  Score=106.04  Aligned_cols=77  Identities=25%  Similarity=0.403  Sum_probs=65.9

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCc-EEEEEeCCHHHHHHHHHcCCceecCc
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-FAFVEMRTVEEASNAMALDGIIFEGV  107 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g-~afV~f~~~~~a~~ai~l~~~~i~g~  107 (380)
                      ....++|||+|||.++++++|+++|++||.            |..+...+..+ ||||+|.+.++|.+|+.+++..|.|+
T Consensus         5 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~------------v~~v~~~~~~g~~afV~f~~~~~a~~ai~l~g~~~~g~   72 (94)
T 2e5g_A            5 SSGLRSVFVSGFPRGVDSAQLSEYFLAFGP------------VASVVMDKDKGVFAIVEMGDVGAREAVLSQSQHSLGGH   72 (94)
T ss_dssp             CTTCCEEEEECCCTTCCHHHHHHHGGGTSC------------EEEEEECSSSCCEEEEEESSHHHHHHHHTCSCCEETTE
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHHhcCC------------eEEEEEcCCCCcEEEEEECCHHHHHHHHhcCCeEECCE
Confidence            456789999999999999999999999998            55554333222 99999999999999999999999999


Q ss_pred             eEEEecCCCC
Q 016936          108 AVRVRRPTDY  117 (380)
Q Consensus       108 ~i~v~~~~~~  117 (380)
                      +|+|.++..+
T Consensus        73 ~l~V~~a~~~   82 (94)
T 2e5g_A           73 RLRVRPREQK   82 (94)
T ss_dssp             ECCCBCSCCS
T ss_pred             EEEEEECCcC
Confidence            9999987654

>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=99.50  E-value=3e-14  Score=113.11  Aligned_cols=78  Identities=26%  Similarity=0.299  Sum_probs=69.1

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecC------CCcEEEEEeCCHHHHHHHH-HcC
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH------EKKFAFVEMRTVEEASNAM-ALD  100 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~------~~g~afV~f~~~~~a~~ai-~l~  100 (380)
                      ...+.++|||+|||+.+++++|+++|++||.            |..+.+..      ++|||||+|.+.++|++|+ .|+
T Consensus        18 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~   85 (126)
T 3ex7_B           18 RSVEGWILFVTGVHEEATEEDIHDKFAEYGE------------IKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLN   85 (126)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHHHHHTTSC------------EEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------eEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhC
Confidence            4456899999999999999999999999997            67776643      3799999999999999999 799


Q ss_pred             CceecCceEEEecCCCC
Q 016936          101 GIIFEGVAVRVRRPTDY  117 (380)
Q Consensus       101 ~~~i~g~~i~v~~~~~~  117 (380)
                      +..|.|++|+|.++...
T Consensus        86 g~~~~g~~l~v~~a~~~  102 (126)
T 3ex7_B           86 GQDLMGQPISVDWCFVR  102 (126)
T ss_dssp             TCBSSSSBCEEEESEES
T ss_pred             CCeeCCeEEEEEEecCC
Confidence            99999999999997543

>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=99.50  E-value=2.6e-14  Score=111.50  Aligned_cols=75  Identities=21%  Similarity=0.298  Sum_probs=66.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeE-----EE
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKT-----LT  225 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~-----i~  225 (380)
                      ...+|||+|||+++++++|+++|++||.|..|.++.+       |||||+|.+.++|++|++.||+..+.|+.     |+
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            3479999999999999999999999999999999764       79999999999999999999999999998     77


Q ss_pred             EEEcccC
Q 016936          226 VRRATAS  232 (380)
Q Consensus       226 v~~~~~~  232 (380)
                      |..+.++
T Consensus        88 v~~~~~~   94 (115)
T 3beg_B           88 VKVDGPR   94 (115)
T ss_dssp             EEECC--
T ss_pred             eccCCCC
Confidence            7766543

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.50  E-value=3.7e-14  Score=108.41  Aligned_cols=77  Identities=25%  Similarity=0.417  Sum_probs=66.3

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe------cCCCcEEEEEeCCHHHHHHHHHcCCc
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAMALDGI  102 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~------~~~~g~afV~f~~~~~a~~ai~l~~~  102 (380)
                      ..+.++|||+|||+++++++|+++|++||             |..+.+      .+++|||||+|.+.++|.+|+.+++.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-------------i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~   78 (103)
T 2dng_A           12 TEPPYTAYVGNLPFNTVQGDIDAIFKDLS-------------IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGA   78 (103)
T ss_dssp             SSSCEEEEEESCCTTCCHHHHHHHTTTSC-------------EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHGGGTTC
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCC-------------ceEEEEeecCCCCccceEEEEEECCHHHHHHHHhhCCC
Confidence            34579999999999999999999999995             344444      23478999999999999999999999


Q ss_pred             eecCceEEEecCCCCC
Q 016936          103 IFEGVAVRVRRPTDYN  118 (380)
Q Consensus       103 ~i~g~~i~v~~~~~~~  118 (380)
                      .|.|++|+|.++....
T Consensus        79 ~~~g~~l~V~~a~~~~   94 (103)
T 2dng_A           79 LLGDRSLRVDIAEGRK   94 (103)
T ss_dssp             EETTEECEEEECCCCC
T ss_pred             eECCeEEEEEEecCCC
Confidence            9999999999976543

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.50  E-value=2e-14  Score=110.26  Aligned_cols=80  Identities=20%  Similarity=0.351  Sum_probs=68.6

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec------CCCcEEEEEeCCHHHHHHHHHcC
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN------HEKKFAFVEMRTVEEASNAMALD  100 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~------~~~g~afV~f~~~~~a~~ai~l~  100 (380)
                      ....+.++|||+|||+.+++++|+++|++||.            |..+.+.      .++|||||+|.+.++|.+|+..+
T Consensus        11 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~~   78 (105)
T 2dh8_A           11 SGADEIGKLFVGGLDWSTTQETLRSYFSQYGE------------VVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASR   78 (105)
T ss_dssp             CCSSSSSEECCBSCCTTCCHHHHHHHHHTTSC------------EEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHHC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------eEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHhC
Confidence            34567899999999999999999999999998            5555543      34689999999999999999559


Q ss_pred             CceecCceEEEecCCCCC
Q 016936          101 GIIFEGVAVRVRRPTDYN  118 (380)
Q Consensus       101 ~~~i~g~~i~v~~~~~~~  118 (380)
                      +..|.|++|+|.++..+.
T Consensus        79 ~~~~~g~~l~V~~a~~~~   96 (105)
T 2dh8_A           79 PHTLDGRNIDPKPCTPRG   96 (105)
T ss_dssp             SEEETTEEEBCCCSCCSS
T ss_pred             CCeECCEEEEEEEccCCC
Confidence            999999999999976553

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.50  E-value=1.4e-13  Score=108.92  Aligned_cols=78  Identities=15%  Similarity=0.224  Sum_probs=68.4

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec-----CCCcEEEEEeCCHHHHHHHH-HcCC
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN-----HEKKFAFVEMRTVEEASNAM-ALDG  101 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~-----~~~g~afV~f~~~~~a~~ai-~l~~  101 (380)
                      .....++|||+|||..+++++|+++|++||.            |..+.+.     .++|||||+|.+.++|.+|+ .+++
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g   98 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGT------------LKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKG   98 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSC------------CSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------eeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCC
Confidence            4567799999999999999999999999998            4445443     46899999999999999999 6999


Q ss_pred             ceecCceEEEecCCCC
Q 016936          102 IIFEGVAVRVRRPTDY  117 (380)
Q Consensus       102 ~~i~g~~i~v~~~~~~  117 (380)
                      ..+.|++|+|.++...
T Consensus        99 ~~~~g~~l~V~~a~~~  114 (124)
T 2kt5_A           99 VPLDGRPMDIQLVASQ  114 (124)
T ss_dssp             EESSSCEEEEEEECCT
T ss_pred             CEECCcEEEEEEeCCC
Confidence            9999999999997654

>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=99.50  E-value=4.3e-14  Score=116.61  Aligned_cols=79  Identities=23%  Similarity=0.402  Sum_probs=69.3

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe------cCCCcEEEEEeCCHHHHHHHH-HcC
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-ALD  100 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~------~~~~g~afV~f~~~~~a~~ai-~l~  100 (380)
                      ...+.++|||+|||..+++++|+++|++||.            |..+.+      ..++|||||+|.+.++|++|+ .|+
T Consensus        35 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~  102 (156)
T 1h2v_Z           35 LLKKSCTLYVGNLSFYTTEEQIYELFSKSGD------------IKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYIN  102 (156)
T ss_dssp             TTTTCCEEEEESCCTTCCHHHHHHHHGGGSC------------EEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTT
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------eEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhC
Confidence            4467899999999999999999999999998            556665      335689999999999999999 699


Q ss_pred             CceecCceEEEecCCCCC
Q 016936          101 GIIFEGVAVRVRRPTDYN  118 (380)
Q Consensus       101 ~~~i~g~~i~v~~~~~~~  118 (380)
                      +..|.|++|+|.|+....
T Consensus       103 g~~~~g~~l~V~~a~~~~  120 (156)
T 1h2v_Z          103 GTRLDDRIIRTDWDAGFK  120 (156)
T ss_dssp             TSEETTEECEEEEESCCC
T ss_pred             CCEECCeEEEEEECCCCC
Confidence            999999999999986543

>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=99.49  E-value=1.4e-14  Score=112.91  Aligned_cols=80  Identities=13%  Similarity=0.107  Sum_probs=67.5

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe-----cCCCcEEEEEeCCHHHHHHHHHcCCc
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-----NHEKKFAFVEMRTVEEASNAMALDGI  102 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~-----~~~~g~afV~f~~~~~a~~ai~l~~~  102 (380)
                      ...+.++|||+|||+++++++|+++|++||.+.           ..+.+     ++++|||||+|.+.++|.+||.+++.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~-----------~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~~~~   79 (114)
T 2cpy_A           11 VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDE-----------NAVHVLVDNNGQGLGQALVQFKNEDDARKSERLHRK   79 (114)
T ss_dssp             CCSCCCEEEEESCCTTSCHHHHHHHTTTSCCCS-----------TTEEECCCTTSSCSSCEEEECSSHHHHHHHGGGCSE
T ss_pred             CCCCccEEEEeCcCCcCCHHHHHHHHHhCCCcC-----------CeEEEEECCCCCcceEEEEEECCHHHHHHHHHhCCC
Confidence            345679999999999999999999999998740           22333     45789999999999999999967999


Q ss_pred             eecCceEEEecCCCCC
Q 016936          103 IFEGVAVRVRRPTDYN  118 (380)
Q Consensus       103 ~i~g~~i~v~~~~~~~  118 (380)
                      .|.|++|+|.++....
T Consensus        80 ~~~gr~i~v~~a~~~~   95 (114)
T 2cpy_A           80 KLNGREAFVHVVTLED   95 (114)
T ss_dssp             EETTEEEEEEEECHHH
T ss_pred             ccCCeEEEEEECCHHH
Confidence            9999999999876543

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.49  E-value=9.3e-14  Score=101.53  Aligned_cols=72  Identities=14%  Similarity=0.146  Sum_probs=62.5

Q ss_pred             ccce-EEEcCCCCcCcHHH----HHHHHHHHH-HhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCce
Q 016936           31 HARR-VYVGGLPPLANEQA----IATFFSQVM-TAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGII  103 (380)
Q Consensus        31 ~~~~-v~V~nLp~~~t~~~----l~~~f~~~G-~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~  103 (380)
                      ++.| |||+|||..+++++    |+++|++|| .            |+++.    .|+|||+|.+.++|++|+ .|+|..
T Consensus         7 p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~------------Vl~Vt----gG~AfV~F~~~esA~~A~~~l~G~~   70 (96)
T 2diu_A            7 GCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGK------------VLSIT----GCSAILRFINQDSAERAQKRMENED   70 (96)
T ss_dssp             CSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCC------------EEECC----TTCEEEEESSHHHHHHHHHHHTTCC
T ss_pred             CcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCe------------eEEEe----cCEEEEEECCHHHHHHHHHHhcCCc
Confidence            4555 99999999999988    558999995 7            66662    399999999999999999 899999


Q ss_pred             ecCceEEEecCCCCC
Q 016936          104 FEGVAVRVRRPTDYN  118 (380)
Q Consensus       104 i~g~~i~v~~~~~~~  118 (380)
                      +.|++|+|.++....
T Consensus        71 l~gr~i~v~~A~~~s   85 (96)
T 2diu_A           71 VFGNRIIVSFTPKNR   85 (96)
T ss_dssp             SSSSCCEEESSCCSC
T ss_pred             cCCceEEEEecCCCc
Confidence            999999999987653

>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=99.49  E-value=6.3e-14  Score=122.64  Aligned_cols=101  Identities=33%  Similarity=0.504  Sum_probs=86.3

Q ss_pred             CccceEEEEeccCCcccCCChHHHHHHHHHHHHhhcccCCeEEEEecCCCCCCCC-CCCccEEEEEeechhhHHHHHHHH
Q 016936          275 ETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGE-TPGVGKVFLEYYDAVGCATAKNAL  353 (380)
Q Consensus       275 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~~f~~~G~I~~v~i~~~~~~~~~-~~g~g~afV~f~~~~~A~~A~~~l  353 (380)
                      .....++.+.+.++.+++.++..     ++|++.|++||.|.++.++++...+.. .++.|++||+|.+.++|.+|++.|
T Consensus       121 ~~~s~v~~l~n~v~~~e~~~e~~-----~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l  195 (222)
T 3dxb_A          121 AMESTVMVLRNMVDPKDIDDDLE-----GEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQAL  195 (222)
T ss_dssp             CCBCSEEEEESSCCGGGCCTTHH-----HHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHH
T ss_pred             ccccccchhhcCCCHHHHHHHHH-----HHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHh
Confidence            45567889999998887765543     699999999999999999866544321 255688899999999999999999


Q ss_pred             cCcccCCeEEEEEeccccccccccCCC
Q 016936          354 SGRKFGGNTVNAFYYPEDKYFNKDYSA  380 (380)
Q Consensus       354 ~g~~i~gr~l~v~~~~~~~~~~~~~~~  380 (380)
                      ||++|+||.|+++|++++.|+.++|++
T Consensus       196 ~gr~~~gr~i~~~~~~~~~f~~~~~~~  222 (222)
T 3dxb_A          196 NGRWFAGRKVVAEVYDQERFDNSDLSA  222 (222)
T ss_dssp             TTCBSSSSBCEEEECCHHHHHTTCCCC
T ss_pred             cCceECCeEEEEEEcCHHHhhhcccCC
Confidence            999999999999999999999999986

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.48  E-value=8.4e-14  Score=112.63  Aligned_cols=76  Identities=25%  Similarity=0.446  Sum_probs=67.6

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec------CCCcEEEEEeCCHHHHHHHH-Hc
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN------HEKKFAFVEMRTVEEASNAM-AL   99 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~------~~~g~afV~f~~~~~a~~ai-~l   99 (380)
                      ....+.++|||+|||+.+++++|+++|++||.            |..+.+.      +++|||||+|.+.++|++|+ .+
T Consensus        58 ~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~------------i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l  125 (140)
T 2ku7_A           58 GSATTKRVLYVGGLAEEVDDKVLHAAFIPFGD------------ITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM  125 (140)
T ss_dssp             SSCSSCCEEEEECCCTTCCHHHHHHHHGGGSC------------EEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHS
T ss_pred             CCCCCCcEEEEEeCCCCCCHHHHHHHHHhcCC------------EEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHh
Confidence            44567899999999999999999999999997            6667663      35899999999999999999 79


Q ss_pred             CCceecCceEEEecC
Q 016936          100 DGIIFEGVAVRVRRP  114 (380)
Q Consensus       100 ~~~~i~g~~i~v~~~  114 (380)
                      ++..|.|++|+|.++
T Consensus       126 ~g~~~~g~~l~v~~A  140 (140)
T 2ku7_A          126 NESELFGRTIRVNLA  140 (140)
T ss_dssp             TEEEETTEEEEEEC-
T ss_pred             CCCEECCEEEEEEeC
Confidence            999999999999874

>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=99.48  E-value=7.2e-14  Score=108.86  Aligned_cols=80  Identities=15%  Similarity=0.307  Sum_probs=67.6

Q ss_pred             chhhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec-----CCCcEEEEEeCCHHHHHHHH-H
Q 016936           25 TQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN-----HEKKFAFVEMRTVEEASNAM-A   98 (380)
Q Consensus        25 ~~~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~-----~~~g~afV~f~~~~~a~~ai-~   98 (380)
                      ....+.+.++|||+|||+.+++++|+++|++||.            |..+.+.     .++|||||+|.+.++|.+|+ .
T Consensus        18 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~   85 (114)
T 1x5o_A           18 AKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQ------------VISTRILRDSSGTSRGVGFARMESTEKCEAVIGH   85 (114)
T ss_dssp             CSCCCCCTTEEEEESCCTTCCHHHHHHTTTTTSC------------EEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHH
T ss_pred             hcccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------EEEEEEEECCCCCcceEEEEEECCHHHHHHHHHH
Confidence            3355678899999999999999999999999997            5555543     34799999999999999999 7


Q ss_pred             cCCcee--------cCceEEEecCCC
Q 016936           99 LDGIIF--------EGVAVRVRRPTD  116 (380)
Q Consensus        99 l~~~~i--------~g~~i~v~~~~~  116 (380)
                      +|+..|        .+++|.|.++.+
T Consensus        86 l~g~~~~~~~~~~~~~~~l~v~~a~p  111 (114)
T 1x5o_A           86 FNGKFIKTPPGVSAPTEPLLCKFSGP  111 (114)
T ss_dssp             HBTCCCCCCTTSCCCSSCBEEEECCC
T ss_pred             hCCCEEcCCccccCCCCceeEEccCC
Confidence            999999        567899988653

>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=99.48  E-value=1.6e-14  Score=107.49  Aligned_cols=72  Identities=36%  Similarity=0.524  Sum_probs=62.4

Q ss_pred             ceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe------cCCCcEEEEEeCCHHHHHHHH-HcCCceec
Q 016936           33 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-ALDGIIFE  105 (380)
Q Consensus        33 ~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~------~~~~g~afV~f~~~~~a~~ai-~l~~~~i~  105 (380)
                      ++|||+|||.++++++|+++|++||.            |.++.+      +.++|||||+|.+.+ |.+|+ .+++..+.
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~------------i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~   68 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGK------------VFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFM   68 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTC------------CSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCS
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCC------------EEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEEC
Confidence            78999999999999999999999998            445554      345899999999999 99999 79999999


Q ss_pred             CceEEEecCCCC
Q 016936          106 GVAVRVRRPTDY  117 (380)
Q Consensus       106 g~~i~v~~~~~~  117 (380)
                      |++|+|.++...
T Consensus        69 g~~l~V~~a~~~   80 (90)
T 2ki2_A           69 GRTIRVTEANPK   80 (90)
T ss_dssp             SSSCSEEEC---
T ss_pred             CeEEEEEEcCCC
Confidence            999999997654

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.48  E-value=4e-14  Score=104.91  Aligned_cols=78  Identities=19%  Similarity=0.420  Sum_probs=66.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      ..++|||+|||..+++++|+++|++||.|..|+++.+     ++|||||+|.+.++|++|...  ...+.|+.|.|.++.
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            3479999999999999999999999999999999754     689999999999999865331  345699999999987


Q ss_pred             cCCCC
Q 016936          231 ASSGQ  235 (380)
Q Consensus       231 ~~~~~  235 (380)
                      ++...
T Consensus        77 ~~~~~   81 (88)
T 1wf0_A           77 PKHNS   81 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            76443

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A

Probab=99.47  E-value=1.7e-13  Score=116.98  Aligned_cols=78  Identities=22%  Similarity=0.256  Sum_probs=72.3

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccC
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  232 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~  232 (380)
                      ++|||+|||+.+++++|+++|++||.|..|++++++ +++++|||||+|.+.++|++|+..+ +..+.|+.|.|.++..-
T Consensus       110 ~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~~y  187 (193)
T 2voo_A          110 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDDY  187 (193)
T ss_dssp             TEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETTTC
T ss_pred             CEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhHHH
Confidence            699999999999999999999999999999999986 5999999999999999999999865 56999999999997653

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.47  E-value=1.6e-14  Score=110.18  Aligned_cols=80  Identities=20%  Similarity=0.309  Sum_probs=67.2

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEE---ecCCCcEEEEEeCCHHHHHHHH-HcCCc
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVY---INHEKKFAFVEMRTVEEASNAM-ALDGI  102 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~---~~~~~g~afV~f~~~~~a~~ai-~l~~~  102 (380)
                      ....+.++|||+|||.++++++|+++|++|+.            +..+.   ...++|||||+|.+.++|.+|+ .|++.
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~------------~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~   77 (102)
T 2fc8_A           10 ARSQPSKTLFVKGLSEDTTEETLKESFDGSVR------------ARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDG   77 (102)
T ss_dssp             SSSCCCSSEEEECCCTTCCHHHHHHTSTTCSE------------EEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTC
T ss_pred             CCCCCCCEEEEeCCCCccCHHHHHHHhcCCeE------------EEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCC
Confidence            44567899999999999999999999997743            33333   2345799999999999999999 69999


Q ss_pred             eecCceEEEecCCCCC
Q 016936          103 IFEGVAVRVRRPTDYN  118 (380)
Q Consensus       103 ~i~g~~i~v~~~~~~~  118 (380)
                      .|.|++|+|.++..+.
T Consensus        78 ~~~g~~l~V~~a~~~~   93 (102)
T 2fc8_A           78 EIDGNKVTLDWAKPKG   93 (102)
T ss_dssp             EETTEECEEEECCCCC
T ss_pred             eECCeEEEEEEecCCC
Confidence            9999999999976643

>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=99.47  E-value=6.7e-14  Score=113.69  Aligned_cols=88  Identities=16%  Similarity=0.176  Sum_probs=70.6

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecCc
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  107 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g~  107 (380)
                      ..+.++|||+|||+++|+++|+++|++||.|..... .....+.....++++|||||+|.+.++|.+|+ .+|+..|.|+
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~-~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~  120 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQ-RIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGK  120 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHH-HHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccc-cceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCc
Confidence            467899999999999999999999999998642100 00000233456788999999999999999999 6999999999


Q ss_pred             eEEEecCCCC
Q 016936          108 AVRVRRPTDY  117 (380)
Q Consensus       108 ~i~v~~~~~~  117 (380)
                      +|+|.++...
T Consensus       121 ~l~V~~a~~~  130 (143)
T 3egn_A          121 PMVVQFARSA  130 (143)
T ss_dssp             ECEEEECCCS
T ss_pred             EEEEEECCCC
Confidence            9999997654

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.47  E-value=1.6e-13  Score=103.32  Aligned_cols=77  Identities=19%  Similarity=0.328  Sum_probs=67.1

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEE-EecC--CCcEEEEEeCCHHHHHHHH-HcCCcee
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNV-YINH--EKKFAFVEMRTVEEASNAM-ALDGIIF  104 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~-~~~~--~~g~afV~f~~~~~a~~ai-~l~~~~i  104 (380)
                      ....++|||+|||+++++++|+++|++||.            |..+ .+..  ..+.|||+|.+.++|.+|+ .+++..|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------v~~~~~i~~~~~~~~afV~f~~~~~a~~Ai~~l~g~~~   79 (96)
T 2e44_A           12 RQRIRKLQIRNIPPHLQWEVLDSLLVQYGV------------VESCEQVNTDSETAVVNVTYSSKDQARQALDKLNGFQL   79 (96)
T ss_dssp             CCSCCCEEEEEECSSSCHHHHHHHHHHHSC------------EEEEEEECCSSSSEEEEEEESSHHHHHHHHHHHTTCBC
T ss_pred             CCCCCEEEEEcCCCCCCHHHHHHHHHhcCC------------eEEEEEeecCCCCCEEEEEECCHHHHHHHHHHhCCCEE
Confidence            345789999999999999999999999997            6666 3443  3466999999999999999 7999999


Q ss_pred             cCceEEEecCCCC
Q 016936          105 EGVAVRVRRPTDY  117 (380)
Q Consensus       105 ~g~~i~v~~~~~~  117 (380)
                      .|++|+|.++.+.
T Consensus        80 ~g~~l~V~~a~~~   92 (96)
T 2e44_A           80 ENFTLKVAYIPDE   92 (96)
T ss_dssp             SSCBCEEEECCCC
T ss_pred             CCcEEEEEEcCcc
Confidence            9999999997665

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.47  E-value=4.7e-14  Score=113.28  Aligned_cols=79  Identities=25%  Similarity=0.403  Sum_probs=69.3

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe------cCCCcEEEEEeCCHHHHHHHH-Hc
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-AL   99 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~------~~~~g~afV~f~~~~~a~~ai-~l   99 (380)
                      ....+.++|||+|||+++++++|+++|++||.            |..+.+      .+++|||||+|.+.++|++|+ .+
T Consensus        42 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~------------i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l  109 (135)
T 2lea_A           42 PDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGR------------VGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM  109 (135)
T ss_dssp             SSGGGCCCEEEECCCSSCHHHHHHHHHGGGSC------------CSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTT
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------EEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHc
Confidence            45567899999999999999999999999997            455554      345789999999999999999 79


Q ss_pred             CCceecCceEEEecCCCC
Q 016936          100 DGIIFEGVAVRVRRPTDY  117 (380)
Q Consensus       100 ~~~~i~g~~i~v~~~~~~  117 (380)
                      ++..|.|++|+|.++...
T Consensus       110 ~g~~i~g~~l~V~~a~~~  127 (135)
T 2lea_A          110 DGAVLDGRELRVQMARYG  127 (135)
T ss_dssp             TTCCSSSSCCEEEECCCC
T ss_pred             CCCEECCEEEEEEECCCC
Confidence            999999999999997654

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.46  E-value=6.6e-14  Score=111.94  Aligned_cols=88  Identities=15%  Similarity=0.269  Sum_probs=70.2

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCc---
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGI---  102 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~---  102 (380)
                      ......++|||+|||+++|+++|+++|++||.|...+    ..++.+...++++|||||+|.+. +|.+|+ .+++.   
T Consensus        18 ~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~----v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~   92 (131)
T 2m2b_A           18 SSENANDTIILRNLNPHSTMDSILGALAPYAVLSSSN----VRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPP   92 (131)
T ss_dssp             CCSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTT----EECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCS
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceee----EEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCC
Confidence            4557789999999999999999999999999853210    01122222456789999999999 999999 89999   


Q ss_pred             -eecCceEEEecCCCCCc
Q 016936          103 -IFEGVAVRVRRPTDYNP  119 (380)
Q Consensus       103 -~i~g~~i~v~~~~~~~~  119 (380)
                       .+.|++|+|.++.....
T Consensus        93 ~~~~gr~l~V~~a~~~~~  110 (131)
T 2m2b_A           93 LTIDGKTINVEFAKGSKR  110 (131)
T ss_dssp             CCGGGCCCCCEECCCSCC
T ss_pred             ccCCCEEEEEEECCCCCC
Confidence             99999999999876543

>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=99.46  E-value=2.3e-13  Score=111.26  Aligned_cols=77  Identities=18%  Similarity=0.160  Sum_probs=66.4

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec--CCCcEEEEEeCCHHHHHHHH-HcCCceecC
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN--HEKKFAFVEMRTVEEASNAM-ALDGIIFEG  106 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~--~~~g~afV~f~~~~~a~~ai-~l~~~~i~g  106 (380)
                      ....+|||+||++.+|+++|+++|++||.            |.++.+.  ..+|||||+|.+.++|++|+ .|+|..|.|
T Consensus        44 s~vl~l~VgNL~~~vted~L~~~Fs~fG~------------V~~V~i~~k~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g  111 (164)
T 1sjr_A           44 SPVLRIIVENLFYPVTLDVLHQIFSKFGT------------VLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYN  111 (164)
T ss_dssp             CCEEEEEECSCCSCCCHHHHHHHHHHHSC------------EEEEEEEESSSCEEEEEEESCHHHHHHHHHHSTTBCSSS
T ss_pred             CceEEEEEeCcCCCCCHHHHHHHHHhcCC------------EEEEEEEeCCCCCEEEEEECCHHHHHHHHHHhCCCEecC
Confidence            44567999999999999999999999998            5555553  34689999999999999999 799999966


Q ss_pred             --ceEEEecCCCCC
Q 016936          107 --VAVRVRRPTDYN  118 (380)
Q Consensus       107 --~~i~v~~~~~~~  118 (380)
                        ++|+|.|+....
T Consensus       112 ~g~~L~V~~Ak~~~  125 (164)
T 1sjr_A          112 ACCTLRIDFSKLTS  125 (164)
T ss_dssp             SCSCEEEEECSSSS
T ss_pred             CCcEEEEEEecCCc
Confidence              999999987653

>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=99.46  E-value=2.3e-14  Score=109.28  Aligned_cols=79  Identities=28%  Similarity=0.176  Sum_probs=65.2

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEE--ecCCCcEEEEEeCCHHHHHHHHHcCCceecC
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVY--INHEKKFAFVEMRTVEEASNAMALDGIIFEG  106 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~--~~~~~g~afV~f~~~~~a~~ai~l~~~~i~g  106 (380)
                      ....++|||+|||+++|++||+++|++||.+ .         |..+.  ..+++|||||+|.+.++|++||++++..|.|
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~---------v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~~~~~~~g   81 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPLNPM-R---------VHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANMQH   81 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-E---------EEEEESSSSCEEEEEEEECSSSHHHHHHHTTSSCCSSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-E---------EEEEECCCCCEeeEEEEEECCHHHHHHHHHhCCCeECC
Confidence            4557899999999999999999999999842 1         22222  2355799999999999999999889999999


Q ss_pred             ceEEEecCCCC
Q 016936          107 VAVRVRRPTDY  117 (380)
Q Consensus       107 ~~i~v~~~~~~  117 (380)
                      +.|+|.++...
T Consensus        82 r~i~V~~~~~~   92 (102)
T 1wez_A           82 RYVELFLNSTA   92 (102)
T ss_dssp             SCCEEEEECCC
T ss_pred             cEEEEEECCCC
Confidence            99999876543

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.45  E-value=2.8e-14  Score=102.83  Aligned_cols=72  Identities=11%  Similarity=0.268  Sum_probs=60.1

Q ss_pred             ceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEE---ecCCCcEEEEEeCCHHHHHHHH-HcCCceecCce
Q 016936           33 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVY---INHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  108 (380)
Q Consensus        33 ~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~---~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g~~  108 (380)
                      ++|||+|||+++++++|+++|++||.|..         +....   .+.++|||||+|.+.++|.+|+ .++ ..+.|++
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~---------v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~   70 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKE---------CLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKT   70 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCC---------EEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEE---------EEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEE
Confidence            58999999999999999999999998432         22111   2345799999999999999999 566 8999999


Q ss_pred             EEEecC
Q 016936          109 VRVRRP  114 (380)
Q Consensus       109 i~v~~~  114 (380)
                      |+|.++
T Consensus        71 l~v~~a   76 (77)
T 1uaw_A           71 IDPKVA   76 (77)
T ss_dssp             CEEEEC
T ss_pred             EEEEec
Confidence            999875

>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=99.45  E-value=1.4e-13  Score=102.12  Aligned_cols=78  Identities=24%  Similarity=0.419  Sum_probs=59.8

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecC-CCcEEEEEeCCHHHHHHHHHcCCceec
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH-EKKFAFVEMRTVEEASNAMALDGIIFE  105 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~-~~g~afV~f~~~~~a~~ai~l~~~~i~  105 (380)
                      .+..+.++|||+|||+++|+++|+++|++||.            |.++.+.. ++|||||+|.+.++|.++... ...+.
T Consensus         6 ~~~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~------------i~~v~i~~~srGfaFV~F~~~~~A~~~~~~-~~~~~   72 (89)
T 3d2w_A            6 HHHHHGSKVFVGRCTEDMTAEELQQFFCQYGE------------VVDVFIPKPFRAFAFVTFADDKVAQSLCGE-DLIIK   72 (89)
T ss_dssp             -----CCEEEEESCCTTCCHHHHHHHHTTTSC------------EEEEECCSSCCSEEEEEESCHHHHHHHTTC-EEEET
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhccCC------------EEEEEEeeCCCCEEEEEECCHHHHHHHcCC-CcccC
Confidence            45678899999999999999999999999998            77777654 689999999999999853221 33456


Q ss_pred             CceEEEecCCCC
Q 016936          106 GVAVRVRRPTDY  117 (380)
Q Consensus       106 g~~i~v~~~~~~  117 (380)
                      |++|.|.++..+
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            899999987654

>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=99.45  E-value=1.2e-13  Score=107.83  Aligned_cols=74  Identities=26%  Similarity=0.353  Sum_probs=63.8

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecCce
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  108 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g~~  108 (380)
                      ...++|||+|||+++++++|+++|++||.            |..+.+..+ |||||+|.+.++|++|| .||+..|.|++
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~------------v~~~~i~~~-g~afV~f~~~~~a~~Ai~~l~g~~~~gr~   80 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGD------------VCYADVYRD-GTGVVEFVRKEDMTYAVRKLDNTKFRSHE   80 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSC------------EEEEEECTT-SEEEEEESSHHHHHHHHHHHTTCBCCCTT
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCC------------eEEEEEecC-CEEEEEECCHHHHHHHHHHhCCCEECCcE
Confidence            46799999999999999999999999987            778887766 99999999999999999 69999999988


Q ss_pred             -----EEEecCCC
Q 016936          109 -----VRVRRPTD  116 (380)
Q Consensus       109 -----i~v~~~~~  116 (380)
                           |+|..+..
T Consensus        81 ~~~~~i~v~~~~~   93 (115)
T 3beg_B           81 GETAYIRVKVDGP   93 (115)
T ss_dssp             SCCCBCEEEECC-
T ss_pred             eeeEEEEeccCCC
Confidence                 77765443

>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=99.44  E-value=1.4e-14  Score=111.66  Aligned_cols=81  Identities=16%  Similarity=0.217  Sum_probs=67.3

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe-----cCCCcEEEEEeCCHHHHHHHHHcCC
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-----NHEKKFAFVEMRTVEEASNAMALDG  101 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~-----~~~~g~afV~f~~~~~a~~ai~l~~  101 (380)
                      ......++|||+|||+++|+++|+++|++||.+-+         |..+.+     ++++|||||+|.+.++|.+|+.+++
T Consensus         6 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~---------v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~~~~   76 (107)
T 2lmi_A            6 EEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNG---------ENGIHFLLNRDGKRRGDALIEMESEQDVQKALEKHR   76 (107)
T ss_dssp             CCCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTT---------TTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHTTTT
T ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCC---------cceEEEEECCCCCEeeEEEEEECCHHHHHHHHHhCc
Confidence            34567899999999999999999999999887210         222222     4578999999999999999999999


Q ss_pred             ceecCceEEEecCCC
Q 016936          102 IIFEGVAVRVRRPTD  116 (380)
Q Consensus       102 ~~i~g~~i~v~~~~~  116 (380)
                      ..+.|+.|+|.++..
T Consensus        77 ~~~~gr~i~V~~a~~   91 (107)
T 2lmi_A           77 MYMGQRYVEVYEINN   91 (107)
T ss_dssp             CCSSSSCCCCEECCH
T ss_pred             ceeCCeEEEEEECCH
Confidence            999999999998654

>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=99.44  E-value=1e-12  Score=101.94  Aligned_cols=81  Identities=17%  Similarity=0.299  Sum_probs=69.2

Q ss_pred             CCCCCEEEEcCCCCCCC-----------HHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCC
Q 016936          149 AEGPDRVFVGGLPYYFT-----------ETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGL  217 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t-----------~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~  217 (380)
                      ....++|+|.||.....           +++|+++|++||.|..|.+ .++   .++|||||+|.+.++|++|+..|||.
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            34558999999944432           5799999999999999966 442   37999999999999999999999999


Q ss_pred             eeCCeEEEEEEcccCC
Q 016936          218 KMGDKTLTVRRATASS  233 (380)
Q Consensus       218 ~~~g~~i~v~~~~~~~  233 (380)
                      .+.|+.|.|.++.++.
T Consensus        88 ~~~gr~l~v~~a~~~~  103 (112)
T 2dit_A           88 WFGGRQITAQAWDGTT  103 (112)
T ss_dssp             EETTEECEEEECCSCC
T ss_pred             EECCcEEEEEEeCCCC
Confidence            9999999999987754

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.44  E-value=3.4e-14  Score=111.69  Aligned_cols=84  Identities=24%  Similarity=0.266  Sum_probs=66.6

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEE--ecCCCcEEEEEeCCHHHHHHHHHcCCceec
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVY--INHEKKFAFVEMRTVEEASNAMALDGIIFE  105 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~--~~~~~g~afV~f~~~~~a~~ai~l~~~~i~  105 (380)
                      ...+.++|||+|||+++|++||+++|++||.|.+.     ...|..+.  .++++|||||+|.+.++|++|+..++..|.
T Consensus        19 ~~~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~-----v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~~~~~l~   93 (123)
T 2dha_A           19 SKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGG-----KEGILFVTYPDGRPTGDAFVLFACEEYAQNALRKHKDLLG   93 (123)
T ss_dssp             HCCSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTG-----GGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTTTTEESS
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCC-----cceEEEEECCCCCEeeEEEEEECCHHHHHHHHHhCCCeeC
Confidence            35678999999999999999999999999864210     00133222  345679999999999999999977999999


Q ss_pred             CceEEEecCCC
Q 016936          106 GVAVRVRRPTD  116 (380)
Q Consensus       106 g~~i~v~~~~~  116 (380)
                      |+.|.|..+..
T Consensus        94 gR~i~V~~a~~  104 (123)
T 2dha_A           94 KRYIELFRSTA  104 (123)
T ss_dssp             SCEECCEEECH
T ss_pred             CeEEEEEECCH
Confidence            99999987643

>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=99.43  E-value=3.9e-13  Score=102.75  Aligned_cols=81  Identities=11%  Similarity=0.205  Sum_probs=70.2

Q ss_pred             CCCEEEEcCC--CCCCC--------HHHHHHHHHhcCCeeEEEEeeCCCC--CCCceEEEEEEcChhHHHHHHHHhCCCe
Q 016936          151 GPDRVFVGGL--PYYFT--------ETQIKELLESFGTLHGFDLVKDRDT--GNSKGYGFCVYQDPAVTDIACAALNGLK  218 (380)
Q Consensus       151 ~~~~l~V~nl--p~~~t--------~~~l~~~F~~~G~i~~v~l~~~~~~--~~~~g~afV~f~~~~~A~~Ai~~l~g~~  218 (380)
                      .++.|.|.|+  |..+.        +++|++.|++||.|.+|.+++++.+  ++++|+|||+|.+.++|.+|+..|||+.
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            3478999998  44443        3689999999999999999988653  3689999999999999999999999999


Q ss_pred             eCCeEEEEEEccc
Q 016936          219 MGDKTLTVRRATA  231 (380)
Q Consensus       219 ~~g~~i~v~~~~~  231 (380)
                      +.||.|+|.++..
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            9999999999753

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.43  E-value=5.9e-13  Score=104.38  Aligned_cols=74  Identities=18%  Similarity=0.125  Sum_probs=63.5

Q ss_pred             ceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcE-EEEEeCCHHHHHHHH-HcCCceecC--ce
Q 016936           33 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKF-AFVEMRTVEEASNAM-ALDGIIFEG--VA  108 (380)
Q Consensus        33 ~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~-afV~f~~~~~a~~ai-~l~~~~i~g--~~  108 (380)
                      ..|||+|||+.+++++|+++|++||.            |.++.+....|+ |||+|.+.++|..|+ .|+|..|.|  ++
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            44789999999999999999999998            555555444586 999999999999999 799999987  68


Q ss_pred             EEEecCCCCC
Q 016936          109 VRVRRPTDYN  118 (380)
Q Consensus       109 i~v~~~~~~~  118 (380)
                      |+|.++....
T Consensus        94 l~V~~Ak~~~  103 (124)
T 2e5i_A           94 LKIEYARPTR  103 (124)
T ss_dssp             EEEECCSCSC
T ss_pred             EEEEEecCCc
Confidence            9999876653

>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=1.9e-13  Score=113.80  Aligned_cols=78  Identities=24%  Similarity=0.264  Sum_probs=67.8

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecC------CCcEEEEEeCCHHHHHHHH-HcC
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH------EKKFAFVEMRTVEEASNAM-ALD  100 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~------~~g~afV~f~~~~~a~~ai-~l~  100 (380)
                      ...+.++|||+|||+.+++++|+++|++||.            |..+.+..      ++|||||+|.+.++|.+|| .||
T Consensus        68 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~------------i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~  135 (165)
T 1rk8_A           68 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGE------------IKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALN  135 (165)
T ss_dssp             CCC-CEEEEEESCCTTCCHHHHHHHHGGGSC------------EEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHhhcCCC------------EEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhC
Confidence            3466789999999999999999999999998            56666543      4799999999999999999 799


Q ss_pred             CceecCceEEEecCCCC
Q 016936          101 GIIFEGVAVRVRRPTDY  117 (380)
Q Consensus       101 ~~~i~g~~i~v~~~~~~  117 (380)
                      +..|.|++|.|.|+...
T Consensus       136 g~~~~g~~l~V~~a~~~  152 (165)
T 1rk8_A          136 GAEIMGQTIQVDWCFVK  152 (165)
T ss_dssp             TCEETTEECEEEESEEC
T ss_pred             CCEECCEEEEEEEecCC
Confidence            99999999999997543

>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=99.42  E-value=2.1e-13  Score=116.36  Aligned_cols=90  Identities=22%  Similarity=0.340  Sum_probs=73.0

Q ss_pred             CCCCccccch--hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec-----CCCcEEEEEeCC
Q 016936           17 PLMPVQVMTQ--QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN-----HEKKFAFVEMRT   89 (380)
Q Consensus        17 ~~~~~~~~~~--~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~-----~~~g~afV~f~~   89 (380)
                      |..|.+...+  ..+...++|||+|||+++++++|+++|++||.            |..+.+.     .++|||||+|.+
T Consensus        92 ~~~p~p~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~------------v~~v~i~~~~~~~~kG~aFVeF~~  159 (193)
T 2voo_A           92 PSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQ------------VLNIQMRRTLHKAFKGSIFVVFDS  159 (193)
T ss_dssp             TTSCCCCCCHHHHHHHHHTEEEEECCCTTCCHHHHHHHHTTSCC------------EEEEEEEECTTCCEEEEEEEEESS
T ss_pred             ccCCCcccchhhhhccccCEEEecCCCCcCCHHHHHHHHhcCCC------------EEEEEEEECCCCCcccEEEEEECC
Confidence            4444444432  25667899999999999999999999999998            5555543     357999999999


Q ss_pred             HHHHHHHHHcCCceecCceEEEecCCCCC
Q 016936           90 VEEASNAMALDGIIFEGVAVRVRRPTDYN  118 (380)
Q Consensus        90 ~~~a~~ai~l~~~~i~g~~i~v~~~~~~~  118 (380)
                      .++|.+|+...+..+.|++|.|.|..++.
T Consensus       160 ~e~A~~A~~~~~~~~~Gr~l~V~~~~~y~  188 (193)
T 2voo_A          160 IESAKKFVETPGQKYKETDLLILFKDDYF  188 (193)
T ss_dssp             HHHHHHHHHCTTCEETTEECEEEETTTC-
T ss_pred             HHHHHHHHHhCCCeECCEEEEEEEhHHHH
Confidence            99999999766779999999999987764

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.42  E-value=3.9e-13  Score=105.86  Aligned_cols=77  Identities=19%  Similarity=0.216  Sum_probs=65.7

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec-CCCcE-EEEEeCCHHHHHHHH-HcCCceecC
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN-HEKKF-AFVEMRTVEEASNAM-ALDGIIFEG  106 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~-~~~g~-afV~f~~~~~a~~ai-~l~~~~i~g  106 (380)
                      ..--+|||+||++.+|+++|+++|++||.            |.++.+. +.+|+ |||+|.+.++|.+|+ .|+|..|.|
T Consensus        26 s~VL~I~V~NL~~~vte~~L~~lFs~yG~------------V~~V~i~~~~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g   93 (130)
T 3zzy_A           26 SPVLRIIVENLFYPVTLDVLHQIFSKFGT------------VLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYN   93 (130)
T ss_dssp             CSEEEEEEESCCSCCCHHHHHHHHTTSSC------------EEEEEEEEETTEEEEEEEESCHHHHHHHHHHHTTCEEET
T ss_pred             CceEEEEECCCCCCCCHHHHHHHHhCcCC------------EEEEEEEcCCCCcEEEEEECCHHHHHHHHHHcCCCeecC
Confidence            34456889999999999999999999998            5555543 45677 999999999999999 899999998


Q ss_pred             --ceEEEecCCCCC
Q 016936          107 --VAVRVRRPTDYN  118 (380)
Q Consensus       107 --~~i~v~~~~~~~  118 (380)
                        +.|+|.++...+
T Consensus        94 ~~~~LrI~~ak~~~  107 (130)
T 3zzy_A           94 ACCTLRIDFSKLTS  107 (130)
T ss_dssp             TEEEEEEEECSCSS
T ss_pred             CCcEEEEEecCCCc
Confidence              899999987654

>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=99.42  E-value=1.4e-13  Score=101.94  Aligned_cols=76  Identities=25%  Similarity=0.384  Sum_probs=63.4

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec-CCCcEEEEEeCCHHHHHHHHHcCCceecCce
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN-HEKKFAFVEMRTVEEASNAMALDGIIFEGVA  108 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~-~~~g~afV~f~~~~~a~~ai~l~~~~i~g~~  108 (380)
                      .++++|||+|||.++++++|+++|++||.            |.++.+. .++|||||+|.+.++|++|+.. ...+.|++
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~------------i~~v~i~~~~~g~afV~f~~~~~a~~~~~~-~~~~~g~~   69 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGD------------VMDVFIPKPFRAFAFVTFADDQIAQSLCGE-DLIIKGIS   69 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSC------------CCEEECCSSCCSCCEEECSCHHHHHHTTTC-EEEETTEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCC------------eeEEEEecCCCCEEEEEECCHHHHHHHhcC-CceeCCEE
Confidence            46799999999999999999999999997            6667664 3689999999999999875532 35568999


Q ss_pred             EEEecCCCCC
Q 016936          109 VRVRRPTDYN  118 (380)
Q Consensus       109 i~v~~~~~~~  118 (380)
                      |+|.++..+.
T Consensus        70 l~v~~a~~~~   79 (88)
T 1wf0_A           70 VHISNAEPKH   79 (88)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEEecCCCC
Confidence            9999876653

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.13  E-value=1.5e-14  Score=113.18  Aligned_cols=91  Identities=21%  Similarity=0.234  Sum_probs=70.2

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCC--CCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCce
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAG--PGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGII  103 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~--~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~  103 (380)
                      +...+.++|||+|||.++++++|+++|++||.|......+  ....+.+.....++|||||+|.+.++|.+|+ .|++..
T Consensus         2 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~   81 (116)
T 2lcw_A            2 QDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKE   81 (116)
Confidence            4567789999999999999999999999999864300000  0011122233456899999999999999999 699999


Q ss_pred             ecCceEEEecCCCC
Q 016936          104 FEGVAVRVRRPTDY  117 (380)
Q Consensus       104 i~g~~i~v~~~~~~  117 (380)
                      |.|++|+|.++...
T Consensus        82 ~~g~~l~V~~a~~~   95 (116)
T 2lcw_A           82 FSGNPIKVSFATRR   95 (116)
Confidence            99999999997654

>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=99.41  E-value=1.4e-13  Score=108.48  Aligned_cols=75  Identities=21%  Similarity=0.251  Sum_probs=64.5

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeE--EEEec-----CCCcEEEEEeCCHHHHHHHHHcC
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVV--NVYIN-----HEKKFAFVEMRTVEEASNAMALD  100 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~--~~~~~-----~~~g~afV~f~~~~~a~~ai~l~  100 (380)
                      .....++|||+|||+++|+++|+++|++|+             |+  ++.+.     +++|||||+|.+.++|++|+.++
T Consensus        38 ~~~~~~~lfVgnLp~~~te~dL~~~F~~~~-------------i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~~~  104 (126)
T 2hgm_A           38 DSANDGFVRLRGLPFGCTKEEIVQFFSGLE-------------IVPNGITLPVDPEGKITGEAFVQFASQELAEKALGKH  104 (126)
T ss_dssp             CSSSCCEEEEECCCTTCCHHHHHHHTTTSC-------------EEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHTTT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCC-------------ceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHHHC
Confidence            445678999999999999999999999993             33  55553     46899999999999999999778


Q ss_pred             CceecCceEEEecCC
Q 016936          101 GIIFEGVAVRVRRPT  115 (380)
Q Consensus       101 ~~~i~g~~i~v~~~~  115 (380)
                      +..|.|+.|+|.++.
T Consensus       105 ~~~l~gR~I~V~~a~  119 (126)
T 2hgm_A          105 KERIGHRYIEVFKSS  119 (126)
T ss_dssp             TCCBTTBCCCCEEEC
T ss_pred             CCEECCEEEEEEECC
Confidence            899999999998754

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.41  E-value=6.4e-14  Score=106.85  Aligned_cols=77  Identities=22%  Similarity=0.348  Sum_probs=66.8

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec-----CCCcEEEEEeCCHHHHHHHHHcCCc
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN-----HEKKFAFVEMRTVEEASNAMALDGI  102 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~-----~~~g~afV~f~~~~~a~~ai~l~~~  102 (380)
                      .+..+++|||+|||+++++++|+++|++||.            |..+.+.     .++|||||+|.+.++|.+|+. ++.
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~------------i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~-~~~   71 (102)
T 2xs2_A            5 GKIMPNTVFVGGIDVRMDETEIRSFFARYGS------------VKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE-SQI   71 (102)
T ss_dssp             CEEEEEEEEEECCCTTCCHHHHHHHHGGGSC------------EEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT-CCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCC------------eEEEEEEECCCCCccceEEEEECCHHHHHHHHh-CCC
Confidence            4556799999999999999999999999998            5555543     357999999999999999999 999


Q ss_pred             eecCceEEEecCCCC
Q 016936          103 IFEGVAVRVRRPTDY  117 (380)
Q Consensus       103 ~i~g~~i~v~~~~~~  117 (380)
                      .+.|++|.|.++..+
T Consensus        72 ~~~g~~l~v~~a~~~   86 (102)
T 2xs2_A           72 NFHGKKLKLGPAIRK   86 (102)
T ss_dssp             EETTEECEEEEEEEC
T ss_pred             eECCEEEEEEECCcC
Confidence            999999999886543

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.41  E-value=3.7e-13  Score=117.55  Aligned_cols=77  Identities=21%  Similarity=0.389  Sum_probs=69.6

Q ss_pred             CCCCEEEEcCCCCCC---------CHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCee-
Q 016936          150 EGPDRVFVGGLPYYF---------TETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM-  219 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~---------t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~-  219 (380)
                      ...++|||+|||..+         ++++|+++|++||.|..|+++.+      +|||||+|.+.++|+.|++.|+|..+ 
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         79999999999999999999853      68999999999999999999999999 


Q ss_pred             -----------CCeEEEEEEcccC
Q 016936          220 -----------GDKTLTVRRATAS  232 (380)
Q Consensus       220 -----------~g~~i~v~~~~~~  232 (380)
                                 .|+.|.|.|+...
T Consensus       206 ~~~~~e~~~~~~gr~L~V~wA~~~  229 (240)
T 3u1l_A          206 LPSDKEWDDRREGTGLLVKWANED  229 (240)
T ss_dssp             CTTSTTGGGGGGSCCCEEEECC--
T ss_pred             ccccccccccCCCCEEEEEEccCC
Confidence                       8999999999764

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.40  E-value=4e-13  Score=112.93  Aligned_cols=76  Identities=16%  Similarity=0.227  Sum_probs=67.4

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe-----cCCCcEEEEEeCCHHHHHHHH-HcCCc
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-----NHEKKFAFVEMRTVEEASNAM-ALDGI  102 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~-----~~~~g~afV~f~~~~~a~~ai-~l~~~  102 (380)
                      ....++|||+|||+.+++++|+++|++||.            |..+.+     ..++|||||+|.+.++|.+|+ .+++.
T Consensus        85 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~------------I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~  152 (177)
T 2f3j_A           85 VETGAKLLVSNLDFGVSDADIQELFAEFGT------------LKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGV  152 (177)
T ss_dssp             CTTCEEEEEECCCSCCCHHHHHHHHHHTSC------------CSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------eEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCC
Confidence            456789999999999999999999999998            555555     346799999999999999999 69999


Q ss_pred             eecCceEEEecCCC
Q 016936          103 IFEGVAVRVRRPTD  116 (380)
Q Consensus       103 ~i~g~~i~v~~~~~  116 (380)
                      .|.|++|+|.++..
T Consensus       153 ~l~Gr~l~V~~a~~  166 (177)
T 2f3j_A          153 PLDGRPMDIQLVAS  166 (177)
T ss_dssp             BCSSSBCEEEEESS
T ss_pred             EECCEEEEEEEecC
Confidence            99999999998754

>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=99.40  E-value=7.8e-13  Score=103.03  Aligned_cols=79  Identities=15%  Similarity=0.189  Sum_probs=69.1

Q ss_pred             CCEEEEcCC--CCCC---CHHHHHHHHHhcCCeeEEEEeeCCC----CCCCceEEEEEEcChhHHHHHHHHhCCCeeCCe
Q 016936          152 PDRVFVGGL--PYYF---TETQIKELLESFGTLHGFDLVKDRD----TGNSKGYGFCVYQDPAVTDIACAALNGLKMGDK  222 (380)
Q Consensus       152 ~~~l~V~nl--p~~~---t~~~l~~~F~~~G~i~~v~l~~~~~----~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~  222 (380)
                      ++.|+|.|+  |.++   .+++|++.|++||.|.+|.+++++.    +++++|++||+|.+.++|.+|+..|||+.+.||
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            369999999  3222   3689999999999999999998753    356789999999999999999999999999999


Q ss_pred             EEEEEEcc
Q 016936          223 TLTVRRAT  230 (380)
Q Consensus       223 ~i~v~~~~  230 (380)
                      .|+|.++.
T Consensus       100 ~i~v~~~~  107 (118)
T 3ue2_A          100 KVVAEVYD  107 (118)
T ss_dssp             ECEEEEEC
T ss_pred             EEEEEEcC
Confidence            99999974

>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=99.39  E-value=3e-13  Score=118.57  Aligned_cols=76  Identities=14%  Similarity=0.217  Sum_probs=64.8

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHH--HhccCCCCCCCCeeEEEEe------cCCCcEEEEEeCCHHHHHHHH-HcC
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVM--TAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-ALD  100 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G--~i~~~~~~~~~~~i~~~~~------~~~~g~afV~f~~~~~a~~ai-~l~  100 (380)
                      ...++|||+|||+++|+++|+++|++||  .            |.++.+      .+++|||||+|.+.++|.+|| .||
T Consensus        66 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~~~------------v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~ln  133 (229)
T 3q2s_C           66 GKRIALYIGNLTWWTTDEDLTEAVHSLGVND------------ILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLP  133 (229)
T ss_dssp             ---CEEEEESCCTTCCHHHHHHHHHTTTCCC------------EEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTST
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHHCCcc------------eEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcC
Confidence            3678999999999999999999999999  6            555554      345799999999999999999 699


Q ss_pred             CceecCceEEEecCCCC
Q 016936          101 GIIFEGVAVRVRRPTDY  117 (380)
Q Consensus       101 ~~~i~g~~i~v~~~~~~  117 (380)
                      +..|.|++|+|.++...
T Consensus       134 g~~~~Gr~l~V~~a~~~  150 (229)
T 3q2s_C          134 KRELHGQNPVVTPVNKQ  150 (229)
T ss_dssp             TSCBTTBCCEEEECCHH
T ss_pred             CCeECCEEeEEEECCCC
Confidence            99999999999987643

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.39  E-value=3.7e-13  Score=117.54  Aligned_cols=78  Identities=22%  Similarity=0.327  Sum_probs=70.5

Q ss_pred             hhcccceEEEcCCCCcC---------cHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-
Q 016936           28 ATRHARRVYVGGLPPLA---------NEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-   97 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~---------t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-   97 (380)
                      .....++|||+|||..+         ++++|+++|++||.            |.++.+..++|||||+|.+.++|+.|+ 
T Consensus       130 ~~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~------------I~~v~v~~~kG~AFV~F~~~~~Ae~A~~  197 (240)
T 3u1l_A          130 FRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGD------------IDRIRYVESKNCGFVKFKYQANAEFAKE  197 (240)
T ss_dssp             -CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSC------------EEEEEEEGGGTEEEEEESSHHHHHHHHH
T ss_pred             cccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCC------------EEEEEEECCCCEEEEEeCCHHHHHHHHH
Confidence            35678999999999998         89999999999998            888888889999999999999999999 


Q ss_pred             HcCCcee------------cCceEEEecCCCC
Q 016936           98 ALDGIIF------------EGVAVRVRRPTDY  117 (380)
Q Consensus        98 ~l~~~~i------------~g~~i~v~~~~~~  117 (380)
                      +|++..|            .|+.|.|.|+...
T Consensus       198 am~g~~l~~~~~~e~~~~~~gr~L~V~wA~~~  229 (240)
T 3u1l_A          198 AMSNQTLLLPSDKEWDDRREGTGLLVKWANED  229 (240)
T ss_dssp             HHTTCCCCCTTSTTGGGGGGSCCCEEEECC--
T ss_pred             HhCCCEEeccccccccccCCCCEEEEEEccCC
Confidence            8999999            8999999998754

>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=99.38  E-value=9.6e-14  Score=111.51  Aligned_cols=78  Identities=29%  Similarity=0.250  Sum_probs=64.7

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe-----cCCCcEEEEEeCCHHHHHHHHHcCC
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-----NHEKKFAFVEMRTVEEASNAMALDG  101 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~-----~~~~g~afV~f~~~~~a~~ai~l~~  101 (380)
                      ......++|||+|||+++|++||+++|++|| +           + ++.+     .+++|||||+|.+.++|++||.+++
T Consensus        41 ~~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i-----------~-~v~i~~d~~g~srGfaFV~F~~~e~A~~Al~~~g  107 (139)
T 2hgn_A           41 VQSTTGHCVHMRGLPYKATENDIYNFFSPLN-P-----------V-RVHIEIGPDGRVTGEADVEFATHEEAVAAMSKDR  107 (139)
T ss_dssp             ----CCCCEECCSCCTTCCHHHHHHHHCSCC-C-----------S-EEECCCSSSSCSSCCCEEECSHHHHHHHHTTCCS
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-C-----------e-EEEEEECCCCCCceEEEEEeCCHHHHHHHHhhCC
Confidence            3456789999999999999999999999998 3           2 3333     4568999999999999999999999


Q ss_pred             ceecCceEEEecCCCC
Q 016936          102 IIFEGVAVRVRRPTDY  117 (380)
Q Consensus       102 ~~i~g~~i~v~~~~~~  117 (380)
                      ..|.|+.|+|.++...
T Consensus       108 ~~l~gR~i~V~~a~~~  123 (139)
T 2hgn_A          108 ANMQHRYIELFLNSTT  123 (139)
T ss_dssp             CSSSSCCCCCEECCCS
T ss_pred             CEECCEEEEEEECCCC
Confidence            9999999999876543

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.37  E-value=9.1e-13  Score=102.56  Aligned_cols=69  Identities=26%  Similarity=0.330  Sum_probs=54.7

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe---------cCCCcEEEEEeCCHHHHHHHH-H
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI---------NHEKKFAFVEMRTVEEASNAM-A   98 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~---------~~~~g~afV~f~~~~~a~~ai-~   98 (380)
                      ....++|||+|||+++++++|+++|++||.|            . +.+         ++++|||||+|.+.++|++|+ .
T Consensus         5 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i------------~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~   71 (114)
T 2dnl_A            5 SSGSRKVFVGGLPPDIDEDEITASFRRFGPL------------V-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDA   71 (114)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHTTTTCCC------------C-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHH
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCE------------E-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHh
Confidence            4567999999999999999999999999974            3 332         356899999999999999999 6


Q ss_pred             cCCceecCceEEEe
Q 016936           99 LDGIIFEGVAVRVR  112 (380)
Q Consensus        99 l~~~~i~g~~i~v~  112 (380)
                      ++  .+.|+.+.+.
T Consensus        72 ~~--~~~G~~~~~~   83 (114)
T 2dnl_A           72 CL--EEDGKLYLCV   83 (114)
T ss_dssp             SE--EETTEEEEEE
T ss_pred             hh--hcCCcEEEec
Confidence            62  2444444443

>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=99.37  E-value=3.2e-13  Score=103.08  Aligned_cols=72  Identities=13%  Similarity=0.259  Sum_probs=62.4

Q ss_pred             EcCCCCCCCHHHHHHHH------------HhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEE
Q 016936          157 VGGLPYYFTETQIKELL------------ESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTL  224 (380)
Q Consensus       157 V~nlp~~~t~~~l~~~F------------~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i  224 (380)
                      +.+||+.+++++|+++|            ++||.|.+|.+++++ .++++|||||+|.+.++|.+|+..|||..+.|+.|
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            44566666776666655            999999999999886 48899999999999999999999999999999999


Q ss_pred             EEEEc
Q 016936          225 TVRRA  229 (380)
Q Consensus       225 ~v~~~  229 (380)
                      +|.++
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99986

>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=99.31  E-value=4.2e-12  Score=121.66  Aligned_cols=76  Identities=16%  Similarity=0.208  Sum_probs=66.8

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe------cCCCcEEEEEeCCHHHHHHHH-HcCCc
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-ALDGI  102 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~------~~~~g~afV~f~~~~~a~~ai-~l~~~  102 (380)
                      .+.++|||+|||+.+|+++|.++|++||.|            ..+.+      +.++|||||+|.+.++|.+|| .||+.
T Consensus       100 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~I------------~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~  167 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEVYGPI------------KRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGK  167 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCe------------eEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCC
Confidence            345899999999999999999999999984            44443      446899999999999999999 89999


Q ss_pred             eecCceEEEecCCCC
Q 016936          103 IFEGVAVRVRRPTDY  117 (380)
Q Consensus       103 ~i~g~~i~v~~~~~~  117 (380)
                      .|.|++|.|.++...
T Consensus       168 ~i~gr~i~V~~a~~~  182 (437)
T 3pgw_S          168 KIDGRRVLVDVERGR  182 (437)
T ss_pred             EECCEEEEEEEeCCC
Confidence            999999999997654

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.26  E-value=5.7e-11  Score=89.49  Aligned_cols=76  Identities=11%  Similarity=0.166  Sum_probs=63.6

Q ss_pred             CCEEEEcCCC-------CCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEE
Q 016936          152 PDRVFVGGLP-------YYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTL  224 (380)
Q Consensus       152 ~~~l~V~nlp-------~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i  224 (380)
                      .++|.|.-.+       ..+++++|+++|++||.|..|.++     ++++|||||+|.+.++|++|++.+  ..+.|++|
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~--~~~~g~~l   82 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNE--VGLVDNPL   82 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTC--CBCSSSBC
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhc--CCCCCCeE
Confidence            3566666554       458999999999999999999987     467899999999999999999974  44679999


Q ss_pred             EEEEcccCCC
Q 016936          225 TVRRATASSG  234 (380)
Q Consensus       225 ~v~~~~~~~~  234 (380)
                      +|.|+..+..
T Consensus        83 ~V~~a~~~~~   92 (100)
T 2d9o_A           83 KISWLEGQPQ   92 (100)
T ss_dssp             EEECSSCCCC
T ss_pred             EEEEccCCCC
Confidence            9999876643

>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=99.20  E-value=8.1e-11  Score=90.91  Aligned_cols=75  Identities=16%  Similarity=0.150  Sum_probs=64.3

Q ss_pred             CCEEEEcCC--CCCCC--------HHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCC
Q 016936          152 PDRVFVGGL--PYYFT--------ETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD  221 (380)
Q Consensus       152 ~~~l~V~nl--p~~~t--------~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g  221 (380)
                      ++.|.|.|+  |....        +++|++.|++||.|.+|.+.++.    ++|+|||+|.+.++|.+|+..|||..+.|
T Consensus         7 s~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~f~G   82 (114)
T 3s6e_A            7 TQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRWFAG   82 (114)
T ss_dssp             CSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCEETT
T ss_pred             CcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            468999999  33211        25889999999999999996652    58999999999999999999999999999


Q ss_pred             eEEEEEEcc
Q 016936          222 KTLTVRRAT  230 (380)
Q Consensus       222 ~~i~v~~~~  230 (380)
                      +.|.|.++.
T Consensus        83 R~i~v~~~~   91 (114)
T 3s6e_A           83 KMITAAYVP   91 (114)
T ss_dssp             EECEEEEEC
T ss_pred             EEEEEEEEc
Confidence            999999974

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*

Probab=99.17  E-value=6.4e-11  Score=108.94  Aligned_cols=75  Identities=21%  Similarity=0.291  Sum_probs=64.0

Q ss_pred             CCCCEEEEcC--CCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeC---Ce--
Q 016936          150 EGPDRVFVGG--LPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG---DK--  222 (380)
Q Consensus       150 ~~~~~l~V~n--lp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~---g~--  222 (380)
                      ..+++|||+|  |+..+++++|+++|++||.|.+|.+..      ++|||||+|.+.++|++|++.|||+.+.   |+  
T Consensus        16 ~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~   89 (345)
T 3tht_A           16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKI   89 (345)
T ss_dssp             SCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEE
T ss_pred             CCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCccccccCCce
Confidence            3447999999  588999999999999999999987753      4689999999999999999999999882   44  


Q ss_pred             EEEEEEcc
Q 016936          223 TLTVRRAT  230 (380)
Q Consensus       223 ~i~v~~~~  230 (380)
                      .+.+.++.
T Consensus        90 ~ly~~~~~   97 (345)
T 3tht_A           90 TLYLNFVE   97 (345)
T ss_dssp             ECEEEECS
T ss_pred             EEEEEEee
Confidence            57777763

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.14  E-value=6.3e-11  Score=91.65  Aligned_cols=66  Identities=12%  Similarity=0.087  Sum_probs=56.3

Q ss_pred             HHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeec----hhh----HHHHHH--HHcCcccCCeEEEEEecccc
Q 016936          303 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYD----AVG----CATAKN--ALSGRKFGGNTVNAFYYPED  371 (380)
Q Consensus       303 ~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~----~~~----A~~A~~--~l~g~~i~gr~l~v~~~~~~  371 (380)
                      .+|+++|++||.|.++.++.++.+|. ++  |++||+|.+    +++    |.+|+.  .|||..|+||+|+|.+-...
T Consensus        21 ~~Lk~~Fs~fGeV~~~~li~Dp~Tg~-sl--GfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~I~Gr~irV~ln~~g   96 (136)
T 2j8a_A           21 ISIKNYFKKYGEISHFEAFNDPNSAL-PL--HVYLIKYASSDGKINDAAKAAFSAVRKHESSGCFIMGFKFEVILNKHS   96 (136)
T ss_dssp             HHHHHHHHTTSCCSEEEEEECTTTCC-EE--EEEEEECC------CCHHHHHHHHHHHTTTTCEEETTEEEEEEECCTT
T ss_pred             HHHHHHHHhcCCeEEEEEEecCCCCc-ee--eEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCeecCcEEEEEECccc
Confidence            69999999999999999999998876 44  566999997    555    789988  89999999999999986654

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.12  E-value=5.7e-10  Score=80.78  Aligned_cols=61  Identities=8%  Similarity=0.275  Sum_probs=54.4

Q ss_pred             HHHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEeccccccc
Q 016936          302 LEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYF  374 (380)
Q Consensus       302 ~~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~~~~~  374 (380)
                      ..+|.+.|++||.|..+++..+           .+||+|.+.++|.+|++ |||..++||+|+|+++.++=..
T Consensus        29 ~~~L~~~F~~~G~Vi~vr~~~d-----------~~fVtF~d~~sAlaAi~-mnG~~v~Gr~LkV~lkt~dW~~   89 (91)
T 2dnr_A           29 IDELLQQFASFGEVILIRFVED-----------KMWVTFLEGSSALNVLS-LNGKELLNRTITIALKSPSGPS   89 (91)
T ss_dssp             HHHHHHHHHTTCCEEEEEECSS-----------SEEEEESSHHHHHHGGG-GTTCEETTEEEEEEECCCSSCS
T ss_pred             HHHHHHHHHhCCCeEEEEEecC-----------CEEEEECChHHHHHHHh-cCCeEeCCeEEEEEeCCCCccc
Confidence            3689999999999999999874           34999999999999998 9999999999999999876443

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.11  E-value=8.3e-11  Score=88.59  Aligned_cols=60  Identities=17%  Similarity=0.270  Sum_probs=51.9

Q ss_pred             HHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEeccccc
Q 016936          303 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  372 (380)
Q Consensus       303 ~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~~~  372 (380)
                      ++|+++|++||.|.+|.++..      +  .|+|||+|.+.++|.+|++.+++  +.|+.|+|.|+....
T Consensus        32 ~~L~~~F~~~G~V~~v~i~~~------~--rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a~~~~   91 (100)
T 2d9o_A           32 DVLLRLLQKYGEVLNLVLSSK------K--PGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWLEGQP   91 (100)
T ss_dssp             HHHHHHHHTTSCEEEEEEESS------S--SSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECSSCCC
T ss_pred             HHHHHHHHhcCCEEEEEEccC------C--CCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEccCCC
Confidence            699999999999999999842      2  36779999999999999998665  689999999987653

>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=99.11  E-value=1.1e-10  Score=107.32  Aligned_cols=75  Identities=17%  Similarity=0.236  Sum_probs=65.6

Q ss_pred             hhcccceEEEcC--CCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCcee
Q 016936           28 ATRHARRVYVGG--LPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIF  104 (380)
Q Consensus        28 ~~~~~~~v~V~n--Lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i  104 (380)
                      .+.++++|||+|  |+..+|+++|+++|++||.            |.++.+..+||||||+|.+.++|++|+ .|||..+
T Consensus        14 ~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~------------V~~v~~~~~kgfaFV~f~~~~~A~~Ai~~lnG~~~   81 (345)
T 3tht_A           14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGL------------VDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEV   81 (345)
T ss_dssp             CSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSC------------EEEEECCTTCSEEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             cCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCC------------eEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCcc
Confidence            467889999999  5789999999999999998            788888889999999999999999999 8999887


Q ss_pred             c---Cc--eEEEecC
Q 016936          105 E---GV--AVRVRRP  114 (380)
Q Consensus       105 ~---g~--~i~v~~~  114 (380)
                      .   |+  +|.+.+.
T Consensus        82 ~~~~g~~~~ly~~~~   96 (345)
T 3tht_A           82 VDDLGQKITLYLNFV   96 (345)
T ss_dssp             ECTTSCEEECEEEEC
T ss_pred             ccccCCceEEEEEEe
Confidence            3   44  5777664

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.92  E-value=4.6e-09  Score=76.01  Aligned_cols=70  Identities=20%  Similarity=0.306  Sum_probs=60.1

Q ss_pred             EEEEcCCCC----CCCH----HHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEE
Q 016936          154 RVFVGGLPY----YFTE----TQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  225 (380)
Q Consensus       154 ~l~V~nlp~----~~t~----~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~  225 (380)
                      +|+|.-.|.    .+-.    .+|.+.|++||.|..+++..++        +||+|.+.++|.+|++ |||..+.|+.|+
T Consensus         9 tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~-mnG~~v~Gr~Lk   79 (91)
T 2dnr_A            9 TVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLS-LNGKELLNRTIT   79 (91)
T ss_dssp             EEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGG-GTTCEETTEEEE
T ss_pred             eEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHh-cCCeEeCCeEEE
Confidence            788877762    3333    5789999999999999998763        8999999999999999 999999999999


Q ss_pred             EEEcccC
Q 016936          226 VRRATAS  232 (380)
Q Consensus       226 v~~~~~~  232 (380)
                      |+.+++.
T Consensus        80 V~lkt~d   86 (91)
T 2dnr_A           80 IALKSPS   86 (91)
T ss_dssp             EEECCCS
T ss_pred             EEeCCCC
Confidence            9998754

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.91  E-value=5.1e-09  Score=80.93  Aligned_cols=72  Identities=14%  Similarity=0.148  Sum_probs=65.1

Q ss_pred             CCEEEEcCCCCC-CCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcC-hhHHHHHHHHhC--CCeeCCeEEEEE
Q 016936          152 PDRVFVGGLPYY-FTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD-PAVTDIACAALN--GLKMGDKTLTVR  227 (380)
Q Consensus       152 ~~~l~V~nlp~~-~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~-~~~A~~Ai~~l~--g~~~~g~~i~v~  227 (380)
                      ...|+|+||++. ++.++|+++|++||.|..|.+.++..      .|||+|.+ +++|..|+..++  +..|.|..+.++
T Consensus        18 G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~e   91 (121)
T 1owx_A           18 GCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWE   91 (121)
T ss_dssp             CCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEE
T ss_pred             CeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEEE
Confidence            368999999999 99999999999999999999988753      69999999 799999999985  789999999988


Q ss_pred             Ec
Q 016936          228 RA  229 (380)
Q Consensus       228 ~~  229 (380)
                      ..
T Consensus        92 vL   93 (121)
T 1owx_A           92 VL   93 (121)
T ss_dssp             EC
T ss_pred             EC
Confidence            75

>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=98.82  E-value=7.9e-09  Score=75.11  Aligned_cols=57  Identities=21%  Similarity=0.345  Sum_probs=51.4

Q ss_pred             HHHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEeccc
Q 016936          302 LEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPE  370 (380)
Q Consensus       302 ~~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~  370 (380)
                      ..+|.+.|++||.|..+++..+           .+||+|.+.++|.+|++ |||..++||.|+|.+...
T Consensus        38 ~~~L~~~F~~~G~Vilvr~v~d-----------~~fVtF~d~~sAl~AI~-ldG~~v~Gr~L~V~~k~~   94 (95)
T 1ufw_A           38 RTELMQTLGSYGTIVLVRINQG-----------QMLVTFADSHSALSVLD-VDGMKVKGRAVKISGPSS   94 (95)
T ss_dssp             HHHHHHHHHHHSCCSEEEEETT-----------EEEEECSCSHHHHHHHH-GGGSEETTEEEEEECCCC
T ss_pred             HHHHHHHHHHCCCEEEEEEecC-----------cEEEEEcChHHHHHHHh-cCCeeeCCeEEEEeccCC
Confidence            3589999999999999999874           35999999999999998 999999999999998653

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=98.73  E-value=3.2e-08  Score=86.11  Aligned_cols=67  Identities=16%  Similarity=0.161  Sum_probs=60.1

Q ss_pred             CCHHHHHHHHHhcCCeeEEEEeeCCC----CCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          164 FTETQIKELLESFGTLHGFDLVKDRD----TGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       164 ~t~~~l~~~F~~~G~i~~v~l~~~~~----~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      -.+++|.+.|++||.|.++.++++..    +++++|++||+|.+.++|.+|+..|||+.+.||.|.+.+..
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            35679999999999999999986533    44899999999999999999999999999999999999974

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.70  E-value=2.6e-08  Score=76.94  Aligned_cols=73  Identities=10%  Similarity=0.043  Sum_probs=64.8

Q ss_pred             hcccceEEEcCCCCc-CcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCC-HHHHHHHH-HcC--Cce
Q 016936           29 TRHARRVYVGGLPPL-ANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRT-VEEASNAM-ALD--GII  103 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~-~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~-~~~a~~ai-~l~--~~~  103 (380)
                      -...+.|+|+||+++ ++.++|+++|++||.            |..+.+..+.-.|||+|.+ ..+|..|+ +++  +..
T Consensus        15 ~~~G~il~v~~l~~~~~sredLke~F~~~G~------------V~~Vd~~~g~~tgfVrf~~~~~~A~~av~~ln~~~~~   82 (121)
T 1owx_A           15 EKIGCLLKFSGDLDDQTCREDLHILFSNHGE------------IKWIDFVRGAKEGIILFKEKAKEALGKAKDANNGNLQ   82 (121)
T ss_dssp             CCCCCEEEEEESCCSSCCHHHHHHHTCSSCC------------EEEEECCTTCSEEEEEESSCHHHHHHHHHHTTTSCBC
T ss_pred             ccCCeEEEEecCCCCcCCHHHHHHHHHhcCC------------EEEEEEecCCCEEEEEECCChHHHHHHHHHhhcCCcE
Confidence            356789999999999 999999999999987            8888888888899999999 89999999 774  677


Q ss_pred             ecCceEEEec
Q 016936          104 FEGVAVRVRR  113 (380)
Q Consensus       104 i~g~~i~v~~  113 (380)
                      |.|..+++..
T Consensus        83 i~g~~~~~ev   92 (121)
T 1owx_A           83 LRNKEVTWEV   92 (121)
T ss_dssp             TTSSSEEEEE
T ss_pred             EeCcEEEEEE
Confidence            8998888864

>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=98.70  E-value=5.1e-08  Score=70.88  Aligned_cols=69  Identities=14%  Similarity=0.200  Sum_probs=59.5

Q ss_pred             CEEEEcCCCCC-----CCH----HHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeE
Q 016936          153 DRVFVGGLPYY-----FTE----TQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKT  223 (380)
Q Consensus       153 ~~l~V~nlp~~-----~t~----~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~  223 (380)
                      -+|+|.-++..     +-.    .+|.+.|++||.|..+++..++        +||+|.+.++|.+|++ |+|..+.||.
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            48999888743     322    4789999999999999998773        9999999999999999 9999999999


Q ss_pred             EEEEEcc
Q 016936          224 LTVRRAT  230 (380)
Q Consensus       224 i~v~~~~  230 (380)
                      |+|++..
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

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.53  E-value=9.2e-07  Score=65.51  Aligned_cols=72  Identities=15%  Similarity=0.152  Sum_probs=67.0

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhc-----CCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEE
Q 016936          152 PDRVFVGGLPYYFTETQIKELLESF-----GTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  226 (380)
Q Consensus       152 ~~~l~V~nlp~~~t~~~l~~~F~~~-----G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v  226 (380)
                      .++|-+-|||+.++...|+.+.+++     |.+..+.+..|.      +-|+|+|.+...|-+|.-.|+|.+|.|++|+|
T Consensus        21 ~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH------~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~   94 (117)
T 2l9w_A           21 ETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF------NGAIIIFRDSKFAAKMLMILNGSQFQGKVIRS   94 (117)
T ss_dssp             TSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT------TEEEEECSCHHHHHHHHHHHSSEEETTEEEEE
T ss_pred             CcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC------CceEEEEccchhhHHHHhhcCCeeecCeEEEe
Confidence            4799999999999999999999999     999999998884      36999999999999999999999999999999


Q ss_pred             EEc
Q 016936          227 RRA  229 (380)
Q Consensus       227 ~~~  229 (380)
                      ...
T Consensus        95 gTv   97 (117)
T 2l9w_A           95 GTI   97 (117)
T ss_dssp             ECH
T ss_pred             cCH
Confidence            865

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.37  E-value=2.1e-06  Score=63.19  Aligned_cols=94  Identities=20%  Similarity=0.294  Sum_probs=74.7

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHHHcCCceecCceE
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  109 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai~l~~~~i~g~~i  109 (380)
                      .-.++|.|.|||+++.++.|.-+|..-- .      ..+..|.++....  +-|+|+|.+.+.|++.++...+.|.+.+|
T Consensus         6 ~~~~~I~V~~lPp~~~~e~L~LYFEn~r-r------sGGG~V~~v~~~~--~~AvItF~d~~va~rVL~k~~H~L~~~~L   76 (104)
T 2dhx_A            6 SGGVAVEVRGLPPAVPDELLTLYFENRR-R------SGGGPVLSWQRLG--CGGVLTFREPADAERVLAQADHELHGAQL   76 (104)
T ss_dssp             CCCCEEEEESCCTTSCHHHHHHHHHCTT-T------TCCCCEEEEEEET--TEEEEEESSHHHHHHHHTCSCCBSSSSBC
T ss_pred             cCccEEEEECCCCCCChhHheEEEeCCC-c------CCCceeeEEEEcC--CcEEEEEcChHHHHHHhcCCcceecCeEE
Confidence            3468999999999999999999998731 0      1123588888766  88999999999999999888889999999


Q ss_pred             EEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCC
Q 016936          110 RVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFT  165 (380)
Q Consensus       110 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t  165 (380)
                      .|.+....                                 .+.++++++||+.++
T Consensus        77 sV~P~~~~---------------------------------~~~r~ll~gl~~~t~   99 (104)
T 2dhx_A           77 SLRPAPPR---------------------------------APARLLLQGLPPGTS   99 (104)
T ss_dssp             EEEECCCC---------------------------------CCCCCCCCSCCCCCC
T ss_pred             EEEcCCCC---------------------------------CcceEeeecCCCCCC
Confidence            99763322                                 235889999988765

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.34  E-value=2.8e-06  Score=62.96  Aligned_cols=78  Identities=14%  Similarity=0.204  Sum_probs=67.8

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecCc
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  107 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g~  107 (380)
                      ....|+|-+-|||..++...|+.++..+-.|..       +.+..+.+.++-+-|+|+|.+...|.+|. .|+|..|.|+
T Consensus        18 ~~~~rtiaL~~ipDtvndarIr~lve~~~~i~~-------g~i~KI~L~pDH~GAivef~d~~~AgKasLaL~G~ef~gr   90 (117)
T 2l9w_A           18 KELETLICLFPLSDKVSPSLICQFLQEEIHINE-------KDIRKILLVSDFNGAIIIFRDSKFAAKMLMILNGSQFQGK   90 (117)
T ss_dssp             TTTTSCEEEECCCTTCCHHHHHHHHHHHTCCCT-------TTCSEEEEETTTTEEEEECSCHHHHHHHHHHHSSEEETTE
T ss_pred             ccCCcEEEEecCCCCCCHHHHHHHHhhhhccCc-------cceeEEEEecCCCceEEEEccchhhHHHHhhcCCeeecCe
Confidence            345899999999999999999999999933221       12778888899999999999999999999 9999999999


Q ss_pred             eEEEec
Q 016936          108 AVRVRR  113 (380)
Q Consensus       108 ~i~v~~  113 (380)
                      +|++.-
T Consensus        91 ~Lr~gT   96 (117)
T 2l9w_A           91 VIRSGT   96 (117)
T ss_dssp             EEEEEC
T ss_pred             EEEecC
Confidence            999974

>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=97.84  E-value=8.5e-05  Score=54.88  Aligned_cols=60  Identities=12%  Similarity=0.178  Sum_probs=53.1

Q ss_pred             HHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEecccc
Q 016936          303 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  371 (380)
Q Consensus       303 ~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~~  371 (380)
                      +.++++|..|+++......+.-         .-+.|.|.++++|.+|-..||+..|+|++++|.|+...
T Consensus        25 ~~~e~Lf~~~~~~~tF~~lkSF---------RRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YFgq~~   84 (104)
T 1wey_A           25 AKFESLFRTYDKDTTFQYFKSF---------KRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQTL   84 (104)
T ss_dssp             HHHHHHHHTTCSSCEEEEETTT---------TEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCCS
T ss_pred             HHHHHHHHhhCcCcceeecCcc---------eEEEEEeCChHHHHHHHHHhccceecCceeEEEecCCC
Confidence            5788999999999888887743         36799999999999999999999999999999998753

>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=97.78  E-value=9e-05  Score=54.76  Aligned_cols=77  Identities=12%  Similarity=0.087  Sum_probs=64.1

Q ss_pred             CCCCEEEEcCCCCCC-C----HHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEE
Q 016936          150 EGPDRVFVGGLPYYF-T----ETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTL  224 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~-t----~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i  224 (380)
                      ..+++|+|.||+..+ .    .+.++++|++|+.+....+.+.-  .    -..|.|.++++|.+|...||+..+.|.+|
T Consensus         3 ~~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSF--R----Rirv~F~~~~~A~~AR~~Lh~~~f~g~~~   76 (104)
T 1wey_A            3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF--K----RVRINFSNPLSAADARLRLHKTEFLGKEM   76 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT--T----EEEEECSSTTHHHHHHHTSTTSEETTEEC
T ss_pred             CCCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcc--e----EEEEEeCChHHHHHHHHHhccceecCcee
Confidence            445799999998754 2    25789999999999888777652  1    46799999999999999999999999999


Q ss_pred             EEEEcccC
Q 016936          225 TVRRATAS  232 (380)
Q Consensus       225 ~v~~~~~~  232 (380)
                      +|-++.+.
T Consensus        77 r~YFgq~~   84 (104)
T 1wey_A           77 KLYFAQTL   84 (104)
T ss_dssp             EEECCCCS
T ss_pred             EEEecCCC
Confidence            99998643

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.70  E-value=0.00046  Score=50.74  Aligned_cols=76  Identities=20%  Similarity=0.284  Sum_probs=62.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHh-c----CCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLES-F----GTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKT  223 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~-~----G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~  223 (380)
                      .....+|.|.|||..++++.|.-+|+. .    |.|..++...        +-|+|+|.+.+.|++.++. ..+.|.+..
T Consensus         5 ~~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k-~~H~L~~~~   75 (104)
T 2dhx_A            5 SSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQ-ADHELHGAQ   75 (104)
T ss_dssp             CCCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTC-SCCBSSSSB
T ss_pred             ccCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcC-CcceecCeE
Confidence            344579999999999999999999996 2    4687776643        3699999999999999984 478999999


Q ss_pred             EEEEEcccCC
Q 016936          224 LTVRRATASS  233 (380)
Q Consensus       224 i~v~~~~~~~  233 (380)
                      |.|....++.
T Consensus        76 LsV~P~~~~~   85 (104)
T 2dhx_A           76 LSLRPAPPRA   85 (104)
T ss_dssp             CEEEECCCCC
T ss_pred             EEEEcCCCCC
Confidence            9998866553

>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=97.44  E-value=0.00063  Score=49.34  Aligned_cols=54  Identities=20%  Similarity=0.414  Sum_probs=46.1

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHh
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL  214 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l  214 (380)
                      .+||.-++|..|...||.++|+.||.| .|+++.|-       .|||.|.+++.|..|+..+
T Consensus        16 ~HVf~l~FP~ewKt~DI~~lFs~fggv-~I~WidDT-------sAlvvf~~~~~a~~al~~i   69 (100)
T 1whv_A           16 DHVLHVTFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVQIAVNTS   69 (100)
T ss_dssp             CSEEEEECCTTCCHHHHHHHHTTTCSC-CCEEEETT-------EEEEECSCHHHHHHHHHHH
T ss_pred             CeEEEEeCChhhhhHHHHHHhhccCCE-EEEEEcCC-------eEEEEecCHHHHHHHHHhc
Confidence            355555999999999999999999955 57887762       6999999999999999976

>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=97.33  E-value=0.00088  Score=50.91  Aligned_cols=77  Identities=19%  Similarity=0.305  Sum_probs=59.9

Q ss_pred             cchhhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHHHcCCce
Q 016936           24 MTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGII  103 (380)
Q Consensus        24 ~~~~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai~l~~~~  103 (380)
                      +........+-|-|-+.|+.. -..|..+|++||.            |++.........-.|.|.++.+|++||..||+.
T Consensus        16 l~~~~~~~~~wVtVFGFp~~~-~~~VL~~F~~~G~------------Iv~~~~~~~~NWihI~Y~s~~~A~rAL~kNG~i   82 (119)
T 1wwh_A           16 LTSEDHLDDTWVTVFGFPQAS-ASYILLQFAQYGN------------ILKHVMSNTGNWMHIRYQSKLQARKALSKDGRI   82 (119)
T ss_dssp             -----CGGGGEEEEECCCGGG-HHHHHHHHHTTSC------------EEEEEECSSSSEEEEEESSHHHHHHHHTTTTCE
T ss_pred             cCCCCCCCCCEEEEECCCHHH-HHHHHHHHHhhCc------------EEEeccCCCCCeEEEEeCCHHHHHHHHHhCCeE
Confidence            333455678899999999885 6788899999998            555555567789999999999999999999999


Q ss_pred             ecC-ceEEEec
Q 016936          104 FEG-VAVRVRR  113 (380)
Q Consensus       104 i~g-~~i~v~~  113 (380)
                      +.| -.|=|.+
T Consensus        83 i~g~~mIGV~p   93 (119)
T 1wwh_A           83 FGESIMIGVKP   93 (119)
T ss_dssp             ETTTEECEEEE
T ss_pred             ecCCEEEEEEE
Confidence            986 4455654

>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=97.20  E-value=0.0017  Score=47.12  Aligned_cols=68  Identities=13%  Similarity=0.204  Sum_probs=57.1

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCC--CceEEEEEEcChhHHHHHHHHhCCCeeC
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGN--SKGYGFCVYQDPAVTDIACAALNGLKMG  220 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~--~~g~afV~f~~~~~A~~Ai~~l~g~~~~  220 (380)
                      .+|.|++||+.+|++++.+.+.....+....+..++.+..  .-.-|+|.|.+.+++....+.++|+.+.
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~   71 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEE
Confidence            4799999999999999999999988887777777643322  3346999999999999999999998773

>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=97.18  E-value=0.0011  Score=50.32  Aligned_cols=71  Identities=17%  Similarity=0.216  Sum_probs=58.3

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCC-eEEEEEEcc
Q 016936          152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD-KTLTVRRAT  230 (380)
Q Consensus       152 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g-~~i~v~~~~  230 (380)
                      .+.|.|-+.|.. ....|..+|++||.|.+......      ..+--|+|.++.+|++|+.. ||..+.| ..|=|.+..
T Consensus        24 ~~wVtVFGFp~~-~~~~VL~~F~~~G~Iv~~~~~~~------~NWihI~Y~s~~~A~rAL~k-NG~ii~g~~mIGV~p~~   95 (119)
T 1wwh_A           24 DTWVTVFGFPQA-SASYILLQFAQYGNILKHVMSNT------GNWMHIRYQSKLQARKALSK-DGRIFGESIMIGVKPCI   95 (119)
T ss_dssp             GGEEEEECCCGG-GHHHHHHHHHTTSCEEEEEECSS------SSEEEEEESSHHHHHHHHTT-TTCEETTTEECEEEECC
T ss_pred             CCEEEEECCCHH-HHHHHHHHHHhhCcEEEeccCCC------CCeEEEEeCCHHHHHHHHHh-CCeEecCCEEEEEEECC
Confidence            468999999988 57889999999999988876322      24888999999999999995 9999975 666777653

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=97.12  E-value=0.00078  Score=49.05  Aligned_cols=54  Identities=19%  Similarity=0.388  Sum_probs=46.4

Q ss_pred             EEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhC
Q 016936          154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN  215 (380)
Q Consensus       154 ~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~  215 (380)
                      .||.-++|..|...||..+|+.||.| .|.++.|-       .|||.|.+++.|..|+..+.
T Consensus         7 HV~~l~FP~ewKt~Di~~lFs~fggv-~I~WidDT-------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHVTFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEEECCTTCCHHHHHHHTTTSEEE-EEEEEETT-------EEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEEeCChhhhhHHHHHHHhccCCE-EEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            56655999999999999999999944 57887762       69999999999999999764

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=96.79  E-value=0.0012  Score=47.85  Aligned_cols=62  Identities=15%  Similarity=0.227  Sum_probs=47.8

Q ss_pred             ceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec--C------CCcEEEEEeCCHHHHHHHH-HcCCce
Q 016936           33 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN--H------EKKFAFVEMRTVEEASNAM-ALDGII  103 (380)
Q Consensus        33 ~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~--~------~~g~afV~f~~~~~a~~ai-~l~~~~  103 (380)
                      ++|-|++||+.+||+++.+.++....            +......  +      .-.-|||.|.+.+++.... .++|..
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            68999999999999999988876632            3333321  1      1257999999999999999 799988


Q ss_pred             ecC
Q 016936          104 FEG  106 (380)
Q Consensus       104 i~g  106 (380)
                      +.+
T Consensus        70 F~D   72 (91)
T 1uw4_A           70 FLD   72 (91)
T ss_dssp             EEC
T ss_pred             EEc
Confidence            764

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=96.21  E-value=0.0055  Score=44.45  Aligned_cols=53  Identities=17%  Similarity=0.202  Sum_probs=41.5

Q ss_pred             ccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHHH
Q 016936           31 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA   98 (380)
Q Consensus        31 ~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai~   98 (380)
                      ..+.++| ++|+++.-.||.++|+.||.+           .+...   +--.|||.|.+++.|..|+.
T Consensus        15 r~HVf~l-~FP~ewKt~DI~~lFs~fggv-----------~I~Wi---dDTsAlvvf~~~~~a~~al~   67 (100)
T 1whv_A           15 RDHVLHV-TFPKEWKTSDLYQLFSAFGNI-----------QISWI---DDTSAFVSLSQPEQVQIAVN   67 (100)
T ss_dssp             CCSEEEE-ECCTTCCHHHHHHHHTTTCSC-----------CCEEE---ETTEEEEECSCHHHHHHHHH
T ss_pred             CCeEEEE-eCChhhhhHHHHHHhhccCCE-----------EEEEE---cCCeEEEEecCHHHHHHHHH
Confidence            3455666 999999999999999999853           22222   23469999999999999993

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=95.90  E-value=0.0022  Score=60.89  Aligned_cols=68  Identities=16%  Similarity=0.178  Sum_probs=49.1

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCc-EEEEEeCCHHHHHHHHHcCCceec
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-FAFVEMRTVEEASNAMALDGIIFE  105 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g-~afV~f~~~~~a~~ai~l~~~~i~  105 (380)
                      ..++..|+|+|. .|...++++|.++|++||+            |.++...+++| ||.|+|.+.+++..++....+...
T Consensus        48 r~~qa~rsv~v~-~~~~~~~~~l~~y~~~~g~------------i~~~~~~~~~g~~~~vef~~~~~~~~~~~~~~~p~~  114 (464)
T 3pq1_A           48 RREQAQRTVLIH-CPEKISENKFLKYLSQFGP------------INNHFFYESFGLYAVVEFCQKESIGSLQNGTHTPXX  114 (464)
T ss_dssp             HHHHHHTEEEEE-ECCC---CHHHHHHGGGSC------------CCCEEEECSSSEEEEEECC---CCHHHHSSCCCCCC
T ss_pred             HHHHhcceEEEE-cCCCCCHHHHHHHHHhcCC------------cceEEEEccCCeEEEEEeCCHHHHHHHHhccCCCcc
Confidence            356888999997 7999999999999999998            56666666766 899999999999988854444444


Q ss_pred             Cc
Q 016936          106 GV  107 (380)
Q Consensus       106 g~  107 (380)
                      +.
T Consensus       115 ~~  116 (464)
T 3pq1_A          115 XX  116 (464)
T ss_dssp             BC
T ss_pred             cc
Confidence            43

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=95.89  E-value=0.012  Score=45.25  Aligned_cols=76  Identities=22%  Similarity=0.316  Sum_probs=56.4

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeE-EEEeeCCC--------CC-----CCceEEEEEEcChhHHHHHHHHhCCCe
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHG-FDLVKDRD--------TG-----NSKGYGFCVYQDPAVTDIACAALNGLK  218 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~-v~l~~~~~--------~~-----~~~g~afV~f~~~~~A~~Ai~~l~g~~  218 (380)
                      ..|.|-+.|.. ....+.++|++||.|.+ ....+...        ..     ...++.-|+|.++.+|.+|+.. ||..
T Consensus         8 ~~VtVFGFp~~-~~~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~-NG~i   85 (132)
T 3p3d_A            8 LAILVFGYPET-MANQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLE-NGAV   85 (132)
T ss_dssp             CEEEEECCCGG-GHHHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTT-TTCE
T ss_pred             eEEEEEecCHH-HHHHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHh-CCeE
Confidence            47888899776 66778899999999865 22221000        00     1235778999999999999995 9999


Q ss_pred             eCCeEEEEEEcc
Q 016936          219 MGDKTLTVRRAT  230 (380)
Q Consensus       219 ~~g~~i~v~~~~  230 (380)
                      +.|.-|=|.+..
T Consensus        86 i~G~mIGV~Py~   97 (132)
T 3p3d_A           86 FNGVLLGVIPYT   97 (132)
T ss_dssp             ETTEECEEEECC
T ss_pred             eCcEEEEEEECC
Confidence            999988888763

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=95.66  E-value=0.011  Score=43.01  Aligned_cols=68  Identities=15%  Similarity=0.190  Sum_probs=50.7

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCC--CceEEEEEEcChhHHHHHHHHhCCCee
Q 016936          152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGN--SKGYGFCVYQDPAVTDIACAALNGLKM  219 (380)
Q Consensus       152 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~--~~g~afV~f~~~~~A~~Ai~~l~g~~~  219 (380)
                      +-+|.|+.||+..|++++.+.++..-.+....+..++.+..  .-..|+|.|.+.++.....+..+|..+
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F   78 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIF   78 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEE
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEE
Confidence            35899999999999999988888655544433433322211  123599999999999999999999877

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=95.62  E-value=0.0091  Score=45.97  Aligned_cols=82  Identities=15%  Similarity=0.220  Sum_probs=54.3

Q ss_pred             cceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCee-----E-EEEec--CCCcEEEEEeCCHHHHHHHHHcCCce
Q 016936           32 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAV-----V-NVYIN--HEKKFAFVEMRTVEEASNAMALDGII  103 (380)
Q Consensus        32 ~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i-----~-~~~~~--~~~g~afV~f~~~~~a~~ai~l~~~~  103 (380)
                      ..-|-|=+.|+. ....+-++|++||.|..-.........     . ..+..  ...+...|.|+++.+|.+||..||+.
T Consensus         7 e~~VtVFGFp~~-~~~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~NG~i   85 (132)
T 3p3d_A            7 ELAILVFGYPET-MANQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLENGAV   85 (132)
T ss_dssp             -CEEEEECCCGG-GHHHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTTTTCE
T ss_pred             ceEEEEEecCHH-HHHHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHhCCeE
Confidence            455777789755 456778899999998652211000000     0 00011  13568899999999999999999999


Q ss_pred             ecCceEEEecC
Q 016936          104 FEGVAVRVRRP  114 (380)
Q Consensus       104 i~g~~i~v~~~  114 (380)
                      |.|.-|-|.+-
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            99987777653

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=95.34  E-value=0.0098  Score=56.51  Aligned_cols=55  Identities=15%  Similarity=0.240  Sum_probs=42.3

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHH
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA  213 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~  213 (380)
                      +.|+|. .|...++.+|.++|++||.|..+.+..+  .|   -||+|+|.+.+++..++..
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            789998 6999999999999999999999988765  23   5999999999999977654

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=94.89  E-value=0.011  Score=43.08  Aligned_cols=52  Identities=17%  Similarity=0.176  Sum_probs=40.7

Q ss_pred             cceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHHH
Q 016936           32 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA   98 (380)
Q Consensus        32 ~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai~   98 (380)
                      .+.++| ++|+++.-.||.++|+.||.+            . +.+. +--.|||.|.+++.|..|+.
T Consensus         6 ~HV~~l-~FP~ewKt~Di~~lFs~fggv------------~-I~Wi-dDTsAlvvf~~~~~a~~al~   57 (101)
T 3ctr_A            6 DHVLHV-TFPKEWKTSDLYQLFSAFGNI------------Q-ISWI-DDTSAFVSLSQPEQVKIAVN   57 (101)
T ss_dssp             EEEEEE-ECCTTCCHHHHHHHTTTSEEE------------E-EEEE-ETTEEEEEEEEECHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHHhccCCE------------E-EEEE-cCCeEEEEecCHHHHHHHHH
Confidence            345556 999999999999999999852            2 2222 23469999999999999993

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=94.89  E-value=0.012  Score=42.95  Aligned_cols=64  Identities=17%  Similarity=0.212  Sum_probs=45.6

Q ss_pred             ccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecC--------CCcEEEEEeCCHHHHHHHH-HcCC
Q 016936           31 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH--------EKKFAFVEMRTVEEASNAM-ALDG  101 (380)
Q Consensus        31 ~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~--------~~g~afV~f~~~~~a~~ai-~l~~  101 (380)
                      .+-+|-|+.||+.+||+++.+.++..=.            +.-....+        .-.-|||.|.+.++..... ..+|
T Consensus         8 ~~~KvVIRrLPP~Ltee~F~~~l~~~~~------------~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g   75 (97)
T 2l08_A            8 HSHMVVIRRLPPGLTKEQLEEQLRPLPA------------HDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDG   75 (97)
T ss_dssp             CCCCEEEECCCSCSCHHHHTTTTSCCSS------------EEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTT
T ss_pred             cceeEEEeCCCCCCCHHHHHHHhCCcCc------------cceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCC
Confidence            4568999999999999997766654311            21111111        1146999999999999999 7999


Q ss_pred             ceecC
Q 016936          102 IIFEG  106 (380)
Q Consensus       102 ~~i~g  106 (380)
                      ..+.+
T Consensus        76 ~~F~D   80 (97)
T 2l08_A           76 YIFLD   80 (97)
T ss_dssp             EEEEC
T ss_pred             cEEEe
Confidence            87754

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}

Probab=88.14  E-value=1.4  Score=42.49  Aligned_cols=54  Identities=19%  Similarity=0.385  Sum_probs=44.4

Q ss_pred             EEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhC
Q 016936          154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN  215 (380)
Q Consensus       154 ~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~  215 (380)
                      .+++-.+|..|...+|.+.|+.||.+ .|+++.+       ..|||.|.+.+.|..++..++
T Consensus       441 ~vl~v~f~~~~~~~~i~~~fs~fg~v-~V~widd-------t~a~V~~~~~~~a~~~l~~~~  494 (507)
T 3d45_A          441 HVLHVTFPKEWKTSDLYQLFSAFGNI-QISWIDD-------TSAFVSLSQPEQVQIAVNTSK  494 (507)
T ss_dssp             GEEEEECCTTCCHHHHHHHGGGGCCC-EEEECSS-------SEEEEECSCHHHHHHHHHHHT
T ss_pred             cEEEEeCCCCCCHHHHHHHHHhcCCE-EEEEEcC-------CeEEEEECCHHHHHHHHHHHH
Confidence            35554599999999999999999954 5666544       279999999999999999885

---

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	380
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-24
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	4e-19
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	2e-06
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-18
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-13
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	5e-17
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-09
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	3e-16
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	0.002
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	9e-16
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	1e-08
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	8e-15
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	2e-07
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	1e-14
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	2e-06
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	1e-14
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	2e-09
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	2e-14
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	4e-09
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	7e-04
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-14
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-11
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	4e-14
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	4e-12
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
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	7e-14
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	7e-10
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	8e-14
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	4e-06
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	8e-14
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	9e-06
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	8e-14
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	6e-06
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	9e-14
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	4e-04
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	1e-13
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	3e-08
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	2e-13
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	1e-10
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	2e-13
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	7e-10
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	3e-13
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	9e-07
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	3e-13
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	5e-07
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	3e-13
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	2e-06
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	4e-13
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	4e-08
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	5e-13
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	3e-10
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	6e-13
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	3e-07
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	6e-13
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	7e-07
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	6e-13
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	4e-08
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	8e-13
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	1e-05
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	1e-12
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	1e-10
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	1e-12
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	2e-06
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	1e-12
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	6e-06
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	1e-12
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	1e-06
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	2e-12
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	5e-10
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	2e-12
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	2e-06
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	2e-12
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	2e-08
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	2e-12
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	8e-06
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	2e-12
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	3e-05
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	2e-12
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	1e-07
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	3e-12
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	4e-07
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	6e-12
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	0.002
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	8e-12
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	4e-06
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	9e-12
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	2e-08
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	1e-11
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	4e-05
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	2e-04
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	2e-11
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	3e-08
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	2e-11
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	4e-05
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-11
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-06
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	9e-11
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	0.001
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	1e-10
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	3e-09
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	2e-10
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	1e-09
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	2e-10
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	6e-07
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	2e-10
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	1e-06
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	4e-10
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	3e-04
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	1e-09
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	1e-04
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	1e-09
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	3e-08
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	1e-09
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	2e-09
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	4e-05
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	3e-09
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	3e-04
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	3e-09
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	9e-04
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	1e-08
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	1e-06
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	1e-08
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	2e-04
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	2e-08
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	1e-07
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	2e-08
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	2e-06
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-08
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	4e-08
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	4e-08
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	8e-08
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	7e-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:) 8e-08
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 3e-07
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	8e-08
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	9e-05
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	9e-08
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-06
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	2e-07
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	8e-06
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	3e-07
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	3e-07
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	8e-05
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	1e-06
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	5e-06
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	2e-06
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	2e-05
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-06
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	3e-05
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	4e-04
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-05
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-04
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	6e-05
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	7e-05
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	8e-05
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	4e-04
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	0.001
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	0.001
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	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 = 93.9 bits (233), Expect = 2e-24
 Identities = 44/100 (44%), Positives = 60/100 (60%), Gaps = 1/100 (1%)

Query: 279 KVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFL 338
           +VLCL   +  + L DDEEYEEI+ED+R+EC KYG + ++ IPR   +G E PG GK+F+
Sbjct: 5   EVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPR-PVDGVEVPGCGKIFV 63

Query: 339 EYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 378
           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 = 82.0 bits (201), Expect = 4e-19
 Identities = 42/215 (19%), Positives = 73/215 (33%), Gaps = 41/215 (19%)

Query: 31  HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI---NHEKKFAFVEM 87
             R++++GGL     ++++ + F Q          G     V +        + F FV  
Sbjct: 5   QLRKLFIGGLSFETTDESLRSHFEQ---------WGTLTDCVVMRDPNTKRSRGFGFVTY 55

Query: 88  RTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIG 147
            TVEE   AM       +G  V  +R      +                          G
Sbjct: 56  ATVEEVDAAMNARPHKVDGRVVEPKRAVSREDS-----------------------QRPG 92

Query: 148 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 207
                 ++FVGG+     E  +++  E +G +   +++ DR +G  +G+ F  + D    
Sbjct: 93  AHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV 152

Query: 208 DIACAALNGLKMGDKTLTVRRATASSGQSKTEQES 242
           D          +      VR+A      SK E  S
Sbjct: 153 DKIV-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 = 45.4 bits (106), Expect = 2e-06
 Identities = 14/95 (14%), Positives = 29/95 (30%), Gaps = 6/95 (6%)

Query: 19  MPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH 78
                    A    ++++VGG+     E  +  +F Q             + + +     
Sbjct: 84  SREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY------GKIEVIEIMTDRGSGK 137

Query: 79  EKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRR 113
           ++ 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 = 77.9 bits (191), Expect = 1e-18
 Identities = 43/89 (48%), Positives = 60/89 (67%), Gaps = 1/89 (1%)

Query: 32  ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 91
           ARR+YVG +P    E+A+  FF+  M   G   A PG+ V+ V IN +K FAF+E R+V+
Sbjct: 1   ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQA-PGNPVLAVQINQDKNFAFLEFRSVD 59

Query: 92  EASNAMALDGIIFEGVAVRVRRPTDYNPT 120
           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 = 63.6 bits (154), Expect = 2e-13
 Identities = 18/81 (22%), Positives = 33/81 (40%), Gaps = 6/81 (7%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDL-----VKDRDTGNSKGYGFCVYQDPAVTD 208
           R++VG +P+  TE  + +   +   L G        V        K + F  ++    T 
Sbjct: 3   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 209 IACAALNGLKMGDKTLTVRRA 229
            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 = 73.1 bits (179), Expect = 5e-17
 Identities = 45/83 (54%), Positives = 58/83 (69%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG SKGY FC Y D  VTD A A 
Sbjct: 3   KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62

Query: 214 LNGLKMGDKTLTVRRATASSGQS 236
           LNG+++GDK L V+RA+  +  +
Sbjct: 63  LNGMQLGDKKLLVQRASVGAKNA 85

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.6 bits (123), Expect = 2e-09
 Identities = 16/83 (19%), Positives = 32/83 (38%), Gaps = 7/83 (8%)

Query: 32  ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 91
           A ++++GGLP   N+  +    +              + V +      K +AF E   + 
Sbjct: 1   AHKLFIGGLPNYLNDDQVKELLTSF------GPLKAFNLVKDSATGLSKGYAFCEYVDIN 54

Query: 92  EASNAM-ALDGIIFEGVAVRVRR 113
               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 = 71.2 bits (174), Expect = 3e-16
 Identities = 16/86 (18%), Positives = 32/86 (37%)

Query: 144 GAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD 203
           GA  G  GP  + V  +P+  +  +I +    +  + G   +K  + G   G     ++ 
Sbjct: 1   GASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFES 60

Query: 204 PAVTDIACAALNGLKMGDKTLTVRRA 229
                 A   LN   +G + + +   
Sbjct: 61  RDEATAAVIDLNDRPIGSRKVKLVLG 86

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.0 bits (80), Expect = 0.002
 Identities = 12/81 (14%), Positives = 23/81 (28%), Gaps = 7/81 (8%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 92
             + V  +P   +   I  FF                 +           A V   + +E
Sbjct: 10  TIIKVQNMPFTVSIDEILDFFYGYQVIP------GSVCLKYNEKGMPTGEAMVAFESRDE 63

Query: 93  ASNAM-ALDGIIFEGVAVRVR 112
           A+ A+  L+        V++ 
Sbjct: 64  ATAAVIDLNDRPIGSRKVKLV 84

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 70.0 bits (171), Expect = 9e-16
 Identities = 20/80 (25%), Positives = 36/80 (45%), Gaps = 2/80 (2%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRD-TGNSKGYGFCVYQDPAVTDIACA 212
           ++ V  +P+   + +I+EL  +FG L    L K    TG  +G+GF  +        A  
Sbjct: 10  KILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFN 69

Query: 213 AL-NGLKMGDKTLTVRRATA 231
           AL +   +  + L +  A +
Sbjct: 70  ALCHSTHLYGRRLVLEWADS 89

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 49.6 bits (118), Expect = 1e-08
 Identities = 15/86 (17%), Positives = 27/86 (31%), Gaps = 7/86 (8%)

Query: 30  RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRT 89
           +   ++ V  +P  AN++ I   FS       G                 + F FV+  T
Sbjct: 6   QTTSKILVRNIPFQANQREIRELFSTF-----GELKTVRLPKKMTGTGAHRGFGFVDFIT 60

Query: 90  VEEASNAMA--LDGIIFEGVAVRVRR 113
            ++A  A           G  + +  
Sbjct: 61  KQDAKKAFNALCHSTHLYGRRLVLEW 86

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.4 bits (164), Expect = 8e-15
 Identities = 25/80 (31%), Positives = 40/80 (50%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
            V+VGGL    +E  + EL    G +    + KDR TG  +GYGF  +      D A   
Sbjct: 11  TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI 70

Query: 214 LNGLKMGDKTLTVRRATASS 233
           ++ +K+  K + V +A+A +
Sbjct: 71  MDMIKLYGKPIRVNKASAHN 90

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.6 bits (110), Expect = 2e-07
 Identities = 22/90 (24%), Positives = 37/90 (41%), Gaps = 7/90 (7%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 92
             VYVGGL    +E  +   F Q    +  +         +      + + FVE  + E+
Sbjct: 10  ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHM------PKDRVTGQHQGYGFVEFLSEED 63

Query: 93  ASNAM-ALDGIIFEGVAVRVRRPTDYNPTL 121
           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 = 66.5 bits (162), Expect = 1e-14
 Identities = 18/76 (23%), Positives = 32/76 (42%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           ++VG L    TE  + E     G +    + +D  T  S GY +  +Q PA  + A   +
Sbjct: 3   LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 62

Query: 215 NGLKMGDKTLTVRRAT 230
           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 = 43.0 bits (101), Expect = 2e-06
 Identities = 15/79 (18%), Positives = 30/79 (37%), Gaps = 7/79 (8%)

Query: 35  VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEAS 94
           +YVG L P   E  +   FS     +            ++       +A+V  +   +A 
Sbjct: 3   LYVGDLHPDVTEAMLYEKFSPAGPILSIR------VCRDMITRRSLGYAYVNFQQPADAE 56

Query: 95  NAM-ALDGIIFEGVAVRVR 112
            A+  ++  + +G  VR+ 
Sbjct: 57  RALDTMNFDVIKGKPVRIM 75

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 66.2 bits (161), Expect = 1e-14
 Identities = 21/76 (27%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           ++F+GGL +  T+  ++E    FG +    +++D  T  S+G+GF  + D A  D    A
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVD-KVLA 60

Query: 214 LNGLKMGDKTLTVRRA 229
            +  ++  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: 34  RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEA 93
           ++++GGL     ++ +  +F Q               + +      + F FV        
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQF------GEVKECLVMRDPLTKRSRGFGFVTFMDQAGV 55

Query: 94  SNAMALDGIIFEGVAVRVRR 113
              +A      +   +  + 
Sbjct: 56  DKVLAQSRHELDSKTIDPKV 75

>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 = 67.0 bits (163), Expect = 2e-14
 Identities = 19/96 (19%), Positives = 41/96 (42%), Gaps = 3/96 (3%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           +++  LPY  T  ++ ++   +G +         +T  ++G  + VY+D      AC  L
Sbjct: 10  LYIRNLPYKITAEEMYDIFGKYGPIRQIR---VGNTPETRGTAYVVYEDIFDAKNACDHL 66

Query: 215 NGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQH 250
           +G  + ++ L V    A+    K + +    Q +  
Sbjct: 67  SGFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLL 102

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.9 bits (124), Expect = 4e-09
 Identities = 15/81 (18%), Positives = 26/81 (32%), Gaps = 10/81 (12%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 92
           R +Y+  LP     + +   F +          GP   +        +  A+V    + +
Sbjct: 8   RILYIRNLPYKITAEEMYDIFGKY---------GPIRQIRVGNTPETRGTAYVVYEDIFD 58

Query: 93  ASNAM-ALDGIIFEGVAVRVR 112
           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 = 36.9 bits (85), Expect = 7e-04
 Identities = 17/74 (22%), Positives = 29/74 (39%), Gaps = 6/74 (8%)

Query: 303 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNT 362
           E+M +  GKYG +  + +    +        G  ++ Y D      A + LSG       
Sbjct: 22  EEMYDIFGKYGPIRQIRVGNTPET------RGTAYVVYEDIFDAKNACDHLSGFNVCNRY 75

Query: 363 VNAFYYPEDKYFNK 376
           +   YY  ++ F K
Sbjct: 76  LVVLYYNANRAFQK 89

>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 = 65.4 bits (159), Expect = 2e-14
 Identities = 21/76 (27%), Positives = 38/76 (50%), Gaps = 1/76 (1%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           ++F+GGL +  T+  +K+    FG +    L  D  TG S+G+GF ++++    D     
Sbjct: 1   KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVD-KVMD 59

Query: 214 LNGLKMGDKTLTVRRA 229
               K+  K +  +RA
Sbjct: 60  QKEHKLNGKVIDPKRA 75

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.9 bits (137), Expect = 2e-11
 Identities = 12/80 (15%), Positives = 26/80 (32%), Gaps = 6/80 (7%)

Query: 34  RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEA 93
           ++++GGL     ++ +  +FS+    +                   + F FV  +  E  
Sbjct: 1   KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPIT------GRSRGFGFVLFKESESV 54

Query: 94  SNAMALDGIIFEGVAVRVRR 113
              M        G  +  +R
Sbjct: 55  DKVMDQKEHKLNGKVIDPKR 74

>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 = 65.1 bits (158), Expect = 4e-14
 Identities = 23/82 (28%), Positives = 42/82 (51%), Gaps = 1/82 (1%)

Query: 150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 209
           E   ++F+GGL +  T+  ++   E +GTL    +++D +T  S+G+GF  Y      D 
Sbjct: 4   EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 63

Query: 210 ACAALNGLKMGDKTLTVRRATA 231
           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 = 59.7 bits (144), Expect = 4e-12
 Identities = 18/83 (21%), Positives = 33/83 (39%), Gaps = 6/83 (7%)

Query: 31  HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTV 90
             R++++GGL     ++++ + F Q        +      + +      + F FV   TV
Sbjct: 5   QLRKLFIGGLSFETTDESLRSHFEQW------GTLTDCVVMRDPNTKRSRGFGFVTYATV 58

Query: 91  EEASNAMALDGIIFEGVAVRVRR 113
           EE   AM       +G  V  +R
Sbjct: 59  EEVDAAMNARPHKVDGRVVEPKR 81

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 64.6 bits (157), Expect = 6e-14
 Identities = 21/78 (26%), Positives = 39/78 (50%), Gaps = 2/78 (2%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
            ++V  LP   T+ Q+  +   +G++   ++++D+ TG  +G  F  Y        A +A
Sbjct: 8   NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 67

Query: 214 LNG--LKMGDKTLTVRRA 229
           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 = 48.0 bits (114), Expect = 5e-08
 Identities = 19/81 (23%), Positives = 31/81 (38%), Gaps = 7/81 (8%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 92
             +YV  LP    +  + T F +  + +  N                +  AFV     EE
Sbjct: 7   TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLT------GRPRGVAFVRYNKREE 60

Query: 93  ASNAM-ALDGIIFEGVAVRVR 112
           A  A+ AL+ +I EG +  + 
Sbjct: 61  AQEAISALNNVIPEGGSQPLS 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 = 64.4 bits (156), Expect = 7e-14
 Identities = 17/76 (22%), Positives = 34/76 (44%), Gaps = 1/76 (1%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           ++FVGG+     E  +++  E +G +   +++ DR +G  +G+ F  + D    D     
Sbjct: 4   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVD-KIVI 62

Query: 214 LNGLKMGDKTLTVRRA 229
                +      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 = 52.8 bits (126), Expect = 7e-10
 Identities = 13/81 (16%), Positives = 28/81 (34%), Gaps = 6/81 (7%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 92
           ++++VGG+     E  +  +F Q             + + +     ++ FAFV     + 
Sbjct: 3   KKIFVGGIKEDTEEHHLRDYFEQYGKIE------VIEIMTDRGSGKKRGFAFVTFDDHDS 56

Query: 93  ASNAMALDGIIFEGVAVRVRR 113
               +        G    VR+
Sbjct: 57  VDKIVIQKYHTVNGHNCEVRK 77

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 64.7 bits (157), Expect = 8e-14
 Identities = 24/91 (26%), Positives = 40/91 (43%)

Query: 148 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 207
           G+ G  R+FV  L Y  +E  +++L  ++G L       D  T   KG+ F  +  P   
Sbjct: 4   GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHA 63

Query: 208 DIACAALNGLKMGDKTLTVRRATASSGQSKT 238
             A A ++G     + L V  +T     S++
Sbjct: 64  VKAYAEVDGQVFQGRMLHVLPSTIKKEASQS 94

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.2 bits (101), Expect = 4e-06
 Identities = 19/83 (22%), Positives = 31/83 (37%), Gaps = 7/83 (8%)

Query: 32  ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 91
           + R++V  L   ++E+ +   FS        +                K FAFV     E
Sbjct: 8   SGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSL------TKKPKGFAFVTFMFPE 61

Query: 92  EASNAM-ALDGIIFEGVAVRVRR 113
            A  A   +DG +F+G  + V  
Sbjct: 62  HAVKAYAEVDGQVFQGRMLHVLP 84

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.0 bits (155), Expect = 8e-14
 Identities = 30/79 (37%), Positives = 41/79 (51%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
            + V  LP   T+ + + L  S G +    LV+D+ TG S GYGF  Y DP   + A   
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 214 LNGLKMGDKTLTVRRATAS 232
           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 = 41.2 bits (96), Expect = 9e-06
 Identities = 13/86 (15%), Positives = 28/86 (32%), Gaps = 9/86 (10%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 92
             + V  LP    ++   + F  +                         + FV     ++
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKIT------GQSLGYGFVNYIDPKD 56

Query: 93  ASNAM-ALDGIIFEGVAVRVR--RPT 115
           A  A+  L+G+  +   ++V   RP+
Sbjct: 57  AEKAINTLNGLRLQTKTIKVSYARPS 82

>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 = 64.2 bits (156), Expect = 8e-14
 Identities = 21/77 (27%), Positives = 36/77 (46%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
            + V  LP   T+ ++  L  + G ++   +++D  TG S GY F  +     +  A   
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 214 LNGLKMGDKTLTVRRAT 230
           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 = 41.9 bits (98), Expect = 6e-06
 Identities = 12/81 (14%), Positives = 29/81 (35%), Gaps = 7/81 (8%)

Query: 34  RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEA 93
            + V  LP    ++ +   F  +              + +    +   +AFV+  +  ++
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPIN------TCRIMRDYKTGYSYGYAFVDFTSEMDS 57

Query: 94  SNAM-ALDGIIFEGVAVRVRR 113
             A+  L+GI      ++V  
Sbjct: 58  QRAIKVLNGITVRNKRLKVSY 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 = 63.9 bits (155), Expect = 9e-14
 Identities = 15/84 (17%), Positives = 30/84 (35%), Gaps = 7/84 (8%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           ++++G L    T   +++L                      GY F  Y D      A   
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKL------PLAGQVLLKSGYAFVDYPDQNWAIRAIET 56

Query: 214 LNG-LKMGDKTLTVRRATASSGQS 236
           L+G +++  K + V  + +   +S
Sbjct: 57  LSGKVELHGKIMEVDYSVSKKLRS 80

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.6 bits (84), Expect = 4e-04
 Identities = 14/82 (17%), Positives = 26/82 (31%), Gaps = 14/82 (17%)

Query: 34  RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEA 93
           ++Y+G L P      +   F                  +   +  +  +AFV+      A
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKL------------PLAGQVLLKSGYAFVDYPDQNWA 50

Query: 94  SNAM-ALDG-IIFEGVAVRVRR 113
             A+  L G +   G  + V  
Sbjct: 51  IRAIETLSGKVELHGKIMEVDY 72

>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 = 63.9 bits (155), Expect = 1e-13
 Identities = 24/90 (26%), Positives = 44/90 (48%), Gaps = 2/90 (2%)

Query: 142 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 201
           +SG       P R+ V  +P+ F +  ++++   FG +   D+    +   SKG+GF  +
Sbjct: 1   SSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKIL--DVEIIFNERGSKGFGFVTF 58

Query: 202 QDPAVTDIACAALNGLKMGDKTLTVRRATA 231
           ++ 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 = 48.9 bits (116), Expect = 3e-08
 Identities = 17/88 (19%), Positives = 29/88 (32%), Gaps = 9/88 (10%)

Query: 27  QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVE 86
           ++    +R++V  +P    +  +   F Q             D  +       K F FV 
Sbjct: 6   ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGK--------ILDVEIIFNERGSKGFGFVT 57

Query: 87  MRTVEEASNAM-ALDGIIFEGVAVRVRR 113
                +A  A   L G + EG  + V  
Sbjct: 58  FENSADADRAREKLHGTVVEGRKIEVNN 85

>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 = 63.9 bits (155), Expect = 2e-13
 Identities = 21/78 (26%), Positives = 39/78 (50%), Gaps = 1/78 (1%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           ++F+GGL +  TE  ++   E +G L    +++D  +  S+G+GF  +   A  D A  A
Sbjct: 22  KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM-A 80

Query: 214 LNGLKMGDKTLTVRRATA 231
                +  + +  +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 = 55.8 bits (134), Expect = 1e-10
 Identities = 16/88 (18%), Positives = 34/88 (38%), Gaps = 6/88 (6%)

Query: 26  QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFV 85
           ++     R++++GGL     E+++  ++ Q               + +      + F FV
Sbjct: 14  KREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVV------MRDPASKRSRGFGFV 67

Query: 86  EMRTVEEASNAMALDGIIFEGVAVRVRR 113
              ++ E   AMA      +G  V  +R
Sbjct: 68  TFSSMAEVDAAMAARPHSIDGRVVEPKR 95

>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 = 63.4 bits (154), Expect = 2e-13
 Identities = 20/76 (26%), Positives = 34/76 (44%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
            ++VG L +Y TE QI EL    G +    +  D+    + G+ F  Y   A  + A   
Sbjct: 9   TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 68

Query: 214 LNGLKMGDKTLTVRRA 229
           +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 = 53.4 bits (128), Expect = 7e-10
 Identities = 18/87 (20%), Positives = 33/87 (37%), Gaps = 7/87 (8%)

Query: 26  QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFV 85
           ++  + +  +YVG L     E+ I   FS+                ++        F FV
Sbjct: 1   EKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIK------KIIMGLDKMKKTACGFCFV 54

Query: 86  EMRTVEEASNAM-ALDGIIFEGVAVRV 111
           E  +  +A NAM  ++G   +   +R 
Sbjct: 55  EYYSRADAENAMRYINGTRLDDRIIRT 81

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.1 bits (153), Expect = 3e-13
 Identities = 24/80 (30%), Positives = 35/80 (43%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
            + V  L     ET ++EL   FG++    L KD+ TG SKG+ F  +        A A 
Sbjct: 10  TIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAG 69

Query: 214 LNGLKMGDKTLTVRRATASS 233
           ++G       L V  A  S+
Sbjct: 70  VSGFGYDHLILNVEWAKPST 89

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.3 bits (104), Expect = 9e-07
 Identities = 13/82 (15%), Positives = 26/82 (31%), Gaps = 7/82 (8%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 92
             + V  L     E  +   F    +              +      K FAF+     E+
Sbjct: 9   ATIRVTNLSEDTRETDLQELFRPFGSISRIYL------AKDKTTGQSKGFAFISFHRRED 62

Query: 93  ASNAM-ALDGIIFEGVAVRVRR 113
           A+ A+  + G  ++ + + V  
Sbjct: 63  AARAIAGVSGFGYDHLILNVEW 84

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.8 bits (152), Expect = 3e-13
 Identities = 24/80 (30%), Positives = 45/80 (56%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           ++FVGGL +   E  ++++   +G +    +VKDR+T  S+G+GF  +++      A  A
Sbjct: 7   KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 66

Query: 214 LNGLKMGDKTLTVRRATASS 233
           +NG  +  + + V +A  SS
Sbjct: 67  MNGKSVDGRQIRVDQAGKSS 86

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.1 bits (106), Expect = 5e-07
 Identities = 21/83 (25%), Positives = 38/83 (45%), Gaps = 7/83 (8%)

Query: 32  ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 91
             +++VGGL    NEQ++   FS+               V +      + F FV    ++
Sbjct: 5   EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVV------VKDRETQRSRGFGFVTFENID 58

Query: 92  EASNAM-ALDGIIFEGVAVRVRR 113
           +A +AM A++G   +G  +RV +
Sbjct: 59  DAKDAMMAMNGKSVDGRQIRVDQ 81

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.4 bits (151), Expect = 3e-13
 Identities = 15/76 (19%), Positives = 31/76 (40%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
            ++VGGL     +  +      FG +    +  D +T   +G+ F  ++       A   
Sbjct: 7   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 66

Query: 214 LNGLKMGDKTLTVRRA 229
           +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 = 43.5 bits (102), Expect = 2e-06
 Identities = 18/82 (21%), Positives = 32/82 (39%), Gaps = 7/82 (8%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 92
           R +YVGGL    +++ +   F                  ++      + FAFVE    E+
Sbjct: 6   RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQI------PLDYETEKHRGFAFVEFELAED 59

Query: 93  ASNAM-ALDGIIFEGVAVRVRR 113
           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 = 62.3 bits (151), Expect = 4e-13
 Identities = 22/88 (25%), Positives = 38/88 (43%), Gaps = 7/88 (7%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
            + V GLP+  TE  +KE   +FG +    + KD  TG+SKG+GF  + +        + 
Sbjct: 10  DLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ 69

Query: 214 LNGLKMGDKTLTVRRATASSGQSKTEQE 241
            + +    +    +        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 = 48.4 bits (115), Expect = 4e-08
 Identities = 18/91 (19%), Positives = 31/91 (34%), Gaps = 7/91 (7%)

Query: 26  QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFV 85
           ++A +    + V GLP    EQ +  +FS     +            ++   H K F FV
Sbjct: 2   KRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVL------MVQVKKDLKTGHSKGFGFV 55

Query: 86  EMRTVEEASNAMALDGIIFEGVAVRVRRPTD 116
                E     M+    + +G     + P  
Sbjct: 56  RFTEYETQVKVMS-QRHMIDGRWCDCKLPNS 85

>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 = 61.9 bits (150), Expect = 5e-13
 Identities = 17/76 (22%), Positives = 31/76 (40%), Gaps = 1/76 (1%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           ++FVGGL     E +I+E    FG +   +L  D  T   +G+ F  +++          
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 214 LNGLKMGDKTLTVRRA 229
                +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 = 53.8 bits (129), Expect = 3e-10
 Identities = 13/80 (16%), Positives = 26/80 (32%), Gaps = 6/80 (7%)

Query: 34  RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEA 93
           +++VGGL P   E+ I  +F               +  ++   N  + F F+  +  E  
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGF------GEVESIELPMDNKTNKRRGFCFITFKEEEPV 54

Query: 94  SNAMALDGIIFEGVAVRVRR 113
              M             ++ 
Sbjct: 55  KKIMEKKYHNVGLSKCEIKV 74

>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 = 62.0 bits (150), Expect = 6e-13
 Identities = 12/81 (14%), Positives = 33/81 (40%), Gaps = 1/81 (1%)

Query: 154 RVFVGGLPYYFTETQIKELLES-FGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA 212
            +++  L     + ++K+ L + F        +    +   +G  F ++++ +    A  
Sbjct: 5   TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALR 64

Query: 213 ALNGLKMGDKTLTVRRATASS 233
           ++ G    DK + ++ A   S
Sbjct: 65  SMQGFPFYDKPMRIQYAKTDS 85

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.8 bits (108), Expect = 3e-07
 Identities = 15/89 (16%), Positives = 31/89 (34%), Gaps = 14/89 (15%)

Query: 30  RHARRVYVGGLPPLANEQAI----ATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFV 85
           R    +Y+  L     +  +       FS+               ++       +  AFV
Sbjct: 1   RPNHTIYINNLNEKIKKDELKKSLHAIFSRFG---------QILDILVSRSLKMRGQAFV 51

Query: 86  EMRTVEEASNAM-ALDGIIFEGVAVRVRR 113
             + V  A+NA+ ++ G  F    +R++ 
Sbjct: 52  IFKEVSSATNALRSMQGFPFYDKPMRIQY 80

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.0 bits (150), Expect = 6e-13
 Identities = 24/87 (27%), Positives = 36/87 (41%), Gaps = 3/87 (3%)

Query: 150 EGPDR-VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 208
           +G  R ++VG L    TE  I +L    G           +  ++  Y F  + +     
Sbjct: 5   DGQPRTLYVGNLSRDVTEVLILQLFSQIG--PCKSCKMITEHTSNDPYCFVEFYEHRDAA 62

Query: 209 IACAALNGLKMGDKTLTVRRATASSGQ 235
            A AA+NG K+  K + V  AT  S Q
Sbjct: 63  AALAAMNGRKILGKEVKVNWATTPSSQ 89

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.6 bits (105), Expect = 7e-07
 Identities = 20/85 (23%), Positives = 30/85 (35%), Gaps = 9/85 (10%)

Query: 30  RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRT 89
              R +YVG L     E  I   FSQ+               +         + FVE   
Sbjct: 6   GQPRTLYVGNLSRDVTEVLILQLFSQIGPCK--------SCKMITEHTSNDPYCFVEFYE 57

Query: 90  VEEASNAM-ALDGIIFEGVAVRVRR 113
             +A+ A+ A++G    G  V+V  
Sbjct: 58  HRDAAAALAAMNGRKILGKEVKVNW 82

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 62.0 bits (150), Expect = 6e-13
 Identities = 19/81 (23%), Positives = 33/81 (40%), Gaps = 3/81 (3%)

Query: 156 FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRD---TGNSKGYGFCVYQDPAVTDIACA 212
           F+  L +  TE  +K +    G +    + K ++      S G+GF  Y+ P     A  
Sbjct: 2   FIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALK 61

Query: 213 ALNGLKMGDKTLTVRRATASS 233
            L G  +    L VR +  ++
Sbjct: 62  QLQGHTVDGHKLEVRISERAT 82

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.1 bits (114), Expect = 4e-08
 Identities = 17/79 (21%), Positives = 30/79 (37%), Gaps = 4/79 (5%)

Query: 36  YVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASN 95
           ++  L     E+ +   FS+V        +   +      +     F FVE +  E+A  
Sbjct: 2   FIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKN---KAGVLLSMGFGFVEYKKPEQAQK 58

Query: 96  AM-ALDGIIFEGVAVRVRR 113
           A+  L G   +G  + VR 
Sbjct: 59  ALKQLQGHTVDGHKLEVRI 77

>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 = 62.0 bits (150), Expect = 8e-13
 Identities = 27/94 (28%), Positives = 46/94 (48%), Gaps = 3/94 (3%)

Query: 143 SGAIGG-AEGPD--RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC 199
            GA G   EGP+   +F+  LP  F +  + ++   FG +    +  D+ T  SK +GF 
Sbjct: 6   IGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFV 65

Query: 200 VYQDPAVTDIACAALNGLKMGDKTLTVRRATASS 233
            Y +P     A  ++NG ++G K L V+   + +
Sbjct: 66  SYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKN 99

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.6 bits (97), Expect = 1e-05
 Identities = 13/82 (15%), Positives = 28/82 (34%), Gaps = 7/82 (8%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 92
             +++  LP    +Q +   F      +           ++   N  K F FV       
Sbjct: 19  ANLFIYHLPQEFGDQDLLQMFMPFGNVV------SAKVFIDKQTNLSKCFGFVSYDNPVS 72

Query: 93  ASNAM-ALDGIIFEGVAVRVRR 113
           A  A+ +++G       ++V+ 
Sbjct: 73  AQAAIQSMNGFQIGMKRLKVQL 94

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.6 bits (149), Expect = 1e-12
 Identities = 13/78 (16%), Positives = 30/78 (38%), Gaps = 1/78 (1%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
            VF   L        +++   + G +    ++ DR++  SKG  +  + +          
Sbjct: 20  TVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVP-LAIG 78

Query: 214 LNGLKMGDKTLTVRRATA 231
           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 = 55.8 bits (134), Expect = 1e-10
 Identities = 21/94 (22%), Positives = 35/94 (37%), Gaps = 7/94 (7%)

Query: 20  PVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE 79
           PV  ++ +  R AR V+   L      + +  FFS V              + +      
Sbjct: 7   PVDNLSPEE-RDARTVFCMQLAARIRPRDLEDFFSAVGKVR------DVRIISDRNSRRS 59

Query: 80  KKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRR 113
           K  A+VE   ++    A+ L G    GV + V+ 
Sbjct: 60  KGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQA 93

>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 = 60.8 bits (147), Expect = 1e-12
 Identities = 23/78 (29%), Positives = 40/78 (51%), Gaps = 2/78 (2%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
            ++V GLP   T+ ++++L   +G +    ++ D+ TG S+G GF  +      + A   
Sbjct: 8   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 67

Query: 214 LNGLKMGDKT--LTVRRA 229
           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 = 43.5 bits (102), Expect = 2e-06
 Identities = 18/81 (22%), Positives = 27/81 (33%), Gaps = 7/81 (8%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 92
             +YV GLP    ++ +   FSQ      G        V  V     +   F+      E
Sbjct: 7   ANLYVSGLPKTMTQKELEQLFSQY-----GRIITSRILVDQVTGVS-RGVGFIRFDKRIE 60

Query: 93  ASNAM-ALDGIIFEGVAVRVR 112
           A  A+  L+G    G    + 
Sbjct: 61  AEEAIKGLNGQKPSGATEPIT 81

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.5 bits (146), Expect = 1e-12
 Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 1/77 (1%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLV-KDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           +F+G L     E  + +   +FG +     + +D DTGNSKGY F  +     +D A  A
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 214 LNGLKMGDKTLTVRRAT 230
           +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 = 42.0 bits (98), Expect = 6e-06
 Identities = 14/80 (17%), Positives = 32/80 (40%), Gaps = 6/80 (7%)

Query: 35  VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEAS 94
           +++G L P  +E+ +   FS       G        + +    + K +AF+   + + + 
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAF-----GVILQTPKIMRDPDTGNSKGYAFINFASFDASD 55

Query: 95  NAM-ALDGIIFEGVAVRVRR 113
            A+ A++G       + V  
Sbjct: 56  AAIEAMNGQYLCNRPITVSY 75

>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 = 60.5 bits (146), Expect = 1e-12
 Identities = 20/83 (24%), Positives = 39/83 (46%), Gaps = 3/83 (3%)

Query: 147 GGAEGPD---RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD 203
           G    PD    + V GL  Y TE  ++E+   +G +    +V D+ +  S+G+ F  +++
Sbjct: 1   GNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 60

Query: 204 PAVTDIACAALNGLKMGDKTLTV 226
                 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 = 43.9 bits (103), Expect = 1e-06
 Identities = 14/80 (17%), Positives = 27/80 (33%), Gaps = 7/80 (8%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 92
             + V GL     E+ +   FS+       +      +  +           V    V++
Sbjct: 10  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAF------VYFENVDD 63

Query: 93  ASNAM-ALDGIIFEGVAVRV 111
           A  A    +G+  +G  +RV
Sbjct: 64  AKEAKERANGMELDGRRIRV 83

>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 = 60.1 bits (145), Expect = 2e-12
 Identities = 19/76 (25%), Positives = 39/76 (51%), Gaps = 1/76 (1%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           ++FVGGL    T   +K   E FG +    L+ D+ T   +G+GF  ++   + +  C  
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-E 59

Query: 214 LNGLKMGDKTLTVRRA 229
           ++  ++ +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 = 53.2 bits (127), Expect = 5e-10
 Identities = 11/80 (13%), Positives = 25/80 (31%), Gaps = 6/80 (7%)

Query: 34  RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEA 93
           +++VGGL      + +  +F Q               + +   N  + F FV   + +  
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVD------DAMLMFDKTTNRHRGFGFVTFESEDIV 54

Query: 94  SNAMALDGIIFEGVAVRVRR 113
                +         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 = 60.9 bits (147), Expect = 2e-12
 Identities = 15/80 (18%), Positives = 29/80 (36%), Gaps = 4/80 (5%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGF--DLVKDRDTGNSKGYGFCVYQDPAVTDIAC 211
           R+F+GG+P      +I E +                 D   ++G+ F  Y+      +A 
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 212 AALNG--LKMGDKTLTVRRA 229
             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 = 43.5 bits (102), Expect = 2e-06
 Identities = 15/83 (18%), Positives = 29/83 (34%), Gaps = 7/83 (8%)

Query: 34  RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEA 93
           R+++GG+P +   + I    ++    +                   + FAFVE  +   A
Sbjct: 3   RLFIGGIPKMKKREEILEEIAK----VTEGVLDVIVYASAADKMKNRGFAFVEYESHRAA 58

Query: 94  SNA---MALDGIIFEGVAVRVRR 113
           + A   +    I   G  + V  
Sbjct: 59  AMARRKLMPGRIQLWGHQIAVDW 81

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 59.9 bits (145), Expect = 2e-12
 Identities = 19/78 (24%), Positives = 36/78 (46%), Gaps = 1/78 (1%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           ++ V  L +  ++  I+EL   FGTL    +  DR +G S G     ++  A    A   
Sbjct: 2   KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQ 60

Query: 214 LNGLKMGDKTLTVRRATA 231
            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 = 48.8 bits (116), Expect = 2e-08
 Identities = 13/80 (16%), Positives = 26/80 (32%), Gaps = 8/80 (10%)

Query: 34  RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEA 93
           ++ V  L    ++  I   F++  T            V           A V      +A
Sbjct: 2   KLLVSNLDFGVSDADIQELFAEFGTLKKAA-------VHYDRSGRSLGTADVHFERKADA 54

Query: 94  SNAM-ALDGIIFEGVAVRVR 112
             AM   +G+  +G  + ++
Sbjct: 55  LKAMKQYNGVPLDGRPMNIQ 74

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.5 bits (146), Expect = 2e-12
 Identities = 18/90 (20%), Positives = 33/90 (36%), Gaps = 5/90 (5%)

Query: 142 ASGAIGGAEGPD--RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC 199
             G I G  G +  R++VG LP       I+++   +G       +  ++      + F 
Sbjct: 2   GGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYG---AIRDIDLKNRRGGPPFAFV 58

Query: 200 VYQDPAVTDIACAALNGLKMGDKTLTVRRA 229
            ++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 = 42.0 bits (98), Expect = 8e-06
 Identities = 23/87 (26%), Positives = 34/87 (39%), Gaps = 10/87 (11%)

Query: 28  ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEM 87
           A  +  R+YVG LPP    + I   F +          G    +          FAFVE 
Sbjct: 10  AGNNDCRIYVGNLPPDIRTKDIEDVFYKY---------GAIRDIDLKNRRGGPPFAFVEF 60

Query: 88  RTVEEASNAM-ALDGIIFEGVAVRVRR 113
               +A +A+   DG  ++G  +RV  
Sbjct: 61  EDPRDAEDAVYGRDGYDYDGYRLRVEF 87

>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 = 60.6 bits (146), Expect = 2e-12
 Identities = 18/85 (21%), Positives = 28/85 (32%), Gaps = 8/85 (9%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLV--------KDRDTGNSKGYGFCVYQDPA 205
            ++V GL    T   + +  +  G +               D++TG  KG     Y+DP 
Sbjct: 10  AIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPP 69

Query: 206 VTDIACAALNGLKMGDKTLTVRRAT 230
               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 = 40.5 bits (94), Expect = 3e-05
 Identities = 20/90 (22%), Positives = 28/90 (31%), Gaps = 3/90 (3%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK--FAFVEMRTV 90
             +YV GL        +A FF Q          G     + +     K    A V     
Sbjct: 9   SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDP 68

Query: 91  EEASNAM-ALDGIIFEGVAVRVRRPTDYNP 119
             A  A+   DG  F+G  ++V       P
Sbjct: 69  PTAKAAVEWFDGKDFQGSKLKVSLARKKPP 98

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.5 bits (146), Expect = 2e-12
 Identities = 24/99 (24%), Positives = 40/99 (40%), Gaps = 4/99 (4%)

Query: 142 ASGAIGG---AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGF 198
           +SG+ G       P   F+G LPY  TE  IKE              +  +    KG+G+
Sbjct: 2   SSGSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGY 61

Query: 199 CVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSK 237
             ++D      +  +LN   +G+K + V  A  +  +  
Sbjct: 62  AEFEDLDSLL-SALSLNEESLGNKRIRVDVADQAQDKDS 99

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.4 bits (112), Expect = 1e-07
 Identities = 14/81 (17%), Positives = 28/81 (34%), Gaps = 6/81 (7%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 92
              ++G LP    E++I  FF  +  +                    K F + E   ++ 
Sbjct: 16  YTAFLGNLPYDVTEESIKEFFRGLNISA------VRLPREPSNPERLKGFGYAEFEDLDS 69

Query: 93  ASNAMALDGIIFEGVAVRVRR 113
             +A++L+        +RV  
Sbjct: 70  LLSALSLNEESLGNKRIRVDV 90

>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 = 60.1 bits (145), Expect = 3e-12
 Identities = 19/80 (23%), Positives = 35/80 (43%), Gaps = 2/80 (2%)

Query: 151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA 210
           G   +F+  L        + +   +FG +    +V D +   SKGYGF  ++     + A
Sbjct: 7   GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERA 64

Query: 211 CAALNGLKMGDKTLTVRRAT 230
              +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 = 45.4 bits (107), Expect = 4e-07
 Identities = 17/81 (20%), Positives = 29/81 (35%), Gaps = 9/81 (11%)

Query: 34  RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEA 93
            +++  L    + +A+   FS                 V    N  K + FV   T E A
Sbjct: 10  NIFIKNLDKSIDNKALYDTFSAFGN--------ILSCKVVCDENGSKGYGFVHFETQEAA 61

Query: 94  SNAM-ALDGIIFEGVAVRVRR 113
             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 = 59.4 bits (143), Expect = 6e-12
 Identities = 17/83 (20%), Positives = 30/83 (36%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
            +++  L    TE  +  L   F    G  +     TG  +G  F  + +  +   A   
Sbjct: 20  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 79

Query: 214 LNGLKMGDKTLTVRRATASSGQS 236
           +NG K+  K L +        +S
Sbjct: 80  VNGYKLYGKILVIEFGKNKKQRS 102

>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 = 35.1 bits (80), Expect = 0.002
 Identities = 13/82 (15%), Positives = 29/82 (35%), Gaps = 7/82 (8%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 92
           + +Y+  L P   E+ + + F++     G            +     +  AF+     E 
Sbjct: 19  KVLYLKNLSPRVTERDLVSLFARFQEKKGPPI------QFRMMTGRMRGQAFITFPNKEI 72

Query: 93  ASNAM-ALDGIIFEGVAVRVRR 113
           A  A+  ++G    G  + +  
Sbjct: 73  AWQALHLVNGYKLYGKILVIEF 94

>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 = 59.0 bits (142), Expect = 8e-12
 Identities = 27/80 (33%), Positives = 42/80 (52%), Gaps = 1/80 (1%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           ++FVGGLPY+ T+  +++  E FG +    ++ DR TG S+GYGF    D A  + AC  
Sbjct: 12  KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 71

Query: 214 LNGLKMGDKTLTVRRATASS 233
            N   +  +   V  A   +
Sbjct: 72  PNP-IIDGRKANVNLAYLGA 90

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.8 bits (100), Expect = 4e-06
 Identities = 14/81 (17%), Positives = 26/81 (32%), Gaps = 6/81 (7%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 92
            +++VGGLP    + ++  +F                 + +      + + FV M     
Sbjct: 11  TKIFVGGLPYHTTDASLRKYFEGF------GDIEEAVVITDRQTGKSRGYGFVTMADRAA 64

Query: 93  ASNAMALDGIIFEGVAVRVRR 113
           A  A      I +G    V  
Sbjct: 65  AERACKDPNPIIDGRKANVNL 85

>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 = 58.9 bits (142), Expect = 9e-12
 Identities = 13/83 (15%), Positives = 30/83 (36%), Gaps = 5/83 (6%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
            +    L +  TE ++KE+ E    +           G SKG  +  ++  A  +     
Sbjct: 18  TLLAKNLSFNITEDELKEVFEDALEIR-----LVSQDGKSKGIAYIEFKSEADAEKNLEE 72

Query: 214 LNGLKMGDKTLTVRRATASSGQS 236
             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 = 49.3 bits (117), Expect = 2e-08
 Identities = 15/89 (16%), Positives = 29/89 (32%), Gaps = 12/89 (13%)

Query: 25  TQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAF 84
           T +  R AR +    L     E  +   F   +     +  G             K  A+
Sbjct: 9   TSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDG-----------KSKGIAY 57

Query: 85  VEMRTVEEASNAM-ALDGIIFEGVAVRVR 112
           +E ++  +A   +    G   +G +V + 
Sbjct: 58  IEFKSEADAEKNLEEKQGAEIDGRSVSLY 86

>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 = 58.8 bits (142), Expect = 1e-11
 Identities = 22/97 (22%), Positives = 36/97 (37%), Gaps = 9/97 (9%)

Query: 279 KVLCLTEAIT-ADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVF 337
           +V+ +       D   D     EI ED+R EC K+G +  +++     +       G   
Sbjct: 9   RVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPD-------GVAS 61

Query: 338 LEYYDAVGCATAKNALSGRKFGGNTVNA-FYYPEDKY 373
           + + 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 = 39.9 bits (93), Expect = 4e-05
 Identities = 19/95 (20%), Positives = 32/95 (33%), Gaps = 7/95 (7%)

Query: 29  TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI--NHEKKFAFVE 86
            RH R V +  +    + +      +++   +          +  + +   H    A V 
Sbjct: 5   MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLR-VECSKFGQIRKLLLFDRHPDGVASVS 63

Query: 87  MRTVEEASNAM-ALDGIIFEGVAVRV---RRPTDY 117
            R  EEA   +  LDG  F G  +        TDY
Sbjct: 64  FRDPEEADYCIQTLDGRWFGGRQITAQAWDGTTDY 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 = 2e-04
 Identities = 9/59 (15%), Positives = 18/59 (30%), Gaps = 1/59 (1%)

Query: 171 ELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA 229
           +L            +      +  G     ++DP   D     L+G   G + +T +  
Sbjct: 35  DLRVECSKFGQIRKLL-LFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAW 92

>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 = 57.7 bits (139), Expect = 2e-11
 Identities = 24/83 (28%), Positives = 41/83 (49%), Gaps = 6/83 (7%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           R+FVG LP   TE ++++L E +G      + KD+       +GF   +   + +IA   
Sbjct: 10  RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG------FGFIRLETRTLAEIAKVE 63

Query: 214 LNGLKMGDKTLTVRRATASSGQS 236
           L+ + +  K L VR A  S+  +
Sbjct: 64  LDNMPLRGKQLRVRFACHSASLT 86

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.4 bits (115), Expect = 3e-08
 Identities = 22/84 (26%), Positives = 34/84 (40%), Gaps = 13/84 (15%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 92
            R++VG LPP   E+ +   F +                  V+I+ +K F F+ + T   
Sbjct: 9   SRLFVGNLPPDITEEEMRKLFEKYGK------------AGEVFIHKDKGFGFIRLETRTL 56

Query: 93  ASNAM-ALDGIIFEGVAVRVRRPT 115
           A  A   LD +   G  +RVR   
Sbjct: 57  AEIAKVELDNMPLRGKQLRVRFAC 80

>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 = 57.8 bits (139), Expect = 2e-11
 Identities = 23/77 (29%), Positives = 34/77 (44%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
            +FV  +     E +I+E    +G +    L  DR TG SKGY    Y+       A  A
Sbjct: 9   ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 68

Query: 214 LNGLKMGDKTLTVRRAT 230
           LNG ++  +T+ V    
Sbjct: 69  LNGAEIMGQTIQVDWCF 85

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 39.7 bits (92), Expect = 4e-05
 Identities = 18/88 (20%), Positives = 30/88 (34%), Gaps = 7/88 (7%)

Query: 27  QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVE 86
           Q +     ++V  +   A E  I   F                  ++      K +A VE
Sbjct: 2   QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIK------NIHLNLDRRTGFSKGYALVE 55

Query: 87  MRTVEEASNAM-ALDGIIFEGVAVRVRR 113
             T ++A  A  AL+G    G  ++V  
Sbjct: 56  YETHKQALAAKEALNGAEIMGQTIQVDW 83

>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 = 56.4 bits (136), Expect = 5e-11
 Identities = 18/93 (19%), Positives = 35/93 (37%), Gaps = 12/93 (12%)

Query: 142 ASGAIGGAEGPD---RVFVGGLPYYFT-ETQIKELLESFGTLHGFDLVKDRDTGNSKGYG 197
           +SG+ G  +      RVF+G L      ++ ++ +   +G +              KG+ 
Sbjct: 2   SSGSSGKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKI--------VGCSVHKGFA 53

Query: 198 FCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT 230
           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 = 44.1 bits (104), Expect = 1e-06
 Identities = 17/83 (20%), Positives = 31/83 (37%), Gaps = 16/83 (19%)

Query: 33  RRVYVGGLPP-LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 91
            RV++G L   +  +  +   FS+          G    +V   ++    FAFV+     
Sbjct: 16  SRVFIGNLNTLVVKKSDVEAIFSKY---------GK---IVGCSVHK--GFAFVQYVNER 61

Query: 92  EASNAM-ALDGIIFEGVAVRVRR 113
            A  A+   DG +  G  + +  
Sbjct: 62  NARAAVAGEDGRMIAGQVLDINL 84

>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 = 55.5 bits (133), Expect = 9e-11
 Identities = 17/93 (18%), Positives = 28/93 (30%), Gaps = 11/93 (11%)

Query: 148 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 207
           G+ G   + V  LP      ++ +LL+ +         K      +K   F    +    
Sbjct: 1   GSSGSSGILVKNLPQDSNCQEVHDLLKDYDL-------KYCYVDRNKRTAFVTLLNGEQA 53

Query: 208 DIACAALNGLKMGDKTLTVRRAT----ASSGQS 236
             A    +      K L V+         SG S
Sbjct: 54  QNAIQMFHQYSFRGKDLIVQLQPTDALLCSGPS 86

>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 = 35.5 bits (81), Expect = 0.001
 Identities = 17/82 (20%), Positives = 30/82 (36%), Gaps = 14/82 (17%)

Query: 32  ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 91
           +  + V  LP  +N Q +                     +   Y++  K+ AFV +   E
Sbjct: 5   SSGILVKNLPQDSNCQEVHDLLKDY-------------DLKYCYVDRNKRTAFVTLLNGE 51

Query: 92  EASNAM-ALDGIIFEGVAVRVR 112
           +A NA+       F G  + V+
Sbjct: 52  QAQNAIQMFHQYSFRGKDLIVQ 73

>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 = 55.7 bits (134), Expect = 1e-10
 Identities = 20/89 (22%), Positives = 39/89 (43%), Gaps = 13/89 (14%)

Query: 24  MTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFA 83
           +  Q++     VY GG+     +Q +   FS                ++ + +  EK ++
Sbjct: 10  VVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQ------------IMEIRVFPEKGYS 57

Query: 84  FVEMRTVEEASNAM-ALDGIIFEGVAVRV 111
           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 = 51.9 bits (124), Expect = 3e-09
 Identities = 11/76 (14%), Positives = 26/76 (34%), Gaps = 6/76 (7%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
            V+ GG+    T+  +++    FG +    +  ++       Y F  +        A  +
Sbjct: 20  TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG------YSFVRFSTHESAAHAIVS 73

Query: 214 LNGLKMGDKTLTVRRA 229
           +NG  +    +     
Sbjct: 74  VNGTTIEGHVVKCYWG 89

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.0 bits (132), Expect = 2e-10
 Identities = 13/76 (17%), Positives = 24/76 (31%), Gaps = 6/76 (7%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
            ++V  L    +E  I++   +                  + Y F  + +      A  A
Sbjct: 10  ILYVRNLMLSTSEEMIEKEFNNIKP------GAVERVKKIRDYAFVHFSNREDAVEAMKA 63

Query: 214 LNGLKMGDKTLTVRRA 229
           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 = 52.3 bits (125), Expect = 1e-09
 Identities = 18/82 (21%), Positives = 32/82 (39%), Gaps = 13/82 (15%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 92
           + +YV  L    +E+ I   F+ +                   +   + +AFV     E+
Sbjct: 9   KILYVRNLMLSTSEEMIEKEFNNIKP------------GAVERVKKIRDYAFVHFSNRED 56

Query: 93  ASNAM-ALDGIIFEGVAVRVRR 113
           A  AM AL+G + +G  + V  
Sbjct: 57  AVEAMKALNGKVLDGSPIEVTL 78

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.1 bits (132), Expect = 2e-10
 Identities = 34/87 (39%), Positives = 46/87 (52%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
            VFVG +PY  TE Q+K++    G +  F LV DR+TG  KGYGFC YQD      A   
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 214 LNGLKMGDKTLTVRRATASSGQSKTEQ 240
           LNG +   + L V  A +   + + + 
Sbjct: 70  LNGREFSGRALRVDNAASEKNKEELKS 96

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.5 bits (107), Expect = 6e-07
 Identities = 31/103 (30%), Positives = 46/103 (44%), Gaps = 8/103 (7%)

Query: 30  RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRT 89
           R  R V+VG +P  A E+ +   FS+V   +          V +      K + F E + 
Sbjct: 6   RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRL------VYDRETGKPKGYGFCEYQD 59

Query: 90  VEEASNAM-ALDGIIFEGVAVRVRR-PTDYNPTLAAALGPGQP 130
            E A +AM  L+G  F G A+RV    ++ N     +LG G P
Sbjct: 60  QETALSAMRNLNGREFSGRALRVDNAASEKNKEELKSLGTGAP 102

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.7 bits (131), Expect = 2e-10
 Identities = 15/90 (16%), Positives = 31/90 (34%), Gaps = 7/90 (7%)

Query: 148 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 207
           G+ G   VFVG      TE +++E    +G      ++        + + F  + D  + 
Sbjct: 1   GSSGSSGVFVGRCTGDMTEDELREFFSQYGD-----VMDVFIPKPFRAFAFVTFADDQIA 55

Query: 208 DIACAALNGLKMGDKTLTVRRATASSGQSK 237
              C     L +   ++ +  A      + 
Sbjct: 56  QSLCG--EDLIIKGISVHISNAEPKHNSNS 83

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.3 bits (104), Expect = 1e-06
 Identities = 18/81 (22%), Positives = 30/81 (37%), Gaps = 12/81 (14%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 92
             V+VG       E  +  FFSQ            GD +        + FAFV     + 
Sbjct: 6   SGVFVGRCTGDMTEDELREFFSQY-----------GDVMDVFIPKPFRAFAFVTFADDQI 54

Query: 93  ASNAMALDGIIFEGVAVRVRR 113
           A +    + +I +G++V +  
Sbjct: 55  AQSLCG-EDLIIKGISVHISN 74

>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 = 53.6 bits (128), Expect = 4e-10
 Identities = 13/76 (17%), Positives = 29/76 (38%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
            +++   P  +T+  I++LL+    +     +       S+ + +               
Sbjct: 3   TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEK 62

Query: 214 LNGLKMGDKTLTVRRA 229
           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 = 37.1 bits (85), Expect = 3e-04
 Identities = 13/81 (16%), Positives = 35/81 (43%), Gaps = 7/81 (8%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 92
             +++   PP   ++ I      +      N       + ++  N  ++FA++++ + E+
Sbjct: 2   CTLWMTNFPPSYTQRNIRDLLQDI------NVVALSIRLPSLRFNTSRRFAYIDVTSKED 55

Query: 93  ASNAM-ALDGIIFEGVAVRVR 112
           A   +  L+G+  EG  +  +
Sbjct: 56  ARYCVEKLNGLKIEGYTLVTK 76

>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 = 53.3 bits (127), Expect = 1e-09
 Identities = 11/76 (14%), Positives = 25/76 (32%), Gaps = 1/76 (1%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
             +  +P+  T+  + + LE          V   + G   G     +++      +   L
Sbjct: 11  AHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSE-RL 69

Query: 215 NGLKMGDKTLTVRRAT 230
           +  K+  +   V   T
Sbjct: 70  HRKKLNGREAFVHVVT 85

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.7 bits (89), Expect = 1e-04
 Identities = 10/84 (11%), Positives = 22/84 (26%), Gaps = 6/84 (7%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 92
              ++  +P    +  +  F   +              V+          A V+ +  ++
Sbjct: 9   VCAHITNIPFSITKMDVLQFLEGIPVDE------NAVHVLVDNNGQGLGQALVQFKNEDD 62

Query: 93  ASNAMALDGIIFEGVAVRVRRPTD 116
           A  +  L      G    V   T 
Sbjct: 63  ARKSERLHRKKLNGREAFVHVVTL 86

>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 = 52.4 bits (125), Expect = 1e-09
 Identities = 15/85 (17%), Positives = 26/85 (30%), Gaps = 7/85 (8%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 92
           R VY+ G P  A    I  +       +          +        K   FV   ++E 
Sbjct: 7   RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQ-------MRRTLHKAFKGSIFVVFDSIES 59

Query: 93  ASNAMALDGIIFEGVAVRVRRPTDY 117
           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 = 48.6 bits (115), Expect = 3e-08
 Identities = 17/76 (22%), Positives = 25/76 (32%), Gaps = 2/76 (2%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
            V++ G P   T   IKE LE  G +     ++       KG  F V+            
Sbjct: 8   SVYIKGFPTDATLDDIKEWLEDKGQVLNIQ-MRRTLHKAFKGSIFVVFDSIESAKKFV-E 65

Query: 214 LNGLKMGDKTLTVRRA 229
             G K  +  L +   
Sbjct: 66  TPGQKYKETDLLILFK 81

>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 = 52.5 bits (125), Expect = 1e-09
 Identities = 15/79 (18%), Positives = 25/79 (31%), Gaps = 6/79 (7%)

Query: 154 RVFVGGLPYYFTETQI---KELLESFGTLHGFDLVKDRDTGNS---KGYGFCVYQDPAVT 207
            VFV GL     + ++    E    FG +H   +        S       +  Y      
Sbjct: 10  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 69

Query: 208 DIACAALNGLKMGDKTLTV 226
             A   +N + +  +TL  
Sbjct: 70  LRAIQCVNNVVVDGRTLKA 88

>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 = 53.0 bits (126), Expect = 2e-09
 Identities = 26/81 (32%), Positives = 41/81 (50%)

Query: 150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 209
           +    + V  +P    E Q+++L E +G +    +V DR+T  S+GYGF  +Q  +    
Sbjct: 40  DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQ 99

Query: 210 ACAALNGLKMGDKTLTVRRAT 230
           A A LNG  + +K L V  A 
Sbjct: 100 AIAGLNGFNILNKRLKVALAA 120

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 41.0 bits (95), Expect = 4e-05
 Identities = 18/100 (18%), Positives = 35/100 (35%), Gaps = 9/100 (9%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 92
           R + V  +P   +E  +   F +               V +      + + FV+ ++   
Sbjct: 43  RNLMVNYIPTTVDEVQLRQLFERYGPIE------SVKIVCDRETRQSRGYGFVKFQSGSS 96

Query: 93  ASNAM-ALDGIIFEGVAVRVR--RPTDYNPTLAAALGPGQ 129
           A  A+  L+G       ++V         P +A A+G G 
Sbjct: 97  AQQAIAGLNGFNILNKRLKVALAASGHQRPGIAGAVGDGN 136

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.3 bits (125), Expect = 3e-09
 Identities = 19/99 (19%), Positives = 34/99 (34%), Gaps = 6/99 (6%)

Query: 146 IGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPA 205
           + G     R+ V  L Y  T   + ++   FGT+             ++      Y DP 
Sbjct: 1   MAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPV 56

Query: 206 VTDIACAALNG--LKMGDKTLTVRRATASSGQSKTEQES 242
               A  +L+G  +     TL +  +  +S   K   + 
Sbjct: 57  SAQHAKLSLDGQNIYNACCTLRIDFSKLTSLNVKYNNDK 95

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.7 bits (87), Expect = 3e-04
 Identities = 16/92 (17%), Positives = 29/92 (31%), Gaps = 17/92 (18%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-FAFVEMRTVE 91
            R+ V  L        +   FS+            G  +  +      +  A ++     
Sbjct: 8   LRIIVENLFYPVTLDVLHQIFSK-----------FGTVLKIITFTKNNQFQALLQYADPV 56

Query: 92  EASNAM-ALDG--IIFEGVAVRVR--RPTDYN 118
            A +A  +LDG  I      +R+   + T  N
Sbjct: 57  SAQHAKLSLDGQNIYNACCTLRIDFSKLTSLN 88

>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 = 3e-09
 Identities = 13/83 (15%), Positives = 29/83 (34%), Gaps = 14/83 (16%)

Query: 35  VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEAS 94
           V V G P  +    +  F                   +   +++   +  +  ++  +A 
Sbjct: 7   VTVFGFPQASASYILLQFAQYGNI-------------LKHVMSNTGNWMHIRYQSKLQAR 53

Query: 95  NAMALDGIIFEG-VAVRVRRPTD 116
            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 = 9e-04
 Identities = 13/77 (16%), Positives = 23/77 (29%), Gaps = 9/77 (11%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           V V G P          +L  F     +  +      N+  +    YQ       A  + 
Sbjct: 7   VTVFGFPQASAS----YILLQF---AQYGNILKHVMSNTGNWMHIRYQSKLQARKAL-SK 58

Query: 215 NGLKMGDKT-LTVRRAT 230
           +G   G+   + V+   
Sbjct: 59  DGRIFGESIMIGVKPCI 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 = 49.5 bits (117), Expect = 1e-08
 Identities = 9/76 (11%), Positives = 22/76 (28%), Gaps = 3/76 (3%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           V V  LP  + + ++ +  +  G +   D+        +  +    +             
Sbjct: 3   VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK--KNFRFARIEFARYDGALA-AITK 59

Query: 215 NGLKMGDKTLTVRRAT 230
               +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 = 1e-06
 Identities = 15/81 (18%), Positives = 25/81 (30%), Gaps = 8/81 (9%)

Query: 35  VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEAS 94
           V V  LP   N+  +  +F      I           V   +    +FA +E    + A 
Sbjct: 3   VLVKNLPKSYNQNKVYKYFKHCGPII--------HVDVADSLKKNFRFARIEFARYDGAL 54

Query: 95  NAMALDGIIFEGVAVRVRRPT 115
            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 = 50.2 bits (119), Expect = 1e-08
 Identities = 24/83 (28%), Positives = 35/83 (42%), Gaps = 6/83 (7%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
            VF+  L +   E  + E+L+ FG L    +V   DT +SKG  F  +          AA
Sbjct: 10  TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAA 69

Query: 214 LN------GLKMGDKTLTVRRAT 230
            +      GLK+  + L V  A 
Sbjct: 70  ASLEAEGGGLKLDGRQLKVDLAV 92

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 38.3 bits (88), Expect = 2e-04
 Identities = 17/92 (18%), Positives = 31/92 (33%), Gaps = 13/92 (14%)

Query: 29  TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMR 88
               + V++  L   + E+A+     Q               V++    H K  AF +  
Sbjct: 5   VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRV------VLHPDTEHSKGCAFAQFM 58

Query: 89  TVEEASNAMA-------LDGIIFEGVAVRVRR 113
           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 = 49.0 bits (116), Expect = 2e-08
 Identities = 12/86 (13%), Positives = 25/86 (29%), Gaps = 6/86 (6%)

Query: 29  TRHARRVYVGGLPP-LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEM 87
           T   R + +  L   L +E  +   F    +    N             +     AF+  
Sbjct: 1   TLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQK-----EHSFNNCCAFMVF 55

Query: 88  RTVEEASNAMALDGIIFEGVAVRVRR 113
              + 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 = 47.0 bits (111), Expect = 1e-07
 Identities = 8/79 (10%), Positives = 25/79 (31%), Gaps = 3/79 (3%)

Query: 154 RVFVGGLPYYFTETQIKELL--ESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 211
            + +  L     +  +                    ++   +    F V+++    + A 
Sbjct: 6   EIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL 65

Query: 212 AALNGLKMGDKTLTVRRAT 230
             +N   +G++ ++V  A 
Sbjct: 66  -QMNRSLLGNREISVSLAD 83

>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 = 49.4 bits (117), Expect = 2e-08
 Identities = 20/92 (21%), Positives = 30/92 (32%), Gaps = 13/92 (14%)

Query: 144 GAIGGAEGPD------RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYG 197
           G+ G + GP       RV V GLP   +   +K+ +   G +   D+ KD         G
Sbjct: 1   GSSGSSGGPPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKDG-------MG 53

Query: 198 FCVYQDPAVTDIACAALNGLKMGDKTLTVRRA 229
              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 = 43.6 bits (102), Expect = 2e-06
 Identities = 17/87 (19%), Positives = 23/87 (26%), Gaps = 14/87 (16%)

Query: 28  ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEM 87
             R   RV V GLPP  + Q +     +                V      +     VE 
Sbjct: 11  TRRSDFRVLVSGLPPSGSWQDLKDHMREAGD-------------VCYADVQKDGMGMVEY 57

Query: 88  RTVEEASNAM-ALDGIIFEGVAVRVRR 113
              E+   A+  LD   F         
Sbjct: 58  LRKEDMEYALRKLDDTKFRSHEGETSY 84

>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 = 49.4 bits (117), Expect = 2e-08
 Identities = 12/89 (13%), Positives = 33/89 (37%), Gaps = 1/89 (1%)

Query: 142 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 201
           +SG          V + GLP+  ++ +I +       +     +     G S G  F  +
Sbjct: 5   SSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQF 64

Query: 202 QDPAVTDIACAALNGLKMGDKTLTVRRAT 230
               + +      +  ++G + + + +++
Sbjct: 65  ASQEIAE-KALKKHKERIGHRYIEIFKSS 92

>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 = 48.0 bits (113), Expect = 4e-08
 Identities = 12/79 (15%), Positives = 29/79 (36%), Gaps = 7/79 (8%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           + + GLP   T  ++ +LL  +   +             KG  F    +    + A    
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDYELKY-------CFVDKYKGTAFVTLLNGEQAEAAINTF 53

Query: 215 NGLKMGDKTLTVRRATASS 233
           +  ++ ++ L+V+     +
Sbjct: 54  HQSRLRERELSVQLQPTDA 72

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.0 bits (116), Expect = 4e-08
 Identities = 16/93 (17%), Positives = 32/93 (34%), Gaps = 6/93 (6%)

Query: 151 GPDRVFVGGL-PYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 209
           G   + V  L P   T   +  L   +G +    ++ ++              D     +
Sbjct: 1   GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKE-----NALVQMADGNQAQL 55

Query: 210 ACAALNGLKMGDKTLTVRRATASSGQSKTEQES 242
           A + LNG K+  K + +  +   + Q   E + 
Sbjct: 56  AMSHLNGHKLHGKPIRITLSKHQNVQLPREGQE 88

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 47.6 bits (112), Expect = 8e-08
 Identities = 15/81 (18%), Positives = 34/81 (41%), Gaps = 2/81 (2%)

Query: 150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 209
             P  +F+G L    +  ++K  +      +   +V  R TG ++ +G+  ++     + 
Sbjct: 11  TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFESAEDLEK 69

Query: 210 ACAALNGLKMGDKTLTVRRAT 230
           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 = 36.5 bits (83), Expect = 7e-04
 Identities = 12/81 (14%), Positives = 30/81 (37%), Gaps = 7/81 (8%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 92
             +++G L P  +   +    S++                       +KF +V+  + E+
Sbjct: 14  FNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRT-------GTNRKFGYVDFESAED 66

Query: 93  ASNAMALDGIIFEGVAVRVRR 113
              A+ L G+   G  +++ +
Sbjct: 67  LEKALELTGLKVFGNEIKLEK 87

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.7 bits (113), Expect = 8e-08
 Identities = 12/85 (14%), Positives = 27/85 (31%), Gaps = 1/85 (1%)

Query: 142 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 201
           +  A G       V +      F E    E+ E +G +   ++  +    +  G  +  +
Sbjct: 17  SQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKF 75

Query: 202 QDPAVTDIACAALNGLKMGDKTLTV 226
           +     + 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 = 46.2 bits (109), Expect = 3e-07
 Identities = 15/76 (19%), Positives = 29/76 (38%), Gaps = 5/76 (6%)

Query: 295 DEEYEEILEDMREEC-GKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNAL 353
            E Y+E  E++  E   KYG +  + +     +          ++++        A   L
Sbjct: 33  QEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNV----YVKFRREEDAEKAVIDL 88

Query: 354 SGRKFGGNTVNAFYYP 369
           + R F G  ++A   P
Sbjct: 89  NNRWFNGQPIHAELSP 104

>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 = 8e-08
 Identities = 16/70 (22%), Positives = 31/70 (44%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           +++ GL    T+  + +L + +G +     + D+ T   KGYGF  +  P+    A  AL
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 215 NGLKMGDKTL 224
               +  +  
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 = 38.2 bits (88), Expect = 9e-05
 Identities = 13/77 (16%), Positives = 28/77 (36%), Gaps = 7/77 (9%)

Query: 35  VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEAS 94
           +Y+ GL P   +Q +          +   +      +++   N  K + FV+  +   A 
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKA------ILDKTTNKCKGYGFVDFDSPSAAQ 54

Query: 95  NAM-ALDGIIFEGVAVR 110
            A+ AL     +    +
Sbjct: 55  KAVTALKASGVQAQMAK 71

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.4 bits (112), Expect = 9e-08
 Identities = 13/83 (15%), Positives = 23/83 (27%), Gaps = 3/83 (3%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           V + GLPY  TE  I               ++    G   G     +        A  A 
Sbjct: 18  VHMRGLPYRATENDIYNFFSPLN--PMRVHIEIGPDGRVTGEADVEFATHEDAVAAM-AK 74

Query: 215 NGLKMGDKTLTVRRATASSGQSK 237
           +   M  + + +   + +     
Sbjct: 75  DKANMQHRYVELFLNSTAGTSGS 97

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.6 bits (102), Expect = 3e-06
 Identities = 21/81 (25%), Positives = 29/81 (35%), Gaps = 8/81 (9%)

Query: 35  VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEAS 94
           V++ GLP  A E  I  FFS +              +           A VE  T E+A 
Sbjct: 18  VHMRGLPYRATENDIYNFFSPLNP--------MRVHIEIGPDGRVTGEADVEFATHEDAV 69

Query: 95  NAMALDGIIFEGVAVRVRRPT 115
            AMA D    +   V +   +
Sbjct: 70  AAMAKDKANMQHRYVELFLNS 90

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.8 bits (108), Expect = 2e-07
 Identities = 18/77 (23%), Positives = 27/77 (35%), Gaps = 8/77 (10%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
            ++V G     T T ++     FG +       D      +   F  Y+     D A A 
Sbjct: 7   TLYVYGED--MTPTLLRGAFSPFGNII------DLSMDPPRNCAFVTYEKMESADQAVAE 58

Query: 214 LNGLKMGDKTLTVRRAT 230
           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 = 41.5 bits (97), Expect = 8e-06
 Identities = 19/92 (20%), Positives = 35/92 (38%), Gaps = 19/92 (20%)

Query: 28  ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEM 87
           A R    +YV G         +   FS                ++++ ++  +  AFV  
Sbjct: 1   APRKGNTLYVYGED--MTPTLLRGAFSPF------------GNIIDLSMDPPRNCAFVTY 46

Query: 88  RTVEEASNAM-ALDGIIFEGVAVRV----RRP 114
             +E A  A+  L+G   E V ++V    ++P
Sbjct: 47  EKMESADQAVAELNGTQVESVQLKVNIARKQP 78

>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 = 46.3 bits (109), Expect = 3e-07
 Identities = 15/107 (14%), Positives = 30/107 (28%), Gaps = 7/107 (6%)

Query: 144 GAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD 203
           G++    G    F G L        +  L  + G +   D V+          G  ++++
Sbjct: 3   GSLEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGA------KEGIILFKE 56

Query: 204 P-AVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQ 249
                       N   +  +   V          K   + I+   Q+
Sbjct: 57  KAKEALGKAKDANNGNLQLRNKEVTWEVLEGEVEKEALKKIIEDQQE 103

>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 = 46.3 bits (109), Expect = 3e-07
 Identities = 14/80 (17%), Positives = 29/80 (36%), Gaps = 1/80 (1%)

Query: 150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 209
           + P  +++  LP    E +++ +L+ FG       +    +G S+G GF   +     + 
Sbjct: 16  QDPTNLYISNLPLSMDEQELENMLKPFGQ-VISTRILRDSSGTSRGVGFARMESTEKCEA 74

Query: 210 ACAALNGLKMGDKTLTVRRA 229
                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 = 39.4 bits (91), Expect = 8e-05
 Identities = 12/90 (13%), Positives = 26/90 (28%), Gaps = 8/90 (8%)

Query: 24  MTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFA 83
           M +Q  +    +Y+  LP   +EQ +          I          ++       +   
Sbjct: 10  MAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTR-------ILRDSSGTSRGVG 62

Query: 84  FVEMRTVEEASNAM-ALDGIIFEGVAVRVR 112
           F  M + E+    +   +G   +       
Sbjct: 63  FARMESTEKCEAVIGHFNGKFIKTPPGVSA 92

>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 = 44.3 bits (104), Expect = 1e-06
 Identities = 24/99 (24%), Positives = 41/99 (41%), Gaps = 12/99 (12%)

Query: 142 ASGAIGGAEGPD--RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC 199
           +SG IG  +     R++VGGL    +   +    + FG++   D VK         + + 
Sbjct: 5   SSGKIGYGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDS------FAYI 58

Query: 200 VYQDPAVTDIACAALNGLKMGDKTLTVR----RATASSG 234
            Y+       ACA + G  +G     +R    ++  SSG
Sbjct: 59  QYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGPSSG 97

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 42.7 bits (100), Expect = 5e-06
 Identities = 17/81 (20%), Positives = 33/81 (40%), Gaps = 13/81 (16%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 92
            R++VGGL P  +  A+A  F +              ++  +       FA+++  +++ 
Sbjct: 18  TRLWVGGLGPNTSLAALAREFDRF------------GSIRTIDHVKGDSFAYIQYESLDA 65

Query: 93  ASNAM-ALDGIIFEGVAVRVR 112
           A  A   + G    G   R+R
Sbjct: 66  AQAACAKMRGFPLGGPDRRLR 86

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.5 bits (104), Expect = 2e-06
 Identities = 15/86 (17%), Positives = 32/86 (37%), Gaps = 1/86 (1%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           V++ GLP+      + +  +    +     +     G + G GF  +++ A    A    
Sbjct: 21  VYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYK-AALCR 79

Query: 215 NGLKMGDKTLTVRRATASSGQSKTEQ 240
           +   MG++ + V   T      K + 
Sbjct: 80  HKQYMGNRFIQVHPITKKGMLEKIDM 105

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.4 bits (96), Expect = 2e-05
 Identities = 15/86 (17%), Positives = 25/86 (29%), Gaps = 6/86 (6%)

Query: 30  RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRT 89
                VY+ GLP  A  + +  FF ++              +            FVE R 
Sbjct: 16  EAGFCVYLKGLPFEAENKHVIDFFKKLDIVE------DSIYIAYGPNGKATGEGFVEFRN 69

Query: 90  VEEASNAMALDGIIFEGVAVRVRRPT 115
             +   A+           ++V   T
Sbjct: 70  EADYKAALCRHKQYMGNRFIQVHPIT 95

>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 = 44.2 bits (103), Expect = 2e-06
 Identities = 18/111 (16%), Positives = 30/111 (27%), Gaps = 14/111 (12%)

Query: 147 GGAEGPDR----VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQ 202
           G +    R    +    LP      +I+E      T   F  +               + 
Sbjct: 1   GSSGSSGRSKTVILAKNLPAGTLAAEIQE------TFSRFGSLGRVLLPEGGITAIVEFL 54

Query: 203 DPAVTDIACAALNGLKMGDKTLTVRRAT----ASSGQSKTEQESILAQAQQ 249
           +P     A   L   K     L +  A      ++ Q K  Q    A+  +
Sbjct: 55  EPLEARKAFRHLAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAEKAE 105

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.3 bits (93), Expect = 3e-05
 Identities = 14/89 (15%), Positives = 25/89 (28%), Gaps = 7/89 (7%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
           RV V GLP   +   +K+ +   G +   D+ +D         G   +        A   
Sbjct: 2   RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG-------TGVVEFVRKEDMTYAVRK 54

Query: 214 LNGLKMGDKTLTVRRATASSGQSKTEQES 242
           L+  K                  ++    
Sbjct: 55  LDNTKFRSHEGETAYIRVKVDGPRSPSYG 83

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.8 bits (84), Expect = 4e-04
 Identities = 16/81 (19%), Positives = 23/81 (28%), Gaps = 14/81 (17%)

Query: 34  RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEA 93
           RV V GLPP  + Q +     +                V     +      VE    E+ 
Sbjct: 2   RVVVSGLPPSGSWQDLKDHMREAGD-------------VCYADVYRDGTGVVEFVRKEDM 48

Query: 94  SNAM-ALDGIIFEGVAVRVRR 113
           + A+  LD   F         
Sbjct: 49  TYAVRKLDNTKFRSHEGETAY 69

>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 = 40.6 bits (94), Expect = 3e-05
 Identities = 16/104 (15%), Positives = 29/104 (27%), Gaps = 11/104 (10%)

Query: 142 ASGAIGGAEGPD---RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGF 198
           +SG+ G          V V GL     E  + E       L  F  +        K    
Sbjct: 2   SSGSSGSHHKVSVSPVVHVRGLCESVVEADLVEA------LEKFGTICYVMMMPFKRQAL 55

Query: 199 CVYQDP--AVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQ 240
             +++   A   +  AA   + +  +      +T+         
Sbjct: 56  VEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRITRPGNS 99

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 38.6 bits (89), Expect = 1e-04
 Identities = 16/106 (15%), Positives = 28/106 (26%), Gaps = 23/106 (21%)

Query: 26  QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFV 85
                 +  V+V GL     E  +     +               +  V +   K+ A V
Sbjct: 9   HHKVSVSPVVHVRGLCESVVEADLVEALEKF------------GTICYVMMMPFKRQALV 56

Query: 86  EMRTVEEASNA---MALDGIIFEGVAVRV--------RRPTDYNPT 120
           E   ++ A       A   +   G              RP +  P+
Sbjct: 57  EFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRITRPGNSGPS 102

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.0 bits (90), Expect = 6e-05
 Identities = 12/76 (15%), Positives = 24/76 (31%), Gaps = 5/76 (6%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           + +  +P   +E  +K L  S G +        +D    +               A   L
Sbjct: 13  LHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD----RKMALIQMGSVEEAVQALIDL 68

Query: 215 NGLKMGD-KTLTVRRA 229
           +   +G+   L V  +
Sbjct: 69  HNHDLGENHHLRVSFS 84

>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 = 39.3 bits (91), Expect = 7e-05
 Identities = 16/87 (18%), Positives = 31/87 (35%), Gaps = 15/87 (17%)

Query: 27  QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVE 86
            AT+    V  GGL    +   +     +               V  + +   K ++F  
Sbjct: 16  YATQS-LVVANGGLGNGVSRNQLLPVLEKC------------GLVDALLMPPNKPYSFAR 62

Query: 87  MRTVEEASNAM-ALDG-IIFEGVAVRV 111
            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 = 39.3 bits (91), Expect = 8e-05
 Identities = 16/68 (23%), Positives = 27/68 (39%), Gaps = 6/68 (8%)

Query: 155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 214
           V  GGL    +  Q+  +LE  G +    +  ++       Y F  Y+    +  A   L
Sbjct: 23  VANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP------YSFARYRTTEESKRAYVTL 76

Query: 215 NGLKMGDK 222
           NG ++ D 
Sbjct: 77  NGKEVVDD 84

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.1 bits (85), Expect = 4e-04
 Identities = 13/80 (16%), Positives = 35/80 (43%), Gaps = 5/80 (6%)

Query: 152 PDR-VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA 210
           P R + +  LP   TET++  L   FG +    ++K ++      +     ++ A+T + 
Sbjct: 7   PSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQ----AFLELATEEAAITMVN 62

Query: 211 CAALNGLKMGDKTLTVRRAT 230
             +     + ++ + ++ + 
Sbjct: 63  YYSAVTPHLRNQPIYIQYSN 82

>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 = 0.001
 Identities = 13/83 (15%), Positives = 25/83 (30%), Gaps = 15/83 (18%)

Query: 33  RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 92
           R +++  LP    E  +                     V N+ +   K  AF+E+ T E 
Sbjct: 9   RVLHIRKLPGEVTETEVIALGLPF------------GKVTNILMLKGKNQAFLELATEEA 56

Query: 93  ASNA---MALDGIIFEGVAVRVR 112
           A       +          + ++
Sbjct: 57  AITMVNYYSAVTPHLRNQPIYIQ 79

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.9 bits (82), Expect = 0.001
 Identities = 11/107 (10%), Positives = 22/107 (20%), Gaps = 20/107 (18%)

Query: 34  RVYVGGLPPL-----ANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMR 88
            +                    + F               D           K   +   
Sbjct: 7   GLIACVANDDVFSESETRAKFESLFRTY------------DKDTTFQYFKSFKRVRINFS 54

Query: 89  TVEEASNAM-ALDGIIFEGVAVRVR--RPTDYNPTLAAALGPGQPSP 132
               A++A   L    F G  +++   +      +  A   P +  P
Sbjct: 55  NPLSAADARLRLHKTEFLGKEMKLYFAQTLHIGSSHLAPPNPDKSGP 101

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 34.8 bits (79), Expect = 0.002
 Identities = 15/77 (19%), Positives = 25/77 (32%), Gaps = 6/77 (7%)

Query: 154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 213
            +F+  LP    E  +  L   F         + R   N     F  +     ++ A  A
Sbjct: 10  ILFLTNLPEETNEMMLSMLFNQF-----PGFKEVRLVPNRHDIAFVEFTTELQSNAAKEA 64

Query: 214 LNGLKMGD-KTLTVRRA 229
           L G K+     + +  A
Sbjct: 65  LQGFKITPTHAMKITFA 81

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	380
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.96
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.93
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.84
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.82
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.81
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.81
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.81
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.81
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.8
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.8
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.79
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.79
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.79
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.79
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.79
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.79
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.78
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.78
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.78
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.78
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.78
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.78
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.77
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.77
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.77
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.77
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.76
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.76
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.76
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.76
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.75
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.75
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.75
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.75
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.75
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.75
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.75
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.74
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.73
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.73
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.73
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.73
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.72
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.72
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.72
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.71
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.7
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.7
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.7
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.7
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.69
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.69
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.68
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.68
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.68
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.68
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.68
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.68
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.68
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.68
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.67
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.67
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.67
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.67
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.67
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.67
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.67
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.66
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.66
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.66
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.66
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.66
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.66
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.66
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.66
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.66
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.66
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.65
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.65
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.65
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.65
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.65
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.65
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.65
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.65
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.65
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.65
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.65
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.65
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.65
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.64
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.64
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.64
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.64
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.64
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.64
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.64
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.64
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.64
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.64
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.64
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.64
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.64
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.63
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.63
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.63
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.63
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.63
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.63
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.63
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.63
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.63
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.62
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.62
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.62
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.62
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.62
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.62
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.62
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.62
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.62
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.62
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.61
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.61
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.61
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.61
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.6
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.6
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.6
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.6
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.6
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.6
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.6
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.59
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.59
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.59
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.59
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.59
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.59
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.58
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.58
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.58
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.57
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.57
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.56
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.56
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.56
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.56
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.56
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.55
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.54
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.54
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.54
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.53
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.53
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.52
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.51
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.5
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.5
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	U2	99.49
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.49
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.47
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.46
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	99.46
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.4
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.4
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.38
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.35
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.35
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.31
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.27
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.2
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	98.52
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.56
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.43
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.28
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.24
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	96.84
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	96.57
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	90.44

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.96  E-value=4.1e-29  Score=211.18  Aligned_cols=166  Identities=22%  Similarity=0.438  Sum_probs=141.9

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe------cCCCcEEEEEeCCHHHHHHHHHcCCce
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAMALDGII  103 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~------~~~~g~afV~f~~~~~a~~ai~l~~~~  103 (380)
                      ++.|+|||+|||+.+|+++|+++|++||.            |.++.+      +.++|+|||+|.+.++|.+|+..++..
T Consensus         4 ~~~r~lfV~nLp~~~te~~L~~~F~~~G~------------v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~~~   71 (183)
T d1u1qa_           4 EQLRKLFIGGLSFETTDESLRSHFEQWGT------------LTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHK   71 (183)
T ss_dssp             HHHHEEEEESCCTTCCHHHHHHHHGGGSC------------EEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHcCC------------EEEEEeeecccCCCccCceecccCCHHHHHHHHHhcCCc
Confidence            35689999999999999999999999997            555543      355799999999999999999988889


Q ss_pred             ecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEE
Q 016936          104 FEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFD  183 (380)
Q Consensus       104 i~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~  183 (380)
                      +.++.+.+.+.........                       .......++|||+|||+.+++++|+++|+.||.|..+.
T Consensus        72 ~~~~~~~~~~~~~~~~~~~-----------------------~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~  128 (183)
T d1u1qa_          72 VDGRVVEPKRAVSREDSQR-----------------------PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIE  128 (183)
T ss_dssp             ETTEECEEEECCCTTGGGS-----------------------TTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEE
T ss_pred             ccccchhhhhhhhcccccc-----------------------cccccccceeEEccCCCcCCHHHHhhhhccCCceeeee
Confidence            9999988876544332211                       01123347999999999999999999999999999999


Q ss_pred             EeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEccc
Q 016936          184 LVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  231 (380)
Q Consensus       184 l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~  231 (380)
                      +..++.++.++|+|||+|.+.++|++|++ +++..+.|++|+|.++.+
T Consensus       129 i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~A~~  175 (183)
T d1u1qa_         129 IMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKALS  175 (183)
T ss_dssp             EEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEECCC
T ss_pred             eecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEecCC
Confidence            99998889999999999999999999998 688999999999999854

>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=99.93  E-value=1e-25  Score=190.14  Aligned_cols=170  Identities=19%  Similarity=0.310  Sum_probs=138.8

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEccc
Q 016936          152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  231 (380)
Q Consensus       152 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~  231 (380)
                      .++|||+|||+.+++++|+++|++||.|..+.+++++.++.++|+|||+|.+.++|++|+.. ++..+.++.+.+.+...
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~-~~~~~~~~~~~~~~~~~   84 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVS   84 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHh-cCCcccccchhhhhhhh
Confidence            37999999999999999999999999999999999988999999999999999999999985 67888888888887644


Q ss_pred             CCCCChhHHHHHHHHHHHHHHHHHHHhhhcCccccCCCCCccCCccceEEEEeccC-CcccCCChHHHHHHHHHHHHhhc
Q 016936          232 SSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAI-TADALADDEEYEEILEDMREECG  310 (380)
Q Consensus       232 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~~~~~~~~~~~~~~~L~~~f~  310 (380)
                      ......                                  .......+.+.+.++. +.++           ++|+++|+
T Consensus        85 ~~~~~~----------------------------------~~~~~~~~~i~V~~lp~~~te-----------~~L~~~f~  119 (183)
T d1u1qa_          85 REDSQR----------------------------------PGAHLTVKKIFVGGIKEDTEE-----------HHLRDYFE  119 (183)
T ss_dssp             TTGGGS----------------------------------TTTTCCCSEEEEECCCTTCCH-----------HHHHHHHG
T ss_pred             cccccc----------------------------------cccccccceeEEccCCCcCCH-----------HHHhhhhc
Confidence            321110                                  0013334556666632 2322           69999999


Q ss_pred             ccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEecccc
Q 016936          311 KYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  371 (380)
Q Consensus       311 ~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~~  371 (380)
                      .||.|..+.+..+..++.   ..|+|||+|.+.++|.+|++ +++..++|++|+|.++..+
T Consensus       120 ~~G~v~~~~i~~~~~~~~---~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~A~~k  176 (183)
T d1u1qa_         120 QYGKIEVIEIMTDRGSGK---KRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKALSK  176 (183)
T ss_dssp             GGSCEEEEEEEECTTTCC---EEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEECCCH
T ss_pred             cCCceeeeeeecccccCc---cceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEecCCc
Confidence            999999999998776554   34677999999999999997 7999999999999998543

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=5.9e-21  Score=144.40  Aligned_cols=102  Identities=43%  Similarity=0.836  Sum_probs=93.8

Q ss_pred             ccceEEEEeccCCcccCCChHHHHHHHHHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcC
Q 016936          276 TLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSG  355 (380)
Q Consensus       276 ~~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g  355 (380)
                      .|++++.|.|++++.++.++.++.++.+||++.|++||.|.+|.|+++... ....+.|+|||+|.+.++|.+|+..|||
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 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDG-VEVPGCGKIFVEFTSVFDCQKAMQGLTG   80 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTS-SSCTTCCEEEEEESCHHHHHHHHHHHSS
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCC-CccCCceEEEEEECCHHHHHHHHHHHCC
Confidence            468999999999999999999999999999999999999999999876543 3345668899999999999999999999


Q ss_pred             cccCCeEEEEEeccccccccccC
Q 016936          356 RKFGGNTVNAFYYPEDKYFNKDY  378 (380)
Q Consensus       356 ~~i~gr~l~v~~~~~~~~~~~~~  378 (380)
                      ++|+||.|.|.|++++.|++++|
T Consensus        81 r~f~gR~v~v~f~~~~~y~~~~f  103 (104)
T d1o0pa_          81 RKFANRVVVTKYCDPDSYHRRDF  103 (104)
T ss_dssp             CCSSSSCCEEEEECHHHHHHTSC
T ss_pred             CEECCeEEEEEEcCHHHhhhccC
Confidence            99999999999999999999987

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.82  E-value=3.6e-20  Score=134.10  Aligned_cols=79  Identities=27%  Similarity=0.452  Sum_probs=76.3

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEccc
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  231 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~  231 (380)
                      ++|||+|||..+++++|+++|++||.|..+++.+++.+|+++|||||+|.+.++|++|++.|||..+.|+.|+|+++.+
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            5899999999999999999999999999999999988899999999999999999999999999999999999999864

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=4.4e-20  Score=135.66  Aligned_cols=82  Identities=18%  Similarity=0.328  Sum_probs=78.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      ..++|||+|||+++++++|+++|++||+|.+|.++.++.+|+++|||||+|.+.++|++|++.+|+..+.|++|+|.++.
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~   83 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   83 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            34799999999999999999999999999999999998899999999999999999999999999999999999999997


Q ss_pred             cC
Q 016936          231 AS  232 (380)
Q Consensus       231 ~~  232 (380)
                      ++
T Consensus        84 p~   85 (89)
T d2cqba1          84 PM   85 (89)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>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=99.81  E-value=9.4e-20  Score=133.49  Aligned_cols=81  Identities=28%  Similarity=0.350  Sum_probs=77.6

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEccc
Q 016936          152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  231 (380)
Q Consensus       152 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~  231 (380)
                      .++|||+|||..+++++|+++|++||.|.+|++++++.+|+++|||||+|.+.++|++|+..|||..+.|+.|+|+|+.+
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            36899999999999999999999999999999999988999999999999999999999999999999999999999976


Q ss_pred             C
Q 016936          232 S  232 (380)
Q Consensus       232 ~  232 (380)
                      +
T Consensus        87 k   87 (88)
T d1rk8a_          87 K   87 (88)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=7.6e-20  Score=135.41  Aligned_cols=82  Identities=30%  Similarity=0.465  Sum_probs=78.4

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEccc
Q 016936          152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  231 (380)
Q Consensus       152 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~  231 (380)
                      .++|||+|||+.+++++|+++|++||.|.+|++++++.++.++|||||+|.+.++|++|++.|||..+.|+.|+|++|.+
T Consensus         9 ~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A~~   88 (93)
T d1x5ua1           9 DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASA   88 (93)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETTT
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCC
Confidence            46999999999999999999999999999999999988999999999999999999999999999999999999999977


Q ss_pred             CC
Q 016936          232 SS  233 (380)
Q Consensus       232 ~~  233 (380)
                      +.
T Consensus        89 ~~   90 (93)
T d1x5ua1          89 HN   90 (93)
T ss_dssp             TS
T ss_pred             CC
Confidence            54

>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=99.81  E-value=1.3e-19  Score=131.16  Aligned_cols=79  Identities=37%  Similarity=0.606  Sum_probs=76.1

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEccc
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  231 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~  231 (380)
                      ++|||+|||+.+++++|+++|++||.|..|++++++.++.++|||||+|.++++|++|++.|||..+.|++|+|.++.|
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            5799999999999999999999999999999999988899999999999999999999999999999999999999865

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.80  E-value=1.5e-19  Score=135.63  Aligned_cols=85  Identities=26%  Similarity=0.439  Sum_probs=79.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      ...+.+|||+|||+.+++++|+++|++||.|.+|+++.++.+++++|||||+|.+.++|++|++.||+..+.|+.|+|.+
T Consensus         5 ~~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~   84 (99)
T d1whwa_           5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34457899999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             cccCC
Q 016936          229 ATASS  233 (380)
Q Consensus       229 ~~~~~  233 (380)
                      +..+.
T Consensus        85 a~~~~   89 (99)
T d1whwa_          85 STIKK   89 (99)
T ss_dssp             CCCCS
T ss_pred             CCCCC
Confidence            88753

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=1.7e-19  Score=129.69  Aligned_cols=77  Identities=23%  Similarity=0.327  Sum_probs=74.9

Q ss_pred             EEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       154 ~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      .|||+|||+.+++++|+++|++||+|.++++++++.+|+++|||||+|.++++|.+|++.|+|..+.|++|+|.|+.
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            69999999999999999999999999999999999899999999999999999999999999999999999999984

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=1.8e-19  Score=132.62  Aligned_cols=81  Identities=30%  Similarity=0.434  Sum_probs=77.7

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEccc
Q 016936          152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  231 (380)
Q Consensus       152 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~  231 (380)
                      ..+|||+|||..+++++|+++|++||.|..|+++.++.++.++|||||+|.+.++|++|++.|+|..+.|+.|+|+++.+
T Consensus         8 ~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~akp   87 (90)
T d2cq0a1           8 NATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKP   87 (90)
T ss_dssp             SEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEeeeC
Confidence            36899999999999999999999999999999999988899999999999999999999999999999999999999976


Q ss_pred             C
Q 016936          232 S  232 (380)
Q Consensus       232 ~  232 (380)
                      +
T Consensus        88 ~   88 (90)
T d2cq0a1          88 S   88 (90)
T ss_dssp             C
T ss_pred             C
Confidence            5

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=3.2e-19  Score=134.35  Aligned_cols=83  Identities=25%  Similarity=0.497  Sum_probs=78.6

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEccc
Q 016936          152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  231 (380)
Q Consensus       152 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~  231 (380)
                      .++|||+|||+++++++|+++|++||.|..+.++.++.+|+++|||||+|.+.++|++|++.|||..+.|+.|+|+++.+
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            35799999999999999999999999999999999988999999999999999999999999999999999999999987


Q ss_pred             CCC
Q 016936          232 SSG  234 (380)
Q Consensus       232 ~~~  234 (380)
                      +..
T Consensus        98 k~~  100 (102)
T d2cpza1          98 KND  100 (102)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            644

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=4.7e-19  Score=131.06  Aligned_cols=82  Identities=24%  Similarity=0.383  Sum_probs=77.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      .+++|||+|||+.+++++|+++|++||.|.+|.++.++.++.++|||||+|.+.++|+.|++.|||..+.|++|+|.|+.
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            34699999999999999999999999999999999998899999999999999999999999999999999999999985


Q ss_pred             cC
Q 016936          231 AS  232 (380)
Q Consensus       231 ~~  232 (380)
                      ..
T Consensus        86 ~~   87 (93)
T d1h2vz_          86 GF   87 (93)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.79  E-value=1.3e-19  Score=131.71  Aligned_cols=80  Identities=56%  Similarity=0.973  Sum_probs=77.0

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccC
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  232 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~  232 (380)
                      .+|||+|||+.+++++|+++|++||+|.+|++++++.+|.++|||||+|.++++|+.|++.||+..+.|++|.|.++.+.
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            37999999999999999999999999999999999989999999999999999999999999999999999999999754

>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=99.79  E-value=3e-19  Score=129.97  Aligned_cols=79  Identities=25%  Similarity=0.458  Sum_probs=74.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCC--eEEEEEE
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD--KTLTVRR  228 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g--~~i~v~~  228 (380)
                      ..++|||+|||+++++++|+++|++||.|..+++++++.+++++|||||+|.+.++|.+|++.||+..+.|  ++|+|+|
T Consensus         5 ~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~   84 (85)
T d1b7fa2           5 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRL   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEE
Confidence            34689999999999999999999999999999999998899999999999999999999999999999876  8899998


Q ss_pred             c
Q 016936          229 A  229 (380)
Q Consensus       229 ~  229 (380)
                      |
T Consensus        85 A   85 (85)
T d1b7fa2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.79  E-value=3.7e-19  Score=128.87  Aligned_cols=75  Identities=23%  Similarity=0.449  Sum_probs=72.3

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEE
Q 016936          152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  226 (380)
Q Consensus       152 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v  226 (380)
                      .++|||+|||+.+++++|+++|++||.|.+|+++.++.+++++|||||+|.+.++|++|+..||+..+.|++|+|
T Consensus         9 ~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           9 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             GGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            368999999999999999999999999999999999888999999999999999999999999999999999987

>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=99.78  E-value=3.5e-19  Score=131.17  Aligned_cols=83  Identities=29%  Similarity=0.569  Sum_probs=78.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      ..++|||+|||+.+++++|+++|++||.|..+.++.++.++.++|||||+|.++++|++|+..|+|..+.|++|+|+++.
T Consensus         4 ~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~   83 (90)
T d1x5sa1           4 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAG   83 (90)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEE
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            34789999999999999999999999999999999988889999999999999999999999999999999999999987


Q ss_pred             cCC
Q 016936          231 ASS  233 (380)
Q Consensus       231 ~~~  233 (380)
                      ++.
T Consensus        84 ~~~   86 (90)
T d1x5sa1          84 KSS   86 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=8.6e-19  Score=129.69  Aligned_cols=83  Identities=25%  Similarity=0.574  Sum_probs=76.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      ...+++|||+|||+.+++++|+++|++||.|..|+++.++  +.++|||||+|.+.++|++|+..||+..+.|+.|+|++
T Consensus         8 ~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~--~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~   85 (93)
T d2cq3a1           8 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN   85 (93)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT--TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccc--cCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            4455799999999999999999999999999999999884  45799999999999999999999999999999999999


Q ss_pred             cccCC
Q 016936          229 ATASS  233 (380)
Q Consensus       229 ~~~~~  233 (380)
                      +.++.
T Consensus        86 A~~r~   90 (93)
T d2cq3a1          86 ATARV   90 (93)
T ss_dssp             CCSSC
T ss_pred             cCcCC
Confidence            98753

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=4.6e-19  Score=128.43  Aligned_cols=79  Identities=27%  Similarity=0.518  Sum_probs=74.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      ..++|||+|||+.+++++|+++|++||.|..++++.++.+|+++|||||+|.+.++|++|++ ++++.+.|+.|+|+.|.
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            34799999999999999999999999999999999999899999999999999999999998 58999999999999874

>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=99.78  E-value=5.5e-19  Score=126.20  Aligned_cols=76  Identities=25%  Similarity=0.413  Sum_probs=73.3

Q ss_pred             EEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       154 ~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      +|||+|||+.+++++|+++|++||.|.++++..++ +++++|||||+|.+.++|++|++.|||..+.|++|+|+++.
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            79999999999999999999999999999999986 79999999999999999999999999999999999999875

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=6.5e-19  Score=129.18  Aligned_cols=82  Identities=23%  Similarity=0.391  Sum_probs=75.5

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      ...++|||+|||+++++++|+++|++||.|..|+++.++.+|+++|||||+|.+.++|++|++.  ...+.|+.|.|+++
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            3446899999999999999999999999999999999988999999999999999999999984  45899999999998


Q ss_pred             ccCC
Q 016936          230 TASS  233 (380)
Q Consensus       230 ~~~~  233 (380)
                      .++.
T Consensus        84 ~~k~   87 (90)
T d2cqga1          84 NSKQ   87 (90)
T ss_dssp             CTTC
T ss_pred             CCCC
Confidence            7653

>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=99.78  E-value=5.5e-19  Score=128.42  Aligned_cols=77  Identities=29%  Similarity=0.509  Sum_probs=73.1

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCC--eEEEEEEc
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD--KTLTVRRA  229 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g--~~i~v~~~  229 (380)
                      ++|||+|||+.+++++|+++|++||.|.++++++++.+|+++|||||+|.+.++|++|++.|||..+.|  ++|+|.||
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            589999999999999999999999999999999998889999999999999999999999999999987  55899885

>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=99.77  E-value=1e-18  Score=139.62  Aligned_cols=86  Identities=30%  Similarity=0.521  Sum_probs=80.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      ....++|||+|||+++++++|+++|++||.|.+|++++++.+++++|||||+|.+.++|++|++.|||..|.|++|+|.+
T Consensus        39 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~  118 (139)
T d1u6fa1          39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL  118 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            34457899999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             cccCCC
Q 016936          229 ATASSG  234 (380)
Q Consensus       229 ~~~~~~  234 (380)
                      +..+..
T Consensus       119 a~~~~~  124 (139)
T d1u6fa1         119 AASGHQ  124 (139)
T ss_dssp             SSCCCC
T ss_pred             cCCCCC
Confidence            876543

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=6.4e-19  Score=127.65  Aligned_cols=79  Identities=30%  Similarity=0.521  Sum_probs=74.2

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCeeEE-EEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccCC
Q 016936          155 VFVGGLPYYFTETQIKELLESFGTLHGF-DLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASS  233 (380)
Q Consensus       155 l~V~nlp~~~t~~~l~~~F~~~G~i~~v-~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~~  233 (380)
                      |||+|||+++++++|+++|++||.|..+ ++++++.+|+++|||||+|.+.++|++|++.++|..+.|++|+|.++.++.
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            7999999999999999999999998764 788888889999999999999999999999999999999999999997654

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.77  E-value=9.3e-19  Score=129.71  Aligned_cols=82  Identities=24%  Similarity=0.468  Sum_probs=76.1

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCC-CCCCceEEEEEEcChhHHHHHHHHh-CCCeeCCeEEEEEEc
Q 016936          152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRD-TGNSKGYGFCVYQDPAVTDIACAAL-NGLKMGDKTLTVRRA  229 (380)
Q Consensus       152 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l-~g~~~~g~~i~v~~~  229 (380)
                      .++|||+|||..+++++|+++|++||.|..|+|+++.. +|+++|||||+|.+.++|.+|+..| |+..+.|++|.|.|+
T Consensus         8 ~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~~A   87 (94)
T d2cpha1           8 TSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWA   87 (94)
T ss_dssp             CCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEEEc
Confidence            36899999999999999999999999999999988743 7899999999999999999999998 899999999999999


Q ss_pred             ccCC
Q 016936          230 TASS  233 (380)
Q Consensus       230 ~~~~  233 (380)
                      ....
T Consensus        88 ~~~~   91 (94)
T d2cpha1          88 DSEV   91 (94)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>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=99.77  E-value=2.5e-18  Score=126.41  Aligned_cols=81  Identities=27%  Similarity=0.415  Sum_probs=74.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      .+++|||+|||..+++++|+++|++||.|..|+++.++.+  .+|||||+|.+.++|.+|+..++|..+.|+.|+|.++.
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            3579999999999999999999999999999999988543  47899999999999999999999999999999999997


Q ss_pred             cCC
Q 016936          231 ASS  233 (380)
Q Consensus       231 ~~~  233 (380)
                      +..
T Consensus        85 ~~~   87 (90)
T d2cqia1          85 TPS   87 (90)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            653

>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=99.76  E-value=5.4e-19  Score=125.18  Aligned_cols=75  Identities=28%  Similarity=0.570  Sum_probs=71.4

Q ss_pred             EEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       154 ~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      +|||+|||+++++++|+++|++||.|..+.++.++.+++++|||||+|.++++|++|++ +++..+.|+.|.|++|
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            58999999999999999999999999999999999999999999999999999999998 6899999999999754

>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=99.76  E-value=9.7e-19  Score=126.05  Aligned_cols=79  Identities=16%  Similarity=0.257  Sum_probs=69.0

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEccc
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  231 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~  231 (380)
                      .+|||+|||+++++++|+++|++||.|..+.++.+...|.++|||||+|.+.++|++|++.|||..+.|++|+|+++.|
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            4899999999999999999999999999888887777899999999999999999999999999999999999999865

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.76  E-value=4.3e-19  Score=126.20  Aligned_cols=75  Identities=28%  Similarity=0.516  Sum_probs=72.4

Q ss_pred             EEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       154 ~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      +|||+|||+++++++|+++|++||.|.++++++++.+|+++|||||+|.++++|++|++ ++++.+.|+.|+|+.|
T Consensus         2 klfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            69999999999999999999999999999999999899999999999999999999998 6999999999999876

>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=99.76  E-value=1e-18  Score=130.98  Aligned_cols=77  Identities=17%  Similarity=0.362  Sum_probs=74.3

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      ++|||+|||+.+++++|+++|+.||.|.+|++++++.+|+++|||||+|.+.++|++|++ |||..+.|+.|.|.++.
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            689999999999999999999999999999999998899999999999999999999996 89999999999999974

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=9.3e-19  Score=132.49  Aligned_cols=79  Identities=43%  Similarity=0.754  Sum_probs=76.2

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEccc
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  231 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~  231 (380)
                      ++|||+|||+++++++|+++|++||.|.+|+++.++.+|+++|||||+|.+.++|++|++.|++..+.|+.|+|.++.+
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            6899999999999999999999999999999999988899999999999999999999999999999999999999864

>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=99.75  E-value=3.4e-18  Score=128.91  Aligned_cols=79  Identities=34%  Similarity=0.658  Sum_probs=74.7

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccC
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  232 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~  232 (380)
                      ++|||+|||+.+++++|+++|++||.|.+|+++.++.+|+++|||||+|.+.++|++|++.+++ .+.|++|+|.++...
T Consensus        11 ~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a~~~   89 (103)
T d2cqda1          11 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAYLG   89 (103)
T ss_dssp             SEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEESTTT
T ss_pred             cEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEcCCC
Confidence            6899999999999999999999999999999999988999999999999999999999998875 799999999998654

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=3.7e-18  Score=122.34  Aligned_cols=76  Identities=22%  Similarity=0.530  Sum_probs=73.0

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      ++|||+|||+++|+++|+++|++||.|..+.+..++.++.++|||||+|.++++|++|+. ++++.|.|+.|+|++|
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            799999999999999999999999999999999999899999999999999999999996 7999999999999876

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.75  E-value=2.2e-18  Score=125.39  Aligned_cols=77  Identities=25%  Similarity=0.480  Sum_probs=71.8

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCC---CCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEccc
Q 016936          155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTG---NSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  231 (380)
Q Consensus       155 l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~---~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~  231 (380)
                      |||+|||+++++++|+++|++||.|.++++++++.++   .++|||||+|.+.++|++|++.+||..+.|+.|+|+++..
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            7999999999999999999999999999999886554   4689999999999999999999999999999999999854

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=2.5e-18  Score=129.29  Aligned_cols=80  Identities=26%  Similarity=0.519  Sum_probs=76.0

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccC
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  232 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~  232 (380)
                      ++|||+|||+++++++|+++|++||.|..+.|+.++.++.++|||||+|.+.++|++|++ +++..|.|+.|.|.++.++
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            689999999999999999999999999999999998889999999999999999999997 6999999999999998776


Q ss_pred             C
Q 016936          233 S  233 (380)
Q Consensus       233 ~  233 (380)
                      .
T Consensus       100 e  100 (103)
T d1x4ba1         100 E  100 (103)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=2.1e-18  Score=126.55  Aligned_cols=78  Identities=23%  Similarity=0.483  Sum_probs=73.4

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccC
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  232 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~  232 (380)
                      .+|||+|||+.+++++|+++|++||.|..++++.++  +.++|||||+|.+.++|++|++.|||..+.|+.|.|.++.++
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            589999999999999999999999999999999885  457899999999999999999999999999999999999765

>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=99.75  E-value=1.1e-18  Score=123.15  Aligned_cols=75  Identities=23%  Similarity=0.439  Sum_probs=70.9

Q ss_pred             EEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       154 ~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      +|||+|||+++++++|+++|++||.|..|+|+.++.+++++|||||+|.+.++|++|++. +++.+.|+.|.|+.|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~~-~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTC-SSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhh-CCCEECCEEeEEEEC
Confidence            589999999999999999999999999999999998999999999999999999999985 778999999998764

>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=99.74  E-value=9.4e-18  Score=125.53  Aligned_cols=84  Identities=29%  Similarity=0.428  Sum_probs=77.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhC------CCeeCCeE
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN------GLKMGDKT  223 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~------g~~~~g~~  223 (380)
                      ...++|||+|||+.+++++|+++|++||.|..+.+..++.++.++|||||+|.+.++|.+|++.++      |..+.|+.
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            344799999999999999999999999999999999998889999999999999999999999886      57889999


Q ss_pred             EEEEEcccCC
Q 016936          224 LTVRRATASS  233 (380)
Q Consensus       224 i~v~~~~~~~  233 (380)
                      |+|.++.++.
T Consensus        86 l~v~~a~~k~   95 (98)
T d1x4ha1          86 LKVDLAVTRD   95 (98)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEEECCCCC
Confidence            9999997653

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.73  E-value=7.8e-18  Score=123.72  Aligned_cols=83  Identities=19%  Similarity=0.418  Sum_probs=74.4

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHHHcCCceecC
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEG  106 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai~l~~~~i~g  106 (380)
                      ..+...++|||+|||+++|+++|+++|++||.|....       +.+...++++|||||+|.+.++|.+||++++..|.|
T Consensus         8 ~~~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~-------v~~~~~g~~kg~afv~F~~~e~a~~Al~~~g~~~~g   80 (91)
T d1fjeb1           8 SESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLA-------VVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFG   80 (91)
T ss_dssp             SSCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCC-------CCEEEEETTTTEEEEEESSHHHHHHHHHGGGEEETT
T ss_pred             CCCCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEee-------eeecCCCCccEEeEEeeCCHHHHHHHHhcCCcEECC
Confidence            4456678999999999999999999999999987653       556678899999999999999999999999999999


Q ss_pred             ceEEEecCCC
Q 016936          107 VAVRVRRPTD  116 (380)
Q Consensus       107 ~~i~v~~~~~  116 (380)
                      ++|+|.++..
T Consensus        81 ~~i~V~~ak~   90 (91)
T d1fjeb1          81 NEIKLEKPKG   90 (91)
T ss_dssp             EEEEEECCCC
T ss_pred             EEEEEEecCC
Confidence            9999998754

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=1e-17  Score=128.99  Aligned_cols=79  Identities=20%  Similarity=0.435  Sum_probs=73.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      .+++|||+|||..+++++|+++|++||.|..|++..+   +.++|||||+|.+.++|..|++.|||..|.|+.|+|.++.
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 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYN   82 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc---CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            3479999999999999999999999999999999764   6678999999999999999999999999999999999986


Q ss_pred             cC
Q 016936          231 AS  232 (380)
Q Consensus       231 ~~  232 (380)
                      ..
T Consensus        83 ~~   84 (114)
T d2f9da1          83 AN   84 (114)
T ss_dssp             HH
T ss_pred             CC
Confidence            53

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.73  E-value=4.2e-18  Score=123.98  Aligned_cols=80  Identities=16%  Similarity=0.360  Sum_probs=70.0

Q ss_pred             CCEEEEcCCCCCCC-HHHHHHHHHhcCCeeEEEEeeC-CCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          152 PDRVFVGGLPYYFT-ETQIKELLESFGTLHGFDLVKD-RDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       152 ~~~l~V~nlp~~~t-~~~l~~~F~~~G~i~~v~l~~~-~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      .++|||+|||++++ +++|+++|++||.|.+|+++.+ ..+++++|||||+|.+.++|++|++ +|+..+.|+.|+|.++
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            47999999999876 5669999999999999998764 4578999999999999999999996 8999999999999998


Q ss_pred             ccC
Q 016936          230 TAS  232 (380)
Q Consensus       230 ~~~  232 (380)
                      .++
T Consensus        83 ~~k   85 (86)
T d2ghpa3          83 DKK   85 (86)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            754

>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=99.73  E-value=3.5e-18  Score=121.21  Aligned_cols=75  Identities=25%  Similarity=0.585  Sum_probs=71.9

Q ss_pred             EEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       154 ~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      +|||+|||+++++++|+++|++||.|..+.+..++.++.++|+|||+|.+.++|++|++ +|++.+.|++|+|++|
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            58999999999999999999999999999999998889999999999999999999997 8999999999999875

>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=99.72  E-value=1.5e-17  Score=125.10  Aligned_cols=82  Identities=22%  Similarity=0.386  Sum_probs=75.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCee--------EEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCe
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLH--------GFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDK  222 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~--------~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~  222 (380)
                      ..++|||+|||..+++++|+++|++||.|.        .+.+..++.+++++|||||+|.++++|.+|++.|||..+.|+
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            347999999999999999999999999874        566777777899999999999999999999999999999999


Q ss_pred             EEEEEEcccC
Q 016936          223 TLTVRRATAS  232 (380)
Q Consensus       223 ~i~v~~~~~~  232 (380)
                      +|+|.++.++
T Consensus        87 ~i~V~~a~~~   96 (101)
T d2cpea1          87 KLKVSLARKK   96 (101)
T ss_dssp             ECEEECSSCC
T ss_pred             EEEEEEcCCC
Confidence            9999999765

>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=1.8e-18  Score=127.26  Aligned_cols=80  Identities=18%  Similarity=0.336  Sum_probs=73.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      ...++|||+|||+++++++|+++|+.||.|..++++.+ .+|+++|||||+|.+.++|++|++ +|+..+.|++|+|.++
T Consensus        11 ~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~a   88 (91)
T d1fjeb1          11 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   88 (91)
T ss_dssp             SSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECC
T ss_pred             CCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEec
Confidence            34468999999999999999999999999999888765 479999999999999999999996 8999999999999998


Q ss_pred             cc
Q 016936          230 TA  231 (380)
Q Consensus       230 ~~  231 (380)
                      ..
T Consensus        89 k~   90 (91)
T d1fjeb1          89 KG   90 (91)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=1.3e-17  Score=123.77  Aligned_cols=78  Identities=26%  Similarity=0.437  Sum_probs=72.5

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceec
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE  105 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~  105 (380)
                      +.....++|||+|||..+++++|+++|++||.            |.++++.+++|||||+|.+.++|.+|+ .+++..|.
T Consensus        13 ~~~~~~~~l~v~nL~~~~te~~L~~~F~~fG~------------i~~v~i~~~kg~afV~f~~~~~A~~Ai~~l~~~~i~   80 (96)
T d1x4ga1          13 QSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQ------------IMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTIE   80 (96)
T ss_dssp             HSCSSCCEEEEECCSSCCCHHHHHHHHHHHSC------------EEEEEEETTTTEEEEEESSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHHHhCC------------ceEEEEEecceEEEEEECCHHHHHHHHHHhCCCEEC
Confidence            45566789999999999999999999999998            888999999999999999999999999 79999999


Q ss_pred             CceEEEecCCC
Q 016936          106 GVAVRVRRPTD  116 (380)
Q Consensus       106 g~~i~v~~~~~  116 (380)
                      |++|+|.|+.+
T Consensus        81 g~~l~v~~ak~   91 (96)
T d1x4ga1          81 GHVVKCYWGKE   91 (96)
T ss_dssp             TEECEEECCCC
T ss_pred             CEEEEEEEcCC
Confidence            99999999754

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=6.9e-17  Score=119.77  Aligned_cols=79  Identities=20%  Similarity=0.404  Sum_probs=72.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      ..++|||+|||+.+++++|+++|++||.|..+.+..+   ..++|||||+|.+.++|++|++.||+..+.|++|+|+++.
T Consensus        13 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~   89 (95)
T d1x4aa1          13 NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPR   89 (95)
T ss_dssp             CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEecc
Confidence            3468999999999999999999999999999887654   5578999999999999999999999999999999999987


Q ss_pred             cC
Q 016936          231 AS  232 (380)
Q Consensus       231 ~~  232 (380)
                      ..
T Consensus        90 ~~   91 (95)
T d1x4aa1          90 SG   91 (95)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.70  E-value=1.5e-17  Score=121.20  Aligned_cols=77  Identities=16%  Similarity=0.333  Sum_probs=69.9

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeE-EEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          152 PDRVFVGGLPYYFTETQIKELLESFGTLHG-FDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       152 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~-v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      ...|||+|||+++++++|+++|+.||.+.. +.+..+ .+++++|+|||+|.+.++|++|++.||+..+.|++|+|..+
T Consensus         9 ~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~-~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           9 PTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYN-EKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             SEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEEC-SSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeC-CCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            457999999999999999999999999876 455555 57999999999999999999999999999999999999864

>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=99.70  E-value=3.4e-17  Score=118.65  Aligned_cols=76  Identities=22%  Similarity=0.270  Sum_probs=71.9

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      ++|||+|||.++++++|+++|+.||.|..|++..++ +++++|||||+|.++++|++|++ +++..+.|+.|.|.+..
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            699999999999999999999999999999998885 79999999999999999999997 69999999999999864

>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=99.70  E-value=8e-18  Score=126.88  Aligned_cols=82  Identities=20%  Similarity=0.263  Sum_probs=77.2

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEccc
Q 016936          152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  231 (380)
Q Consensus       152 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~  231 (380)
                      +++|||+|||..+++++|+++|++||.|..+.+..+..+|+++|||||+|.+.++|++|++.|||..+.|++|+|+++.+
T Consensus        18 s~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~ak~   97 (102)
T d2cpxa1          18 NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKN   97 (102)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeCCC
Confidence            47999999999999999999999999999998888777899999999999999999999999999999999999999987


Q ss_pred             CC
Q 016936          232 SS  233 (380)
Q Consensus       232 ~~  233 (380)
                      +.
T Consensus        98 k~   99 (102)
T d2cpxa1          98 KK   99 (102)
T ss_dssp             CS
T ss_pred             cc
Confidence            53

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=5.1e-17  Score=120.53  Aligned_cols=74  Identities=19%  Similarity=0.406  Sum_probs=70.1

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccC
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  232 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~  232 (380)
                      ++|||+|||..+++++|+++|++||.|.+|++.++      +|||||+|.+.++|++|+..|++..+.|+.|+|.|+.++
T Consensus        19 ~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~~   92 (96)
T d1x4ga1          19 CTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKES   92 (96)
T ss_dssp             CEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             CEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            68999999999999999999999999999999865      579999999999999999999999999999999998764

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.69  E-value=6.1e-17  Score=117.58  Aligned_cols=76  Identities=34%  Similarity=0.568  Sum_probs=70.6

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEccc
Q 016936          152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  231 (380)
Q Consensus       152 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~  231 (380)
                      .++|||+|||.++++++|+++|++||.|.+|++.++      +|||||+|.+.++|++|+..|||..+.|+.|+|+++..
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            358999999999999999999999999999999765      56999999999999999999999999999999999976


Q ss_pred             CC
Q 016936          232 SS  233 (380)
Q Consensus       232 ~~  233 (380)
                      ..
T Consensus        82 ~~   83 (86)
T d2cpja1          82 SA   83 (86)
T ss_dssp             CS
T ss_pred             cC
Confidence            53

>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=99.69  E-value=2.8e-17  Score=123.41  Aligned_cols=80  Identities=20%  Similarity=0.422  Sum_probs=69.5

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe------cCCCcEEEEEeCCHHHHHHHHHcC
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAMALD  100 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~------~~~~g~afV~f~~~~~a~~ai~l~  100 (380)
                      ......++|||+|||+++++++|+++|++||.            |..+.+      ..++|||||+|.+.++|.+|++++
T Consensus        15 ~~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~------------i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~~~   82 (103)
T d1x4ba1          15 REKEQFRKLFIGGLSFETTEESLRNYYEQWGK------------LTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAAR   82 (103)
T ss_dssp             CHHHHHTEEEEECCTTCCCHHHHHHHHTSSCC------------CSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSC
T ss_pred             CCcCCCCEEEEeCCCCcCCHHHHHHHHHhhCc------------ccceeecccccCCCccCeEEEEECCHHHHHHHHHhC
Confidence            44556789999999999999999999999998            444544      356899999999999999999999


Q ss_pred             CceecCceEEEecCCCCC
Q 016936          101 GIIFEGVAVRVRRPTDYN  118 (380)
Q Consensus       101 ~~~i~g~~i~v~~~~~~~  118 (380)
                      +..|.|++|.|.++..++
T Consensus        83 ~~~l~G~~i~V~~a~~ke  100 (103)
T d1x4ba1          83 PHSIDGRVVEPKRAVARE  100 (103)
T ss_dssp             SEEETTEEEEEECCSSCC
T ss_pred             CCeECCEEEEEEECcccC
Confidence            999999999999877653

>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=99.68  E-value=2.4e-17  Score=123.77  Aligned_cols=79  Identities=19%  Similarity=0.444  Sum_probs=73.6

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEccc
Q 016936          152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  231 (380)
Q Consensus       152 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~  231 (380)
                      +++|||+|||+++++++|+++|++||.|..+.+..+. ++.++|||||+|.+.++|++|++.|||..+.|+++.|.++.+
T Consensus        18 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~~P   96 (101)
T d1x5oa1          18 PTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEP   96 (101)
T ss_dssp             TTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSSC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccc-ccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCCCC
Confidence            4789999999999999999999999999999998885 789999999999999999999999999999999998877653

>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=99.68  E-value=3.2e-17  Score=119.91  Aligned_cols=76  Identities=20%  Similarity=0.327  Sum_probs=69.4

Q ss_pred             CCEEEEcCCCCCCCHHHH---HHHHHhcCCeeEEEEeeCCCCCCC---ceEEEEEEcChhHHHHHHHHhCCCeeCCeEEE
Q 016936          152 PDRVFVGGLPYYFTETQI---KELLESFGTLHGFDLVKDRDTGNS---KGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  225 (380)
Q Consensus       152 ~~~l~V~nlp~~~t~~~l---~~~F~~~G~i~~v~l~~~~~~~~~---~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~  225 (380)
                      .++|||+|||+.+++++|   .++|++||.|..|.+++++.++.+   +|||||+|.+.++|.+|++.|||..+.|+.|+
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            368999999999999999   678999999999999998766554   48999999999999999999999999999999


Q ss_pred             EE
Q 016936          226 VR  227 (380)
Q Consensus       226 v~  227 (380)
                      |.
T Consensus        88 vS   89 (89)
T d2cpia1          88 AS   89 (89)
T ss_dssp             EE
T ss_pred             EC
Confidence            84

>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=99.68  E-value=9.3e-17  Score=121.30  Aligned_cols=84  Identities=27%  Similarity=0.489  Sum_probs=72.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDR-DTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  227 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~  227 (380)
                      ...+.+|||+|||+++++++|+++|++|| +..++++.++ .+++++|||||+|.+.++|++|++ +|+..+.|+.|+|.
T Consensus        12 ~~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~-~~~~~~~gr~l~V~   89 (104)
T d1wi8a_          12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNKRIRVD   89 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHG-GGTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHH-cCCCEECCEEEEEE
Confidence            33457999999999999999999999999 7777777664 468899999999999999987775 89999999999999


Q ss_pred             EcccCCC
Q 016936          228 RATASSG  234 (380)
Q Consensus       228 ~~~~~~~  234 (380)
                      ++.++..
T Consensus        90 ~a~~~~~   96 (104)
T d1wi8a_          90 VADQAQD   96 (104)
T ss_dssp             ECCCCCC
T ss_pred             ECCCCCC
Confidence            9876543

>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=99.68  E-value=1.2e-16  Score=116.18  Aligned_cols=76  Identities=17%  Similarity=0.175  Sum_probs=69.3

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEccc
Q 016936          152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  231 (380)
Q Consensus       152 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~  231 (380)
                      .++|||+|||+.+++++|+++|++||.|..+.+.      +++|||||+|.++++|.+|+..|||..+.|+.|.|.++.+
T Consensus         8 ~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~------~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP   81 (86)
T d2cpda1           8 VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKP   81 (86)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEE------ECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCC
T ss_pred             CCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEc------cccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccC
Confidence            4789999999999999999999999999877764      3468999999999999999999999999999999999976


Q ss_pred             CC
Q 016936          232 SS  233 (380)
Q Consensus       232 ~~  233 (380)
                      ..
T Consensus        82 ~~   83 (86)
T d2cpda1          82 VD   83 (86)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=2.2e-17  Score=123.63  Aligned_cols=77  Identities=29%  Similarity=0.405  Sum_probs=68.4

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe------cCCCcEEEEEeCCHHHHHHHHHcC
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAMALD  100 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~------~~~~g~afV~f~~~~~a~~ai~l~  100 (380)
                      +.+++.++|||+|||+++++++|+++|++||.            |.++.+      ++++|||||+|.+.++|.+|++++
T Consensus        13 ~~~~~~~tifV~nL~~~~te~~l~~~F~~~G~------------V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~l~   80 (101)
T d2cq4a1          13 PEERDARTVFCMQLAARIRPRDLEDFFSAVGK------------VRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLT   80 (101)
T ss_dssp             TTHHHHTEEEEESCCTTCCHHHHHHHHTTTSC------------EEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHT
T ss_pred             ccccCCCEEEEECCCCCCCHHHHHHHHcCCCe------------EEEEEeeecCCCccccceEEEEECCHHHHHHHHHHC
Confidence            45567799999999999999999999999998            555655      356899999999999999999999


Q ss_pred             CceecCceEEEecCC
Q 016936          101 GIIFEGVAVRVRRPT  115 (380)
Q Consensus       101 ~~~i~g~~i~v~~~~  115 (380)
                      +..|.|++|+|.++.
T Consensus        81 g~~~~G~~l~V~~a~   95 (101)
T d2cq4a1          81 GQRLLGVPIIVQASQ   95 (101)
T ss_dssp             TEEETTEEEEEEEHH
T ss_pred             CCEECCEEEEEEECC
Confidence            999999999998753

>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=99.68  E-value=6.1e-17  Score=117.83  Aligned_cols=75  Identities=24%  Similarity=0.383  Sum_probs=68.0

Q ss_pred             ccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecCceE
Q 016936           31 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  109 (380)
Q Consensus        31 ~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g~~i  109 (380)
                      ..++|||+|||+++++++|+++|++||.            +..+.+.+++|||||+|.+.++|..|+ .||+..|.|++|
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            4589999999999999999999999987            455666788999999999999999999 799999999999


Q ss_pred             EEecCCCC
Q 016936          110 RVRRPTDY  117 (380)
Q Consensus       110 ~v~~~~~~  117 (380)
                      +|.|+.+.
T Consensus        75 ~V~~akP~   82 (86)
T d2cpda1          75 EVTLAKPV   82 (86)
T ss_dssp             EEECCCCC
T ss_pred             EEEeccCC
Confidence            99997654

>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=99.68  E-value=4.7e-17  Score=120.12  Aligned_cols=76  Identities=32%  Similarity=0.478  Sum_probs=67.9

Q ss_pred             ccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe------cCCCcEEEEEeCCHHHHHHHH-HcCCce
Q 016936           31 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-ALDGII  103 (380)
Q Consensus        31 ~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~------~~~~g~afV~f~~~~~a~~ai-~l~~~~  103 (380)
                      ..++|||+|||+++|+++|+++|++||.            |.++.+      +.++|||||+|.+.++|++|+ .|++..
T Consensus         8 ~~~tlfV~nLp~~~t~~~l~~~F~~~G~------------v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~   75 (93)
T d1x5ua1           8 QDATVYVGGLDEKVSEPLLWELFLQAGP------------VVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIK   75 (93)
T ss_dssp             TTTEEEEECCCTTCCHHHHHHHHHTTSC------------EEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCB
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhCC------------ccccceeecccccccccceEEEECCHHHHHHHHHHcCCCE
Confidence            4579999999999999999999999997            666665      346789999999999999999 799999


Q ss_pred             ecCceEEEecCCCCC
Q 016936          104 FEGVAVRVRRPTDYN  118 (380)
Q Consensus       104 i~g~~i~v~~~~~~~  118 (380)
                      |.|++|+|.|+...+
T Consensus        76 ~~g~~l~V~~A~~~~   90 (93)
T d1x5ua1          76 LYGKPIRVNKASAHN   90 (93)
T ss_dssp             CSSCBCEEEETTTTS
T ss_pred             ECCEEEEEEEcCCCC
Confidence            999999999987654

>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=99.68  E-value=1.3e-16  Score=117.05  Aligned_cols=77  Identities=27%  Similarity=0.399  Sum_probs=68.2

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec----CCCcEEEEEeCCHHHHHHHH-HcCCc
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN----HEKKFAFVEMRTVEEASNAM-ALDGI  102 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~----~~~g~afV~f~~~~~a~~ai-~l~~~  102 (380)
                      .+.+.++|||+|||+++++++|+++|++||.            |.++.+.    ..+|||||+|.+.++|.+|+ .+++.
T Consensus         4 d~~~~~tl~V~nLp~~~te~~l~~~F~~~G~------------i~~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~l~~~   71 (90)
T d2cqia1           4 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGP------------CKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGR   71 (90)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSC------------EEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCC------------ceeeeeecccCccceeeEEEECCHHHHHHHHHHcCCC
Confidence            3556789999999999999999999999998            6666653    35789999999999999999 79999


Q ss_pred             eecCceEEEecCCC
Q 016936          103 IFEGVAVRVRRPTD  116 (380)
Q Consensus       103 ~i~g~~i~v~~~~~  116 (380)
                      .+.|++|+|.|+..
T Consensus        72 ~~~g~~i~v~~a~~   85 (90)
T d2cqia1          72 KILGKEVKVNWATT   85 (90)
T ss_dssp             EETTEEEEEEECCC
T ss_pred             EECCEEEEEEEcCC
Confidence            99999999999764

>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=99.67  E-value=5.1e-17  Score=117.46  Aligned_cols=75  Identities=25%  Similarity=0.451  Sum_probs=65.7

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe------cCCCcEEEEEeCCHHHHHHHHHcCCc
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAMALDGI  102 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~------~~~~g~afV~f~~~~~a~~ai~l~~~  102 (380)
                      +...++|||+|||+++|+++|+++|++||.            |.++.+      ++++|||||+|.+.++|.+|+++++.
T Consensus         3 pe~~~~lfV~nlp~~~te~~l~~~F~~~G~------------i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~~~~~   70 (84)
T d1l3ka1           3 PEQLRKLFIGGLSFETTDESLRSHFEQWGT------------LTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPH   70 (84)
T ss_dssp             CGGGGEEEEESCCTTCCHHHHHHHHGGGSC------------EEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSC
T ss_pred             CCCCcEEEEECCCCCCCHHHHHHHHHhhcc------------ccceeecccccCCCcccEEEEEEcCHHHHHHHHHhCCC
Confidence            345689999999999999999999999998            555544      34679999999999999999988999


Q ss_pred             eecCceEEEecCC
Q 016936          103 IFEGVAVRVRRPT  115 (380)
Q Consensus       103 ~i~g~~i~v~~~~  115 (380)
                      .|.|+.|+|.++.
T Consensus        71 ~i~Gr~i~V~~A~   83 (84)
T d1l3ka1          71 KVDGRVVEPKRAV   83 (84)
T ss_dssp             EETTEECEEEECC
T ss_pred             EECCEEEEEEeee
Confidence            9999999998753

>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=99.67  E-value=1.1e-17  Score=117.46  Aligned_cols=71  Identities=23%  Similarity=0.452  Sum_probs=67.9

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEE
Q 016936          155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  225 (380)
Q Consensus       155 l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~  225 (380)
                      |||+|||.++++++|+++|++||.|..+++.+++.++.++|+|||+|.+.++|++|++.|||..+.|+.|+
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            79999999999999999999999999999999988999999999999999999999999999999998763

>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=99.67  E-value=1.2e-16  Score=120.54  Aligned_cols=86  Identities=13%  Similarity=0.227  Sum_probs=75.3

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEE
Q 016936          148 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  227 (380)
Q Consensus       148 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~  227 (380)
                      +......|||+|||+++++++|+++|+.+|.+....++.+..+++++|+|||+|.++++|++|++ +|+..|.|+.|+|.
T Consensus        11 ~~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~   89 (104)
T d1wg5a_          11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIF   89 (104)
T ss_dssp             SCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEE
Confidence            34445689999999999999999999999998876666665689999999999999999999997 79999999999999


Q ss_pred             EcccCCC
Q 016936          228 RATASSG  234 (380)
Q Consensus       228 ~~~~~~~  234 (380)
                      ++.....
T Consensus        90 ~~~~~~~   96 (104)
T d1wg5a_          90 KSSRAEV   96 (104)
T ss_dssp             EECTTTS
T ss_pred             ECCHHHh
Confidence            9876543

>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=2.4e-17  Score=126.28  Aligned_cols=78  Identities=21%  Similarity=0.155  Sum_probs=72.3

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceec
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE  105 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~  105 (380)
                      ...+..++|||+|||+++++++|+++|++||.            |..+.+.+++|||||+|.+.++|.+|+ .||+..|.
T Consensus         5 ~~~r~~~~l~V~nLp~~~t~~~L~~~F~~fG~------------I~~v~l~~~kg~afV~f~~~~~A~~A~~~lng~~~~   72 (111)
T d1whxa_           5 SSGRSKTVILAKNLPAGTLAAEIQETFSRFGS------------LGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKFH   72 (111)
T ss_dssp             GTSEEEEEEEEESCCTTCCHHHHHHHHHTTSC------------EEEEECCSSSSCEEEEESCHHHHHHHHHHHTTCBSS
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHhhhhccCC------------ccEEEeeccCceEEEEEcCHHHHHHHHHHHcCCccC
Confidence            44567789999999999999999999999997            888999999999999999999999999 89999999


Q ss_pred             CceEEEecCCC
Q 016936          106 GVAVRVRRPTD  116 (380)
Q Consensus       106 g~~i~v~~~~~  116 (380)
                      |++|+|.|+..
T Consensus        73 gr~l~v~~a~~   83 (111)
T d1whxa_          73 HVPLYLEWAPI   83 (111)
T ss_dssp             SSBCEEEEEET
T ss_pred             CCeEEEEECCC
Confidence            99999998754

>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=99.67  E-value=1.4e-16  Score=112.47  Aligned_cols=74  Identities=12%  Similarity=0.188  Sum_probs=68.1

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      ++|||+|||+.+++++|+++|+.||.|..+++..++.  ..+++|||+|.++++|++|+. ++++.|+|++|.|..+
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            3899999999999999999999999999999999853  446799999999999999996 7999999999999875

>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=99.67  E-value=4.5e-17  Score=117.13  Aligned_cols=78  Identities=15%  Similarity=0.377  Sum_probs=62.2

Q ss_pred             cceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecCceEE
Q 016936           32 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVR  110 (380)
Q Consensus        32 ~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g~~i~  110 (380)
                      .|||||+|||+++|+++|+++|++||.+...      ..+.+...++++|||||+|.+.++|.+|+ .+|+..+.|++|+
T Consensus         1 d~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~------~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~   74 (81)
T d2ghpa1           1 ECTLWMTNFPPSYTQRNIRDLLQDINVVALS------IRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLV   74 (81)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHHHTTCCCCE------EECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CcEEEEECCCCcCCHHHHHHHHHHhCcEEee------eeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            4899999999999999999999999985321      01222234567899999999999999999 7999999999999


Q ss_pred             EecCC
Q 016936          111 VRRPT  115 (380)
Q Consensus       111 v~~~~  115 (380)
                      |.++.
T Consensus        75 V~~a~   79 (81)
T d2ghpa1          75 TKVSN   79 (81)
T ss_dssp             EEECC
T ss_pred             EEEcc
Confidence            99864

>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=99.67  E-value=2.5e-17  Score=119.70  Aligned_cols=75  Identities=29%  Similarity=0.503  Sum_probs=69.7

Q ss_pred             ccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecCceE
Q 016936           31 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  109 (380)
Q Consensus        31 ~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g~~i  109 (380)
                      ..++|||+|||+++++++|+++|++||.            |.++.+.+++|||||+|.+.++|.+|+ .+|+..|.|++|
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~------------i~~i~~~~~k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l   74 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGK------------AGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQL   74 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCC------------CSEEEEETTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCC------------ceEeeeecccceEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            4578999999999999999999999997            778888899999999999999999999 799999999999


Q ss_pred             EEecCCCC
Q 016936          110 RVRRPTDY  117 (380)
Q Consensus       110 ~v~~~~~~  117 (380)
                      +|.|+...
T Consensus        75 ~V~~A~~~   82 (86)
T d2cpja1          75 RVRFACHS   82 (86)
T ss_dssp             EEEESSCC
T ss_pred             EEEECCCc
Confidence            99997654

>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=99.66  E-value=9.2e-17  Score=118.50  Aligned_cols=76  Identities=24%  Similarity=0.395  Sum_probs=67.5

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec------CCCcEEEEEeCCHHHHHHHH-HcCC
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN------HEKKFAFVEMRTVEEASNAM-ALDG  101 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~------~~~g~afV~f~~~~~a~~ai-~l~~  101 (380)
                      ...+|+|||+|||+.+|+++|+++|++||.            |.++.+.      .++|||||+|.+.++|..|+ .||+
T Consensus         4 ~~~s~tlfV~nlp~~~te~~l~~~F~~~G~------------i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g   71 (93)
T d1h2vz_           4 LKKSCTLYVGNLSFYTTEEQIYELFSKSGD------------IKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYING   71 (93)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSC------------EEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTT
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHHHCC------------cceeccccccccccccceEEEEECCHHHHHHHHHHhCC
Confidence            467899999999999999999999999997            5666653      34689999999999999999 7999


Q ss_pred             ceecCceEEEecCCC
Q 016936          102 IIFEGVAVRVRRPTD  116 (380)
Q Consensus       102 ~~i~g~~i~v~~~~~  116 (380)
                      ..+.|++|+|.|+..
T Consensus        72 ~~~~gr~i~V~~a~~   86 (93)
T d1h2vz_          72 TRLDDRIIRTDWDAG   86 (93)
T ss_dssp             SEETTEECEEEEESC
T ss_pred             CEECCEEEEEEEcCC
Confidence            999999999999654

>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=99.66  E-value=9.6e-17  Score=119.23  Aligned_cols=78  Identities=17%  Similarity=0.325  Sum_probs=71.3

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEccc
Q 016936          152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  231 (380)
Q Consensus       152 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~  231 (380)
                      .++|||+|||+++++++|+++|++||.|..+..     ++.++|||||+|.+.++|++|++.||+..+.|++|+|.++.+
T Consensus        16 ~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~-----~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~~   90 (96)
T d1fjca_          16 ARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE   90 (96)
T ss_dssp             GGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE-----TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcccceeeee-----cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            479999999999999999999999998876643     578899999999999999999999999999999999999987


Q ss_pred             CCC
Q 016936          232 SSG  234 (380)
Q Consensus       232 ~~~  234 (380)
                      +..
T Consensus        91 k~~   93 (96)
T d1fjca_          91 KGG   93 (96)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            644

>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=99.66  E-value=5e-16  Score=123.66  Aligned_cols=79  Identities=18%  Similarity=0.314  Sum_probs=68.2

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe------cCCCcEEEEEeCCHHHHHHHH-HcC
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-ALD  100 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~------~~~~g~afV~f~~~~~a~~ai-~l~  100 (380)
                      .....++|||+|||+++|+++|+++|++||.            |.++.+      ++++|||||+|.+.++|.+|+ .+|
T Consensus        38 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~------------i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~ln  105 (139)
T d1u6fa1          38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGP------------IESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLN  105 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSC------------EEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhcc------------ccccccccccccccccceeeEEECCHHHHHHHHHHhC
Confidence            3455678999999999999999999999998            555554      345799999999999999999 799


Q ss_pred             CceecCceEEEecCCCCC
Q 016936          101 GIIFEGVAVRVRRPTDYN  118 (380)
Q Consensus       101 ~~~i~g~~i~v~~~~~~~  118 (380)
                      +..|.|++|+|.++....
T Consensus       106 g~~~~gr~l~V~~a~~~~  123 (139)
T d1u6fa1         106 GFNILNKRLKVALAASGH  123 (139)
T ss_dssp             TEECSSCEEEEEESSCCC
T ss_pred             CCEECCEEEEEEEcCCCC
Confidence            999999999999976543

>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=99.66  E-value=7.7e-18  Score=119.60  Aligned_cols=76  Identities=12%  Similarity=0.243  Sum_probs=63.6

Q ss_pred             ceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHHHcCCceecCceEEEe
Q 016936           33 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVR  112 (380)
Q Consensus        33 ~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai~l~~~~i~g~~i~v~  112 (380)
                      |+|||+|||+++|+++|+++|++||.|...      ..+.+-..++++|||||+|.+.++|.+|++++++.+.|++|+|.
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            789999999999999999999999985321      11112223567899999999999999999989999999999998


Q ss_pred             cC
Q 016936          113 RP  114 (380)
Q Consensus       113 ~~  114 (380)
                      .+
T Consensus        75 ~A   76 (77)
T d1uawa_          75 VA   76 (77)
T ss_dssp             EC
T ss_pred             EC
Confidence            65

>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=99.66  E-value=1.5e-16  Score=118.35  Aligned_cols=75  Identities=21%  Similarity=0.454  Sum_probs=67.7

Q ss_pred             CCCCEEEEcCCC-CCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          150 EGPDRVFVGGLP-YYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       150 ~~~~~l~V~nlp-~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      ....+|||+||| ..+++++|+++|++||.|.+|++.        +|||||+|.+.++|++|++.|||..+.|++|+|.+
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~--------rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~   84 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH--------KGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINL   84 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE--------TEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe--------CCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            344689999996 578899999999999999999883        57999999999999999999999999999999999


Q ss_pred             cccC
Q 016936          229 ATAS  232 (380)
Q Consensus       229 ~~~~  232 (380)
                      +...
T Consensus        85 a~~~   88 (98)
T d1wf2a_          85 AAEP   88 (98)
T ss_dssp             TTSC
T ss_pred             CCCC
Confidence            8754

>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=99.66  E-value=9.6e-17  Score=117.84  Aligned_cols=76  Identities=28%  Similarity=0.519  Sum_probs=66.5

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe------cCCCcEEEEEeCCHHHHHHHH-HcCCc
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-ALDGI  102 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~------~~~~g~afV~f~~~~~a~~ai-~l~~~  102 (380)
                      .+.++|||+|||+++++++|+++|++||.|            ..+.+      +.++|||||+|.+.++|+.|+ .+++.
T Consensus         3 ~~~~kifV~nLp~~~t~~~l~~~F~~~G~i------------~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~   70 (90)
T d1x5sa1           3 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQI------------SEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGK   70 (90)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCC------------CEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTC
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhccccc------------cceeeccccccccccceEEEEECCHHHHHHHHHHcCCC
Confidence            467889999999999999999999999984            33332      346899999999999999999 79999


Q ss_pred             eecCceEEEecCCCC
Q 016936          103 IFEGVAVRVRRPTDY  117 (380)
Q Consensus       103 ~i~g~~i~v~~~~~~  117 (380)
                      .|.|++|+|.++...
T Consensus        71 ~~~g~~l~V~~a~~~   85 (90)
T d1x5sa1          71 SVDGRQIRVDQAGKS   85 (90)
T ss_dssp             CTTSCCCEEEEEECC
T ss_pred             EECCEEEEEEEcCCC
Confidence            999999999987554

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=9.5e-17  Score=114.90  Aligned_cols=75  Identities=19%  Similarity=0.319  Sum_probs=67.8

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCC-eeCCeEEEEEEccc
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGL-KMGDKTLTVRRATA  231 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~-~~~g~~i~v~~~~~  231 (380)
                      ++|||+|||.++++++|+++|++||.|..+++...      +|||||+|.+.++|++|++.|||. .+.|++|+|+++.+
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            47999999999999999999999999987766543      679999999999999999999996 69999999999987


Q ss_pred             CC
Q 016936          232 SS  233 (380)
Q Consensus       232 ~~  233 (380)
                      +.
T Consensus        76 k~   77 (80)
T d2cqha1          76 KK   77 (80)
T ss_dssp             CC
T ss_pred             cC
Confidence            53

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=1.1e-16  Score=116.70  Aligned_cols=77  Identities=16%  Similarity=0.231  Sum_probs=66.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      ..+++|||+|||.++++++|+++|++||. ..+.+      +.++|||||+|.+.++|++|+..||+..+.|++|+|+++
T Consensus         3 s~s~~i~V~nLp~~~t~~~l~~lF~~~G~-~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a   75 (88)
T d1wg1a_           3 SGSSGILVKNLPQDSNCQEVHDLLKDYDL-KYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQ   75 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSSCC-CCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCccChHHHHHHHHhcCc-eeeee------eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            34578999999999999999999999993 23333      445789999999999999999999999999999999998


Q ss_pred             ccCC
Q 016936          230 TASS  233 (380)
Q Consensus       230 ~~~~  233 (380)
                      ..+.
T Consensus        76 ~~~~   79 (88)
T d1wg1a_          76 PTDA   79 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6553

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=1.6e-16  Score=118.00  Aligned_cols=81  Identities=19%  Similarity=0.322  Sum_probs=72.5

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCC-eeEEEEeeCC-CCCCCceEEEEEEcChhHHHHHHHHhCC--CeeCCeEEEEEE
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGT-LHGFDLVKDR-DTGNSKGYGFCVYQDPAVTDIACAALNG--LKMGDKTLTVRR  228 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~-i~~v~l~~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g--~~~~g~~i~v~~  228 (380)
                      .+|||+|||..+++++|+++|++||. |..+.++++. .+++++|||||+|.+.++|.+|++.|++  ..+.|+.|+|.|
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 8999998874 4689999999999999999999999864  566899999999


Q ss_pred             cccCC
Q 016936          229 ATASS  233 (380)
Q Consensus       229 ~~~~~  233 (380)
                      |.+..
T Consensus        82 A~p~~   86 (96)
T d2disa1          82 AEPEI   86 (96)
T ss_dssp             SCSSC
T ss_pred             cCCCC
Confidence            97653

>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=99.66  E-value=3.7e-16  Score=117.56  Aligned_cols=84  Identities=15%  Similarity=0.260  Sum_probs=73.0

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecC
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  106 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g  106 (380)
                      +..++++|||+|||.++++++|+++|++||.+...      ..+.+...++++|||||+|.+.++|..|+ .+|+..|.|
T Consensus        14 ~~~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~------~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g   87 (102)
T d2cpxa1          14 PGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGP------PIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYG   87 (102)
T ss_dssp             CCSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSS------CCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhhccceeeE------EeecccccccccccceEEeccHHHHHHHHHHhCCCEECC
Confidence            34567999999999999999999999999998653      23444456788999999999999999999 799999999


Q ss_pred             ceEEEecCCCC
Q 016936          107 VAVRVRRPTDY  117 (380)
Q Consensus       107 ~~i~v~~~~~~  117 (380)
                      ++|+|.|+..+
T Consensus        88 ~~l~V~~ak~k   98 (102)
T d2cpxa1          88 KILVIEFGKNK   98 (102)
T ss_dssp             CBCEEEECCCC
T ss_pred             EEEEEEeCCCc
Confidence            99999998764

>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=99.65  E-value=1e-16  Score=122.72  Aligned_cols=75  Identities=19%  Similarity=0.170  Sum_probs=69.5

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccC
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  232 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~  232 (380)
                      ++|||+|||+.+++++|+++|++||.|..|.|..      ++|||||+|.+.++|++|++.|||..|.|++|.|.|+...
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            5899999999999999999999999999998843      4689999999999999999999999999999999998765


Q ss_pred             C
Q 016936          233 S  233 (380)
Q Consensus       233 ~  233 (380)
                      .
T Consensus        85 ~   85 (111)
T d1whxa_          85 V   85 (111)
T ss_dssp             T
T ss_pred             c
Confidence            4

>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=99.65  E-value=2.7e-16  Score=113.40  Aligned_cols=73  Identities=21%  Similarity=0.338  Sum_probs=67.4

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCee-CCeEEEEEEcc
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM-GDKTLTVRRAT  230 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~-~g~~i~v~~~~  230 (380)
                      ++|||+|||..+++++|+++|++||.|..|++.++     .+|||||+|.+.++|..|+..|+|..+ +|++|+|.|++
T Consensus         9 ~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~ak   82 (83)
T d2b0ga1           9 QILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN-----RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAK   82 (83)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT-----TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEECC
T ss_pred             CEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc-----cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEec
Confidence            69999999999999999999999999999999754     367999999999999999999999988 56899999985

>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=99.65  E-value=9.2e-17  Score=123.49  Aligned_cols=74  Identities=18%  Similarity=0.219  Sum_probs=66.3

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe---cCCCcEEEEEeCCHHHHHHHH-HcCCceec
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI---NHEKKFAFVEMRTVEEASNAM-ALDGIIFE  105 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~---~~~~g~afV~f~~~~~a~~ai-~l~~~~i~  105 (380)
                      ..+++|||+|||.++++++|+++|++||.            |.++.+   ..++|||||+|.+.++|..|+ .|||..|.
T Consensus         5 ~~~r~l~V~nLp~~~te~~l~~~F~~~G~------------v~~i~~~~~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~   72 (114)
T d2f9da1           5 EVNRILYIRNLPYKITAEEMYDIFGKYGP------------IRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVC   72 (114)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSC------------EEEEEEECSTTTTTEEEEEESSHHHHHHHHHHHTTCEET
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCC------------eEeecccccCCcCCeEEEEECCHHHHHHHHHHhCCCEEC
Confidence            45789999999999999999999999998            555554   456899999999999999999 89999999


Q ss_pred             CceEEEecCC
Q 016936          106 GVAVRVRRPT  115 (380)
Q Consensus       106 g~~i~v~~~~  115 (380)
                      |++|+|.++.
T Consensus        73 gr~l~V~~a~   82 (114)
T d2f9da1          73 NRYLVVLYYN   82 (114)
T ss_dssp             TEECEEEECC
T ss_pred             CEEEEEEEcC
Confidence            9999999864

>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=99.65  E-value=2e-16  Score=120.60  Aligned_cols=77  Identities=17%  Similarity=0.271  Sum_probs=70.1

Q ss_pred             CCEEEEcCCC-CCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          152 PDRVFVGGLP-YYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       152 ~~~l~V~nlp-~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      +++|||+||| ..+++++|+++|+.||.|..|.+++++     +|||||+|.+.++|.+|++.|+|..+.|+.|+|.++.
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            3699999995 569999999999999999999998763     6899999999999999999999999999999999986


Q ss_pred             cCC
Q 016936          231 ASS  233 (380)
Q Consensus       231 ~~~  233 (380)
                      ...
T Consensus        77 ~~~   79 (109)
T d2adca1          77 HQN   79 (109)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=99.65  E-value=3.7e-17  Score=117.08  Aligned_cols=73  Identities=19%  Similarity=0.337  Sum_probs=64.4

Q ss_pred             ceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCc-eecCceEE
Q 016936           33 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGI-IFEGVAVR  110 (380)
Q Consensus        33 ~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~-~i~g~~i~  110 (380)
                      .+|||+|||.++|+++|+++|++||.+            .+..+.+++|||||+|.+.++|.+|+ .+||. .+.|++|+
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            579999999999999999999999974            44444567899999999999999999 79986 59999999


Q ss_pred             EecCCCC
Q 016936          111 VRRPTDY  117 (380)
Q Consensus       111 v~~~~~~  117 (380)
                      |.|+.++
T Consensus        70 V~~a~~k   76 (80)
T d2cqha1          70 VDYSVSK   76 (80)
T ss_dssp             EEECCCC
T ss_pred             EEEcCCc
Confidence            9997764

>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=99.65  E-value=2.5e-16  Score=112.11  Aligned_cols=70  Identities=19%  Similarity=0.269  Sum_probs=63.3

Q ss_pred             eEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec-----CCCcEEEEEeCCHHHHHHHH-HcCCceecCc
Q 016936           34 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN-----HEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  107 (380)
Q Consensus        34 ~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~-----~~~g~afV~f~~~~~a~~ai-~l~~~~i~g~  107 (380)
                      +|||+|||+++++++|+++|++||.            |.++.+.     +++|||||+|.+.++|.+|+ .+|+..+.|+
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 KLLVSNLDFGVSDADIQELFAEFGT------------LKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGR   69 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSC------------EEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTE
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCC------------CeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            6999999999999999999999998            6666654     45789999999999999999 7999999999


Q ss_pred             eEEEecCC
Q 016936          108 AVRVRRPT  115 (380)
Q Consensus       108 ~i~v~~~~  115 (380)
                      +|+|.++.
T Consensus        70 ~l~V~~a~   77 (78)
T d1no8a_          70 PMNIQLVT   77 (78)
T ss_dssp             ECEEEEEC
T ss_pred             EEEEEEee
Confidence            99998754

>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=99.65  E-value=1.3e-16  Score=115.05  Aligned_cols=73  Identities=18%  Similarity=0.306  Sum_probs=64.8

Q ss_pred             cceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec------CCCcEEEEEeCCHHHHHHHH-HcCCcee
Q 016936           32 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN------HEKKFAFVEMRTVEEASNAM-ALDGIIF  104 (380)
Q Consensus        32 ~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~------~~~g~afV~f~~~~~a~~ai-~l~~~~i  104 (380)
                      .++|||+|||+++|+++|+++|++||.            |.++.+.      .++|||||+|.+.++|++|+ .||+..+
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~------------v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~   69 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGP------------INTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITV   69 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSC------------EEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCC------------cceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEE
Confidence            578999999999999999999999998            5555542      34789999999999999999 7999999


Q ss_pred             cCceEEEecCCC
Q 016936          105 EGVAVRVRRPTD  116 (380)
Q Consensus       105 ~g~~i~v~~~~~  116 (380)
                      .|++|+|.|+.+
T Consensus        70 ~g~~l~v~~a~p   81 (82)
T d1b7fa1          70 RNKRLKVSYARP   81 (82)
T ss_dssp             TTEECEEEECCC
T ss_pred             CCEEEEEEEcCC
Confidence            999999999653

>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=99.65  E-value=3.1e-17  Score=123.28  Aligned_cols=80  Identities=18%  Similarity=0.245  Sum_probs=66.9

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEE---EecCCCcEEEEEeCCHHHHHHHH-HcCCceec
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNV---YINHEKKFAFVEMRTVEEASNAM-ALDGIIFE  105 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~---~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~  105 (380)
                      .+.++|||+|||+++++++|+++|++||.+..         +..+   ..+.++|||||+|.+.++|..|+ .+|+..|.
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~---------~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~   86 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVS---------AKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIG   86 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSE---------EEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccc---------cceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEEC
Confidence            34678999999999999999999999998432         2212   12356799999999999999999 79999999


Q ss_pred             CceEEEecCCCCC
Q 016936          106 GVAVRVRRPTDYN  118 (380)
Q Consensus       106 g~~i~v~~~~~~~  118 (380)
                      |++|+|.|+..++
T Consensus        87 g~~i~V~~a~~k~   99 (102)
T d2cpza1          87 MKRLKVQLKRSKN   99 (102)
T ss_dssp             TEECEEECCCCSC
T ss_pred             CEEEEEEEeCCCC
Confidence            9999999977654

>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=99.65  E-value=3.2e-17  Score=120.08  Aligned_cols=82  Identities=22%  Similarity=0.339  Sum_probs=67.1

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecCce
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  108 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g~~  108 (380)
                      ...++|||+|||+++++++|+++|++||.|....      .+.+...+.++|||||+|.+.++|++|+ .+++..+.|++
T Consensus         3 ~~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~------i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~   76 (89)
T d2cqba1           3 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQ------IPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRT   76 (89)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEE------CCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEE
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecc------cccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEE
Confidence            3568999999999999999999999999843210      1111123467899999999999999999 79999999999


Q ss_pred             EEEecCCCC
Q 016936          109 VRVRRPTDY  117 (380)
Q Consensus       109 i~v~~~~~~  117 (380)
                      |+|.++.+.
T Consensus        77 l~v~~a~p~   85 (89)
T d2cqba1          77 IRVNLAKPM   85 (89)
T ss_dssp             EEEEECCCC
T ss_pred             EEEEEeCCC
Confidence            999997643

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=2.3e-16  Score=112.61  Aligned_cols=74  Identities=23%  Similarity=0.369  Sum_probs=67.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      ..++|||+|++  +|+++|+++|++||.|.++++.++      +|||||+|.+.++|.+|+..|||..+.|++|+|.|+.
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            34799999996  899999999999999999998654      5699999999999999999999999999999999997


Q ss_pred             cC
Q 016936          231 AS  232 (380)
Q Consensus       231 ~~  232 (380)
                      ++
T Consensus        76 ~~   77 (79)
T d2bz2a1          76 KQ   77 (79)
T ss_dssp             SS
T ss_pred             CC
Confidence            54

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.65  E-value=1.7e-16  Score=117.25  Aligned_cols=77  Identities=22%  Similarity=0.351  Sum_probs=67.8

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe-------cCCCcEEEEEeCCHHHHHHHH-Hc-
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-------NHEKKFAFVEMRTVEEASNAM-AL-   99 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~-------~~~~g~afV~f~~~~~a~~ai-~l-   99 (380)
                      ...+++|||+|||+++++++|+++|++||.            |.++.+       +.++|||||+|.+.++|.+|+ .| 
T Consensus         5 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~------------i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~   72 (94)
T d2cpha1           5 KQTTSKILVRNIPFQANQREIRELFSTFGE------------LKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALC   72 (94)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSC------------EEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCC------------ceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHcc
Confidence            356788999999999999999999999997            666665       245799999999999999999 67 


Q ss_pred             CCceecCceEEEecCCCC
Q 016936          100 DGIIFEGVAVRVRRPTDY  117 (380)
Q Consensus       100 ~~~~i~g~~i~v~~~~~~  117 (380)
                      |+..|.|++|+|.|+...
T Consensus        73 ~~~~~~Gr~l~V~~A~~~   90 (94)
T d2cpha1          73 HSTHLYGRRLVLEWADSE   90 (94)
T ss_dssp             TCCBSSSCBCEEEECCCC
T ss_pred             CCcEECCEEEEEEEcCCC
Confidence            899999999999997654

>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=99.65  E-value=7.8e-17  Score=116.74  Aligned_cols=76  Identities=21%  Similarity=0.306  Sum_probs=66.6

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe-----cCCCcEEEEEeCCHHHHHHHHHcCCce
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-----NHEKKFAFVEMRTVEEASNAMALDGII  103 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~-----~~~~g~afV~f~~~~~a~~ai~l~~~~  103 (380)
                      +...++|||+|||.++|+++|+++|++||.            |.++.+     +.++|||||+|.+.++|.+|+++++..
T Consensus         3 ~~~~rtvfV~nlp~~~te~~l~~~F~~~G~------------v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~~~~~~   70 (85)
T d1zh5a2           3 DVKNRSVYIKGFPTDATLDDIKEWLEDKGQ------------VLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQK   70 (85)
T ss_dssp             HHHTTEEEEECCCTTCCHHHHHHHHTTSCC------------EEEEEEEECTTCCEEEEEEEEESCHHHHHHHHTCCCCE
T ss_pred             CCCcCEEEEECCCCCCCHHHHHHHHHHhcc------------cccceeeeeccCCcceEEEEEEcCHHHHHHHHHHCCCE
Confidence            456789999999999999999999999998            445544     234689999999999999999999999


Q ss_pred             ecCceEEEecCCC
Q 016936          104 FEGVAVRVRRPTD  116 (380)
Q Consensus       104 i~g~~i~v~~~~~  116 (380)
                      +.|++|.|.|..+
T Consensus        71 ~~g~~l~v~~~~d   83 (85)
T d1zh5a2          71 YKETDLLILFKDD   83 (85)
T ss_dssp             ETTEECEEEEGGG
T ss_pred             ECCEEEEEEEcCC
Confidence            9999999998654

>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=3.6e-16  Score=117.85  Aligned_cols=81  Identities=17%  Similarity=0.139  Sum_probs=71.8

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-Hc--CCce
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-AL--DGII  103 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l--~~~~  103 (380)
                      ....++++|||+|||.+++++||+++|++||.            |..+.+.+.+++|||+|.+.++|+.|+ .+  ++..
T Consensus        10 ~~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~------------I~~~~~~~~k~~AfV~f~~~e~A~~ai~~~~~~~~~   77 (104)
T d1wexa_          10 HKVSVSPVVHVRGLCESVVEADLVEALEKFGT------------ICYVMMMPFKRQALVEFENIDSAKECVTFAADVPVY   77 (104)
T ss_dssp             CCCCCCSEEEEESCCSSCCHHHHHHHHTTTSC------------EEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCB
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHhhhhccc------------ceEEEEEecceeEEEEeCCHHHHHHHHHHHcCCCcE
Confidence            34467899999999999999999999999997            788888999999999999999999999 55  5677


Q ss_pred             ecCceEEEecCCCCCc
Q 016936          104 FEGVAVRVRRPTDYNP  119 (380)
Q Consensus       104 i~g~~i~v~~~~~~~~  119 (380)
                      +.|++|+|.++..++.
T Consensus        78 ~~g~~l~v~~s~~~~~   93 (104)
T d1wexa_          78 IAGQQAFFNYSTSKRI   93 (104)
T ss_dssp             SSSSBCEEEECSSSSC
T ss_pred             EeeEEEEEEEcCCCcc
Confidence            8999999999876543

>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=99.64  E-value=3.8e-16  Score=114.02  Aligned_cols=76  Identities=13%  Similarity=0.103  Sum_probs=68.3

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCee-CCeEEEEEEccc
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM-GDKTLTVRRATA  231 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~-~g~~i~v~~~~~  231 (380)
                      ++|||+|||.++++++|+++|++||.|..+.+..    +.++|+|||+|.+.++|.+|+..|+|..+ .|+.|+|.+++.
T Consensus        11 ~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~----~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk~   86 (88)
T d2adca2          11 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF----QKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS   86 (88)
T ss_dssp             SEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEEC----SSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSS
T ss_pred             CEEEEECCCCCCCHHHHHHHhhccCCEEEEEEee----ecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCCC
Confidence            6899999999999999999999999998887654    34578999999999999999999999988 589999999865


Q ss_pred             C
Q 016936          232 S  232 (380)
Q Consensus       232 ~  232 (380)
                      +
T Consensus        87 ~   87 (88)
T d2adca2          87 T   87 (88)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.64  E-value=8.1e-17  Score=115.02  Aligned_cols=74  Identities=23%  Similarity=0.385  Sum_probs=68.1

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecCc
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  107 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g~  107 (380)
                      ++..++|||+||+  +|+++|+++|++||.            |.++.+.+.+|||||+|.+.++|..|+ .+|+..+.|+
T Consensus         2 p~~~~ti~V~~~~--~te~~L~~~F~~~G~------------I~~v~~~~~~~~afV~f~~~~~A~~Ai~~lng~~~~g~   67 (79)
T d2bz2a1           2 PRKGNTLYVYGED--MTPTLLRGAFSPFGN------------IIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESV   67 (79)
T ss_dssp             CCCCCEEEEECSS--CCHHHHHHHHSTTCC------------CSCEEEETTTTEEEEECSSHHHHHHHHHHHTTCBCSSC
T ss_pred             CCCCCEEEEECCC--CCHHHHHHHHhccCc------------cceeeeccCCCEEEEEEcccHHHHHHHHHhCCCEECCE
Confidence            4567899999995  999999999999998            677888899999999999999999999 8999999999


Q ss_pred             eEEEecCCC
Q 016936          108 AVRVRRPTD  116 (380)
Q Consensus       108 ~i~v~~~~~  116 (380)
                      +|+|.|+..
T Consensus        68 ~l~V~~a~~   76 (79)
T d2bz2a1          68 QLKVNIARK   76 (79)
T ss_dssp             BCEEEECCS
T ss_pred             EEEEEEecC
Confidence            999999754

>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=99.64  E-value=1.4e-16  Score=118.16  Aligned_cols=77  Identities=29%  Similarity=0.494  Sum_probs=67.5

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe---cCCCcEEEEEeCCHHHHHHHH-HcCCcee
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI---NHEKKFAFVEMRTVEEASNAM-ALDGIIF  104 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~---~~~~g~afV~f~~~~~a~~ai-~l~~~~i  104 (380)
                      ..+.++|||+|||+++|+++|+++|++||.            |..+.+   ..+++||||+|.+.++|+.|| .||+..|
T Consensus        11 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~------------v~~~~~~~~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~   78 (95)
T d1x4aa1          11 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGA------------IRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDY   78 (95)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSC------------EEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhcCCc------------eEEEEecccccccceEEEEECCHHHHHHHHHHhCCCEE
Confidence            355689999999999999999999999997            455544   456899999999999999999 7999999


Q ss_pred             cCceEEEecCCCC
Q 016936          105 EGVAVRVRRPTDY  117 (380)
Q Consensus       105 ~g~~i~v~~~~~~  117 (380)
                      .|++|+|.|+...
T Consensus        79 ~g~~l~V~~a~~~   91 (95)
T d1x4aa1          79 DGYRLRVEFPRSG   91 (95)
T ss_dssp             TTEECEEECCCCC
T ss_pred             CCEEEEEEeccCC
Confidence            9999999997653

>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=99.64  E-value=3.2e-16  Score=117.08  Aligned_cols=78  Identities=26%  Similarity=0.361  Sum_probs=68.9

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec------CCCcEEEEEeCCHHHHHHHH-HcCC
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN------HEKKFAFVEMRTVEEASNAM-ALDG  101 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~------~~~g~afV~f~~~~~a~~ai-~l~~  101 (380)
                      +..+++|||+|||+++++++|+++|++||.            |.++.+.      .++|||||+|.+.++|.+|+ .||+
T Consensus         5 ~~~~~~lfV~nL~~~~t~~~l~~~F~~~g~------------v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g   72 (99)
T d1whwa_           5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGP------------LSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDG   72 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSC------------EEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTT
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCC------------ceeeeecccccccccCcceEEEECCHHHHHHHHHHcCC
Confidence            356788999999999999999999999987            6666653      45789999999999999999 7999


Q ss_pred             ceecCceEEEecCCCCC
Q 016936          102 IIFEGVAVRVRRPTDYN  118 (380)
Q Consensus       102 ~~i~g~~i~v~~~~~~~  118 (380)
                      ..|.|++|+|.++..+.
T Consensus        73 ~~~~gr~i~V~~a~~~~   89 (99)
T d1whwa_          73 QVFQGRMLHVLPSTIKK   89 (99)
T ss_dssp             EESSSCEEEEEECCCCS
T ss_pred             CEECCEEEEEEECCCCC
Confidence            99999999999977653

>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=99.64  E-value=1.9e-16  Score=116.39  Aligned_cols=77  Identities=14%  Similarity=0.383  Sum_probs=69.9

Q ss_pred             CEEEEcCCCCCCCHHHHH----HHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          153 DRVFVGGLPYYFTETQIK----ELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~----~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      ++|||+|||+.+++++|+    ++|++||.|.+|++.+   ++.++|||||+|.+.++|.+|++.+||..+.|+.|+|.+
T Consensus         4 ~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~   80 (91)
T d1nu4a_           4 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY   80 (91)
T ss_dssp             SEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            699999999999999886    4689999999998865   367889999999999999999999999999999999999


Q ss_pred             cccC
Q 016936          229 ATAS  232 (380)
Q Consensus       229 ~~~~  232 (380)
                      +..+
T Consensus        81 ak~~   84 (91)
T d1nu4a_          81 AKTD   84 (91)
T ss_dssp             CSSC
T ss_pred             eCCC
Confidence            9754

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=3e-17  Score=120.55  Aligned_cols=86  Identities=49%  Similarity=0.868  Sum_probs=74.7

Q ss_pred             cceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHHHcCCceecCceEEE
Q 016936           32 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRV  111 (380)
Q Consensus        32 ~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai~l~~~~i~g~~i~v  111 (380)
                      .|+|||+|||+++|+++|+++|++||.+...... ....+.+....+++|||||+|.+.++|++|+++|+..+.|++|+|
T Consensus         1 aRrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~-~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~l~g~~~~Gr~l~V   79 (90)
T d1u2fa_           1 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQA-PGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKI   79 (90)
T ss_dssp             CCEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCS-SSCSEEECCEETTTTEEEEEESSCTTTTTGGGGSSCCSSSSCCCC
T ss_pred             CCEEEEcCCCCccchHHHHHHHHhhCcEEEEEEe-ccceeeecccCCCceEEEEEeCCHHHHHHHHhhCCcEECCEEEEE
Confidence            4899999999999999999999999998765432 233466777788999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 016936          112 RRPTDYN  118 (380)
Q Consensus       112 ~~~~~~~  118 (380)
                      .++.+++
T Consensus        80 ~r~k~~~   86 (90)
T d1u2fa_          80 RRPHDYQ   86 (90)
T ss_dssp             BCTTCCS
T ss_pred             CCCCCCC
Confidence            9877664

>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=99.64  E-value=2.4e-16  Score=113.58  Aligned_cols=72  Identities=15%  Similarity=0.322  Sum_probs=63.8

Q ss_pred             cceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec------CCCcEEEEEeCCHHHHHHHH-HcCCcee
Q 016936           32 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN------HEKKFAFVEMRTVEEASNAM-ALDGIIF  104 (380)
Q Consensus        32 ~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~------~~~g~afV~f~~~~~a~~ai-~l~~~~i  104 (380)
                      .++|||+|||+++++++|+++|++||.            |.++.+.      +++|||||+|.+.++|++|+ .+++..|
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~------------v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~   69 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGE------------IESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRL   69 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSC------------EEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCC------------cccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEE
Confidence            357999999999999999999999997            5555542      45689999999999999999 7999999


Q ss_pred             cCceEEEecCC
Q 016936          105 EGVAVRVRRPT  115 (380)
Q Consensus       105 ~g~~i~v~~~~  115 (380)
                      .|++|+|.|+.
T Consensus        70 ~g~~l~v~~Ak   80 (82)
T d1fxla1          70 QTKTIKVSYAR   80 (82)
T ss_dssp             TTEECEEEECC
T ss_pred             CCEEEEEEEee
Confidence            99999999965

>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=99.64  E-value=1.2e-16  Score=116.72  Aligned_cols=76  Identities=24%  Similarity=0.276  Sum_probs=66.1

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe------cCCCcEEEEEeCCHHHHHHHH-HcCC
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-ALDG  101 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~------~~~~g~afV~f~~~~~a~~ai-~l~~  101 (380)
                      +.+.++|||+|||.++|+++|+++|++||.            |.++++      ++++|||||+|.+.++|++|+ .+|+
T Consensus         4 s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~------------i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng   71 (88)
T d1rk8a_           4 SVEGWILFVTSIHEEAQEDEIQEKFCDYGE------------IKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNG   71 (88)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSC------------EEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCC------------cccccccccccccccccceeEEECCHHHHHHHHHHcCC
Confidence            456789999999999999999999999998            555544      245789999999999999999 7999


Q ss_pred             ceecCceEEEecCCC
Q 016936          102 IIFEGVAVRVRRPTD  116 (380)
Q Consensus       102 ~~i~g~~i~v~~~~~  116 (380)
                      ..+.|++|+|.|+..
T Consensus        72 ~~l~g~~l~V~~a~~   86 (88)
T d1rk8a_          72 AEIMGQTIQVDWCFV   86 (88)
T ss_dssp             CEETTEECEEEESEE
T ss_pred             CEECCEEEEEEEecC
Confidence            999999999999753

>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=1.2e-16  Score=116.68  Aligned_cols=79  Identities=18%  Similarity=0.400  Sum_probs=69.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      ..+++|||+|||+.+++++|+++|++||.|..|++.     ..++|||||+|.+.++|++|+.  +++.+.|++|+|.++
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~-----~~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a   75 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIP-----KPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNA   75 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECC-----SSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEe-----eccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeC
Confidence            345799999999999999999999999999999874     3457899999999999999985  788999999999999


Q ss_pred             ccCCCC
Q 016936          230 TASSGQ  235 (380)
Q Consensus       230 ~~~~~~  235 (380)
                      .++...
T Consensus        76 ~~k~~~   81 (88)
T d1wf0a_          76 EPKHNS   81 (88)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            776443

>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=99.64  E-value=1.6e-16  Score=114.65  Aligned_cols=70  Identities=27%  Similarity=0.411  Sum_probs=62.0

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe------cCCCcEEEEEeCCHHHHHHHH-HcCCc
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-ALDGI  102 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~------~~~~g~afV~f~~~~~a~~ai-~l~~~  102 (380)
                      .+.++|||+|||+.+|+++|+++|++||.            |.++.+      ++++|||||+|.+.++|.+|+ .+++.
T Consensus         7 ~~~~~l~V~nL~~~~te~~l~~~F~~~G~------------i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~   74 (83)
T d2cqca1           7 DPNCCLGVFGLSLYTTERDLREVFSKYGP------------IADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGM   74 (83)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSC------------EEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCC------------CccccccccccccccccceEEEECCHHHHHHHHHHcCCC
Confidence            35689999999999999999999999998            555554      345789999999999999999 79999


Q ss_pred             eecCceEEE
Q 016936          103 IFEGVAVRV  111 (380)
Q Consensus       103 ~i~g~~i~v  111 (380)
                      .|.|++|+|
T Consensus        75 ~~~gr~i~V   83 (83)
T d2cqca1          75 ELDGRRIRV   83 (83)
T ss_dssp             EETTEEEEE
T ss_pred             EECCEEeEC
Confidence            999999987

>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=99.64  E-value=9.5e-17  Score=119.28  Aligned_cols=80  Identities=18%  Similarity=0.268  Sum_probs=69.6

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEE-EecCCCcEEEEEeCCHHHHHHHH-HcCCcee
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNV-YINHEKKFAFVEMRTVEEASNAM-ALDGIIF  104 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~-~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i  104 (380)
                      ...++.++|||+|||.++|+++|+++|++||.+            ..+ ...+++|||||+|.+.++|.+|+ .||+..|
T Consensus        11 ~~~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v------------~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~   78 (96)
T d1fjca_          11 KKVRAARTLLAKNLSFNITEDELKEVFEDALEI------------RLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEI   78 (96)
T ss_dssp             STTTGGGEEEEESCCSSCCHHHHHHHHCSEEEE------------CCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEE
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHHHHhcccc------------eeeeecCccccEEEEEeCCHHHHHHHHHHcCCCEE
Confidence            445678999999999999999999999999974            223 34567899999999999999999 7999999


Q ss_pred             cCceEEEecCCCCC
Q 016936          105 EGVAVRVRRPTDYN  118 (380)
Q Consensus       105 ~g~~i~v~~~~~~~  118 (380)
                      .|++|+|.|+..+.
T Consensus        79 ~gr~i~V~~a~~k~   92 (96)
T d1fjca_          79 DGRSVSLYYTGEKG   92 (96)
T ss_dssp             TTEEEEEEECSSSC
T ss_pred             CCEEEEEEEeCCCC
Confidence            99999999977653

>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=99.64  E-value=3.5e-16  Score=115.40  Aligned_cols=79  Identities=24%  Similarity=0.398  Sum_probs=69.6

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec----CCCcEEEEEeCCHHHHHHHH-HcCC
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN----HEKKFAFVEMRTVEEASNAM-ALDG  101 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~----~~~g~afV~f~~~~~a~~ai-~l~~  101 (380)
                      +.....++|||+|||+.+++++|+++|++||.            |..+.+.    .++|||||+|.+.++|.+|+ .+|+
T Consensus         6 ~~~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~------------v~~v~~~~~~~~~kg~afV~f~~~~~a~~Ai~~l~~   73 (93)
T d2cq3a1           6 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGK------------ILDVEIIFNERGSKGFGFVTFENSADADRAREKLHG   73 (93)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHGGGTSC------------EEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTT
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHhhcce------------eeeccccccccCCcceeEEEECCHHHHHHHHHHcCC
Confidence            45567789999999999999999999999997            6666543    34789999999999999999 7999


Q ss_pred             ceecCceEEEecCCCC
Q 016936          102 IIFEGVAVRVRRPTDY  117 (380)
Q Consensus       102 ~~i~g~~i~v~~~~~~  117 (380)
                      ..|.|++|+|.++..+
T Consensus        74 ~~~~g~~l~V~~A~~r   89 (93)
T d2cq3a1          74 TVVEGRKIEVNNATAR   89 (93)
T ss_dssp             CEETTEECEEEECCSS
T ss_pred             CEECCEEEEEEecCcC
Confidence            9999999999997654

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=3.3e-16  Score=117.58  Aligned_cols=82  Identities=16%  Similarity=0.189  Sum_probs=72.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      .....+|||+|||+++|+++|+++|+.||. ..+.++.+. ++.++|||||+|.+.++|++|++ +|+..|.||.|+|.+
T Consensus        12 ~~~~~~v~v~nLp~~~te~dl~~~F~~~~~-~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~   88 (102)
T d1weza_          12 STTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFL   88 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHhccCc-ceeeeEEec-CCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEE
Confidence            344579999999999999999999999985 467788775 58999999999999999999987 799999999999999


Q ss_pred             cccCC
Q 016936          229 ATASS  233 (380)
Q Consensus       229 ~~~~~  233 (380)
                      +....
T Consensus        89 s~~~~   93 (102)
T d1weza_          89 NSTAG   93 (102)
T ss_dssp             ECCCC
T ss_pred             cCCCC
Confidence            87653

>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=99.63  E-value=2.4e-16  Score=111.31  Aligned_cols=69  Identities=20%  Similarity=0.436  Sum_probs=61.9

Q ss_pred             eEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe------cCCCcEEEEEeCCHHHHHHHHHcCCceecCc
Q 016936           34 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAMALDGIIFEGV  107 (380)
Q Consensus        34 ~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~------~~~~g~afV~f~~~~~a~~ai~l~~~~i~g~  107 (380)
                      +|||+|||+++|+++|+++|++||.            |.++.+      ++++|||||+|.+.++|++|+++++..|.|+
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~------------i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~~~~~~l~Gr   68 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGE------------VVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEHKLNGK   68 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSC------------EEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHHTCCCCBTTB
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhcc------------ccccccccCCCCCCcCceEEEEECCHHHHHHHHhcCCCEECCC
Confidence            5999999999999999999999998            666665      3467999999999999999999899999999


Q ss_pred             eEEEecC
Q 016936          108 AVRVRRP  114 (380)
Q Consensus       108 ~i~v~~~  114 (380)
                      +|+|..+
T Consensus        69 ~i~V~rA   75 (75)
T d1hd0a_          69 VIDPKRA   75 (75)
T ss_dssp             CCEECCC
T ss_pred             EEEeeEC
Confidence            9999753

>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=99.63  E-value=2.3e-16  Score=113.76  Aligned_cols=77  Identities=22%  Similarity=0.314  Sum_probs=67.5

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecC-CCcEEEEEeCCHHHHHHHH-HcCCcee
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH-EKKFAFVEMRTVEEASNAM-ALDGIIF  104 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~-~~g~afV~f~~~~~a~~ai-~l~~~~i  104 (380)
                      ....++++|||+|||..+++++|+++|++||.            |..+++.+ .+|||||+|.+.++|..|+ .|+|..|
T Consensus         3 ~~~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~------------i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~   70 (83)
T d2b0ga1           3 TEQPPNQILFLTNLPEETNEMMLSMLFNQFPG------------FKEVRLVPNRHDIAFVEFTTELQSNAAKEALQGFKI   70 (83)
T ss_dssp             CCCSCCSEEEEESCCTTCCHHHHHHHHTTSTT------------EEEEEECTTTCSCEEEEESSHHHHHHHHHHHTTCBS
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHhhhccCcc------------EEEeeeecccceeEEEecCCHHHHHHHHHHhCCcEe
Confidence            34456799999999999999999999999998            77777654 5689999999999999999 7999888


Q ss_pred             c-CceEEEecCC
Q 016936          105 E-GVAVRVRRPT  115 (380)
Q Consensus       105 ~-g~~i~v~~~~  115 (380)
                      . |++|+|.|++
T Consensus        71 ~~~~~i~v~~ak   82 (83)
T d2b0ga1          71 TPTHAMKITFAK   82 (83)
T ss_dssp             STTCBCEEEECC
T ss_pred             CCCcEEEEEEec
Confidence            5 6899999964

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.63  E-value=3.1e-16  Score=110.57  Aligned_cols=69  Identities=19%  Similarity=0.290  Sum_probs=64.4

Q ss_pred             EEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecCceEEEec
Q 016936           35 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRR  113 (380)
Q Consensus        35 v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g~~i~v~~  113 (380)
                      |||+|||+++++++|+++|++||             +..+.+.+++|||||+|.+.++|++|+ .+|+..+.|++|+|.+
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 8999999999999999


Q ss_pred             CCC
Q 016936          114 PTD  116 (380)
Q Consensus       114 ~~~  116 (380)
                      +..
T Consensus        68 a~~   70 (75)
T d1wi6a1          68 QPT   70 (75)
T ss_dssp             CCS
T ss_pred             eCC
Confidence            754

>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=99.63  E-value=1.9e-16  Score=114.99  Aligned_cols=75  Identities=13%  Similarity=0.224  Sum_probs=65.2

Q ss_pred             cccceEEEcCCCCcCc-HHHHHHHHHHHHHhccCCCCCCCCeeEEEEe-------cCCCcEEEEEeCCHHHHHHHHHcCC
Q 016936           30 RHARRVYVGGLPPLAN-EQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-------NHEKKFAFVEMRTVEEASNAMALDG  101 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t-~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~-------~~~~g~afV~f~~~~~a~~ai~l~~  101 (380)
                      .+.++|||+|||++++ +++|+++|++||.            |.++.+       .+++|||||+|.+.++|++|+++|+
T Consensus         2 ~e~~~l~V~nLp~~~t~ed~l~~~F~~~G~------------i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~~n~   69 (86)
T d2ghpa3           2 LEGREIMIRNLSTELLDENLLRESFEGFGS------------IEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQMNR   69 (86)
T ss_dssp             CTTTEEEEEEECTTTCCHHHHHHHHGGGSC------------EEEEECCSCCC---CCCEEEEEEESSHHHHHHHGGGTT
T ss_pred             CCCCEEEEECCCCCcccHHHHHHHHHhhhh------------ccceeeecccCCccccceeeeEEECCHHHHHHHHhcCC
Confidence            4689999999999986 5669999999998            566654       3457899999999999999999999


Q ss_pred             ceecCceEEEecCCC
Q 016936          102 IIFEGVAVRVRRPTD  116 (380)
Q Consensus       102 ~~i~g~~i~v~~~~~  116 (380)
                      ..+.|++|+|.++..
T Consensus        70 ~~~~gr~l~V~~a~~   84 (86)
T d2ghpa3          70 SLLGNREISVSLADK   84 (86)
T ss_dssp             EEETTEEEEEEECCC
T ss_pred             CEECCEEEEEEEcCC
Confidence            999999999999764

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=1.1e-16  Score=116.72  Aligned_cols=74  Identities=23%  Similarity=0.316  Sum_probs=66.4

Q ss_pred             ccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecCceE
Q 016936           31 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  109 (380)
Q Consensus        31 ~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g~~i  109 (380)
                      .+++|||+|||++++++||+++|++||.             ..+.+.+++|||||+|.+.++|++|+ .||+..+.|++|
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G~-------------~~~~~~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l   70 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYDL-------------KYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDL   70 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSCC-------------CCEEEEGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcCc-------------eeeeeeccCCceEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            4679999999999999999999999973             33556788999999999999999999 899999999999


Q ss_pred             EEecCCCC
Q 016936          110 RVRRPTDY  117 (380)
Q Consensus       110 ~v~~~~~~  117 (380)
                      +|.++...
T Consensus        71 ~V~~a~~~   78 (88)
T d1wg1a_          71 IVQLQPTD   78 (88)
T ss_dssp             EEEECCCC
T ss_pred             EEEEcCCC
Confidence            99997543

>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=99.63  E-value=3.3e-16  Score=114.56  Aligned_cols=76  Identities=20%  Similarity=0.333  Sum_probs=67.0

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecC----CCcEEEEEeCCHHHHHHHH-HcCCcee
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH----EKKFAFVEMRTVEEASNAM-ALDGIIF  104 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~----~~g~afV~f~~~~~a~~ai-~l~~~~i  104 (380)
                      ....+|||+|||+++++++|+++|++||.            |..+.+..    ++|||||+|.+.++|++|+ .||+..|
T Consensus         6 s~~~~l~V~nLp~~~t~~~l~~~F~~~G~------------v~~~~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~   73 (89)
T d1cvja2           6 SGVGNIFIKNLDKSIDNKALYDTFSAFGN------------ILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLL   73 (89)
T ss_dssp             TTTTEEEEESCCSSCCHHHHHHHHHTTSC------------EEEEEECCBTTBCCSCEEEEESCHHHHHHHTTSSSEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------ceEEEEEeecCCCcceeEEEECCHHHHHHHHHHcCCCEE
Confidence            34568999999999999999999999997            66666543    4799999999999999999 7999999


Q ss_pred             cCceEEEecCCCC
Q 016936          105 EGVAVRVRRPTDY  117 (380)
Q Consensus       105 ~g~~i~v~~~~~~  117 (380)
                      .|++|.|.++..+
T Consensus        74 ~g~~i~V~~a~~~   86 (89)
T d1cvja2          74 NDRKVFVGRFKSR   86 (89)
T ss_dssp             TTEEEEEEECCCT
T ss_pred             CCEEEEEEECCCC
Confidence            9999999997654

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.63  E-value=5.9e-16  Score=109.11  Aligned_cols=71  Identities=18%  Similarity=0.355  Sum_probs=63.8

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccC
Q 016936          155 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  232 (380)
Q Consensus       155 l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~  232 (380)
                      |||+|||+++++++|+++|++|| +..+.+      ++++|+|||+|.+.++|++|++.|||..+.|++|+|+++...
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~------~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee------cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            79999999999999999999999 444443      456789999999999999999999999999999999998654

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.63  E-value=5.3e-16  Score=115.32  Aligned_cols=74  Identities=23%  Similarity=0.404  Sum_probs=68.6

Q ss_pred             ccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecC--c
Q 016936           31 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG--V  107 (380)
Q Consensus        31 ~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g--~  107 (380)
                      ++++|||+|||+++++++|+++|++||.            |..+.+.++++||||+|.+.++|++|+ .|++..|.|  +
T Consensus        16 Ps~tl~V~nLp~~~t~~~l~~~f~~~G~------------i~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~   83 (97)
T d1whya_          16 PTTRLWVGGLGPNTSLAALAREFDRFGS------------IRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFPLGGPDR   83 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSC------------EEEEEECSSSCCEEEEESSHHHHHHHHHHHTTCBCSSSSC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhhcc------------cceEeeeccccEEEeccCCHHHHHHHHHHhCCCEeCCCce
Confidence            4689999999999999999999999987            888999999999999999999999999 899999987  5


Q ss_pred             eEEEecCCC
Q 016936          108 AVRVRRPTD  116 (380)
Q Consensus       108 ~i~v~~~~~  116 (380)
                      +|+|.|+..
T Consensus        84 ~l~v~~ak~   92 (97)
T d1whya_          84 RLRVDFAKS   92 (97)
T ss_dssp             BCEEEECCC
T ss_pred             EEEEEeCCC
Confidence            899999764

>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=99.63  E-value=3.1e-16  Score=112.10  Aligned_cols=71  Identities=20%  Similarity=0.385  Sum_probs=62.7

Q ss_pred             cceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe------cCCCcEEEEEeCCHHHHHHHHHcCCceec
Q 016936           32 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAMALDGIIFE  105 (380)
Q Consensus        32 ~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~------~~~~g~afV~f~~~~~a~~ai~l~~~~i~  105 (380)
                      .|+|||+|||+++|+++|+++|++||.+            ..+.+      +.++|||||+|.+.++|.+|+++++..|.
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i------------~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~~~~~~l~   69 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKI------------EVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVN   69 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCE------------EEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHCSCCEET
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccc------------cccccccCCCCcccccEEEEEEcCHHHHHHHHHhCCCEEC
Confidence            5899999999999999999999999984            44443      24579999999999999999999999999


Q ss_pred             CceEEEecC
Q 016936          106 GVAVRVRRP  114 (380)
Q Consensus       106 g~~i~v~~~  114 (380)
                      |++|+|..+
T Consensus        70 Gr~i~V~~A   78 (79)
T d1l3ka2          70 GHNCEVRKA   78 (79)
T ss_dssp             TEECEEEEC
T ss_pred             CEEEEEEEC
Confidence            999999864

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=3.9e-16  Score=114.00  Aligned_cols=77  Identities=22%  Similarity=0.354  Sum_probs=65.1

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCcee-cCc
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIF-EGV  107 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i-~g~  107 (380)
                      .++++|||+|||+++++++|+++|++||.+.          -......+++|+|||+|.+.++|.+|+ .|++..+ .|+
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~----------~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~   77 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVV----------KGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENH   77 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCE----------EEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEE----------EEEEeeecccceeEEEECCHHHHHHHHHhccCCEecCCC
Confidence            3578999999999999999999999999742          122234567899999999999999999 8999988 589


Q ss_pred             eEEEecCCC
Q 016936          108 AVRVRRPTD  116 (380)
Q Consensus       108 ~i~v~~~~~  116 (380)
                      +|+|.+++.
T Consensus        78 ~l~v~~sk~   86 (88)
T d2adca2          78 HLRVSFSKS   86 (88)
T ss_dssp             BCEEEECSS
T ss_pred             EEEEEeCCC
Confidence            999998653

>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=99.62  E-value=7e-16  Score=115.95  Aligned_cols=79  Identities=19%  Similarity=0.315  Sum_probs=66.6

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe------cCCCcEEEEEeCCHHHHHHHHHcC
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAMALD  100 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~------~~~~g~afV~f~~~~~a~~ai~l~  100 (380)
                      +.+...++|||+|||+.++++||+++|++||.            |.++.+      ++++|||||+|.+.++|++|++..
T Consensus         5 ~~d~~~~~lfV~nLp~~~te~~l~~~F~~~G~------------i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~   72 (103)
T d2cqda1           5 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGD------------IEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP   72 (103)
T ss_dssp             CCSCSSSEEEEECCCSSCCHHHHHHHHHTTSC------------EEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCS
T ss_pred             CCCCCCcEEEEeCCCCcCcHHHHHHHHhhccc------------ccceeccccccccccCCeEEEEECCHHHHHHHHHHC
Confidence            34455688999999999999999999999997            666665      346899999999999999999544


Q ss_pred             CceecCceEEEecCCCC
Q 016936          101 GIIFEGVAVRVRRPTDY  117 (380)
Q Consensus       101 ~~~i~g~~i~v~~~~~~  117 (380)
                      +..|.|++|+|.++...
T Consensus        73 ~~~l~Gr~l~V~~a~~~   89 (103)
T d2cqda1          73 NPIIDGRKANVNLAYLG   89 (103)
T ss_dssp             SCEETTEECEEEESTTT
T ss_pred             CCcCCCEEEEEEEcCCC
Confidence            45799999999987654

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=3.9e-16  Score=117.54  Aligned_cols=79  Identities=14%  Similarity=0.184  Sum_probs=70.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      ...+|||+|||+.+++++|+++|+.||.+..+.++....+|+++|+|||+|.+.++|++|++ +|+..|.|+.|.|.++.
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            34689999999999999999999999999875444444589999999999999999999997 89999999999999874

>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=99.62  E-value=5.8e-16  Score=115.14  Aligned_cols=77  Identities=21%  Similarity=0.220  Sum_probs=69.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      ....+|||+|||+.+++++|+++|++||.|..+.+..       +|||||+|.+.++|++|++.||+..|.|+.|+|.++
T Consensus        13 ~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~   85 (98)
T d1wg4a_          13 RSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYI   85 (98)
T ss_dssp             SCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEE
Confidence            3456899999999999999999999999999998853       379999999999999999999999999999999998


Q ss_pred             ccCC
Q 016936          230 TASS  233 (380)
Q Consensus       230 ~~~~  233 (380)
                      ..+.
T Consensus        86 ~~~~   89 (98)
T d1wg4a_          86 RVYP   89 (98)
T ss_dssp             EEEC
T ss_pred             ecCC
Confidence            6543

>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=99.62  E-value=9.2e-17  Score=116.98  Aligned_cols=72  Identities=21%  Similarity=0.240  Sum_probs=66.7

Q ss_pred             EEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcccC
Q 016936          154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  232 (380)
Q Consensus       154 ~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~~~  232 (380)
                      +|||+|||+.+++++|+++|++||.|..+++..+       |||||+|.+.++|++|+..|||..|.|+.|+|.++...
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~   73 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   73 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhccccccccccc-------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecC
Confidence            6999999999999999999999999999988643       79999999999999999999999999999998876554

>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=99.62  E-value=2.2e-16  Score=115.74  Aligned_cols=78  Identities=18%  Similarity=0.368  Sum_probs=67.9

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec------CCCcEEEEEeCCHHHHHHHH-HcC
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN------HEKKFAFVEMRTVEEASNAM-ALD  100 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~------~~~g~afV~f~~~~~a~~ai-~l~  100 (380)
                      ...+.++|||+|||.++++++|+++|++||.            |..+.+.      .++|||||+|.+.++|.+|+ .++
T Consensus         4 ~~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~------------v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~   71 (90)
T d2cq0a1           4 RADDNATIRVTNLSEDTRETDLQELFRPFGS------------ISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVS   71 (90)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCC------------EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTT
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHhcc------------cccccccccccccccccceeEEECCHHHHHHHHHHhC
Confidence            3446789999999999999999999999998            5555543      45789999999999999999 799


Q ss_pred             CceecCceEEEecCCCC
Q 016936          101 GIIFEGVAVRVRRPTDY  117 (380)
Q Consensus       101 ~~~i~g~~i~v~~~~~~  117 (380)
                      +..+.|++|+|.|+..+
T Consensus        72 g~~~~g~~i~v~~akp~   88 (90)
T d2cq0a1          72 GFGYDHLILNVEWAKPS   88 (90)
T ss_dssp             TCEETTEECEEEESSCC
T ss_pred             CCEECCEEEEEEeeeCC
Confidence            99999999999997654

>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=99.62  E-value=2.4e-16  Score=114.14  Aligned_cols=73  Identities=19%  Similarity=0.422  Sum_probs=65.5

Q ss_pred             ceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe------cCCCcEEEEEeCCHHHHHHHH-HcCCceec
Q 016936           33 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-ALDGIIFE  105 (380)
Q Consensus        33 ~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~------~~~~g~afV~f~~~~~a~~ai-~l~~~~i~  105 (380)
                      .+|||+|||+.+|+++|+++|++||.            |.++++      ++++|||||+|.+.++|+.|+ .+++..|.
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~------------v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~   69 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGP------------LKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLG   69 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSC------------EEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCS
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCc------------cceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEEC
Confidence            58999999999999999999999998            555655      456899999999999999999 69999999


Q ss_pred             CceEEEecCCCC
Q 016936          106 GVAVRVRRPTDY  117 (380)
Q Consensus       106 g~~i~v~~~~~~  117 (380)
                      |++|.|.++...
T Consensus        70 g~~l~V~~A~~~   81 (85)
T d2u2fa_          70 DKKLLVQRASVG   81 (85)
T ss_dssp             SSCCEEEECCCC
T ss_pred             CEEEEEEECCCC
Confidence            999999997643

>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=99.62  E-value=5.7e-16  Score=113.21  Aligned_cols=78  Identities=26%  Similarity=0.394  Sum_probs=65.8

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe------cCCCcEEEEEeCCHHHHHHHHHcCC
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAMALDG  101 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~------~~~~g~afV~f~~~~~a~~ai~l~~  101 (380)
                      ..+..++|||+|||+++|+++|+++|++||.            |.++.+      +.++|||||+|.+.++|.+||+ +.
T Consensus         4 ~~~~~~~lfV~nLp~~~te~~l~~~F~~~G~------------i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~-~~   70 (90)
T d2cqga1           4 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGE------------VLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS-QR   70 (90)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGGSC------------EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH-SC
T ss_pred             CCcCCCeEEEECCCCCCCHHHHHHHHHhhcc------------cceeeeccCCCCcccCCEEEEEECCHHHHHHHHh-cC
Confidence            4456789999999999999999999999998            444443      4567999999999999999996 34


Q ss_pred             ceecCceEEEecCCCCC
Q 016936          102 IIFEGVAVRVRRPTDYN  118 (380)
Q Consensus       102 ~~i~g~~i~v~~~~~~~  118 (380)
                      ..|.|+.|+|.++..++
T Consensus        71 ~~l~Gr~i~v~~a~~k~   87 (90)
T d2cqga1          71 HMIDGRWCDCKLPNSKQ   87 (90)
T ss_dssp             EEETTEEEEEECCCTTC
T ss_pred             CccCCEEeEEEeCCCCC
Confidence            57999999999976643

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=5.8e-16  Score=115.31  Aligned_cols=89  Identities=22%  Similarity=0.376  Sum_probs=78.3

Q ss_pred             CccceEEEEeccCCcccCC-ChHHHHHHHHHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHH
Q 016936          275 ETLAKVLCLTEAITADALA-DDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNAL  353 (380)
Q Consensus       275 ~~~~~~~~l~~~~~~~~~~-~~~~~~~~~~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l  353 (380)
                      ....+++.+.|++++.++. ++..+.++.++|++.|++||.|..|.+..++.       .|+|||+|.++++|.+|+..|
T Consensus         5 ~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~~-------~G~~fV~f~~~e~A~~A~~~l   77 (99)
T d2dita1           5 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHP-------DGVASVSFRDPEEADYCIQTL   77 (99)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCT-------TCEEEEECSCHHHHHHHHHHS
T ss_pred             CCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCCC-------ccEEEEEECCHHHHHHHHHHh
Confidence            5678999999999888764 34458889999999999999999999987643       268899999999999999999


Q ss_pred             cCcccCCeEEEEEeccc
Q 016936          354 SGRKFGGNTVNAFYYPE  370 (380)
Q Consensus       354 ~g~~i~gr~l~v~~~~~  370 (380)
                      ||++|+||+|+|+|+..
T Consensus        78 ng~~~~gr~i~v~~~~g   94 (99)
T d2dita1          78 DGRWFGGRQITAQAWDG   94 (99)
T ss_dssp             TTCEETTEECEEEECCS
T ss_pred             CCcEECCEEEEEEEeCC
Confidence            99999999999999865

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=4.5e-16  Score=113.57  Aligned_cols=78  Identities=17%  Similarity=0.146  Sum_probs=70.8

Q ss_pred             hhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-H--cCCcee
Q 016936           28 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-A--LDGIIF  104 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~--l~~~~i  104 (380)
                      ...++++|||+|||+++++++|+++|++||.            |.++.+.+++++|||+|.+.++|..|+ .  +++..+
T Consensus         4 ~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~------------i~~v~~~~~~~~afV~f~~~e~A~~a~~~~~~~~~~~   71 (88)
T d2cq1a1           4 DGAPSRVLHIRKLPGEVTETEVIALGLPFGK------------VTNILMLKGKNQAFLELATEEAAITMVNYYSAVTPHL   71 (88)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSC------------EEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcccc------------cccccccccceEEEEEeCCHHHHHHHHHHHccCCCcc
Confidence            3568999999999999999999999999997            888889999999999999999999999 3  467889


Q ss_pred             cCceEEEecCCCC
Q 016936          105 EGVAVRVRRPTDY  117 (380)
Q Consensus       105 ~g~~i~v~~~~~~  117 (380)
                      .|++|+|.+++.+
T Consensus        72 ~g~~l~v~~sk~~   84 (88)
T d2cq1a1          72 RNQPIYIQYSNHK   84 (88)
T ss_dssp             TTEECEEEECSCS
T ss_pred             CCCEEEEEECCCC
Confidence            9999999997654

>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=99.61  E-value=1.9e-16  Score=114.32  Aligned_cols=78  Identities=17%  Similarity=0.321  Sum_probs=63.5

Q ss_pred             EEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecCceEEEec
Q 016936           35 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRR  113 (380)
Q Consensus        35 v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g~~i~v~~  113 (380)
                      |||+|||+++|+++|+++|++||.+....     .++.+...++++|||||+|.+.++|.+|+ .+++..+.|++|+|.|
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            79999999999999999999999863210     00111122456899999999999999999 7999999999999999


Q ss_pred             CCCC
Q 016936          114 PTDY  117 (380)
Q Consensus       114 ~~~~  117 (380)
                      +..+
T Consensus        76 a~~k   79 (83)
T d1x5ta1          76 AFKK   79 (83)
T ss_dssp             SCCC
T ss_pred             ecCC
Confidence            7654

>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=99.61  E-value=1.2e-16  Score=113.09  Aligned_cols=75  Identities=15%  Similarity=0.284  Sum_probs=61.8

Q ss_pred             eEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHHHcCCceecCceEEEec
Q 016936           34 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRR  113 (380)
Q Consensus        34 ~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai~l~~~~i~g~~i~v~~  113 (380)
                      +|||+|||+++|+++|+++|++||.+....      .+.+-..+..++||||+|.+.++|.+|+++++..|.|++|+|.+
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~------~~~~~~~~~~~~~afV~F~~~~~a~~al~~~~~~l~gr~i~V~~   74 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAM------LMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKK   74 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEEC------CBCCTTCTTSCCEEEEECSCHHHHHHHHHCSSCCBTTBCCEEEE
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceee------eeeeccccccCceeEEEECCHHHHHHHHhcCCCEECCeEEEEEE
Confidence            599999999999999999999999853211      01111124567999999999999999999999999999999987


Q ss_pred             C
Q 016936          114 P  114 (380)
Q Consensus       114 ~  114 (380)
                      |
T Consensus        75 A   75 (75)
T d2msta_          75 A   75 (75)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=2.4e-16  Score=118.99  Aligned_cols=78  Identities=33%  Similarity=0.514  Sum_probs=67.1

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe------cCCCcEEEEEeCCHHHHHHHH-HcCC
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-ALDG  101 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~------~~~~g~afV~f~~~~~a~~ai-~l~~  101 (380)
                      +++.|+|||+|||+++++++|+++|++||.|            .++.+      ++++|||||+|.+.++|.+|+ .+++
T Consensus         5 ~~~~rtl~V~nLp~~~te~~l~~~f~~~G~i------------~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~   72 (104)
T d1p1ta_           5 DRSLRSVFVGNIPYEATEEQLKDIFSEVGPV------------VSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNG   72 (104)
T ss_dssp             HHHHSCEEEESCCTTSCHHHHHHHHHTTSCC------------SEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSS
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHhhhccccc------------cccccccccceeccCCceEEEECCHHHHHHHHHHcCC
Confidence            4567899999999999999999999999984            33433      335789999999999999999 7999


Q ss_pred             ceecCceEEEecCCCCC
Q 016936          102 IIFEGVAVRVRRPTDYN  118 (380)
Q Consensus       102 ~~i~g~~i~v~~~~~~~  118 (380)
                      ..|.|++|+|.++....
T Consensus        73 ~~~~g~~i~V~~a~~~~   89 (104)
T d1p1ta_          73 REFSGRALRVDNAASEK   89 (104)
T ss_dssp             BSCSSSCBEEEETTCTT
T ss_pred             CEECCEEEEEEECCCCC
Confidence            99999999999976543

>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=99.61  E-value=6e-16  Score=108.90  Aligned_cols=69  Identities=19%  Similarity=0.356  Sum_probs=61.5

Q ss_pred             eEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec------CCCcEEEEEeCCHHHHHHHHHcCCceecCc
Q 016936           34 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN------HEKKFAFVEMRTVEEASNAMALDGIIFEGV  107 (380)
Q Consensus        34 ~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~------~~~g~afV~f~~~~~a~~ai~l~~~~i~g~  107 (380)
                      +|||+|||+++|+++|+++|++||.            |.++.+.      +++|||||+|.+.++|++||+.+++.+.|+
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~------------I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~~~~~~i~g~   68 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGE------------VESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLS   68 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSC------------EEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTCSSCCBTTB
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCC------------cccccccccccccccccEEEEEECCHHHHHHHHhhCCCEECCE
Confidence            6999999999999999999999998            6666653      467999999999999999998888899999


Q ss_pred             eEEEecC
Q 016936          108 AVRVRRP  114 (380)
Q Consensus       108 ~i~v~~~  114 (380)
                      .|+|..+
T Consensus        69 ~i~vk~A   75 (75)
T d1x0fa1          69 KCEIKVA   75 (75)
T ss_dssp             CCEEECC
T ss_pred             EeEEEEC
Confidence            9998753

>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=99.60  E-value=3.2e-15  Score=112.55  Aligned_cols=79  Identities=16%  Similarity=0.138  Sum_probs=70.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHh--CCCeeCCeEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL--NGLKMGDKTLTV  226 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l--~g~~~~g~~i~v  226 (380)
                      ...+++|||+|||..+++++|+++|++||.|..+.+.++      +|+|||+|.+.++|++|+..+  ++..+.|++|+|
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            345579999999999999999999999999999998654      579999999999999999987  567889999999


Q ss_pred             EEcccCC
Q 016936          227 RRATASS  233 (380)
Q Consensus       227 ~~~~~~~  233 (380)
                      .++....
T Consensus        86 ~~s~~~~   92 (104)
T d1wexa_          86 NYSTSKR   92 (104)
T ss_dssp             EECSSSS
T ss_pred             EEcCCCc
Confidence            9987643

>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=99.60  E-value=7.2e-16  Score=111.76  Aligned_cols=70  Identities=26%  Similarity=0.414  Sum_probs=61.8

Q ss_pred             EEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec---------CCCcEEEEEeCCHHHHHHHH-HcCCcee
Q 016936           35 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN---------HEKKFAFVEMRTVEEASNAM-ALDGIIF  104 (380)
Q Consensus        35 v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~---------~~~g~afV~f~~~~~a~~ai-~l~~~~i  104 (380)
                      |||+|||+++|+++|+++|++||.            |.++.+.         .++|||||+|.+.++|.+|+ .+|+..+
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~------------v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~   68 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGA------------IKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTV   68 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSC------------EEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEE
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCC------------ccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEE
Confidence            799999999999999999999998            4444442         24689999999999999999 7999999


Q ss_pred             cCceEEEecCCC
Q 016936          105 EGVAVRVRRPTD  116 (380)
Q Consensus       105 ~g~~i~v~~~~~  116 (380)
                      .|++|+|.++..
T Consensus        69 ~g~~i~V~~a~~   80 (85)
T d2cpfa1          69 DGHKLEVRISER   80 (85)
T ss_dssp             TTEECEEECSSC
T ss_pred             CCEEEEEEECCC
Confidence            999999999754

>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=99.60  E-value=8.8e-16  Score=109.83  Aligned_cols=70  Identities=21%  Similarity=0.395  Sum_probs=62.7

Q ss_pred             eEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec------CCCcEEEEEeCCHHHHHHHH-HcCCceecC
Q 016936           34 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN------HEKKFAFVEMRTVEEASNAM-ALDGIIFEG  106 (380)
Q Consensus        34 ~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~------~~~g~afV~f~~~~~a~~ai-~l~~~~i~g  106 (380)
                      +|||+|||+++|+++|+++|++||.            |.++++.      +++|||||+|.+.++|.+|+ .++|..+.|
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~------------i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~g   69 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGP------------ILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKG   69 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSC------------EEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETT
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCC------------EeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECC
Confidence            5999999999999999999999997            5555543      34689999999999999999 799999999


Q ss_pred             ceEEEecCC
Q 016936          107 VAVRVRRPT  115 (380)
Q Consensus       107 ~~i~v~~~~  115 (380)
                      ++|+|.|+.
T Consensus        70 r~i~v~~a~   78 (80)
T d1cvja1          70 KPVRIMWSQ   78 (80)
T ss_dssp             EECEEEECC
T ss_pred             EEEEEEEeC
Confidence            999999864

>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=99.60  E-value=6.9e-16  Score=111.73  Aligned_cols=74  Identities=23%  Similarity=0.399  Sum_probs=63.8

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe------cCCCcEEEEEeCCHHHHHHHH-HcCC
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-ALDG  101 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~------~~~~g~afV~f~~~~~a~~ai-~l~~  101 (380)
                      +...++|||+|||+.+|+++|+++|++||.            |.++++      +.++|||||+|.+.++|.+|+ .||+
T Consensus         3 s~k~~~lfV~nLp~~~te~~L~~~F~~~G~------------v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng   70 (85)
T d1fxla2           3 SIRDANLYVSGLPKTMTQKELEQLFSQYGR------------IITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNG   70 (85)
T ss_dssp             GGTTCEEEEESCCTTCCHHHHHHHHGGGSC------------EEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCC------------ccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCC
Confidence            345688999999999999999999999998            555554      245789999999999999999 7999


Q ss_pred             ceecC--ceEEEecC
Q 016936          102 IIFEG--VAVRVRRP  114 (380)
Q Consensus       102 ~~i~g--~~i~v~~~  114 (380)
                      ..+.|  ++|+|.|+
T Consensus        71 ~~~~G~~~~i~V~~A   85 (85)
T d1fxla2          71 QKPSGATEPITVKFA   85 (85)
T ss_dssp             CCCTTCSSCCEEEEC
T ss_pred             CEeCCCCEEEEEEeC
Confidence            99988  56999874

>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=99.60  E-value=2.6e-15  Score=111.49  Aligned_cols=75  Identities=25%  Similarity=0.525  Sum_probs=68.5

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCC--eEEEEEEc
Q 016936          152 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD--KTLTVRRA  229 (380)
Q Consensus       152 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g--~~i~v~~~  229 (380)
                      .++|||+|||+.+++++|+++|++||.|..+++.++      ++||||+|.+.++|++|++.||+..+.|  ++|+|.|+
T Consensus        17 s~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~a   90 (97)
T d1whya_          17 TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFA   90 (97)
T ss_dssp             CSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEEC
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeC
Confidence            479999999999999999999999999999998654      5699999999999999999999999976  58999998


Q ss_pred             ccC
Q 016936          230 TAS  232 (380)
Q Consensus       230 ~~~  232 (380)
                      ++.
T Consensus        91 k~~   93 (97)
T d1whya_          91 KSG   93 (97)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            764

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=2.8e-15  Score=114.10  Aligned_cols=74  Identities=26%  Similarity=0.307  Sum_probs=66.2

Q ss_pred             cceEEEcCCCC-cCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecC-CCcEEEEEeCCHHHHHHHH-HcCCceecCce
Q 016936           32 ARRVYVGGLPP-LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH-EKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  108 (380)
Q Consensus        32 ~~~v~V~nLp~-~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~-~~g~afV~f~~~~~a~~ai-~l~~~~i~g~~  108 (380)
                      +++|||+|||+ .+|+++|+++|++||.            |..+.+.+ .+|||||+|.+.++|.+|+ .+++..|.|+.
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            58999999965 5999999999999998            77787654 4689999999999999999 89999999999


Q ss_pred             EEEecCCCC
Q 016936          109 VRVRRPTDY  117 (380)
Q Consensus       109 i~v~~~~~~  117 (380)
                      |+|.++...
T Consensus        70 l~v~~s~~~   78 (109)
T d2adca1          70 IRITLSKHQ   78 (109)
T ss_dssp             CEEECCSCC
T ss_pred             EEEEECCCC
Confidence            999997644

>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=99.60  E-value=1.8e-16  Score=118.83  Aligned_cols=80  Identities=15%  Similarity=0.310  Sum_probs=67.7

Q ss_pred             cchhhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe-----cCCCcEEEEEeCCHHHHHHHH-
Q 016936           24 MTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-----NHEKKFAFVEMRTVEEASNAM-   97 (380)
Q Consensus        24 ~~~~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~-----~~~~g~afV~f~~~~~a~~ai-   97 (380)
                      +..+.+.+.++|||+|||+++++++|+++|++||.|            ..+.+     .+++|||||+|.+.++|.+|+ 
T Consensus        10 ~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i------------~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~   77 (101)
T d1x5oa1          10 MAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQV------------ISTRILRDSSGTSRGVGFARMESTEKCEAVIG   77 (101)
T ss_dssp             CCSCCCCCTTEEEEESCCTTCCHHHHHHTTTTTSCE------------EEEEEEECSSSCEEEEEEEEESCHHHHHHHHH
T ss_pred             hhccccCCCCEEEEeCCCCCCCHHHHHHHHhhcccc------------cceeeecccccccccceeEEeCCHHHHHHHHH
Confidence            344566778999999999999999999999999984            33332     345789999999999999999 


Q ss_pred             HcCCceecCceEEEecCC
Q 016936           98 ALDGIIFEGVAVRVRRPT  115 (380)
Q Consensus        98 ~l~~~~i~g~~i~v~~~~  115 (380)
                      .|||..|.|+++.+.++.
T Consensus        78 ~lng~~i~gr~~~v~~~~   95 (101)
T d1x5oa1          78 HFNGKFIKTPPGVSAPTE   95 (101)
T ss_dssp             HHBTCCCCCCTTSCCCSS
T ss_pred             HhCCCEECCcCCccCCCC
Confidence            799999999999887643

>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=99.59  E-value=3.4e-15  Score=108.84  Aligned_cols=77  Identities=14%  Similarity=0.161  Sum_probs=68.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHh--CCCeeCCeEEEEE
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL--NGLKMGDKTLTVR  227 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l--~g~~~~g~~i~v~  227 (380)
                      ..+++|||+|||.++++++|+++|++||.|..+++.++      +|+|||+|.+.++|++|++.+  ++..+.|++|+|.
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            34479999999999999999999999999999998765      469999999999999999865  5789999999999


Q ss_pred             EcccC
Q 016936          228 RATAS  232 (380)
Q Consensus       228 ~~~~~  232 (380)
                      ++..+
T Consensus        80 ~sk~~   84 (88)
T d2cq1a1          80 YSNHK   84 (88)
T ss_dssp             ECSCS
T ss_pred             ECCCC
Confidence            98754

>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=99.59  E-value=8.6e-16  Score=108.25  Aligned_cols=70  Identities=19%  Similarity=0.272  Sum_probs=62.1

Q ss_pred             ceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec----CCCcEEEEEeCCHHHHHHHHHcCCceecCce
Q 016936           33 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN----HEKKFAFVEMRTVEEASNAMALDGIIFEGVA  108 (380)
Q Consensus        33 ~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~----~~~g~afV~f~~~~~a~~ai~l~~~~i~g~~  108 (380)
                      ++|||+|||+++++++|+++|++||.            |..+.+.    ..+++|||+|.+.++|.+|+.+++..|.|++
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~------------I~~v~~~~~~~~~~~~afV~F~~~~~a~~Al~~~~~~i~g~~   68 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGP------------IIHVDVADSLKKNFRFARIEFARYDGALAAITKTHKVVGQNE   68 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSC------------EEEEEEEECTTSSSEEEEEEESSHHHHHHHHTTTTCEETTEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCc------------eEEEEEEeeccccceEEEEEEcchHHhHHHHHhcCcEECCEE
Confidence            48999999999999999999999998            5555553    3457999999999999999999999999999


Q ss_pred             EEEecC
Q 016936          109 VRVRRP  114 (380)
Q Consensus       109 i~v~~~  114 (380)
                      |.|...
T Consensus        69 i~V~~~   74 (75)
T d2ghpa2          69 IIVSHL   74 (75)
T ss_dssp             CEEEEC
T ss_pred             EEEEEC
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=99.59  E-value=1.1e-15  Score=116.00  Aligned_cols=79  Identities=22%  Similarity=0.259  Sum_probs=70.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCee--CCeEEEEEE
Q 016936          151 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM--GDKTLTVRR  228 (380)
Q Consensus       151 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~--~g~~i~v~~  228 (380)
                      ...+|||+|||+.+|+++|+++|++||.|..|.+..++    ++|+|||+|.+.++|++|+..||+..+  .++.|+|.+
T Consensus         6 ~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~   81 (108)
T d2adba1           6 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF   81 (108)
T ss_dssp             CEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEE
T ss_pred             CeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEe
Confidence            34689999999999999999999999999999998763    479999999999999999999999988  578899998


Q ss_pred             cccCC
Q 016936          229 ATASS  233 (380)
Q Consensus       229 ~~~~~  233 (380)
                      +....
T Consensus        82 s~~~~   86 (108)
T d2adba1          82 SKLTS   86 (108)
T ss_dssp             CSSCS
T ss_pred             cCCcc
Confidence            86643

>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=99.59  E-value=2.1e-15  Score=112.41  Aligned_cols=77  Identities=22%  Similarity=0.341  Sum_probs=65.3

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec------CCCcEEEEEeCCHHHHHHHH-HcC-
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN------HEKKFAFVEMRTVEEASNAM-ALD-  100 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~------~~~g~afV~f~~~~~a~~ai-~l~-  100 (380)
                      ..+.++|||+|||+++|+++|+++|++||.            +.++.+.      .++|||||+|.+.++|.+|+ .++ 
T Consensus         5 ~~~~~tlfV~nLp~~~te~~l~~~f~~~G~------------v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~   72 (98)
T d1x4ha1           5 VTEGKTVFIRNLSFDSEEEALGEVLQQFGD------------LKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASL   72 (98)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSC------------EEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCT
T ss_pred             CCCCCEEEEcCCCCcCCHHHHHHHHhcccc------------ceeeeeccccccccccceEEEEEcCHHHHHHHHHHccc
Confidence            345789999999999999999999999987            5555542      35799999999999999999 565 


Q ss_pred             -----CceecCceEEEecCCCC
Q 016936          101 -----GIIFEGVAVRVRRPTDY  117 (380)
Q Consensus       101 -----~~~i~g~~i~v~~~~~~  117 (380)
                           +..+.|++|+|.++..+
T Consensus        73 ~~~~~g~~~~gr~l~v~~a~~k   94 (98)
T d1x4ha1          73 EAEGGGLKLDGRQLKVDLAVTR   94 (98)
T ss_dssp             TTTTCCEESSSCEEEEECCCCC
T ss_pred             ccccCCcEECCEEEEEEECCCC
Confidence                 56789999999997654

>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=99.59  E-value=1.6e-15  Score=114.38  Aligned_cols=75  Identities=20%  Similarity=0.346  Sum_probs=63.8

Q ss_pred             ccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe-------cCCCcEEEEEeCCHHHHHHHHHcCCce
Q 016936           31 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-------NHEKKFAFVEMRTVEEASNAMALDGII  103 (380)
Q Consensus        31 ~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~-------~~~~g~afV~f~~~~~a~~ai~l~~~~  103 (380)
                      +.++|||+|||+++|+++|+++|++||.             +.+.+       ..++|||||+|.+.++|++|+.+|+..
T Consensus        14 p~~~v~V~nLp~~~te~~l~~~f~~~g~-------------~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~~~~~~   80 (104)
T d1wi8a_          14 PPYTAFLGNLPYDVTEESIKEFFRGLNI-------------SAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEES   80 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSCE-------------EEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhcc-------------ccceeeeeeccCCCcceeeeEEECCHHHHHHHHHcCCCE
Confidence            4589999999999999999999999973             22222       235689999999999999888999999


Q ss_pred             ecCceEEEecCCCCC
Q 016936          104 FEGVAVRVRRPTDYN  118 (380)
Q Consensus       104 i~g~~i~v~~~~~~~  118 (380)
                      |.|++|+|.++...+
T Consensus        81 ~~gr~l~V~~a~~~~   95 (104)
T d1wi8a_          81 LGNKRIRVDVADQAQ   95 (104)
T ss_dssp             ETTEECEEEECCCCC
T ss_pred             ECCEEEEEEECCCCC
Confidence            999999999976543

>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=99.59  E-value=1.1e-15  Score=112.23  Aligned_cols=76  Identities=20%  Similarity=0.414  Sum_probs=65.9

Q ss_pred             cccceEEEcCCCCcCcHHHHHH----HHHHHHHhccCCCCCCCCeeEEEEec---CCCcEEEEEeCCHHHHHHHH-HcCC
Q 016936           30 RHARRVYVGGLPPLANEQAIAT----FFSQVMTAIGGNSAGPGDAVVNVYIN---HEKKFAFVEMRTVEEASNAM-ALDG  101 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~----~f~~~G~i~~~~~~~~~~~i~~~~~~---~~~g~afV~f~~~~~a~~ai-~l~~  101 (380)
                      +++++|||+|||++++++||++    +|++||.            |.++.+.   +++|||||+|.+.++|.+|+ .+|+
T Consensus         1 ~P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~------------i~~i~~~~~~~~~g~afV~F~~~~~A~~A~~~~~~   68 (91)
T d1nu4a_           1 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQ------------ILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQG   68 (91)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSC------------EEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhccccc------------ccceEEeeeccCCCceEEEECCHHHHHHHHHHhCC
Confidence            4689999999999999999975    5678876            6666654   46899999999999999999 7999


Q ss_pred             ceecCceEEEecCCCC
Q 016936          102 IIFEGVAVRVRRPTDY  117 (380)
Q Consensus       102 ~~i~g~~i~v~~~~~~  117 (380)
                      ..+.|++|+|.|+...
T Consensus        69 ~~~~g~~l~v~~ak~~   84 (91)
T d1nu4a_          69 FPFYDKPMRIQYAKTD   84 (91)
T ss_dssp             CEETTEECEEEECSSC
T ss_pred             CEECCEEEEEEEeCCC
Confidence            9999999999997654

>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=5.1e-16  Score=115.75  Aligned_cols=80  Identities=24%  Similarity=0.329  Sum_probs=71.4

Q ss_pred             hhhhcccceEEEcCCCCc-CcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH---HcCC
Q 016936           26 QQATRHARRVYVGGLPPL-ANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM---ALDG  101 (380)
Q Consensus        26 ~~~~~~~~~v~V~nLp~~-~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai---~l~~  101 (380)
                      ++....+++|||+|||.+ +|+++|.++|++||.            |.++.+.+++|+|||+|.+.++|..|+   .+++
T Consensus        12 ~~~~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~------------V~~v~~~~~k~~afV~f~~~~~A~~Ai~~~~~~~   79 (99)
T d1x4fa1          12 DQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGK------------IKNYILMRMKSQAFIEMETREDAMAMVDHCLKKA   79 (99)
T ss_dssp             CCSSCCCCEEEEESCCCSSCCSHHHHTTTTTTSC------------CSEEEEETTTTEEEEECSSHHHHHHHHHHHHHSC
T ss_pred             ccCCCCCCEEEEeCCcCCccCHHHHHhhhccccc------------eeEEEEeecCCcEEEEecchHHHHHHHHHHhcCC
Confidence            345677899999999986 899999999999998            778888899999999999999999998   3788


Q ss_pred             ceecCceEEEecCCCC
Q 016936          102 IIFEGVAVRVRRPTDY  117 (380)
Q Consensus       102 ~~i~g~~i~v~~~~~~  117 (380)
                      ..+.|++|+|.++..+
T Consensus        80 ~~~~gr~l~V~~s~~~   95 (99)
T d1x4fa1          80 LWFQGRCVKVDLSEKY   95 (99)
T ss_dssp             CCSSSSCCEEEEECSC
T ss_pred             ceECCEEEEEEEcCCc
Confidence            8999999999997654

>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=99.58  E-value=5.1e-16  Score=113.22  Aligned_cols=76  Identities=25%  Similarity=0.415  Sum_probs=66.4

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe-cCCCcEEEEEeCCHHHHHHHHHcCCceecCce
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-NHEKKFAFVEMRTVEEASNAMALDGIIFEGVA  108 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~-~~~~g~afV~f~~~~~a~~ai~l~~~~i~g~~  108 (380)
                      ..+++|||+|||+++|+++|+++|++||.            |.++.+ ..+++||||+|.+.++|++|+. ++..|.|++
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~------------v~~v~~~~~~~gfafV~f~~~~~a~~a~~-~~~~i~g~~   69 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGD------------VMDVFIPKPFRAFAFVTFADDQIAQSLCG-EDLIIKGIS   69 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSC------------CCEEECCSSCCSCCEEECSCHHHHHHTTT-CEEEETTEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCC------------ceEEEEeeccCceEEEEECCHHHHHHHHh-CCCEECCEE
Confidence            46789999999999999999999999997            555654 4568999999999999999995 778899999


Q ss_pred             EEEecCCCCC
Q 016936          109 VRVRRPTDYN  118 (380)
Q Consensus       109 i~v~~~~~~~  118 (380)
                      |+|.++..+.
T Consensus        70 l~v~~a~~k~   79 (88)
T d1wf0a_          70 VHISNAEPKH   79 (88)
T ss_dssp             EEEECCCCCC
T ss_pred             eEEEeCCCCC
Confidence            9999976543

>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=99.58  E-value=1.1e-15  Score=116.65  Aligned_cols=81  Identities=19%  Similarity=0.315  Sum_probs=71.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEE
Q 016936          149 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  228 (380)
Q Consensus       149 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~  228 (380)
                      .....+|||+|||+++++++|+++|+.||.+..+.++.+..+|.++|+|||+|.+.++|++|+. +|+..|+|+.|.|.+
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            3445799999999999999999999999998775555554689999999999999999999997 899999999999998


Q ss_pred             cc
Q 016936          229 AT  230 (380)
Q Consensus       229 ~~  230 (380)
                      +.
T Consensus        94 ~~   95 (112)
T d1wela1          94 IT   95 (112)
T ss_dssp             EC
T ss_pred             cC
Confidence            74

>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=99.57  E-value=1.4e-15  Score=114.08  Aligned_cols=88  Identities=22%  Similarity=0.212  Sum_probs=68.7

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEE---EecCCCcEEEEEeCCHHHHHHHH-HcCCcee
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNV---YINHEKKFAFVEMRTVEEASNAM-ALDGIIF  104 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~---~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i  104 (380)
                      +.+.++|||+|||..+|+++|+++|++||.|.......... +...   ..++++|||||+|.+.++|.+|+ .+++..|
T Consensus         5 ~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~-~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~   83 (101)
T d2cpea1           5 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPM-IHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   83 (101)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBS-EECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccce-eEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEE
Confidence            45678999999999999999999999999864322111110 1111   11356799999999999999999 7999999


Q ss_pred             cCceEEEecCCCC
Q 016936          105 EGVAVRVRRPTDY  117 (380)
Q Consensus       105 ~g~~i~v~~~~~~  117 (380)
                      .|++|+|.++..+
T Consensus        84 ~gr~i~V~~a~~~   96 (101)
T d2cpea1          84 QGSKLKVSLARKK   96 (101)
T ss_dssp             TTEECEEECSSCC
T ss_pred             CCEEEEEEEcCCC
Confidence            9999999997654

>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=99.57  E-value=1.1e-15  Score=113.57  Aligned_cols=74  Identities=23%  Similarity=0.411  Sum_probs=65.3

Q ss_pred             cccceEEEcCCC-CcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecCc
Q 016936           30 RHARRVYVGGLP-PLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  107 (380)
Q Consensus        30 ~~~~~v~V~nLp-~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g~  107 (380)
                      ...++|||+||| ..+++++|+++|++||.            |.++.+  .+|||||+|.+.++|.+|+ .||+..|.|+
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~------------i~~~~i--~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~   78 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGK------------IVGCSV--HKGFAFVQYVNERNARAAVAGEDGRMIAGQ   78 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSC------------EEEEEE--ETEEEEEEESSHHHHHHHHHTTTTCEETTE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCC------------EEEEEE--eCCeEEEEECCHHHHHHHHHHcCCCEECCE
Confidence            445689999997 56889999999999998            677776  5799999999999999999 7999999999


Q ss_pred             eEEEecCCCC
Q 016936          108 AVRVRRPTDY  117 (380)
Q Consensus       108 ~i~v~~~~~~  117 (380)
                      +|+|.++...
T Consensus        79 ~l~V~~a~~~   88 (98)
T d1wf2a_          79 VLDINLAAEP   88 (98)
T ss_dssp             ECEEEETTSC
T ss_pred             EEEEEECCCC
Confidence            9999997653

>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=99.56  E-value=2.2e-15  Score=109.08  Aligned_cols=73  Identities=30%  Similarity=0.447  Sum_probs=63.3

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec------CCCcEEEEEeCCHHHHHHHH-HcCCc
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN------HEKKFAFVEMRTVEEASNAM-ALDGI  102 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~------~~~g~afV~f~~~~~a~~ai-~l~~~  102 (380)
                      ...++|||+|||+++++++|+++|++||.            |.++++.      +++|||||+|.+.++|.+|+ .+|+.
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~~~G~------------i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~   71 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFGKYGS------------IVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNV   71 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSC------------EEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCC------------EeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCC
Confidence            35678999999999999999999999998            5555543      45689999999999999999 79999


Q ss_pred             eecC--ceEEEecC
Q 016936          103 IFEG--VAVRVRRP  114 (380)
Q Consensus       103 ~i~g--~~i~v~~~  114 (380)
                      .+.|  ++|+|.|+
T Consensus        72 ~~~g~~~~l~V~~A   85 (85)
T d1b7fa2          72 IPEGGSQPLSVRLA   85 (85)
T ss_dssp             CCTTCSSCCEEEEC
T ss_pred             EeCCCCeEEEEEEC
Confidence            9877  88999875

>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=99.56  E-value=8.5e-15  Score=108.51  Aligned_cols=76  Identities=25%  Similarity=0.386  Sum_probs=63.9

Q ss_pred             cceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec-------CCCcEEEEEeCCHHHHHHHH-HcCC--
Q 016936           32 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN-------HEKKFAFVEMRTVEEASNAM-ALDG--  101 (380)
Q Consensus        32 ~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~-------~~~g~afV~f~~~~~a~~ai-~l~~--  101 (380)
                      .|+|||+|||.++++++|+++|++||..           +..+.+.       +++|||||+|.+.++|..|+ .|++  
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~-----------i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~   69 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEG-----------VLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGR   69 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTT-----------EEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCC
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCc-----------ceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCC
Confidence            3799999999999999999999999852           5666652       46789999999999999999 6764  


Q ss_pred             ceecCceEEEecCCCCC
Q 016936          102 IIFEGVAVRVRRPTDYN  118 (380)
Q Consensus       102 ~~i~g~~i~v~~~~~~~  118 (380)
                      ..+.|++|+|.|+..++
T Consensus        70 ~~~~g~~i~V~~A~p~~   86 (96)
T d2disa1          70 IQLWGHQIAVDWAEPEI   86 (96)
T ss_dssp             SCBTTBCCEEEESCSSC
T ss_pred             eEECCEEEEEEEcCCCC
Confidence            45678999999986543

>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=99.56  E-value=3.6e-15  Score=112.25  Aligned_cols=79  Identities=19%  Similarity=0.199  Sum_probs=66.0

Q ss_pred             hcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe-----cCCCcEEEEEeCCHHHHHHHHHcCCce
Q 016936           29 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-----NHEKKFAFVEMRTVEEASNAMALDGII  103 (380)
Q Consensus        29 ~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~-----~~~~g~afV~f~~~~~a~~ai~l~~~~  103 (380)
                      .....+|||+|||+++|++||+++|+++|.+           +..+.+     .+.+|+|||+|.++++|++|+++++..
T Consensus        12 ~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v-----------~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~~~~~~   80 (104)
T d1wg5a_          12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIV-----------PNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKER   80 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEE-----------EEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTTTTCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCc-----------eEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHhhCCCE
Confidence            3466689999999999999999999999873           222222     345799999999999999999999999


Q ss_pred             ecCceEEEecCCCCC
Q 016936          104 FEGVAVRVRRPTDYN  118 (380)
Q Consensus       104 i~g~~i~v~~~~~~~  118 (380)
                      |+|+.|+|.++...+
T Consensus        81 i~gR~i~V~~~~~~~   95 (104)
T d1wg5a_          81 IGHRYIEIFKSSRAE   95 (104)
T ss_dssp             SSSSCCEEEEECTTT
T ss_pred             EcceEEEEEECCHHH
Confidence            999999999876543

>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=99.56  E-value=8.9e-16  Score=111.66  Aligned_cols=69  Identities=23%  Similarity=0.262  Sum_probs=62.7

Q ss_pred             ceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecCceEEE
Q 016936           33 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV  111 (380)
Q Consensus        33 ~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g~~i~v  111 (380)
                      .+|||+|||+++++++|+++|++||.            |..+.+. ..|||||+|.+.++|++|| .|++..|.|+.|+|
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            37999999999999999999999997            7777765 4599999999999999999 79999999999988


Q ss_pred             ecC
Q 016936          112 RRP  114 (380)
Q Consensus       112 ~~~  114 (380)
                      .+.
T Consensus        68 ~~~   70 (87)
T d3begb1          68 AYI   70 (87)
T ss_dssp             CBC
T ss_pred             eEE
Confidence            764

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.56  E-value=1.3e-15  Score=110.61  Aligned_cols=77  Identities=17%  Similarity=0.126  Sum_probs=64.2

Q ss_pred             ccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecCceE
Q 016936           31 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  109 (380)
Q Consensus        31 ~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g~~i  109 (380)
                      ...+|||+|||++++++||+++|++||.+...      ..+.....+.++|+|||+|.+.++|.+|+ .+|+..+.|++|
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~------~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i   81 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGS------VCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKV   81 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTT------CEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcccceeE------EEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEE
Confidence            34679999999999999999999999986432      11222234566899999999999999999 799999999999


Q ss_pred             EEec
Q 016936          110 RVRR  113 (380)
Q Consensus       110 ~v~~  113 (380)
                      +|.+
T Consensus        82 ~v~l   85 (86)
T d2cqpa1          82 KLVL   85 (86)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            9975

>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=99.55  E-value=1.1e-15  Score=114.71  Aligned_cols=81  Identities=27%  Similarity=0.155  Sum_probs=66.5

Q ss_pred             hhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEE--ecCCCcEEEEEeCCHHHHHHHHHcCCcee
Q 016936           27 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVY--INHEKKFAFVEMRTVEEASNAMALDGIIF  104 (380)
Q Consensus        27 ~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~--~~~~~g~afV~f~~~~~a~~ai~l~~~~i  104 (380)
                      ..+....+|||+|||+++|++||+++|..+|.+.          +..+.  ....+|||||+|.+.++|++|+++|+..|
T Consensus        10 ~~~~~~~~v~v~nLp~~~te~dl~~~F~~~~~~~----------v~~~~~~~g~~~G~afVeF~~~~~a~~Al~~~~~~i   79 (102)
T d1weza_          10 FQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMR----------VHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANM   79 (102)
T ss_dssp             CCCSSSCEEEEESCCTTCCHHHHHHSSCSCCCSE----------EEEEESSSSCEEEEEEEECSSSHHHHHHHTTSSCCS
T ss_pred             CcCCCCCEEEEeCCCCcCCHHHHHHHHhccCcce----------eeeEEecCCcceEEEEEEECCHHHHHHHHHcCCCEE
Confidence            3456668999999999999999999999987421          22222  23457999999999999999999999999


Q ss_pred             cCceEEEecCCCC
Q 016936          105 EGVAVRVRRPTDY  117 (380)
Q Consensus       105 ~g~~i~v~~~~~~  117 (380)
                      .|+.|+|.++...
T Consensus        80 ~gR~I~V~~s~~~   92 (102)
T d1weza_          80 QHRYVELFLNSTA   92 (102)
T ss_dssp             SSSCCEEEEECCC
T ss_pred             CCEEEEEEEcCCC
Confidence            9999999986654

>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=99.54  E-value=1.3e-14  Score=105.71  Aligned_cols=77  Identities=14%  Similarity=0.092  Sum_probs=68.4

Q ss_pred             CCCCEEEEcCCCCC-CCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHh--CCCeeCCeEEEE
Q 016936          150 EGPDRVFVGGLPYY-FTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL--NGLKMGDKTLTV  226 (380)
Q Consensus       150 ~~~~~l~V~nlp~~-~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l--~g~~~~g~~i~v  226 (380)
                      ..++.|||+|||.. +|++||.++|++||.|..+.+.++      +++|||+|.+.++|..|+..+  ++..+.|++|+|
T Consensus         6 ~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~------k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V   79 (89)
T d1x4da1           6 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRV   79 (89)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc------ceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEE
Confidence            45589999999986 789999999999999999999765      358999999999999999966  678999999999


Q ss_pred             EEcccC
Q 016936          227 RRATAS  232 (380)
Q Consensus       227 ~~~~~~  232 (380)
                      .++...
T Consensus        80 ~~s~~~   85 (89)
T d1x4da1          80 HLSQKY   85 (89)
T ss_dssp             EEECCC
T ss_pred             EECCCc
Confidence            998643

>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=99.54  E-value=1e-15  Score=116.95  Aligned_cols=94  Identities=17%  Similarity=0.168  Sum_probs=73.7

Q ss_pred             CCCCccccchhhhcccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHH
Q 016936           17 PLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNA   96 (380)
Q Consensus        17 ~~~~~~~~~~~~~~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~a   96 (380)
                      |..+-....+.+....++|||+|||+++|++||+++|+.+|.+...      ..+..-..+.++|+|||+|.+.++|++|
T Consensus         3 p~~~~~~~~~~~~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~------~~~~~~~~g~~~G~afVeF~~~e~a~~a   76 (112)
T d1wela1           3 PSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDS------IYIAYGPNGKATGEGFVEFRNEADYKAA   76 (112)
T ss_dssp             CCCCCCCCCSSCCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTT------CEEEECTTSSEEEEEEEEBSSSHHHHHH
T ss_pred             CCCCCCCCCCCCCCCCeEEEEecCCCcCcHHHHhhHHhhccccccc------eeeecCcccceeeEEEEEECCHHHHHHH
Confidence            4444445555666778899999999999999999999999876431      1112222345679999999999999999


Q ss_pred             HHcCCceecCceEEEecCCC
Q 016936           97 MALDGIIFEGVAVRVRRPTD  116 (380)
Q Consensus        97 i~l~~~~i~g~~i~v~~~~~  116 (380)
                      +.+|+..|+|+.|+|.++..
T Consensus        77 l~~~~~~i~gR~i~V~~~~~   96 (112)
T d1wela1          77 LCRHKQYMGNRFIQVHPITK   96 (112)
T ss_dssp             HTSCSBCSTTSCBEEEEECH
T ss_pred             HHcCCCcCCCEEEEEEEcCh
Confidence            99999999999999987543

>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=99.54  E-value=4.7e-15  Score=108.03  Aligned_cols=78  Identities=22%  Similarity=0.214  Sum_probs=70.2

Q ss_pred             hhcccceEEEcCCCCc-CcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-Hc--CCce
Q 016936           28 ATRHARRVYVGGLPPL-ANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-AL--DGII  103 (380)
Q Consensus        28 ~~~~~~~v~V~nLp~~-~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l--~~~~  103 (380)
                      ....+++|||+|||.. +|++||.++|++||.            |.++.+.+++++|||.|.+.++|..|+ .+  ++..
T Consensus         4 ~~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~------------I~~i~i~~~k~~afV~f~~~~~A~~A~~~l~~~~~~   71 (89)
T d1x4da1           4 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGV------------ISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPAL   71 (89)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHHHHTTTGGGSC------------EEEEEECSSSSCEEEEESSHHHHHHHHHHHHHSCCE
T ss_pred             CCCCCcEEEEECCCCCcCCHHHHHHHHHhhCC------------eEEEEeeccceEEEEEEcchhhHHHHHHHHhhCCCc
Confidence            3567899999999986 899999999999998            888999999999999999999999999 44  6788


Q ss_pred             ecCceEEEecCCCC
Q 016936          104 FEGVAVRVRRPTDY  117 (380)
Q Consensus       104 i~g~~i~v~~~~~~  117 (380)
                      +.|++|+|.++..+
T Consensus        72 ~~gr~l~V~~s~~~   85 (89)
T d1x4da1          72 VFGKPVRVHLSQKY   85 (89)
T ss_dssp             ETTEECEEEEECCC
T ss_pred             cCCceEEEEECCCc
Confidence            99999999997654

>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=99.53  E-value=6.4e-15  Score=109.37  Aligned_cols=73  Identities=23%  Similarity=0.283  Sum_probs=65.8

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCceecCce
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  108 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g~~  108 (380)
                      +..++|||+|||++++++||+++|++||.            |..+.+. .+|||||+|.+.++|++|| .||+..|.|+.
T Consensus        13 ~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~------------v~~~~i~-~~g~afV~f~~~~~a~~Ai~~lng~~~~g~~   79 (98)
T d1wg4a_          13 RSDFRVLVSGLPPSGSWQDLKDHMREAGD------------VCYADVQ-KDGMGMVEYLRKEDMEYALRKLDDTKFRSHE   79 (98)
T ss_dssp             SCSCEEEEECCCSSCCHHHHHHHHTTSSC------------EEEEEEE-TTTEEEEEESSHHHHHHHHHHHSSEEEECTT
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhhcc------------ccccccc-ccceEEEEECCHHHHHHHHHHhCCCEeCCeE
Confidence            45778999999999999999999999997            6677665 5799999999999999999 79999999999


Q ss_pred             EEEecCC
Q 016936          109 VRVRRPT  115 (380)
Q Consensus       109 i~v~~~~  115 (380)
                      |+|.+..
T Consensus        80 i~v~~~~   86 (98)
T d1wg4a_          80 GETSYIR   86 (98)
T ss_dssp             SCEEEEE
T ss_pred             EEEEEEe
Confidence            9998754

>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=99.53  E-value=2.9e-16  Score=115.15  Aligned_cols=78  Identities=22%  Similarity=0.439  Sum_probs=68.2

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEe-----eCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEE
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLV-----KDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  227 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~-----~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~  227 (380)
                      ++|||+|||+++++++|+++|++||.+..+.+.     .+..+++++|||||+|.+.++|++|++ |||..+.|+.|+|+
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            689999999999999999999999998766553     233467889999999999999999986 99999999999998


Q ss_pred             Eccc
Q 016936          228 RATA  231 (380)
Q Consensus       228 ~~~~  231 (380)
                      ++..
T Consensus        81 r~k~   84 (90)
T d1u2fa_          81 RPHD   84 (90)
T ss_dssp             CTTC
T ss_pred             CCCC
Confidence            6543

>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=99.52  E-value=1.1e-14  Score=108.24  Aligned_cols=76  Identities=13%  Similarity=0.218  Sum_probs=67.9

Q ss_pred             CCCEEEEcCCCCC-CCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHH--HhCCCeeCCeEEEEE
Q 016936          151 GPDRVFVGGLPYY-FTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA--ALNGLKMGDKTLTVR  227 (380)
Q Consensus       151 ~~~~l~V~nlp~~-~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~--~l~g~~~~g~~i~v~  227 (380)
                      .+++|||+|||.+ +|+++|.++|++||.|.++.+.++      +|+|||+|.+.++|.+|++  .+++..+.|+.|+|.
T Consensus        17 ~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~   90 (99)
T d1x4fa1          17 LGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVD   90 (99)
T ss_dssp             CCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEE
T ss_pred             CCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEE
Confidence            3478999999985 899999999999999999999765      4799999999999999997  467889999999999


Q ss_pred             EcccC
Q 016936          228 RATAS  232 (380)
Q Consensus       228 ~~~~~  232 (380)
                      ++...
T Consensus        91 ~s~~~   95 (99)
T d1x4fa1          91 LSEKY   95 (99)
T ss_dssp             EECSC
T ss_pred             EcCCc
Confidence            98654

>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=99.51  E-value=1.3e-15  Score=114.62  Aligned_cols=79  Identities=13%  Similarity=0.071  Sum_probs=65.6

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEE--EEecCCCcEEEEEeCCHHHHHHHHHcCCceecCc
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVN--VYINHEKKFAFVEMRTVEEASNAMALDGIIFEGV  107 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~--~~~~~~~g~afV~f~~~~~a~~ai~l~~~~i~g~  107 (380)
                      ....+|||+|||+++|++||+++|+.||.+...        +..  -..+.++|+|||+|.+.++|++|+.+++..|.|+
T Consensus         6 ~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~--------~~~~~~~~g~~~G~afV~F~s~~~a~~Al~~n~~~i~gr   77 (103)
T d2cpya1           6 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENA--------VHVLVDNNGQGLGQALVQFKNEDDARKSERLHRKKLNGR   77 (103)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTT--------EEECCCTTSSCSSCEEEECSSHHHHHHHGGGCSEEETTE
T ss_pred             CCceEEEEeCCCCCCCHHHHhhhhcccceEEEE--------EEEEeCCCCCcCccEEEEECCHHHHHHHHhcCCCeECCc
Confidence            345679999999999999999999999975321        211  1234578999999999999999999999999999


Q ss_pred             eEEEecCCC
Q 016936          108 AVRVRRPTD  116 (380)
Q Consensus       108 ~i~v~~~~~  116 (380)
                      .|.|.++..
T Consensus        78 ~i~V~~~~~   86 (103)
T d2cpya1          78 EAFVHVVTL   86 (103)
T ss_dssp             EEEEEEECH
T ss_pred             EEEEEECCH
Confidence            999988654

>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=99.50  E-value=6.7e-15  Score=111.58  Aligned_cols=77  Identities=18%  Similarity=0.178  Sum_probs=65.8

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe--cCCCcEEEEEeCCHHHHHHHH-HcCCcee--
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI--NHEKKFAFVEMRTVEEASNAM-ALDGIIF--  104 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~--~~~~g~afV~f~~~~~a~~ai-~l~~~~i--  104 (380)
                      .+..+|||+|||+.+|+++|+++|++||.            |..+.+  .+++|+|||+|.+.++|++|+ .+++..|  
T Consensus         5 s~~~~v~V~NL~~~vte~~L~~~F~~~G~------------i~~~~i~~~~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~   72 (108)
T d2adba1           5 SPVLRIIVENLFYPVTLDVLHQIFSKFGT------------VLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYN   72 (108)
T ss_dssp             CCEEEEESCSCCSTTHHHHHHHHHTTTSC------------EEEEEEEEETTEEEEEEEESCHHHHHHHHHHHHSCCSST
T ss_pred             CCeEEEEEeCcCCCCCHHHHHHHHccCCc------------EEEEEEEeeCCCCeEEEEECCHHHHHHHHHHHCCCEecc
Confidence            45678999999999999999999999998            444443  457899999999999999999 8999988  


Q ss_pred             cCceEEEecCCCCC
Q 016936          105 EGVAVRVRRPTDYN  118 (380)
Q Consensus       105 ~g~~i~v~~~~~~~  118 (380)
                      ++++|+|.++...+
T Consensus        73 ~~~~l~v~~s~~~~   86 (108)
T d2adba1          73 ACCTLRIDFSKLTS   86 (108)
T ss_dssp             TCCCCEEEECSSCS
T ss_pred             CCcEEEEEecCCcc
Confidence            46889998876543

>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=99.50  E-value=1.6e-14  Score=108.25  Aligned_cols=78  Identities=13%  Similarity=0.098  Sum_probs=68.3

Q ss_pred             CCCCEEEEcCCCCCC-CH----HHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEE
Q 016936          150 EGPDRVFVGGLPYYF-TE----TQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTL  224 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~-t~----~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i  224 (380)
                      ....+|||+||+.++ ++    ++|.++|++||.|..+++.+.      +++|||+|.+.++|.+|+..|||..+.|++|
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            345799999999875 33    579999999999999999754      5699999999999999999999999999999


Q ss_pred             EEEEcccCC
Q 016936          225 TVRRATASS  233 (380)
Q Consensus       225 ~v~~~~~~~  233 (380)
                      +|.|+....
T Consensus        77 ~v~~a~~~~   85 (104)
T d1weya_          77 KLYFAQTLH   85 (104)
T ss_dssp             EEECCCCSS
T ss_pred             EEeecccCC
Confidence            999997653

>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=99.49  E-value=3.7e-14  Score=106.20  Aligned_cols=66  Identities=23%  Similarity=0.269  Sum_probs=57.7

Q ss_pred             HHHHHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEecc
Q 016936          300 EILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYP  369 (380)
Q Consensus       300 ~~~~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~  369 (380)
                      .++++|+++|++||.|.+|.|+++. ++.   ..|+|||+|.+.++|.+|++.|||++|+||+|+|+|.|
T Consensus        39 ~~ed~l~e~f~k~G~I~~v~I~~~~-~~~---~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~sP  104 (104)
T d1jmta_          39 FFEEVFTEMEEKYGEVEEMNVCDNL-GDH---LVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELSP  104 (104)
T ss_dssp             HHHHHHHHHHHHTCCEEEEEECCSS-SSS---SEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEECC
T ss_pred             hhHHHHHHHhccCCCEEEEEeecCC-CCC---EeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEECC
Confidence            3457899999999999999998764 332   35778999999999999999999999999999999976

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.49  E-value=1.6e-14  Score=108.17  Aligned_cols=77  Identities=9%  Similarity=-0.011  Sum_probs=68.6

Q ss_pred             cccceEEEcCCCCcCcH-----HHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCce
Q 016936           30 RHARRVYVGGLPPLANE-----QAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGII  103 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~-----~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~  103 (380)
                      ..+++|||+||+.++..     ++|+++|++||.            |.++.+.++++||||+|.+.++|.+|+ .||+..
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~------------i~~~~~~k~~~~afV~f~~~~~A~~Ai~~lng~~   70 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDK------------DTTFQYFKSFKRVRINFSNPLSAADARLRLHKTE   70 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCS------------SCEEEEETTTTEEEEECSSTTHHHHHHHTSTTSE
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhccccc------------ceEEEEecCCCEEEEEECCHHHHHHHHHHhcccc
Confidence            45789999999998733     569999999987            788898999999999999999999999 899999


Q ss_pred             ecCceEEEecCCCCC
Q 016936          104 FEGVAVRVRRPTDYN  118 (380)
Q Consensus       104 i~g~~i~v~~~~~~~  118 (380)
                      |.|++|+|.|+....
T Consensus        71 ~~g~~l~v~~a~~~~   85 (104)
T d1weya_          71 FLGKEMKLYFAQTLH   85 (104)
T ss_dssp             ETTEECEEECCCCSS
T ss_pred             cCCCEeEEeecccCC
Confidence            999999999986544

>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=99.47  E-value=7.4e-14  Score=101.66  Aligned_cols=64  Identities=20%  Similarity=0.335  Sum_probs=56.2

Q ss_pred             HHH---HHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEE
Q 016936          303 EDM---REECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAF  366 (380)
Q Consensus       303 ~~L---~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~  366 (380)
                      ++|   +++|++||.|.+|.++++...+......|+|||+|.++++|.+|++.|||..|+||.|+|+
T Consensus        23 ~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~lkvS   89 (89)
T d2cpia1          23 PEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKAS   89 (89)
T ss_dssp             HHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             HHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEEEEC
Confidence            577   6789999999999999887665544445789999999999999999999999999999986

>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=99.46  E-value=7e-15  Score=102.83  Aligned_cols=64  Identities=22%  Similarity=0.368  Sum_probs=56.4

Q ss_pred             EEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEe------cCCCcEEEEEeCCHHHHHHHH-HcCCceecCc
Q 016936           35 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  107 (380)
Q Consensus        35 v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~------~~~~g~afV~f~~~~~a~~ai-~l~~~~i~g~  107 (380)
                      |||+|||+++|+++|+++|++||.            |..+.+      ..++|+|||+|.+.++|++|+ .|||..+.|+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~------------v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr   68 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGK------------IVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQ   68 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSC------------EEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEE
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhcc------------ccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCE
Confidence            799999999999999999999998            444443      346799999999999999999 7999999998


Q ss_pred             eEE
Q 016936          108 AVR  110 (380)
Q Consensus       108 ~i~  110 (380)
                      .|+
T Consensus        69 ~~k   71 (72)
T d1x4ea1          69 MAK   71 (72)
T ss_dssp             SCC
T ss_pred             ECc
Confidence            764

>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=99.46  E-value=6.1e-15  Score=110.58  Aligned_cols=75  Identities=13%  Similarity=0.171  Sum_probs=70.5

Q ss_pred             EEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          154 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       154 ~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      .++|.+++..+++++|+++|++||.|.+|+|+++. +++++|+|||+|.+.++|.+|++.|||+.+.|++|+|++.
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 DVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             hHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCC-CCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            58888888889999999999999999999998874 7999999999999999999999999999999999999875

>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=99.40  E-value=2.7e-13  Score=96.25  Aligned_cols=73  Identities=19%  Similarity=0.285  Sum_probs=64.3

Q ss_pred             ccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHHHcCCceecCce-E
Q 016936           31 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVA-V  109 (380)
Q Consensus        31 ~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai~l~~~~i~g~~-i  109 (380)
                      +.+.|+|.|+|++++++.| .+|++||.            |.++++.++++||||+|.++++|++||++||..|.|+. |
T Consensus         3 ~~~wV~V~G~p~~~~~~il-~~F~~~G~------------I~~~~~~~~~~~~fV~f~~~~~A~~Al~~nG~~~~g~~~v   69 (81)
T d1wwha1           3 DDTWVTVFGFPQASASYIL-LQFAQYGN------------ILKHVMSNTGNWMHIRYQSKLQARKALSKDGRIFGESIMI   69 (81)
T ss_dssp             GGGEEEEECCCGGGHHHHH-HHHHTTSC------------EEEEEECSSSSEEEEEESSHHHHHHHHTTTTCEETTTEEC
T ss_pred             cccEEEEECCChHHHHHHH-HHHHhhhh------------hheEEecCCCCEEEEEEcccHHHHHHHhcCCCeECCcEEE
Confidence            5678999999999997655 68999998            88899999999999999999999999999999999975 6


Q ss_pred             EEecCCC
Q 016936          110 RVRRPTD  116 (380)
Q Consensus       110 ~v~~~~~  116 (380)
                      .|.+..+
T Consensus        70 gV~~~~~   76 (81)
T d1wwha1          70 GVKPCID   76 (81)
T ss_dssp             EEEECCC
T ss_pred             EEEeCCC
Confidence            7876544

>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=99.40  E-value=7.2e-13  Score=100.82  Aligned_cols=77  Identities=14%  Similarity=0.136  Sum_probs=66.8

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcCh-hHHHHHHHHhCCCeeCCeEEEE
Q 016936          148 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP-AVTDIACAALNGLKMGDKTLTV  226 (380)
Q Consensus       148 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~-~~A~~Ai~~l~g~~~~g~~i~v  226 (380)
                      ...+...+||+|||+.+|+++|+++|++||+|..|.++++      +|||||.|.++ ++|..|+..+++..+.++.+.|
T Consensus         7 ~~~g~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v   80 (113)
T d1owxa_           7 EKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEV   80 (113)
T ss_dssp             CCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSE
T ss_pred             CCCCCeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEE
Confidence            3445568899999999999999999999999999999754      57999999996 6799999999999888777777


Q ss_pred             EEcc
Q 016936          227 RRAT  230 (380)
Q Consensus       227 ~~~~  230 (380)
                      .+..
T Consensus        81 ~~~~   84 (113)
T d1owxa_          81 TWEV   84 (113)
T ss_dssp             EEEE
T ss_pred             EEee
Confidence            7764

>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=99.38  E-value=4.7e-13  Score=99.55  Aligned_cols=66  Identities=18%  Similarity=0.254  Sum_probs=59.9

Q ss_pred             hhcccceEEEcC--CCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHH-HcCCcee
Q 016936           28 ATRHARRVYVGG--LPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIF  104 (380)
Q Consensus        28 ~~~~~~~v~V~n--Lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai-~l~~~~i  104 (380)
                      .+.+.++++|.|  ||.++|+++|+++|++||.            |.++.+.++++||||+|.+.++|.+|+ .|||..+
T Consensus        14 ~~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~------------i~~i~~~~~k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGL------------VDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSC------------EEEEECCTTCSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCCCceEEEECCCCCCCCCHHHHHHHHHhhCc------------ccEEeeccCccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            346678899955  9999999999999999998            888999999999999999999999999 8999887


Q ss_pred             c
Q 016936          105 E  105 (380)
Q Consensus       105 ~  105 (380)
                      .
T Consensus        82 ~   82 (101)
T d2cq2a1          82 V   82 (101)
T ss_dssp             E
T ss_pred             C
Confidence            3

>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=99.35  E-value=1.3e-12  Score=97.05  Aligned_cols=62  Identities=23%  Similarity=0.360  Sum_probs=56.2

Q ss_pred             CCEEEEcC--CCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCee
Q 016936          152 PDRVFVGG--LPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM  219 (380)
Q Consensus       152 ~~~l~V~n--lp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~  219 (380)
                      .++++|.|  ||..+|+++|+++|++||.|..+++..+      ++||||+|.+.++|.+|+..|||+.+
T Consensus        18 t~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          18 TQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             CSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            46888855  9999999999999999999999988755      46999999999999999999999877

>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=99.35  E-value=1.9e-12  Score=95.91  Aligned_cols=80  Identities=18%  Similarity=0.361  Sum_probs=67.7

Q ss_pred             CCCCEEEEcCC--CCCCC---------HHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCe
Q 016936          150 EGPDRVFVGGL--PYYFT---------ETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLK  218 (380)
Q Consensus       150 ~~~~~l~V~nl--p~~~t---------~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~  218 (380)
                      ...++|+|+|+  |.++.         .++|++.|++||.|..+.+..+    ..+|+|||+|.+.++|.+|+..|||..
T Consensus         6 ~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~lng~~   81 (99)
T d2dita1           6 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDGRW   81 (99)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhCCcE
Confidence            34579999999  54321         2688999999999999988654    457999999999999999999999999


Q ss_pred             eCCeEEEEEEcccCC
Q 016936          219 MGDKTLTVRRATASS  233 (380)
Q Consensus       219 ~~g~~i~v~~~~~~~  233 (380)
                      +.|++|.|.+...+.
T Consensus        82 ~~gr~i~v~~~~g~~   96 (99)
T d2dita1          82 FGGRQITAQAWDGTT   96 (99)
T ss_dssp             ETTEECEEEECCSCC
T ss_pred             ECCEEEEEEEeCCcC
Confidence            999999999986543

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.31  E-value=1.8e-12  Score=91.86  Aligned_cols=71  Identities=18%  Similarity=0.218  Sum_probs=60.7

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeE-EEEEEccc
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKT-LTVRRATA  231 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~-i~v~~~~~  231 (380)
                      +.|+|.++|+..++ ++..+|++||.|.++++.      +++|||||+|.++++|++|++ +||..+.|+. |.|.++.+
T Consensus         5 ~wV~V~G~p~~~~~-~il~~F~~~G~I~~~~~~------~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~~   76 (81)
T d1wwha1           5 TWVTVFGFPQASAS-YILLQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCID   76 (81)
T ss_dssp             GEEEEECCCGGGHH-HHHHHHHTTSCEEEEEEC------SSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCC
T ss_pred             cEEEEECCChHHHH-HHHHHHHhhhhhheEEec------CCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCCC
Confidence            57999999999875 455689999999999874      346899999999999999996 8999999975 57888754

>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=99.27  E-value=1.2e-12  Score=99.59  Aligned_cols=70  Identities=11%  Similarity=0.050  Sum_probs=61.2

Q ss_pred             cceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCH-HHHHHHH-HcCCceecCceE
Q 016936           32 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTV-EEASNAM-ALDGIIFEGVAV  109 (380)
Q Consensus        32 ~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~-~~a~~ai-~l~~~~i~g~~i  109 (380)
                      ...+||+|||+.+|+++|+++|++||+            |.++.+.+++|||||.|.++ ++|..|+ .+++..+.++.+
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~fG~------------V~~v~i~~~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~   78 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSNHGE------------IKWIDFVRGAKEGIILFKEKAKEALGKAKDANNGNLQLRNK   78 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSSCC------------EEEEECCTTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSS
T ss_pred             CeEEEECCCCCCCCHHHHHHHHHhcCC------------hheEEEecCCceEEEEecCcHHHHHHHHHHhcCCceecCce
Confidence            345699999999999999999999998            89999999999999999996 6788888 899988877666


Q ss_pred             EEec
Q 016936          110 RVRR  113 (380)
Q Consensus       110 ~v~~  113 (380)
                      .|.|
T Consensus        79 ~v~~   82 (113)
T d1owxa_          79 EVTW   82 (113)
T ss_dssp             SEEE
T ss_pred             EEEE
Confidence            6655

>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=99.20  E-value=8.4e-12  Score=93.28  Aligned_cols=79  Identities=11%  Similarity=0.215  Sum_probs=67.4

Q ss_pred             CCEEEEcCC--CCCCC--------HHHHHHHHHhcCCeeEEEEeeCCCC--CCCceEEEEEEcChhHHHHHHHHhCCCee
Q 016936          152 PDRVFVGGL--PYYFT--------ETQIKELLESFGTLHGFDLVKDRDT--GNSKGYGFCVYQDPAVTDIACAALNGLKM  219 (380)
Q Consensus       152 ~~~l~V~nl--p~~~t--------~~~l~~~F~~~G~i~~v~l~~~~~~--~~~~g~afV~f~~~~~A~~Ai~~l~g~~~  219 (380)
                      ++.|.|.|+  |..+.        .+||++.|++||.|.+|.++++++.  ....|++||+|.+.++|.+|+..|||+.+
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            368999999  55443        3578999999999999999886543  24568999999999999999999999999


Q ss_pred             CCeEEEEEEcc
Q 016936          220 GDKTLTVRRAT  230 (380)
Q Consensus       220 ~g~~i~v~~~~  230 (380)
                      .||.|.+.+..
T Consensus        84 ~gR~v~v~f~~   94 (104)
T d1o0pa_          84 ANRVVVTKYCD   94 (104)
T ss_dssp             SSSCCEEEEEC
T ss_pred             CCeEEEEEEcC
Confidence            99999999975

>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=98.52  E-value=2.9e-07  Score=60.40  Aligned_cols=66  Identities=15%  Similarity=0.162  Sum_probs=57.8

Q ss_pred             HHHHHHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEeccc
Q 016936          299 EEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPE  370 (380)
Q Consensus       299 ~~~~~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~~  370 (380)
                      .++.+-|.+.|.++|.|.++.+....+..      -.|-|...+.++|..|+..||.+.|++++|.|+|++.
T Consensus         7 kelqq~L~~~f~~h~~V~sv~l~~~~dg~------~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~~   72 (73)
T d2dgxa1           7 KELQQLLQEAFARHGKVKSVELSPHTDYQ------LKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATG   72 (73)
T ss_dssp             HHHHHHHHHHHHHHSCEEEEEECSCCSTT------CCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             HHHHHHHHHHHHhheeEEEEEEEeccCCc------EEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEecC
Confidence            35667899999999999999998765322      3689999999999999999999999999999999874

>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=97.56  E-value=0.0001  Score=50.70  Aligned_cols=57  Identities=21%  Similarity=0.360  Sum_probs=50.4

Q ss_pred             HHHHHHHhhcccCCeEEEEecCCCCCCCCCCCccEEEEEeechhhHHHHHHHHcCcccCCeEEEEEecc
Q 016936          301 ILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYP  369 (380)
Q Consensus       301 ~~~~L~~~f~~~G~I~~v~i~~~~~~~~~~~g~g~afV~f~~~~~A~~A~~~l~g~~i~gr~l~v~~~~  369 (380)
                      ....|.+.|..||+|.-|++..+           ...|.|.+-..|.+|+. |+|..+.|+.|.++...
T Consensus        37 l~~~Llq~l~~~GeViLvRFv~d-----------~mwVTF~dG~SAL~al~-l~g~~v~G~~l~It~~~   93 (95)
T d1ufwa_          37 LRTELMQTLGSYGTIVLVRINQG-----------QMLVTFADSHSALSVLD-VDGMKVKGRAVKISGPS   93 (95)
T ss_dssp             HHHHHHHHHHHHSCCSEEEEETT-----------EEEEECSCSHHHHHHHH-GGGSEETTEEEEEECCC
T ss_pred             HHHHHHHHHhhCCeEEEEEEeCC-----------eEEEEECCcHHHHHHhc-cCCeEEcceEEEEecCC
Confidence            34789999999999999999763           56999999999999998 79999999999998653

>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=97.43  E-value=0.00051  Score=44.72  Aligned_cols=61  Identities=18%  Similarity=0.192  Sum_probs=52.2

Q ss_pred             HHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEcc
Q 016936          167 TQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  230 (380)
Q Consensus       167 ~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~~  230 (380)
                      +-|.+.|+++|.|.++.+.... .+..  .|-|...+..+|..|+..|+...+++++|.|.++.
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            3467889999999999987653 2433  58999999999999999999999999999999874

>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=97.28  E-value=0.00043  Score=47.49  Aligned_cols=54  Identities=15%  Similarity=0.290  Sum_probs=48.6

Q ss_pred             HHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhCCCeeCCeEEEEEEc
Q 016936          167 TQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  229 (380)
Q Consensus       167 ~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~~  229 (380)
                      .+|.+.|..||+|.=+++..+        ..+|.|.+-.+|-+|+. ++|.++.|+.|.|.-.
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            478899999999998999876        58999999999999998 6999999999999754

>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=97.24  E-value=0.00071  Score=47.17  Aligned_cols=67  Identities=13%  Similarity=0.229  Sum_probs=57.4

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCC--CceEEEEEEcChhHHHHHHHHhCCCee
Q 016936          153 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGN--SKGYGFCVYQDPAVTDIACAALNGLKM  219 (380)
Q Consensus       153 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~--~~g~afV~f~~~~~A~~Ai~~l~g~~~  219 (380)
                      ++|.|+.||+.+|++++.+.+...|.+........+.+..  .-.-|+|.|.+.++.....+..+|+.+
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            4899999999999999999999999988888877654432  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=96.84  E-value=0.0029  Score=44.05  Aligned_cols=58  Identities=19%  Similarity=0.389  Sum_probs=48.5

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCCceEEEEEEcChhHHHHHHHHhC
Q 016936          150 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN  215 (380)
Q Consensus       150 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~l~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~  215 (380)
                      .....||.-.+|..|...||.++|+.||.|. |.++.+-       -|||...+.++|+.++..++
T Consensus        13 p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~-VswIddT-------Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          13 PKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDDT-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCSEEEEECCTTCCHHHHHHHHTTTCSCC-CEEEETT-------EEEEECSCHHHHHHHHHHHH
T ss_pred             CCcceeEEEeCCcccchhHHHHHhcCCCceE-EEEecCc-------eEEEEecCHHHHHHHHHHhc
Confidence            3446899999999999999999999999984 5555442       69999999999999988654

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.57  E-value=0.001  Score=46.34  Aligned_cols=62  Identities=15%  Similarity=0.240  Sum_probs=47.3

Q ss_pred             ceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEec--C-----C-CcEEEEEeCCHHHHHHHH-HcCCce
Q 016936           33 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN--H-----E-KKFAFVEMRTVEEASNAM-ALDGII  103 (380)
Q Consensus        33 ~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~--~-----~-~g~afV~f~~~~~a~~ai-~l~~~~  103 (380)
                      ++|.|+.||+.+||+++.+.++..|.            +.-....  +     + -.-|||.|.+.++..... ..+|..
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~------------~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~   69 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPE------------HDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYV   69 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCC------------EEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCc------------eEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcE
Confidence            58999999999999999998875543            3333322  1     1 257999999999999999 799888


Q ss_pred             ecC
Q 016936          104 FEG  106 (380)
Q Consensus       104 i~g  106 (380)
                      +.+
T Consensus        70 F~D   72 (91)
T d1uw4a_          70 FLD   72 (91)
T ss_dssp             EEC
T ss_pred             EEc
Confidence            754

>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=90.44  E-value=0.12  Score=35.74  Aligned_cols=55  Identities=18%  Similarity=0.235  Sum_probs=43.4

Q ss_pred             cccceEEEcCCCCcCcHHHHHHHHHHHHHhccCCCCCCCCeeEEEEecCCCcEEEEEeCCHHHHHHHHH
Q 016936           30 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA   98 (380)
Q Consensus        30 ~~~~~v~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~i~~~~~~~~~g~afV~f~~~~~a~~ai~   98 (380)
                      .....||.-..|..+...||.++|+.||.|.           ++ -+  +--.|||...+.++|..++.
T Consensus        13 p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~-----------Vs-wI--ddTSa~V~L~~~e~~~~v~~   67 (100)
T d1whva_          13 PKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQ-----------IS-WI--DDTSAFVSLSQPEQVQIAVN   67 (100)
T ss_dssp             CCCCSEEEEECCTTCCHHHHHHHHTTTCSCC-----------CE-EE--ETTEEEEECSCHHHHHHHHH
T ss_pred             CCcceeEEEeCCcccchhHHHHHhcCCCceE-----------EE-Ee--cCceEEEEecCHHHHHHHHH
Confidence            3445689999999999999999999998742           22 22  22369999999999998884