Citrus Sinensis ID: 013141

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------45
Protein Sequence
MQQSNGGDANAAAAAAAAVSGGAGGGSQPTPQQPYHWVPPHQQQWMAMMQYPAAAMAMMQQQQMMMYPHHYMPYGGGGHPYYQNGGGVKQQQQQQHGLSNGKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQWRGDHSNHWNGAHYGGQGYSGNGYAFPPNQDPNMYAATAVPGAS
Secondary Structure (PSIPRED)
cccccccccHHHHHHHHHcccccccccccccccccccccccHHHHHHHHccHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccccHHHHHHHHHcccccEEEEEEEcccccccccEEEEEcccHHHHHHHHHHHcccccccccccEEEEcccccccccccccccccEEEEccccccccHHHHHHHHccccccccEEEEEEcccccccccEEEEEEccHHHHHHHHHHHcccccccccEEEEEcccccccccccccHHHHHHHcccccccccccccccccccccccEEEEccccccccHHHHHHHHcccccEEEEEEEccccEEEEEcccHHHHHHHHHHHcccEEccEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHccccccccccEEEEEccccccccHHHHHHHHcccccEEEEEEEEEccccccccEEEEEEccHHHHHHHHHHHcccEcccccEEEEEEccccccccccccccccEEEEEEcccccccHHHHHHHHcHHcccEEEEEEEEccccccccccEEEEcccHHHHHHHHHHHcccEEcccEEEEEcccccHHHHHHHHHHHHHHHHHcccccccccccccccccccccEEEEEEcccccccHHHHHHHHcccccEEEEEEEcccccEEEEEccHHHHHHHHHHHcccEEcccEEEEEEcccHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mqqsnggdANAAAAAAAAVsggagggsqptpqqpyhwvpphQQQWMAMMQYPAAAMAMMQQQQMmmyphhympygggghpyyqngggvkqqqqqqhglsngkqngsnnnftndetktiwiGDLFhwmdetflhncfshtgQVVNVKVIRnkqtgqsegygfVEFYSRAAAEKVLQSysgslmpntdqpfrlnwatfsgsdrrteacsdlsifvgdlapdvtdsilqetfsskypsvkgakviidsntgrtkgygfvrfgdeneRSRAMTEmngvycssrpmridvatpkkasgyqqqYSSQALvlaggpgsngarvqgsqsdgesnnatIFVGaldsdvsdedlrepfsqfgeilsvkipvgkgcgfvqfANRKDAEVALQKLQGTAIGKQTVrlswgrnpgnkqwrgdhsnhwngahyggqgysgngyafppnqdpnmyaatavpgas
Flexible Loop (DISEMBL)
MQQSNGGDANAAAAAAAAVSGGAGGGSQPTPQQPYHWVPPHQQQWMAMMQYPAAAMAMMQQQQMMMYPHHYMPYGGGGHPYYQNGGGVKQQQQQQHGLSngkqngsnnnfTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSlmpntdqpfrLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQEtfsskypsvkgakviidsntgrtkgygfvrfgdenersrAMTEmngvycssrpMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQgtaigkqtvrlswgRNPGNKQWRGDHSNHWNGAHYGGQGYSGNGYAFPPNQDPNMYAATAVPGAS
Low Complexity Region (SEG)
MQQSNggdanaaaaaaaavsggagggSQPTPQQPYHWVPPHqqqwmammqypaaamammqqqqmmmyphhympygggghpyyqngggvkqqqqqqhglsngkqNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKASGyqqqyssqALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQWRGDHSNHWNGAHYGGQGYSGNGYAFPPNQDPNMYAATAVPGAS
Disordered region (IsUnstruct)
***********************************HWVPPHQQQWMAMMQYPAAAMAMMQQQQMMMYPHHYMPYGGGGHPYY********************************TKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFG**************VYC*****************************************************IFVGAL**********EPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQWRGDHSNHWNGAHYGGQGYSGNGYA*******************
Disordered Region (DISOPRED)
*********************************************************************************************************************IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRL*******************IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRID****************************************SNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLS***************************************DPNMY*********
Disordered Region (DISEMBL)
*******************************QQPYHWVPPHQQQWMAMMQYPAAAMAMMQQQQMMMYPHHYMPYGGGGHPYYQNGG**************GKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVAT*********QYSSQALVLAGG****************SNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQWRGDHSNHWNGAHYGGQGYSGNGYAFPPNQDPNMYAATAVPGAS
Disordered Region (DISPRO)
***********************************HW*******WMAMMQYPAAAMAMMQQQQMMMYPHHYMPYGGGGHPYYQNGGGV*Q******GLSNGKQ**SNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATFSGS**R*EACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGP*************GESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQWRGDHSNHWNGAHYGGQGYSGNGYAFPPNQDPNMYAATAVP***
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MQQSNGGDANAAAAAAAAVSGGAGGGSQPTPQQPYHWVPPHQQQWMAMMQYPAAAMAMMQQQQMMMYPHHYMPYGGGGHPYYQNGGGVKQQQQQQHGLSNGKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQWRGDHSNHWNGAHYGGQGYSGNGYAFPPNQDPNMYAATAVPGAS
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	449	2.2.26 [Sep-21-2011]
Q0WW84	435	Polyadenylate-binding pro	yes	no	0.815	0.841	0.683	1e-141
Q9LEB3	428	Polyadenylate-binding pro	N/A	no	0.752	0.789	0.672	1e-136
F4I3B3	445	Polyadenylate-binding pro	no	no	0.728	0.734	0.711	1e-136
Q9SX79	432	Polyadenylate-binding pro	no	no	0.828	0.861	0.548	1e-121
Q9SX80	434	Polyadenylate-binding pro	no	no	0.757	0.783	0.606	1e-119
Q8VXZ9	425	Polyadenylate-binding pro	no	no	0.730	0.771	0.547	1e-100
Q9SAB3	405	Polyadenylate-binding pro	no	no	0.685	0.760	0.569	2e-98
Q9LEB4	409	Polyadenylate-binding pro	N/A	no	0.752	0.826	0.519	1e-95
Q9FPJ8	387	Polyadenylate-binding pro	no	no	0.719	0.834	0.518	3e-92
Q93W34	415	Polyadenylate-binding pro	no	no	0.688	0.744	0.529	4e-88

>sp|Q0WW84|RB47B_ARATH Polyadenylate-binding protein RBP47B OS=Arabidopsis thaliana GN=RBP47B PE=2 SV=1

 Score =  502 bits (1293), Expect = e-141,   Method: Compositional matrix adjust.
 Identities = 259/379 (68%), Positives = 305/379 (80%), Gaps = 13/379 (3%)

Query: 45  WMAMMQYP-AAAMAMMQQQQMMMYPHHYMPYGGGGHPYYQNGGGVKQQQQQQHG---LSN 100
           WMA MQYP AAAM MMQQQQM+MYPH Y+PY  G  PY Q+       Q  Q+G      
Sbjct: 40  WMAAMQYPPAAAMMMMQQQQMLMYPHQYVPYNQG--PYQQH-----HPQLHQYGSYQQHQ 92

Query: 101 GKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYG 160
            +Q+ + +  + D+ KT+W+GDL HWMDET+LH+CFSHTG+V +VKVIRNK T QSEGYG
Sbjct: 93  HQQHKAIDRGSGDDVKTLWVGDLLHWMDETYLHSCFSHTGEVSSVKVIRNKLTSQSEGYG 152

Query: 161 FVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATFS-GSDRRTEACSDLSIFVGDLAPD 219
           FVEF SRAAAE+VLQ+YSGS+MPN+DQPFR+NWA+FS G  R  E   DLS+FVGDL+PD
Sbjct: 153 FVEFLSRAAAEEVLQNYSGSVMPNSDQPFRINWASFSTGEKRAVENGPDLSVFVGDLSPD 212

Query: 220 VTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSR 279
           VTD +L ETFS +YPSVK AKV+IDSNTGR+KGYGFVRFGDENERSRA+TEMNG YCS+R
Sbjct: 213 VTDVLLHETFSDRYPSVKSAKVVIDSNTGRSKGYGFVRFGDENERSRALTEMNGAYCSNR 272

Query: 280 PMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDV 339
            MR+ +ATPK+A   QQQ+SSQA++LAGG GSNG+   GSQSDGES NATIFVG +D DV
Sbjct: 273 QMRVGIATPKRAIANQQQHSSQAVILAGGHGSNGSMGYGSQSDGESTNATIFVGGIDPDV 332

Query: 340 SDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGR 399
            DEDLR+PFSQFGE++SVKIPVGKGCGFVQFA+RK AE A++ L GT IGK TVRLSWGR
Sbjct: 333 IDEDLRQPFSQFGEVVSVKIPVGKGCGFVQFADRKSAEDAIESLNGTVIGKNTVRLSWGR 392

Query: 400 NPGNKQWRGDHSNHWNGAH 418
           +P NKQWRGD    WNG +
Sbjct: 393 SP-NKQWRGDSGQQWNGGY 410

Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation.
Arabidopsis thaliana (taxid: 3702)

>sp|Q9LEB3|RBP47_NICPL Polyadenylate-binding protein RBP47 OS=Nicotiana plumbaginifolia GN=RBP47 PE=1 SV=1

 Score =  486 bits (1250), Expect = e-136,   Method: Compositional matrix adjust.
 Identities = 228/339 (67%), Positives = 279/339 (82%), Gaps = 1/339 (0%)

Query: 111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAA 170
           ++++ KTIWIGDL  WMDE++LH+CFS  G+V++VK+IRNKQTGQSE YGFVEF + AAA
Sbjct: 79  SSEDNKTIWIGDLQQWMDESYLHSCFSQAGEVISVKIIRNKQTGQSERYGFVEFNTHAAA 138

Query: 171 EKVLQSYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFS 230
           EKVLQSY+G++MPNT+QPFRLNWA FS  ++R E  SD SIFVGDLA DVTD++L++TF+
Sbjct: 139 EKVLQSYNGTMMPNTEQPFRLNWAGFSTGEKRAETGSDFSIFVGDLASDVTDTMLRDTFA 198

Query: 231 SKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKK 290
           S+YPS+KGAKV++D+NTG +KGYGFVRFGDE+ERSRAMTEMNGVYCSSR MRI VATPKK
Sbjct: 199 SRYPSLKGAKVVVDANTGHSKGYGFVRFGDESERSRAMTEMNGVYCSSRAMRIGVATPKK 258

Query: 291 ASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQ 350
            S + +QYSSQA++L+GG  SNGA   GSQSDG+S+N TIFVG LDS+V+DE+LR+ F+Q
Sbjct: 259 PSAH-EQYSSQAVILSGGYASNGAATHGSQSDGDSSNTTIFVGGLDSEVTDEELRQSFNQ 317

Query: 351 FGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQWRGDH 410
           FGE++SVKIP GKGCGFVQF++R  A+ A+QKL G  IGKQ VRLSWGR+P NKQ R D 
Sbjct: 318 FGEVVSVKIPAGKGCGFVQFSDRSSAQEAIQKLSGAIIGKQAVRLSWGRSPANKQMRTDS 377

Query: 411 SNHWNGAHYGGQGYSGNGYAFPPNQDPNMYAATAVPGAS 449
            + WNG + G Q Y G GY    NQD  MYA  A  GAS
Sbjct: 378 GSQWNGGYNGRQNYGGYGYGASQNQDSGMYATGAAYGAS 416

Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation.

Nicotiana plumbaginifolia (taxid: 4092)

>sp|F4I3B3|RB47A_ARATH Polyadenylate-binding protein RBP47A OS=Arabidopsis thaliana GN=RBP47A PE=2 SV=1

 Score =  484 bits (1247), Expect = e-136,   Method: Compositional matrix adjust.
 Identities = 242/340 (71%), Positives = 278/340 (81%), Gaps = 13/340 (3%)

Query: 113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEK 172
           D+ KT+W+GDL HWMDET+LH CFSHT +V +VKVIRNKQT QSEGYGFVEF SR+AAE+
Sbjct: 116 DDVKTLWVGDLLHWMDETYLHTCFSHTNEVSSVKVIRNKQTCQSEGYGFVEFLSRSAAEE 175

Query: 173 VLQSYSGSLMPNTDQPFRLNWATFS-GSDRRTEACSDLSIFVGDLAPDVTDSILQETFSS 231
            LQS+SG  MPN +QPFRLNWA+FS G  R +E   DLSIFVGDLAPDV+D++L ETF+ 
Sbjct: 176 ALQSFSGVTMPNAEQPFRLNWASFSTGEKRASENGPDLSIFVGDLAPDVSDAVLLETFAG 235

Query: 232 KYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKA 291
           +YPSVKGAKV+IDSNTGR+KGYGFVRFGDENERSRAMTEMNG +CSSR MR+ +ATPK+A
Sbjct: 236 RYPSVKGAKVVIDSNTGRSKGYGFVRFGDENERSRAMTEMNGAFCSSRQMRVGIATPKRA 295

Query: 292 SGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQF 351
           + Y QQ  SQAL LAGG G N     GS SDGESNN+TIFVG LD+DV++EDL +PFS F
Sbjct: 296 AAYGQQNGSQALTLAGGHGGN-----GSMSDGESNNSTIFVGGLDADVTEEDLMQPFSDF 350

Query: 352 GEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQWRGDHS 411
           GE++SVKIPVGKGCGFVQFANR+ AE A+  L GT IGK TVRLSWGR+P NKQWR D  
Sbjct: 351 GEVVSVKIPVGKGCGFVQFANRQSAEEAIGNLNGTVIGKNTVRLSWGRSP-NKQWRSDSG 409

Query: 412 NHWNGAHYGGQGYSGNGYAFPPNQDPNMY--AATAVPGAS 449
           N WNG +  GQGY+ NGYA   NQD NMY  AA AVPGAS
Sbjct: 410 NQWNGGYSRGQGYN-NGYA---NQDSNMYATAAAAVPGAS 445

Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SX79|RB47C_ARATH Polyadenylate-binding protein RBP47C OS=Arabidopsis thaliana GN=RBP47C PE=2 SV=1

 Score =  435 bits (1118), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 230/419 (54%), Positives = 280/419 (66%), Gaps = 47/419 (11%)

Query: 27  SQPTPQQPYHWVPPHQQQWMAMMQYPAAAMAMMQQQQMMMYPHHYMPYGGGGHPYYQNGG 86
           + PTP  P HW           M+YP   +      QMM  P  + PY            
Sbjct: 43  TSPTP--PPHW-----------MRYPPTVII---PHQMMYAPPPFPPY------------ 74

Query: 87  GVKQQQQQQHGLSNGKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFS--HTGQVVN 144
               Q    H L +  +   + N  N E KTIW+GDL HWMDE +L++ F+     ++V+
Sbjct: 75  ---HQYPNHHHLHHQSRGNKHQNAFNGENKTIWVGDLHHWMDEAYLNSSFASGDEREIVS 131

Query: 145 VKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATFSGSDRRTE 204
           VKVIRNK  G SEGYGFVEF S   A+KVL+ ++G+ MPNTDQPFRLNWA+FS  ++R E
Sbjct: 132 VKVIRNKNNGLSEGYGFVEFESHDVADKVLREFNGTTMPNTDQPFRLNWASFSTGEKRLE 191

Query: 205 AC-SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENE 263
               DLSIFVGDL+PDV+D++L ETFS KYPSVK AKV++D+NTGR+KGYGFVRFGDENE
Sbjct: 192 NNGPDLSIFVGDLSPDVSDNLLHETFSEKYPSVKAAKVVLDANTGRSKGYGFVRFGDENE 251

Query: 264 RSRAMTEMNGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDG 323
           R++AMTEMNGV CSSR MRI  ATP+K +GYQQQ         GG   NG     ++ +G
Sbjct: 252 RTKAMTEMNGVKCSSRAMRIGPATPRKTNGYQQQ---------GGYMPNGTL---TRPEG 299

Query: 324 ESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKL 383
           +  N TIFVG LDS V+DEDL++PF++FGEI+SVKIPVGKGCGFVQF NR +AE AL+KL
Sbjct: 300 DIMNTTIFVGGLDSSVTDEDLKQPFNEFGEIVSVKIPVGKGCGFVQFVNRPNAEEALEKL 359

Query: 384 QGTAIGKQTVRLSWGRNPGNKQWRGDHSNHWNGAHYGGQGYSGNGYAFPPNQDPNMYAA 442
            GT IGKQTVRLSWGRNP NKQ R  + N W   +YGGQ Y+G GY   P  DP MY A
Sbjct: 360 NGTVIGKQTVRLSWGRNPANKQPRDKYGNQWVDPYYGGQFYNGYGYMV-PQPDPRMYPA 417

Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SX80|R47CP_ARATH Polyadenylate-binding protein RBP47C' OS=Arabidopsis thaliana GN=RBP47C' PE=2 SV=1

 Score =  427 bits (1098), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 216/356 (60%), Positives = 263/356 (73%), Gaps = 16/356 (4%)

Query: 90  QQQQQQHGLSNGKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFS--HTGQVVNVKV 147
            Q    H   +  +   + N  N E KTIW+GDL +WMDE +L++ F+     ++V++KV
Sbjct: 77  HQYPNHHHFHHQSRGNKHQNAFNGENKTIWVGDLQNWMDEAYLNSAFTSAEEREIVSLKV 136

Query: 148 IRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATFSGSDRRTEAC- 206
           IRNK  G SEGYGFVEF S   A+KVLQ ++G+ MPNTDQPFRLNWA+FS  ++R E   
Sbjct: 137 IRNKHNGSSEGYGFVEFESHDVADKVLQEFNGAPMPNTDQPFRLNWASFSTGEKRLENNG 196

Query: 207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSR 266
            DLSIFVGDLAPDV+D++L ETFS KYPSVK AKV++D+NTGR+KGYGFVRFGDENER++
Sbjct: 197 PDLSIFVGDLAPDVSDALLHETFSEKYPSVKAAKVVLDANTGRSKGYGFVRFGDENERTK 256

Query: 267 AMTEMNGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESN 326
           AMTEMNGV CSSR MRI  ATP+K +GYQQQ         GG   +GA    ++S+G++ 
Sbjct: 257 AMTEMNGVKCSSRAMRIGPATPRKTNGYQQQ---------GGYMPSGAF---TRSEGDTI 304

Query: 327 NATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGT 386
           N TIFVG LDS V+DEDL++PFS+FGEI+SVKIPVGKGCGFVQF NR +AE AL+KL GT
Sbjct: 305 NTTIFVGGLDSSVTDEDLKQPFSEFGEIVSVKIPVGKGCGFVQFVNRPNAEEALEKLNGT 364

Query: 387 AIGKQTVRLSWGRNPGNKQWRGDHSNHWNGAHYGGQGYSGNGYAFPPNQDPNMYAA 442
            IGKQTVRLSWGRNP NKQ R  + N W   +YGGQ Y+G GY   P  DP MY A
Sbjct: 365 VIGKQTVRLSWGRNPANKQPRDKYGNQWVDPYYGGQFYNGYGYMV-PQPDPRMYPA 419

Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation.

Arabidopsis thaliana (taxid: 3702)

>sp|Q8VXZ9|R47BP_ARATH Polyadenylate-binding protein RBP47B' OS=Arabidopsis thaliana GN=RBP47B' PE=2 SV=1

 Score =  366 bits (939), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 183/334 (54%), Positives = 240/334 (71%), Gaps = 6/334 (1%)

Query: 111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAA 170
           T +E +T+WIGDL +W+DE +L +CFS TG++V+VKVIRNK TGQ EGYGF+EF S AAA
Sbjct: 19  TLEEVRTLWIGDLQYWVDENYLTSCFSQTGELVSVKVIRNKITGQPEGYGFIEFISHAAA 78

Query: 171 EKVLQSYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFS 230
           E+ LQ+Y+G+ MP T+  FRLNWA+F GS ++ +A  D SIFVGDLAPDVTD +LQETF 
Sbjct: 79  ERTLQTYNGTQMPGTELTFRLNWASF-GSGQKVDAGPDHSIFVGDLAPDVTDYLLQETFR 137

Query: 231 SKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKK 290
             Y SV+GAKV+ D +TGR+KGYGFV+F +E+ER+RAM EMNG+YCS+RPMRI  ATPKK
Sbjct: 138 VHYSSVRGAKVVTDPSTGRSKGYGFVKFAEESERNRAMAEMNGLYCSTRPMRISAATPKK 197

Query: 291 ASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESN--NATIFVGALDSDVSDEDLREPF 348
             G QQQY ++A+     P +  A VQ   +  ES+    TI V  LD +V++E+L++ F
Sbjct: 198 NVGVQQQYVTKAVYPVTVPSAVAAPVQAYVAPPESDVTCTTISVANLDQNVTEEELKKAF 257

Query: 349 SQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQWRG 408
           SQ GE++ VKIP  KG G+VQF  R  AE A+Q++QG  IG+Q VR+SW +NPG   W  
Sbjct: 258 SQLGEVIYVKIPATKGYGYVQFKTRPSAEEAVQRMQGQVIGQQAVRISWSKNPGQDGWVT 317

Query: 409 D-HSNHWNGAHYGGQGYSGNGYAFPPNQDPNMYA 441
               N WNG +  GQ    + YA+   QDP++YA
Sbjct: 318 QADPNQWNGYYGYGQ--GYDAYAYGATQDPSVYA 349

Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SAB3|RB45B_ARATH Polyadenylate-binding protein RBP45B OS=Arabidopsis thaliana GN=RBP45B PE=1 SV=1

 Score =  359 bits (922), Expect = 2e-98,   Method: Compositional matrix adjust.
 Identities = 188/330 (56%), Positives = 232/330 (70%), Gaps = 22/330 (6%)

Query: 111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAA 170
           T DE +T+WIGDL +WMDE FL+ CF+HTG++V+ KVIRNKQTGQ EGYGF+EF S AAA
Sbjct: 57  TADEIRTLWIGDLQYWMDENFLYGCFAHTGEMVSAKVIRNKQTGQVEGYGFIEFASHAAA 116

Query: 171 EKVLQSYSGSLMPN-TDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETF 229
           E+VLQ+++ + +P+  DQ FRLNWA+ S  D+R ++  D +IFVGDLA DVTD IL ETF
Sbjct: 117 ERVLQTFNNAPIPSFPDQLFRLNWASLSSGDKRDDS-PDYTIFVGDLAADVTDYILLETF 175

Query: 230 SSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPK 289
            + YPSVKGAKV+ID  TGRTKGYGFVRF DE+E+ RAMTEMNGV CS+RPMRI  A  K
Sbjct: 176 RASYPSVKGAKVVIDRVTGRTKGYGFVRFSDESEQIRAMTEMNGVPCSTRPMRIGPAASK 235

Query: 290 K-ASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPF 348
           K  +G +  Y S A               G  +D + NN T+FVG LD+ V+D+ L+  F
Sbjct: 236 KGVTGQRDSYQSSA--------------AGVTTDNDPNNTTVFVGGLDASVTDDHLKNVF 281

Query: 349 SQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQWRG 408
           SQ+GEI+ VKIP GK CGFVQF+ +  AE AL+ L G  +G  TVRLSWGR+P NKQ  G
Sbjct: 282 SQYGEIVHVKIPAGKRCGFVQFSEKSCAEEALRMLNGVQLGGTTVRLSWGRSPSNKQ-SG 340

Query: 409 DHSNHWNGAHYGGQGYSGNGYAFPPNQDPN 438
           D S  + G +  GQG    GY  P  QDPN
Sbjct: 341 DPSQFYYGGY--GQGQEQYGYTMP--QDPN 366

Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LEB4|RBP45_NICPL Polyadenylate-binding protein RBP45 OS=Nicotiana plumbaginifolia GN=RBP45 PE=1 SV=1

 Score =  350 bits (899), Expect = 1e-95,   Method: Compositional matrix adjust.
 Identities = 183/352 (51%), Positives = 233/352 (66%), Gaps = 14/352 (3%)

Query: 89  KQQQQQQHGLSNGKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVI 148
           +Q  QQQ+G         +     +E +++WIGDL +WMDE +L  CF HTG++V+ KVI
Sbjct: 57  QQPSQQQYGAMATTNPNPSPTGNPNEVRSLWIGDLQYWMDENYLSTCFYHTGELVSAKVI 116

Query: 149 RNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATFSGSDRRTEACSD 208
           RNKQTGQSEGYGF+EF S AAAE +LQ+Y+G+LMPN +Q FR+NWA+    +RR ++ ++
Sbjct: 117 RNKQTGQSEGYGFLEFRSHAAAETILQTYNGTLMPNVEQNFRMNWASLGAGERRDDS-AE 175

Query: 209 LSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAM 268
            +IFVGDLA DVTD ILQETF S Y SV+GAKV+ D  TGR+KGYGFV+F DE+E+ RAM
Sbjct: 176 HTIFVGDLAADVTDYILQETFKSVYSSVRGAKVVTDRITGRSKGYGFVKFADESEQLRAM 235

Query: 269 TEMNGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNA 328
           TEMNGV CS+RPMRI  A  KK  G  Q+ + Q               Q +Q + + NN 
Sbjct: 236 TEMNGVLCSTRPMRIGPAANKKPVGTPQKATYQ-------------NPQATQGESDPNNT 282

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAI 388
           TIFVG LD  V++E LR+ FS +GE++ VKI  GK CGFVQF  R  AE AL  L GT +
Sbjct: 283 TIFVGGLDPTVAEEHLRQVFSPYGELVHVKIVAGKRCGFVQFGTRASAEQALSSLNGTQL 342

Query: 389 GKQTVRLSWGRNPGNKQWRGDHSNHWNGAHYGGQGYSGNGYAFPPNQDPNMY 440
           G Q++RLSWGR+P +KQ          GA+YG           PP QDPNMY
Sbjct: 343 GGQSIRLSWGRSPSSKQTDQTQWGGSGGAYYGYGQGYEAYGYAPPAQDPNMY 394

Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation.

Nicotiana plumbaginifolia (taxid: 4092)

>sp|Q9FPJ8|RB45A_ARATH Polyadenylate-binding protein RBP45A OS=Arabidopsis thaliana GN=RBP45A PE=2 SV=1

 Score =  339 bits (869), Expect = 3e-92,   Method: Compositional matrix adjust.
 Identities = 182/351 (51%), Positives = 232/351 (66%), Gaps = 28/351 (7%)

Query: 93  QQQHGLSNGKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQ 152
           Q Q+G+      GS N  +  + K++WIGDL  WMDE ++ + F+ +G+  + KVIRNK 
Sbjct: 43  QHQYGI------GSQNPGSASDVKSLWIGDLQQWMDENYIMSVFAQSGEATSAKVIRNKL 96

Query: 153 TGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATFSGSDRRTEA-CSDLSI 211
           TGQSEGYGF+EF S + AE+VLQ+Y+G+ MP+T+Q FRLNWA     ++R +    D +I
Sbjct: 97  TGQSEGYGFIEFVSHSVAERVLQTYNGAPMPSTEQTFRLNWAQAGAGEKRFQTEGPDHTI 156

Query: 212 FVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEM 271
           FVGDLAP+VTD +L +TF + Y SVKGAKV++D  TGR+KGYGFVRF DENE+ RAMTEM
Sbjct: 157 FVGDLAPEVTDYMLSDTFKNVYGSVKGAKVVLDRTTGRSKGYGFVRFADENEQMRAMTEM 216

Query: 272 NGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIF 331
           NG YCS+RPMRI  A  K A         Q  +     G+N         D + NN TIF
Sbjct: 217 NGQYCSTRPMRIGPAANKNA------LPMQPAMYQNTQGANAG-------DNDPNNTTIF 263

Query: 332 VGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQ 391
           VG LD++V+D++L+  F QFGE+L VKIP GK CGFVQ+AN+  AE AL  L GT +G Q
Sbjct: 264 VGGLDANVTDDELKSIFGQFGELLHVKIPPGKRCGFVQYANKASAEHALSVLNGTQLGGQ 323

Query: 392 TVRLSWGRNPGNKQWRGDHSNHWNGAHYGG---QGYSGNGYAF-PPNQDPN 438
           ++RLSWGR+P NKQ        WNG  Y G   Q   G GYA  PP QDPN
Sbjct: 324 SIRLSWGRSP-NKQ---SDQAQWNGGGYYGYPPQPQGGYGYAAQPPTQDPN 370

Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation.

Arabidopsis thaliana (taxid: 3702)

>sp|Q93W34|RP45C_ARATH Polyadenylate-binding protein RBP45C OS=Arabidopsis thaliana GN=RBP45C PE=2 SV=1

 Score =  325 bits (833), Expect = 4e-88,   Method: Compositional matrix adjust.
 Identities = 173/327 (52%), Positives = 215/327 (65%), Gaps = 18/327 (5%)

Query: 114 ETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKV 173
           E +++WIGDL  WMDE +L N F  TG+    KVIRNKQ G SEGYGF+EF + A AE+ 
Sbjct: 78  EIRSLWIGDLQPWMDENYLMNVFGLTGEATAAKVIRNKQNGYSEGYGFIEFVNHATAERN 137

Query: 174 LQSYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKY 233
           LQ+Y+G+ MP+++Q FRLNWA     +RR     + ++FVGDLAPDVTD +L ETF + Y
Sbjct: 138 LQTYNGAPMPSSEQAFRLNWAQLGAGERRQAEGPEHTVFVGDLAPDVTDHMLTETFKAVY 197

Query: 234 PSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKASG 293
            SVKGAKV+ D  TGR+KGYGFVRF DE+E+ RAMTEMNG YCSSRPMR   A  KK   
Sbjct: 198 SSVKGAKVVNDRTTGRSKGYGFVRFADESEQIRAMTEMNGQYCSSRPMRTGPAANKKPLT 257

Query: 294 YQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGE 353
            Q             P S     QG+  + +  N TIFVGA+D  V+++DL+  F QFGE
Sbjct: 258 MQ-------------PASY-QNTQGNSGESDPTNTTIFVGAVDQSVTEDDLKSVFGQFGE 303

Query: 354 ILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQWRGDHSNH 413
           ++ VKIP GK CGFVQ+ANR  AE AL  L GT +G Q++RLSWGR+P NKQ + D + +
Sbjct: 304 LVHVKIPAGKRCGFVQYANRACAEQALSVLNGTQLGGQSIRLSWGRSPSNKQTQPDQAQY 363

Query: 414 WNGAHYGGQGYSGN---GYAFPPNQDP 437
             G  Y G    G    GYA PP QDP
Sbjct: 364 GGGGGYYGYPPQGYEAYGYA-PPPQDP 389

Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation.

Arabidopsis thaliana (taxid: 3702)

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	449
224105517	412	predicted protein [Populus trichocarpa]	0.879	0.958	0.723	1e-155
224123466	397	predicted protein [Populus trichocarpa]	0.752	0.851	0.790	1e-154
225428741	416	PREDICTED: uncharacterized RNA-binding p	0.846	0.913	0.695	1e-150
255555523	438	nuclear acid binding protein, putative [	0.748	0.767	0.783	1e-150
356521484	431	PREDICTED: uncharacterized RNA-binding p	0.886	0.923	0.675	1e-149
449523756	437	PREDICTED: polyadenylate-binding protein	0.879	0.903	0.693	1e-149
297741313	342	unnamed protein product [Vitis vinifera]	0.755	0.991	0.758	1e-148
449455232	436	PREDICTED: polyadenylate-binding protein	0.877	0.903	0.688	1e-146
359492060	418	PREDICTED: uncharacterized RNA-binding p	0.826	0.887	0.660	1e-144
356500047	431	PREDICTED: uncharacterized RNA-binding p	0.879	0.916	0.668	1e-142

>gi|224105517|ref|XP_002313840.1| predicted protein [Populus trichocarpa] gi|222850248|gb|EEE87795.1| predicted protein [Populus trichocarpa]

 Score =  555 bits (1431), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 295/408 (72%), Positives = 331/408 (81%), Gaps = 13/408 (3%)

Query: 45  WMAMMQYPAAAMAMMQQQQMMMYP---HHYMPYGGGGHPYYQNGGGVKQQQQQQHGLSNG 101
           WMA MQYPAAAM MMQQQ MM      HHYM Y       YQ       Q+QQ+     G
Sbjct: 15  WMAAMQYPAAAMVMMQQQMMMYPQQQHHHYMAYYHQQQQQYQKQQQQYHQKQQKQLQQQG 74

Query: 102 KQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGF 161
                    +N+E KT+W+GDL HWMDET+LHNCFSHTG+V +VK+IRNKQTGQ EGYGF
Sbjct: 75  ---------SNEEAKTVWVGDLLHWMDETYLHNCFSHTGEVSSVKIIRNKQTGQLEGYGF 125

Query: 162 VEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVT 221
           VEFYS AAAEKVLQSYSGS+MPNTDQPFRLNWA+F+G +RR +A SDLSIFVGDLA DVT
Sbjct: 126 VEFYSHAAAEKVLQSYSGSMMPNTDQPFRLNWASFAG-ERRADAGSDLSIFVGDLAADVT 184

Query: 222 DSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPM 281
           D++LQETF++KY SVKGAKV+ DSNTGR+KGYGFVRFGDENE++RA+TEMNG YCSSRPM
Sbjct: 185 DAMLQETFATKYASVKGAKVVADSNTGRSKGYGFVRFGDENEKTRAITEMNGAYCSSRPM 244

Query: 282 RIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSD 341
           RI VATPKK S YQQQYSSQALVLAGG  SNG   QGSQSDG+SNN TIFVG +DSDV+D
Sbjct: 245 RIGVATPKKPSAYQQQYSSQALVLAGGHASNGTMAQGSQSDGDSNNTTIFVGGIDSDVTD 304

Query: 342 EDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNP 401
           EDLR+PFSQFGE++SVK+P GKGC FVQFANRK+AE ALQ L GT IGKQTVRLSWGR P
Sbjct: 305 EDLRQPFSQFGEVVSVKMPTGKGCAFVQFANRKNAEDALQSLNGTTIGKQTVRLSWGRTP 364

Query: 402 GNKQWRGDHSNHWNGAHYGGQGYSGNGYAFPPNQDPNMYAATAVPGAS 449
            NKQWRGDH N W+GA++GGQGY+G GYA PPNQDP MY A A  GAS
Sbjct: 365 ANKQWRGDHGNQWHGAYFGGQGYAGYGYAMPPNQDPGMYVAAAASGAS 412

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224123466|ref|XP_002330321.1| predicted protein [Populus trichocarpa] gi|222871356|gb|EEF08487.1| predicted protein [Populus trichocarpa]

 Score =  550 bits (1416), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 268/339 (79%), Positives = 299/339 (88%), Gaps = 1/339 (0%)

Query: 111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAA 170
           +N+E KTIW+GDL HWMDE +LHNCFSHTG+V +VK+IRNKQTGQ EGYGFVEFYSRAAA
Sbjct: 60  SNEEAKTIWVGDLLHWMDEAYLHNCFSHTGEVSSVKIIRNKQTGQLEGYGFVEFYSRAAA 119

Query: 171 EKVLQSYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFS 230
           EKVLQSYSGS+MPNT+QPFRLNWA+F+G +RR +  SDLSIFVGDLA DVTDS+LQETF+
Sbjct: 120 EKVLQSYSGSMMPNTEQPFRLNWASFAG-ERRADPGSDLSIFVGDLAADVTDSMLQETFA 178

Query: 231 SKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKK 290
            KYPSVKGAKV+IDSNTGR+KGYGFVRFGDENE++RAM EMNG +CSSRPMRI VATPKK
Sbjct: 179 GKYPSVKGAKVVIDSNTGRSKGYGFVRFGDENEKTRAMMEMNGAFCSSRPMRIGVATPKK 238

Query: 291 ASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQ 350
            S YQQQYSSQALVLAGG  SNGA  QGSQSDG+SNN TIFVG +DSDV+DEDLR+PFSQ
Sbjct: 239 PSAYQQQYSSQALVLAGGHASNGAMAQGSQSDGDSNNTTIFVGGIDSDVTDEDLRQPFSQ 298

Query: 351 FGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQWRGDH 410
           FGE++SVKIPVGKGC FVQFANRK+AE ALQ L GT IGKQTVRLSWGR P NKQWRGDH
Sbjct: 299 FGEVVSVKIPVGKGCAFVQFANRKNAEDALQSLNGTTIGKQTVRLSWGRTPANKQWRGDH 358

Query: 411 SNHWNGAHYGGQGYSGNGYAFPPNQDPNMYAATAVPGAS 449
            N W+G ++GGQGY+G GYA PPNQDP MY A A  G S
Sbjct: 359 GNQWHGGYFGGQGYAGYGYAMPPNQDPGMYVAAAASGVS 397

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225428741|ref|XP_002285031.1| PREDICTED: uncharacterized RNA-binding protein C23E6.01c-like isoform 1 [Vitis vinifera]

 Score =  537 bits (1384), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 279/401 (69%), Positives = 315/401 (78%), Gaps = 21/401 (5%)

Query: 51  YPAAAMAMMQQQQMMMYPHHYMPYGGGGHPYYQNGGGVKQQQQQQHGLSNGKQNGSNNNF 110
           YPAAAM M  Q   MMYP HYMP     HP        +  Q Q HG             
Sbjct: 35  YPAAAMVMQHQ---MMYPQHYMP---YHHPQPPQQYQNQPPQHQMHG------------- 75

Query: 111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQV--VNVKVIRNKQTGQSEGYGFVEFYSRA 168
           + DE KT+W+GDL  WMD+ +L  CF HTG+V   ++K+IRNKQTGQSEGYGFVEF+SRA
Sbjct: 76  STDEIKTLWVGDLHQWMDDNYLRTCFGHTGEVKVSSIKIIRNKQTGQSEGYGFVEFFSRA 135

Query: 169 AAEKVLQSYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQET 228
            AEK+L SY+G+LMPNT+QPFRLNWATFS  DRRT+A SDLSIFVGDLA DVTD++LQET
Sbjct: 136 TAEKILHSYNGTLMPNTEQPFRLNWATFSTGDRRTDAGSDLSIFVGDLASDVTDALLQET 195

Query: 229 FSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATP 288
           F+++YPSVKGAKV+ DSNTGR+KGYGFVRFGDENERSRAM EMNG+YCSSRPMRI VATP
Sbjct: 196 FATRYPSVKGAKVVTDSNTGRSKGYGFVRFGDENERSRAMNEMNGIYCSSRPMRIGVATP 255

Query: 289 KKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPF 348
           KKASGYQQQYSSQALVLAGG  SNGA  QGSQ++G+S N TIFVG LDS+V+DEDLR+ F
Sbjct: 256 KKASGYQQQYSSQALVLAGGNASNGAVAQGSQANGDSTNTTIFVGGLDSEVTDEDLRQSF 315

Query: 349 SQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQWRG 408
           SQFGE++SVKIPVGKGCGFVQFANR  AE ALQ+L GT IGKQTVRLSWGRNP +KQWR 
Sbjct: 316 SQFGEVVSVKIPVGKGCGFVQFANRNSAEDALQRLNGTVIGKQTVRLSWGRNPASKQWRN 375

Query: 409 DHSNHWNGAHYGGQGYSGNGYAFPPNQDPNMYAATAVPGAS 449
           D +N WNGA+YGGQGY G      P  DPNMYAA A  GAS
Sbjct: 376 DSNNQWNGAYYGGQGYGGGYGYAMPQNDPNMYAAAATYGAS 416

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255555523|ref|XP_002518798.1| nuclear acid binding protein, putative [Ricinus communis] gi|223542179|gb|EEF43723.1| nuclear acid binding protein, putative [Ricinus communis]

 Score =  537 bits (1383), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 264/337 (78%), Positives = 296/337 (87%), Gaps = 1/337 (0%)

Query: 113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEK 172
           +++KTIW+GDL HWMDET+LH+CFSHTG+V +VKVIRNKQTGQ EGYGF+EFYS A AEK
Sbjct: 103 EDSKTIWVGDLLHWMDETYLHSCFSHTGEVTSVKVIRNKQTGQPEGYGFIEFYSHATAEK 162

Query: 173 VLQSYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSK 232
           VLQ+Y+GS+MPN DQPFRLNWA+F+G +RRTE  SDLSIFVGDLA DVTD++LQETFSSK
Sbjct: 163 VLQNYNGSMMPNADQPFRLNWASFAG-ERRTETGSDLSIFVGDLAADVTDAMLQETFSSK 221

Query: 233 YPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKAS 292
           Y SVKGAKV+ D NTGR+KGYGFVRFGDENERSRAM EMNGVYCSSRPMRI VATPKK+ 
Sbjct: 222 YLSVKGAKVVTDLNTGRSKGYGFVRFGDENERSRAMMEMNGVYCSSRPMRIGVATPKKSP 281

Query: 293 GYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFG 352
            YQQQYSSQALVLAGG   NG+  QGSQSDG+SNN TIFVG +DSD+SDEDLR+PFSQFG
Sbjct: 282 AYQQQYSSQALVLAGGHAPNGSMAQGSQSDGDSNNTTIFVGGIDSDISDEDLRQPFSQFG 341

Query: 353 EILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQWRGDHSN 412
           E++SVKIP GKGCGFVQFA+RK AE ALQ L GT IGKQTVRLSWGR+P NKQWRGDH+N
Sbjct: 342 EVVSVKIPAGKGCGFVQFADRKSAEDALQSLNGTTIGKQTVRLSWGRSPANKQWRGDHNN 401

Query: 413 HWNGAHYGGQGYSGNGYAFPPNQDPNMYAATAVPGAS 449
            WNGA++GGQGY G GYA  PNQD NMY A A  GAS
Sbjct: 402 QWNGAYFGGQGYGGYGYAMAPNQDQNMYVAAAASGAS 438

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356521484|ref|XP_003529385.1| PREDICTED: uncharacterized RNA-binding protein C23E6.01c-like [Glycine max]

 Score =  536 bits (1380), Expect = e-149,   Method: Compositional matrix adjust.
 Identities = 277/410 (67%), Positives = 322/410 (78%), Gaps = 12/410 (2%)

Query: 41  HQQQWMAMMQYPAAAMAMMQQQQMMMYPHHYMPYGGGGHPYYQNGGGVKQQQQQQHGLSN 100
           +QQQWMAM QYPA A   M QQQMMMYP HYMP     + +          Q   H    
Sbjct: 33  YQQQWMAM-QYPATA-MAMMQQQMMMYPQHYMP-----YAHPHYPPPPPPPQSSHHHHHK 85

Query: 101 GKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYG 160
                +    ++DE +T+W+GDL HWMDE +LHNCF+HTG+VV+ KVIRNKQTGQSEGYG
Sbjct: 86  QAAAAAAAAASSDEIRTVWLGDLHHWMDENYLHNCFAHTGEVVSAKVIRNKQTGQSEGYG 145

Query: 161 FVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATFSGSDRR-TEACSDLSIFVGDLAPD 219
           FVEFYSRA AEKVLQ+Y+G++MPNTDQ FRLNWATFS  +RR ++A SDLSIFVGDLA D
Sbjct: 146 FVEFYSRATAEKVLQNYNGTMMPNTDQAFRLNWATFSAGERRSSDATSDLSIFVGDLAID 205

Query: 220 VTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSR 279
           VTD++LQETF+ +Y S+KGAKV+IDSNTGR+KGYGFVRFGDENER+RAMTEMNGVYCSSR
Sbjct: 206 VTDAMLQETFAGRYSSIKGAKVVIDSNTGRSKGYGFVRFGDENERTRAMTEMNGVYCSSR 265

Query: 280 PMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDV 339
           PMRI VATPKK  GYQQQYSSQA++LAGG  +NGA  QGS S+G+ NN TIFVG LDSD 
Sbjct: 266 PMRIGVATPKKTYGYQQQYSSQAVLLAGGHAANGAVAQGSHSEGDLNNTTIFVGGLDSDT 325

Query: 340 SDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGR 399
           SDEDLR+PF QFGE++SVKIPVGKGCGFVQFA+RK+AE A+  L GT IGKQTVRLSWGR
Sbjct: 326 SDEDLRQPFLQFGEVVSVKIPVGKGCGFVQFADRKNAEEAIHALNGTVIGKQTVRLSWGR 385

Query: 400 NPGNKQWRGDHSNHWNGAHYGGQGYSGNGYAFPPNQDPNMYAATAVPGAS 449
           +PGNK WR D     NG ++GGQ Y G+G+A   NQD  M  ATA+ GAS
Sbjct: 386 SPGNKHWRSDS----NGGYFGGQSYGGHGFAVRQNQDIAMQPATAIQGAS 431

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449523756|ref|XP_004168889.1| PREDICTED: polyadenylate-binding protein RBP47-like [Cucumis sativus]

 Score =  535 bits (1379), Expect = e-149,   Method: Compositional matrix adjust.
 Identities = 281/405 (69%), Positives = 320/405 (79%), Gaps = 10/405 (2%)

Query: 51  YPAAAMAMMQQQQMMMYP-HHYMPYGGGGHPYYQNGGGVKQQQQQQHGLSNGKQNGSNNN 109
           YPAAAMAMM QQQM+MYP  HYM Y    HPY Q     +Q   QQ       Q      
Sbjct: 37  YPAAAMAMMHQQQMVMYPPQHYMAYSH--HPYQQQQQQQQQPSSQQQQQHAQSQRPRRQG 94

Query: 110 FTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAA 169
            T DE KT+WIGDL  WMDET+L+NCF+HTG+V +VKVI NKQTGQSEGYGFVEF+S   
Sbjct: 95  ST-DEVKTLWIGDLQPWMDETYLNNCFAHTGEVSSVKVICNKQTGQSEGYGFVEFFSHTT 153

Query: 170 AEKVLQSYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETF 229
           AEKVLQ+Y+G++MPNT+ PFRLNWATFS +DRR +  SDLSIFVGDLA DVTD+ILQETF
Sbjct: 154 AEKVLQNYNGTIMPNTELPFRLNWATFSANDRRPDTGSDLSIFVGDLAADVTDAILQETF 213

Query: 230 SSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPK 289
           SS+Y SVKGAKV+IDSN+GR+KGYGFVRFGDENER+RAMTEMNG+YCSSRPMRI VATPK
Sbjct: 214 SSRYTSVKGAKVVIDSNSGRSKGYGFVRFGDENERTRAMTEMNGIYCSSRPMRIGVATPK 273

Query: 290 KASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFS 349
           KASGYQQ Y+SQALVLAGG   NG  VQGSQSD ESNN TIFVG LDSDVSDEDL++ FS
Sbjct: 274 KASGYQQGYASQALVLAGG-HPNGMAVQGSQSDSESNNTTIFVGGLDSDVSDEDLKQAFS 332

Query: 350 QFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQWRGD 409
           +FG+++SVKIP+GKGCGFVQFANRK+AE A+Q L GT IGKQTVRLSWGR+ GNKQWRGD
Sbjct: 333 KFGDVVSVKIPIGKGCGFVQFANRKNAEDAIQGLNGTVIGKQTVRLSWGRSTGNKQWRGD 392

Query: 410 HSNHWN--GAHYGGQGYSGNGYAFPPNQDPNMY---AATAVPGAS 449
            +N WN         G  G  Y+ P +QDPNM+   AA AV G+S
Sbjct: 393 SNNQWNGGRYGGQSYGGYGGYYSVPQHQDPNMHPTAAAAAVNGSS 437

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297741313|emb|CBI32444.3| unnamed protein product [Vitis vinifera]

 Score =  530 bits (1365), Expect = e-148,   Method: Compositional matrix adjust.
 Identities = 257/339 (75%), Positives = 292/339 (86%)

Query: 111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAA 170
           + DE KT+W+GDL  WMD+ +L  CF HTG+V ++K+IRNKQTGQSEGYGFVEF+SRA A
Sbjct: 4   STDEIKTLWVGDLHQWMDDNYLRTCFGHTGEVSSIKIIRNKQTGQSEGYGFVEFFSRATA 63

Query: 171 EKVLQSYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFS 230
           EK+L SY+G+LMPNT+QPFRLNWATFS  DRRT+A SDLSIFVGDLA DVTD++LQETF+
Sbjct: 64  EKILHSYNGTLMPNTEQPFRLNWATFSTGDRRTDAGSDLSIFVGDLASDVTDALLQETFA 123

Query: 231 SKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKK 290
           ++YPSVKGAKV+ DSNTGR+KGYGFVRFGDENERSRAM EMNG+YCSSRPMRI VATPKK
Sbjct: 124 TRYPSVKGAKVVTDSNTGRSKGYGFVRFGDENERSRAMNEMNGIYCSSRPMRIGVATPKK 183

Query: 291 ASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQ 350
           ASGYQQQYSSQALVLAGG  SNGA  QGSQ++G+S N TIFVG LDS+V+DEDLR+ FSQ
Sbjct: 184 ASGYQQQYSSQALVLAGGNASNGAVAQGSQANGDSTNTTIFVGGLDSEVTDEDLRQSFSQ 243

Query: 351 FGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQWRGDH 410
           FGE++SVKIPVGKGCGFVQFANR  AE ALQ+L GT IGKQTVRLSWGRNP +KQWR D 
Sbjct: 244 FGEVVSVKIPVGKGCGFVQFANRNSAEDALQRLNGTVIGKQTVRLSWGRNPASKQWRNDS 303

Query: 411 SNHWNGAHYGGQGYSGNGYAFPPNQDPNMYAATAVPGAS 449
           +N WNGA+YGGQGY G      P  DPNMYAA A  GAS
Sbjct: 304 NNQWNGAYYGGQGYGGGYGYAMPQNDPNMYAAAATYGAS 342

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449455232|ref|XP_004145357.1| PREDICTED: polyadenylate-binding protein RBP47-like [Cucumis sativus]

 Score =  526 bits (1354), Expect = e-146,   Method: Compositional matrix adjust.
 Identities = 279/405 (68%), Positives = 318/405 (78%), Gaps = 11/405 (2%)

Query: 51  YPAAAMAMMQQQQMMMYP-HHYMPYGGGGHPYYQNGGGVKQQQQQQHGLSNGKQNGSNNN 109
           YPAAAMAMM QQQM+MYP  HYM Y    HPY Q     +Q   QQ       Q      
Sbjct: 37  YPAAAMAMMHQQQMVMYPPQHYMAYSH--HPYQQQQQQQQQPSSQQQQQHAQSQRPRRQG 94

Query: 110 FTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAA 169
            T DE KT+WIGDL  WMDET+L+NCF+HTG+V +VKVI NKQTGQSEGYGFVEF+S   
Sbjct: 95  ST-DEVKTLWIGDLQPWMDETYLNNCFAHTGEVSSVKVICNKQTGQSEGYGFVEFFSHTT 153

Query: 170 AEKVLQSYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETF 229
           AEKVLQ+Y+G++MPNT+ PFRLNWATFS +DRR +  SDLSIFVGDLA DVTD+ILQETF
Sbjct: 154 AEKVLQNYNGTIMPNTELPFRLNWATFSANDRRPDTGSDLSIFVGDLAADVTDAILQETF 213

Query: 230 SSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPK 289
           SS+Y SVKGAKV+IDSN+G +KGYGF RFGDENER+RAMTEMNG+YCSSRPMRI VATPK
Sbjct: 214 SSRYTSVKGAKVVIDSNSGPSKGYGF-RFGDENERTRAMTEMNGIYCSSRPMRIGVATPK 272

Query: 290 KASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFS 349
           KASGYQQ Y+SQALVLAGG   NG  VQGSQSD ESNN TIFVG LDSDVSDEDL++ FS
Sbjct: 273 KASGYQQGYASQALVLAGG-HPNGMAVQGSQSDSESNNTTIFVGGLDSDVSDEDLKQAFS 331

Query: 350 QFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQWRGD 409
           +FG+++SVKIP+GKGCGFVQFANRK+AE A+Q L GT IGKQTVRLSWGR+ GNKQWRGD
Sbjct: 332 KFGDVVSVKIPIGKGCGFVQFANRKNAEDAIQGLNGTVIGKQTVRLSWGRSTGNKQWRGD 391

Query: 410 HSNHWN--GAHYGGQGYSGNGYAFPPNQDPNMY---AATAVPGAS 449
            +N WN         G  G  Y+ P +QDPNM+   AA AV G+S
Sbjct: 392 SNNQWNGGRYGGQSYGGYGGYYSVPQHQDPNMHPTAAAAAVNGSS 436

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359492060|ref|XP_003634360.1| PREDICTED: uncharacterized RNA-binding protein C23E6.01c-like isoform 2 [Vitis vinifera]

 Score =  517 bits (1332), Expect = e-144,   Method: Compositional matrix adjust.
 Identities = 265/401 (66%), Positives = 301/401 (75%), Gaps = 30/401 (7%)

Query: 45  WMAMMQYPAAAMAMMQQQQMM---MYPHHYMPYGGGGHPYYQNGGGVKQQQQQQHGLSNG 101
           WMAM QYPAAAM M  Q QMM    YP H+                V    Q        
Sbjct: 29  WMAM-QYPAAAMVM--QHQMMPPQHYPQHF----------------VAYHHQPHQYQHQH 69

Query: 102 KQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGF 161
           +Q       +N + +TIW+GDL +WMDE +LH+CF+ TG++ ++KVIRNKQTG SEGYGF
Sbjct: 70  QQQHQQQQGSNADNRTIWVGDLHNWMDENYLHSCFAATGELASMKVIRNKQTGSSEGYGF 129

Query: 162 VEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVT 221
           VEF+S AAAEKVLQ Y+G LMPNTDQPFRLNWATFS  D+R++   DLSIFVGDLA DV+
Sbjct: 130 VEFFSHAAAEKVLQGYAGVLMPNTDQPFRLNWATFSMGDKRSDNGPDLSIFVGDLASDVS 189

Query: 222 DSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPM 281
           DS+L ETF+ KYPSVK AKV+ D+NTGR+KGYGFVRFGDENERS+AMTEMNGVYCSSRPM
Sbjct: 190 DSLLHETFAGKYPSVKAAKVVFDANTGRSKGYGFVRFGDENERSQAMTEMNGVYCSSRPM 249

Query: 282 RIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSD 341
           RI  ATP+K+SGYQQQYSS      GG  SNGA V   QSDG+S N TIFVG LD +VSD
Sbjct: 250 RIGAATPRKSSGYQQQYSSH-----GGYASNGASV---QSDGDSMNTTIFVGGLDPNVSD 301

Query: 342 EDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNP 401
           EDLR+PFSQ+GEI+SVKIPVGKGCGFVQFANR +AE ALQKL GT IGKQTVRLSWGRNP
Sbjct: 302 EDLRQPFSQYGEIVSVKIPVGKGCGFVQFANRNNAEDALQKLNGTVIGKQTVRLSWGRNP 361

Query: 402 GNKQWRGDHSNHWNGAHYGGQGYSGNGYAFPPNQDPNMYAA 442
            NKQ R D  N W+GA+YGGQ Y G GYA PP  DP MYAA
Sbjct: 362 ANKQMRADFGNQWSGAYYGGQVYDGYGYALPPPHDPTMYAA 402

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356500047|ref|XP_003518846.1| PREDICTED: uncharacterized RNA-binding protein C23E6.01c-like [Glycine max]

 Score =  509 bits (1312), Expect = e-142,   Method: Compositional matrix adjust.
 Identities = 276/413 (66%), Positives = 323/413 (78%), Gaps = 18/413 (4%)

Query: 40  PHQ--QQWMAMMQYPAAAMAMMQQQQMMMYPHHYMPYGGGGHPYYQNGGGVKQQQQQQHG 97
           PHQ  QQWMAM QYPA AMAMMQQQ +M YP HYM         + +           H 
Sbjct: 34  PHQYQQQWMAM-QYPATAMAMMQQQMLM-YPQHYM------PYAHPHYPPPPPPPPSSHH 85

Query: 98  LSNGKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSE 157
             + KQ  +    ++DE +T+W+GDL HWMDE +LHNCF+HTG+VV+ KVIRNKQTGQSE
Sbjct: 86  HHHHKQAAA----SSDEIRTVWLGDLHHWMDENYLHNCFAHTGEVVSAKVIRNKQTGQSE 141

Query: 158 GYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATFSGSDRRT-EACSDLSIFVGDL 216
           GYGFVEFYSR  AEKVLQ+Y+G++MPNTDQ FRLNWATFS  +RR+ +A SDLSIFVGDL
Sbjct: 142 GYGFVEFYSRGTAEKVLQNYNGTMMPNTDQAFRLNWATFSAGERRSSDATSDLSIFVGDL 201

Query: 217 APDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYC 276
           A DVTD++LQ+TF+ +Y S+KGAKV+IDSNTGR+KGYGFVRFGDENER+RAMTEMNGVYC
Sbjct: 202 AIDVTDAMLQDTFAGRYSSIKGAKVVIDSNTGRSKGYGFVRFGDENERTRAMTEMNGVYC 261

Query: 277 SSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALD 336
           SSRPMRI VATPKK  G+QQQYSSQA+VLAGG  +NGA  QGS S+G+ NN TIFVG LD
Sbjct: 262 SSRPMRIGVATPKKTYGFQQQYSSQAVVLAGGHSANGAVAQGSHSEGDINNTTIFVGGLD 321

Query: 337 SDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLS 396
           SD SDEDLR+PF QFGE++SVKIPVGKGCGFVQFA+RK+AE A+Q L GT IGKQTVRLS
Sbjct: 322 SDTSDEDLRQPFLQFGEVVSVKIPVGKGCGFVQFADRKNAEEAIQGLNGTVIGKQTVRLS 381

Query: 397 WGRNPGNKQWRGDHSNHWNGAHYGGQGYSGNGYAFPPNQDPNMYAATAVPGAS 449
           WGR+PGNK WR D +      + G QGY G+G+A   NQD  M  A A+ GAS
Sbjct: 382 WGRSPGNKHWRSDSNGG---HYGGHQGYGGHGFAVRQNQDIAMQPAAAIQGAS 431

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	449
TAIR|locus:2012211	445	RBP47A "RNA-binding protein 47	0.728	0.734	0.697	3.4e-125
TAIR|locus:2094098	435	RBP47B "RNA-binding protein 47	0.728	0.751	0.692	3.4e-125
UNIPROTKB|Q9LEB3	428	RBP47 "Polyadenylate-binding p	0.752	0.789	0.657	1.5e-122
TAIR|locus:2015398	434	RBP47C' "RNA-binding protein 4	0.723	0.748	0.619	6.3e-110
TAIR|locus:2015403	432	RBP47C "RNA-binding protein 47	0.723	0.752	0.614	2.7e-109
TAIR|locus:2150215	425	AT5G19350 [Arabidopsis thalian	0.726	0.767	0.547	6.1e-95
UNIPROTKB|Q9LEB4	409	RBP45 "Polyadenylate-binding p	0.710	0.779	0.553	2.4e-92
TAIR|locus:2027372	405	RBP45B [Arabidopsis thaliana (	0.683	0.758	0.562	2.7e-92
TAIR|locus:2116322	415	ATRBP45C [Arabidopsis thaliana	0.714	0.773	0.530	1.6e-88
TAIR|locus:2160210	387	RBP45A "RNA-binding protein 45	0.708	0.821	0.532	3.7e-87

TAIR|locus:2012211 RBP47A "RNA-binding protein 47A" [Arabidopsis thaliana (taxid:3702)]

 Score = 1230 (438.0 bits), Expect = 3.4e-125, P = 3.4e-125
 Identities = 237/340 (69%), Positives = 273/340 (80%)

Query:   113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEK 172
             D+ KT+W+GDL HWMDET+LH CFSHT +V +VKVIRNKQT QSEGYGFVEF SR+AAE+
Sbjct:   116 DDVKTLWVGDLLHWMDETYLHTCFSHTNEVSSVKVIRNKQTCQSEGYGFVEFLSRSAAEE 175

Query:   173 VLQSYSGSLMPNTDQPFRLNWATFS-GSDRRTEACSDLSIFVGDLAPDVTDSILQETFSS 231
              LQS+SG  MPN +QPFRLNWA+FS G  R +E   DLSIFVGDLAPDV+D++L ETF+ 
Sbjct:   176 ALQSFSGVTMPNAEQPFRLNWASFSTGEKRASENGPDLSIFVGDLAPDVSDAVLLETFAG 235

Query:   232 KYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKA 291
             +YPSVKGAKV+IDSNTGR+KGYGFVRFGDENERSRAMTEMNG +CSSR MR+ +ATPK+A
Sbjct:   236 RYPSVKGAKVVIDSNTGRSKGYGFVRFGDENERSRAMTEMNGAFCSSRQMRVGIATPKRA 295

Query:   292 SGXXXXXXXXALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQF 351
             +         AL LAGG G NG     S SDGESNN+TIFVG LD+DV++EDL +PFS F
Sbjct:   296 AAYGQQNGSQALTLAGGHGGNG-----SMSDGESNNSTIFVGGLDADVTEEDLMQPFSDF 350

Query:   352 GEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQWRGDHS 411
             GE++SVKIPVGKGCGFVQFANR+ AE A+  L GT IGK TVRLSWGR+P NKQWR D  
Sbjct:   351 GEVVSVKIPVGKGCGFVQFANRQSAEEAIGNLNGTVIGKNTVRLSWGRSP-NKQWRSDSG 409

Query:   412 NHWNGAHYGGQGYSGNGYAFPPNQDPNMYA--ATAVPGAS 449
             N WNG +  GQGY+ NGYA   NQD NMYA  A AVPGAS
Sbjct:   410 NQWNGGYSRGQGYN-NGYA---NQDSNMYATAAAAVPGAS 445

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005829 "cytosol" evidence=IDA

TAIR|locus:2094098 RBP47B "RNA-binding protein 47B" [Arabidopsis thaliana (taxid:3702)]

 Score = 1230 (438.0 bits), Expect = 3.4e-125, P = 3.4e-125
 Identities = 230/332 (69%), Positives = 269/332 (81%)

Query:   111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAA 170
             + D+ KT+W+GDL HWMDET+LH+CFSHTG+V +VKVIRNK T QSEGYGFVEF SRAAA
Sbjct:   103 SGDDVKTLWVGDLLHWMDETYLHSCFSHTGEVSSVKVIRNKLTSQSEGYGFVEFLSRAAA 162

Query:   171 EKVLQSYSGSLMPNTDQPFRLNWATFS-GSDRRTEACSDLSIFVGDLAPDVTDSILQETF 229
             E+VLQ+YSGS+MPN+DQPFR+NWA+FS G  R  E   DLS+FVGDL+PDVTD +L ETF
Sbjct:   163 EEVLQNYSGSVMPNSDQPFRINWASFSTGEKRAVENGPDLSVFVGDLSPDVTDVLLHETF 222

Query:   230 SSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPK 289
             S +YPSVK AKV+IDSNTGR+KGYGFVRFGDENERSRA+TEMNG YCS+R MR+ +ATPK
Sbjct:   223 SDRYPSVKSAKVVIDSNTGRSKGYGFVRFGDENERSRALTEMNGAYCSNRQMRVGIATPK 282

Query:   290 KASGXXXXXXXXALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFS 349
             +A          A++LAGG GSNG+   GSQSDGES NATIFVG +D DV DEDLR+PFS
Sbjct:   283 RAIANQQQHSSQAVILAGGHGSNGSMGYGSQSDGESTNATIFVGGIDPDVIDEDLRQPFS 342

Query:   350 QFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQWRGD 409
             QFGE++SVKIPVGKGCGFVQFA+RK AE A++ L GT IGK TVRLSWGR+P NKQWRGD
Sbjct:   343 QFGEVVSVKIPVGKGCGFVQFADRKSAEDAIESLNGTVIGKNTVRLSWGRSP-NKQWRGD 401

Query:   410 HSNHWNGAHYGGQGYS-GNGYAFPPNQDPNMY 440
                 WNG +  G GY+ G GYA   + D N Y
Sbjct:   402 SGQQWNGGYSRGHGYNNGGGYA--NHHDSNNY 431

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

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

GO:0005829 "cytosol" evidence=IDA

GO:0042991 "transcription factor import into nucleus" evidence=RCA

UNIPROTKB|Q9LEB3 RBP47 "Polyadenylate-binding protein RBP47" [Nicotiana plumbaginifolia (taxid:4092)]

 Score = 1205 (429.2 bits), Expect = 1.5e-122, P = 1.5e-122
 Identities = 223/339 (65%), Positives = 272/339 (80%)

Query:   111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAA 170
             ++++ KTIWIGDL  WMDE++LH+CFS  G+V++VK+IRNKQTGQSE YGFVEF + AAA
Sbjct:    79 SSEDNKTIWIGDLQQWMDESYLHSCFSQAGEVISVKIIRNKQTGQSERYGFVEFNTHAAA 138

Query:   171 EKVLQSYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFS 230
             EKVLQSY+G++MPNT+QPFRLNWA FS  ++R E  SD SIFVGDLA DVTD++L++TF+
Sbjct:   139 EKVLQSYNGTMMPNTEQPFRLNWAGFSTGEKRAETGSDFSIFVGDLASDVTDTMLRDTFA 198

Query:   231 SKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKK 290
             S+YPS+KGAKV++D+NTG +KGYGFVRFGDE+ERSRAMTEMNGVYCSSR MRI VATPKK
Sbjct:   199 SRYPSLKGAKVVVDANTGHSKGYGFVRFGDESERSRAMTEMNGVYCSSRAMRIGVATPKK 258

Query:   291 ASGXXXXXXXXALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQ 350
              S         A++L+GG  SNGA   GSQSDG+S+N TIFVG LDS+V+DE+LR+ F+Q
Sbjct:   259 PSAHEQYSSQ-AVILSGGYASNGAATHGSQSDGDSSNTTIFVGGLDSEVTDEELRQSFNQ 317

Query:   351 FGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQWRGDH 410
             FGE++SVKIP GKGCGFVQF++R  A+ A+QKL G  IGKQ VRLSWGR+P NKQ R D 
Sbjct:   318 FGEVVSVKIPAGKGCGFVQFSDRSSAQEAIQKLSGAIIGKQAVRLSWGRSPANKQMRTDS 377

Query:   411 SNHWNGAHYGGQGYSGNGYAFPPNQDPNMYAATAVPGAS 449
              + WNG + G Q Y G GY    NQD  MYA  A  GAS
Sbjct:   378 GSQWNGGYNGRQNYGGYGYGASQNQDSGMYATGAAYGAS 416

GO:0005634 "nucleus" evidence=IDA

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

GO:0010494 "cytoplasmic stress granule" evidence=IDA

GO:0034605 "cellular response to heat" evidence=IDA

TAIR|locus:2015398 RBP47C' "RNA-binding protein 47C'" [Arabidopsis thaliana (taxid:3702)]

 Score = 1064 (379.6 bits), Expect = 6.3e-110, Sum P(2) = 6.3e-110
 Identities = 212/342 (61%), Positives = 256/342 (74%)

Query:   104 NGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQ--VVNVKVIRNKQTGQSEGYGF 161
             N   N F N E KTIW+GDL +WMDE +L++ F+   +  +V++KVIRNK  G SEGYGF
Sbjct:    92 NKHQNAF-NGENKTIWVGDLQNWMDEAYLNSAFTSAEEREIVSLKVIRNKHNGSSEGYGF 150

Query:   162 VEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATFSGSDRRTEACS-DLSIFVGDLAPDV 220
             VEF S   A+KVLQ ++G+ MPNTDQPFRLNWA+FS  ++R E    DLSIFVGDLAPDV
Sbjct:   151 VEFESHDVADKVLQEFNGAPMPNTDQPFRLNWASFSTGEKRLENNGPDLSIFVGDLAPDV 210

Query:   221 TDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRP 280
             +D++L ETFS KYPSVK AKV++D+NTGR+KGYGFVRFGDENER++AMTEMNGV CSSR 
Sbjct:   211 SDALLHETFSEKYPSVKAAKVVLDANTGRSKGYGFVRFGDENERTKAMTEMNGVKCSSRA 270

Query:   281 MRIDVATPKKASGXXXXXXXXALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVS 340
             MRI  ATP+K +G             GG   +GA    ++S+G++ N TIFVG LDS V+
Sbjct:   271 MRIGPATPRKTNGYQQQ---------GGYMPSGAF---TRSEGDTINTTIFVGGLDSSVT 318

Query:   341 DEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRN 400
             DEDL++PFS+FGEI+SVKIPVGKGCGFVQF NR +AE AL+KL GT IGKQTVRLSWGRN
Sbjct:   319 DEDLKQPFSEFGEIVSVKIPVGKGCGFVQFVNRPNAEEALEKLNGTVIGKQTVRLSWGRN 378

Query:   401 PGNKQWRGDHSNHWNGAHYGGQGYSGNGYAFPPNQDPNMYAA 442
             P NKQ R  + N W   +YGGQ Y+G GY  P   DP MY A
Sbjct:   379 PANKQPRDKYGNQWVDPYYGGQFYNGYGYMVP-QPDPRMYPA 419

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

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

TAIR|locus:2015403 RBP47C "RNA-binding protein 47C" [Arabidopsis thaliana (taxid:3702)]

 Score = 1059 (377.8 bits), Expect = 2.7e-109, Sum P(2) = 2.7e-109
 Identities = 210/342 (61%), Positives = 253/342 (73%)

Query:   104 NGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQ--VVNVKVIRNKQTGQSEGYGF 161
             N   N F N E KTIW+GDL HWMDE +L++ F+   +  +V+VKVIRNK  G SEGYGF
Sbjct:    90 NKHQNAF-NGENKTIWVGDLHHWMDEAYLNSSFASGDEREIVSVKVIRNKNNGLSEGYGF 148

Query:   162 VEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATFSGSDRRTEACS-DLSIFVGDLAPDV 220
             VEF S   A+KVL+ ++G+ MPNTDQPFRLNWA+FS  ++R E    DLSIFVGDL+PDV
Sbjct:   149 VEFESHDVADKVLREFNGTTMPNTDQPFRLNWASFSTGEKRLENNGPDLSIFVGDLSPDV 208

Query:   221 TDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRP 280
             +D++L ETFS KYPSVK AKV++D+NTGR+KGYGFVRFGDENER++AMTEMNGV CSSR 
Sbjct:   209 SDNLLHETFSEKYPSVKAAKVVLDANTGRSKGYGFVRFGDENERTKAMTEMNGVKCSSRA 268

Query:   281 MRIDVATPKKASGXXXXXXXXALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVS 340
             MRI  ATP+K +G             GG   NG     ++ +G+  N TIFVG LDS V+
Sbjct:   269 MRIGPATPRKTNGYQQQ---------GGYMPNGTL---TRPEGDIMNTTIFVGGLDSSVT 316

Query:   341 DEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRN 400
             DEDL++PF++FGEI+SVKIPVGKGCGFVQF NR +AE AL+KL GT IGKQTVRLSWGRN
Sbjct:   317 DEDLKQPFNEFGEIVSVKIPVGKGCGFVQFVNRPNAEEALEKLNGTVIGKQTVRLSWGRN 376

Query:   401 PGNKQWRGDHSNHWNGAHYGGQGYSGNGYAFPPNQDPNMYAA 442
             P NKQ R  + N W   +YGGQ Y+G GY  P   DP MY A
Sbjct:   377 PANKQPRDKYGNQWVDPYYGGQFYNGYGYMVP-QPDPRMYPA 417

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0009507 "chloroplast" evidence=ISM

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

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

TAIR|locus:2150215 AT5G19350 [Arabidopsis thaliana (taxid:3702)]

 Score = 924 (330.3 bits), Expect = 6.1e-95, Sum P(2) = 6.1e-95
 Identities = 184/336 (54%), Positives = 240/336 (71%)

Query:   111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAA 170
             T +E +T+WIGDL +W+DE +L +CFS TG++V+VKVIRNK TGQ EGYGF+EF S AAA
Sbjct:    19 TLEEVRTLWIGDLQYWVDENYLTSCFSQTGELVSVKVIRNKITGQPEGYGFIEFISHAAA 78

Query:   171 EKVLQSYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFS 230
             E+ LQ+Y+G+ MP T+  FRLNWA+F GS ++ +A  D SIFVGDLAPDVTD +LQETF 
Sbjct:    79 ERTLQTYNGTQMPGTELTFRLNWASF-GSGQKVDAGPDHSIFVGDLAPDVTDYLLQETFR 137

Query:   231 SKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKK 290
               Y SV+GAKV+ D +TGR+KGYGFV+F +E+ER+RAM EMNG+YCS+RPMRI  ATPKK
Sbjct:   138 VHYSSVRGAKVVTDPSTGRSKGYGFVKFAEESERNRAMAEMNGLYCSTRPMRISAATPKK 197

Query:   291 ASGXXXXXXXXALVLAGGPGSNGARVQGSQSDGESNNA--TIFVGALDSDVSDEDLREPF 348
               G        A+     P +  A VQ   +  ES+    TI V  LD +V++E+L++ F
Sbjct:   198 NVGVQQQYVTKAVYPVTVPSAVAAPVQAYVAPPESDVTCTTISVANLDQNVTEEELKKAF 257

Query:   349 SQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQW-- 406
             SQ GE++ VKIP  KG G+VQF  R  AE A+Q++QG  IG+Q VR+SW +NPG   W  
Sbjct:   258 SQLGEVIYVKIPATKGYGYVQFKTRPSAEEAVQRMQGQVIGQQAVRISWSKNPGQDGWVT 317

Query:   407 RGDHSNHWNGAHYG-GQGYSGNGYAFPPNQDPNMYA 441
             + D  N WNG +YG GQGY  + YA+   QDP++YA
Sbjct:   318 QAD-PNQWNG-YYGYGQGY--DAYAYGATQDPSVYA 349

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

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

GO:0010048 "vernalization response" evidence=RCA

UNIPROTKB|Q9LEB4 RBP45 "Polyadenylate-binding protein RBP45" [Nicotiana plumbaginifolia (taxid:4092)]

 Score = 920 (328.9 bits), Expect = 2.4e-92, P = 2.4e-92
 Identities = 186/336 (55%), Positives = 231/336 (68%)

Query:   113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEK 172
             +E +++WIGDL +WMDE +L  CF HTG++V+ KVIRNKQTGQSEGYGF+EF S AAAE 
Sbjct:    81 NEVRSLWIGDLQYWMDENYLSTCFYHTGELVSAKVIRNKQTGQSEGYGFLEFRSHAAAET 140

Query:   173 VLQSYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSK 232
             +LQ+Y+G+LMPN +Q FR+NWA+    +RR ++ ++ +IFVGDLA DVTD ILQETF S 
Sbjct:   141 ILQTYNGTLMPNVEQNFRMNWASLGAGERRDDS-AEHTIFVGDLAADVTDYILQETFKSV 199

Query:   233 YPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKAS 292
             Y SV+GAKV+ D  TGR+KGYGFV+F DE+E+ RAMTEMNGV CS+RPMRI  A  KK  
Sbjct:   200 YSSVRGAKVVTDRITGRSKGYGFVKFADESEQLRAMTEMNGVLCSTRPMRIGPAANKKPV 259

Query:   293 GXXXXXXXXALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFG 352
             G               P       Q +Q + + NN TIFVG LD  V++E LR+ FS +G
Sbjct:   260 GTPQKATYQ------NP-------QATQGESDPNNTTIFVGGLDPTVAEEHLRQVFSPYG 306

Query:   353 EILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQWRGDHSN 412
             E++ VKI  GK CGFVQF  R  AE AL  L GT +G Q++RLSWGR+P +KQ       
Sbjct:   307 ELVHVKIVAGKRCGFVQFGTRASAEQALSSLNGTQLGGQSIRLSWGRSPSSKQTDQTQWG 366

Query:   413 HWNGAHYG-GQGYSGNGYAFPPNQDPNMYAATAVPG 447
                GA+YG GQGY   GYA PP QDPNMY     PG
Sbjct:   367 GSGGAYYGYGQGYEAYGYA-PPAQDPNMYYGN-YPG 400

GO:0005634 "nucleus" evidence=IDA

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

TAIR|locus:2027372 RBP45B [Arabidopsis thaliana (taxid:3702)]

 Score = 896 (320.5 bits), Expect = 2.7e-92, Sum P(2) = 2.7e-92
 Identities = 184/327 (56%), Positives = 228/327 (69%)

Query:   111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAA 170
             T DE +T+WIGDL +WMDE FL+ CF+HTG++V+ KVIRNKQTGQ EGYGF+EF S AAA
Sbjct:    57 TADEIRTLWIGDLQYWMDENFLYGCFAHTGEMVSAKVIRNKQTGQVEGYGFIEFASHAAA 116

Query:   171 EKVLQSYSGSLMPN-TDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETF 229
             E+VLQ+++ + +P+  DQ FRLNWA+ S  D+R ++  D +IFVGDLA DVTD IL ETF
Sbjct:   117 ERVLQTFNNAPIPSFPDQLFRLNWASLSSGDKRDDS-PDYTIFVGDLAADVTDYILLETF 175

Query:   230 SSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPK 289
              + YPSVKGAKV+ID  TGRTKGYGFVRF DE+E+ RAMTEMNGV CS+RPMRI  A  K
Sbjct:   176 RASYPSVKGAKVVIDRVTGRTKGYGFVRFSDESEQIRAMTEMNGVPCSTRPMRIGPAASK 235

Query:   290 KASGXXXXXXXXALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFS 349
             K              + G   S  +   G  +D + NN T+FVG LD+ V+D+ L+  FS
Sbjct:   236 KG-------------VTGQRDSYQSSAAGVTTDNDPNNTTVFVGGLDASVTDDHLKNVFS 282

Query:   350 QFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQWRGD 409
             Q+GEI+ VKIP GK CGFVQF+ +  AE AL+ L G  +G  TVRLSWGR+P NKQ  GD
Sbjct:   283 QYGEIVHVKIPAGKRCGFVQFSEKSCAEEALRMLNGVQLGGTTVRLSWGRSPSNKQ-SGD 341

Query:   410 HSNHWNGAHYGGQGYSGNGYAFP--PN 434
              S  + G +  GQG    GY  P  PN
Sbjct:   342 PSQFYYGGY--GQGQEQYGYTMPQDPN 366

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

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

GO:0005634 "nucleus" evidence=ISS

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

GO:0010193 "response to ozone" evidence=IEP

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

TAIR|locus:2116322 ATRBP45C [Arabidopsis thaliana (taxid:3702)]

 Score = 884 (316.2 bits), Expect = 1.6e-88, P = 1.6e-88
 Identities = 180/339 (53%), Positives = 223/339 (65%)

Query:   105 GSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEF 164
             GS N  +  E +++WIGDL  WMDE +L N F  TG+    KVIRNKQ G SEGYGF+EF
Sbjct:    69 GSQNPGSAGEIRSLWIGDLQPWMDENYLMNVFGLTGEATAAKVIRNKQNGYSEGYGFIEF 128

Query:   165 YSRAAAEKVLQSYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSI 224
              + A AE+ LQ+Y+G+ MP+++Q FRLNWA     +RR     + ++FVGDLAPDVTD +
Sbjct:   129 VNHATAERNLQTYNGAPMPSSEQAFRLNWAQLGAGERRQAEGPEHTVFVGDLAPDVTDHM 188

Query:   225 LQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRID 284
             L ETF + Y SVKGAKV+ D  TGR+KGYGFVRF DE+E+ RAMTEMNG YCSSRPMR  
Sbjct:   189 LTETFKAVYSSVKGAKVVNDRTTGRSKGYGFVRFADESEQIRAMTEMNGQYCSSRPMRTG 248

Query:   285 VATPKKASGXXXXXXXXALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDL 344
              A  KK              L   P S     QG+  + +  N TIFVGA+D  V+++DL
Sbjct:   249 PAANKKP-------------LTMQPASY-QNTQGNSGESDPTNTTIFVGAVDQSVTEDDL 294

Query:   345 REPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNK 404
             +  F QFGE++ VKIP GK CGFVQ+ANR  AE AL  L GT +G Q++RLSWGR+P NK
Sbjct:   295 KSVFGQFGELVHVKIPAGKRCGFVQYANRACAEQALSVLNGTQLGGQSIRLSWGRSPSNK 354

Query:   405 QWRGDHSNHWNGAHYGG---QGYSGNGYAFPPNQDPNMY 440
             Q + D + +  G  Y G   QGY   GYA PP QDPN Y
Sbjct:   355 QTQPDQAQYGGGGGYYGYPPQGYEAYGYA-PPPQDPNAY 392

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005829 "cytosol" evidence=IDA

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

TAIR|locus:2160210 RBP45A "RNA-binding protein 45A" [Arabidopsis thaliana (taxid:3702)]

 Score = 871 (311.7 bits), Expect = 3.7e-87, P = 3.7e-87
 Identities = 182/342 (53%), Positives = 232/342 (67%)

Query:   105 GSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEF 164
             GS N  +  + K++WIGDL  WMDE ++ + F+ +G+  + KVIRNK TGQSEGYGF+EF
Sbjct:    49 GSQNPGSASDVKSLWIGDLQQWMDENYIMSVFAQSGEATSAKVIRNKLTGQSEGYGFIEF 108

Query:   165 YSRAAAEKVLQSYSGSLMPNTDQPFRLNWATFSGSDRR--TEACSDLSIFVGDLAPDVTD 222
              S + AE+VLQ+Y+G+ MP+T+Q FRLNWA     ++R  TE   D +IFVGDLAP+VTD
Sbjct:   109 VSHSVAERVLQTYNGAPMPSTEQTFRLNWAQAGAGEKRFQTEG-PDHTIFVGDLAPEVTD 167

Query:   223 SILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMR 282
              +L +TF + Y SVKGAKV++D  TGR+KGYGFVRF DENE+ RAMTEMNG YCS+RPMR
Sbjct:   168 YMLSDTFKNVYGSVKGAKVVLDRTTGRSKGYGFVRFADENEQMRAMTEMNGQYCSTRPMR 227

Query:   283 IDVATPKKASGXXXXXXXXALVLAGGPGSNGARVQGSQS-DGESNNATIFVGALDSDVSD 341
             I  A  K A           L +      N    QG+ + D + NN TIFVG LD++V+D
Sbjct:   228 IGPAANKNA-----------LPMQPAMYQN---TQGANAGDNDPNNTTIFVGGLDANVTD 273

Query:   342 EDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNP 401
             ++L+  F QFGE+L VKIP GK CGFVQ+AN+  AE AL  L GT +G Q++RLSWGR+P
Sbjct:   274 DELKSIFGQFGELLHVKIPPGKRCGFVQYANKASAEHALSVLNGTQLGGQSIRLSWGRSP 333

Query:   402 GNKQWRGDHSNHWNGAHYG--GQGYSGNGYAF-PPNQDPNMY 440
              NKQ   D +    G +YG   Q   G GYA  PP QDPN Y
Sbjct:   334 -NKQ--SDQAQWNGGGYYGYPPQPQGGYGYAAQPPTQDPNAY 372

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

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

GO:0005829 "cytosol" evidence=IDA

GO:0009220 "pyrimidine ribonucleotide biosynthetic process" evidence=RCA

---

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)
Q0WW84	RB47B_ARATH	No assigned EC number	0.6833	0.8151	0.8413	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	449
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	2e-47
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	1e-42
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	7e-35
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	4e-32
cd12612	82	cd12612, RRM2_SECp43, RNA recognition motif 2 in t	5e-32
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	8e-32
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	2e-27
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	4e-25
cd12610	84	cd12610, RRM1_SECp43, RNA recognition motif 1 in t	9e-25
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	5e-24
cd12611	81	cd12611, RRM1_NGR1_NAM8_like, RNA recognition moti	3e-22
smart00360	73	smart00360, RRM, RNA recognition motif	1e-19
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	2e-19
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	9e-19
smart00360	73	smart00360, RRM, RNA recognition motif	1e-18
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-18
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	3e-18
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	8e-18
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	1e-17
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	3e-17
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	5e-17
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	6e-17
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	3e-16
smart00360	73	smart00360, RRM, RNA recognition motif	4e-16
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	9e-16
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	1e-15
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	3e-15
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	4e-15
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	7e-15
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	8e-15
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-14
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	2e-14
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	3e-14
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	9e-14
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	1e-13
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-13
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	2e-13
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	4e-13
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	5e-13
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	6e-13
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	8e-13
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	2e-12
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	3e-12
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	4e-12
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	8e-12
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	8e-12
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	1e-11
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	1e-11
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	1e-11
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	1e-11
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	1e-11
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	1e-11
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	2e-11
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	3e-11
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	3e-11
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	4e-11
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	5e-11
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	5e-11
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	6e-11
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	6e-11
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	8e-11
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	9e-11
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	1e-10
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	1e-10
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	1e-10
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	1e-10
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	1e-10
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	1e-10
cd12265	86	cd12265, RRM_SLT11, RNA recognition motif of pre-m	2e-10
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	2e-10
cd12462	79	cd12462, RRM_SCAF8, RNA recognition motif in SR-re	2e-10
cd12262	82	cd12262, RRM2_4_MRN1, RNA recognition motif 2 and	2e-10
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	2e-10
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	3e-10
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	3e-10
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	4e-10
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	4e-10
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	5e-10
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	5e-10
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	5e-10
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	6e-10
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	7e-10
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	8e-10
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	8e-10
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	9e-10
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	9e-10
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	1e-09
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	1e-09
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	1e-09
cd12461	81	cd12461, RRM_SCAF4, RNA recognition motif found in	1e-09
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	1e-09
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	1e-09
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	1e-09
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	2e-09
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	2e-09
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	2e-09
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	2e-09
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	2e-09
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	2e-09
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	3e-09
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	3e-09
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	3e-09
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	3e-09
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	3e-09
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	4e-09
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	4e-09
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	4e-09
cd12523	78	cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA	4e-09
cd12622	74	cd12622, RRM3_PUB1, RNA recognition motif 3 in yea	4e-09
cd12610	84	cd12610, RRM1_SECp43, RNA recognition motif 1 in t	5e-09
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	5e-09
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	5e-09
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	5e-09
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	5e-09
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	5e-09
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	6e-09
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	6e-09
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	6e-09
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	6e-09
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	7e-09
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	8e-09
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	8e-09
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	9e-09
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	1e-08
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	1e-08
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	1e-08
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	1e-08
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	1e-08
cd12620	73	cd12620, RRM3_TIAR, RNA recognition motif 3 in nuc	1e-08
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	1e-08
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	1e-08
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	1e-08
cd12612	82	cd12612, RRM2_SECp43, RNA recognition motif 2 in t	2e-08
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	2e-08
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	2e-08
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	2e-08
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	2e-08
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	2e-08
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	2e-08
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	2e-08
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	2e-08
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	2e-08
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	2e-08
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	2e-08
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	2e-08
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	2e-08
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-08
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	3e-08
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	3e-08
cd12621	74	cd12621, RRM3_TIA1, RNA recognition motif 3 in nuc	3e-08
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	4e-08
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	4e-08
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	4e-08
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	4e-08
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	4e-08
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	5e-08
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	5e-08
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	6e-08
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	6e-08
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	7e-08
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	7e-08
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	8e-08
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	8e-08
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	8e-08
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	9e-08
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	1e-07
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	1e-07
cd12587	71	cd12587, RRM1_PSF, RNA recognition motif 1 in vert	1e-07
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	1e-07
cd12453	86	cd12453, RRM1_RIM4_like, RNA recognition motif 1 i	1e-07
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	1e-07
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	2e-07
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	2e-07
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	2e-07
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	2e-07
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	2e-07
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	2e-07
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	2e-07
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	2e-07
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	2e-07
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	2e-07
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	2e-07
cd12635	81	cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2	2e-07
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	3e-07
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	3e-07
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	3e-07
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	3e-07
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	3e-07
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	3e-07
cd12529	71	cd12529, RRM2_MEI2_like, RNA recognition motif 2 i	3e-07
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	3e-07
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	3e-07
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	3e-07
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	3e-07
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	4e-07
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	4e-07
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	4e-07
cd12257	72	cd12257, RRM1_RBM26_like, RNA recognition motif 1	4e-07
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	4e-07
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	5e-07
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	5e-07
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	5e-07
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	5e-07
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	5e-07
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	5e-07
cd12555	87	cd12555, RRM2_RBM15, RNA recognition motif 2 in ve	5e-07
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	6e-07
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	6e-07
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	6e-07
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	6e-07
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	6e-07
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	6e-07
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	7e-07
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	7e-07
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	7e-07
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	7e-07
cd12522	79	cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA	7e-07
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	7e-07
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	7e-07
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	8e-07
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	8e-07
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	8e-07
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	8e-07
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	8e-07
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	9e-07
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	9e-07
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	1e-06
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	1e-06
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	1e-06
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	1e-06
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	1e-06
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	1e-06
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	1e-06
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	1e-06
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	1e-06
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	1e-06
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	1e-06
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	1e-06
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	1e-06
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	1e-06
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	2e-06
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	2e-06
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	2e-06
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	2e-06
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	2e-06
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	2e-06
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	2e-06
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	2e-06
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	2e-06
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	2e-06
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	3e-06
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	3e-06
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	3e-06
cd12331	79	cd12331, RRM_NRD1_SEB1_like, RNA recognition motif	3e-06
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	3e-06
cd12527	71	cd12527, RRM2_EAR1_like, RNA recognition motif 2 i	3e-06
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	4e-06
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	4e-06
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	4e-06
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	4e-06
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	4e-06
cd12662	77	cd12662, RRM3_MYEF2, RNA recognition motif 3 in ve	4e-06
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	5e-06
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	5e-06
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	5e-06
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	5e-06
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	5e-06
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	5e-06
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	5e-06
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	5e-06
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	6e-06
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	6e-06
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	6e-06
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	7e-06
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	7e-06
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	7e-06
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	7e-06
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	7e-06
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	7e-06
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	7e-06
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	7e-06
cd12358	73	cd12358, RRM1_VICKZ, RNA recognition motif 1 in th	7e-06
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	7e-06
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	8e-06
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	8e-06
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	8e-06
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	8e-06
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	8e-06
cd12402	77	cd12402, RRM_eIF4B, RNA recognition motif in eukar	8e-06
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	8e-06
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	8e-06
cd12232	89	cd12232, RRM3_U2AF65, RNA recognition motif 3 foun	8e-06
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	9e-06
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	1e-05
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	1e-05
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	1e-05
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	1e-05
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	1e-05
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	1e-05
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	1e-05
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	1e-05
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	1e-05
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	1e-05
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	1e-05
cd12360	78	cd12360, RRM_cwf2, RNA recognition motif in yeast	1e-05
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	1e-05
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	1e-05
cd12561	81	cd12561, RRM1_RBM5_like, RNA recognition motif 1 i	1e-05
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	1e-05
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	1e-05
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	1e-05
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	1e-05
cd12610	84	cd12610, RRM1_SECp43, RNA recognition motif 1 in t	2e-05
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	2e-05
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	2e-05
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	2e-05
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	2e-05
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	2e-05
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	2e-05
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	2e-05
cd12616	81	cd12616, RRM1_TIAR, RNA recognition motif 1 in nuc	2e-05
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	2e-05
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	2e-05
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	2e-05
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	2e-05
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	2e-05
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	2e-05
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	3e-05
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	3e-05
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	3e-05
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	3e-05
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	3e-05
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	3e-05
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	3e-05
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	3e-05
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	3e-05
cd12426	79	cd12426, RRM4_PTBPH3, RNA recognition motif 4 in p	3e-05
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	3e-05
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	3e-05
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	3e-05
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	4e-05
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	4e-05
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	4e-05
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	4e-05
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	4e-05
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	4e-05
cd12317	72	cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition mot	4e-05
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	4e-05
cd12631	84	cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif	4e-05
cd12634	81	cd12634, RRM2_CELF1_2, RNA recognition motif 2 in	4e-05
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	4e-05
cd12296	71	cd12296, RRM1_Prp24, RNA recognition motif 1 in fu	4e-05
cd12595	70	cd12595, RRM1_SRSF5, RNA recognition motif 1 in ve	4e-05
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	5e-05
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	5e-05
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	5e-05
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	5e-05
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	5e-05
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	5e-05
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	5e-05
cd12568	72	cd12568, RRM3_MRD1, RNA recognition motif 3 in yea	5e-05
cd12626	77	cd12626, RRM1_IGF2BP2, RNA recognition motif 1 in	5e-05
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	5e-05
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	5e-05
cd12369	68	cd12369, RRM4_RBM45, RNA recognition motif 4 in RN	5e-05
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	5e-05
pfam08777	102	pfam08777, RRM_3, RNA binding motif	5e-05
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	6e-05
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	6e-05
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	6e-05
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	6e-05
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	6e-05
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	6e-05
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	7e-05
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	7e-05
cd12556	85	cd12556, RRM2_RBM15B, RNA recognition motif 2 in p	7e-05
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	7e-05
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	7e-05
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	7e-05
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	8e-05
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	8e-05
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	8e-05
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	8e-05
cd12631	84	cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif	8e-05
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	8e-05
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	8e-05
cd12234	72	cd12234, RRM1_AtRSp31_like, RNA recognition motif	8e-05
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	9e-05
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	9e-05
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	9e-05
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	9e-05
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	9e-05
cd12603	71	cd12603, RRM_hnRNPC, RNA recognition motif in vert	9e-05
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	9e-05
cd12612	82	cd12612, RRM2_SECp43, RNA recognition motif 2 in t	1e-04
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	1e-04
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	1e-04
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	1e-04
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	1e-04
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	1e-04
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	1e-04
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	1e-04
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	1e-04
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	1e-04
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	1e-04
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	1e-04
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	1e-04
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	1e-04
cd12275	71	cd12275, RRM1_MEI2_EAR1_like, RNA recognition moti	1e-04
cd12419	80	cd12419, RRM_Ssp2_like, RNA recognition motif in y	1e-04
cd12431	80	cd12431, RRM_ALKBH8, RNA recognition motif in alky	1e-04
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	1e-04
cd12596	70	cd12596, RRM1_SRSF6, RNA recognition motif 1 in ve	1e-04
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	1e-04
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	1e-04
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	1e-04
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	1e-04
cd12598	72	cd12598, RRM1_SRSF9, RNA recognition motif 1 in ve	1e-04
cd12357	89	cd12357, RRM_PPARGC1A_like, RNA recognition motif	1e-04
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	2e-04
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	2e-04
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	2e-04
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	2e-04
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	2e-04
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	2e-04
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	2e-04
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	2e-04
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	2e-04
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	2e-04
cd12584	80	cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in	2e-04
cd12583	75	cd12583, RRM2_hnRNPD, RNA recognition motif 2 in h	2e-04
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	2e-04
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	2e-04
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	2e-04
cd12333	80	cd12333, RRM2_p54nrb_like, RNA recognition motif 2	2e-04
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	2e-04
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	2e-04
cd12245	79	cd12245, RRM_scw1_like, RNA recognition motif in y	2e-04
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	2e-04
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	2e-04
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	2e-04
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	3e-04
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	3e-04
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	3e-04
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	3e-04
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	3e-04
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	3e-04
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	3e-04
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	3e-04
cd12583	75	cd12583, RRM2_hnRNPD, RNA recognition motif 2 in h	3e-04
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	3e-04
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	3e-04
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	3e-04
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	3e-04
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	3e-04
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	4e-04
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	4e-04
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	4e-04
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	4e-04
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	4e-04
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	4e-04
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	4e-04
cd12429	74	cd12429, RRM_DNAJC17, RNA recognition motif in the	4e-04
cd12615	74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	4e-04
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	5e-04
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	5e-04
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	5e-04
cd12604	76	cd12604, RRM_RALY, RNA recognition motif in verteb	5e-04
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	6e-04
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	6e-04
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	6e-04
cd12333	80	cd12333, RRM2_p54nrb_like, RNA recognition motif 2	6e-04
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	6e-04
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	6e-04
cd12416	98	cd12416, RRM4_RBM28_like, RNA recognition motif 4	6e-04
cd12459	80	cd12459, RRM1_CID8_like, RNA recognition motif 1 i	6e-04
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	6e-04
pfam09606	768	pfam09606, Med15, ARC105 or Med15 subunit of Media	6e-04
cd12477	89	cd12477, RRM1_U1A, RNA recognition motif 1 found i	6e-04
cd12597	73	cd12597, RRM1_SRSF1, RNA recognition motif 1 in se	6e-04
cd12458	70	cd12458, RRM_AtC3H46_like, RNA recognition motif i	6e-04
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	7e-04
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	7e-04
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	7e-04
cd12245	79	cd12245, RRM_scw1_like, RNA recognition motif in y	7e-04
cd12497	74	cd12497, RRM3_RBM47, RNA recognition motif 3 in ve	7e-04
cd12569	72	cd12569, RRM4_RBM19, RNA recognition motif 4 in RN	7e-04
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	7e-04
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	7e-04
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	8e-04
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	8e-04
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	8e-04
cd12429	74	cd12429, RRM_DNAJC17, RNA recognition motif in the	8e-04
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	8e-04
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	9e-04
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	0.001
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	0.001
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	0.001
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	0.001
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	0.001
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	0.001
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	0.001
cd12453	86	cd12453, RRM1_RIM4_like, RNA recognition motif 1 i	0.001
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	0.001
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	0.001
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	0.001
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	0.001
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	0.001
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	0.001
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	0.001
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	0.001
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	0.001
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	0.001
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	0.001
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	0.001
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	0.001
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	0.001
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	0.001
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	0.001
cd12478	91	cd12478, RRM1_U2B, RNA recognition motif 1 in U2 s	0.001
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	0.001
cd12476	78	cd12476, RRM1_SNF, RNA recognition motif 1 found i	0.001
cd12661	77	cd12661, RRM3_hnRNPM, RNA recognition motif 3 in v	0.001
cd12589	80	cd12589, RRM2_PSP1, RNA recognition motif 2 in ver	0.001
cd12473	85	cd12473, RRM2_MSSP1, RNA recognition motif 2 found	0.001
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	0.001
cd12441	73	cd12441, RRM_Nup53_like, RNA recognition motif in	0.001
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	0.002
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	0.002
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	0.002
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	0.002
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	0.002
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	0.002
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	0.002
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	0.002
cd12616	81	cd12616, RRM1_TIAR, RNA recognition motif 1 in nuc	0.002
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	0.002
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	0.002
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	0.002
cd12615	74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	0.002
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	0.002
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	0.002
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	0.002
cd12420	79	cd12420, RRM_RBPMS_like, RNA recognition motif in	0.002
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	0.002
cd12238	73	cd12238, RRM1_RBM40_like, RNA recognition motif 1	0.002
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	0.002
cd12679	76	cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in	0.002
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	0.002
cd12422	85	cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition m	0.002
cd12594	74	cd12594, RRM1_SRSF4, RNA recognition motif 1 in ve	0.002
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	0.002
cd12292	75	cd12292, RRM2_La_like, RNA recognition motif 2 in	0.002
cd12342	71	cd12342, RRM_Nab3p, RNA recognition motif in yeast	0.002
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	0.003
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	0.003
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	0.003
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	0.003
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	0.003
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	0.003
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	0.003
cd12661	77	cd12661, RRM3_hnRNPM, RNA recognition motif 3 in v	0.003
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	0.003
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	0.003
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	0.003
cd12520	74	cd12520, RRM1_MRN1, RNA recognition motif 1 of RNA	0.003
cd12424	71	cd12424, RRM3_hnRNPL_like, RNA recognition motif 1	0.003
cd12755	86	cd12755, RRM2_RBM5, RNA recognition motif 2 in ver	0.003
cd12590	80	cd12590, RRM2_PSF, RNA recognition motif 2 in vert	0.003
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	0.003
cd12764	72	cd12764, RRM2_SRSF4, RNA recognition motif 2 in ve	0.003
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	0.004
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	0.004
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	0.004
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	0.004
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	0.004
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	0.004
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	0.004
cd12291	72	cd12291, RRM1_La, RNA recognition motif 1 in La au	0.004
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	0.004
cd12562	86	cd12562, RRM2_RBM5_like, RNA recognition motif 2 i	0.004
cd12356	79	cd12356, RRM_PPARGC1B, RNA recognition motif in pe	0.004

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

 Score =  157 bits (399), Expect = 2e-47
 Identities = 62/80 (77%), Positives = 72/80 (90%)

Query: 208 DLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRA 267
           D SIFVGDLAPDVTD +LQETF ++YPSV+GAKV++D  TGR+KGYGFVRFGDE+ER RA
Sbjct: 1   DHSIFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRA 60

Query: 268 MTEMNGVYCSSRPMRIDVAT 287
           +TEMNGVYCSSRPMR+  AT
Sbjct: 61  LTEMNGVYCSSRPMRVSPAT 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|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score =  144 bits (366), Expect = 1e-42
 Identities = 47/81 (58%), Positives = 62/81 (76%)

Query: 117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQS 176
           T+W+GDL  WMDE ++++ F+  G+V +VK+IRNKQTG+S GYGFVEF +  AAE+ LQS
Sbjct: 1   TLWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQS 60

Query: 177 YSGSLMPNTDQPFRLNWATFS 197
            +G  +PNT Q FRLNWA F 
Sbjct: 61  LNGKPIPNTQQRFRLNWANFG 81

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

 Score =  123 bits (312), Expect = 7e-35
 Identities = 44/72 (61%), Positives = 54/72 (75%)

Query: 327 NATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGT 386
           N T+FVG LD  V++++LR  F  FGEI+ VKIP GKGCGFVQF +R  AE A+Q+LQGT
Sbjct: 1   NTTVFVGGLDPAVTEDELRSLFGPFGEIVYVKIPPGKGCGFVQFVHRAAAEAAIQQLQGT 60

Query: 387 AIGKQTVRLSWG 398
            IG   +RLSWG
Sbjct: 61  IIGGSRIRLSWG 72

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

>gnl|CDD|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins

 Score =  116 bits (293), Expect = 4e-32
 Identities = 46/78 (58%), Positives = 58/78 (74%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           SIFVGDL+P+V +S L   F S++PS K AK++ D  TG ++GYGFVRF DEN++ RA+ 
Sbjct: 3   SIFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALI 62

Query: 270 EMNGVYCSSRPMRIDVAT 287
           EM GVYC  RPMRI  AT
Sbjct: 63  EMQGVYCGGRPMRISTAT 80

This subgroup corresponds to the RRM2 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both, RNA and single-stranded DNA (ssDNA), in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs. . Length = 80

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

 Score =  116 bits (293), Expect = 5e-32
 Identities = 46/83 (55%), Positives = 60/83 (72%), Gaps = 2/83 (2%)

Query: 208 DLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRA 267
           + S+FVGDL PDV D  L E FS +YPS KGAKV++D N G ++GYGFVRF DE+E+ RA
Sbjct: 1   EFSLFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLDQN-GNSRGYGFVRFSDESEQKRA 59

Query: 268 MTEMNG-VYCSSRPMRIDVATPK 289
           +TEM G      +P+R+ +A PK
Sbjct: 60  LTEMQGASGLGGKPIRVSLAIPK 82

This subgroup corresponds to the RRM2 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. . Length = 82

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

 Score =  127 bits (320), Expect = 8e-32
 Identities = 78/278 (28%), Positives = 133/278 (47%), Gaps = 39/278 (14%)

Query: 117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQS 176
           ++++GDL   + E  L++ F   G V++V+V R+  T +S GYG+V F + A AE+ L++
Sbjct: 2   SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALET 61

Query: 177 YSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSV 236
            +   +    +P R+ W+    S RR+      +IFV +L   V +  L +TF SK+ ++
Sbjct: 62  MNFKRL--GGKPIRIMWSQRDPSLRRS---GVGNIFVKNLDKSVDNKALFDTF-SKFGNI 115

Query: 237 KGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKASGYQQ 296
              KV  D N G+++GYGFV F  E     A+ ++NG+  + + + +     K       
Sbjct: 116 LSCKVATDEN-GKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKKHEREAAP 174

Query: 297 QYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILS 356
                                            ++V  LD  V+++ LRE F++FGEI S
Sbjct: 175 ---------------------------LKKFTNLYVKNLDPSVNEDKLRELFAKFGEITS 207

Query: 357 VKI---PVG--KGCGFVQFANRKDAEVALQKLQGTAIG 389
             +     G  +G  FV F   +DA  A++++ G  IG
Sbjct: 208 AAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIG 245

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

 Score =  110 bits (276), Expect = 2e-27
 Identities = 52/243 (21%), Positives = 99/243 (40%), Gaps = 9/243 (3%)

Query: 163 EFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTD 222
                    ++ +   G      +    L  ++ S   R+     + ++FVG+L  DVT+
Sbjct: 70  SERKEENEREMEEQNDGERGYTKEFEEELFRSSESPKSRQKSKEENNTLFVGNLPYDVTE 129

Query: 223 SILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMR 282
             L+E F  K+  VK  +++ D  TG+++G+ FV F  E    +A+ E+NG     RP+R
Sbjct: 130 EDLRELFK-KFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLR 188

Query: 283 IDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDE 342
           +  A P       +   S  L  +     +  +    +      +  ++VG L    ++E
Sbjct: 189 VQKAQPAS---QPRSELSNNLDASFAKKLSRGKALLLEK-----SDNLYVGNLPLKTAEE 240

Query: 343 DLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPG 402
           +L + F   G+I+   +P  K     +  +    E +   L+  + G +   L  G    
Sbjct: 241 ELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGNEASKDALESNSRGNKKKILGRGPRKA 300

Query: 403 NKQ 405
             Q
Sbjct: 301 FSQ 303

Length = 306

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

 Score = 98.1 bits (245), Expect = 4e-25
 Identities = 41/77 (53%), Positives = 54/77 (70%), Gaps = 1/77 (1%)

Query: 207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSR 266
           +D  IFVGDL  +VTD +L   FS KYPS + AKV+ D  TG++KGYGFV F D N+  +
Sbjct: 5   NDFRIFVGDLGNEVTDEVLARAFS-KYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLK 63

Query: 267 AMTEMNGVYCSSRPMRI 283
           AM EMNG Y  +RP+++
Sbjct: 64  AMKEMNGKYVGNRPIKL 80

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

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

 Score = 97.0 bits (242), Expect = 9e-25
 Identities = 37/84 (44%), Positives = 54/84 (64%), Gaps = 3/84 (3%)

Query: 117 TIWIGDLFHWMDETFLHNCFSHTGQ-VVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQ 175
           ++W+GDL  +MDE F+   F+  G+ V++VK+IRNK TG   GY FVEF   A AE+ L 
Sbjct: 1   SLWMGDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLH 60

Query: 176 SYSGSLMPNTDQP--FRLNWATFS 197
             +G  +P ++ P  F+LN AT+ 
Sbjct: 61  KLNGKPIPGSNPPKRFKLNRATYG 84

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

 Score =  104 bits (260), Expect = 5e-24
 Identities = 74/283 (26%), Positives = 134/283 (47%), Gaps = 32/283 (11%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY 177
           I++ +L   +D   L + FS  G +++ KV  + + G+S GYGFV F    +A+  +Q  
Sbjct: 91  IFVKNLDKSVDNKALFDTFSKFGNILSCKVATD-ENGKSRGYGFVHFEKEESAKAAIQKV 149

Query: 178 SGSLMPNTD---QPFRLNWATFSGSDRR-TEACSDLSIFVGDLAPDVTDSILQETFSSKY 233
           +G L+ + +     F          +R         +++V +L P V +  L+E F +K+
Sbjct: 150 NGMLLNDKEVYVGRFIKK------HEREAAPLKKFTNLYVKNLDPSVNEDKLRELF-AKF 202

Query: 234 PSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCS--SRPMRIDVATPKKA 291
             +  A V+ D + GR++G+ FV F    + ++A+ EMNG          ++ V   +K 
Sbjct: 203 GEITSAAVMKDGS-GRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKR 261

Query: 292 SGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQF 351
           +  + +   +                  +   ++    ++V  LD  V+DE LRE FS+ 
Sbjct: 262 AEREAELRRK------------FEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSEC 309

Query: 352 GEILSVKI-----PVGKGCGFVQFANRKDAEVALQKLQGTAIG 389
           GEI S K+      V +G GFV F+N ++A  A+ ++ G  +G
Sbjct: 310 GEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLG 352

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|241055 cd12611, RRM1_NGR1_NAM8_like, RNA recognition motif 1 in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins

 Score = 89.8 bits (223), Expect = 3e-22
 Identities = 38/82 (46%), Positives = 56/82 (68%), Gaps = 2/82 (2%)

Query: 117 TIWIGDLFHWMDETFLHNCFSHTGQV-VNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQ 175
           T+W+GDL  WMDE F+   ++  G   VNVKVIR++ +G + GY FVEF S  AA+  L 
Sbjct: 1   TLWMGDLEPWMDENFIKQVWASLGLEPVNVKVIRSRNSGLNAGYCFVEFPSPHAAQNAL- 59

Query: 176 SYSGSLMPNTDQPFRLNWATFS 197
           S +G+ +PN+++ F+LNWA+  
Sbjct: 60  SLNGTPIPNSNRTFKLNWASGG 81

This subgroup corresponds to the RRM1 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both, RNA and single-stranded DNA (ssDNA), in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The subgroup also includes NAM8, a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs. . Length = 81

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

 Score = 82.6 bits (205), Expect = 1e-19
 Identities = 28/73 (38%), Positives = 46/73 (63%), Gaps = 6/73 (8%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVALQK 382
           T+FVG L  D ++E+LRE FS+FG++ SV++         KG  FV+F + +DAE AL+ 
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 383 LQGTAIGKQTVRL 395
           L G  +  + +++
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score = 81.4 bits (201), Expect = 2e-19
 Identities = 35/75 (46%), Positives = 52/75 (69%), Gaps = 1/75 (1%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           +IFVGDL+P+VTD+ L   FS+ +PS   A+V+ D  +GR++GYGFV F  + +   A+ 
Sbjct: 1   NIFVGDLSPEVTDATLFAAFSA-FPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAIN 59

Query: 270 EMNGVYCSSRPMRID 284
           EMNG +  SRP+R +
Sbjct: 60  EMNGKWLGSRPIRCN 74

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

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

 Score = 80.0 bits (198), Expect = 9e-19
 Identities = 32/72 (44%), Positives = 46/72 (63%), Gaps = 5/72 (6%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIP-----VGKGCGFVQFANRKDAEVALQKLQ 384
           +FVG L  D ++EDLRE FS+FGEI SV+I        KG  FV+F + +DAE AL+ L 
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 385 GTAIGKQTVRLS 396
           G  +  + +++S
Sbjct: 61  GKELDGRKLKVS 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|214636 smart00360, RRM, RNA recognition motif

 Score = 79.2 bits (196), Expect = 1e-18
 Identities = 27/74 (36%), Positives = 47/74 (63%), Gaps = 1/74 (1%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           ++FVG+L PD T+  L+E FS K+  V+  +++ D  TG++KG+ FV F  E +  +A+ 
Sbjct: 1   TLFVGNLPPDTTEEELRELFS-KFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALE 59

Query: 270 EMNGVYCSSRPMRI 283
            +NG     RP+++
Sbjct: 60  ALNGKELDGRPLKV 73

Length = 73

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

 Score = 87.6 bits (217), Expect = 2e-18
 Identities = 58/189 (30%), Positives = 84/189 (44%), Gaps = 36/189 (19%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           S++VGDL PDVT++ L + F   +  V   +V  DS T R+ GYG+V F +  +  RA+ 
Sbjct: 2   SLYVGDLDPDVTEAKLYDLFK-PFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALE 60

Query: 270 EMNGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNAT 329
            MN      +P+RI                                 Q   S   S    
Sbjct: 61  TMNFKRLGGKPIRI------------------------------MWSQRDPSLRRSGVGN 90

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPV-----GKGCGFVQFANRKDAEVALQKLQ 384
           IFV  LD  V ++ L + FS+FG ILS K+        +G GFV F   + A+ A+QK+ 
Sbjct: 91  IFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVN 150

Query: 385 GTAIGKQTV 393
           G  +  + V
Sbjct: 151 GMLLNDKEV 159

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|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 = 78.4 bits (194), Expect = 3e-18
 Identities = 28/72 (38%), Positives = 44/72 (61%)

Query: 328 ATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTA 387
            T++VG L   +++E+L+  FS FG I  V++   KG  FV+F   + A  A+  + GT+
Sbjct: 1   TTVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDKGYAFVRFDTHEAAATAIVAVNGTS 60

Query: 388 IGKQTVRLSWGR 399
           I  QTV+ SWG+
Sbjct: 61  INGQTVKCSWGK 72

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

 Score = 77.4 bits (191), Expect = 8e-18
 Identities = 27/74 (36%), Positives = 44/74 (59%), Gaps = 1/74 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           IFVGDL+P++    L+  F+  +  +  A+V+ D  TG++KGYGFV F  + +   A+  
Sbjct: 2   IFVGDLSPEIDTETLRAAFA-PFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQS 60

Query: 271 MNGVYCSSRPMRID 284
           MNG +   R +R +
Sbjct: 61  MNGQWLGGRAIRTN 74

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

 Score = 76.8 bits (190), Expect = 1e-17
 Identities = 28/74 (37%), Positives = 42/74 (56%), Gaps = 1/74 (1%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           S++VGDL PDVT+++L E FS     V   +V  D  T R+ GY +V F +  +  RA+ 
Sbjct: 1   SLYVGDLHPDVTEAMLYEIFS-PAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALD 59

Query: 270 EMNGVYCSSRPMRI 283
            +N      +P+RI
Sbjct: 60  TLNFDVIKGKPIRI 73

This subfamily corresponds to the RRM1 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammals, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 80

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

 Score = 75.3 bits (186), Expect = 3e-17
 Identities = 29/70 (41%), Positives = 44/70 (62%), Gaps = 5/70 (7%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-----KGCGFVQFANRKDAEVALQKLQ 384
           +FVG L  D ++EDL++ FS+FG I S++I        KG  FV+F + +DAE AL+ L 
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 385 GTAIGKQTVR 394
           G  +G + +R
Sbjct: 61  GKELGGRELR 70

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

>gnl|CDD|240673 cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins

 Score = 75.1 bits (185), Expect = 5e-17
 Identities = 26/74 (35%), Positives = 46/74 (62%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAI 388
           T+++G L   V++EDL+  F ++GEI S+ +   +GC +V    R+DA  ALQKL+   +
Sbjct: 4   TLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIPPRGCAYVCMETRQDAHRALQKLRNVKL 63

Query: 389 GKQTVRLSWGRNPG 402
             + ++++W  N G
Sbjct: 64  AGKKIKVAWAPNKG 77

This subfamily corresponds to the RRM in a new class of SCAFs (SR-like CTD-associated factors), including SCAF4, SCAF8 and similar proteins. The biological role of SCAF4 remains unclear, but it shows high sequence similarity to SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8). SCAF8 is a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. In addition, SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8 and SCAF4 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain), and serine/arginine-rich motifs. Length = 77

>gnl|CDD|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins

 Score = 75.0 bits (185), Expect = 6e-17
 Identities = 29/72 (40%), Positives = 44/72 (61%), Gaps = 1/72 (1%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQG-TA 387
           T++VG L   V+++DLR+ F QFGEI S+ +   + C FV F  R+ AE A ++L     
Sbjct: 3   TLYVGGLGERVTEKDLRDHFYQFGEIRSITVVPRQQCAFVTFTTREAAEKAAERLFNKLI 62

Query: 388 IGKQTVRLSWGR 399
           I  + ++L WGR
Sbjct: 63  INGRRLKLKWGR 74

This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines. Length = 74

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

 Score = 72.9 bits (179), Expect = 3e-16
 Identities = 27/80 (33%), Positives = 43/80 (53%), Gaps = 1/80 (1%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           ++FV +LA  VT   L + FS   P +K A V+ D  TG ++GYGFV F    +   A+ 
Sbjct: 1   TLFVRNLAFSVTQEDLTDFFSDVAP-IKHAVVVTDPETGESRGYGFVTFAMLEDAQEALA 59

Query: 270 EMNGVYCSSRPMRIDVATPK 289
           ++       R +R+D+A  +
Sbjct: 60  KLKNKKLHGRILRLDIAERR 79

This subgroup corresponds to the RRM1 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 72.6 bits (179), Expect = 4e-16
 Identities = 26/66 (39%), Positives = 44/66 (66%)

Query: 117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQS 176
           T+++G+L     E  L   FS  G+V +V+++R+K+TG+S+G+ FVEF S   AEK L++
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 177 YSGSLM 182
            +G  +
Sbjct: 61  LNGKEL 66

Length = 73

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

 Score = 71.7 bits (176), Expect = 9e-16
 Identities = 28/76 (36%), Positives = 46/76 (60%), Gaps = 1/76 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +FVG+L+  V D  L+  F  K+ +V GA+VI D  TGR++G+G+V F    +  +A+  
Sbjct: 2   LFVGNLSWSVDDEWLKAEFE-KFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 271 MNGVYCSSRPMRIDVA 286
           M+G     RP+ +D +
Sbjct: 61  MDGKELDGRPINVDFS 76

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

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

 Score = 71.1 bits (175), Expect = 1e-15
 Identities = 31/80 (38%), Positives = 45/80 (56%), Gaps = 9/80 (11%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKI--P-------VGKGCGFVQFANRKDAEVAL 380
           ++VG L+  V++E L + F +FG + SVKI  P         + CGFV F NR DAE AL
Sbjct: 4   LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERAL 63

Query: 381 QKLQGTAIGKQTVRLSWGRN 400
            +L G  +    ++L WG+ 
Sbjct: 64  DELDGKDVMGYELKLGWGKA 83

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

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

 Score = 76.6 bits (188), Expect = 3e-15
 Identities = 69/280 (24%), Positives = 122/280 (43%), Gaps = 22/280 (7%)

Query: 67  YPHHYMPYGGGGHPYYQNGGGVKQ---------QQQQQHGLSNGKQNGSNNNFTNDETKT 117
           YP     +  G + +Y NGG                  + L++    GS++N TN+    
Sbjct: 50  YPSTGRQHRQGYNDFYGNGGSSACGLGSMGNMANMASTNSLNSLGSGGSDDNDTNNSGTN 109

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY 177
           + +  L   M +  L+  F   G +   +++R+ +TG S GY FV+F S A +++ +++ 
Sbjct: 110 LIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNL 169

Query: 178 SGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVK 237
           +G  + N  +  ++++A   G     E+  D +++V +L   +TD  L +T   KY  + 
Sbjct: 170 NGITVRN--KRLKVSYARPGG-----ESIKDTNLYVTNLPRTITDDQL-DTIFGKYGQIV 221

Query: 238 GAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVY--CSSRPMRIDVATPK-KASGY 294
              ++ D  TG  +G  FVRF    E   A++ +N V     S+P+ + +A    KA   
Sbjct: 222 QKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAEEHGKAKA- 280

Query: 295 QQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGA 334
              Y SQ      G   +G       S     N   F+G 
Sbjct: 281 -HHYMSQMGHGNMGNMGHGNMGMAGGSGMNPPNPPAFMGM 319

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

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

 Score = 69.6 bits (171), Expect = 4e-15
 Identities = 26/78 (33%), Positives = 45/78 (57%), Gaps = 1/78 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           ++VG+L  +VT+  L++ F   +  V  A+VI D  TGR++G+GFV      E + A+ +
Sbjct: 2   LYVGNLPYNVTEEDLKDLFGQ-FGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 271 MNGVYCSSRPMRIDVATP 288
           +NG     R + ++ A P
Sbjct: 61  LNGTDFGGRTLTVNEARP 78

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

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

 Score = 75.4 bits (185), Expect = 7e-15
 Identities = 53/200 (26%), Positives = 89/200 (44%), Gaps = 18/200 (9%)

Query: 127 MDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTD 186
           M +  + + F+  G++ + K++R+K TGQS GYGFV +     AEK + S +G       
Sbjct: 15  MTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNG------- 67

Query: 187 QPFRLNWATFSGSDRR--TEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIID 244
              RL   T   S  R  +++    +++V  L   +T   L+  F S +  +  ++++ D
Sbjct: 68  --LRLQNKTIKVSYARPSSDSIKGANLYVSGLPKTMTQHELESIF-SPFGQIITSRILSD 124

Query: 245 SNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV------ATPKKASGYQQQY 298
           + TG +KG GF+RF   +E  RA+  +NG   S     I V      ++        Q  
Sbjct: 125 NVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKFANNPSSSNSKGLLSQLE 184

Query: 299 SSQALVLAGGPGSNGARVQG 318
           + Q       P S      G
Sbjct: 185 AVQNPQTTRVPLSTILTAAG 204

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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 68.8 bits (169), Expect = 8e-15
 Identities = 27/72 (37%), Positives = 45/72 (62%), Gaps = 2/72 (2%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +FVG+L PD T+  L++ FS K+  ++  +++ D  TGR+KG+ FV F DE +  +A+  
Sbjct: 1   LFVGNLPPDTTEEDLKDLFS-KFGPIESIRIVRD-ETGRSKGFAFVEFEDEEDAEKALEA 58

Query: 271 MNGVYCSSRPMR 282
           +NG     R +R
Sbjct: 59  LNGKELGGRELR 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|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 76.0 bits (187), Expect = 1e-14
 Identities = 51/208 (24%), Positives = 96/208 (46%), Gaps = 25/208 (12%)

Query: 109 NFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRA 168
            FTN     +++ +L   ++E  L   F+  G++ +  V+++  +G+S G+ FV F    
Sbjct: 177 KFTN-----LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKD-GSGRSRGFAFVNFEKHE 230

Query: 169 AAEKVLQSYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDL---------------SIFV 213
            A K ++  +G  +    +  +L          R                      +++V
Sbjct: 231 DAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYV 290

Query: 214 GDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNG 273
            +L   VTD  L+E FS +   +  AKV++D   G ++G+GFV F +  E +RA+TEM+G
Sbjct: 291 KNLDDTVTDEKLRELFS-ECGEITSAKVMLDE-KGVSRGFGFVCFSNPEEANRAVTEMHG 348

Query: 274 VYCSSRPMRIDVATPKKA--SGYQQQYS 299
                +P+ + +A  K+   +  Q Q+ 
Sbjct: 349 RMLGGKPLYVALAQRKEQRRAHLQDQFM 376

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

 Score = 74.9 bits (184), Expect = 2e-14
 Identities = 44/163 (26%), Positives = 88/163 (53%), Gaps = 11/163 (6%)

Query: 128 DETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQ 187
            E  L+  FS  G+V +V+ I+++ + +S+G  +VEFY   +  K L   +G ++    +
Sbjct: 102 RERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALAL-TGQMLLG--R 158

Query: 188 PFRL-------NWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAK 240
           P  +       N A  + + +  +  + L ++VG+L  ++T+  L++ F   +  ++  +
Sbjct: 159 PIIVQSSQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEP-FGDIEDVQ 217

Query: 241 VIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRI 283
           +  D  TGR+KG+GF++F D  E   A+  MNG   + RP+++
Sbjct: 218 LHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKV 260

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

 Score = 67.0 bits (164), Expect = 3e-14
 Identities = 28/74 (37%), Positives = 41/74 (55%), Gaps = 6/74 (8%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKI------PVGKGCGFVQFANRKDAEVALQKL 383
           IFVG L  ++  E LR  F+ FGEI   ++         KG GFV F  ++DAE A+Q +
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 384 QGTAIGKQTVRLSW 397
            G  +G + +R +W
Sbjct: 62  NGQWLGGRAIRTNW 75

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

 Score = 66.0 bits (162), Expect = 9e-14
 Identities = 27/78 (34%), Positives = 41/78 (52%), Gaps = 7/78 (8%)

Query: 331 FVGALDSDVSDEDLREPFSQFGEILSVKI---PVGK---GCGFVQFANRKDAEVALQKLQ 384
           +VG L  DV++  L E FS  G +LS+++    + +   G  +V F N  DAE AL  L 
Sbjct: 3   YVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTLN 62

Query: 385 GTAIGKQTVRLSWG-RNP 401
              I  + +R+ W  R+P
Sbjct: 63  FDVIKGKPIRIMWSQRDP 80

This subfamily corresponds to the RRM1 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammals, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 80

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

 Score = 65.4 bits (160), Expect = 1e-13
 Identities = 24/65 (36%), Positives = 36/65 (55%), Gaps = 5/65 (7%)

Query: 338 DVSDEDLREPFSQFGEILSVKIP---VGKGCGF--VQFANRKDAEVALQKLQGTAIGKQT 392
             ++ DL++ FS FG +  V IP    GK  GF  VQF ++ DAE A++ + G  I  + 
Sbjct: 10  KCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGVNGKKIKGRP 69

Query: 393 VRLSW 397
           V + W
Sbjct: 70  VAVDW 74

This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 76

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

 Score = 65.0 bits (159), Expect = 2e-13
 Identities = 23/74 (31%), Positives = 44/74 (59%), Gaps = 2/74 (2%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +FVG+L PD T+  L+E FS K+  ++  +++ D + G++KG+ FV F    +  +A+  
Sbjct: 1   LFVGNLPPDTTEEDLRELFS-KFGEIESVRIVRDKD-GKSKGFAFVEFESPEDAEKALEA 58

Query: 271 MNGVYCSSRPMRID 284
           +NG     R +++ 
Sbjct: 59  LNGKELDGRKLKVS 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|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 71.5 bits (175), Expect = 2e-13
 Identities = 51/197 (25%), Positives = 89/197 (45%), Gaps = 28/197 (14%)

Query: 208 DLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRA 267
           D ++FV  LA    +  L E FS K   V+  + I D N+ R+KG  +V F D  E    
Sbjct: 89  DRTVFVLQLALKARERDLYEFFS-KVGKVRDVQCIKDRNSRRSKGVAYVEFYDV-ESVIK 146

Query: 268 MTEMNGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNN 327
              + G     RP+ +               SSQA        +  A+    Q     N 
Sbjct: 147 ALALTGQMLLGRPIIVQ--------------SSQA------EKNRAAKAATHQPGDIPNF 186

Query: 328 ATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVALQ 381
             ++VG L  ++++++LR+ F  FG+I  V++         KG GF+QF + ++A+ AL+
Sbjct: 187 LKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALE 246

Query: 382 KLQGTAIGKQTVRLSWG 398
            + G  +  + +++ + 
Sbjct: 247 VMNGFELAGRPIKVGYA 263

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

 Score = 64.2 bits (157), Expect = 4e-13
 Identities = 25/80 (31%), Positives = 41/80 (51%), Gaps = 1/80 (1%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           ++FV +L  D TD  L+E FS   P +K   V+ D  + + +G+G+V F  E +  RA+ 
Sbjct: 1   TLFVRNLPYDTTDEQLEEFFSEVGP-IKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALE 59

Query: 270 EMNGVYCSSRPMRIDVATPK 289
           E        R + ++ A  K
Sbjct: 60  EKKKTKFGGRKIHVEFAKKK 79

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

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

 Score = 69.2 bits (168), Expect = 5e-13
 Identities = 46/229 (20%), Positives = 91/229 (39%), Gaps = 22/229 (9%)

Query: 81  YYQNGGGVKQQQQQQHGLSNGKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTG 140
             QN G     ++ +  L    ++  +   + +E  T+++G+L + + E  L   F   G
Sbjct: 81  EEQNDGERGYTKEFEEELFRSSESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFG 140

Query: 141 QVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATFSGSD 200
            V  V+++R+++TG+S G+ FVEF S  +AEK ++  +G  +    +P R+  A  +   
Sbjct: 141 PVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKEL--EGRPLRVQKAQPASQP 198

Query: 201 RRTEAC-------------------SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKV 241
           R   +                       +++VG+L     +  L + F S    +  A +
Sbjct: 199 RSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKS-RGDIVRASL 257

Query: 242 IIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKK 290
               +    K   FV      +   + +  N      R  R   + P+ 
Sbjct: 258 PPSKDGKIPKSRSFVGNEASKDALESNSRGNKKKILGRGPRKAFSQPRL 306

Length = 306

>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 = 63.4 bits (155), Expect = 6e-13
 Identities = 28/76 (36%), Positives = 43/76 (56%), Gaps = 1/76 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +FVG++  D T+  L E FS   P V   +++ D +TG+ KGYGF  F D    + A+  
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEVGP-VVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRN 59

Query: 271 MNGVYCSSRPMRIDVA 286
           +NG   + R +R+D A
Sbjct: 60  LNGYEFNGRALRVDFA 75

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

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

 Score = 63.4 bits (155), Expect = 8e-13
 Identities = 21/59 (35%), Positives = 35/59 (59%), Gaps = 6/59 (10%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKI---PVG---KGCGFVQFANRKDAEVALQ 381
           T+F+  L  D ++E+L+E FSQFGE+   +I    +    KG  FV+F  ++ A+  L+
Sbjct: 2   TVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLE 60

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

 Score = 61.9 bits (151), Expect = 2e-12
 Identities = 23/65 (35%), Positives = 40/65 (61%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIG 389
           +FVG L +D+++E+ +E FS++GE+  V +   KG GF++   R +AE A  +L G    
Sbjct: 4   LFVGNLPNDITEEEFKELFSKYGEVSEVFLNKEKGFGFIRLDTRTNAEKAKAELDGIMRK 63

Query: 390 KQTVR 394
            + +R
Sbjct: 64  GRQLR 68

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

 Score = 61.5 bits (150), Expect = 3e-12
 Identities = 26/58 (44%), Positives = 35/58 (60%), Gaps = 5/58 (8%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKI-----PVGKGCGFVQFANRKDAEVALQ 381
            IFVG +  D ++E+LR+ FS+FG +  VKI      V KG GFV F  ++DAE  L 
Sbjct: 4   RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDAEKILA 61

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

 Score = 61.0 bits (149), Expect = 4e-12
 Identities = 24/74 (32%), Positives = 42/74 (56%), Gaps = 7/74 (9%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKI------PVGKGCGFVQFANRKDAEVALQK 382
           ++FVG L  D+ +E+LR+ F   G++ +V+I       +GKG G+V F  +    +AL K
Sbjct: 1   SVFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALAL-K 59

Query: 383 LQGTAIGKQTVRLS 396
           L G  +  + +R+ 
Sbjct: 60  LNGIKLKGRKIRVK 73

This subfamily corresponds to the RRM2 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein. . Length = 73

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

 Score = 60.3 bits (147), Expect = 8e-12
 Identities = 27/69 (39%), Positives = 44/69 (63%), Gaps = 4/69 (5%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIP----VGKGCGFVQFANRKDAEVALQKLQG 385
           ++V  L   V++EDLRE FS +G++  V++       +G  FV+FA+ +DAE AL+KL G
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60

Query: 386 TAIGKQTVR 394
             +  +T+R
Sbjct: 61  LVLDGRTLR 69

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

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

 Score = 60.3 bits (147), Expect = 8e-12
 Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 11/72 (15%)

Query: 328 ATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK-----------GCGFVQFANRKDA 376
            T+FV  L+   ++E L++ F + G + SV I   K           G GFV+F +++ A
Sbjct: 1   TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAA 60

Query: 377 EVALQKLQGTAI 388
           + AL++LQGT +
Sbjct: 61  QKALKRLQGTVL 72

This subfamily corresponds to the RRM5 of RBM19 and RRM4 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 82

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

 Score = 59.6 bits (145), Expect = 1e-11
 Identities = 23/62 (37%), Positives = 40/62 (64%), Gaps = 1/62 (1%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY 177
           +++G+L     E  L   FS  G++ +V+++R+K  G+S+G+ FVEF S   AEK L++ 
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDK-DGKSKGFAFVEFESPEDAEKALEAL 59

Query: 178 SG 179
           +G
Sbjct: 60  NG 61

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

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

 Score = 65.7 bits (160), Expect = 1e-11
 Identities = 62/282 (21%), Positives = 102/282 (36%), Gaps = 42/282 (14%)

Query: 127 MDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTD 186
           M +  L + FS  GQ++  +++ +  TG S+G GF+ F  R  A++ +++ +G+      
Sbjct: 101 MTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCT 160

Query: 187 QPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQE--TFSSKYPSVKGAKVIID 244
           +P  + +A    S       S L        P  T   L    T +   P    A     
Sbjct: 161 EPITVKFANNPSSSNSKGLLSQLEAV---QNPQTTRVPLSTILTAAGIGPMHHAAARF-R 216

Query: 245 SNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKASGYQQQYSSQALV 304
            + G        +        +   +         P   D  T   A+G           
Sbjct: 217 PSAGDFTAVLAHQQQQHAVAQQHAAQRAS------PPATDGQTAGLAAG----------- 259

Query: 305 LAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-- 362
            A    S+GA               IFV  L  D  +  L + F  FG + +VKI     
Sbjct: 260 -AQIAASDGA------------GYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLT 306

Query: 363 ----KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRN 400
               KG GFV   N  +A +A+  L G  +G + +++S+  N
Sbjct: 307 TNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTN 348

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

 Score = 66.5 bits (162), Expect = 1e-11
 Identities = 42/198 (21%), Positives = 82/198 (41%), Gaps = 16/198 (8%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           I++G+L   + +  ++E   S +  +K   +I D  TG +KGY F  + D +    A+  
Sbjct: 298 IYIGNLPLYLGEDQIKELLES-FGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAA 356

Query: 271 MNGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATI 330
           +NG       + +  A            +  A V       + + +Q      +    T 
Sbjct: 357 LNGKDTGDNKLHVQRACVGANQATIDTSNGMAPVTLLAKALSQSILQIGGKPTKVVQLTN 416

Query: 331 FVGALD-SDVSD-----EDLREPFSQFGEILSVKIP-------VGKGCG--FVQFANRKD 375
            V   D  D  +     ED++  FS++G ++++ IP          G G  F+++A+ + 
Sbjct: 417 LVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRS 476

Query: 376 AEVALQKLQGTAIGKQTV 393
           AE A++ + G     + V
Sbjct: 477 AEKAMEGMNGRKFNDRVV 494

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

 Score = 62.0 bits (150), Expect = 1e-11
 Identities = 33/103 (32%), Positives = 56/103 (54%), Gaps = 1/103 (0%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +F+G L+    D+ L++ F+  +  V  AKVI+D  TGR++G+GFV F DE   + A++E
Sbjct: 37  LFIGGLSWGTDDASLRDAFAH-FGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISE 95

Query: 271 MNGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNG 313
           M+G   + R +R++ A  + ++              GG G  G
Sbjct: 96  MDGKELNGRHIRVNPANDRPSAPRAYGGGGGYSGGGGGYGGGG 138

Length = 144

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

 Score = 59.6 bits (145), Expect = 1e-11
 Identities = 22/68 (32%), Positives = 36/68 (52%), Gaps = 2/68 (2%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIG 389
           ++V  L    ++E LRE FS++GE+  VK    K   FV F  R DA  A++++ G  + 
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGEVERVKKI--KDYAFVHFEERDDAVKAMEEMNGKELE 61

Query: 390 KQTVRLSW 397
              + +S 
Sbjct: 62  GSPIEVSL 69

This subfamily corresponds to the RRM3 in hnRNP R, hnRNP Q, and APOBEC-1 complementation factor (ACF). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches and has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members contain three conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Length = 72

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

 Score = 59.7 bits (145), Expect = 1e-11
 Identities = 27/72 (37%), Positives = 44/72 (61%), Gaps = 6/72 (8%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKL 383
           +FVG L  D  ++ + E F ++GEI SV++P        KG G+V+F++++ A+ AL  L
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 384 QGTAIGKQTVRL 395
            GT +  + VRL
Sbjct: 61  GGTDLLGRPVRL 72

This subfamily corresponds to the RRM2 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues. . Length = 73

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

 Score = 59.3 bits (144), Expect = 2e-11
 Identities = 22/74 (29%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +FVG+L+ D  +  + E F  +Y  +   ++  D ++GR KG+G+V F  +     A+  
Sbjct: 1   LFVGNLSFDADEDSIYEAFG-EYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDA 59

Query: 271 MNGVYCSSRPMRID 284
           + G     RP+R+D
Sbjct: 60  LGGTDLLGRPVRLD 73

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

 Score = 58.9 bits (143), Expect = 3e-11
 Identities = 27/76 (35%), Positives = 45/76 (59%), Gaps = 2/76 (2%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY 177
           I++GDL   +D   L   F+  G++ + +V+++ QTG+S+GYGFV F  +  AE  +QS 
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 178 SGSLMPNTDQPFRLNW 193
           +G  +    +  R NW
Sbjct: 62  NGQWL--GGRAIRTNW 75

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|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 = 58.7 bits (142), Expect = 3e-11
 Identities = 27/76 (35%), Positives = 43/76 (56%), Gaps = 1/76 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +F+G L+ D  +  L++ FS KY  +    V+ D  T R++G+GFV F + ++   AM  
Sbjct: 3   LFIGGLSFDTNEQSLEQVFS-KYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMA 61

Query: 271 MNGVYCSSRPMRIDVA 286
           MNG     R +R+D A
Sbjct: 62  MNGKSVDGRQIRVDQA 77

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

 Score = 58.4 bits (142), Expect = 4e-11
 Identities = 28/64 (43%), Positives = 39/64 (60%), Gaps = 4/64 (6%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDEN--ERSRAM 268
           IFVG + PD T+  L++ FS ++ SVK  K+I D   G +KGYGFV F  +   E+  AM
Sbjct: 5   IFVGGIPPDTTEEELRDFFS-RFGSVKDVKIITD-RAGVSKGYGFVTFETQEDAEKILAM 62

Query: 269 TEMN 272
             +N
Sbjct: 63  GNLN 66

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

 Score = 58.0 bits (141), Expect = 5e-11
 Identities = 28/76 (36%), Positives = 46/76 (60%), Gaps = 2/76 (2%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           ++V +L   + D  L+E FS  + ++  AKV+ D   GR+KG+GFV F    E ++A+TE
Sbjct: 4   LYVKNLDDSIDDERLREEFS-PFGTITSAKVMTDEK-GRSKGFGFVCFSSPEEATKAVTE 61

Query: 271 MNGVYCSSRPMRIDVA 286
           MNG     +P+ + +A
Sbjct: 62  MNGRIIGGKPLYVALA 77

This subfamily corresponds to the RRM4 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in theThe CD corresponds to the RRM. regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 79

>gnl|CDD|240753 cd12307, RRM_NIFK_like, RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) and similar proteins

 Score = 58.0 bits (141), Expect = 5e-11
 Identities = 25/66 (37%), Positives = 39/66 (59%)

Query: 117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQS 176
            ++IG L H   E  L   FS  G V  +++ R+K+TG+S+GY FVEF S   A+ V ++
Sbjct: 1   VVYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAET 60

Query: 177 YSGSLM 182
            +  L+
Sbjct: 61  MNNYLL 66

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

 Score = 57.7 bits (140), Expect = 6e-11
 Identities = 22/73 (30%), Positives = 46/73 (63%), Gaps = 1/73 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           ++VG+L  ++T+  L+  F   +  ++  ++  D  TGR+KGYGF++F D  +  +A+ +
Sbjct: 1   LYVGNLHFNITEDDLRGIFEP-FGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQ 59

Query: 271 MNGVYCSSRPMRI 283
           +NG   + RP+++
Sbjct: 60  LNGFELAGRPIKV 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|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 = 58.0 bits (141), Expect = 6e-11
 Identities = 22/77 (28%), Positives = 41/77 (53%), Gaps = 1/77 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +FV  L+   T+  L+  FS K+  V+   ++ D  TG ++G+GFV F    +   A+ +
Sbjct: 4   LFVSGLSTRTTEKELEALFS-KFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRD 62

Query: 271 MNGVYCSSRPMRIDVAT 287
           +NG     R ++++ A 
Sbjct: 63  LNGKELEGRVIKVEKAK 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|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins

 Score = 57.6 bits (140), Expect = 8e-11
 Identities = 25/72 (34%), Positives = 43/72 (59%), Gaps = 6/72 (8%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVALQK 382
            ++VG L  +V++EDL++ F QFGE+ S ++         +G GFV+    ++A  A++K
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 383 LQGTAIGKQTVR 394
           L GT  G +T+ 
Sbjct: 61  LNGTDFGGRTLT 72

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

 Score = 57.7 bits (140), Expect = 9e-11
 Identities = 28/81 (34%), Positives = 49/81 (60%), Gaps = 2/81 (2%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERS-RAMT 269
           +F+G+L P+V + +L +TFS+    ++  K++ D +TG +KG+ F+ + D  E S  A+ 
Sbjct: 4   LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISY-DSFEASDAAIE 62

Query: 270 EMNGVYCSSRPMRIDVATPKK 290
            MNG Y  +RP+ +  A  K 
Sbjct: 63  AMNGQYLCNRPITVSYAFKKD 83

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

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

 Score = 56.6 bits (137), Expect = 1e-10
 Identities = 22/66 (33%), Positives = 42/66 (63%)

Query: 117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQS 176
           T+++G+L   +D+ +L   F   G VV  +VI +++TG+S G+G+V+F S   A+K +++
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 177 YSGSLM 182
             G  +
Sbjct: 61  MDGKEL 66

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

 Score = 62.3 bits (151), Expect = 1e-10
 Identities = 44/190 (23%), Positives = 84/190 (44%), Gaps = 43/190 (22%)

Query: 226 QETFSSKYPS---VKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMR 282
           QE   S + S   ++  K++ D  TG++ GYGFV +    +  +A+  +NG+   ++ ++
Sbjct: 17  QEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIK 76

Query: 283 IDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDE 342
           +  A P   S                       ++G         A ++V  L   ++  
Sbjct: 77  VSYARPSSDS-----------------------IKG---------ANLYVSGLPKTMTQH 104

Query: 343 DLREPFSQFGEILSVKI------PVGKGCGFVQFANRKDAEVALQKLQGTAIGKQT--VR 394
           +L   FS FG+I++ +I       + KG GF++F  R +A+ A++ L GT     T  + 
Sbjct: 105 ELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPIT 164

Query: 395 LSWGRNPGNK 404
           + +  NP + 
Sbjct: 165 VKFANNPSSS 174

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

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

 Score = 57.2 bits (139), Expect = 1e-10
 Identities = 24/69 (34%), Positives = 40/69 (57%), Gaps = 5/69 (7%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKI---PVGK--GCGFVQFANRKDAEVALQKLQ 384
           ++V  L  D+ DE L+E F ++G+I S K+     GK  G GFV F N + A+ A+++L 
Sbjct: 4   VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEELN 63

Query: 385 GTAIGKQTV 393
           G  +  + +
Sbjct: 64  GKEVNGKKL 72

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

>gnl|CDD|241030 cd12586, RRM1_PSP1, RNA recognition motif 1 in vertebrate paraspeckle protein 1 (PSP1)

 Score = 56.9 bits (137), Expect = 1e-10
 Identities = 23/66 (34%), Positives = 42/66 (63%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIG 389
           +FVG L +D+++ED ++ F ++GE   V I   +G GF++  +R  AE+A  +L GT + 
Sbjct: 4   LFVGNLPTDITEEDFKKLFEKYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTILK 63

Query: 390 KQTVRL 395
            + +R+
Sbjct: 64  NRPLRI 69

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

>gnl|CDD|240768 cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 56.9 bits (138), Expect = 1e-10
 Identities = 29/57 (50%), Positives = 36/57 (63%), Gaps = 5/57 (8%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-KGCGFVQFANRKDAEVALQKLQG 385
           +FVG L  D+++EDLR+ FSQFGE+  V IP   +   FV FA   D EVA Q L G
Sbjct: 3   VFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKPFRAFAFVTFA---DPEVA-QSLCG 55

This subfamily corresponds to the RRM2 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. . Length = 71

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

 Score = 56.5 bits (137), Expect = 1e-10
 Identities = 22/76 (28%), Positives = 38/76 (50%), Gaps = 4/76 (5%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           ++VG+L   VT+ +L E FS   P +K  K+I +        Y FV + D    + A+  
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGP-IKSCKLIREHGN---DPYAFVEYYDHRSAAAALQT 56

Query: 271 MNGVYCSSRPMRIDVA 286
           MNG     + ++++ A
Sbjct: 57  MNGRLILGQEIKVNWA 72

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

>gnl|CDD|240711 cd12265, RRM_SLT11, RNA recognition motif of pre-mRNA-splicing factor SLT11 and similar proteins

 Score = 57.0 bits (138), Expect = 2e-10
 Identities = 20/83 (24%), Positives = 38/83 (45%), Gaps = 12/83 (14%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTA- 387
           + F+  ++ D+ +  +R+ F QFG+  SV +     CGFV+F  R+ AE     +     
Sbjct: 4   SFFLFGVEDDLPEYKIRDYFEQFGKSKSVIVNHRAKCGFVRFETREAAEKFAAAISENGL 63

Query: 388 -----------IGKQTVRLSWGR 399
                      +    +R++WG+
Sbjct: 64  NAGLSRGGLLVLEGCPLRVAWGK 86

This subfamily corresponds to the RRM of SLT11, also known as extracellular mutant protein 2, or synthetic lethality with U2 protein 11, and is a splicing factor required for spliceosome assembly in yeast. It contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). SLT11 can facilitate the cooperative formation of U2/U6 helix II in association with stem II in the yeast spliceosome by utilizing its RNA-annealing and -binding activities. . Length = 86

>gnl|CDD|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 = 56.8 bits (138), Expect = 2e-10
 Identities = 23/64 (35%), Positives = 36/64 (56%), Gaps = 6/64 (9%)

Query: 331 FVGALDSDVSDEDLREPFSQFGEILSVKI------PVGKGCGFVQFANRKDAEVALQKLQ 384
           FVG L    ++ED+R  F ++G I  V I         KGC FV+F++R++A+ A++ L 
Sbjct: 3   FVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEALH 62

Query: 385 GTAI 388
           G   
Sbjct: 63  GKVT 66

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|240908 cd12462, RRM_SCAF8, RNA recognition motif in SR-related and CTD-associated factor 8 (SCAF8) and similar proteins

 Score = 56.6 bits (136), Expect = 2e-10
 Identities = 27/78 (34%), Positives = 47/78 (60%), Gaps = 2/78 (2%)

Query: 327 NATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGT 386
           + T++VG +D   + +DL   F +FG+I S+ +   +GC +V   +R+DA  ALQKL   
Sbjct: 2   STTLWVGQVDKKATQQDLTNLFEEFGQIESINMIPPRGCAYVCMVHRQDAYRALQKLSSG 61

Query: 387 A--IGKQTVRLSWGRNPG 402
           +  IG + ++++W  N G
Sbjct: 62  SYKIGSKVIKIAWALNKG 79

This subgroup corresponds to the RRM of SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8), a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8, together with SCAF4, represents a new class of SCAFs (SR-like CTD-associated factors). They contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and serine/arginine-rich motifs. Length = 79

>gnl|CDD|240708 cd12262, RRM2_4_MRN1, RNA recognition motif 2 and 4 in RNA-binding protein MRN1 and similar proteins

 Score = 56.4 bits (136), Expect = 2e-10
 Identities = 22/75 (29%), Positives = 42/75 (56%), Gaps = 5/75 (6%)

Query: 330 IFVGALD-----SDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQ 384
           +++G +       ++ +++LR+   ++GEI S++I   K C F+ F N  +A  ALQ L 
Sbjct: 5   VYIGNVSDVGDERNLPEKELRKECEKYGEIESIRILREKACAFINFMNIPNAIAALQTLN 64

Query: 385 GTAIGKQTVRLSWGR 399
           G       VR+++G+
Sbjct: 65  GKKPYDTIVRINYGK 79

This subgroup corresponds to the RRM2 and RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, and is an RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 82

>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 = 56.3 bits (136), Expect = 2e-10
 Identities = 26/76 (34%), Positives = 43/76 (56%), Gaps = 1/76 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +FVG++  + T+  L++ FS   P V   +++ D  TG+ KGYGF  + D+     AM  
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGP-VVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRN 59

Query: 271 MNGVYCSSRPMRIDVA 286
           +NG   + R +R+D A
Sbjct: 60  LNGYELNGRQLRVDNA 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|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins

 Score = 55.7 bits (135), Expect = 3e-10
 Identities = 19/64 (29%), Positives = 39/64 (60%)

Query: 117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQS 176
            +++G+L + + E  L + F   G+V + +VI +++TG+S G+GFVE  +   A   ++ 
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 177 YSGS 180
            +G+
Sbjct: 61  LNGT 64

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

 Score = 56.1 bits (136), Expect = 3e-10
 Identities = 23/62 (37%), Positives = 36/62 (58%), Gaps = 1/62 (1%)

Query: 117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQS 176
            I++G +     E  L + FS  G V +VK+I ++  G S+GYGFV F ++  AEK+L  
Sbjct: 4   RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDR-AGVSKGYGFVTFETQEDAEKILAM 62

Query: 177 YS 178
            +
Sbjct: 63  GN 64

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

 Score = 55.3 bits (134), Expect = 4e-10
 Identities = 25/62 (40%), Positives = 40/62 (64%), Gaps = 6/62 (9%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIP------VGKGCGFVQFANRKDAEVALQKL 383
           ++VG L  +++++DLR  F  FGEI  V++         KG GF+QFA+ +DA+ AL++L
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 384 QG 385
            G
Sbjct: 61  NG 62

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

>gnl|CDD|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 = 55.6 bits (135), Expect = 4e-10
 Identities = 25/70 (35%), Positives = 37/70 (52%), Gaps = 1/70 (1%)

Query: 120 IGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSG 179
           +G L     E  +   F   G +  V +IR+K TGQS+G  FV+F SR  A+K +++  G
Sbjct: 4   VGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEALHG 63

Query: 180 S-LMPNTDQP 188
              MP   +P
Sbjct: 64  KVTMPGASRP 73

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|240759 cd12313, RRM1_RRM2_RBM5_like, RNA recognition motif 1 and 2 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 55.6 bits (135), Expect = 5e-10
 Identities = 19/70 (27%), Positives = 32/70 (45%), Gaps = 2/70 (2%)

Query: 114 ETKTIWIGDLFHWMDETFLHNCFSHTG--QVVNVKVIRNKQTGQSEGYGFVEFYSRAAAE 171
            T T+ +  L     E  +    S      + +V++IR+K TG S G+ FVEF S   A 
Sbjct: 1   PTNTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDAT 60

Query: 172 KVLQSYSGSL 181
           + + + +   
Sbjct: 61  QWMDALNNLD 70

This subfamily includes the RRM1 and RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37) and RNA-binding protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs share high sequence homology and may play an important role in regulating apoptosis. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM6 has been predicted to be a nuclear factor based on its nuclear localization signal. Both, RBM6 and RBM5, specifically bind poly(G) RNA. RBM10 is a paralog of RBM5. It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. All family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. . Length = 84

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

 Score = 54.4 bits (132), Expect = 5e-10
 Identities = 18/55 (32%), Positives = 30/55 (54%), Gaps = 1/55 (1%)

Query: 344 LREPFSQFGEILSVKI-PVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSW 397
           L + FS FG +  +K+     G  FV+F+  + AE A+Q L G   G + +R+ +
Sbjct: 1   LYKLFSPFGNVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDY 55

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

 Score = 55.1 bits (133), Expect = 5e-10
 Identities = 24/51 (47%), Positives = 35/51 (68%), Gaps = 1/51 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDE 261
           IFVG L PDVT+   +E FS ++  V  A+++ D +TGR++G+GFV F  E
Sbjct: 2   IFVGGLPPDVTEEEFKEYFS-QFGKVVDAQLMQDHDTGRSRGFGFVTFDSE 51

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

 Score = 55.2 bits (133), Expect = 6e-10
 Identities = 26/66 (39%), Positives = 37/66 (56%)

Query: 117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQS 176
            I+IG L H   E  L   FS  G V NV+V R+K+TG S+ YGF++F +   A    +S
Sbjct: 1   VIYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKS 60

Query: 177 YSGSLM 182
            +  L+
Sbjct: 61  MNNYLL 66

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

 Score = 55.0 bits (133), Expect = 7e-10
 Identities = 28/69 (40%), Positives = 39/69 (56%), Gaps = 10/69 (14%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK---------GCGFVQFANRKDAEVAL 380
           I+V  LD  + ++DLR  FS+FGE+ S++IP  +         G  FV F +   AE AL
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62

Query: 381 QKLQGTAIG 389
           Q L GT +G
Sbjct: 63  Q-LNGTELG 70

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

 Score = 55.1 bits (132), Expect = 8e-10
 Identities = 27/77 (35%), Positives = 47/77 (61%), Gaps = 1/77 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +FVGDL+P++T   ++  F+  +  +  A+V+ D  TG++KGYGFV F ++ +   A+  
Sbjct: 4   VFVGDLSPEITTEDIKSAFAP-FGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 62

Query: 271 MNGVYCSSRPMRIDVAT 287
           M G +   R +R + AT
Sbjct: 63  MGGQWLGGRQIRTNWAT 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|240819 cd12373, RRM_SRSF3_like, RNA recognition motif in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins

 Score = 54.5 bits (132), Expect = 8e-10
 Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 7/75 (9%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKI----PVGKGCGFVQFANRKDAEVALQKLQG 385
           ++VG L    +  +L + F ++G + SV +    P   G  FV+F + +DAE A++ L G
Sbjct: 2   VYVGNLGPRATKRELEDEFEKYGPLRSVWVARNPP---GFAFVEFEDPRDAEDAVRALDG 58

Query: 386 TAIGKQTVRLSWGRN 400
             I    VR+   R 
Sbjct: 59  RRICGNRVRVELSRG 73

This subfamily corresponds to the RRM of two serine/arginine (SR) proteins, serine/arginine-rich splicing factor 3 (SRSF3) and serine/arginine-rich splicing factor 7 (SRSF7). SRSF3, also termed pre-mRNA-splicing factor SRp20, modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation, and tumor induction and maintenance. It can shuttle between the nucleus and cytoplasm. SRSF7, also termed splicing factor 9G8, plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. Moreover, SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. Both SRSF3 and SRSF7 contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 73

>gnl|CDD|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split end) protein family

 Score = 54.7 bits (132), Expect = 9e-10
 Identities = 23/76 (30%), Positives = 40/76 (52%), Gaps = 5/76 (6%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKI-----PVGKGCGFVQFANRKDAEVALQKL 383
           T+FVG L+  +++E+LR  F ++G +  V I       G    FV+F N   A  A   +
Sbjct: 4   TLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRAKVAM 63

Query: 384 QGTAIGKQTVRLSWGR 399
            G  IG+  +++ +G+
Sbjct: 64  SGQYIGRNQIKIGYGK 79

This subfamily corresponds to the RRM2 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which share a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 79

>gnl|CDD|240796 cd12350, RRM3_SHARP, RNA recognition motif 3 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 54.3 bits (131), Expect = 9e-10
 Identities = 23/70 (32%), Positives = 38/70 (54%), Gaps = 3/70 (4%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKI---PVGKGCGFVQFANRKDAEVALQKLQG 385
           T+F+G L+   +  DLRE F +FGEI+ + I          F+Q+A+      A++K+ G
Sbjct: 4   TLFIGNLEKTTTYSDLREAFERFGEIIDIDIKKQGGNPAYAFIQYADIASVVKAMRKMDG 63

Query: 386 TAIGKQTVRL 395
             +G   V+L
Sbjct: 64  EYLGNNRVKL 73

This subfamily corresponds to the RRM3 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 74

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

 Score = 54.1 bits (131), Expect = 1e-09
 Identities = 26/63 (41%), Positives = 33/63 (52%), Gaps = 6/63 (9%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIP------VGKGCGFVQFANRKDAEVALQK 382
           TI V  L  D  ++DLRE F  FG I  V +         +G  FV F  R+DAE A++K
Sbjct: 1   TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60

Query: 383 LQG 385
           L G
Sbjct: 61  LNG 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|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate Hu-antigen B (HuB)

 Score = 54.3 bits (130), Expect = 1e-09
 Identities = 30/79 (37%), Positives = 45/79 (56%), Gaps = 1/79 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           IFV +LAPD  +SIL + F   + +V   KVI D NT + KG+GFV   + +E + A+  
Sbjct: 6   IFVYNLAPDADESILWQMFGP-FGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIAS 64

Query: 271 MNGVYCSSRPMRIDVATPK 289
           +NG     R +++   T K
Sbjct: 65  LNGYRLGDRVLQVSFKTNK 83

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

 Score = 54.2 bits (131), Expect = 1e-09
 Identities = 21/80 (26%), Positives = 39/80 (48%), Gaps = 9/80 (11%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKI-------PVGK--GCGFVQFANRKDAEVA 379
            +++G LDS +++  L + FS++G+I              G+  G  FV F  +++AE A
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 380 LQKLQGTAIGKQTVRLSWGR 399
           L+ L G     + + + W  
Sbjct: 61  LKSLNGKTALGKKLVVRWAH 80

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|240907 cd12461, RRM_SCAF4, RNA recognition motif found in SR-related and CTD-associated factor 4 (SCAF4) and similar proteins

 Score = 54.3 bits (130), Expect = 1e-09
 Identities = 23/76 (30%), Positives = 44/76 (57%), Gaps = 2/76 (2%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTA- 387
           T++VG LD   + +D+     +FG I S+ +   +GC ++   +R+DA  ALQKL     
Sbjct: 6   TLWVGQLDKRTTQQDVTSLLEEFGPIESINMIPPRGCAYIVMVHRQDAYRALQKLSRGNV 65

Query: 388 -IGKQTVRLSWGRNPG 402
            + +++++++W  N G
Sbjct: 66  KVNQKSIKIAWALNKG 81

The CD corresponds to the RRM of SCAF4 (also termed splicing factor, arginine/serine-rich 15 or SFR15, or CTD-binding SR-like protein RA4) that belongs to a new class of SCAFs (SR-like CTD-associated factors). Although its biological function remains unclear, SCAF4 shows high sequence similarity to SCAF8 that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II) and may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF4 and SCAF8 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and serine/arginine-rich motifs. Length = 81

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

 Score = 54.1 bits (131), Expect = 1e-09
 Identities = 24/69 (34%), Positives = 36/69 (52%), Gaps = 5/69 (7%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-----KGCGFVQFANRKDAEVALQKLQ 384
           IF+  LD  + ++ L + FS FG ILS K+        KG GFV F   + A  A++K+ 
Sbjct: 5   IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAVRAIEKVN 64

Query: 385 GTAIGKQTV 393
           G  +  + V
Sbjct: 65  GMLLNDKKV 73

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

 Score = 53.8 bits (130), Expect = 1e-09
 Identities = 21/69 (30%), Positives = 36/69 (52%), Gaps = 6/69 (8%)

Query: 332 VGALDSDVSDEDLREPFSQFGEILSVKIP------VGKGCGFVQFANRKDAEVALQKLQG 385
           V  L    + +DLR  F ++GE+  V IP        +G  FV+F +++DAE A+  + G
Sbjct: 3   VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDG 62

Query: 386 TAIGKQTVR 394
             +  + +R
Sbjct: 63  KELDGRELR 71

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

 Score = 54.3 bits (130), Expect = 1e-09
 Identities = 27/77 (35%), Positives = 48/77 (62%), Gaps = 1/77 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +FVGDL+P++T   ++  F+  +  +  A+V+ D  TG++KGYGFV F ++ +   A+ +
Sbjct: 4   VFVGDLSPEITTDDIKAAFAP-FGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 62

Query: 271 MNGVYCSSRPMRIDVAT 287
           M G +   R +R + AT
Sbjct: 63  MGGQWLGGRQIRTNWAT 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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 53.4 bits (129), Expect = 2e-09
 Identities = 21/68 (30%), Positives = 41/68 (60%), Gaps = 1/68 (1%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY 177
           +++G+L     E  L + FS  G + +++++R+ +TG+S+G+ FVEF     AEK L++ 
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRD-ETGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 178 SGSLMPNT 185
           +G  +   
Sbjct: 60  NGKELGGR 67

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

 Score = 53.3 bits (129), Expect = 2e-09
 Identities = 21/74 (28%), Positives = 40/74 (54%), Gaps = 2/74 (2%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           S+FVG+L  D+ +  L++ F      V+  +++ D  TG  KG+G+V F  + +      
Sbjct: 1   SVFVGNLPFDIEEEELRKHFEDCGD-VEAVRIVRDRKTGIGKGFGYVLFKTK-DSVALAL 58

Query: 270 EMNGVYCSSRPMRI 283
           ++NG+    R +R+
Sbjct: 59  KLNGIKLKGRKIRV 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|240841 cd12395, RRM2_RBM34, RNA recognition motif 2 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 53.3 bits (129), Expect = 2e-09
 Identities = 16/59 (27%), Positives = 36/59 (61%)

Query: 117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQ 175
           ++++G+L   ++E  L   F   G V  V+++R+++TG  +G+G+V F ++ +    L+
Sbjct: 1   SVFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALK 59

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

 Score = 53.8 bits (130), Expect = 2e-09
 Identities = 31/65 (47%), Positives = 41/65 (63%), Gaps = 3/65 (4%)

Query: 330 IFVGALDSD-VSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAI 388
           +FVG L++D VS EDL E FS++G+IL   I + KG GFVQF N +DA  A+    G  I
Sbjct: 3   VFVGNLNTDKVSKEDLEEIFSKYGKILG--ISLHKGYGFVQFDNEEDARAAVAGENGREI 60

Query: 389 GKQTV 393
             Q +
Sbjct: 61  AGQKL 65

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

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

 Score = 53.4 bits (129), Expect = 2e-09
 Identities = 25/69 (36%), Positives = 36/69 (52%), Gaps = 5/69 (7%)

Query: 328 ATIFVGALDSDVSDEDLREPFSQFGEILSVKI---PVGK--GCGFVQFANRKDAEVALQK 382
             + V  L  DV++EDL E F + GE+  VKI     G+  G   V F  R+DAE A+++
Sbjct: 1   TRLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIKQ 60

Query: 383 LQGTAIGKQ 391
             G  +  Q
Sbjct: 61  FNGVLLDGQ 69

This subfamily corresponds to the RRM of Aly/REF family which includes THO complex subunit 4 (THOC4, also termed Aly/REF), S6K1 Aly/REF-like target (SKAR, also termed PDIP3 or PDIP46) and similar proteins. THOC4 is an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus, and was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid, and might be a novel transcription cofactor for erythroid-specific genes. SKAR shows high sequence homology with THOC4 and possesses one RRM as well. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion. . Length = 75

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

 Score = 53.8 bits (130), Expect = 2e-09
 Identities = 24/74 (32%), Positives = 37/74 (50%), Gaps = 8/74 (10%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +FV  L  D T+S L+  F   Y  +K  +++ D  TG+ +GY F+ F  E+ER      
Sbjct: 4   LFVARLNYDTTESKLRREFEE-YGPIKRIRLVRDKKTGKPRGYAFIEF--EHERD----- 55

Query: 271 MNGVYCSSRPMRID 284
           M   Y  +   +ID
Sbjct: 56  MKAAYKYADGKKID 69

This subfamily corresponds to the RRM of U1-70K, also termed snRNP70, a key component of the U1 snRNP complex, which is one of the key factors facilitating the splicing of pre-mRNA via interaction at the 5' splice site, and is involved in regulation of polyadenylation of some viral and cellular genes, enhancing or inhibiting efficient poly(A) site usage. U1-70K plays an essential role in targeting the U1 snRNP to the 5' splice site through protein-protein interactions with regulatory RNA-binding splicing factors, such as the RS protein ASF/SF2. Moreover, U1-70K protein can specifically bind to stem-loop I of the U1 small nuclear RNA (U1 snRNA) contained in the U1 snRNP complex. It also mediates the binding of U1C, another U1-specific protein, to the U1 snRNP complex. U1-70K contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region at the N-terminal half, and two serine/arginine-rich (SR) domains at the C-terminal half. The RRM is responsible for the binding of stem-loop I of U1 snRNA molecule. Additionally, the most prominent immunodominant region that can be recognized by auto-antibodies from autoimmune patients may be located within the RRM. The SR domains are involved in protein-protein interaction with SR proteins that mediate 5' splice site recognition. For instance, the first SR domain is necessary and sufficient for ASF/SF2 Binding. The family also includes Drosophila U1-70K that is an essential splicing factor required for viability in flies, but its SR domain is dispensable. The yeast U1-70k doesn't contain easily recognizable SR domains and shows low sequence similarity in the RRM region with other U1-70k proteins and therefore not included in this family. The RRM domain is dispensable for yeast U1-70K function. Length = 91

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

 Score = 53.0 bits (128), Expect = 3e-09
 Identities = 24/63 (38%), Positives = 38/63 (60%), Gaps = 2/63 (3%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           ++V +L  D+ D  L+E F  KY  +  AKV+ D   G++KG+GFV F +     +A+ E
Sbjct: 4   VYVKNLGEDMDDEKLKELFG-KYGKITSAKVMKDDE-GKSKGFGFVNFENHEAAQKAVEE 61

Query: 271 MNG 273
           +NG
Sbjct: 62  LNG 64

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

>gnl|CDD|240808 cd12362, RRM3_CELF1-6, RNA recognition motif 3 in CELF/Bruno-like family of RNA binding proteins CELF1, CELF2, CELF3, CELF4, CELF5, CELF6 and similar proteins

 Score = 53.0 bits (128), Expect = 3e-09
 Identities = 22/63 (34%), Positives = 36/63 (57%), Gaps = 1/63 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +F+  L  + TD  L + F+  + +V  AKV +D NTG++K +GFV + +      A+  
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAP-FGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKA 59

Query: 271 MNG 273
           MNG
Sbjct: 60  MNG 62

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

 Score = 53.1 bits (128), Expect = 3e-09
 Identities = 27/73 (36%), Positives = 40/73 (54%), Gaps = 1/73 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           IFV +L PD  +S+L + FS  + +V   KVI D  T + KGYGFV   +  E   A+  
Sbjct: 4   IFVYNLPPDADESLLWQLFSP-FGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIAS 62

Query: 271 MNGVYCSSRPMRI 283
           +NG     R +++
Sbjct: 63  LNGYRLGGRVLQV 75

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

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

 Score = 53.0 bits (128), Expect = 3e-09
 Identities = 21/60 (35%), Positives = 34/60 (56%)

Query: 116 KTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQ 175
             I++G L +   +  L   FS  G++    VI ++QTG+S GYGFV F  + +AE+  +
Sbjct: 1   TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60

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

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

 Score = 53.4 bits (129), Expect = 3e-09
 Identities = 19/60 (31%), Positives = 31/60 (51%)

Query: 113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEK 172
           D   T+++G L     E  L   FS  G +  ++++R+  TG S+GY FVE+     A +
Sbjct: 1   DPYLTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALR 60

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

 Score = 53.0 bits (128), Expect = 4e-09
 Identities = 20/66 (30%), Positives = 37/66 (56%), Gaps = 5/66 (7%)

Query: 210 SIFVGDLAPDVTDSILQETFSS--KYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRA 267
           ++++GDL P + ++ +   F+   +  SVK   +I +  TG++ GYGFV F       +A
Sbjct: 1   TLWMGDLEPWMDEAYIYSAFAECGEVTSVK---IIRNKQTGKSAGYGFVEFATHEAAEQA 57

Query: 268 MTEMNG 273
           +  +NG
Sbjct: 58  LQSLNG 63

This subfamily corresponds to the RRM1 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs. . Length = 81

>gnl|CDD|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 = 53.0 bits (128), Expect = 4e-09
 Identities = 21/70 (30%), Positives = 37/70 (52%), Gaps = 7/70 (10%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKI---PVGK---GCGFVQFANRKDAEVALQK 382
            +FV  L +  ++++L   FS+FG +  V +   P      G GFV F + +DA+ A++ 
Sbjct: 3   KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRD 62

Query: 383 LQGTAI-GKQ 391
           L G  + G+ 
Sbjct: 63  LNGKELEGRV 72

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

 Score = 53.0 bits (128), Expect = 4e-09
 Identities = 23/77 (29%), Positives = 42/77 (54%), Gaps = 1/77 (1%)

Query: 209 LSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAM 268
           L++FVG L+   T+  L+E FS +Y  ++  +++ D  TG +KGY FV +  E +  RA 
Sbjct: 4   LTLFVGRLSLQTTEETLREVFS-RYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAY 62

Query: 269 TEMNGVYCSSRPMRIDV 285
            + + +      + +D 
Sbjct: 63  RDAHKLVIDGSEIFVDF 79

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|240967 cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA-binding protein MRN1 and similar proteins

 Score = 52.8 bits (127), Expect = 4e-09
 Identities = 21/61 (34%), Positives = 31/61 (50%), Gaps = 2/61 (3%)

Query: 323 GESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQK 382
           G S N  +++G L    S+E+LRE   +FG I  +KI   K   FV F +  +A   +  
Sbjct: 1   GASRN--VYIGNLPESYSEEELREDLEKFGPIDQIKIVKEKNIAFVHFLSIANAIKVVTT 58

Query: 383 L 383
           L
Sbjct: 59  L 59

This subgroup corresponds to the RRM2 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 78

>gnl|CDD|241066 cd12622, RRM3_PUB1, RNA recognition motif 3 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 52.5 bits (126), Expect = 4e-09
 Identities = 21/72 (29%), Positives = 37/72 (51%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAI 388
           T++VG +    +  DL   F  FG IL  +    +G  FV+    + A +A+ +LQG  +
Sbjct: 2   TVYVGNIPPYTTQADLIPLFQNFGYILEFRHQPDRGFAFVKLDTHEQAAMAIVQLQGFPV 61

Query: 389 GKQTVRLSWGRN 400
             + +R  WG++
Sbjct: 62  HGRPLRCGWGKD 73

This subfamily corresponds to the RRM3 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 74

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

 Score = 52.7 bits (127), Expect = 5e-09
 Identities = 22/64 (34%), Positives = 37/64 (57%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           S+++GDL P + ++ ++  F+S   +V   K+I +  TG   GY FV F DE    R + 
Sbjct: 1   SLWMGDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLH 60

Query: 270 EMNG 273
           ++NG
Sbjct: 61  KLNG 64

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

 Score = 52.3 bits (126), Expect = 5e-09
 Identities = 21/50 (42%), Positives = 33/50 (66%), Gaps = 1/50 (2%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGD 260
           +FVG L  DVT+  L+E FS +Y +V+  +++ D  TG+ +G+ FV F D
Sbjct: 2   LFVGGLKEDVTEEDLREYFS-QYGNVESVEIVTDKETGKKRGFAFVTFDD 50

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

 Score = 52.7 bits (127), Expect = 5e-09
 Identities = 16/41 (39%), Positives = 26/41 (63%)

Query: 132 LHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEK 172
           L   FS  G++ + +VIR+K+TG S  Y F+EF ++   E+
Sbjct: 20  LEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEE 60

This subfamily corresponds to the RRM of PPIase, also termed cyclophilin-like protein PPIL4, or rotamase PPIL4, a novel nuclear RNA-binding protein encoded by cyclophilin-like PPIL4 gene. The precise role of PPIase remains unclear. PPIase contains a conserved N-terminal peptidyl-prolyl cistrans isomerase (PPIase) motif, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a lysine rich domain, and a pair of bipartite nuclear targeting sequences (NLS) at the C-terminus. Length = 83

>gnl|CDD|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic activator RIM4 and similar proteins

 Score = 52.3 bits (126), Expect = 5e-09
 Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 3/75 (4%)

Query: 209 LSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAM 268
            SIFVG L+PDVT   L E F S++  +    +I  +N      + F++F  E   +RA+
Sbjct: 4   YSIFVGQLSPDVTKEELNERF-SRHGKILEVNLIKRANHTNA--FAFIKFEREQAAARAV 60

Query: 269 TEMNGVYCSSRPMRI 283
              N     ++ M +
Sbjct: 61  ESENHSMLKNKTMHV 75

This subfamily corresponds to the RRM2 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. . Length = 80

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

 Score = 52.2 bits (126), Expect = 5e-09
 Identities = 22/71 (30%), Positives = 39/71 (54%), Gaps = 6/71 (8%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKL 383
           + VG L  +V+ + L+E FS +G +  V +P+       +G  +V+F + +DAE A++ +
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 384 QGTAIGKQTVR 394
            G  I  Q V 
Sbjct: 61  DGGQIDGQEVT 71

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

 Score = 52.3 bits (126), Expect = 5e-09
 Identities = 28/77 (36%), Positives = 41/77 (53%), Gaps = 2/77 (2%)

Query: 208 DLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRA 267
           D ++FVG+L   VT+ IL E F    P ++G K+  D N G+ K + FV F  E     A
Sbjct: 1   DRTLFVGNLDARVTEEILYELFLQAGP-LEGVKIPKDPN-GKPKSFAFVTFKHEVSVPYA 58

Query: 268 MTEMNGVYCSSRPMRID 284
           +  +NG+    R +RI 
Sbjct: 59  IQLLNGIRLFGRELRIK 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|240722 cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in Mei2-like proteins and terminal EAR1-like proteins

 Score = 52.2 bits (126), Expect = 6e-09
 Identities = 25/61 (40%), Positives = 36/61 (59%), Gaps = 1/61 (1%)

Query: 327 NATIFVGALDSDVSDEDLREPFSQFGEILSVK-IPVGKGCGFVQFANRKDAEVALQKLQG 385
             T+ V  LDS +SD++LR  FSQFGE+  ++  P+     FV+F + + AE AL  L G
Sbjct: 1   QGTLLVFNLDSPISDQELRSLFSQFGEVKDIRETPLRPSQKFVEFYDIRAAEAALDALNG 60

Query: 386 T 386
            
Sbjct: 61  R 61

This subfamily corresponds to the RRM2 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding proteins family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins. . Length = 71

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

 Score = 52.3 bits (126), Expect = 6e-09
 Identities = 18/53 (33%), Positives = 32/53 (60%)

Query: 127 MDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSG 179
           M +  L + F   G + + K++R++ TGQS GYGFV++     A+K + + +G
Sbjct: 12  MTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNG 64

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

 Score = 51.8 bits (125), Expect = 6e-09
 Identities = 22/58 (37%), Positives = 35/58 (60%), Gaps = 1/58 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAM 268
           +F+G L+ D T+  L+E FS KY  V    ++ D  TGR++G+GFV F D +   + +
Sbjct: 1   LFIGGLSWDTTEESLREYFS-KYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVL 57

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

 Score = 51.8 bits (125), Expect = 6e-09
 Identities = 20/73 (27%), Positives = 40/73 (54%), Gaps = 6/73 (8%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVALQKL 383
           ++VG L  +V ++ L   F  FG+I  ++IP+       +G  FV+F   +DA  A+  +
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 384 QGTAIGKQTVRLS 396
             + +  +T+R++
Sbjct: 61  NESELFGRTIRVN 73

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|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic activator RIM4 and similar proteins

 Score = 51.9 bits (125), Expect = 7e-09
 Identities = 21/70 (30%), Positives = 36/70 (51%), Gaps = 4/70 (5%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKI----PVGKGCGFVQFANRKDAEVALQKLQ 384
           +IFVG L  DV+ E+L E FS+ G+IL V +           F++F   + A  A++   
Sbjct: 5   SIFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNAFAFIKFEREQAAARAVESEN 64

Query: 385 GTAIGKQTVR 394
            + +  +T+ 
Sbjct: 65  HSMLKNKTMH 74

This subfamily corresponds to the RRM2 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. . Length = 80

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

 Score = 52.0 bits (125), Expect = 8e-09
 Identities = 20/73 (27%), Positives = 39/73 (53%), Gaps = 6/73 (8%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVALQK 382
           T+FVG L   V DE L+  F +FG ++  ++         +G G+V F + +DA+ A++ 
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 383 LQGTAIGKQTVRL 395
           + G  +  + + +
Sbjct: 61  MDGKELDGRPINV 73

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

 Score = 51.9 bits (125), Expect = 8e-09
 Identities = 26/60 (43%), Positives = 35/60 (58%), Gaps = 7/60 (11%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK------GCGFVQFANRKDAE-VALQK 382
           +FVG L  DV++EDLRE FSQ+G + SV+I   K      G  FV F +    + + LQK
Sbjct: 2   LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQK 61

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

 Score = 51.8 bits (125), Expect = 9e-09
 Identities = 26/67 (38%), Positives = 35/67 (52%), Gaps = 6/67 (8%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFG---EILSVKIPVGKGC---GFVQFANRKDAEVALQK 382
           T+FV  L  D +DE L E FS+ G       VK    K C   G+V FA  +DA+ AL++
Sbjct: 1   TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEE 60

Query: 383 LQGTAIG 389
            + T  G
Sbjct: 61  KKKTKFG 67

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

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

 Score = 56.2 bits (135), Expect = 1e-08
 Identities = 66/276 (23%), Positives = 105/276 (38%), Gaps = 45/276 (16%)

Query: 182 MPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKV 241
           M N      LN     GSD      S  ++ V  L  D+TD  L   F +  P +   ++
Sbjct: 81  MANMASTNSLNSLGSGGSDDNDTNNSGTNLIVNYLPQDMTDRELYALFRTIGP-INTCRI 139

Query: 242 IIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKASGYQQQYSSQ 301
           + D  TG + GY FV FG E +  RA+  +NG+   ++ +++  A P             
Sbjct: 140 MRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYARP------------- 186

Query: 302 ALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV 361
                           G +S  ++N   ++V  L   ++D+ L   F ++G+I+   I  
Sbjct: 187 ----------------GGESIKDTN---LYVTNLPRTITDDQLDTIFGKYGQIVQKNILR 227

Query: 362 GK------GCGFVQFANRKDAEVALQKLQGT----AIGKQTVRLSWGRNPGNKQWRGDHS 411
            K      G  FV+F  R++A+ A+  L            TVRL+               
Sbjct: 228 DKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAEEHGKAKAHHYMSQM 287

Query: 412 NHWNGAH--YGGQGYSGNGYAFPPNQDPNMYAATAV 445
            H N  +  +G  G +G     PPN    M     V
Sbjct: 288 GHGNMGNMGHGNMGMAGGSGMNPPNPPAFMGMNNMV 323

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

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

 Score = 51.5 bits (124), Expect = 1e-08
 Identities = 26/65 (40%), Positives = 37/65 (56%), Gaps = 5/65 (7%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKI-----PVGKGCGFVQFANRKDAEVALQKLQ 384
           ++V  LD  + DE LRE FS FG I S K+        KG GFV F++ ++A  A+ ++ 
Sbjct: 4   LYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVTEMN 63

Query: 385 GTAIG 389
           G  IG
Sbjct: 64  GRIIG 68

This subfamily corresponds to the RRM4 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in theThe CD corresponds to the RRM. regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 79

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

 Score = 51.1 bits (123), Expect = 1e-08
 Identities = 26/62 (41%), Positives = 37/62 (59%), Gaps = 1/62 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           IFVG L    TD  L++ FS ++  ++ A VI D  TG+++GYGFV F D+    RA  +
Sbjct: 3   IFVGGLPYHTTDDSLRKYFS-QFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKD 61

Query: 271 MN 272
            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|240782 cd12336, RRM_RBM7_like, RNA recognition motif in RNA-binding protein 7 (RBM7) and similar proteins

 Score = 51.5 bits (124), Expect = 1e-08
 Identities = 26/75 (34%), Positives = 38/75 (50%), Gaps = 5/75 (6%)

Query: 327 NATIFVGALDSDVSDEDLREPFSQFGEILSVKIP-----VGKGCGFVQFANRKDAEVALQ 381
           + T+FVG LD+ V++E L E F Q G +  VKIP       K   FV F +      A+Q
Sbjct: 1   DRTLFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKPKSFAFVTFKHEVSVPYAIQ 60

Query: 382 KLQGTAIGKQTVRLS 396
            L G  +  + +R+ 
Sbjct: 61  LLNGIRLFGRELRIK 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|240766 cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition motif 6 in RNA-binding protein 19 (RBM19 or RBD-1) and RNA recognition motif 5 in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 51.5 bits (124), Expect = 1e-08
 Identities = 18/53 (33%), Positives = 34/53 (64%), Gaps = 5/53 (9%)

Query: 339 VSDEDLREPFSQFGEILSVKIPVG-----KGCGFVQFANRKDAEVALQKLQGT 386
            + ++LRE FS FG++ SV++P       +G  FV+F  +++A+ A++ L+ T
Sbjct: 12  ATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEALKST 64

This subfamily corresponds to the RRM6 of RBM19 and RRM5 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 76

>gnl|CDD|241064 cd12620, RRM3_TIAR, RNA recognition motif 3 in nucleolysin TIAR and similar proteins

 Score = 51.6 bits (123), Expect = 1e-08
 Identities = 21/71 (29%), Positives = 43/71 (60%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAI 388
           T++ G + S ++++ +R+ FS FG+I+ +++   KG  F++F+  + A  A+  + GT I
Sbjct: 2   TVYCGGIASGLTEQLMRQTFSPFGQIMEIRVFPEKGYSFIRFSTHESAAHAIVSVNGTTI 61

Query: 389 GKQTVRLSWGR 399
               V+  WG+
Sbjct: 62  EGHVVKCYWGK 72

This subgroup corresponds to the RRM3 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 73

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

 Score = 51.6 bits (124), Expect = 1e-08
 Identities = 21/73 (28%), Positives = 39/73 (53%), Gaps = 5/73 (6%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIP-----VGKGCGFVQFANRKDAEVALQKL 383
            +FV  L   V+ E+L + F + G + SV++        KG  +V++ N   A  A+ K+
Sbjct: 4   KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKM 63

Query: 384 QGTAIGKQTVRLS 396
            GT I ++T+ ++
Sbjct: 64  DGTEIKEKTISVA 76

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

 Score = 51.1 bits (123), Expect = 1e-08
 Identities = 20/57 (35%), Positives = 33/57 (57%), Gaps = 2/57 (3%)

Query: 117 TIWIGDL-FHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEK 172
            + +G+L   + DE F        G V    ++ ++ TG+S+GYGFVE+ S+A+A K
Sbjct: 1   LLCVGNLPLEFTDEQFRELVSPF-GAVERCFLVYSESTGESKGYGFVEYASKASALK 56

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

 Score = 51.1 bits (123), Expect = 1e-08
 Identities = 23/69 (33%), Positives = 39/69 (56%), Gaps = 1/69 (1%)

Query: 216 LAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVY 275
           L+   T+  L+E FS +Y  ++  +V+ D  TGR++G+GFV F    +   A   +NG+ 
Sbjct: 7   LSLYTTERDLREVFS-RYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGME 65

Query: 276 CSSRPMRID 284
              R +R+D
Sbjct: 66  IDGRRIRVD 74

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

 Score = 50.8 bits (122), Expect = 2e-08
 Identities = 24/75 (32%), Positives = 43/75 (57%), Gaps = 7/75 (9%)

Query: 329 TIFVGALDSDVSDEDLREPFSQ-FGEILSVKIPVG-----KGCGFVQFANRKDAEVALQK 382
           ++FVG L  DV D  L E FS+ +      K+ +      +G GFV+F++  + + AL +
Sbjct: 3   SLFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLDQNGNSRGYGFVRFSDESEQKRALTE 62

Query: 383 LQG-TAIGKQTVRLS 396
           +QG + +G + +R+S
Sbjct: 63  MQGASGLGGKPIRVS 77

This subgroup corresponds to the RRM2 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. . Length = 82

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

 Score = 50.6 bits (121), Expect = 2e-08
 Identities = 24/74 (32%), Positives = 39/74 (52%), Gaps = 6/74 (8%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKI------PVGKGCGFVQFANRKDAEVALQKL 383
           IFVG L  +V+D  L   FS F      ++         +G GFV F +++DAE A+ ++
Sbjct: 2   IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61

Query: 384 QGTAIGKQTVRLSW 397
            G  +G + +R +W
Sbjct: 62  NGKWLGSRPIRCNW 75

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

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

 Score = 50.6 bits (121), Expect = 2e-08
 Identities = 24/76 (31%), Positives = 40/76 (52%), Gaps = 2/76 (2%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY 177
           I++GDL   + +  L   FS      + +V+ + ++G+S GYGFV F S+  AE  +   
Sbjct: 2   IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61

Query: 178 SGSLMPNTDQPFRLNW 193
           +G  +    +P R NW
Sbjct: 62  NGKWL--GSRPIRCNW 75

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

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

 Score = 50.4 bits (121), Expect = 2e-08
 Identities = 25/71 (35%), Positives = 40/71 (56%), Gaps = 3/71 (4%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGC---GFVQFANRKDAEVALQKLQGT 386
           ++VG LD  V+++ L E FSQ G I S K+    G     FV++ + + A  ALQ + G 
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDPYAFVEYYDHRSAAAALQTMNGR 60

Query: 387 AIGKQTVRLSW 397
            I  Q ++++W
Sbjct: 61  LILGQEIKVNW 71

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

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

 Score = 50.7 bits (122), Expect = 2e-08
 Identities = 23/59 (38%), Positives = 32/59 (54%), Gaps = 6/59 (10%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQ 381
            IFVG L    +D+ LR+ FSQFGEI    +         +G GFV F +++ AE A +
Sbjct: 2   KIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60

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

>gnl|CDD|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate Hu-antigen D (HuD)

 Score = 51.2 bits (122), Expect = 2e-08
 Identities = 28/79 (35%), Positives = 45/79 (56%), Gaps = 1/79 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           IFV +L+PD  +S+L + F   + +V   KVI D NT + KG+GFV   + +E + A+  
Sbjct: 6   IFVYNLSPDSDESVLWQLFGP-FGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIAS 64

Query: 271 MNGVYCSSRPMRIDVATPK 289
           +NG     R +++   T K
Sbjct: 65  LNGYRLGDRVLQVSFKTNK 83

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|240718 cd12272, RRM2_PHIP1, RNA recognition motif 2 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 50.9 bits (122), Expect = 2e-08
 Identities = 26/76 (34%), Positives = 43/76 (56%), Gaps = 5/76 (6%)

Query: 210 SIFVGDLAPDVTDSILQETFSS-KYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAM 268
           ++++G+LA D+T+  ++E F   +  SV+ A    D  TG  KG+G V F DE     A+
Sbjct: 1   TVYIGNLAWDITEDDVREFFKGCEITSVRLAT---DKETGEFKGFGHVDFADEESLDAAL 57

Query: 269 TEMNGVYCSSRPMRID 284
            +++G     RP+RI 
Sbjct: 58  -KLDGTVLCGRPIRIA 72

The CD corresponds to the RRM2 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

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

 Score = 50.8 bits (122), Expect = 2e-08
 Identities = 22/77 (28%), Positives = 40/77 (51%), Gaps = 1/77 (1%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY 177
           ++I +L   MDE  L       GQV++ +++R+ + GQS G GF    SR   E ++  +
Sbjct: 3   LYISNLPLHMDEQDLETMLKPYGQVISTRILRDSK-GQSRGVGFARMESREKCEDIISKF 61

Query: 178 SGSLMPNTDQPFRLNWA 194
           +G  +    +P  + +A
Sbjct: 62  NGKYLKGEGEPLLVKFA 78

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

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

 Score = 50.8 bits (122), Expect = 2e-08
 Identities = 20/65 (30%), Positives = 37/65 (56%), Gaps = 6/65 (9%)

Query: 328 ATIFVGALDSDVSDEDLREPFSQFGEILSVKI------PVGKGCGFVQFANRKDAEVALQ 381
           A ++V  L   ++ ++L   FS +G I++ +I       + +G GF++F  R +AE A++
Sbjct: 1   ANLYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIK 60

Query: 382 KLQGT 386
            L GT
Sbjct: 61  ALNGT 65

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

 Score = 51.0 bits (122), Expect = 2e-08
 Identities = 26/58 (44%), Positives = 36/58 (62%), Gaps = 5/58 (8%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKI-----PVGKGCGFVQFANRKDAEVALQK 382
           IFVG +D   ++ DLR+ FSQ+G +  VKI      V KG GFV F  ++DA+  LQ+
Sbjct: 5   IFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRAGVSKGYGFVTFETQEDAQKILQE 62

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

 Score = 50.7 bits (122), Expect = 2e-08
 Identities = 20/71 (28%), Positives = 39/71 (54%), Gaps = 6/71 (8%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKL 383
           I+V ++  D+S++D++  F  FG+I S  +         KG GF+++ N + A+ A+  +
Sbjct: 3   IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASM 62

Query: 384 QGTAIGKQTVR 394
               +G Q +R
Sbjct: 63  NLFDLGGQQLR 73

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

 Score = 50.9 bits (122), Expect = 2e-08
 Identities = 27/52 (51%), Positives = 32/52 (61%), Gaps = 4/52 (7%)

Query: 341 DEDLREPFSQFGEILSVKIPV----GKGCGFVQFANRKDAEVALQKLQGTAI 388
           D DLR+ F QFG IL V+I       KG GFV FAN  DA+ A +KL GT +
Sbjct: 14  DPDLRQMFGQFGPILDVEIIFNERGSKGFGFVTFANSADADRAREKLHGTVV 65

This subfamily corresponds to the RRM of several tissue-specific alternative splicing isoforms of vertebrate RNA binding protein Fox-1 homologs, which show high sequence similarity to the Caenorhabditis elegans feminizing locus on X (Fox-1) gene encoding Fox-1 protein. RNA binding protein Fox-1 homolog 1 (RBFOX1), also termed ataxin-2-binding protein 1 (A2BP1), or Fox-1 homolog A, or hexaribonucleotide-binding protein 1 (HRNBP1), is predominantly expressed in neurons, skeletal muscle and heart. It regulates alternative splicing of tissue-specific exons by binding to UGCAUG elements. Moreover, RBFOX1 binds to the C-terminus of ataxin-2 and forms an ataxin-2/A2BP1 complex involved in RNA processing. RNA binding protein fox-1 homolog 2 (RBFOX2), also termed Fox-1 homolog B, or hexaribonucleotide-binding protein 2 (HRNBP2), or RNA-binding motif protein 9 (RBM9), or repressor of tamoxifen transcriptional activity, is expressed in ovary, whole embryo, and human embryonic cell lines in addition to neurons and muscle. RBFOX2 activates splicing of neuron-specific exons through binding to downstream UGCAUG elements. RBFOX2 also functions as a repressor of tamoxifen activation of the estrogen receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3 or NeuN or HRNBP3), also termed Fox-1 homolog C, is a nuclear RNA-binding protein that regulates alternative splicing of the RBFOX2 pre-mRNA, producing a message encoding a dominant negative form of the RBFOX2 protein. Its message is detected exclusively in post-mitotic regions of embryonic brain. Like RBFOX1, both RBFOX2 and RBFOX3 bind to the hexanucleotide UGCAUG elements and modulate brain and muscle-specific splicing of exon EIIIB of fibronectin, exon N1 of c-src, and calcitonin/CGRP. Members in this family also harbor one RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 76

>gnl|CDD|240751 cd12305, RRM_NELFE, RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins

 Score = 50.7 bits (122), Expect = 2e-08
 Identities = 23/74 (31%), Positives = 42/74 (56%), Gaps = 4/74 (5%)

Query: 327 NATIFV-GALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQG 385
             T++V G     +++E L++ FS FG I+++ +   K CGFV F   + A+ A+ +L G
Sbjct: 4   GNTLYVHGY---GLTEEILKKAFSPFGNIINISMEKEKNCGFVTFEKMESADRAIAELNG 60

Query: 386 TAIGKQTVRLSWGR 399
           T +    +++S  R
Sbjct: 61  TTVQGVQLKVSLAR 74

This subfamily corresponds to the RRM of NELF-E, also termed RNA-binding protein RD. NELF-E is the RNA-binding subunit of cellular negative transcription elongation factor NELF (negative elongation factor) involved in transcriptional regulation of HIV-1 by binding to the stem of the viral transactivation-response element (TAR) RNA which is synthesized by cellular RNA polymerase II at the viral long terminal repeat. NELF is a heterotetrameric protein consisting of NELF A, B, C or the splice variant D, and E. NELF-E contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It plays a role in the control of HIV transcription by binding to TAR RNA. In addition, NELF-E is associated with the NELF-B subunit, probably via a leucine zipper motif. . Length = 75

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

 Score = 50.3 bits (121), Expect = 2e-08
 Identities = 21/59 (35%), Positives = 34/59 (57%), Gaps = 5/59 (8%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPV-----GKGCGFVQFANRKDAEVALQK 382
           T+FV  LD  V +++LR+ FS+ GEI  V++        KG  +V+F N +  + AL+ 
Sbjct: 1   TVFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEALKL 59

This subfamily corresponds to the RRM1 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 72

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

 Score = 55.6 bits (134), Expect = 3e-08
 Identities = 29/81 (35%), Positives = 46/81 (56%), Gaps = 7/81 (8%)

Query: 328 ATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK------GCGFVQFANRKDAEVALQ 381
           A+++VG LD DV++  L + F  FG +LSV++          G G+V F N  DAE AL+
Sbjct: 1   ASLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALE 60

Query: 382 KLQGTAIGKQTVRLSWG-RNP 401
            +    +G + +R+ W  R+P
Sbjct: 61  TMNFKRLGGKPIRIMWSQRDP 81

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

 Score = 55.8 bits (134), Expect = 3e-08
 Identities = 49/236 (20%), Positives = 94/236 (39%), Gaps = 29/236 (12%)

Query: 175 QSYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLS-IFVGDLAPDVTDSILQETFSSKY 233
           QS    L+  T    +          +R +A + +  ++VG ++ ++ +  ++  F    
Sbjct: 73  QSIKQVLLKQTKAHQQQQLENQQRQQQRQQALAIMCRVYVGSISFELREDTIRRAFDPFG 132

Query: 234 PSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKASG 293
           P +K   +  D  TG+ KG+ FV +        A+ +MNG     R   I V  P     
Sbjct: 133 P-IKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGR--NIKVGRPSNMPQ 189

Query: 294 YQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGE 353
            Q                    +   Q + +  N  I+V ++  D+S+ D++  F  FGE
Sbjct: 190 AQPI------------------IDMVQEEAKKFN-RIYVASVHPDLSETDIKSVFEAFGE 230

Query: 354 ILSVKIPVG------KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGN 403
           I+  ++         KG GF+++ N +    A+  +    +G Q +R+     P +
Sbjct: 231 IVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTPPD 286

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

 Score = 50.0 bits (120), Expect = 3e-08
 Identities = 23/65 (35%), Positives = 38/65 (58%), Gaps = 1/65 (1%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSV-KIPVGKGCGFVQFANRKDAEVALQKLQGTA 387
           T+FV  ++S+V DE+LR  F QFG+I ++      +G   V + + + A  A + LQGT 
Sbjct: 3   TLFVRNINSNVEDEELRALFEQFGDIRTLYTACKHRGFIMVSYYDIRAARRAKRALQGTE 62

Query: 388 IGKQT 392
           +G + 
Sbjct: 63  LGGRK 67

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

>gnl|CDD|241065 cd12621, RRM3_TIA1, RNA recognition motif 3 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 50.1 bits (119), Expect = 3e-08
 Identities = 23/71 (32%), Positives = 43/71 (60%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAI 388
           T++ G + S ++++ +R+ FS FG+I+ V++   KG  FV+F + + A  A+  + GT I
Sbjct: 2   TVYCGGVTSGLTEQLMRQTFSPFGQIMEVRVFPDKGYSFVRFNSHESAAHAIVSVNGTTI 61

Query: 389 GKQTVRLSWGR 399
               V+  WG+
Sbjct: 62  EGHVVKCYWGK 72

This subgroup corresponds to the RRM3 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1) and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 74

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

 Score = 50.3 bits (121), Expect = 4e-08
 Identities = 29/78 (37%), Positives = 43/78 (55%), Gaps = 8/78 (10%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK------GCGFVQFANRKDAEVALQK 382
           T+++G L+  + +  +   F++ GE+ SVKI   K      G GFV+FA  + AE ALQ 
Sbjct: 1   TLWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQS 60

Query: 383 LQGTAI--GKQTVRLSWG 398
           L G  I   +Q  RL+W 
Sbjct: 61  LNGKPIPNTQQRFRLNWA 78

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

 Score = 50.0 bits (120), Expect = 4e-08
 Identities = 21/66 (31%), Positives = 33/66 (50%), Gaps = 6/66 (9%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKI----PVGK--GCGFVQFANRKDAEVALQK 382
            +FV  L+   +DEDL   FS+FG+I S ++      G      F++F  ++D E A  K
Sbjct: 5   VLFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFK 64

Query: 383 LQGTAI 388
           +    I
Sbjct: 65  MDNVLI 70

This subfamily corresponds to the RRM of PPIase, also termed cyclophilin-like protein PPIL4, or rotamase PPIL4, a novel nuclear RNA-binding protein encoded by cyclophilin-like PPIL4 gene. The precise role of PPIase remains unclear. PPIase contains a conserved N-terminal peptidyl-prolyl cistrans isomerase (PPIase) motif, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a lysine rich domain, and a pair of bipartite nuclear targeting sequences (NLS) at the C-terminus. Length = 83

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

 Score = 49.5 bits (119), Expect = 4e-08
 Identities = 17/63 (26%), Positives = 34/63 (53%), Gaps = 1/63 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           ++VG LA +V + +L   F   +  +K  ++ +D  T + +G+ FV F +  + + A+  
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIP-FGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDN 59

Query: 271 MNG 273
           MN 
Sbjct: 60  MNE 62

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

>gnl|CDD|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 = 50.0 bits (120), Expect = 4e-08
 Identities = 23/65 (35%), Positives = 32/65 (49%), Gaps = 6/65 (9%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVALQKL 383
           +FV  L    ++E+LRE F  FGEI  V +P+       KG  FV F   + A  A  +L
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 384 QGTAI 388
            G+  
Sbjct: 62  DGSIF 66

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

 Score = 49.9 bits (120), Expect = 4e-08
 Identities = 21/61 (34%), Positives = 34/61 (55%), Gaps = 3/61 (4%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAE---KVL 174
           +++G+L   + E  L   F   G VVNV + +++ T   +GYGFVEF S   A+   K++
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 175 Q 175
            
Sbjct: 61  N 61

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

 Score = 49.9 bits (120), Expect = 5e-08
 Identities = 22/62 (35%), Positives = 35/62 (56%), Gaps = 6/62 (9%)

Query: 327 NATIFVGALDSDVSDEDLREPFSQFGEILSVK----IPVG--KGCGFVQFANRKDAEVAL 380
             T+FVG L    ++E LRE FS++G+I  ++    I  G  KG  FV++ + +DA  A 
Sbjct: 3   YLTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAY 62

Query: 381 QK 382
           + 
Sbjct: 63  RD 64

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|240693 cd12247, RRM2_U1A_like, RNA recognition motif 2 in the U1A/U2B"/SNF protein family

 Score = 49.5 bits (119), Expect = 5e-08
 Identities = 22/62 (35%), Positives = 32/62 (51%)

Query: 327 NATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGT 386
           N  +F+  L  + + E L   F+QF     V++   +G  FV+F   + A VALQ LQG 
Sbjct: 2   NKILFLQNLPEETTKEMLEMLFNQFPGFKEVRLVPRRGIAFVEFETEEQATVALQALQGF 61

Query: 387 AI 388
            I
Sbjct: 62  KI 63

This subfamily corresponds to the RRM2 of U1A/U2B"/SNF protein family, containing Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs) connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B" does not require an auxiliary protein for binding to RNA and its nuclear transport is independent on U2 snRNA binding. . Length = 72

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

 Score = 49.3 bits (118), Expect = 6e-08
 Identities = 21/53 (39%), Positives = 33/53 (62%)

Query: 127 MDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSG 179
           M +  + + FS  G++ + K+IR+K TGQS GYGFV +     AEK + + +G
Sbjct: 13  MTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTLNG 65

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

 Score = 49.6 bits (119), Expect = 6e-08
 Identities = 21/70 (30%), Positives = 40/70 (57%), Gaps = 3/70 (4%)

Query: 219 DVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNG--VYC 276
            VT+  L+E F+  +  ++   V+ D  T  +KG  +V+F   +  +RAM EMNG  +  
Sbjct: 13  SVTEDDLREAFA-PFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCLGG 71

Query: 277 SSRPMRIDVA 286
            ++P+++ +A
Sbjct: 72  DTKPLKVLIA 81

This subfamily corresponds to the RRM1 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 81

>gnl|CDD|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 = 49.2 bits (118), Expect = 7e-08
 Identities = 20/77 (25%), Positives = 42/77 (54%), Gaps = 2/77 (2%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY 177
           +++G++ +   E  L   FS  G VV+ +++ ++ TG+ +GYGF EF     A   +++ 
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60

Query: 178 SGSLMPNTDQPFRLNWA 194
           +G       +  R+++A
Sbjct: 61  NGY--EFNGRALRVDFA 75

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

>gnl|CDD|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 = 49.2 bits (118), Expect = 7e-08
 Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 6/74 (8%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVALQKL 383
           +FVG +  D ++E L E FS+ G ++S ++         KG GF +F + + A  A++ L
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60

Query: 384 QGTAIGKQTVRLSW 397
            G     + +R+ +
Sbjct: 61  NGYEFNGRALRVDF 74

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

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

 Score = 48.7 bits (117), Expect = 8e-08
 Identities = 23/73 (31%), Positives = 43/73 (58%), Gaps = 6/73 (8%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK------GCGFVQFANRKDAEVALQKL 383
           ++VG LD  V++E L E F Q G +++V IP  +      G GFV+F + +DA+ A++ +
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 384 QGTAIGKQTVRLS 396
               +  + +R++
Sbjct: 61  NMIKLYGKPIRVN 73

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|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding protein 7 (RBM7)

 Score = 49.1 bits (117), Expect = 8e-08
 Identities = 27/76 (35%), Positives = 40/76 (52%), Gaps = 2/76 (2%)

Query: 208 DLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRA 267
           D ++FVG+L P VT+ ++ E F    P +K  K+  D   G+ K + FV F  E     A
Sbjct: 1   DRTLFVGNLDPKVTEELIFELFLQAGPVIK-VKIPKD-KDGKPKQFAFVNFKHEVSVPYA 58

Query: 268 MTEMNGVYCSSRPMRI 283
           M  +NG+    RP+ I
Sbjct: 59  MNLLNGIKLYGRPLNI 74

This subfamily corresponds to the RRM of RBM7, a ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. RBM7 interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20. It may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM7 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. . Length = 75

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

 Score = 49.3 bits (117), Expect = 8e-08
 Identities = 26/80 (32%), Positives = 45/80 (56%), Gaps = 1/80 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           IFV +L+P+  +S+L + F   + +V   KVI D  T + KG+GFV   + +E + A+  
Sbjct: 4   IFVYNLSPEADESVLWQLFGP-FGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIAS 62

Query: 271 MNGVYCSSRPMRIDVATPKK 290
           +NG     R +++   T K+
Sbjct: 63  LNGYRLGDRVLQVSFKTSKQ 82

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

 Score = 49.1 bits (118), Expect = 9e-08
 Identities = 24/74 (32%), Positives = 40/74 (54%), Gaps = 2/74 (2%)

Query: 120 IGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSG 179
           +GDL   + E  L+  FS  G V++++V R+  T +S GY +V F + A AE+ L +   
Sbjct: 4   VGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTL-- 61

Query: 180 SLMPNTDQPFRLNW 193
           +      +P R+ W
Sbjct: 62  NFDVIKGKPIRIMW 75

This subfamily corresponds to the RRM1 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammals, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 80

>gnl|CDD|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins

 Score = 49.1 bits (117), Expect = 1e-07
 Identities = 21/74 (28%), Positives = 40/74 (54%), Gaps = 6/74 (8%)

Query: 328 ATIFVGALDSDVSDEDLREPFSQFGEILSVKI------PVGKGCGFVQFANRKDAEVALQ 381
             +F+G L  D +++ L + FS++G+I  V +         +G GFV F N  DA+ A+ 
Sbjct: 1   GKLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMM 60

Query: 382 KLQGTAIGKQTVRL 395
            + G ++  + +R+
Sbjct: 61  AMNGKSVDGRQIRV 74

This subfamily corresponds to the RRM domain of two structurally related heterogenous nuclear ribonucleoproteins, CIRBP (also termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL), both of which belong to a highly conserved cold shock proteins family. The cold shock proteins can be induced after exposure to a moderate cold-shock and other cellular stresses such as UV radiation and hypoxia. CIRBP and RBM3 may function in posttranscriptional regulation of gene expression by binding to different transcripts, thus allowing the cell to response rapidly to environmental signals. However, the kinetics and degree of cold induction are different between CIRBP and RBM3. Tissue distribution of their expression is different. CIRBP and RBM3 may be differentially regulated under physiological and stress conditions and may play distinct roles in cold responses of cells. CIRBP, also termed glycine-rich RNA-binding protein CIRP, is localized in the nucleus and mediates the cold-induced suppression of cell cycle progression. CIRBP also binds DNA and possibly serves as a chaperone that assists in the folding/unfolding, assembly/disassembly and transport of various proteins. RBM3 may enhance global protein synthesis and the formation of active polysomes while reducing the levels of ribonucleoprotein complexes containing microRNAs. RBM3 may also serve to prevent the loss of muscle mass by its ability to decrease cell death. Furthermore, RBM3 may be essential for cell proliferation and mitosis. Both, CIRBP and RBM3, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), that is involved in RNA binding, and C-terminal glycine-rich domain (RGG motif) that probably enhances RNA-binding via protein-protein and/or protein-RNA interactions. Like CIRBP, RBM3 can also bind to both RNA and DNA via its RRM domain. . Length = 80

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

 Score = 48.4 bits (116), Expect = 1e-07
 Identities = 23/68 (33%), Positives = 34/68 (50%), Gaps = 3/68 (4%)

Query: 117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNK---QTGQSEGYGFVEFYSRAAAEKV 173
            +WIG+L   + E  L   FS  G++     + +K     GQ  GY FV F ++  AEK 
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 174 LQSYSGSL 181
           L+S +G  
Sbjct: 61  LKSLNGKT 68

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|241031 cd12587, RRM1_PSF, RNA recognition motif 1 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

 Score = 48.4 bits (115), Expect = 1e-07
 Identities = 22/66 (33%), Positives = 43/66 (65%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIG 389
           +FVG L +D+++++ ++ F+++GE   V I  GKG GF++  +R  AE+A  +L  T + 
Sbjct: 4   LFVGNLPADITEDEFKKLFAKYGEPGEVFINKGKGFGFIKLESRALAEIAKAELDDTPMR 63

Query: 390 KQTVRL 395
            + +R+
Sbjct: 64  GRQLRV 69

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|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 48.3 bits (115), Expect = 1e-07
 Identities = 22/63 (34%), Positives = 38/63 (60%), Gaps = 1/63 (1%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAI- 388
           +FVG L  D+++E++R+ F ++G+   + I   KG GF++   R  AE+A  +L    + 
Sbjct: 4   LFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKDKGFGFIRLETRTLAEIAKAELDNMPLR 63

Query: 389 GKQ 391
           GKQ
Sbjct: 64  GKQ 66

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|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic activator RIM4 and similar proteins

 Score = 49.0 bits (117), Expect = 1e-07
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 7/74 (9%)

Query: 328 ATIFVGALDSDVSDEDL----REPFSQFGEILSVKI---PVGKGCGFVQFANRKDAEVAL 380
           A +FV +L +  SD++L     E FS++G ++ VK+      +   FVQF N  DA+ AL
Sbjct: 3   ACVFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRDWRQRPYAFVQFTNDDDAKNAL 62

Query: 381 QKLQGTAIGKQTVR 394
            K QGT +  + +R
Sbjct: 63  AKGQGTILDGRHIR 76

This subfamily corresponds to the RRM1 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. . Length = 86

>gnl|CDD|240679 cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition motif found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins

 Score = 48.2 bits (115), Expect = 1e-07
 Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 3/72 (4%)

Query: 329 TIFVGALDSD-VSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTA 387
           T+FV   D     +ED+ + F  FG ++   I   K   FV+F + +DA  AL+ L G+ 
Sbjct: 1   TLFVVGFDPGTTREEDIEKLFEPFGPLVRCDIR--KTFAFVEFEDSEDATKALEALHGSR 58

Query: 388 IGKQTVRLSWGR 399
           I    + + + +
Sbjct: 59  IDGSVLTVEFVK 70

This subfamily corresponds to the RRM of Srp1p and RRM2 of plant SR splicing factors. Srp1p is encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but is not essential for growth. Srp1p is closely related to the SR protein family found in Metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. The family also includes a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RRMs at their N-terminus and an RS domain at their C-terminus. Length = 70

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

 Score = 47.5 bits (114), Expect = 2e-07
 Identities = 22/64 (34%), Positives = 36/64 (56%), Gaps = 3/64 (4%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           ++V +L P VT+  L+E FS  Y  V+G  V +  N  R +G+ FV F    +   A+ +
Sbjct: 1   LYVRNLPPSVTEEDLREFFS-PYGKVEG--VRLVRNKDRPRGFAFVEFASPEDAEAALKK 57

Query: 271 MNGV 274
           +NG+
Sbjct: 58  LNGL 61

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

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

 Score = 48.0 bits (115), Expect = 2e-07
 Identities = 25/78 (32%), Positives = 39/78 (50%), Gaps = 9/78 (11%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           ++V +L    T+  L+E FS +Y  V+  K I D        Y FV F + ++  +AM E
Sbjct: 4   LYVRNLPLSTTEEQLRELFS-EYGEVERVKKIKD--------YAFVHFEERDDAVKAMEE 54

Query: 271 MNGVYCSSRPMRIDVATP 288
           MNG      P+ + +A P
Sbjct: 55  MNGKELEGSPIEVSLAKP 72

This subfamily corresponds to the RRM3 in hnRNP R, hnRNP Q, and APOBEC-1 complementation factor (ACF). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches and has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members contain three conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Length = 72

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

 Score = 48.5 bits (115), Expect = 2e-07
 Identities = 25/75 (33%), Positives = 42/75 (56%), Gaps = 6/75 (8%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKI------PVGKGCGFVQFANRKDAEVALQKL 383
           +FVG L  +++ ED++  F+ FG+I   ++         KG GFV F N+ DAE A+  +
Sbjct: 4   VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63

Query: 384 QGTAIGKQTVRLSWG 398
            G  +G + +R +W 
Sbjct: 64  GGQWLGGRQIRTNWA 78

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

 Score = 47.9 bits (115), Expect = 2e-07
 Identities = 24/64 (37%), Positives = 37/64 (57%), Gaps = 2/64 (3%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           IF+ +L   + +  L +TFS  + ++   KV  D N G +KGYGFV F  E    RA+ +
Sbjct: 5   IFIKNLDKSIDNKALYDTFS-AFGNILSCKVATDEN-GGSKGYGFVHFETEEAAVRAIEK 62

Query: 271 MNGV 274
           +NG+
Sbjct: 63  VNGM 66

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

 Score = 48.4 bits (116), Expect = 2e-07
 Identities = 25/75 (33%), Positives = 37/75 (49%), Gaps = 3/75 (4%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +FV  L P  TD  L+  FS ++  +K  +VI D  TG +  Y F+ F  + +   A  +
Sbjct: 6   LFVCKLNPVTTDEDLEIIFS-RFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFK 64

Query: 271 MNGVYCSSRPMRIDV 285
           M+ V    R  RI V
Sbjct: 65  MDNVLIDDR--RIHV 77

This subfamily corresponds to the RRM of PPIase, also termed cyclophilin-like protein PPIL4, or rotamase PPIL4, a novel nuclear RNA-binding protein encoded by cyclophilin-like PPIL4 gene. The precise role of PPIase remains unclear. PPIase contains a conserved N-terminal peptidyl-prolyl cistrans isomerase (PPIase) motif, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a lysine rich domain, and a pair of bipartite nuclear targeting sequences (NLS) at the C-terminus. Length = 83

>gnl|CDD|240771 cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP A and hnRNP D subfamilies and similar proteins

 Score = 48.0 bits (115), Expect = 2e-07
 Identities = 21/58 (36%), Positives = 33/58 (56%), Gaps = 6/58 (10%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKI---PV---GKGCGFVQFANRKDAEVALQ 381
           +F+G L  D ++E LRE FS++GE++   I   P+    +G GFV FA+    +  L 
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLA 58

This subfamily corresponds to the RRM1 in the hnRNP A subfamily which includes hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The hnRNP D subfamily includes hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus, plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this subfamily contain two putative RRMs and a glycine- and tyrosine-rich C-terminus. The family also contains DAZAP1 (Deleted in azoospermia-associated protein 1), RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins. They all harbor two RRMs. . Length = 72

>gnl|CDD|240771 cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP A and hnRNP D subfamilies and similar proteins

 Score = 47.6 bits (114), Expect = 2e-07
 Identities = 22/60 (36%), Positives = 36/60 (60%), Gaps = 2/60 (3%)

Query: 118 IWIGDLFHW-MDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQS 176
           ++IG L  W   E  L   FS  G+VV+  ++++  TG+S G+GFV F   ++ +KVL +
Sbjct: 1   LFIGGL-SWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAA 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|240686 cd12240, RRM_NCBP2, RNA recognition motif found in nuclear cap-binding protein subunit 2 (CBP20) and similar proteins

 Score = 48.3 bits (116), Expect = 2e-07
 Identities = 23/74 (31%), Positives = 43/74 (58%), Gaps = 6/74 (8%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKG----CGF--VQFANRKDAEVALQKL 383
           ++VG L    ++E + E FS+ G+I  + + + +     CGF  V++  R+DAE A++ L
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60

Query: 384 QGTAIGKQTVRLSW 397
            GT +  + +R+ W
Sbjct: 61  NGTKLDDRIIRVDW 74

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

 Score = 48.1 bits (114), Expect = 2e-07
 Identities = 28/80 (35%), Positives = 39/80 (48%), Gaps = 13/80 (16%)

Query: 211 IFVGDLAPDVTDSILQETFS--SKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAM 268
           +FV +LA  VT+ IL+++FS   K   VK           + K Y FV F + +   RAM
Sbjct: 4   LFVRNLATTVTEEILEKSFSEFGKLERVK-----------KLKDYAFVHFEERDAAVRAM 52

Query: 269 TEMNGVYCSSRPMRIDVATP 288
            EMNG       + I +A P
Sbjct: 53  DEMNGKEIEGEEIEIVLAKP 72

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

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

 Score = 47.9 bits (114), Expect = 2e-07
 Identities = 27/77 (35%), Positives = 42/77 (54%), Gaps = 3/77 (3%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY 177
           +++G+L   + E  L   F   G V NVK+I +K   +   YGFVE++    AE  LQ+ 
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNN-KGVNYGFVEYHQSHDAEIALQTL 59

Query: 178 SGSLMPNTDQPFRLNWA 194
           +G  + N +   R+NWA
Sbjct: 60  NGRQIENNE--IRVNWA 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|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 = 19/47 (40%), Positives = 29/47 (61%)

Query: 128 DETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVL 174
            E  L + FS  G+++ V+V ++ +TGQS+G+GFV F       KVL
Sbjct: 12  TEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVL 58

This subfamily corresponds to the RRM1 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. . Length = 77

>gnl|CDD|241079 cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 47.8 bits (114), Expect = 2e-07
 Identities = 23/62 (37%), Positives = 35/62 (56%), Gaps = 5/62 (8%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKI---PVG--KGCGFVQFANRKDAEVALQKLQ 384
           +FVG L    +++D+R  F  FG I    I   P G  KGC FV+F++  +A+ A+  L 
Sbjct: 4   LFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPDGNSKGCAFVKFSSHAEAQAAINALH 63

Query: 385 GT 386
           G+
Sbjct: 64  GS 65

This subgroup corresponds to the RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, being highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, being strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in a muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 81

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

 Score = 47.5 bits (113), Expect = 3e-07
 Identities = 27/75 (36%), Positives = 37/75 (49%), Gaps = 6/75 (8%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEI---LSVKIPVGK---GCGFVQFANRKDAEVALQK 382
           T+FV  L   V+ EDL + FS    I   + V  P      G GFV FA  +DA+ AL K
Sbjct: 1   TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAK 60

Query: 383 LQGTAIGKQTVRLSW 397
           L+   +  + +RL  
Sbjct: 61  LKNKKLHGRILRLDI 75

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

 Score = 47.6 bits (114), Expect = 3e-07
 Identities = 21/58 (36%), Positives = 29/58 (50%), Gaps = 5/58 (8%)

Query: 129 ETFLHNCFSHTGQVVNVKVIRNK-----QTGQSEGYGFVEFYSRAAAEKVLQSYSGSL 181
           E  L   F   G V +V + + K         S GYGFVEF S+ AA+K L+   G++
Sbjct: 14  EETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQKALKRLQGTV 71

This subfamily corresponds to the RRM5 of RBM19 and RRM4 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 82

>gnl|CDD|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 = 47.6 bits (114), Expect = 3e-07
 Identities = 18/55 (32%), Positives = 30/55 (54%)

Query: 117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAE 171
            +++  L     E  L   FS  G+V  V ++++ +TG+S G+GFV F S   A+
Sbjct: 3   KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDAD 57

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

 Score = 47.4 bits (112), Expect = 3e-07
 Identities = 24/78 (30%), Positives = 45/78 (57%), Gaps = 2/78 (2%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY 177
           +++GDL   +    + + F+  G++ + +V+++  TG+S+GYGFV FY++  AE  +   
Sbjct: 4   VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63

Query: 178 SGSLMPNTDQPFRLNWAT 195
            G  +    +  R NWAT
Sbjct: 64  GGQWLGG--RQIRTNWAT 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|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor 3B subunit 4 (SF3B4) and similar proteins

 Score = 47.2 bits (113), Expect = 3e-07
 Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           ++VG+L   VT+ +L E F    P V    +  D  T   +GYGFV F  E +   A+  
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGP-VVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKI 59

Query: 271 MNGVYCSSRPMRI 283
           MN +    +P+R+
Sbjct: 60  MNMIKLYGKPIRV 72

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

>gnl|CDD|240775 cd12329, RRM2_hnRNPD_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 47.4 bits (113), Expect = 3e-07
 Identities = 19/60 (31%), Positives = 35/60 (58%), Gaps = 10/60 (16%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKL 383
           IFVG L  + ++E +RE F +FG I+ +++P+       +G  F+ F    D+E  ++K+
Sbjct: 2   IFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITF----DSEEPVKKI 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|240973 cd12529, RRM2_MEI2_like, RNA recognition motif 2 in plant Mei2-like proteins

 Score = 47.1 bits (112), Expect = 3e-07
 Identities = 22/68 (32%), Positives = 39/68 (57%), Gaps = 1/68 (1%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVK-IPVGKGCGFVQFANRKDAEVALQKLQGTA 387
           T+ V  LD  VS++DL + F  +GEI  ++  P  +   F++F + + AE AL+ L  + 
Sbjct: 3   TLVVFNLDPSVSNDDLHQIFGAYGEIKEIRETPNKRHHKFIEFYDVRSAEAALKALNRSE 62

Query: 388 IGKQTVRL 395
           I  + ++L
Sbjct: 63  IAGKRIKL 70

This subgroup corresponds to the RRM2 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and is highly conserved between plants and fungi. To date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 71

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

 Score = 47.6 bits (114), Expect = 3e-07
 Identities = 22/60 (36%), Positives = 34/60 (56%), Gaps = 3/60 (5%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQ-FA--NRKDAEVALQKLQGT 386
           +FVG L   V++ DL E FS+FG +  V+I   K  G  + FA  + + +E  L+K + T
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKST 61

This model corresponds to the RRM of NOL8 (also termed Nop132) encoded by a novel NOL8 gene that is up-regulated in the majority of diffuse-type, but not intestinal-type, gastric cancers. Thus, NOL8 may be a good molecular target for treatment of diffuse-type gastric cancer. Also, NOL8 is a phosphorylated protein that contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), suggesting NOL8 is likely to function as a novel RNA-binding protein. It may be involved in regulation of gene expression at the post-transcriptional level or in ribosome biogenesis in cancer cells. Length = 78

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

 Score = 47.3 bits (113), Expect = 3e-07
 Identities = 22/53 (41%), Positives = 29/53 (54%), Gaps = 1/53 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENE 263
           +FVG+L   V    L+E FS ++  VK   V  D  TG +KGYGFV F   + 
Sbjct: 2   LFVGNLPWTVGSKELKEYFS-QFGKVKSCNVPFDKETGLSKGYGFVSFSSRDG 53

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

 Score = 47.4 bits (113), Expect = 3e-07
 Identities = 20/52 (38%), Positives = 34/52 (65%), Gaps = 1/52 (1%)

Query: 128 DETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSG 179
           DE F  + F   G V N K++R+K+TG S G+GFV++ S   A++ +++ +G
Sbjct: 14  DEEF-RSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLNG 64

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

 Score = 47.4 bits (113), Expect = 3e-07
 Identities = 27/83 (32%), Positives = 45/83 (54%), Gaps = 11/83 (13%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +F+G L+ + TD  L+  FS ++  +    V+ D NT R++G+GFV F   +E   AM  
Sbjct: 2   LFIGGLSYETTDDSLKNYFS-QWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAM-- 58

Query: 271 MNGVYCSSRPMRID--VATPKKA 291
                 ++RP ++D     PK+A
Sbjct: 59  ------NARPHKVDGREVEPKRA 75

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

 Score = 47.2 bits (113), Expect = 4e-07
 Identities = 23/59 (38%), Positives = 34/59 (57%), Gaps = 5/59 (8%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEF-----YSRAAAE 171
           I++GDL + + +  L   FS        KV+R+K+TG+S+GYGFV F     Y +A  E
Sbjct: 9   IFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKE 67

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

 Score = 47.2 bits (112), Expect = 4e-07
 Identities = 26/73 (35%), Positives = 41/73 (56%), Gaps = 5/73 (6%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKG-----CGFVQFANRKDAEVALQKLQ 384
           ++VG LD  V+++ L++ F   G + +VKI   K       GFV++    DAE+ALQ L 
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVNYGFVEYHQSHDAEIALQTLN 60

Query: 385 GTAIGKQTVRLSW 397
           G  I    +R++W
Sbjct: 61  GRQIENNEIRVNW 73

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

 Score = 47.3 bits (112), Expect = 4e-07
 Identities = 24/69 (34%), Positives = 38/69 (55%), Gaps = 1/69 (1%)

Query: 221 TDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRP 280
           T+  L+E FS +Y  + G  V+ D  TGR++G+ FV F   ++   AM   NG+    R 
Sbjct: 12  TERDLREVFS-RYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGMELDGRR 70

Query: 281 MRIDVATPK 289
           +R+D +  K
Sbjct: 71  IRVDYSITK 79

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|240703 cd12257, RRM1_RBM26_like, RNA recognition motif 1 in vertebrate RNA-binding protein 26 (RBM26) and similar proteins

 Score = 46.8 bits (112), Expect = 4e-07
 Identities = 15/56 (26%), Positives = 32/56 (57%), Gaps = 1/56 (1%)

Query: 327 NATIFVGALDSDVSDED-LREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQ 381
           N T+ V  +  ++++   L E FS+FG I+++++        VQF+  ++A+ A +
Sbjct: 1   NTTLEVRNIPPELNNITKLNEHFSKFGTIVNIQVNYNPESALVQFSTSEEAKKAYR 56

This subfamily corresponds to the RRM1 of RBM26, and the RRM of RBM27. RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, represents a cutaneous lymphoma (CL)-associated antigen. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions. RBM27 contains only one RRM; its biological function remains unclear. . Length = 72

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

 Score = 48.0 bits (114), Expect = 4e-07
 Identities = 25/56 (44%), Positives = 34/56 (60%), Gaps = 1/56 (1%)

Query: 208 DLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENE 263
           D ++FV +L  D T+  L   FS K+ SV+ A  +ID +TGR KG GFV F D+  
Sbjct: 1   DFTLFVRNLPYDATEESLAPHFS-KFGSVRYALPVIDKSTGRAKGTGFVCFKDQYT 55

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

 Score = 46.9 bits (112), Expect = 5e-07
 Identities = 25/75 (33%), Positives = 40/75 (53%), Gaps = 7/75 (9%)

Query: 329 TIFVGALDSDVSDEDLREPFSQ-FGEILSVKI---PV---GKGCGFVQFANRKDAEVALQ 381
           +IFVG L  DV+D  L+E F   +  +   K+   PV    KG GFV+F +  + + AL 
Sbjct: 3   SIFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALT 62

Query: 382 KLQGTAIGKQTVRLS 396
           ++ G     + +R+S
Sbjct: 63  EMNGVYCSSRPMRVS 77

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

 Score = 46.8 bits (112), Expect = 5e-07
 Identities = 19/53 (35%), Positives = 31/53 (58%)

Query: 127 MDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSG 179
            DE  L   F   G +  V + ++K+TGQS G+ FV F++R  AE+ ++  +G
Sbjct: 11  ADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNG 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|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 47.0 bits (111), Expect = 5e-07
 Identities = 24/78 (30%), Positives = 45/78 (57%), Gaps = 2/78 (2%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY 177
           +++GDL   +    +   F+  G++ + +V+++  TG+S+GYGFV F+++  AE  +Q  
Sbjct: 4   VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63

Query: 178 SGSLMPNTDQPFRLNWAT 195
            G  +    +  R NWAT
Sbjct: 64  GGQWLGG--RQIRTNWAT 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|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins family

 Score = 46.9 bits (112), Expect = 5e-07
 Identities = 24/74 (32%), Positives = 37/74 (50%), Gaps = 6/74 (8%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKI------PVGKGCGFVQFANRKDAEVALQK 382
            IFV  L  D  +  L + FS FG + +VK+         KG GFV   N ++A  A+  
Sbjct: 3   CIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIAS 62

Query: 383 LQGTAIGKQTVRLS 396
           L G  +G + +++S
Sbjct: 63  LNGYRLGGRVLQVS 76

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

 Score = 46.6 bits (111), Expect = 5e-07
 Identities = 23/72 (31%), Positives = 40/72 (55%), Gaps = 6/72 (8%)

Query: 332 VGALDSDVSDEDLREPFSQFGEILSVKIPVGK------GCGFVQFANRKDAEVALQKLQG 385
           V  L  +++ +++R  FS  GEI S K+   K      G GFV + + +DAE A+  L G
Sbjct: 6   VNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTLNG 65

Query: 386 TAIGKQTVRLSW 397
             +  +T+++S+
Sbjct: 66  LRLQNKTIKVSY 77

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

 Score = 46.9 bits (112), Expect = 5e-07
 Identities = 23/59 (38%), Positives = 33/59 (55%), Gaps = 5/59 (8%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-----KGCGFVQFANRKDAEVALQK 382
           T+FVG L      +DL E F + GE++ V+I        KG G V+FA  + A+ AL+K
Sbjct: 1   TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALEK 59

This subfamily corresponds to the RRM1 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 77

>gnl|CDD|240999 cd12555, RRM2_RBM15, RNA recognition motif 2 in vertebrate RNA binding motif protein 15 (RBM15)

 Score = 47.2 bits (112), Expect = 5e-07
 Identities = 27/83 (32%), Positives = 44/83 (53%), Gaps = 5/83 (6%)

Query: 322 DGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIP-VGKG----CGFVQFANRKDA 376
           D +  N T+F+G LD  V++ DLR  F +FG I  V I   G+G     GF++F N   A
Sbjct: 2   DDQRANRTLFLGNLDITVTETDLRRAFDRFGVITEVDIKRPGRGQTSTYGFLKFENLDMA 61

Query: 377 EVALQKLQGTAIGKQTVRLSWGR 399
             A   + G  + +  +++ +G+
Sbjct: 62  HRAKLAMSGKVLRRNPIKIGYGK 84

This subgroup corresponds to the RRM2 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contain three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties. . Length = 87

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

 Score = 46.5 bits (111), Expect = 6e-07
 Identities = 20/68 (29%), Positives = 42/68 (61%), Gaps = 1/68 (1%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVV-NVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQS 176
           ++IG+L   +DE  L++ FS  G ++   K++R+  TG S+G+ F+ + S  A++  +++
Sbjct: 4   LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63

Query: 177 YSGSLMPN 184
            +G  + N
Sbjct: 64  MNGQYLCN 71

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

 Score = 46.6 bits (110), Expect = 6e-07
 Identities = 25/75 (33%), Positives = 43/75 (57%), Gaps = 6/75 (8%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKI------PVGKGCGFVQFANRKDAEVALQKL 383
           +FVG L  +++ +D++  F+ FG I   ++         KG GFV F N+ DAE A+Q++
Sbjct: 4   VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63

Query: 384 QGTAIGKQTVRLSWG 398
            G  +G + +R +W 
Sbjct: 64  GGQWLGGRQIRTNWA 78

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

 Score = 46.6 bits (111), Expect = 6e-07
 Identities = 20/78 (25%), Positives = 43/78 (55%), Gaps = 2/78 (2%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +FV  L   VT   L++ F  K+  VK  +++ + + G+ KG  +V + +E+  S+A+ +
Sbjct: 5   LFVSGLPFSVTKEELEKLFK-KHGVVKSVRLVTNRS-GKPKGLAYVEYENESSASQAVLK 62

Query: 271 MNGVYCSSRPMRIDVATP 288
           M+G     + + + ++ P
Sbjct: 63  MDGTEIKEKTISVAISNP 80

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|240762 cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 46.5 bits (111), Expect = 6e-07
 Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 1/63 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +FV +L    T+  L+E F   +  +    + +D  T R+KG+ FV F       +A +E
Sbjct: 2   LFVRNLPFTTTEEELRELFE-AFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSE 60

Query: 271 MNG 273
           ++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|241037 cd12593, RRM_RBM11, RNA recognition motif in vertebrate RNA-binding protein 11 (RBM11)

 Score = 46.5 bits (110), Expect = 6e-07
 Identities = 24/76 (31%), Positives = 36/76 (47%), Gaps = 2/76 (2%)

Query: 208 DLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRA 267
           D ++FVG+L   V + IL E F    P  K    I     G+ K +GFV F        A
Sbjct: 1   DRTLFVGNLECRVREEILYELFLQAGPLTKVT--ICKDKEGKPKSFGFVCFKHSESVPYA 58

Query: 268 MTEMNGVYCSSRPMRI 283
           +  +NG+    RP+++
Sbjct: 59  IALLNGIRLYGRPIKV 74

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

>gnl|CDD|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 46.4 bits (110), Expect = 6e-07
 Identities = 23/57 (40%), Positives = 35/57 (61%), Gaps = 1/57 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRA 267
           +FVG L  DV +  L E FS ++  V+ A+VI D  TG+ +G+GFV F + +   +A
Sbjct: 2   LFVGGLKGDVGEGDLTEHFS-QFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKA 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|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 50.7 bits (121), Expect = 7e-07
 Identities = 26/79 (32%), Positives = 46/79 (58%), Gaps = 1/79 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           IFV +L+PD  +++L + F   + +V+  K+I D  T + KGYGFV   + +E + A+  
Sbjct: 272 IFVYNLSPDTDETVLWQLFG-PFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILS 330

Query: 271 MNGVYCSSRPMRIDVATPK 289
           +NG    +R +++   T K
Sbjct: 331 LNGYTLGNRVLQVSFKTNK 349

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|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 = 46.1 bits (110), Expect = 7e-07
 Identities = 16/48 (33%), Positives = 31/48 (64%)

Query: 132 LHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSG 179
           L+  F+  G V++ KV  +K TGQS+ +GFV + +  +A+  +++ +G
Sbjct: 15  LYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAMNG 62

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

 Score = 46.5 bits (111), Expect = 7e-07
 Identities = 24/75 (32%), Positives = 37/75 (49%), Gaps = 6/75 (8%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEIL------SVKIPVGKGCGFVQFANRKDAEVALQK 382
            + VG L  + +DE  RE  S FG +       S      KG GFV++A++  A  A  +
Sbjct: 1   LLCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQ 60

Query: 383 LQGTAIGKQTVRLSW 397
           L G  IG + +++ W
Sbjct: 61  LDGKQIGGRKLQVDW 75

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

 Score = 46.4 bits (110), Expect = 7e-07
 Identities = 24/76 (31%), Positives = 42/76 (55%), Gaps = 2/76 (2%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           ++VG+L P VT+ IL++ F    P V+  K+I D N  +   YGFV +   ++   A+  
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGP-VQNVKIIPDKNN-KGVNYGFVEYHQSHDAEIALQT 58

Query: 271 MNGVYCSSRPMRIDVA 286
           +NG    +  +R++ A
Sbjct: 59  LNGRQIENNEIRVNWA 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|240966 cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA-binding protein MRN1 and similar proteins

 Score = 46.3 bits (110), Expect = 7e-07
 Identities = 24/62 (38%), Positives = 36/62 (58%), Gaps = 2/62 (3%)

Query: 323 GESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQK 382
           G S N  +++G +D  +++E LR  FSQ+GEI SV     K C FV F N  +A  A+  
Sbjct: 1   GASRN--VYIGNIDDSLTEEKLRNDFSQYGEIESVNYLREKNCAFVNFTNISNAIKAIDG 58

Query: 383 LQ 384
           ++
Sbjct: 59  VK 60

This subgroup corresponds to the RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 79

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

 Score = 46.4 bits (110), Expect = 7e-07
 Identities = 24/60 (40%), Positives = 39/60 (65%), Gaps = 1/60 (1%)

Query: 117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQS 176
           T+++G +   MDET + + F+  G V  VK+I ++ TG S+GYGFV FY     +K+++S
Sbjct: 7   TVFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDR-TGVSKGYGFVSFYDDVDVQKIVES 65

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

 Score = 46.6 bits (110), Expect = 7e-07
 Identities = 26/76 (34%), Positives = 42/76 (55%), Gaps = 6/76 (7%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK------GCGFVQFANRKDAEVALQKL 383
           + V  L  +++ ++LR  FS  GE+ S K+   K      G GFV + N KDAE A+  L
Sbjct: 4   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTL 63

Query: 384 QGTAIGKQTVRLSWGR 399
            G  +  +T+++S+ R
Sbjct: 64  NGLRLQSKTIKVSYAR 79

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

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

 Score = 46.4 bits (111), Expect = 8e-07
 Identities = 20/68 (29%), Positives = 39/68 (57%)

Query: 116 KTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQ 175
           +T++I +L     E  L   FS  G+V   +++++K TG S+G  FV+F ++ +A+K L+
Sbjct: 1   RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLE 60

Query: 176 SYSGSLMP 183
           +   +   
Sbjct: 61  AADNAEDS 68

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

 Score = 46.3 bits (110), Expect = 8e-07
 Identities = 13/68 (19%), Positives = 31/68 (45%), Gaps = 2/68 (2%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIP--VGKGCGFVQFANRKDAEVALQKLQGT 386
           T++ G   +     D++  F   G +  V +     +   F+ F N + A++A++ L G 
Sbjct: 1   TVYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTVQPHAFITFENLEAAQLAIETLNGA 60

Query: 387 AIGKQTVR 394
           ++    ++
Sbjct: 61  SVDGNCIK 68

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

>gnl|CDD|240847 cd12401, RRM_eIF4H, RNA recognition motif in eukaryotic translation initiation factor 4H (eIF-4H) and similar proteins

 Score = 46.2 bits (110), Expect = 8e-07
 Identities = 24/75 (32%), Positives = 37/75 (49%), Gaps = 3/75 (4%)

Query: 212 FVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEM 271
           FVG+L  +     L   F  K  SVK  +++ D  T + KG+ +V F D      A+ E 
Sbjct: 5   FVGNLPFNTVQGDLDAIF--KDLSVKSVRLVRDKETDKFKGFCYVEFEDVESLKEAL-EY 61

Query: 272 NGVYCSSRPMRIDVA 286
           +G     R +R+D+A
Sbjct: 62  DGALFDDRSLRVDIA 76

This subfamily corresponds to the RRM of eIF-4H, also termed Williams-Beuren syndrome chromosomal region 1 protein, which, together with elf-4B/eIF-4G, serves as the accessory protein of RNA helicase eIF-4A. eIF-4H contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It stimulates protein synthesis by enhancing the helicase activity of eIF-4A in the initiation step of mRNA translation. . Length = 76

>gnl|CDD|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 = 46.2 bits (110), Expect = 8e-07
 Identities = 30/82 (36%), Positives = 45/82 (54%), Gaps = 15/82 (18%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCG---------FVQFANRKDAEVA 379
           TI VG +D  +S++DL+E FS  GE+  V++     CG         FV+FA+ + A  A
Sbjct: 2   TIHVGGIDGSLSEDDLKEFFSNCGEVTRVRL-----CGDRQHSARFAFVEFADAESALSA 56

Query: 380 LQKLQGTAIGKQTVRLSWGRNP 401
           L  L GT +G   +R+S  + P
Sbjct: 57  L-NLSGTLLGGHPLRVSPSKTP 77

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

 Score = 46.4 bits (110), Expect = 8e-07
 Identities = 19/66 (28%), Positives = 32/66 (48%)

Query: 129 ETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQP 188
           E  L   F   G +V   ++R+K TG   G  FV +  R  A+  + S +G++ P +  P
Sbjct: 14  EDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSLNGTIPPGSTMP 73

Query: 189 FRLNWA 194
             + +A
Sbjct: 74  LSVRYA 79

This subfamily corresponds to the RRM2 of the sex-lethal protein (SXL) which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 79

>gnl|CDD|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 46.3 bits (110), Expect = 9e-07
 Identities = 22/58 (37%), Positives = 35/58 (60%), Gaps = 1/58 (1%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQ 175
           I++G +    +E  L   FS  G V  VK++ ++  G S+GYGFV F ++  A+K+LQ
Sbjct: 5   IFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDR-AGVSKGYGFVTFETQEDAQKILQ 61

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|240758 cd12312, RRM_SRSF10_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins

 Score = 46.2 bits (110), Expect = 9e-07
 Identities = 21/77 (27%), Positives = 39/77 (50%), Gaps = 6/77 (7%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVALQK 382
           +++V  +      +DLR  F ++G I+ V IP+       +G  +VQF + +DAE AL  
Sbjct: 2   SLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYY 61

Query: 383 LQGTAIGKQTVRLSWGR 399
           L  T    + + + + +
Sbjct: 62  LDRTRFLGREIEIQFAQ 78

This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

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

 Score = 46.1 bits (110), Expect = 1e-06
 Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 6/73 (8%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVALQKL 383
           IFVG L ++V+DE L   FS++      K+         KG GFV F++  D   A++++
Sbjct: 9   IFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKEM 68

Query: 384 QGTAIGKQTVRLS 396
            G  +G + ++L 
Sbjct: 69  NGKYVGNRPIKLR 81

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

 Score = 47.3 bits (112), Expect = 1e-06
 Identities = 29/108 (26%), Positives = 50/108 (46%), Gaps = 8/108 (7%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVALQKL 383
           +F+G L     D  LR+ F+ FG+++  K+ V       +G GFV F +   A  A+ ++
Sbjct: 37  LFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEM 96

Query: 384 QGTAIGKQTVRLSWG--RNPGNKQWRGDHSNHWNGAHYGGQGYSGNGY 429
            G  +  + +R++    R    + + G       G  YGG G  G G+
Sbjct: 97  DGKELNGRHIRVNPANDRPSAPRAYGGGGGYSGGGGGYGGGGDGGGGF 144

Length = 144

>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 = 45.7 bits (109), Expect = 1e-06
 Identities = 20/67 (29%), Positives = 38/67 (56%), Gaps = 6/67 (8%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVALQKL 383
           +F+  L ++ +D+DL + F+ FG ++S K+ V       K  GFV + N + A+ A++ +
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 384 QGTAIGK 390
            G  +G 
Sbjct: 61  NGFQVGG 67

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

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

 Score = 45.8 bits (109), Expect = 1e-06
 Identities = 20/58 (34%), Positives = 34/58 (58%), Gaps = 1/58 (1%)

Query: 216 LAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNG 273
           L  D+T   L+  F +    ++  K++ D  TG++ GYGFV + DEN+  +A+  +NG
Sbjct: 8   LPQDMTQEELRSLFEA-IGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNG 64

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

 Score = 45.7 bits (109), Expect = 1e-06
 Identities = 22/66 (33%), Positives = 36/66 (54%), Gaps = 6/66 (9%)

Query: 335 LDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVALQKLQGTAI 388
           L    ++ DLRE FS++G I  V++         +G GFV F + +DA+ A ++L G  I
Sbjct: 7   LSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEI 66

Query: 389 GKQTVR 394
             + +R
Sbjct: 67  DGRRIR 72

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

 Score = 45.8 bits (109), Expect = 1e-06
 Identities = 18/65 (27%), Positives = 37/65 (56%), Gaps = 4/65 (6%)

Query: 219 DVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE---MNGVY 275
             T+  L++ FS  +  +   +V  D  TG++KG+GFVRF D  ++ + +++   ++G +
Sbjct: 10  KTTEQDLKDYFS-TFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLSQRHMIDGRW 68

Query: 276 CSSRP 280
           C  + 
Sbjct: 69  CDVKI 73

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

 Score = 45.8 bits (109), Expect = 1e-06
 Identities = 26/60 (43%), Positives = 36/60 (60%), Gaps = 6/60 (10%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIP------VGKGCGFVQFANRKDAEVALQK 382
            +FVG L   V  ++L+E FSQFG++ S  +P      + KG GFV F++R   E ALQK
Sbjct: 1   KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK 60

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

 Score = 45.7 bits (109), Expect = 1e-06
 Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 5/64 (7%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-----KGCGFVQFANRKDAEVALQKLQ 384
           IFV  L   V+ +DL++ F + G +L   +        KG G V F + +DA+ A++   
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMFN 60

Query: 385 GTAI 388
           G  +
Sbjct: 61  GYDL 64

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|240852 cd12406, RRM4_NCL, RNA recognition motif 4 in vertebrate nucleolin

 Score = 45.7 bits (108), Expect = 1e-06
 Identities = 25/80 (31%), Positives = 40/80 (50%), Gaps = 4/80 (5%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           ++FV  L+ D T+  L+E+F         A+++ D +TG +KG+GFV F  E +   A  
Sbjct: 2   TLFVKGLSEDTTEETLKESFDGSI----AARIVTDRDTGSSKGFGFVDFSSEEDAKAAKE 57

Query: 270 EMNGVYCSSRPMRIDVATPK 289
            M         + +D A PK
Sbjct: 58  AMEDGEIDGNKVTLDFAKPK 77

This subfamily corresponds to the RRM4 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 78

>gnl|CDD|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast nucleolar protein 13 (Nop13p) and similar proteins

 Score = 45.5 bits (108), Expect = 1e-06
 Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 9/75 (12%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVALQKL 383
           +FVG L  + ++++LR  F + G I  V++         KG  FV F   ++ E A   L
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDF---EEIEFATNAL 57

Query: 384 QGTAIGKQTVRLSWG 398
           +G  +  + +R+ +G
Sbjct: 58  KGKHLNGRALRVEYG 72

This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

>gnl|CDD|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end) protein family

 Score = 45.3 bits (108), Expect = 1e-06
 Identities = 17/66 (25%), Positives = 33/66 (50%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIG 389
           ++VG L    S  +L   F +FG I  +    G+   ++++ + + A+ A + L+G  +G
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGAIRRIDYDPGRNYAYIEYESIEAAQAAKEALRGFPLG 60

Query: 390 KQTVRL 395
               RL
Sbjct: 61  GPGRRL 66

This subfamily corresponds to the RRM3 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B) and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and is a novel component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 72

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

 Score = 45.8 bits (109), Expect = 1e-06
 Identities = 19/66 (28%), Positives = 38/66 (57%)

Query: 117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQS 176
           T+++ +L   +    LH  FS  G+VV V ++++K+T +S+G  F+ F  R  A K +++
Sbjct: 3   TVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKA 62

Query: 177 YSGSLM 182
            +   +
Sbjct: 63  LNNKEL 68

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

 Score = 45.9 bits (108), Expect = 1e-06
 Identities = 26/82 (31%), Positives = 43/82 (52%), Gaps = 6/82 (7%)

Query: 324 ESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK------GCGFVQFANRKDAE 377
           E +   + V  L  +++ E+L+  F   GEI S K+   K      G GFV + + KDAE
Sbjct: 1   EDSKTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAE 60

Query: 378 VALQKLQGTAIGKQTVRLSWGR 399
            A+  L G  +  +T+++S+ R
Sbjct: 61  KAINTLNGLRLQTKTIKVSYAR 82

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

>gnl|CDD|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 45.6 bits (109), Expect = 1e-06
 Identities = 24/82 (29%), Positives = 40/82 (48%), Gaps = 12/82 (14%)

Query: 328 ATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKG------CGFVQFANRKDAEVALQ 381
           +T++V          D+R+ F Q+GEILS++ P  +       C +VQF + + A  A+ 
Sbjct: 1   STLWVTNFPPSFDQSDIRDLFEQYGEILSIRFPSLRFNKTRRFC-YVQFTSPESAAAAVA 59

Query: 382 KLQGTAIG--KQTVRLSWGRNP 401
            L G      K  V++S   +P
Sbjct: 60  LLNGKLGEGYKLVVKIS---DP 78

This subfamily corresponds to the RRM2 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

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

 Score = 45.3 bits (108), Expect = 2e-06
 Identities = 19/49 (38%), Positives = 32/49 (65%), Gaps = 1/49 (2%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRF 258
           ++F+ +L  D T+  L+E FS ++  VK A+++ D  TG +KG  FV+F
Sbjct: 2   TVFIRNLPFDATEEELKELFS-QFGEVKYARIVKDKLTGHSKGTAFVKF 49

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

 Score = 45.1 bits (107), Expect = 2e-06
 Identities = 20/58 (34%), Positives = 30/58 (51%), Gaps = 6/58 (10%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK------GCGFVQFANRKDAEVALQ 381
           IFVG L  DV++E+ +E FSQFG+++  ++          G GFV F +    E    
Sbjct: 2   IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFS 59

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

 Score = 45.7 bits (109), Expect = 2e-06
 Identities = 16/49 (32%), Positives = 30/49 (61%)

Query: 116 KTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEF 164
           KT+++  L +   E+ L   F   G +  ++++R+K+TG+  GY F+EF
Sbjct: 2   KTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEF 50

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

 Score = 45.3 bits (108), Expect = 2e-06
 Identities = 19/66 (28%), Positives = 34/66 (51%), Gaps = 6/66 (9%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKI----PVGK--GCGFVQFANRKDAEVALQK 382
           T+FV  L+ D ++  LR  F ++G I  +++      GK  G  F++F + +D + A + 
Sbjct: 3   TLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKY 62

Query: 383 LQGTAI 388
             G  I
Sbjct: 63  ADGKKI 68

This subfamily corresponds to the RRM of U1-70K, also termed snRNP70, a key component of the U1 snRNP complex, which is one of the key factors facilitating the splicing of pre-mRNA via interaction at the 5' splice site, and is involved in regulation of polyadenylation of some viral and cellular genes, enhancing or inhibiting efficient poly(A) site usage. U1-70K plays an essential role in targeting the U1 snRNP to the 5' splice site through protein-protein interactions with regulatory RNA-binding splicing factors, such as the RS protein ASF/SF2. Moreover, U1-70K protein can specifically bind to stem-loop I of the U1 small nuclear RNA (U1 snRNA) contained in the U1 snRNP complex. It also mediates the binding of U1C, another U1-specific protein, to the U1 snRNP complex. U1-70K contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region at the N-terminal half, and two serine/arginine-rich (SR) domains at the C-terminal half. The RRM is responsible for the binding of stem-loop I of U1 snRNA molecule. Additionally, the most prominent immunodominant region that can be recognized by auto-antibodies from autoimmune patients may be located within the RRM. The SR domains are involved in protein-protein interaction with SR proteins that mediate 5' splice site recognition. For instance, the first SR domain is necessary and sufficient for ASF/SF2 Binding. The family also includes Drosophila U1-70K that is an essential splicing factor required for viability in flies, but its SR domain is dispensable. The yeast U1-70k doesn't contain easily recognizable SR domains and shows low sequence similarity in the RRM region with other U1-70k proteins and therefore not included in this family. The RRM domain is dispensable for yeast U1-70K function. Length = 91

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

 Score = 44.9 bits (107), Expect = 2e-06
 Identities = 17/59 (28%), Positives = 32/59 (54%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQS 176
           +++G L   + E  L   FS  G V +V+++ +K+TG+  G+ FV F      +K++  
Sbjct: 2   LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQ 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|241096 cd12652, RRM2_Hu, RNA recognition motif 2 in the Hu proteins family

 Score = 45.4 bits (108), Expect = 2e-06
 Identities = 20/63 (31%), Positives = 35/63 (55%), Gaps = 1/63 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           ++V  L   +T   L+  FS  Y  +  ++++ D+ TG ++G GF+RF    E  RA+  
Sbjct: 3   LYVSGLPKTMTQQELEALFSP-YGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKA 61

Query: 271 MNG 273
           +NG
Sbjct: 62  LNG 64

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

 Score = 45.1 bits (106), Expect = 2e-06
 Identities = 25/79 (31%), Positives = 43/79 (54%), Gaps = 1/79 (1%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           ++ V  L  ++T   L+  FSS    V+ AK+I D   G + GYGFV + +  +  RA+ 
Sbjct: 3   NLIVNYLPQNMTQDELRSLFSS-IGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAIN 61

Query: 270 EMNGVYCSSRPMRIDVATP 288
            +NG+   S+ +++  A P
Sbjct: 62  TLNGLRLQSKTIKVSYARP 80

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

 Score = 45.7 bits (109), Expect = 2e-06
 Identities = 20/74 (27%), Positives = 42/74 (56%), Gaps = 6/74 (8%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKL 383
           IFV  +  +  +ED+ + F++FGEI ++ + +       KG   +++  +K+A+ A++ L
Sbjct: 9   IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 384 QGTAIGKQTVRLSW 397
            G  +  QT+ + W
Sbjct: 69  NGKELLGQTISVDW 82

This subfamily corresponds to the RRM of RBM8, also termed binder of OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is one of the components of the exon-exon junction complex (EJC). It has two isoforms, RBM8A and RBM8B, both of which are identical except that RBM8B is 16 amino acids shorter at its N-terminus. RBM8, together with other EJC components (such as Magoh, Aly/REF, RNPS1, Srm160, and Upf3), plays critical roles in postsplicing processing, including nuclear export and cytoplasmic localization of the mRNA, and the nonsense-mediated mRNA decay (NMD) surveillance process. RBM8 binds to mRNA 20-24 nucleotides upstream of a spliced exon-exon junction. It is also involved in spliced mRNA nuclear export, and the process of nonsense-mediated decay of mRNAs with premature stop codons. RBM8 forms a specific heterodimer complex with the EJC protein Magoh which then associates with Aly/REF, RNPS1, DEK, and SRm160 on the spliced mRNA, and inhibits ATP turnover by eIF4AIII, thereby trapping the EJC core onto RNA. RBM8 contains an N-terminal putative bipartite nuclear localization signal, one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), in the central region, and a C-terminal serine-arginine rich region (SR domain) and glycine-arginine rich region (RG domain). . Length = 88

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

 Score = 45.4 bits (108), Expect = 2e-06
 Identities = 20/61 (32%), Positives = 33/61 (54%)

Query: 115 TKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVL 174
           TK I++G L   + ET L   FS  G V  V V+ + +  +  G+GF+ F S  + ++V+
Sbjct: 2   TKKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVV 61

Query: 175 Q 175
            
Sbjct: 62  N 62

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|240846 cd12400, RRM_Nop6, RNA recognition motif in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and similar proteins

 Score = 44.6 bits (106), Expect = 2e-06
 Identities = 23/70 (32%), Positives = 31/70 (44%), Gaps = 10/70 (14%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVALQK 382
            +FVG L  D + EDL   F   G   SV++         KGC FV+F   +    AL+ 
Sbjct: 2   ILFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKL 61

Query: 383 ----LQGTAI 388
               L+G  I
Sbjct: 62  HHTLLKGRKI 71

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|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 = 21/77 (27%), Positives = 42/77 (54%), Gaps = 7/77 (9%)

Query: 328 ATIFVGALDSDVSDEDLREPFSQFGEIL-SVKI------PVGKGCGFVQFANRKDAEVAL 380
           A +F+G LD +V ++ L + FS FG IL + KI         KG  F+ + + + ++ A+
Sbjct: 2   ANLFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAI 61

Query: 381 QKLQGTAIGKQTVRLSW 397
           + + G  +  + + +S+
Sbjct: 62  EAMNGQYLCNRPITVSY 78

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

 Score = 44.6 bits (106), Expect = 3e-06
 Identities = 18/62 (29%), Positives = 35/62 (56%)

Query: 127 MDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTD 186
           M +  L   FS  G+++  +++ +  TG S G GF+ F  R  AE+ +++ +G++ P   
Sbjct: 12  MTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKALNGTIPPGAT 71

Query: 187 QP 188
           +P
Sbjct: 72  EP 73

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

 Score = 44.2 bits (105), Expect = 3e-06
 Identities = 17/58 (29%), Positives = 38/58 (65%), Gaps = 1/58 (1%)

Query: 117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVL 174
           T+++ +L + + E  L   FS  G++ +V++++N + G+S+GY +VEF +  + ++ L
Sbjct: 1   TVFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYK-GKSKGYAYVEFENEESVQEAL 57

This subfamily corresponds to the RRM1 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 72

>gnl|CDD|240777 cd12331, RRM_NRD1_SEB1_like, RNA recognition motif in Saccharomyces cerevisiae protein Nrd1, Schizosaccharomyces pombe Rpb7-binding protein seb1 and similar proteins

 Score = 44.9 bits (106), Expect = 3e-06
 Identities = 24/70 (34%), Positives = 38/70 (54%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAI 388
           T+F G +  ++ + DLR  F +FGE+ S  +   K   FV+  NR+DAE A + ++    
Sbjct: 5   TLFPGGVTFNMIEYDLRSGFGRFGEVQSCILNNDKRHAFVKMYNRRDAENAREAMEQYKS 64

Query: 389 GKQTVRLSWG 398
           G   +R  WG
Sbjct: 65  GDMQLRTRWG 74

This subfamily corresponds to the RRM of Nrd1 and Seb1. Nrd1 is a novel heterogeneous nuclear ribonucleoprotein (hnRNP)-like RNA-binding protein encoded by gene NRD1 (for nuclear pre-mRNA down-regulation) from yeast S. cerevisiae. It is implicated in 3' end formation of small nucleolar and small nuclear RNAs transcribed by polymerase II, and plays a critical role in pre-mRNA metabolism. Nrd1 contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a short arginine-, serine-, and glutamate-rich segment similar to the regions rich in RE and RS dipeptides (RE/RS domains) in many metazoan splicing factors, and a proline- and glutamine-rich C-terminal domain (P+Q domain) similar to domains found in several yeast hnRNPs. Disruption of NRD1 gene is lethal to yeast cells. Its N-terminal domain is sufficient for viability, which may facilitate interactions with RNA polymerase II where Nrd1 may function as an auxiliary factor. By contrast, the RRM, RE/RS domains, and P+Q domain are dispensable. Seb1 is an RNA-binding protein encoded by gene seb1 (for seven binding) from fission yeast S. pombe. It is essential for cell viability and bound directly to Rpb7 subunit of RNA polymerase II. Seb1 is involved in processing of polymerase II transcripts. It also contains one RRM motif and a region rich in arginine-serine dipeptides (RS domain). Length = 79

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

 Score = 44.5 bits (106), Expect = 3e-06
 Identities = 19/58 (32%), Positives = 29/58 (50%), Gaps = 1/58 (1%)

Query: 216 LAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNG 273
           L P+ TD  L++     +  +   K I+D  T + KGYGFV F       +A+  +NG
Sbjct: 8   LPPNTTDEDLEK-LCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEGLNG 64

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|240971 cd12527, RRM2_EAR1_like, RNA recognition motif 2 in terminal EAR1-like proteins

 Score = 44.4 bits (105), Expect = 3e-06
 Identities = 21/68 (30%), Positives = 36/68 (52%), Gaps = 1/68 (1%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVK-IPVGKGCGFVQFANRKDAEVALQKLQGTA 387
           T+ +  LD  VS E LR  F  +G++  ++  P  +   FV+F + +DA  AL+ + G  
Sbjct: 3   TLVIFNLDPTVSSETLRSIFQVYGDVKELRETPCKREQRFVEFFDVRDAAKALRAMNGKE 62

Query: 388 IGKQTVRL 395
           I  + V +
Sbjct: 63  ISGKPVVI 70

This subgroup corresponds to the RRM2 of terminal EAR1-like proteins, including terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land plants. They may play a role in the regulation of leaf initiation. The terminal EAR1-like proteins are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and TEL characteristic motifs that allow sequence and putative functional discrimination between the terminal EAR1-like proteins and Mei2-like proteins. . Length = 71

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

 Score = 44.2 bits (105), Expect = 4e-06
 Identities = 26/77 (33%), Positives = 40/77 (51%), Gaps = 8/77 (10%)

Query: 117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQS 176
           T+++G L   + E  L + F   G++V VK+   K      G GFV+F  RAAAE  +Q 
Sbjct: 3   TVFVGGLDPAVTEDELRSLFGPFGEIVYVKIPPGK------GCGFVQFVHRAAAEAAIQQ 56

Query: 177 YSGSLMPNTDQPFRLNW 193
             G+++       RL+W
Sbjct: 57  LQGTIIGG--SRIRLSW 71

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

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

 Score = 43.7 bits (104), Expect = 4e-06
 Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 7/63 (11%)

Query: 132 LHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRL 191
           L+  FS  G V  +K+++ K      G+ FVEF +  AAEK +Q  +G L     +P R+
Sbjct: 1   LYKLFSPFGNVEKIKLLKKKP-----GFAFVEFSTEEAAEKAVQYLNGVLFGG--RPLRV 53

Query: 192 NWA 194
           +++
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|240821 cd12375, RRM1_Hu_like, RNA recognition motif 1 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 44.3 bits (105), Expect = 4e-06
 Identities = 23/72 (31%), Positives = 36/72 (50%), Gaps = 6/72 (8%)

Query: 332 VGALDSDVSDEDLREPFSQFGEILSVKIPVGK------GCGFVQFANRKDAEVALQKLQG 385
           V  L  D++ E+LR  F   G I S KI   +      G GFV + +  DA+ A+  L G
Sbjct: 5   VNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNG 64

Query: 386 TAIGKQTVRLSW 397
             I  + +++S+
Sbjct: 65  FEIRNKRLKVSY 76

This subfamily corresponds to the RRM1 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. This family also includes the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds to its own pre-mRNA and promotes female-specific alternative splicing. It contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 77

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

 Score = 44.3 bits (105), Expect = 4e-06
 Identities = 20/71 (28%), Positives = 40/71 (56%), Gaps = 1/71 (1%)

Query: 216 LAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVY 275
           L  ++T   ++  FSS    ++  K+I D  TG++ GYGFV + D  +  +A+  +NG+ 
Sbjct: 9   LPQNMTQDEIRSLFSS-IGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTLNGLR 67

Query: 276 CSSRPMRIDVA 286
             ++ +++  A
Sbjct: 68  LQNKTIKVSYA 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|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related protein 7 (LARP7) and similar proteins

 Score = 44.3 bits (105), Expect = 4e-06
 Identities = 17/61 (27%), Positives = 33/61 (54%), Gaps = 6/61 (9%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIP----VGKGCG--FVQFANRKDAEVALQK 382
           T++V  L  + + E L+  FS++G ++ V +P     G   G  F++F   ++A+ A + 
Sbjct: 1   TVYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKH 60

Query: 383 L 383
           L
Sbjct: 61  L 61

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|241106 cd12662, RRM3_MYEF2, RNA recognition motif 3 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 44.3 bits (104), Expect = 4e-06
 Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 4/75 (5%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPV----GKGCGFVQFANRKDAEVALQKLQG 385
           IFV  L  D++ + L+E FSQ G ++  +I +     KGCG V+F + + AE A + + G
Sbjct: 2   IFVRNLPFDLTWQKLKEKFSQCGHVMFAEIKMENGKSKGCGTVRFDSPESAEKACRLMNG 61

Query: 386 TAIGKQTVRLSWGRN 400
             I  + + +   RN
Sbjct: 62  IKINGREIDVRLDRN 76

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|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 = 43.8 bits (104), Expect = 5e-06
 Identities = 20/64 (31%), Positives = 31/64 (48%), Gaps = 7/64 (10%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           +++VG+L   +T+  LQ TFS           I +    + KGY FVRF      + A+ 
Sbjct: 2   TVYVGNLPHGLTEEELQRTFSP-------FGAIEEVRVFKDKGYAFVRFDTHEAAATAIV 54

Query: 270 EMNG 273
            +NG
Sbjct: 55  AVNG 58

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

 Score = 43.7 bits (104), Expect = 5e-06
 Identities = 24/73 (32%), Positives = 38/73 (52%), Gaps = 2/73 (2%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           + V +L  DVT+  L+E F      VK  K+  D  +GR++G   V F    +  RA+ +
Sbjct: 3   LRVSNLHYDVTEEDLEELFGRVGE-VKKVKINYDR-SGRSEGTADVVFEKREDAERAIKQ 60

Query: 271 MNGVYCSSRPMRI 283
            NGV    +PM++
Sbjct: 61  FNGVLLDGQPMQV 73

This subfamily corresponds to the RRM of Aly/REF family which includes THO complex subunit 4 (THOC4, also termed Aly/REF), S6K1 Aly/REF-like target (SKAR, also termed PDIP3 or PDIP46) and similar proteins. THOC4 is an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus, and was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid, and might be a novel transcription cofactor for erythroid-specific genes. SKAR shows high sequence homology with THOC4 and possesses one RRM as well. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion. . Length = 75

>gnl|CDD|240775 cd12329, RRM2_hnRNPD_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 43.9 bits (104), Expect = 5e-06
 Identities = 16/52 (30%), Positives = 31/52 (59%), Gaps = 1/52 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDEN 262
           IFVG L+P+ T+  ++E F  K+ ++   ++ +D  T + +G+ F+ F  E 
Sbjct: 2   IFVGGLSPETTEEKIREYF-GKFGNIVEIELPMDKKTNKRRGFCFITFDSEE 52

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

 Score = 43.8 bits (104), Expect = 5e-06
 Identities = 21/44 (47%), Positives = 26/44 (59%)

Query: 132 LHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQ 175
           L   FS  G+V +  V  +K+TG S+GYGFV F SR   E  LQ
Sbjct: 16  LKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQ 59

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|241205 cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 44.3 bits (104), Expect = 5e-06
 Identities = 26/83 (31%), Positives = 44/83 (53%), Gaps = 11/83 (13%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +F+G L+ + TD  L+  F  ++ ++    V+ D NT R++G+GFV +    E   AM  
Sbjct: 5   LFIGGLSFETTDESLRSHFE-QWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMN- 62

Query: 271 MNGVYCSSRPMRID--VATPKKA 291
                  +RP ++D  V  PK+A
Sbjct: 63  -------ARPHKVDGRVVEPKRA 78

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|241217 cd12773, RRM2_HuR, RNA recognition motif 2 in vertebrate Hu-antigen R (HuR)

 Score = 44.2 bits (104), Expect = 5e-06
 Identities = 22/77 (28%), Positives = 44/77 (57%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY 177
           ++I  L   M +  + + FS  G+++N +V+ ++ TG S G  F+ F  R+ AE+ + S+
Sbjct: 3   LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITSF 62

Query: 178 SGSLMPNTDQPFRLNWA 194
           +G   P + +P  + +A
Sbjct: 63  NGHKPPGSSEPITVKFA 79

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

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

 Score = 44.3 bits (104), Expect = 5e-06
 Identities = 25/79 (31%), Positives = 41/79 (51%), Gaps = 1/79 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           IF+ +L  D  + IL + F   + +V   KVI D NT + KG+GFV   +  E + A+  
Sbjct: 4   IFIYNLGQDADEGILWQMFGP-FGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIAS 62

Query: 271 MNGVYCSSRPMRIDVATPK 289
           +NG     + +++   T K
Sbjct: 63  LNGYRLGDKILQVSFKTSK 81

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

 Score = 43.9 bits (104), Expect = 5e-06
 Identities = 19/71 (26%), Positives = 36/71 (50%), Gaps = 6/71 (8%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKI------PVGKGCGFVQFANRKDAEVALQKL 383
           ++V  L S     DL++ FS++G+++  KI      P  +  GFV  A+ ++A   +Q L
Sbjct: 2   LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHL 61

Query: 384 QGTAIGKQTVR 394
             T +  + + 
Sbjct: 62  HRTELHGRVIS 72

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

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

 Score = 43.7 bits (103), Expect = 6e-06
 Identities = 19/76 (25%), Positives = 38/76 (50%), Gaps = 1/76 (1%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           +++V +L   +T+  L++ F   Y ++    ++ D +TG  +G  FVR+    E   A++
Sbjct: 2   NLYVTNLPRQLTEDELRKIFE-AYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAIS 60

Query: 270 EMNGVYCSSRPMRIDV 285
            +NG       M + V
Sbjct: 61  SLNGTIPPGSTMPLSV 76

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|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 = 19/68 (27%), Positives = 34/68 (50%), Gaps = 8/68 (11%)

Query: 127 MDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTD 186
             E  L   F   G +  V ++++K TG+S+G+G+V+F+  + A   L+        N D
Sbjct: 12  YTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVALE--------NCD 63

Query: 187 QPFRLNWA 194
           + F+   A
Sbjct: 64  KSFKAVLA 71

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

 Score = 43.7 bits (103), Expect = 6e-06
 Identities = 16/64 (25%), Positives = 37/64 (57%), Gaps = 5/64 (7%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKI-----PVGKGCGFVQFANRKDAEVALQKLQ 384
           +FVG L+   +++++ E FS +G +  + +        +GC FV++++++ A+ A++ L 
Sbjct: 2   LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQSRGCAFVKYSSKEMAQAAIKALN 61

Query: 385 GTAI 388
           G   
Sbjct: 62  GVYT 65

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|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 = 43.4 bits (103), Expect = 7e-06
 Identities = 20/64 (31%), Positives = 34/64 (53%), Gaps = 6/64 (9%)

Query: 117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQS 176
           T+++G+L H + E  L   FS  G +  V+V ++K      GY FV F +  AA   + +
Sbjct: 2   TVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDK------GYAFVRFDTHEAAATAIVA 55

Query: 177 YSGS 180
            +G+
Sbjct: 56  VNGT 59

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

 Score = 43.4 bits (103), Expect = 7e-06
 Identities = 20/62 (32%), Positives = 38/62 (61%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY 177
           +++G+L   + E  L   F   G++  V++ R+ +TG+S+GYGF++F     A+K L+  
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 178 SG 179
           +G
Sbjct: 61  NG 62

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

>gnl|CDD|241030 cd12586, RRM1_PSP1, RNA recognition motif 1 in vertebrate paraspeckle protein 1 (PSP1)

 Score = 43.4 bits (102), Expect = 7e-06
 Identities = 23/73 (31%), Positives = 38/73 (52%), Gaps = 7/73 (9%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +FVG+L  D+T+   ++ F  KY      +V I+    R +G+GF+R         A  E
Sbjct: 4   LFVGNLPTDITEEDFKKLFE-KYGEPS--EVFIN----RDRGFGFIRLESRTLAEIAKAE 56

Query: 271 MNGVYCSSRPMRI 283
           ++G    +RP+RI
Sbjct: 57  LDGTILKNRPLRI 69

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

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

 Score = 43.3 bits (103), Expect = 7e-06
 Identities = 19/64 (29%), Positives = 34/64 (53%), Gaps = 1/64 (1%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           +I V +L+ D  +  L+E F    P  +   +  D  TG+++G+ FV F    +  RA+ 
Sbjct: 1   TIRVTNLSEDADEDDLRELFRPFGPISR-VYLAKDKETGQSRGFAFVTFHTREDAERAIE 59

Query: 270 EMNG 273
           ++NG
Sbjct: 60  KLNG 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|240817 cd12371, RRM2_PUF60, RNA recognition motif 2 in (U)-binding-splicing factor PUF60 and similar proteins

 Score = 43.4 bits (103), Expect = 7e-06
 Identities = 17/63 (26%), Positives = 33/63 (52%), Gaps = 1/63 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           I+V  + PD+++  ++  F + +  +K   +  D  TG+ KGYGF+ + +      A+  
Sbjct: 3   IYVASVHPDLSEDDIKSVFEA-FGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIAS 61

Query: 271 MNG 273
           MN 
Sbjct: 62  MNL 64

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

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

 Score = 43.5 bits (103), Expect = 7e-06
 Identities = 21/57 (36%), Positives = 32/57 (56%), Gaps = 6/57 (10%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSV---KIPVGK---GCGFVQFANRKDAEVAL 380
           +F+G L  + +D+ L+  FSQ+GEI      K P  K   G GFV FA+  + + A+
Sbjct: 2   LFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAM 58

This subfamily corresponds to the RRM1 in hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 78

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

 Score = 43.4 bits (103), Expect = 7e-06
 Identities = 19/55 (34%), Positives = 29/55 (52%), Gaps = 6/55 (10%)

Query: 340 SDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKLQGTAI 388
           +DEDL +    FG+I+S K  +       KG GFV F + + A  A++ L G  +
Sbjct: 13  TDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEGLNGRGV 67

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

 Score = 44.0 bits (103), Expect = 7e-06
 Identities = 21/69 (30%), Positives = 41/69 (59%), Gaps = 3/69 (4%)

Query: 223 SILQETFSSKYPSV---KGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSR 279
           ++ QE F S + S+   +  K++ D  TG++ GYGFV + D N+  +A+  +NG+   ++
Sbjct: 14  NMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINTLNGLKLQTK 73

Query: 280 PMRIDVATP 288
            +++  A P
Sbjct: 74  TIKVSYARP 82

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|240804 cd12358, RRM1_VICKZ, RNA recognition motif 1 in the VICKZ family proteins

 Score = 43.5 bits (103), Expect = 7e-06
 Identities = 20/80 (25%), Positives = 41/80 (51%), Gaps = 7/80 (8%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +++G+L+ DV +S L++ F      V    V++        GY FV   D++   +A+ +
Sbjct: 1   LYIGNLSSDVNESDLRQLFEEHKIPVSS--VLVKKG-----GYAFVDCPDQSWADKAIEK 53

Query: 271 MNGVYCSSRPMRIDVATPKK 290
           +NG     + + ++ + PKK
Sbjct: 54  LNGKILQGKVIEVEHSVPKK 73

Thid subfamily corresponds to the RRM1 of IGF2BPs (or IMPs) found in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains. Length = 73

>gnl|CDD|241003 cd12559, RRM_SRSF10, RNA recognition motif in serine/arginine-rich splicing factor 10 (SRSF10) and similar proteins

 Score = 43.8 bits (103), Expect = 7e-06
 Identities = 25/71 (35%), Positives = 39/71 (54%), Gaps = 7/71 (9%)

Query: 328 ATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQ 381
           +++FV  +  D   EDLR  F ++G I+ V +P+       +G  +VQF + +DAE AL 
Sbjct: 1   SSLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALH 60

Query: 382 KLQGTAI-GKQ 391
            L    I G+Q
Sbjct: 61  NLDRKWICGRQ 71

This subgroup corresponds to the RRM of SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). SRSF10 is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

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

 Score = 43.5 bits (103), Expect = 8e-06
 Identities = 19/35 (54%), Positives = 23/35 (65%)

Query: 128 DETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFV 162
           DE+ L   FS  G V NVKVIR+  T + +GYGFV
Sbjct: 14  DESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFV 48

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|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 43.4 bits (102), Expect = 8e-06
 Identities = 23/56 (41%), Positives = 29/56 (51%), Gaps = 6/56 (10%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK------GCGFVQFANRKDAEVA 379
           +FVG L  DV + DL E FSQFG +   ++   K      G GFV F N   A+ A
Sbjct: 2   LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKA 57

This subgroup corresponds to the RRM2 of hnRNP A0, a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

>gnl|CDD|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 43.6 bits (102), Expect = 8e-06
 Identities = 25/83 (30%), Positives = 45/83 (54%), Gaps = 11/83 (13%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +F+G L+ + TD  L+E F  K+ ++    V+ D  T R++G+GFV +         + E
Sbjct: 5   LFIGGLSFETTDDSLREHFE-KWGTLTDCVVMRDPQTKRSRGFGFVTYS-------CVEE 56

Query: 271 MNGVYCSSRPMRID--VATPKKA 291
           ++     +RP ++D  V  PK+A
Sbjct: 57  VDAAMS-ARPHKVDGRVVEPKRA 78

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

 Score = 43.3 bits (102), Expect = 8e-06
 Identities = 19/50 (38%), Positives = 30/50 (60%), Gaps = 1/50 (2%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGD 260
           +F+G L  + TD  L+E F  ++  V    V+ DS TGR++G+GF+ F  
Sbjct: 1   MFIGGLNWETTDDSLREYFG-QFGEVTDCTVMRDSATGRSRGFGFLTFKK 49

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

 Score = 43.0 bits (102), Expect = 8e-06
 Identities = 19/57 (33%), Positives = 29/57 (50%), Gaps = 2/57 (3%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGT 386
           +FVG L    + E+LR  F ++G +    +   K  GFV     +DAE A++ L G 
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGTVTECDVV--KNYGFVHMEEEEDAEDAIKALNGY 56

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|240848 cd12402, RRM_eIF4B, RNA recognition motif in eukaryotic translation initiation factor 4B (eIF-4B) and similar proteins

 Score = 43.5 bits (103), Expect = 8e-06
 Identities = 21/81 (25%), Positives = 41/81 (50%), Gaps = 14/81 (17%)

Query: 212 FVGDLAPDVTDSILQETFSSKYPSVKGAKVII------DSNTGRTKGYGFVRFGDENERS 265
           ++G+L  DVT+  ++E F       +G  V          + GR +G+G+  F D +   
Sbjct: 5   YLGNLPYDVTEEDIKEFF-------RGLNVSSVRLPREPGDPGRLRGFGYAEFEDRDSLL 57

Query: 266 RAMTEMNGVYCSSRPMRIDVA 286
           +A++ +N     +R +R+D+A
Sbjct: 58  QALS-LNDESLKNRRIRVDIA 77

This subfamily corresponds to the RRM of eIF-4B, a multi-domain RNA-binding protein that has been primarily implicated in promoting the binding of 40S ribosomal subunits to mRNA during translation initiation. It contains two RNA-binding domains; the N-terminal well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), binds the 18S rRNA of the 40S ribosomal subunit and the C-terminal basic domain (BD), including two arginine-rich motifs (ARMs), binds mRNA during initiation, and is primarily responsible for the stimulation of the helicase activity of eIF-4A. eIF-4B also contains a DRYG domain (a region rich in Asp, Arg, Tyr, and Gly amino acids) in the middle, which is responsible for both, self-association of eIF-4B and binding to the p170 subunit of eIF3. Additional research indicates that eIF-4B can interact with the poly(A) binding protein (PABP) in mammalian cells, which can stimulate both, the eIF-4B-mediated activation of the helicase activity of eIF-4A and binding of poly(A) by PABP. eIF-4B has also been shown to interact specifically with the internal ribosome entry sites (IRES) of several picornaviruses which facilitate cap-independent translation initiation. . Length = 77

>gnl|CDD|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins

 Score = 43.4 bits (103), Expect = 8e-06
 Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 2/64 (3%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           ++FV  L+  V +  L E FS     V+  ++I D N+ R+KG  +V F DE     A+ 
Sbjct: 1   TVFVMQLSLKVRERDLYEFFSKAGK-VRDVRIIRDRNSRRSKGVAYVEFYDEESVPLAL- 58

Query: 270 EMNG 273
            + G
Sbjct: 59  GLTG 62

This subfamily corresponds to the RRM1 of RNA-binding protein 39 (RBM39), RNA-binding protein 23 (RBM23) and similar proteins. RBM39 (also termed HCC1) is a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor. . Length = 73

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

 Score = 43.4 bits (102), Expect = 8e-06
 Identities = 22/79 (27%), Positives = 41/79 (51%), Gaps = 3/79 (3%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           +++V  L   +T   L++ FS +Y  +  ++++ D  TG ++G GF+RF    E   A+ 
Sbjct: 2   NLYVSGLPKTMTQKELEQLFS-QYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIK 60

Query: 270 EMNGVYCS--SRPMRIDVA 286
            +NG      S P+ +  A
Sbjct: 61  GLNGQKPEGASEPITVKFA 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|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 = 43.7 bits (104), Expect = 8e-06
 Identities = 24/72 (33%), Positives = 37/72 (51%), Gaps = 11/72 (15%)

Query: 336 DSDVSD--EDLREPFSQFGEILSVKIP---------VGKGCGFVQFANRKDAEVALQKLQ 384
           D +  +  ED++E   ++G++LSV IP          G G  FV+FA+ +DA+ A   L 
Sbjct: 18  DEEYEEILEDVKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVEDAQKAQLALA 77

Query: 385 GTAIGKQTVRLS 396
           G     +TV  S
Sbjct: 78  GRKFDGRTVVAS 89

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

 Score = 43.6 bits (102), Expect = 9e-06
 Identities = 25/80 (31%), Positives = 41/80 (51%), Gaps = 6/80 (7%)

Query: 326 NNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK------GCGFVQFANRKDAEVA 379
           +   + V  L  +++ E+ R  F   GEI S K+   K      G GFV + + KDAE A
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 380 LQKLQGTAIGKQTVRLSWGR 399
           +  L G  +  +T+++S+ R
Sbjct: 61  INTLNGLRLQTKTIKVSYAR 80

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

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

 Score = 43.4 bits (103), Expect = 1e-05
 Identities = 22/79 (27%), Positives = 39/79 (49%), Gaps = 10/79 (12%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYP--SVKGAKVII----DSNTGRTKGYGFVRFGDENER 264
           ++VG+L P VT+ +L + F    P  SVK    I+    +    R +  GFV F +  + 
Sbjct: 4   LYVGNLNPKVTEEVLCQEFGRFGPLASVK----IMWPRTEEERRRNRNCGFVAFMNRADA 59

Query: 265 SRAMTEMNGVYCSSRPMRI 283
            RA+ E++G       +++
Sbjct: 60  ERALDELDGKDVMGYELKL 78

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

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

 Score = 42.6 bits (101), Expect = 1e-05
 Identities = 23/73 (31%), Positives = 40/73 (54%), Gaps = 7/73 (9%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +FVG+L  D+T+   +E FS KY  V  ++V ++      KG+GF+R        +A  E
Sbjct: 4   LFVGNLPNDITEEEFKELFS-KYGEV--SEVFLNKE----KGFGFIRLDTRTNAEKAKAE 56

Query: 271 MNGVYCSSRPMRI 283
           ++G+    R +R+
Sbjct: 57  LDGIMRKGRQLRV 69

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

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

 Score = 45.0 bits (106), Expect = 1e-05
 Identities = 24/62 (38%), Positives = 36/62 (58%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY 177
           ++IG L    D+  L + F+H G VV+ KVI +++TG+S G+GFV F    AA   +   
Sbjct: 37  LFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEM 96

Query: 178 SG 179
            G
Sbjct: 97  DG 98

Length = 144

>gnl|CDD|241115 cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), cleavage stimulation factor subunit 2 tau variant (CSTF2T) and similar proteins

 Score = 42.9 bits (101), Expect = 1e-05
 Identities = 18/72 (25%), Positives = 41/72 (56%), Gaps = 6/72 (8%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKL 383
           +FVG +  + ++E L++ FS+ G ++S ++         KG GF ++ +++ A  A++ L
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 384 QGTAIGKQTVRL 395
            G  +  + +R+
Sbjct: 61  NGYELNGRQLRV 72

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

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

 Score = 42.5 bits (101), Expect = 1e-05
 Identities = 20/63 (31%), Positives = 31/63 (49%), Gaps = 1/63 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           + VG L  +V    L+E FS  Y +VK   + ID      +GY +V F    +  +A+  
Sbjct: 1   LHVGKLTRNVNKDHLKEIFS-NYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKH 59

Query: 271 MNG 273
           M+G
Sbjct: 60  MDG 62

This subfamily corresponds to the RRM of RNPS1 and its eukaryotic homologs. RNPS1, also termed RNA-binding protein prevalent during the S phase, or SR-related protein LDC2, was originally characterized as a general pre-mRNA splicing activator, which activates both constitutive and alternative splicing of pre-mRNA in vitro.It has been identified as a protein component of the splicing-dependent mRNP complex, or exon-exon junction complex (EJC), and is directly involved in mRNA surveillance. Furthermore, RNPS1 is a splicing regulator whose activator function is controlled in part by CK2 (casein kinase II) protein kinase phosphorylation. It can also function as a squamous-cell carcinoma antigen recognized by T cells-3 (SART3)-binding protein, and is involved in the regulation of mRNA splicing. RNPS1 contains an N-terminal serine-rich (S) domain, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and the C-terminal arginine/serine/proline-rich (RS/P) domain. . Length = 73

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

 Score = 43.2 bits (102), Expect = 1e-05
 Identities = 20/80 (25%), Positives = 40/80 (50%), Gaps = 6/80 (7%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK------GCGFVQFANRKDAEVALQK 382
            + +  L   ++DE+ R  F   G + + KI   K      G GFV + + +DA+ A++ 
Sbjct: 2   NLIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRT 61

Query: 383 LQGTAIGKQTVRLSWGRNPG 402
           L G  +  + +++++ R  G
Sbjct: 62  LNGLQLQNKRIKVAYARPGG 81

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

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

 Score = 43.3 bits (102), Expect = 1e-05
 Identities = 24/75 (32%), Positives = 40/75 (53%), Gaps = 9/75 (12%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKI-----PVGKGCGFVQFANRKDAEVALQKL 383
           T+FVG +D  + + ++R  F+++G +  VKI      V KG GFV F +    +V +QK+
Sbjct: 7   TVFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDRTGVSKGYGFVSFYD----DVDVQKI 62

Query: 384 QGTAIGKQTVRLSWG 398
             + I     +L  G
Sbjct: 63  VESQINFHGKKLKLG 77

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

 Score = 43.2 bits (101), Expect = 1e-05
 Identities = 22/67 (32%), Positives = 36/67 (53%)

Query: 113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEK 172
           D    + +  L   M +  L + F   G++ + K++R+K TGQS GYGFV +     AEK
Sbjct: 2   DSKTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEK 61

Query: 173 VLQSYSG 179
            + + +G
Sbjct: 62  AINTLNG 68

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

 Score = 42.7 bits (101), Expect = 1e-05
 Identities = 21/60 (35%), Positives = 36/60 (60%), Gaps = 1/60 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           IFVG L P+VT++ L++ FS ++ +V    V+ D    R +G+GF+ F  E+   + + E
Sbjct: 5   IFVGGLPPNVTETDLRKYFS-QFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVVNE 63

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

 Score = 43.0 bits (102), Expect = 1e-05
 Identities = 15/37 (40%), Positives = 26/37 (70%)

Query: 140 GQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQS 176
           G++++ K I +K+T + +GYGFV+F S  AA K ++ 
Sbjct: 25  GKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEG 61

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

 Score = 42.7 bits (101), Expect = 1e-05
 Identities = 17/60 (28%), Positives = 27/60 (45%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY 177
           +W+  L        L   FS  G+VV  K++ N ++  +  +GFV   S   A K +Q  
Sbjct: 2   LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHL 61

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

>gnl|CDD|240806 cd12360, RRM_cwf2, RNA recognition motif in yeast pre-mRNA-splicing factor Cwc2 and similar proteins

 Score = 43.0 bits (102), Expect = 1e-05
 Identities = 18/71 (25%), Positives = 36/71 (50%), Gaps = 4/71 (5%)

Query: 327 NATIFVGALDSDVSDED----LREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQK 382
           N T++VG + +  + +     LR  F ++G+I  +++   KG  FV++  R  AE A + 
Sbjct: 1   NRTLYVGGIKAGSALKQIEEILRRHFGEWGDIEDIRVLPSKGIAFVRYKYRASAEFAKEA 60

Query: 383 LQGTAIGKQTV 393
           +   ++    V
Sbjct: 61  MADQSLDGGEV 71

This subfamily corresponds to the RRM of yeast protein Cwc2, also termed Complexed with CEF1 protein 2, or PRP19-associated complex protein 40 (Ntc40), or synthetic lethal with CLF1 protein 3, one of the components of the Prp19-associated complex [nineteen complex (NTC)] that can bind to RNA. NTC is composed of the scaffold protein Prp19 and a number of associated splicing factors, and plays a crucial role in intron removal during premature mRNA splicing in eukaryotes. Cwc2 functions as an RNA-binding protein that can bind both small nuclear RNAs (snRNAs) and pre-mRNA in vitro. It interacts directly with the U6 snRNA to link the NTC to the spliceosome during pre-mRNA splicing. In the N-terminal half, Cwc2 contains a CCCH-type zinc finger (ZnF domain), a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and an intervening loop, also termed RNA-binding loop or RB loop, between ZnF and RRM, all of which are necessary and sufficient for RNA binding. The ZnF is also responsible for mediating protein-protein interaction. The C-terminal flexible region of Cwc2 interacts with the WD40 domain of Prp19. Length = 78

>gnl|CDD|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 42.9 bits (101), Expect = 1e-05
 Identities = 22/70 (31%), Positives = 40/70 (57%), Gaps = 6/70 (8%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIP-----VGKGCGFVQFANRKDAEVALQKLQ 384
           I V  L  + + +D+R  FS +G++ SV++P       +G  FV+F+  K+A  A+  L+
Sbjct: 3   ILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAMNALK 62

Query: 385 GTAI-GKQTV 393
            T + G++ V
Sbjct: 63  DTHLLGRRLV 72

This subgroup corresponds to the RRM5 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

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

 Score = 42.7 bits (101), Expect = 1e-05
 Identities = 18/71 (25%), Positives = 33/71 (46%), Gaps = 5/71 (7%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKI---PVGK--GCGFVQFANRKDAEVALQKLQ 384
           + V  L   + ++ LR+ F  FG I  V++     GK    GFV +   ++A+ AL+   
Sbjct: 3   LIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKHFN 62

Query: 385 GTAIGKQTVRL 395
            + I    + +
Sbjct: 63  NSFIDTSKITV 73

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

>gnl|CDD|241005 cd12561, RRM1_RBM5_like, RNA recognition motif 1 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 43.1 bits (102), Expect = 1e-05
 Identities = 17/45 (37%), Positives = 26/45 (57%)

Query: 137 SHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSL 181
           SH  +  +V+++R K TG S G+ FVEF S   A + ++   G L
Sbjct: 25  SHGVEPKDVRLMRRKTTGASRGFAFVEFMSLEEATRWMELNQGKL 69

This subgroup corresponds to the RRM1 of RNA-binding protein 5 (RBM5 or LUCA15 or H37), RNA-binding protein 10 (RBM10 or S1-1) and similar proteins. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. Both, RBM5 and RBM10, contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. . Length = 81

>gnl|CDD|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 42.6 bits (100), Expect = 1e-05
 Identities = 23/50 (46%), Positives = 31/50 (62%), Gaps = 1/50 (2%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGD 260
           +FVG L+ D T   L+E FS K+  V    + ID  TGR++G+GFV F D
Sbjct: 1   MFVGGLSWDTTKKDLKEYFS-KFGEVVDCTIKIDPVTGRSRGFGFVLFKD 49

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

 Score = 42.6 bits (100), Expect = 1e-05
 Identities = 27/69 (39%), Positives = 36/69 (52%), Gaps = 10/69 (14%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKI---PV---GKGCGFVQFANRKDAEVALQ-- 381
           +FVG L  D + +DL+E FS+FGE++   I   PV    +G GFV F +    E  L   
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60

Query: 382 --KLQGTAI 388
             KL G  I
Sbjct: 61  EHKLDGRVI 69

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

 Score = 42.9 bits (101), Expect = 1e-05
 Identities = 20/59 (33%), Positives = 32/59 (54%), Gaps = 5/59 (8%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEI-----LSVKIPVGKGCGFVQFANRKDAEVALQKL 383
           +FVG L    ++ D+R  F+ FG I     L  +    +GC FV FA+R+ A  A++ +
Sbjct: 4   LFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQNGQSRGCAFVTFASRQCALNAIKAM 62

This subgroup corresponds to the RRM2 of Bruno, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 81

>gnl|CDD|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering time control protein FCA and similar proteins

 Score = 42.6 bits (100), Expect = 1e-05
 Identities = 18/61 (29%), Positives = 36/61 (59%), Gaps = 6/61 (9%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK------GCGFVQFANRKDAEVALQKL 383
           +FVG++   ++++++R  F + G +L V I   K      GC FV+++ R +A+ A++ L
Sbjct: 2   LFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRAL 61

Query: 384 Q 384
            
Sbjct: 62  H 62

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

 Score = 42.7 bits (101), Expect = 2e-05
 Identities = 23/67 (34%), Positives = 36/67 (53%), Gaps = 7/67 (10%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGE-ILSVKIPVGK------GCGFVQFANRKDAEVALQ 381
           ++++G L+  + +  ++  F+  GE +LSVKI   K      G  FV+FA+   AE  L 
Sbjct: 1   SLWMGDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLH 60

Query: 382 KLQGTAI 388
           KL G  I
Sbjct: 61  KLNGKPI 67

This subgroup corresponds to the RRM1 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. . Length = 84

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

 Score = 42.4 bits (100), Expect = 2e-05
 Identities = 21/75 (28%), Positives = 45/75 (60%), Gaps = 2/75 (2%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY 177
           +++G+L    DE  ++  F   G++ +V++  +  +G+ +G+G+VEF S+ AA+  L + 
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 178 SGSLMPNTDQPFRLN 192
            G+ +    +P RL+
Sbjct: 61  GGTDLLG--RPVRLD 73

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

 Score = 42.0 bits (99), Expect = 2e-05
 Identities = 17/40 (42%), Positives = 28/40 (70%)

Query: 136 FSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQ 175
           FS  G+VV+ +++++  TG+S G+GFV F S +A E+V  
Sbjct: 20  FSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFS 59

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

 Score = 42.3 bits (100), Expect = 2e-05
 Identities = 16/56 (28%), Positives = 27/56 (48%)

Query: 127 MDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLM 182
                L   F   G+V +V + R++ T +S G+ FV FY +  AE  + +  G  +
Sbjct: 10  TTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDGKEL 65

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

 Score = 42.3 bits (100), Expect = 2e-05
 Identities = 25/80 (31%), Positives = 41/80 (51%), Gaps = 3/80 (3%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           ++FVG+L+       L+E F      V   ++  D + GR+KG+G V F  E    +A  
Sbjct: 1   TLFVGNLSWSAEQDDLEEFFKECGE-VVDVRIAQDDD-GRSKGFGHVEFATEEGAQKA-L 57

Query: 270 EMNGVYCSSRPMRIDVATPK 289
           E +G     R +R+D+AT +
Sbjct: 58  EKSGEELLGREIRVDLATER 77

This subfamily corresponds to the RRM1 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 77

>gnl|CDD|240939 cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 42.3 bits (99), Expect = 2e-05
 Identities = 23/78 (29%), Positives = 38/78 (48%), Gaps = 9/78 (11%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +FV +LA  VT+ IL++ F  ++  ++  K        + K Y F+ F + +   +AM E
Sbjct: 4   LFVRNLANTVTEEILEKAFG-QFGKLERVK--------KLKDYAFIHFDERDGAVKAMEE 54

Query: 271 MNGVYCSSRPMRIDVATP 288
           MNG       + I  A P
Sbjct: 55  MNGKELEGENIEIVFAKP 72

This subgroup corresponds to the RRM3 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP that is a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. . Length = 72

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

 Score = 42.6 bits (101), Expect = 2e-05
 Identities = 19/76 (25%), Positives = 42/76 (55%), Gaps = 6/76 (7%)

Query: 325 SNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIP------VGKGCGFVQFANRKDAEV 378
            ++A I++G L  ++++ D+   FSQ+GEI+ + +         KG  F+ + +++   +
Sbjct: 7   KDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTIL 66

Query: 379 ALQKLQGTAIGKQTVR 394
           A+  L G  +  +T+R
Sbjct: 67  AVDNLNGIKLLGRTIR 82

This subfamily corresponds to the RRM of the ist3 family that includes fungal U2 small nuclear ribonucleoprotein (snRNP) component increased sodium tolerance protein 3 (ist3), X-linked 2 RNA-binding motif proteins (RBMX2) found in Metazoa and plants, and similar proteins. Gene IST3 encoding ist3, also termed U2 snRNP protein SNU17 (Snu17p), is a novel yeast Saccharomyces cerevisiae protein required for the first catalytic step of splicing and for progression of spliceosome assembly. It binds specifically to the U2 snRNP and is an intrinsic component of prespliceosomes and spliceosomes. Yeast ist3 contains an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In the yeast pre-mRNA retention and splicing complex, the atypical RRM of ist3 functions as a scaffold that organizes the other two constituents, Bud13p (bud site selection 13) and Pml1p (pre-mRNA leakage 1). Fission yeast Schizosaccharomyces pombe gene cwf29 encoding ist3, also termed cell cycle control protein cwf29, is an RNA-binding protein complexed with cdc5 protein 29. It also contains one RRM. The biological function of RBMX2 remains unclear. It shows high sequence similarity to yeast ist3 protein and harbors one RRM as well. . Length = 89

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

 Score = 42.6 bits (101), Expect = 2e-05
 Identities = 16/47 (34%), Positives = 33/47 (70%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEF 164
           I+IG L + + E  +   FS  G++V++ ++R+K+TG+S+G+ F+ +
Sbjct: 12  IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAY 58

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|241060 cd12616, RRM1_TIAR, RNA recognition motif 1 in nucleolysin TIAR and similar proteins

 Score = 42.4 bits (99), Expect = 2e-05
 Identities = 24/81 (29%), Positives = 41/81 (50%), Gaps = 4/81 (4%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCG----FVQFANRKDAEVALQKLQ 384
           T++VG L  DV++  + + FSQ G   S K+           FV+F   +DA  AL  + 
Sbjct: 1   TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMN 60

Query: 385 GTAIGKQTVRLSWGRNPGNKQ 405
           G  I  + V+++W   P +++
Sbjct: 61  GRKILGKEVKVNWATTPSSQK 81

This subgroup corresponds to the RRM1 of nucleolysin TIAR, also termed TIA-1-related protein, and a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 81

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

 Score = 42.5 bits (99), Expect = 2e-05
 Identities = 20/77 (25%), Positives = 40/77 (51%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY 177
           +++  L   M +  L   FS  G+++  +++ ++ TG S G GF+ F  R  AE+ ++  
Sbjct: 8   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 67

Query: 178 SGSLMPNTDQPFRLNWA 194
           +G   P   +P  + +A
Sbjct: 68  NGQKPPGATEPITVKFA 84

This subgroup corresponds to the RRM2 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 90

>gnl|CDD|241043 cd12599, RRM1_SF2_plant_like, RNA recognition motif 1 in plant pre-mRNA-splicing factor SF2 and similar proteins

 Score = 42.1 bits (99), Expect = 2e-05
 Identities = 20/70 (28%), Positives = 40/70 (57%), Gaps = 3/70 (4%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSV--KIPV-GKGCGFVQFANRKDAEVALQKLQG 385
           T++VG L  D+ + ++ + F ++G I+ +  K+P    G  F++F + +DAE A++   G
Sbjct: 1   TVYVGNLPGDIREREVEDLFYKYGPIVDIDLKLPPRPPGYAFIEFEDARDAEDAIRGRDG 60

Query: 386 TAIGKQTVRL 395
                Q +R+
Sbjct: 61  YDFDGQRLRV 70

This subgroup corresponds to the RRM1 of SF2, also termed SR1 protein, a plant serine/arginine (SR)-rich phosphoprotein similar to the mammalian splicing factor SF2/ASF. It promotes splice site switching in mammalian nuclear extracts. SF2 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal domain rich in proline, serine and lysine residues (PSK domain), a composition reminiscent of histones. This PSK domain harbors a putative phosphorylation site for the mitotic kinase cyclin/p34cdc2. . Length = 72

>gnl|CDD|240784 cd12338, RRM1_SRSF1_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 42.0 bits (99), Expect = 2e-05
 Identities = 19/70 (27%), Positives = 36/70 (51%), Gaps = 3/70 (4%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKI---PVGKGCGFVQFANRKDAEVALQKLQG 385
            I+VG L  D+ + D+ + F ++G I ++ +     G    FV+F + +DAE A++   G
Sbjct: 1   RIYVGNLPGDIRERDIEDLFYKYGPIKAIDLKNRRRGPPFAFVEFEDPRDAEDAVRGRDG 60

Query: 386 TAIGKQTVRL 395
                  +R+
Sbjct: 61  YDFDGYRLRV 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|241084 cd12640, RRM3_Bruno_like, RNA recognition motif 3 in Drosophila melanogaster Bruno protein and similar proteins

 Score = 42.3 bits (99), Expect = 2e-05
 Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 6/74 (8%)

Query: 328 ATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGC------GFVQFANRKDAEVALQ 381
             +F+  L  + +D DL + F  FG ++S K+ + K        GFV + N   A+ A+Q
Sbjct: 5   CNLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAIQ 64

Query: 382 KLQGTAIGKQTVRL 395
            + G  IG + +++
Sbjct: 65  AMNGFQIGTKRLKV 78

This subgroup corresponds to the RRM3 of Bruno protein, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 79

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

 Score = 42.3 bits (99), Expect = 2e-05
 Identities = 20/65 (30%), Positives = 39/65 (60%), Gaps = 6/65 (9%)

Query: 327 NATIFVGALDSDVSDEDLREPFSQFGEILSVKI------PVGKGCGFVQFANRKDAEVAL 380
           +A ++V  L   +S +++ + FSQ+G I++ +I       + +G GF++F  R +AE A+
Sbjct: 1   DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAI 60

Query: 381 QKLQG 385
           + L G
Sbjct: 61  KGLNG 65

This subgroup corresponds to the RRM2 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

>gnl|CDD|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 41.8 bits (98), Expect = 2e-05
 Identities = 21/64 (32%), Positives = 36/64 (56%), Gaps = 7/64 (10%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQ-----KLQ 384
           +FVG L  + +++++R  F Q+G++L   I   K  GFV   ++  A+ A++     KL 
Sbjct: 3   LFVGNLPPEATEQEIRSLFEQYGKVLECDII--KNYGFVHMDDKTAADEAIRNLHHYKLH 60

Query: 385 GTAI 388
           G AI
Sbjct: 61  GVAI 64

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

 Score = 45.7 bits (108), Expect = 3e-05
 Identities = 26/85 (30%), Positives = 44/85 (51%), Gaps = 7/85 (8%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK------GCGFVQFANRKDAEVALQKL 383
           + V  L   ++ E++R  F+  GEI S K+   K      G GFV +   +DAE A+  L
Sbjct: 6   LIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSL 65

Query: 384 QGTAIGKQTVRLSWGRNPGNKQWRG 408
            G  +  +T+++S+ R P +   +G
Sbjct: 66  NGLRLQNKTIKVSYAR-PSSDSIKG 89

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

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

 Score = 45.3 bits (107), Expect = 3e-05
 Identities = 28/88 (31%), Positives = 42/88 (47%)

Query: 97  GLSNGKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQS 156
           G + G   G+    ++     I++ +L    DET L   F   G V NVK+IR+  T Q 
Sbjct: 251 GQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQC 310

Query: 157 EGYGFVEFYSRAAAEKVLQSYSGSLMPN 184
           +GYGFV   +   A   + S +G  + N
Sbjct: 311 KGYGFVSMTNYDEAAMAILSLNGYTLGN 338

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|240686 cd12240, RRM_NCBP2, RNA recognition motif found in nuclear cap-binding protein subunit 2 (CBP20) and similar proteins

 Score = 41.8 bits (99), Expect = 3e-05
 Identities = 19/76 (25%), Positives = 42/76 (55%), Gaps = 2/76 (2%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY 177
           +++G+L  +  E  ++  FS  G +  + +  ++ T    G+ FVE+Y+R  AE  ++  
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60

Query: 178 SGSLMPNTDQPFRLNW 193
           +G+ +   D+  R++W
Sbjct: 61  NGTKL--DDRIIRVDW 74

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|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 41.8 bits (98), Expect = 3e-05
 Identities = 21/55 (38%), Positives = 32/55 (58%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEK 172
           +++G L   + E  L   FS  G V   +VI +KQTG+  G+GFV F +  +A+K
Sbjct: 2   LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADK 56

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

 Score = 42.0 bits (98), Expect = 3e-05
 Identities = 20/53 (37%), Positives = 32/53 (60%)

Query: 127 MDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSG 179
           M +  L + FS  G+V + K+IR+K  G S GYGFV + +   AE+ + + +G
Sbjct: 13  MTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTLNG 65

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

 Score = 42.0 bits (98), Expect = 3e-05
 Identities = 19/69 (27%), Positives = 39/69 (56%), Gaps = 3/69 (4%)

Query: 223 SILQETFSSKYPSV---KGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSR 279
           ++ QE   S + S+   +  K++ D  TG++ GYGFV + D  +  +A+  +NG+   ++
Sbjct: 15  NMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTK 74

Query: 280 PMRIDVATP 288
            +++  A P
Sbjct: 75  TIKVSYARP 83

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

 Score = 42.0 bits (98), Expect = 3e-05
 Identities = 20/69 (28%), Positives = 40/69 (57%), Gaps = 3/69 (4%)

Query: 223 SILQETFSSKYPSV---KGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSR 279
           ++ QE F S + S+   +  K++ D  TG++ GYGFV + D  +  +A+  +NG+   ++
Sbjct: 13  NMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTK 72

Query: 280 PMRIDVATP 288
            +++  A P
Sbjct: 73  TIKVSYARP 81

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

 Score = 42.1 bits (98), Expect = 3e-05
 Identities = 24/86 (27%), Positives = 46/86 (53%), Gaps = 8/86 (9%)

Query: 327 NATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVAL 380
           +A ++V  L   ++ ++L + FSQ+G I++ +I V       +G GF++F  R +AE A+
Sbjct: 5   DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 64

Query: 381 QKLQGTAI--GKQTVRLSWGRNPGNK 404
           + L G       + + + +  NP  K
Sbjct: 65  KGLNGQKPPGATEPITVKFANNPSQK 90

This subgroup corresponds to the RRM2 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 90

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

 Score = 42.0 bits (99), Expect = 3e-05
 Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 6/74 (8%)

Query: 326 NNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGC------GFVQFANRKDAEVA 379
           ++  +FVG L  D+++++L+E F +FG +L V+I    G       GFV F + +  +  
Sbjct: 2   DSHQLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKI 61

Query: 380 LQKLQGTAIGKQTV 393
           L        G   +
Sbjct: 62  LANKPIYFRGDHRL 75

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|240872 cd12426, RRM4_PTBPH3, RNA recognition motif 4 in plant polypyrimidine tract-binding protein homolog 3 (PTBPH3)

 Score = 41.7 bits (98), Expect = 3e-05
 Identities = 23/71 (32%), Positives = 39/71 (54%), Gaps = 2/71 (2%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKI--PVGKGCGFVQFANRKDAEVALQKLQGT 386
            I V  L SDV++ED+    ++ G I++VK+    GK    V+FA  + A  AL     +
Sbjct: 9   MIHVSNLPSDVTEEDVINHLAEHGVIVNVKVFESNGKKQALVEFATEEQATEALACKHAS 68

Query: 387 AIGKQTVRLSW 397
           ++   T+RL++
Sbjct: 69  SLNGSTIRLAF 79

This subfamily corresponds to the RRM4 of PTBPH3. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. Like PTB, PTBPH3 contains four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 79

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

 Score = 42.0 bits (98), Expect = 3e-05
 Identities = 21/65 (32%), Positives = 39/65 (60%), Gaps = 6/65 (9%)

Query: 327 NATIFVGALDSDVSDEDLREPFSQFGEILSVKI------PVGKGCGFVQFANRKDAEVAL 380
           +A ++V  L   ++ ++L + FSQ+G I++ +I       V +G GF++F  R +AE A+
Sbjct: 2   DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 61

Query: 381 QKLQG 385
           + L G
Sbjct: 62  KGLNG 66

This subgroup corresponds to the RRM2 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells and also regulates the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

>gnl|CDD|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 41.5 bits (97), Expect = 3e-05
 Identities = 25/83 (30%), Positives = 45/83 (54%), Gaps = 11/83 (13%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +FVG L+ D +   L++ F+ K+  V    + +D NTGR++G+GF+ F D +   + + +
Sbjct: 2   MFVGGLSWDTSKKDLKDYFT-KFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQ 60

Query: 271 MNGVYCSSRPMRID--VATPKKA 291
                   +  R+D  +  PKKA
Sbjct: 61  --------KEHRLDGRLIDPKKA 75

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

 Score = 41.4 bits (97), Expect = 3e-05
 Identities = 17/63 (26%), Positives = 32/63 (50%), Gaps = 3/63 (4%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAI- 388
           IFVG + +  + ++LR  F +FG ++       K   FV     ++A  A++ L G  + 
Sbjct: 3   IFVGNVSATCTSDELRGLFEEFGRVVECDKV--KDYAFVHMEREEEALAAIEALNGKEVK 60

Query: 389 GKQ 391
           G++
Sbjct: 61  GRR 63

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

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

 Score = 41.5 bits (98), Expect = 4e-05
 Identities = 24/80 (30%), Positives = 42/80 (52%), Gaps = 3/80 (3%)

Query: 117 TIWIGDLFHWMDETFLHNCF-SHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQ 175
           +I++GDL   + +  L   F +    V   KV+ +  TG+S+GYGFV F      ++ L 
Sbjct: 3   SIFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALT 62

Query: 176 SYSGSLMPNTDQPFRLNWAT 195
             +G  +  + +P R++ AT
Sbjct: 63  EMNG--VYCSSRPMRVSPAT 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|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 41.5 bits (98), Expect = 4e-05
 Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 7/72 (9%)

Query: 327 NATIFVGALDSDVSDEDLREPFSQFGEILSVKI------PVGKGCGFVQFANRKDAEVAL 380
           N+ +F+      V+++DLRE F+ FGEI  + +         KG  +V+FA    A  A+
Sbjct: 3   NSRLFI-VCGKSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAM 61

Query: 381 QKLQGTAIGKQT 392
           +++ G  +G  T
Sbjct: 62  EEMNGKCLGGDT 73

This subfamily corresponds to the RRM1 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 81

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

 Score = 41.6 bits (98), Expect = 4e-05
 Identities = 17/57 (29%), Positives = 32/57 (56%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVL 174
           ++IG L +   +  L N FS  G++ +  V+++  T +S G+GFV F S +  +  +
Sbjct: 2   LFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAM 58

This subfamily corresponds to the RRM1 in hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 78

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

 Score = 41.4 bits (97), Expect = 4e-05
 Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 6/59 (10%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKI------PVGKGCGFVQFANRKDAEVALQK 382
           +F+G L+ + +D+ LRE F QFGE+    +         +G GF+ F   K     ++K
Sbjct: 1   MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKK 59

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|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins

 Score = 41.1 bits (97), Expect = 4e-05
 Identities = 14/40 (35%), Positives = 25/40 (62%)

Query: 136 FSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQ 175
           FS  G+V +V++IR++ + +S+G  +VEFY   +    L 
Sbjct: 20  FSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALG 59

This subfamily corresponds to the RRM1 of RNA-binding protein 39 (RBM39), RNA-binding protein 23 (RBM23) and similar proteins. RBM39 (also termed HCC1) is a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor. . Length = 73

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

 Score = 41.4 bits (98), Expect = 4e-05
 Identities = 20/65 (30%), Positives = 34/65 (52%), Gaps = 7/65 (10%)

Query: 329 TIFVGALDSDVSDEDLREP----FSQFGEILSV---KIPVGKGCGFVQFANRKDAEVALQ 381
           T+++  L+  +  ++L+      FSQFG +L +   K    +G  FV F + + A  AL+
Sbjct: 1   TLYINNLNEKIKKDELKRSLYALFSQFGPVLDIVASKTLKMRGQAFVVFKDVESATNALR 60

Query: 382 KLQGT 386
            LQG 
Sbjct: 61  ALQGF 65

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

>gnl|CDD|240763 cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition motif 4 in RNA-binding protein 19 (RBM19) and RNA recognition motif 3 in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 41.4 bits (98), Expect = 4e-05
 Identities = 17/55 (30%), Positives = 27/55 (49%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKL 383
            I V  L    ++E+LRE F +FG +  + +P  +    V+F    DA  A + L
Sbjct: 2   VILVKNLPFGTTEEELRELFEKFGSLGRLLLPPSRTIALVEFLEPSDARKAFKSL 56

This subfamily corresponds to the RRM4 of RBM19 and the RRM3 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologues exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 72

>gnl|CDD|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 = 41.6 bits (98), Expect = 4e-05
 Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 6/70 (8%)

Query: 323 GESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKI------PVGKGCGFVQFANRKDA 376
            + +   +FVG +  ++ ++DLR  F QFG+I  + +       + KGC F+ +  R+ A
Sbjct: 1   KDDDAIKLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESA 60

Query: 377 EVALQKLQGT 386
             A   L   
Sbjct: 61  LKAQSALHEQ 70

This subfamily corresponds to the RRM1 of CELF-3, CELF-4, CELF-5, CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In additiona to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 87

>gnl|CDD|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 = 41.7 bits (98), Expect = 4e-05
 Identities = 21/55 (38%), Positives = 29/55 (52%), Gaps = 8/55 (14%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKI--------PVGKGCGFVQFANRKDA 376
           +FVG +    S++DLRE F Q+G +  + +        P  KGC FV F  RK A
Sbjct: 4   MFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKAA 58

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|241078 cd12634, RRM2_CELF1_2, RNA recognition motif 2 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 41.6 bits (97), Expect = 4e-05
 Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 5/60 (8%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-----KGCGFVQFANRKDAEVALQKLQ 384
           +F+G +    ++ D+R  FS FG+I   +I  G     +GC FV F  R  A+ A++ + 
Sbjct: 4   LFIGMVSKKCNENDIRVMFSPFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 63

This subgroup corresponds to the RRM2 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. Human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it preferentially binds to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. . Length = 81

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

 Score = 41.4 bits (97), Expect = 4e-05
 Identities = 19/70 (27%), Positives = 39/70 (55%), Gaps = 8/70 (11%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-----KGCGFVQFANRKDAEVALQKL 383
           T+FV  L  +++ ++L+E F    +I   ++P G     KG  +++F    +AE AL++ 
Sbjct: 5   TLFVKNLPYNITVDELKEVFEDAVDI---RLPSGKDGSSKGIAYIEFKTEAEAEKALEEK 61

Query: 384 QGTAIGKQTV 393
           QG  +  +++
Sbjct: 62  QGAEVDGRSI 71

This subfamily corresponds to the RRM2 of ubiquitously expressed protein nucleolin, also termed protein C23, a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines.RRM2, together with RRM1, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop. . Length = 77

>gnl|CDD|240742 cd12296, RRM1_Prp24, RNA recognition motif 1 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 41.1 bits (97), Expect = 4e-05
 Identities = 20/71 (28%), Positives = 32/71 (45%), Gaps = 3/71 (4%)

Query: 328 ATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGF--VQFANRKDAEVALQKLQG 385
            T+ V  L  D ++  +R+ F   GEI  VKI   +G     ++F    +A  AL K   
Sbjct: 1   LTVKVKNLPKDTTENKIRQFFKDCGEIREVKIVESEGGLVAVIEFETEDEALAALTK-DH 59

Query: 386 TAIGKQTVRLS 396
             +G   + +S
Sbjct: 60  KRLGGNEISVS 70

This subfamily corresponds to the RRM1 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 71

>gnl|CDD|241039 cd12595, RRM1_SRSF5, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 5 (SRSF5)

 Score = 41.1 bits (96), Expect = 4e-05
 Identities = 19/70 (27%), Positives = 38/70 (54%), Gaps = 2/70 (2%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIG 389
           +F+G L+    ++D+   F  +G I  + +   +G GFV+F + +DA+ A+ +L G  + 
Sbjct: 2   VFIGRLNPAAREKDVERFFKGYGRIRDIDLK--RGFGFVEFDDPRDADDAVYELDGKELC 59

Query: 390 KQTVRLSWGR 399
            + V +   R
Sbjct: 60  NERVTIEHAR 69

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|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split end) protein family

 Score = 41.2 bits (97), Expect = 5e-05
 Identities = 21/74 (28%), Positives = 36/74 (48%), Gaps = 2/74 (2%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           ++FVG+L   +T+  L+  F  +Y  V+    I     G+   Y FV+F + +   RA  
Sbjct: 4   TLFVGNLEITITEEELRRAFE-RYGVVEDV-DIKRPPRGQGNAYAFVKFLNLDMAHRAKV 61

Query: 270 EMNGVYCSSRPMRI 283
            M+G Y     ++I
Sbjct: 62  AMSGQYIGRNQIKI 75

This subfamily corresponds to the RRM2 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which share a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 79

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

 Score = 41.0 bits (97), Expect = 5e-05
 Identities = 14/40 (35%), Positives = 23/40 (57%)

Query: 136 FSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQ 175
           FS+ G V +V +  +++     GY +VEF S   AEK ++
Sbjct: 19  FSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIK 58

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

 Score = 41.1 bits (97), Expect = 5e-05
 Identities = 21/66 (31%), Positives = 40/66 (60%), Gaps = 2/66 (3%)

Query: 117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQS 176
           T+++G+L    ++  L   F   G+VV+V++ ++   G+S+G+G VEF +   A+K L+ 
Sbjct: 1   TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDD-GRSKGFGHVEFATEEGAQKALE- 58

Query: 177 YSGSLM 182
            SG  +
Sbjct: 59  KSGEEL 64

This subfamily corresponds to the RRM1 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 77

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

 Score = 41.4 bits (98), Expect = 5e-05
 Identities = 15/63 (23%), Positives = 31/63 (49%), Gaps = 1/63 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           IFV  +  +  +  + + F+ ++  +K   + +D  TG  KGY  + +  + E   A+  
Sbjct: 9   IFVTGVHEEAQEEDVHDKFA-EFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEG 67

Query: 271 MNG 273
           +NG
Sbjct: 68  LNG 70

This subfamily corresponds to the RRM of RBM8, also termed binder of OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is one of the components of the exon-exon junction complex (EJC). It has two isoforms, RBM8A and RBM8B, both of which are identical except that RBM8B is 16 amino acids shorter at its N-terminus. RBM8, together with other EJC components (such as Magoh, Aly/REF, RNPS1, Srm160, and Upf3), plays critical roles in postsplicing processing, including nuclear export and cytoplasmic localization of the mRNA, and the nonsense-mediated mRNA decay (NMD) surveillance process. RBM8 binds to mRNA 20-24 nucleotides upstream of a spliced exon-exon junction. It is also involved in spliced mRNA nuclear export, and the process of nonsense-mediated decay of mRNAs with premature stop codons. RBM8 forms a specific heterodimer complex with the EJC protein Magoh which then associates with Aly/REF, RNPS1, DEK, and SRm160 on the spliced mRNA, and inhibits ATP turnover by eIF4AIII, thereby trapping the EJC core onto RNA. RBM8 contains an N-terminal putative bipartite nuclear localization signal, one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), in the central region, and a C-terminal serine-arginine rich region (SR domain) and glycine-arginine rich region (RG domain). . Length = 88

>gnl|CDD|240846 cd12400, RRM_Nop6, RNA recognition motif in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and similar proteins

 Score = 41.2 bits (97), Expect = 5e-05
 Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 5/60 (8%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +FVG+L  D T   L   F +        +++ D  TG++KG  FV F    + + AMT+
Sbjct: 3   LFVGNLPYDTTAEDLLAHFKNAGAPPS-VRLLTDKKTGKSKGCAFVEF----DTAEAMTK 57

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

 Score = 41.3 bits (96), Expect = 5e-05
 Identities = 19/53 (35%), Positives = 31/53 (58%)

Query: 127 MDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSG 179
           M +    + F   G++ + K++R+K TGQS GYGFV +     AEK + + +G
Sbjct: 14  MTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNG 66

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

 Score = 41.2 bits (97), Expect = 5e-05
 Identities = 21/75 (28%), Positives = 35/75 (46%), Gaps = 4/75 (5%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY 177
           +++G+L H + E  L   F   G V+ V++      G+   +GFV F    A +K+L + 
Sbjct: 6   LFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILANK 65

Query: 178 SGSLMPNTDQPFRLN 192
              +    D   RLN
Sbjct: 66  --PIYFRGDH--RLN 76

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|241012 cd12568, RRM3_MRD1, RNA recognition motif 3 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 41.2 bits (97), Expect = 5e-05
 Identities = 19/70 (27%), Positives = 30/70 (42%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAI 388
           TI V       + E+LR+ F   G++  V +P       V+FAN + A +A + L     
Sbjct: 2   TILVKNFPYGTTAEELRDLFEPHGKLTRVLMPPAGTIAIVEFANPQQARLAFKALAYRRF 61

Query: 389 GKQTVRLSWG 398
               + L  G
Sbjct: 62  KDSILYLEKG 71

This subgroup corresponds to the RRM3 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 72

>gnl|CDD|241070 cd12626, RRM1_IGF2BP2, RNA recognition motif 1 in vertebrate insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2)

 Score = 41.1 bits (96), Expect = 5e-05
 Identities = 25/81 (30%), Positives = 45/81 (55%), Gaps = 8/81 (9%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +++G+L+P VT   L++ F  +   + G +V++ S      GY FV + D+N   RA+  
Sbjct: 4   LYIGNLSPAVTAEDLRQLFGDRKLPLTG-QVLLKS------GYAFVDYPDQNWAIRAIET 56

Query: 271 MNG-VYCSSRPMRIDVATPKK 290
           ++G V    + M +D + PKK
Sbjct: 57  LSGKVELHGKVMEVDYSVPKK 77

This subgroup corresponds to the RRM1 of IGF2BP2 (IGF2 mRNA-binding protein 2 or IMP-2), also termed hepatocellular carcinoma autoantigen p62, or VICKZ family member 2, which is a ubiquitously expressed RNA-binding protein involved in the stimulation of insulin action. It is predominantly nuclear. SNPs in IGF2BP2 gene are implicated in susceptibility to type 2 diabetes. IGF2BP2 plays an important role in cellular motility; it regulates the expression of PINCH-2, an important mediator of cell adhesion and motility, and MURF-3, a microtubule-stabilizing protein, through direct binding to their mRNAs. IGF2BP2 may be involved in the regulation of mRNA stability through the interaction with the AU-rich element-binding factor AUF1. IGF2BP2 binds initially to nascent beta-actin transcripts and facilitates the subsequent binding of the shuttling IGF2BP1. IGF2BP2 contains four hnRNP K-homology (KH) domains, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a RGG RNA-binding domain. . Length = 77

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

 Score = 41.5 bits (98), Expect = 5e-05
 Identities = 27/80 (33%), Positives = 42/80 (52%), Gaps = 7/80 (8%)

Query: 329 TIFVGALDSDVSDED-LREPFSQFGEILSVKIPVG-----KGCGFVQFANRKDAEVALQK 382
            +FV  L     D   LR+ FSQ G+    ++ +      +G  FV++A  +DAE A Q 
Sbjct: 4   CLFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAPNGQPRGFAFVEYATAEDAEEAQQA 63

Query: 383 LQGTAIGKQTVRLSWGRNPG 402
           L G ++    +R+S+G NPG
Sbjct: 64  LNGHSLQGSPIRVSFG-NPG 82

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

 Score = 41.4 bits (98), Expect = 5e-05
 Identities = 22/69 (31%), Positives = 36/69 (52%), Gaps = 9/69 (13%)

Query: 210 SIFVGDLAPDVTDS----ILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERS 265
           ++FVG++   V+D     +L++    K  S K  K   D +TG+ K +GF  F D     
Sbjct: 2   TVFVGNIPEGVSDDFIRKLLEK--CGKVLSWKRVK---DPSTGKLKAFGFCEFEDPEGAL 56

Query: 266 RAMTEMNGV 274
           RA+  +NG+
Sbjct: 57  RALRLLNGL 65

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|240815 cd12369, RRM4_RBM45, RNA recognition motif 4 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 40.8 bits (96), Expect = 5e-05
 Identities = 16/49 (32%), Positives = 28/49 (57%)

Query: 340 SDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAI 388
            D  L + F +FG ++ V +  GK  G+ ++A+R+ AE A+  L G  +
Sbjct: 12  PDYILEDVFCRFGGLIDVYLVPGKNYGYAKYADRESAERAITTLHGKEV 60

This subfamily corresponds to the RRM4 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 68

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

 Score = 41.0 bits (97), Expect = 5e-05
 Identities = 25/72 (34%), Positives = 37/72 (51%), Gaps = 7/72 (9%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKI---PVGKG--CGFVQFANRKDAEVALQKLQ 384
           I V  L   V+++ LRE F   GE+  VK+     GK    GFV F + +DA+ A++   
Sbjct: 3   IIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVKYFN 62

Query: 385 GTAIGKQTVRLS 396
            T I   T ++S
Sbjct: 63  KTFID--TSKIS 72

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|220013 pfam08777, RRM_3, RNA binding motif

 Score = 41.6 bits (98), Expect = 5e-05
 Identities = 22/63 (34%), Positives = 32/63 (50%), Gaps = 2/63 (3%)

Query: 335 LDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQ--GTAIGKQT 392
           L+   S ED++E FSQ GE+  V    G   G+V+F   + A+ AL+K       I +  
Sbjct: 9   LNKPTSREDIKEAFSQHGEVKYVDFLEGDKEGYVRFKTPEAAKKALEKATEAKLKIKEAE 68

Query: 393 VRL 395
           V L
Sbjct: 69  VTL 71

This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif. Length = 102

>gnl|CDD|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins

 Score = 41.0 bits (96), Expect = 6e-05
 Identities = 28/75 (37%), Positives = 43/75 (57%), Gaps = 7/75 (9%)

Query: 329 TIFVGALDSDVSDEDLREPF-SQFGEILSVKI------PVGKGCGFVQFANRKDAEVALQ 381
           +IFVG L  +V++ DL   F S+F    S KI       V +G GFV+F++  D + AL 
Sbjct: 3   SIFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALI 62

Query: 382 KLQGTAIGKQTVRLS 396
           ++QG   G + +R+S
Sbjct: 63  EMQGVYCGGRPMRIS 77

This subgroup corresponds to the RRM2 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both, RNA and single-stranded DNA (ssDNA), in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs. . Length = 80

>gnl|CDD|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 = 41.0 bits (96), Expect = 6e-05
 Identities = 20/62 (32%), Positives = 36/62 (58%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY 177
           ++IG L    +E  L   FS  GQ+  V V+++++T +S G+GFV F +   A+  + + 
Sbjct: 3   LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62

Query: 178 SG 179
           +G
Sbjct: 63  NG 64

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

 Score = 41.1 bits (97), Expect = 6e-05
 Identities = 21/77 (27%), Positives = 41/77 (53%), Gaps = 1/77 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           + VG+L  + TD   +E  S  + +V+   ++   +TG +KGYGFV +  +    +A  +
Sbjct: 2   LCVGNLPLEFTDEQFRELVSP-FGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQ 60

Query: 271 MNGVYCSSRPMRIDVAT 287
           ++G     R +++D A 
Sbjct: 61  LDGKQIGGRKLQVDWAD 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|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related protein 7 (LARP7) and similar proteins

 Score = 41.2 bits (97), Expect = 6e-05
 Identities = 20/57 (35%), Positives = 29/57 (50%)

Query: 132 LHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQP 188
           L   FS  G VV V + R K TG  +G+ F+EF +   A+K  +  +      TD+P
Sbjct: 16  LKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHLNNPPETATDKP 72

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|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 = 6e-05
 Identities = 21/62 (33%), Positives = 33/62 (53%), Gaps = 1/62 (1%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
            +FVG L    +DS L+  F+  Y  +    V++D NT R++G+GF+ F   +E   AM 
Sbjct: 4   KLFVGGLNLKTSDSGLRRHFTR-YGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAME 62

Query: 270 EM 271
             
Sbjct: 63  AQ 64

This subfamily corresponds to the RRM1 of hnRNP A0 which is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 79

>gnl|CDD|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 41.0 bits (96), Expect = 6e-05
 Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 5/61 (8%)

Query: 342 EDLREPFSQFGEILSVKIPVGKG---CGF--VQFANRKDAEVALQKLQGTAIGKQTVRLS 396
             L++ F ++G++    IP  +G   CGF  V    RK+AE+AL+   G  I  + V + 
Sbjct: 16  VKLKKIFGRYGKVREATIPRKRGGKLCGFAFVTMKKRKNAEIALENTNGLEIDGRPVAVD 75

Query: 397 W 397
           W
Sbjct: 76  W 76

This subgroup corresponds to the RRM2 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 83

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

 Score = 40.8 bits (96), Expect = 7e-05
 Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 1/73 (1%)

Query: 216 LAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVY 275
           L   +TD   +  F +  P VK  K++ D  TG + G+GFV +    +  RA+  +NG+ 
Sbjct: 8   LPQTLTDEEFRSLFLAVGP-VKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLNGLQ 66

Query: 276 CSSRPMRIDVATP 288
             ++ +++  A P
Sbjct: 67  LQNKRIKVAYARP 79

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

 Score = 41.0 bits (96), Expect = 7e-05
 Identities = 22/52 (42%), Positives = 34/52 (65%), Gaps = 2/52 (3%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDE 261
           ++FVG +   + ++ ++  F+ KY SVK  K+I D  TG +KGYGFV F D+
Sbjct: 7   TVFVGGIDIRMDETEIRSFFA-KYGSVKEVKIITD-RTGVSKGYGFVSFYDD 56

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|241000 cd12556, RRM2_RBM15B, RNA recognition motif 2 in putative RNA binding motif protein 15B (RBM15B) from vertebrate

 Score = 41.1 bits (96), Expect = 7e-05
 Identities = 25/83 (30%), Positives = 43/83 (51%), Gaps = 5/83 (6%)

Query: 322 DGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIP-VGKGCG----FVQFANRKDA 376
           D +     +F+G LD +VS+ +LR  F ++G I  V I    +G G    F++F N   A
Sbjct: 3   DDQRATRNLFIGNLDHNVSEVELRRAFDKYGIIEEVVIKRPARGQGGAYAFLKFQNLDMA 62

Query: 377 EVALQKLQGTAIGKQTVRLSWGR 399
             A   + G  IG+  +++ +G+
Sbjct: 63  HRAKVAMSGRVIGRNPIKIGYGK 85

This subgroup corresponds to the RRM2 of RBM15B, also termed one twenty-two 3 (OTT3), a paralog of RNA binding motif protein 15 (RBM15), also known as One-twenty two protein 1 (OTT1). Like RBM15, RBM15B has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. RBM15B belongs to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 85

>gnl|CDD|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II polyadenylate-binding proteins

 Score = 40.7 bits (96), Expect = 7e-05
 Identities = 11/40 (27%), Positives = 23/40 (57%)

Query: 136 FSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQ 175
           F   G +  + ++ +K TGQ +G+ ++EF  +++ E  L 
Sbjct: 20  FKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALL 59

This subfamily corresponds to the RRM of type II polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 2 (PABP-2 or PABPN1), embryonic polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and similar proteins. PABPs are highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. ePABP-2 is predominantly located in the cytoplasm and PABP-2 is located in the nucleus. In contrast to the type I PABPs containing four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), the type II PABPs contains a single highly-conserved RRM. This subfamily also includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C) gene encoding cytoplasmic mRNA-binding protein Rbp29 that binds preferentially to poly(A). Although not essential for cell viability, Rbp29 plays a role in modulating the expression of cytoplasmic mRNA. Like other type II PABPs, Rbp29 contains one RRM only. . Length = 73

>gnl|CDD|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II polyadenylate-binding proteins

 Score = 40.4 bits (95), Expect = 7e-05
 Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 6/58 (10%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVALQ 381
           IFVG +D   + E+L+E F   G I  + I         KG  +++F ++   E AL 
Sbjct: 2   IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALL 59

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|241020 cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins

 Score = 40.5 bits (95), Expect = 7e-05
 Identities = 20/50 (40%), Positives = 30/50 (60%), Gaps = 1/50 (2%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGD 260
           +F+G L+   T   L+E FS K+  +K   V+ D  T R++G+GFV F D
Sbjct: 1   MFIGGLSWQTTAEGLREYFS-KFGEIKECMVMRDPTTKRSRGFGFVTFSD 49

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

 Score = 40.3 bits (95), Expect = 8e-05
 Identities = 14/47 (29%), Positives = 27/47 (57%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEF 164
           +++G L   +DE  LH  F   G + ++++  + +T +  G+ FVEF
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEF 47

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

 Score = 40.6 bits (95), Expect = 8e-05
 Identities = 25/79 (31%), Positives = 42/79 (53%), Gaps = 2/79 (2%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           IFVG +     ++ L++ FS +Y +VK  K++ D   G +KGYGFV F  + +  + + E
Sbjct: 5   IFVGGIDFKTNENDLRKFFS-QYGTVKEVKIVND-RAGVSKGYGFVTFETQEDAQKILQE 62

Query: 271 MNGVYCSSRPMRIDVATPK 289
            N +    + + I  A  K
Sbjct: 63  ANRLCFRDKKLNIGQAIRK 81

This subgroup corresponds to the RRM of BOULE, the founder member of the human DAZ gene family. Invertebrates contain a single BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. BOULE encodes an RNA-binding protein containing an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a single copy of the DAZ motif. Although its specific biochemical functions remains to be investigated, BOULE protein may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 81

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

 Score = 40.4 bits (95), Expect = 8e-05
 Identities = 20/74 (27%), Positives = 40/74 (54%), Gaps = 6/74 (8%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKI------PVGKGCGFVQFANRKDAEVALQK 382
           T++V  L   +++ DL + FS++G+++ V I         KG  F+ F +R+DA   ++ 
Sbjct: 3   TVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKA 62

Query: 383 LQGTAIGKQTVRLS 396
           L    +  +T++ S
Sbjct: 63  LNNKELFGRTLKCS 76

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

 Score = 40.8 bits (95), Expect = 8e-05
 Identities = 22/74 (29%), Positives = 41/74 (55%), Gaps = 1/74 (1%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           ++F+  L  + TD+ L +TF   + +V  AKV ID  T  +K +GFV + + +    A+ 
Sbjct: 6   NLFIYHLPQEFTDTDLAQTFLP-FGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAIQ 64

Query: 270 EMNGVYCSSRPMRI 283
            MNG    ++ +++
Sbjct: 65  AMNGFQIGTKRLKV 78

This subgroup corresponds to the RRM3 of Bruno protein, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 79

>gnl|CDD|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 = 40.9 bits (96), Expect = 8e-05
 Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 2/55 (3%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTG--QSEGYGFVEFYSRAAA 170
           +++G +     E  L   F   G V  + V+R++     QS+G  FV FY+R AA
Sbjct: 4   MFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKAA 58

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

 Score = 40.7 bits (96), Expect = 8e-05
 Identities = 24/73 (32%), Positives = 39/73 (53%), Gaps = 2/73 (2%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           + V +L   V+D  ++E F+  + ++K A V  D + GR+ G   V F    +  +AM +
Sbjct: 3   LLVSNLDFGVSDDDIKELFAE-FGALKKAAVHYDRS-GRSLGTADVVFERRADALKAMKQ 60

Query: 271 MNGVYCSSRPMRI 283
            NGV    RPM+I
Sbjct: 61  YNGVPLDGRPMKI 73

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

>gnl|CDD|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 40.7 bits (95), Expect = 8e-05
 Identities = 26/85 (30%), Positives = 42/85 (49%), Gaps = 15/85 (17%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +F+G L+ D T   L++ FS K+  V    + +D  TGR++G+GFV F +     + M +
Sbjct: 1   MFIGGLSWDTTKKDLKDYFS-KFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ 59

Query: 271 ----MNGVYCSSRPMRIDVATPKKA 291
               +NG           V  PK+A
Sbjct: 60  KEHKLNG----------KVIDPKRA 74

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|240680 cd12234, RRM1_AtRSp31_like, RNA recognition motif in Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins from plants

 Score = 40.2 bits (94), Expect = 8e-05
 Identities = 18/67 (26%), Positives = 31/67 (46%), Gaps = 2/67 (2%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIG 389
           +F G  + D    ++   F ++G +  V +    G  FV   + +DAE A++ L     G
Sbjct: 3   VFCGNFEYDARQSEIERLFGKYGRVDRVDMK--SGFAFVYMEDERDAEDAIRGLDNFEFG 60

Query: 390 KQTVRLS 396
           +Q  RL 
Sbjct: 61  RQRRRLR 67

This subfamily corresponds to the RRM1in a family that represents a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at their N-terminus, and an RS domain at their C-terminus. Length = 72

>gnl|CDD|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins

 Score = 40.6 bits (95), Expect = 9e-05
 Identities = 24/80 (30%), Positives = 40/80 (50%), Gaps = 3/80 (3%)

Query: 117 TIWIGDLFHWMDETFLHNCF-SHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQ 175
           +I++GDL   ++E+ L + F S      + K++ +  TG S GYGFV F      ++ L 
Sbjct: 3   SIFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALI 62

Query: 176 SYSGSLMPNTDQPFRLNWAT 195
              G       +P R++ AT
Sbjct: 63  EMQGVYC--GGRPMRISTAT 80

This subgroup corresponds to the RRM2 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both, RNA and single-stranded DNA (ssDNA), in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs. . Length = 80

>gnl|CDD|240753 cd12307, RRM_NIFK_like, RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) and similar proteins

 Score = 40.3 bits (95), Expect = 9e-05
 Identities = 15/57 (26%), Positives = 30/57 (52%), Gaps = 6/57 (10%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIP------VGKGCGFVQFANRKDAEVA 379
            +++G L     + +LR+ FSQFG +  +++         KG  FV+F + + A++ 
Sbjct: 1   VVYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIV 57

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

 Score = 40.3 bits (95), Expect = 9e-05
 Identities = 14/45 (31%), Positives = 26/45 (57%), Gaps = 1/45 (2%)

Query: 136 FSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGS 180
           FS  GQV +V++ + K  G   G+ FVEF ++  A+  +++   +
Sbjct: 21  FSPFGQVKSVRLPK-KFDGSHRGFAFVEFVTKQEAQNAMEALKST 64

This subfamily corresponds to the RRM6 of RBM19 and RRM5 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 76

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

 Score = 40.7 bits (96), Expect = 9e-05
 Identities = 22/76 (28%), Positives = 44/76 (57%), Gaps = 5/76 (6%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSR--AM 268
           I++G L  ++T+  +   FS +Y  +    ++ D  TG++KG+ F+ +  E++RS   A+
Sbjct: 12  IYIGGLPYELTEGDILCVFS-QYGEIVDINLVRDKKTGKSKGFAFLAY--EDQRSTILAV 68

Query: 269 TEMNGVYCSSRPMRID 284
             +NG+    R +R+D
Sbjct: 69  DNLNGIKLLGRTIRVD 84

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

 Score = 40.4 bits (94), Expect = 9e-05
 Identities = 23/71 (32%), Positives = 33/71 (46%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY 177
           ++IG L     +  L   F   G+V    V+R+  T +S G+GFV F  +A  +KVL   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62

Query: 178 SGSLMPNTDQP 188
              L   T  P
Sbjct: 63  RHELDSKTIDP 73

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|241047 cd12603, RRM_hnRNPC, RNA recognition motif in vertebrate heterogeneous nuclear ribonucleoprotein C1/C2 (hnRNP C1/C2)

 Score = 40.4 bits (94), Expect = 9e-05
 Identities = 23/71 (32%), Positives = 39/71 (54%), Gaps = 3/71 (4%)

Query: 327 NATIFVGALDSD-VSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQG 385
           N+ +F+G L++  V   D+   FS++G+I  V   V KG  FVQ+ N ++A  A+    G
Sbjct: 1   NSRVFIGNLNTLVVKKSDVEAIFSKYGKI--VGCSVHKGFAFVQYVNERNARAAVAGEDG 58

Query: 386 TAIGKQTVRLS 396
             I  Q + ++
Sbjct: 59  RMIAGQVLDIN 69

This subgroup corresponds to the RRM of heterogeneous nuclear ribonucleoprotein C (hnRNP) proteins C1 and C2, produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex. They are involved in the packaging of hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. hnRNP C proteins contain two distinct domains, an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain that includes the variable region, the basic region and the KSG box rich in repeated Lys-Ser-Gly sequences, the leucine zipper, and the acidic region. The RRM is capable of binding poly(U). The KSG box may bind to RNA. The leucine zipper may be involved in dimer formation. The acidic and hydrophilic C-teminus harbors a putative nucleoside triphosphate (NTP)-binding fold and a protein kinase phosphorylation site. . Length = 71

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

 Score = 40.0 bits (94), Expect = 9e-05
 Identities = 16/56 (28%), Positives = 30/56 (53%), Gaps = 2/56 (3%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQG 385
           +++G L     + D+   F  +G I  + +    G GFV+F + +DA+ A+ +L G
Sbjct: 2   VYIGRLPYRARERDVERFFKGYGRIREINLK--NGFGFVEFEDPRDADDAVYELNG 55

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

 Score = 40.4 bits (95), Expect = 1e-04
 Identities = 24/69 (34%), Positives = 34/69 (49%), Gaps = 9/69 (13%)

Query: 117 TIWIGDLFHWMDETFLHNCFS-HTGQVVNVKVIRNKQTGQSEGYGFVEF-----YSRAAA 170
           ++++GDL   +D+  L+  FS         KV+ + Q G S GYGFV F       RA  
Sbjct: 3   SLFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLD-QNGNSRGYGFVRFSDESEQKRALT 61

Query: 171 EKVLQSYSG 179
           E  +Q  SG
Sbjct: 62  E--MQGASG 68

This subgroup corresponds to the RRM2 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. . Length = 82

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

 Score = 39.8 bits (94), Expect = 1e-04
 Identities = 21/65 (32%), Positives = 36/65 (55%), Gaps = 2/65 (3%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY 177
           +++ +L   + E  L   FS  G+V  V+++RNK   +  G+ FVEF S   AE  L+  
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD--RPRGFAFVEFASPEDAEAALKKL 58

Query: 178 SGSLM 182
           +G ++
Sbjct: 59  NGLVL 63

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

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

 Score = 39.6 bits (93), Expect = 1e-04
 Identities = 25/77 (32%), Positives = 41/77 (53%), Gaps = 5/77 (6%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY 177
           +++G+L   + E  L   FS  G + + K+IR  + G    Y FVE+Y   +A   LQ+ 
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIR--EHGNDP-YAFVEYYDHRSAAAALQTM 57

Query: 178 SGSLMPNTDQPFRLNWA 194
           +G L+    Q  ++NWA
Sbjct: 58  NGRLI--LGQEIKVNWA 72

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

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

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 3/61 (4%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKV---IRNKQTGQSEGYGFVEFYSRAAAEKVL 174
           I++ +L   +DE  L   FS  G+V ++++      KQ   + G+ FV F   ++AE  L
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62

Query: 175 Q 175
           Q
Sbjct: 63  Q 63

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

 Score = 40.0 bits (94), Expect = 1e-04
 Identities = 22/72 (30%), Positives = 33/72 (45%), Gaps = 1/72 (1%)

Query: 213 VGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMN 272
           V +L    T   L+  F  KY  V    +  D  T  ++G+ FVRF D+ +   AM  M+
Sbjct: 3   VDNLTYRTTPDDLRRVFE-KYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMD 61

Query: 273 GVYCSSRPMRID 284
           G     R +R+ 
Sbjct: 62  GKELDGRELRVQ 73

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

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

 Score = 40.3 bits (94), Expect = 1e-04
 Identities = 16/65 (24%), Positives = 35/65 (53%), Gaps = 6/65 (9%)

Query: 328 ATIFVGALDSDVSDEDLREPFSQFGEILSVKI------PVGKGCGFVQFANRKDAEVALQ 381
             ++V  L   +++++LR+ F  +G I+   +       + +G  FV++  R++A+ A+ 
Sbjct: 1   TNLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAIS 60

Query: 382 KLQGT 386
            L GT
Sbjct: 61  SLNGT 65

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|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast nucleolar protein 13 (Nop13p) and similar proteins

 Score = 39.7 bits (93), Expect = 1e-04
 Identities = 18/76 (23%), Positives = 40/76 (52%), Gaps = 4/76 (5%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +FVG+L+ + T+  L+  F  +   ++  +++   ++G+ KG+ FV F  E     A   
Sbjct: 1   LFVGNLSFETTEDELRAHF-GRVGRIRRVRMMTFEDSGKCKGFAFVDF--EEIEF-ATNA 56

Query: 271 MNGVYCSSRPMRIDVA 286
           + G + + R +R++  
Sbjct: 57  LKGKHLNGRALRVEYG 72

This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

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

 Score = 40.0 bits (94), Expect = 1e-04
 Identities = 23/70 (32%), Positives = 35/70 (50%), Gaps = 10/70 (14%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSV--------KIPVGKGCGFVQFANRKDAEVALQ 381
           IFVG L  +V++ DLR+ FSQFG +  V        K P  +G GF+ F +    +  + 
Sbjct: 5   IFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRP--RGFGFITFESEDSVDQVVN 62

Query: 382 KLQGTAIGKQ 391
           +      GK+
Sbjct: 63  EHFHDINGKK 72

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

 Score = 40.0 bits (94), Expect = 1e-04
 Identities = 15/63 (23%), Positives = 34/63 (53%), Gaps = 1/63 (1%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           +++V  L+     + L++ FS KY  V GAK++ ++ +   + +GFV      E ++ + 
Sbjct: 1   NLWVSGLSSTTKAADLKQLFS-KYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQ 59

Query: 270 EMN 272
            ++
Sbjct: 60  HLH 62

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

>gnl|CDD|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 23/70 (32%), Positives = 35/70 (50%), Gaps = 10/70 (14%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVAL-- 380
           T+FV  L   V + DL E FS+ G++  V+I         KG  +V+F + +   +AL  
Sbjct: 1   TVFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALGL 60

Query: 381 --QKLQGTAI 388
             Q+L G  I
Sbjct: 61  TGQRLLGQPI 70

This subfamily corresponds to the RRM1 of RNA-binding protein 39 (RBM39), RNA-binding protein 23 (RBM23) and similar proteins. RBM39 (also termed HCC1) is a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor. . Length = 73

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

 Score = 40.5 bits (94), Expect = 1e-04
 Identities = 20/66 (30%), Positives = 38/66 (57%), Gaps = 1/66 (1%)

Query: 208 DLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRA 267
           D +++V  L   +T   L++ FS +Y  +  +++++D  TG ++G GF+RF    E   A
Sbjct: 2   DANLYVSGLPKTMTQKELEQLFS-QYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 60

Query: 268 MTEMNG 273
           +  +NG
Sbjct: 61  IKGLNG 66

This subgroup corresponds to the RRM2 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells and also regulates the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

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

 Score = 40.1 bits (93), Expect = 1e-04
 Identities = 19/77 (24%), Positives = 39/77 (50%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY 177
           +++  L   M +  L   FS  G+++  +++ ++ TG S G GF+ F  R  AE+ ++  
Sbjct: 5   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 64

Query: 178 SGSLMPNTDQPFRLNWA 194
           +G       +P  + +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|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 4/76 (5%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           I V +L   VT+  L+E F SK   V   KV+  +  G+++ +GFV F  E +  +A+  
Sbjct: 3   IIVKNLPKYVTEDRLREHFESKG-EVTDVKVM-RTRDGKSRRFGFVGFKSEEDAQQAVKY 60

Query: 271 MNGVYCSSRPMRIDVA 286
            N  +  +   +I V 
Sbjct: 61  FNKTFIDT--SKISVE 74

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|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II polyadenylate-binding proteins

 Score = 40.0 bits (94), Expect = 1e-04
 Identities = 19/59 (32%), Positives = 32/59 (54%), Gaps = 1/59 (1%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAM 268
           SIFVG++    T   LQE F S   ++    ++ D  TG+ KG+ ++ F D++    A+
Sbjct: 1   SIFVGNVDYGTTPEELQEHFKS-CGTINRITILCDKFTGQPKGFAYIEFLDKSSVENAL 58

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|240721 cd12275, RRM1_MEI2_EAR1_like, RNA recognition motif 1 in Mei2-like proteins and terminal EAR1-like proteins

 Score = 40.2 bits (94), Expect = 1e-04
 Identities = 18/65 (27%), Positives = 37/65 (56%), Gaps = 1/65 (1%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIP-VGKGCGFVQFANRKDAEVALQKLQGTA 387
           ++FV  +  DV++  LR  F  +G++  V+   + +G   V F + +DA+ A+++L G  
Sbjct: 3   SLFVINVPRDVTESTLRRLFEVYGDVRGVQTERISEGIVTVHFYDIRDAKRAVRELCGRH 62

Query: 388 IGKQT 392
           + +Q 
Sbjct: 63  MQQQA 67

This subfamily corresponds to the RRM1 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding protein family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins. . Length = 71

>gnl|CDD|240865 cd12419, RRM_Ssp2_like, RNA recognition motif in yeast sporulation-specific protein 2 (Ssp2) and similar protein

 Score = 40.4 bits (95), Expect = 1e-04
 Identities = 20/77 (25%), Positives = 42/77 (54%), Gaps = 8/77 (10%)

Query: 335 LDSDVSDEDLREPFSQFGEILSVKIPVGKG-CGFVQFANRKDAEVALQKLQ--GTAIGKQ 391
           L SD   E+L++ F+ FGEI+ +   + +  C  + FA+ + A  A + L+  G+++  +
Sbjct: 2   LPSDFDVEELKDDFTVFGEIVDISPIISRKLCVSIFFADIRSAIRAKETLEDKGSSLNNK 61

Query: 392 TVRLSW----GRNPGNK 404
            ++  W    G++  +K
Sbjct: 62  YIK-QWSIWYGKDITDK 77

This subfamily corresponds to the RRM of the lineage specific yeast sporulation-specific protein 2 (Ssp2) and similar proteins. Ssp2 is encoded by a sporulation-specific gene necessary for outer spore wall assembly in the yeast Saccharomyces cerevisiae. It localizes to the spore wall and may play an important role after meiosis II and during spore wall formation. Ssp2 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 80

>gnl|CDD|240877 cd12431, RRM_ALKBH8, RNA recognition motif in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and similar proteins

 Score = 40.3 bits (95), Expect = 1e-04
 Identities = 18/53 (33%), Positives = 29/53 (54%)

Query: 333 GALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQG 385
           G L + VS E+L   F ++G +  + +P GK   FV +++ +DA  A   L G
Sbjct: 9   GGLGNGVSREELLRVFEKYGTVEDLVMPPGKPYCFVSYSSIEDAAAAYDALNG 61

This subfamily corresponds to the RRM of ALKBH8, also termed alpha-ketoglutarate-dependent dioxygenase ABH8, or S-adenosyl-L-methionine-dependent tRNA methyltransferase ABH8, expressed in various types of human cancers. It is essential in urothelial carcinoma cell survival mediated by NOX-1-dependent ROS signals. ALKBH8 has also been identified as a tRNA methyltransferase that catalyzes methylation of tRNA to yield 5-methylcarboxymethyl uridine (mcm5U) at the wobble position of the anticodon loop. Thus, ALKBH8 plays a crucial role in the DNA damage survival pathway through a distinct mechanism involving the regulation of tRNA modification. ALKBH8 localizes to the cytoplasm. It contains the characteristic AlkB domain that is composed of a tRNA methyltransferase motif, a motif homologous to the bacterial AlkB DNA/RNA repair enzyme, and a dioxygenase catalytic core domain encompassing cofactor-binding sites for iron and 2-oxoglutarate. In addition, unlike other AlkB homologs, ALKBH8 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal S-adenosylmethionine (SAM)-dependent methyltransferase (MT) domain. . Length = 80

>gnl|CDD|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like proteins mainly from plants

 Score = 40.1 bits (94), Expect = 1e-04
 Identities = 26/71 (36%), Positives = 36/71 (50%), Gaps = 11/71 (15%)

Query: 329 TIFVGALDSDVSDED----LREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEV 378
           TIFV   DS + ++D    L E FS  GEI  V IP        KG  +++F +    E 
Sbjct: 1   TIFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEK 60

Query: 379 ALQKLQGTAIG 389
           AL+ L G+ +G
Sbjct: 61  ALE-LDGSDLG 70

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|241040 cd12596, RRM1_SRSF6, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 6 (SRSF6)

 Score = 39.9 bits (93), Expect = 1e-04
 Identities = 19/70 (27%), Positives = 40/70 (57%), Gaps = 2/70 (2%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIG 389
           +++G L   V ++D++  F  +G++L + +    G GFV+F + +DA+ A+ +L G  + 
Sbjct: 2   VYIGRLSYHVREKDIQRFFGGYGKLLEIDLK--NGYGFVEFEDSRDADDAVYELNGKDLC 59

Query: 390 KQTVRLSWGR 399
            + V +   R
Sbjct: 60  GERVIVEHAR 69

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

 Score = 40.2 bits (94), Expect = 1e-04
 Identities = 16/45 (35%), Positives = 25/45 (55%)

Query: 132 LHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQS 176
           L   FS  G+VV+  ++++K T +S G+GFV+F        VL  
Sbjct: 16  LRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAG 60

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|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 = 39.9 bits (94), Expect = 1e-04
 Identities = 19/63 (30%), Positives = 35/63 (55%), Gaps = 1/63 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           IF+G L   +++  ++E   S +  +K   ++ DS TG +KGY F  + D +   +A+  
Sbjct: 3   IFIGGLPNYLSEDQVKELLES-FGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAG 61

Query: 271 MNG 273
           +NG
Sbjct: 62  LNG 64

This subfamily corresponds to the RRM2 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Length = 77

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

 Score = 40.1 bits (94), Expect = 1e-04
 Identities = 20/63 (31%), Positives = 32/63 (50%), Gaps = 6/63 (9%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIP------VGKGCGFVQFANRKDAEVALQKL 383
           +FV  L     ++DL + FS+FGE+  V +         KG  +V F + +DA  A ++L
Sbjct: 5   LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKEL 64

Query: 384 QGT 386
            G 
Sbjct: 65  DGK 67

This subgroup corresponds to the RRM2 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 79

>gnl|CDD|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 40.2 bits (93), Expect = 1e-04
 Identities = 19/41 (46%), Positives = 28/41 (68%)

Query: 140 GQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGS 180
           G++V+ K I +K T Q +GYGFV+F S AAA+K + S   +
Sbjct: 29  GKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKAVASLKAN 69

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|241042 cd12598, RRM1_SRSF9, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 9 (SRSF9)

 Score = 39.8 bits (93), Expect = 1e-04
 Identities = 23/71 (32%), Positives = 41/71 (57%), Gaps = 3/71 (4%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGC---GFVQFANRKDAEVALQKLQGT 386
           I+VG L SDV ++DL + F ++G I  +++   +G     FV+F + +DAE A+    G 
Sbjct: 2   IYVGNLPSDVREKDLEDLFYKYGRIRDIELKNRRGLVPFAFVRFEDPRDAEDAVFGRNGY 61

Query: 387 AIGKQTVRLSW 397
             G+  +R+ +
Sbjct: 62  DFGQCRLRVEF 72

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|240803 cd12357, RRM_PPARGC1A_like, RNA recognition motif in the peroxisome proliferator-activated receptor gamma coactivator 1A (PGC-1alpha) family of regulated coactivators

 Score = 40.0 bits (94), Expect = 1e-04
 Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 3/54 (5%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKI---PVGKGCGFVQFANRKDAEVAL 380
           I+VG +  D +  +LR+ F  FGEI  + +     G   GFV +    DA  A+
Sbjct: 5   IYVGKIPIDTTRSELRQRFQPFGEIEEITLHFRDDGDNYGFVTYRYACDAFRAI 58

This subfamily corresponds to the RRM of PGC-1alpha, PGC-1beta, and PGC-1-related coactivator (PRC), which serve as mediators between environmental or endogenous signals and the transcriptional machinery governing mitochondrial biogenesis. They play an important integrative role in the control of respiratory gene expression through interacting with a number of transcription factors, such as NRF-1, NRF-2, ERR, CREB and YY1. All family members are multi-domain proteins containing the N-terminal activation domain, an LXXLL coactivator signature, a tetrapeptide motif (DHDY) responsible for HCF binding, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In contrast to PGC-1alpha and PRC, PGC-1beta possesses two glutamic/aspartic acid-rich acidic domains, but lacks most of the arginine/serine (SR)-rich domain that is responsible for the regulation of RNA processing. . Length = 89

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

 Score = 39.5 bits (93), Expect = 2e-04
 Identities = 16/69 (23%), Positives = 29/69 (42%), Gaps = 6/69 (8%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVI-----IDSNTGRTKGYGFVRFGDENER 264
           ++FV +L    T+  L++ F  K   V+   +             + GYGFV F  +   
Sbjct: 2   TLFVKNLNFKTTEETLKKHFE-KCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAA 60

Query: 265 SRAMTEMNG 273
            +A+  + G
Sbjct: 61  QKALKRLQG 69

This subfamily corresponds to the RRM5 of RBM19 and RRM4 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 82

>gnl|CDD|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 = 39.8 bits (94), Expect = 2e-04
 Identities = 22/75 (29%), Positives = 41/75 (54%), Gaps = 4/75 (5%)

Query: 212 FVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEM 271
           FVG L    T+  ++  F  +Y +++   +I D +TG++KG  FV+F    E  +A+  +
Sbjct: 3   FVGQLPKTATEEDVRALFE-EYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEAL 61

Query: 272 NGVYCS---SRPMRI 283
           +G       SRP+++
Sbjct: 62  HGKVTMPGASRPLQV 76

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

>gnl|CDD|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding protein 7 (RBM7)

 Score = 39.5 bits (92), Expect = 2e-04
 Identities = 23/62 (37%), Positives = 31/62 (50%), Gaps = 5/62 (8%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-----KGCGFVQFANRKDAEVALQKL 383
           T+FVG LD  V++E + E F Q G ++ VKIP       K   FV F +      A+  L
Sbjct: 3   TLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKDGKPKQFAFVNFKHEVSVPYAMNLL 62

Query: 384 QG 385
            G
Sbjct: 63  NG 64

This subfamily corresponds to the RRM of RBM7, a ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. RBM7 interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20. It may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM7 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. . Length = 75

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

 Score = 39.6 bits (92), Expect = 2e-04
 Identities = 21/66 (31%), Positives = 35/66 (53%), Gaps = 2/66 (3%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIG 389
           +FV  L + V++E L + FS+FG++  VK    K   FV F  R  A  A+ ++ G  I 
Sbjct: 4   LFVRNLATTVTEEILEKSFSEFGKLERVKKL--KDYAFVHFEERDAAVRAMDEMNGKEIE 61

Query: 390 KQTVRL 395
            + + +
Sbjct: 62  GEEIEI 67

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

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

 Score = 39.7 bits (93), Expect = 2e-04
 Identities = 18/49 (36%), Positives = 29/49 (59%), Gaps = 6/49 (12%)

Query: 338 DVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVAL 380
             +++DL++ FS FGE+L V++         KG GFV+FA+ +D    L
Sbjct: 10  KTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVL 58

This subfamily corresponds to the RRM1 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. . Length = 77

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

 Score = 39.9 bits (93), Expect = 2e-04
 Identities = 20/77 (25%), Positives = 40/77 (51%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY 177
           +++  L   M +  L   FS  G+++  +++R++ TG S G GF+ F  R  AE+ ++  
Sbjct: 3   LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGL 62

Query: 178 SGSLMPNTDQPFRLNWA 194
           +G       +P  + +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|240822 cd12376, RRM2_Hu_like, RNA recognition motif 2 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 39.5 bits (92), Expect = 2e-04
 Identities = 21/64 (32%), Positives = 38/64 (59%), Gaps = 6/64 (9%)

Query: 328 ATIFVGALDSDVSDEDLREPFSQFGEILSVKI------PVGKGCGFVQFANRKDAEVALQ 381
           A ++V  L   ++ ++L + FSQ+G I++ +I       V +G GF++F  R +AE A++
Sbjct: 1   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIK 60

Query: 382 KLQG 385
            L G
Sbjct: 61  GLNG 64

This subfamily corresponds to the RRM2 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. Also included in this subfamily is the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 79

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

 Score = 39.8 bits (92), Expect = 2e-04
 Identities = 20/66 (30%), Positives = 38/66 (57%), Gaps = 1/66 (1%)

Query: 208 DLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRA 267
           D +++V  L   +T   L++ FS +Y  +  +++++D  TG ++G GF+RF    E   A
Sbjct: 5   DANLYVSGLPKTMTQKELEQLFS-QYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 63

Query: 268 MTEMNG 273
           +  +NG
Sbjct: 64  IKGLNG 69

This subgroup corresponds to the RRM2 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 90

>gnl|CDD|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like proteins mainly from plants

 Score = 39.7 bits (93), Expect = 2e-04
 Identities = 16/47 (34%), Positives = 28/47 (59%), Gaps = 1/47 (2%)

Query: 136 FSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLM 182
           FS  G++  V +  +++TG S+G+ ++EF S    EK L+   GS +
Sbjct: 24  FSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKALE-LDGSDL 69

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

 Score = 39.4 bits (92), Expect = 2e-04
 Identities = 20/52 (38%), Positives = 31/52 (59%), Gaps = 1/52 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDEN 262
           +FVG L+ + T   L+  FS +Y  V    ++ D  T R++G+GFV+F D N
Sbjct: 2   LFVGGLSWETTQETLRRYFS-QYGEVVDCVIMKDKTTNRSRGFGFVKFKDPN 52

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|241028 cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 40.0 bits (93), Expect = 2e-04
 Identities = 19/59 (32%), Positives = 34/59 (57%), Gaps = 6/59 (10%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQK 382
           IFVG L+ + ++E +RE F +FGEI ++++P+       +G  F+ F      +  L+K
Sbjct: 7   IFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPVKKVLEK 65

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|241027 cd12583, RRM2_hnRNPD, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 39.6 bits (92), Expect = 2e-04
 Identities = 17/61 (27%), Positives = 35/61 (57%), Gaps = 1/61 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           IFVG L+PD  +  ++E F + +  V+  ++ +D+ T + +G+ F+ F +E    + M +
Sbjct: 2   IFVGGLSPDTPEEKIREYFGA-FGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 271 M 271
            
Sbjct: 61  K 61

This subgroup corresponds to the RRM2 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, 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 = 75

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

 Score = 39.7 bits (93), Expect = 2e-04
 Identities = 19/52 (36%), Positives = 33/52 (63%), Gaps = 1/52 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDEN 262
           IFVG L+ + T+  +++ FS ++  V+ A ++ D  T R +G+GFV F  E+
Sbjct: 2   IFVGGLSANTTEDDVKKYFS-QFGKVEDAMLMFDKQTNRHRGFGFVTFESED 52

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

 Score = 39.7 bits (93), Expect = 2e-04
 Identities = 19/56 (33%), Positives = 30/56 (53%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKV 173
           I++G L     E  +   FS  G+V +  ++ +KQT +  G+GFV F S    +KV
Sbjct: 2   IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKV 57

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

 Score = 39.0 bits (91), Expect = 2e-04
 Identities = 17/54 (31%), Positives = 30/54 (55%), Gaps = 6/54 (11%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK------GCGFVQFANRKDAE 377
           IFVG L ++ +++D+++ FSQFG++    +   K      G GFV F +    +
Sbjct: 2   IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVD 55

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

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 21/74 (28%), Positives = 41/74 (55%), Gaps = 3/74 (4%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           ++ V +L+P V++ +L++ FS ++  V+ A VI+D + GR+ G G V F  +     A+ 
Sbjct: 1   ALRVKNLSPFVSNELLEQAFS-QFGEVERAVVIVD-DRGRSTGEGIVEFSRKPGAQAAIK 58

Query: 270 EMN-GVYCSSRPMR 282
             + G +  +   R
Sbjct: 59  RCSEGCFLLTASPR 72

This subfamily corresponds to the RRM2 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. The family also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contains a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members. . Length = 80

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

 Score = 39.6 bits (92), Expect = 2e-04
 Identities = 20/60 (33%), Positives = 34/60 (56%), Gaps = 10/60 (16%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKL 383
           +FVG L  D ++E ++E F  FGEI ++++P+       +G  FV + +    E  +QKL
Sbjct: 2   VFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTD----EEPVQKL 57

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

 Score = 39.5 bits (93), Expect = 2e-04
 Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 3/62 (4%)

Query: 327 NATIFVGALDSDVSDEDLREPFSQFGEILSVKI---PVGKGCGFVQFANRKDAEVALQKL 383
           N  ++V  L   +S E+L + F ++G I  ++I      +G  FV + +  DA+ A   L
Sbjct: 2   NRILYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKETRGTAFVVYEDIYDAKNACDHL 61

Query: 384 QG 385
            G
Sbjct: 62  SG 63

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

>gnl|CDD|240691 cd12245, RRM_scw1_like, RNA recognition motif in yeast cell wall integrity protein scw1 and similar proteins

 Score = 39.5 bits (93), Expect = 2e-04
 Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 4/63 (6%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKG---CGFVQFANRKDAEVALQKLQG 385
           T+FV  L  + ++E+LR+ FS+      +K+   KG     FV+F +   A  AL  LQG
Sbjct: 4   TLFVANLGPNTTEEELRQLFSRQPGFRRLKM-HNKGGGPVCFVEFEDVSFATQALNSLQG 62

Query: 386 TAI 388
             +
Sbjct: 63  AVL 65

This subfamily corresponds to the RRM of the family including yeast cell wall integrity protein scw1, yeast Whi3 protein, yeast Whi4 protein and similar proteins. The strong cell wall protein 1, scw1, is a nonessential cytoplasmic RNA-binding protein that regulates septation and cell-wall structure in fission yeast. It may function as an inhibitor of septum formation, such that its loss of function allows weak SIN signaling to promote septum formation. It's RRM domain shows high homology to two budding yeast proteins, Whi3 and Whi4. Whi3 is a dose-dependent modulator of cell size and has been implicated in cell cycle control in the yeast Saccharomyces cerevisiae. It functions as a negative regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3), a G1 cyclin that promotes transcription of many genes to trigger the G1/S transition in budding yeast. It specifically binds the CLN3 mRNA and localizes it into discrete cytoplasmic loci that may locally restrict Cln3 synthesis to modulate cell cycle progression. Moreover, Whi3 plays a key role in cell fate determination in budding yeast. The RRM domain is essential for Whi3 function. Whi4 is a partially redundant homolog of Whi3, also containing one RRM. Some uncharacterized family members of this subfamily contain two RRMs; their RRM1 shows high sequence homology to the RRM of RNA-binding protein with multiple splicing (RBP-MS)-like proteins. Length = 79

>gnl|CDD|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 = 39.5 bits (92), Expect = 2e-04
 Identities = 20/64 (31%), Positives = 34/64 (53%), Gaps = 1/64 (1%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           ++F+  L  +  D+ L + F   + +V  AKV +D  T ++K +GFV F +      A+ 
Sbjct: 6   NLFIYHLPQEFGDAELMQMFLP-FGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQ 64

Query: 270 EMNG 273
            MNG
Sbjct: 65  AMNG 68

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

>gnl|CDD|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 39.5 bits (93), Expect = 2e-04
 Identities = 17/66 (25%), Positives = 35/66 (53%), Gaps = 5/66 (7%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKI---PVG--KGCGFVQFANRKDAEVALQKLQ 384
           +FVG +  D+ +++L   F + G I  +++     G  +G  FV + N++ A+ A+++L 
Sbjct: 4   VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGLNRGYAFVTYTNKEAAQRAVKQLH 63

Query: 385 GTAIGK 390
              I  
Sbjct: 64  NYEIRP 69

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|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding protein 19 (RBM19), yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 39.2 bits (92), Expect = 2e-04
 Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 6/74 (8%)

Query: 330 IFVGALDSDVSDEDLREPFSQF-GEILSVKI---PVGK--GCGFVQFANRKDAEVALQKL 383
           + V  L + +++ +L+E FS+  GEI  VK+     GK     F+ +   ++A+ A    
Sbjct: 3   LIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTEEEAQKAKDYF 62

Query: 384 QGTAIGKQTVRLSW 397
             T I    + + +
Sbjct: 63  NNTYINTSKISVEF 76

This subfamily corresponds to the RRM1 of RBM19 and MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 77

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

 Score = 39.2 bits (92), Expect = 3e-04
 Identities = 21/76 (27%), Positives = 38/76 (50%), Gaps = 2/76 (2%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           + V +L    T++ L++ FS  +  V     I     G+ KG+ FV+F  + +  +A+  
Sbjct: 2   LIVRNLPFKCTEADLKKLFS-PFGFVWEVT-IPRKPDGKKKGFAFVQFTSKADAEKAIKG 59

Query: 271 MNGVYCSSRPMRIDVA 286
           +NG     RP+ +D A
Sbjct: 60  VNGKKIKGRPVAVDWA 75

This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 76

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

 Score = 38.8 bits (91), Expect = 3e-04
 Identities = 23/67 (34%), Positives = 36/67 (53%), Gaps = 3/67 (4%)

Query: 128 DETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQ 187
            E  L   FS  G V  V + R K  G+ +G+ FV+F S+A AEK ++  +G  +    +
Sbjct: 12  TEADLKKLFSPFGFVWEVTIPR-KPDGKKKGFAFVQFTSKADAEKAIKGVNGKKIKG--R 68

Query: 188 PFRLNWA 194
           P  ++WA
Sbjct: 69  PVAVDWA 75

This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 76

>gnl|CDD|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 = 38.6 bits (90), Expect = 3e-04
 Identities = 17/62 (27%), Positives = 39/62 (62%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY 177
           +++G++ +   E  L + FS  G VV+ +++ +++TG+ +GYGF E+  +  A   +++ 
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 178 SG 179
           +G
Sbjct: 61  NG 62

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

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

 Score = 38.8 bits (91), Expect = 3e-04
 Identities = 15/64 (23%), Positives = 32/64 (50%), Gaps = 1/64 (1%)

Query: 116 KTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQ 175
           +T+++G+L   + E  L+  F   G +  VK+ ++   G+ + + FV F    +    +Q
Sbjct: 2   RTLFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPN-GKPKSFAFVTFKHEVSVPYAIQ 60

Query: 176 SYSG 179
             +G
Sbjct: 61  LLNG 64

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

>gnl|CDD|240852 cd12406, RRM4_NCL, RNA recognition motif 4 in vertebrate nucleolin

 Score = 39.2 bits (91), Expect = 3e-04
 Identities = 25/80 (31%), Positives = 40/80 (50%), Gaps = 9/80 (11%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVALQK 382
           T+FV  L  D ++E L+E F   G I + +I         KG GFV F++ +DA+ A + 
Sbjct: 2   TLFVKGLSEDTTEETLKESFD--GSI-AARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEA 58

Query: 383 LQGTAIGKQTVRLSWGRNPG 402
           ++   I    V L + +  G
Sbjct: 59  MEDGEIDGNKVTLDFAKPKG 78

This subfamily corresponds to the RRM4 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 78

>gnl|CDD|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast nucleolar protein 13 (Nop13p) and similar proteins

 Score = 38.6 bits (90), Expect = 3e-04
 Identities = 14/57 (24%), Positives = 29/57 (50%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVL 174
           +++G+L     E  L   F   G++  V+++  + +G+ +G+ FV+F     A   L
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNAL 57

This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

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

 Score = 39.2 bits (92), Expect = 3e-04
 Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 5/63 (7%)

Query: 328 ATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV-----GKGCGFVQFANRKDAEVALQK 382
             + V  LD  VSD+D++E F++FG +    +         G   V F  R DA  A+++
Sbjct: 1   TKLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDRSGRSLGTADVVFERRADALKAMKQ 60

Query: 383 LQG 385
             G
Sbjct: 61  YNG 63

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

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

 Score = 38.9 bits (91), Expect = 3e-04
 Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 1/73 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +FV +L     +  L++ FS K+  +    V ID  +G++KG+ +V F D  +  +A  E
Sbjct: 5   LFVRNLPYSCKEDDLEKLFS-KFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKE 63

Query: 271 MNGVYCSSRPMRI 283
           ++G     R + I
Sbjct: 64  LDGKVFQGRLIHI 76

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|241027 cd12583, RRM2_hnRNPD, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 38.8 bits (90), Expect = 3e-04
 Identities = 19/59 (32%), Positives = 32/59 (54%), Gaps = 6/59 (10%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQK 382
           IFVG L  D  +E +RE F  FGE+ S+++P+       +G  F+ F   +  +  ++K
Sbjct: 2   IFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

This subgroup corresponds to the RRM2 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, 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 = 75

>gnl|CDD|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins

 Score = 39.6 bits (92), Expect = 3e-04
 Identities = 20/69 (28%), Positives = 36/69 (52%), Gaps = 1/69 (1%)

Query: 221 TDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRP 280
           T+  L+E FS KY  +    ++ D  + R++G+ FV F + ++   A    NG+    R 
Sbjct: 22  TERDLREVFS-KYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRR 80

Query: 281 MRIDVATPK 289
           +R+D +  K
Sbjct: 81  IRVDFSITK 89

This subgroup corresponds to the RRM of TRA2-beta or TRA-2-beta, also termed splicing factor, arginine/serine-rich 10 (SFRS10), or transformer-2 protein homolog B, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. It contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. TRA2-beta specifically binds to two types of RNA sequences, the CAA and (GAA)2 sequences, through the RRMs in different RNA binding modes. . Length = 89

>gnl|CDD|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP DL) and similar proteins

 Score = 39.2 bits (91), Expect = 3e-04
 Identities = 26/69 (37%), Positives = 35/69 (50%), Gaps = 10/69 (14%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKI---PV---GKGCGFVQFANRKDAEVALQ-- 381
           +F+G L  D S +DL E  S+FGE+L   I   PV    +G GFV F +    +  L+  
Sbjct: 2   MFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLELK 61

Query: 382 --KLQGTAI 388
             KL G  I
Sbjct: 62  EHKLDGKLI 70

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

 Score = 39.3 bits (91), Expect = 3e-04
 Identities = 23/78 (29%), Positives = 40/78 (51%), Gaps = 6/78 (7%)

Query: 328 ATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGC------GFVQFANRKDAEVALQ 381
           A +F+  L  +  D+DL + F  FG ++S K+ + K        GFV + N   A+ A+Q
Sbjct: 8   ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQ 67

Query: 382 KLQGTAIGKQTVRLSWGR 399
            + G  IG + +++   R
Sbjct: 68  AMNGFQIGMKRLKVQLKR 85

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|240818 cd12372, RRM_CFIm68_CFIm59, RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6), pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7), and similar proteins

 Score = 38.8 bits (91), Expect = 3e-04
 Identities = 22/61 (36%), Positives = 36/61 (59%), Gaps = 4/61 (6%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIR---NKQTGQSEGYGFVEFYSRAAAEKVL 174
           +++G+L  W  +  L    +  G VV+VK I+   +K  G+S+G+ +VEF S AAA  V 
Sbjct: 1   LYVGNLTWWTTDEDLEGALAEAG-VVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVK 59

Query: 175 Q 175
           +
Sbjct: 60  E 60

This subfamily corresponds to the RRM of cleavage factor Im (CFIm) subunits. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. Two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. Structurally related CFIm68 and CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59), are functionally redundant. Both contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. Their N-terminal RRM mediates the interaction with CFIm25, and also serves to enhance RNA binding and facilitate RNA looping. . Length = 76

>gnl|CDD|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 39.1 bits (92), Expect = 3e-04
 Identities = 22/76 (28%), Positives = 33/76 (43%), Gaps = 3/76 (3%)

Query: 211 IFVGDLAPDVTDSILQETFSS--KYPSVKGAKVIID-SNTGRTKGYGFVRFGDENERSRA 267
           ++V +L+  VT+  L   F       S +     I     GR KG  FV F  E   ++A
Sbjct: 4   LYVKNLSKRVTEEDLVYIFGRFVDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEIATKA 63

Query: 268 MTEMNGVYCSSRPMRI 283
           +  +NG     +PM I
Sbjct: 64  LNLVNGYVLKGKPMVI 79

This subfamily corresponds to the RRM2 of RBM40 and the RRM of RBM41. RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein). It serves as a bridging factor between the U11 and U12 snRNPs. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. RBM41 contains only one RRM. Its biological function remains unclear. . Length = 82

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

 Score = 38.6 bits (90), Expect = 4e-04
 Identities = 18/63 (28%), Positives = 34/63 (53%), Gaps = 6/63 (9%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVALQK 382
            I++G L     +++L++ FSQFG + +V++         K  GF+QF N + A +A + 
Sbjct: 1   VIYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKS 60

Query: 383 LQG 385
           +  
Sbjct: 61  MNN 63

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

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

 Score = 38.5 bits (90), Expect = 4e-04
 Identities = 15/64 (23%), Positives = 37/64 (57%)

Query: 127 MDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTD 186
           + E  L   F+  G++ ++ V+++KQT +S+G  +V+F   ++A + ++  +G  +    
Sbjct: 14  VTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCLGGDT 73

Query: 187 QPFR 190
           +P +
Sbjct: 74  KPLK 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|241021 cd12577, RRM1_Hrp1p, RNA recognition motif 1 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 38.3 bits (89), Expect = 4e-04
 Identities = 17/57 (29%), Positives = 30/57 (52%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVL 174
           ++IG L     +  L   F   G+V +  V+R+  TG+S G+GF+ F    +  +V+
Sbjct: 1   MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVM 57

This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition, steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway. It binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y. . Length = 76

>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 = 38.7 bits (90), Expect = 4e-04
 Identities = 19/44 (43%), Positives = 26/44 (59%)

Query: 132 LHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQ 175
           L   FS  G+VV+  +  +  TG+S G+GFV F   A+ EKVL 
Sbjct: 15  LKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLD 58

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

 Score = 38.7 bits (91), Expect = 4e-04
 Identities = 25/69 (36%), Positives = 39/69 (56%), Gaps = 6/69 (8%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILS---VKIP-VGKGC--GFVQFANRKDAEVALQK 382
           T+FVG +   VSD+ +R+   + G++LS   VK P  GK    GF +F + + A  AL+ 
Sbjct: 2   TVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALRL 61

Query: 383 LQGTAIGKQ 391
           L G  +G +
Sbjct: 62  LNGLELGGK 70

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|241020 cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins

 Score = 38.6 bits (90), Expect = 4e-04
 Identities = 21/58 (36%), Positives = 31/58 (53%), Gaps = 6/58 (10%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEI---LSVKIPVGK---GCGFVQFANRKDAEVALQ 381
           +F+G L    + E LRE FS+FGEI   + ++ P  K   G GFV F++    +  L 
Sbjct: 1   MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLA 58

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|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 38.6 bits (90), Expect = 4e-04
 Identities = 21/56 (37%), Positives = 30/56 (53%), Gaps = 2/56 (3%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQG 385
           IFVG +D D S E+LR  F  +G +LS    V +   FV       A+ A+++L G
Sbjct: 3   IFVGNVDEDTSQEELRALFEAYGAVLSCA--VMRQFAFVHLRGEAAADRAIEELNG 56

This subgroup corresponds to the RRM1 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs. . Length = 69

>gnl|CDD|240875 cd12429, RRM_DNAJC17, RNA recognition motif in the DnaJ homolog subfamily C member 17

 Score = 38.4 bits (90), Expect = 4e-04
 Identities = 20/68 (29%), Positives = 30/68 (44%), Gaps = 9/68 (13%)

Query: 127 MDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTD 186
             E  L   FS  G V +V V+ +K+ G       VEF S+ AAE  +++  G       
Sbjct: 16  YSEDELRKIFSKYGDVSDV-VVSSKKKGS----AIVEFASKKAAEAAVENECG----LPS 66

Query: 187 QPFRLNWA 194
            P  ++W 
Sbjct: 67  NPLLVSWL 74

The CD corresponds to the RRM of some eukaryotic DnaJ homolog subfamily C member 17 and similar proteins. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Members in this family contains an N-terminal DnaJ domain or J-domain, which mediates the interaction with Hsp70. They also contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the C-terminus, which may play an essential role in RNA binding. . Length = 74

>gnl|CDD|241059 cd12615, RRM1_TIA1, RNA recognition motif 1 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 38.5 bits (89), Expect = 4e-04
 Identities = 22/77 (28%), Positives = 43/77 (55%), Gaps = 3/77 (3%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           +++VG+L+ DVT++++ + FS   P  K  K+I+D  T     Y FV F +    + ++ 
Sbjct: 1   TLYVGNLSRDVTEALILQLFSQIGP-CKSCKMIMD--TAGNDPYCFVEFFEHRHAAASLA 57

Query: 270 EMNGVYCSSRPMRIDVA 286
            MNG     + ++++ A
Sbjct: 58  AMNGRKIMGKEVKVNWA 74

This subgroup corresponds to the RRM1 of TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1) and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and functions as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 74

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

 Score = 38.4 bits (89), Expect = 5e-04
 Identities = 18/66 (27%), Positives = 38/66 (57%), Gaps = 1/66 (1%)

Query: 208 DLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRA 267
           D +++V  L   ++   +++ FS +Y  +  +++++D  TG ++G GF+RF    E   A
Sbjct: 1   DANLYVSGLPKTMSQKEMEQLFS-QYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEA 59

Query: 268 MTEMNG 273
           +  +NG
Sbjct: 60  IKGLNG 65

This subgroup corresponds to the RRM2 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

>gnl|CDD|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 = 38.5 bits (90), Expect = 5e-04
 Identities = 15/61 (24%), Positives = 34/61 (55%)

Query: 112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAE 171
           +D+   +++G +   ++E  L   F   G++  + V+++K TG  +G  F+ + +R +A 
Sbjct: 2   DDDAIKLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESAL 61

Query: 172 K 172
           K
Sbjct: 62  K 62

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|240772 cd12326, RRM1_hnRNPA0, RNA recognition motif 1 found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 38.6 bits (90), Expect = 5e-04
 Identities = 20/73 (27%), Positives = 37/73 (50%), Gaps = 7/73 (9%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK------GCGFVQFANRKDAEVALQKL 383
           +FVG L+   SD  LR  F+++G++    + V        G GF+ F++  +A+ A++  
Sbjct: 5   LFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAME-A 63

Query: 384 QGTAIGKQTVRLS 396
           Q  +I    + L 
Sbjct: 64  QPHSIDGNQIELK 76

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|241048 cd12604, RRM_RALY, RNA recognition motif in vertebrate RNA-binding protein Raly

 Score = 38.5 bits (89), Expect = 5e-04
 Identities = 22/76 (28%), Positives = 40/76 (52%), Gaps = 3/76 (3%)

Query: 327 NATIFVGALDSD-VSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQG 385
           N+ +F+G L++  V   D+   FS++G ++     V KG  FVQ++N + A  A+    G
Sbjct: 1   NSRVFIGNLNTAVVKKSDVETIFSKYGRVVGCS--VHKGYAFVQYSNERHARGAVIGENG 58

Query: 386 TAIGKQTVRLSWGRNP 401
             +  QT+ ++    P
Sbjct: 59  RVLAGQTLDINMAGEP 74

This subgroup corresponds to the RRM of Raly, also termed autoantigen p542, or heterogeneous nuclear ribonucleoprotein C-like 2, or hnRNP core protein C-like 2, or hnRNP associated with lethal yellow protein homolog, an RNA-binding protein that may play a critical role in embryonic development. It is encoded by Raly, a ubiquitously expressed gene of unknown function. Raly shows a high degree of identity with the 5' sequences of p542 gene encoding autoantigen, which can cross-react with EBNA-1 of the Epstein Barr virus. Raly contains two distinct domains, an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain that includes a unique glycine/serine-rich stretch. . Length = 76

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

 Score = 38.3 bits (90), Expect = 6e-04
 Identities = 22/73 (30%), Positives = 42/73 (57%), Gaps = 6/73 (8%)

Query: 110 FTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAA 169
           FTN     +++ +L   MD+  L   F   G++ + KV+++   G+S+G+GFV F +  A
Sbjct: 1   FTN-----VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKD-DEGKSKGFGFVNFENHEA 54

Query: 170 AEKVLQSYSGSLM 182
           A+K ++  +G  +
Sbjct: 55  AQKAVEELNGKEV 67

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

 Score = 38.0 bits (89), Expect = 6e-04
 Identities = 20/63 (31%), Positives = 29/63 (46%), Gaps = 9/63 (14%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +FVG+L    T   L+  F  KY +V    V+        K YGFV   +E +   A+  
Sbjct: 2   LFVGNLPDATTSEELRALF-EKYGTVTECDVV--------KNYGFVHMEEEEDAEDAIKA 52

Query: 271 MNG 273
           +NG
Sbjct: 53  LNG 55

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

 Score = 38.1 bits (88), Expect = 6e-04
 Identities = 18/77 (23%), Positives = 39/77 (50%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY 177
           +++  L   M +  +   FS  G+++  +++ ++ TG S G GF+ F  R  AE+ ++  
Sbjct: 4   LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKGL 63

Query: 178 SGSLMPNTDQPFRLNWA 194
           +G       +P  + +A
Sbjct: 64  NGQKPLGAAEPITVKFA 80

This subgroup corresponds to the RRM2 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

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

 Score = 38.1 bits (89), Expect = 6e-04
 Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 5/59 (8%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPV---GK--GCGFVQFANRKDAEVALQK 382
            + V  L   VS+E L + FSQFGE+    + V   G+  G G V+F+ +  A+ A+++
Sbjct: 1   ALRVKNLSPFVSNELLEQAFSQFGEVERAVVIVDDRGRSTGEGIVEFSRKPGAQAAIKR 59

This subfamily corresponds to the RRM2 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. The family also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contains a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members. . Length = 80

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

 Score = 38.1 bits (88), Expect = 6e-04
 Identities = 16/51 (31%), Positives = 32/51 (62%), Gaps = 1/51 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDE 261
           +FVG L+PD T+  ++E F + +  ++  ++ +D+ T   +G+ FV + DE
Sbjct: 2   VFVGGLSPDTTEEQIKEYFGA-FGEIENIELPMDTKTNERRGFCFVTYTDE 51

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|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 38.7 bits (89), Expect = 6e-04
 Identities = 20/56 (35%), Positives = 34/56 (60%), Gaps = 1/56 (1%)

Query: 125 HWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGS 180
           +  D+  +  C  + G++V+ K I +K T + +GYGFV+F S AAA+K + +   S
Sbjct: 18  NTTDQDLVKLCQPY-GKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQKAVSALKAS 72

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|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 38.7 bits (91), Expect = 6e-04
 Identities = 15/41 (36%), Positives = 24/41 (58%), Gaps = 6/41 (14%)

Query: 140 GQVVNVKVIRNKQ------TGQSEGYGFVEFYSRAAAEKVL 174
            ++  VK++R+ +       G+S+GYGFVEF +   A K L
Sbjct: 34  PKIKQVKIMRDLKRVDPNGKGKSKGYGFVEFTNHEHALKAL 74

This subfamily corresponds to the RRM4 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 98

>gnl|CDD|240905 cd12459, RRM1_CID8_like, RNA recognition motif 1 in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 38.2 bits (89), Expect = 6e-04
 Identities = 22/82 (26%), Positives = 39/82 (47%), Gaps = 15/82 (18%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCG---------FVQFANRKDAEVA 379
           T++V  +D  V++E L   FS  G+++  ++     CG         F++F + + A  A
Sbjct: 4   TVYVSDIDQQVTEEQLAALFSNCGQVVDCRV-----CGDPNSVLRFAFIEFTDEEGARAA 58

Query: 380 LQKLQGTAIGKQTVRLSWGRNP 401
           L  L GT +G   VR+   +  
Sbjct: 59  LS-LSGTMLGFYPVRVLPSKTA 79

This subgroup corresponds to the RRM1 domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 80

>gnl|CDD|240851 cd12405, RRM3_NCL, RNA recognition motif 3 in vertebrate nucleolin

 Score = 38.0 bits (88), Expect = 6e-04
 Identities = 21/74 (28%), Positives = 32/74 (43%), Gaps = 6/74 (8%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           + V +L+   ++  LQE F       K   + I  N GR KGY FV F    +   A+  
Sbjct: 4   LVVNNLSYSASEDSLQEVFE------KATSIRIPQNNGRPKGYAFVEFESAEDAKEALNS 57

Query: 271 MNGVYCSSRPMRID 284
            N      R +R++
Sbjct: 58  CNNTEIEGRSIRLE 71

This subfamily corresponds to the RRM3 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 72

>gnl|CDD|220309 pfam09606, Med15, ARC105 or Med15 subunit of Mediator complex non-fungal

 Score = 41.9 bits (98), Expect = 6e-04
 Identities = 25/117 (21%), Positives = 31/117 (26%), Gaps = 1/117 (0%)

Query: 3   QSNGGDANAAAAAAAAVSGGAGGGSQPTPQQPYHWVPPHQQ-QWMAMMQYPAAAMAMMQQ 61
           Q   G A       + V     GG      Q     P  QQ   M   Q  A   A    
Sbjct: 122 QMPMGAAGMGPHQMSRVGTMQPGGQAGGMMQQSSGQPQSQQPNQMGPQQGQAQGQAGGMN 181

Query: 62  QQMMMYPHHYMPYGGGGHPYYQNGGGVKQQQQQQHGLSNGKQNGSNNNFTNDETKTI 118
           Q          P   G       GG  + QQQ Q G    +         N + + +
Sbjct: 182 QGQQGPVGQQQPPQMGQPGMPGGGGQGQMQQQGQPGGQQQQNPQMQQQLQNQQQQQM 238

The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development. Length = 768

>gnl|CDD|240921 cd12477, RRM1_U1A, RNA recognition motif 1 found in vertebrate U1 small nuclear ribonucleoprotein A (U1A)

 Score = 38.5 bits (89), Expect = 6e-04
 Identities = 21/80 (26%), Positives = 41/80 (51%), Gaps = 7/80 (8%)

Query: 327 NATIFVGALDSDVSDEDLREP----FSQFGEILSVKIPVG---KGCGFVQFANRKDAEVA 379
           N TI++  L+  +  ++L++     FS+FG+IL + +      +G  FV F     A  A
Sbjct: 3   NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 62

Query: 380 LQKLQGTAIGKQTVRLSWGR 399
           L+ +QG     + +R+ + +
Sbjct: 63  LRSMQGFPFYDKPMRIQYAK 82

This subgroup corresponds to the RRM1 of U1A (also termed U1 snRNP A or U1-A), an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein and it also shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins, including polypyrimidine tract binding protein (PTB), polypyrimidine-tract binding protein-associated factor (PSF), and non-POU-domain-containing, octamer-binding (NONO), DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). It also binds to a flavivirus NS5 protein and plays an important role in virus replication. U1A contains two RNA recognition motifs (RRMs); the N-terminal RRM (RRM1) binds tightly and specifically to the U1 snRNA SLII and its own 3'-UTR, while in contrast, the C-terminal RRM (RRM2) does not appear to associate with any RNA and may be free to bind other proteins. U1A also contains a proline-rich region, and a nuclear localization signal (NLS) in the central domain that is responsible for its nuclear import. . Length = 89

>gnl|CDD|241041 cd12597, RRM1_SRSF1, RNA recognition motif 1 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 37.8 bits (88), Expect = 6e-04
 Identities = 18/58 (31%), Positives = 32/58 (55%), Gaps = 2/58 (3%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKG--CGFVQFANRKDAEVALQKLQG 385
           I+VG L  D+  +D+ + F ++G I  + +   +G    FV+F + +DAE A+    G
Sbjct: 2   IYVGNLPPDIRTKDIEDLFYKYGAIRDIDLKNRRGPPFAFVEFEDPRDAEDAVYGRDG 59

This subgroup corresponds to the RRM1 of SRSF1, also termed alternative-splicing factor 1 (ASF-1), or pre-mRNA-splicing factor SF2, P33 subunit. SRSF1 is a splicing regulatory serine/arginine (SR) protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF1 is a shuttling SR protein and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a long glycine-rich spacer, and a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 73

>gnl|CDD|240904 cd12458, RRM_AtC3H46_like, RNA recognition motif in Arabidopsis thaliana zinc finger CCCH domain-containing protein 46 (AtC3H46) and similar proteins

 Score = 37.8 bits (88), Expect = 6e-04
 Identities = 23/61 (37%), Positives = 31/61 (50%), Gaps = 2/61 (3%)

Query: 336 DSDVSDEDLREPFSQFGEILSVKIPVG--KGCGFVQFANRKDAEVALQKLQGTAIGKQTV 393
           DS  ++ED+ E F QFG +L V+IP    +  GFV F N +  +  L K     I    V
Sbjct: 8   DSRFTEEDVSEYFGQFGPVLDVRIPYQQKRMFGFVTFENAETVKRILSKGNPHFICGSRV 67

Query: 394 R 394
           R
Sbjct: 68  R 68

This subfamily corresponds to the RRM domain in AtC3H46, a putative RNA-binding protein that contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCCH class of zinc finger, typically C-X8-C-X5-C-X3-H. It may possess ribonuclease activity. . Length = 70

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

 Score = 41.4 bits (97), Expect = 7e-04
 Identities = 18/62 (29%), Positives = 39/62 (62%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY 177
           +++G+L   + E  L   F   G + +V++ R+ +TG+S+G+GF++F+    A++ L+  
Sbjct: 189 LYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVM 248

Query: 178 SG 179
           +G
Sbjct: 249 NG 250

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

 Score = 38.0 bits (89), Expect = 7e-04
 Identities = 17/45 (37%), Positives = 27/45 (60%)

Query: 128 DETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEK 172
            E  L   FS  G +  V+V+ +++TG+S G+GFV F S   A++
Sbjct: 12  TERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKE 56

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

 Score = 37.9 bits (89), Expect = 7e-04
 Identities = 21/78 (26%), Positives = 43/78 (55%), Gaps = 4/78 (5%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFV--RFGDENERSRAM 268
           +FVG L+P VT+S L+E F S++ +V   ++I   + G  +G+ ++  R  +   + +  
Sbjct: 2   LFVGGLSPSVTESDLEERF-SRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLK-KCK 59

Query: 269 TEMNGVYCSSRPMRIDVA 286
           + +NG       ++I+ 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|240691 cd12245, RRM_scw1_like, RNA recognition motif in yeast cell wall integrity protein scw1 and similar proteins

 Score = 38.0 bits (89), Expect = 7e-04
 Identities = 26/88 (29%), Positives = 42/88 (47%), Gaps = 16/88 (18%)

Query: 205 ACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYG---FVRFGDE 261
            C+ L  FV +L P+ T+  L++ F S+ P  +  K+         KG G   FV F D 
Sbjct: 1   PCNTL--FVANLGPNTTEEELRQLF-SRQPGFRRLKM-------HNKGGGPVCFVEFEDV 50

Query: 262 NERSRAMTEMNGVYCSSR---PMRIDVA 286
           +  ++A+  + G   SS     +RI+ A
Sbjct: 51  SFATQALNSLQGAVLSSSDRGGIRIEYA 78

This subfamily corresponds to the RRM of the family including yeast cell wall integrity protein scw1, yeast Whi3 protein, yeast Whi4 protein and similar proteins. The strong cell wall protein 1, scw1, is a nonessential cytoplasmic RNA-binding protein that regulates septation and cell-wall structure in fission yeast. It may function as an inhibitor of septum formation, such that its loss of function allows weak SIN signaling to promote septum formation. It's RRM domain shows high homology to two budding yeast proteins, Whi3 and Whi4. Whi3 is a dose-dependent modulator of cell size and has been implicated in cell cycle control in the yeast Saccharomyces cerevisiae. It functions as a negative regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3), a G1 cyclin that promotes transcription of many genes to trigger the G1/S transition in budding yeast. It specifically binds the CLN3 mRNA and localizes it into discrete cytoplasmic loci that may locally restrict Cln3 synthesis to modulate cell cycle progression. Moreover, Whi3 plays a key role in cell fate determination in budding yeast. The RRM domain is essential for Whi3 function. Whi4 is a partially redundant homolog of Whi3, also containing one RRM. Some uncharacterized family members of this subfamily contain two RRMs; their RRM1 shows high sequence homology to the RRM of RNA-binding protein with multiple splicing (RBP-MS)-like proteins. Length = 79

>gnl|CDD|240941 cd12497, RRM3_RBM47, RNA recognition motif 3 in vertebrate RNA-binding protein 47 (RBM47)

 Score = 38.1 bits (88), Expect = 7e-04
 Identities = 16/59 (27%), Positives = 31/59 (52%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAI 388
           ++V  L  + S++ +++ F QF      ++   +   FV F +R+DA  A+  L GT +
Sbjct: 4   LYVRNLMIETSEDTIKKTFGQFNPGCVERVKKIRDYAFVHFTSREDAVHAMNNLNGTEL 62

This subgroup corresponds to the RRM3 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

>gnl|CDD|241013 cd12569, RRM4_RBM19, RNA recognition motif 4 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 37.7 bits (88), Expect = 7e-04
 Identities = 18/54 (33%), Positives = 28/54 (51%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKL 383
           I V  L +     +LRE FS+FG +  V +P       V+F    +A++A +KL
Sbjct: 3   ILVKNLPAGTLTAELRELFSKFGSLGRVLLPPAGITAIVEFLEPSEAKLAFRKL 56

This subgroup corresponds to the RRM4 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 72

>gnl|CDD|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 38.4 bits (90), Expect = 7e-04
 Identities = 14/31 (45%), Positives = 19/31 (61%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKI 359
           T+FVG L      +DL++ F QFG I SV+ 
Sbjct: 2   TVFVGNLPLTTKKKDLKKLFKQFGPIESVRF 32

This subfamily corresponds to the RRM1 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein. . Length = 91

>gnl|CDD|241025 cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 38.1 bits (88), Expect = 7e-04
 Identities = 19/63 (30%), Positives = 36/63 (57%), Gaps = 1/63 (1%)

Query: 116 KTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEK-VL 174
           K +++G +    +E  L + F   G++  +++I ++Q+G+  G+GFV F      +K VL
Sbjct: 1   KKLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVL 60

Query: 175 QSY 177
           Q Y
Sbjct: 61  QKY 63

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|240846 cd12400, RRM_Nop6, RNA recognition motif in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and similar proteins

 Score = 37.7 bits (88), Expect = 8e-04
 Identities = 15/40 (37%), Positives = 26/40 (65%)

Query: 136 FSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQ 175
           F + G   +V+++ +K+TG+S+G  FVEF +  A  K L+
Sbjct: 21  FKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALK 60

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|241020 cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins

 Score = 37.8 bits (88), Expect = 8e-04
 Identities = 21/60 (35%), Positives = 31/60 (51%), Gaps = 2/60 (3%)

Query: 118 IWIGDLFHWMDET-FLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQS 176
           ++IG L  W      L   FS  G++    V+R+  T +S G+GFV F   A+ +KVL  
Sbjct: 1   MFIGGL-SWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQ 59

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|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 = 37.9 bits (88), Expect = 8e-04
 Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 6/72 (8%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGC------GFVQFANRKDAEVALQKL 383
           +F+  L  +  D +L + F  FG ++S K+ V +        GFV F N   A+ A+Q +
Sbjct: 7   LFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAM 66

Query: 384 QGTAIGKQTVRL 395
            G  IG + +++
Sbjct: 67  NGFQIGMKRLKV 78

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

>gnl|CDD|240875 cd12429, RRM_DNAJC17, RNA recognition motif in the DnaJ homolog subfamily C member 17

 Score = 37.6 bits (88), Expect = 8e-04
 Identities = 17/45 (37%), Positives = 31/45 (68%), Gaps = 1/45 (2%)

Query: 338 DVSDEDLREPFSQFGEILSVKIPVGK-GCGFVQFANRKDAEVALQ 381
           D S+++LR+ FS++G++  V +   K G   V+FA++K AE A++
Sbjct: 15  DYSEDELRKIFSKYGDVSDVVVSSKKKGSAIVEFASKKAAEAAVE 59

The CD corresponds to the RRM of some eukaryotic DnaJ homolog subfamily C member 17 and similar proteins. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Members in this family contains an N-terminal DnaJ domain or J-domain, which mediates the interaction with Hsp70. They also contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the C-terminus, which may play an essential role in RNA binding. . Length = 74

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

 Score = 37.8 bits (88), Expect = 8e-04
 Identities = 22/76 (28%), Positives = 47/76 (61%), Gaps = 8/76 (10%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKI---PVG---KGCGFVQFANRKDAEVALQKL 383
           ++VG++  ++ ++ +R+ FS FG I S+ +   PV    KG  FV++   + A++AL+++
Sbjct: 3   VYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQM 62

Query: 384 QGTAIGKQTVRLSWGR 399
            G  +G + +++  GR
Sbjct: 63  NGVMLGGRNIKV--GR 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|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 37.4 bits (87), Expect = 9e-04
 Identities = 24/73 (32%), Positives = 35/73 (47%), Gaps = 2/73 (2%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           IFV +L   V    L+E F      V  A +  D   G+++G G V+F    E  +A++ 
Sbjct: 1   IFVANLDYKVGWKKLKEVFKLA-GKVVRADIKEDKE-GKSRGMGVVQFEHPIEAVQAISM 58

Query: 271 MNGVYCSSRPMRI 283
            NG     RPMR+
Sbjct: 59  FNGQMLFDRPMRV 71

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

>gnl|CDD|240673 cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins

 Score = 37.7 bits (88), Expect = 0.001
 Identities = 20/84 (23%), Positives = 36/84 (42%), Gaps = 8/84 (9%)

Query: 115 TKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVL 174
           + T+WIG L   + E  L N F   G++ ++ +I  +      G  +V   +R  A + L
Sbjct: 2   STTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIPPR------GCAYVCMETRQDAHRAL 55

Query: 175 QSYSGSLMPNTDQPFRLNWATFSG 198
           Q      +    +  ++ WA   G
Sbjct: 56  QKLRNVKL--AGKKIKVAWAPNKG 77

This subfamily corresponds to the RRM in a new class of SCAFs (SR-like CTD-associated factors), including SCAF4, SCAF8 and similar proteins. The biological role of SCAF4 remains unclear, but it shows high sequence similarity to SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8). SCAF8 is a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. In addition, SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8 and SCAF4 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain), and serine/arginine-rich motifs. Length = 77

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

 Score = 37.1 bits (86), Expect = 0.001
 Identities = 18/64 (28%), Positives = 30/64 (46%), Gaps = 2/64 (3%)

Query: 132 LHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRL 191
           L + FS    + +  V+ + +TG+S GYGFV F     A++ L       +    +  RL
Sbjct: 16  LTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKLKNKKLHG--RILRL 73

Query: 192 NWAT 195
           + A 
Sbjct: 74  DIAE 77

This subgroup corresponds to the RRM1 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 37.6 bits (88), Expect = 0.001
 Identities = 23/89 (25%), Positives = 37/89 (41%), Gaps = 17/89 (19%)

Query: 115 TKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVI---------RNKQTGQSEGYGFVEFY 165
           T  +++G+L   + E  L   F   G + +VK++         RN+  G      FV F 
Sbjct: 1   TTNLYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCG------FVAFM 54

Query: 166 SRAAAEKVLQSYSGSLMPNTDQPFRLNWA 194
           +RA AE+ L    G  +       +L W 
Sbjct: 55  NRADAERALDELDGKDV--MGYELKLGWG 81

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

>gnl|CDD|240759 cd12313, RRM1_RRM2_RBM5_like, RNA recognition motif 1 and 2 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 37.5 bits (88), Expect = 0.001
 Identities = 19/81 (23%), Positives = 34/81 (41%), Gaps = 11/81 (13%)

Query: 327 NATIFVGALDSDVSDEDLREPFSQFG--EILSVKI------PVGKGCGFVQFANRKDAEV 378
             T+ +  LD   ++ED+ +  S      I  V++         +G  FV+F + +DA  
Sbjct: 2   TNTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQ 61

Query: 379 ALQKLQGTA---IGKQTVRLS 396
            +  L       I  + VR+S
Sbjct: 62  WMDALNNLDPFVIDGRVVRVS 82

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|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate Hu-antigen B (HuB)

 Score = 37.4 bits (86), Expect = 0.001
 Identities = 22/62 (35%), Positives = 33/62 (53%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY 177
           I++ +L    DE+ L   F   G V NVKVIR+  T + +G+GFV   +   A   + S 
Sbjct: 6   IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 178 SG 179
           +G
Sbjct: 66  NG 67

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

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

 Score = 36.9 bits (86), Expect = 0.001
 Identities = 20/81 (24%), Positives = 38/81 (46%), Gaps = 15/81 (18%)

Query: 210 SIFVGDLAPDVTDSILQETFSS--KYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRA 267
           ++FV +L   V +  L++ FS   +   V+    ++ +  G++KGY +V F +E     A
Sbjct: 1   TVFVSNLDYSVPEDELRKLFSKCGEITDVR----LVKNYKGKSKGYAYVEFENEESVQEA 56

Query: 268 M----TEMNGVYCSSRPMRID 284
           +      + G     RPM + 
Sbjct: 57  LKLDRELIKG-----RPMFVS 72

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

 Score = 37.4 bits (86), Expect = 0.001
 Identities = 22/62 (35%), Positives = 33/62 (53%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY 177
           I++ +L    DE+ L   F   G V NVKVIR+  T + +G+GFV   +   A   + S 
Sbjct: 4   IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63

Query: 178 SG 179
           +G
Sbjct: 64  NG 65

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

>gnl|CDD|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic activator RIM4 and similar proteins

 Score = 37.4 bits (87), Expect = 0.001
 Identities = 23/86 (26%), Positives = 40/86 (46%), Gaps = 10/86 (11%)

Query: 204 EACSDLSIFVGDLAPDVTDSILQETFS---SKYPSVKGAKVIIDSNTGRTKGYGFVRFGD 260
            AC    +FV  L    +D  L+   +   SKY ++   KV+ D    R + Y FV+F +
Sbjct: 2   SAC----VFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRDW---RQRPYAFVQFTN 54

Query: 261 ENERSRAMTEMNGVYCSSRPMRIDVA 286
           +++   A+ +  G     R +R + A
Sbjct: 55  DDDAKNALAKGQGTILDGRHIRCERA 80

This subfamily corresponds to the RRM1 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. . Length = 86

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

 Score = 37.5 bits (88), Expect = 0.001
 Identities = 17/64 (26%), Positives = 34/64 (53%), Gaps = 1/64 (1%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFY-SRAAAEKVLQS 176
           +++G L   + E+ L   FS  G V +V++I+ K  G   G+ +++   S A  +K   +
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKST 61

Query: 177 YSGS 180
            +G+
Sbjct: 62  LNGT 65

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

 Score = 37.2 bits (87), Expect = 0.001
 Identities = 26/75 (34%), Positives = 37/75 (49%), Gaps = 4/75 (5%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           IFV +L   VT   L++ F  +  +V  A V  D N GR+KG+G V F    +  RA+  
Sbjct: 1   IFVRNLPFSVTWQDLKDLFR-ECGNVLRADVKTD-NDGRSKGFGTVLFESPEDAQRAIEM 58

Query: 271 MNGVYCSSRPMRIDV 285
            NG     R   ++V
Sbjct: 59  FNGYDLEGRE--LEV 71

This subfamily corresponds to the RRM3 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 72

>gnl|CDD|241217 cd12773, RRM2_HuR, RNA recognition motif 2 in vertebrate Hu-antigen R (HuR)

 Score = 37.3 bits (86), Expect = 0.001
 Identities = 21/79 (26%), Positives = 43/79 (54%), Gaps = 3/79 (3%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           ++++  L   +T   +++ FS ++  +  ++V++D  TG ++G  F+RF   +E   A+T
Sbjct: 2   NLYISGLPRTMTQKDVEDMFS-RFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAIT 60

Query: 270 EMNGVY--CSSRPMRIDVA 286
             NG     SS P+ +  A
Sbjct: 61  SFNGHKPPGSSEPITVKFA 79

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

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

 Score = 37.7 bits (87), Expect = 0.001
 Identities = 23/62 (37%), Positives = 32/62 (51%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY 177
           I+I +L    DE  L   F   G V NVKVIR+  T + +G+GFV   +   A   + S 
Sbjct: 4   IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63

Query: 178 SG 179
           +G
Sbjct: 64  NG 65

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

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

 Score = 37.4 bits (86), Expect = 0.001
 Identities = 23/81 (28%), Positives = 41/81 (50%), Gaps = 6/81 (7%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKL 383
           IF+  L  D  +  L + F  FG + +VK+         KG GFV   N ++A +A+  L
Sbjct: 4   IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63

Query: 384 QGTAIGKQTVRLSWGRNPGNK 404
            G  +G + +++S+  +  +K
Sbjct: 64  NGYRLGDKILQVSFKTSKSHK 84

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

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

 Score = 37.4 bits (87), Expect = 0.001
 Identities = 20/80 (25%), Positives = 40/80 (50%), Gaps = 10/80 (12%)

Query: 211 IFVGDLAP-DVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           +FV  + P   T+  L+E F   +  ++   ++ D NTG +KG+G+V+F   ++ + A+ 
Sbjct: 4   LFV--VIPKSYTEEDLREKFKE-FGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVALE 60

Query: 270 EMNGVYCSSRPMRIDVATPK 289
                    +  +  +A PK
Sbjct: 61  ------NCDKSFKAVLAEPK 74

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

 Score = 37.0 bits (86), Expect = 0.001
 Identities = 22/58 (37%), Positives = 31/58 (53%), Gaps = 7/58 (12%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKI------PVGKGCGFVQFANRKDAEVALQ 381
           +FV  +    ++EDLRE F +FG+I  V I         KG G+V+F     A VAL+
Sbjct: 4   LFV-VIPKSYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVALE 60

This subfamily corresponds to the RRM2 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

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

 Score = 37.8 bits (87), Expect = 0.001
 Identities = 18/53 (33%), Positives = 31/53 (58%)

Query: 127 MDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSG 179
           M +    + F   G++ + K++R+K TGQS GYGFV +     A+K + + +G
Sbjct: 15  MTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINTLNG 67

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|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 37.3 bits (86), Expect = 0.001
 Identities = 20/68 (29%), Positives = 35/68 (51%), Gaps = 6/68 (8%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVALQKL 383
           +FVG L  D S +DL++ F++FGE+    I +       +G GF+ F +    E  L++ 
Sbjct: 2   MFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQK 61

Query: 384 QGTAIGKQ 391
           +    G+ 
Sbjct: 62  EHRLDGRL 69

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|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 37.3 bits (86), Expect = 0.001
 Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 10/69 (14%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVALQ-- 381
           +F+G L  D + +DL++ FS+FGE++   + +       +G GFV F   +  +  +   
Sbjct: 1   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60

Query: 382 --KLQGTAI 388
             KL G  I
Sbjct: 61  EHKLNGKVI 69

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

 Score = 37.5 bits (87), Expect = 0.001
 Identities = 19/58 (32%), Positives = 29/58 (50%), Gaps = 6/58 (10%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILS---VKIPVG---KGCGFVQFANRKDAEVALQ 381
           +FVG L  + + E LR  FSQ+GE++    +K       +G GFV+F +       L 
Sbjct: 2   LFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLA 59

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|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins

 Score = 37.7 bits (87), Expect = 0.001
 Identities = 23/77 (29%), Positives = 37/77 (48%), Gaps = 6/77 (7%)

Query: 327 NATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVAL 380
           N  + V  L    ++ DLRE FS++G I  V I         +G  FV F N  DA+ A 
Sbjct: 9   NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 68

Query: 381 QKLQGTAIGKQTVRLSW 397
           ++  G  +  + +R+ +
Sbjct: 69  ERANGMELDGRRIRVDF 85

This subgroup corresponds to the RRM of TRA2-beta or TRA-2-beta, also termed splicing factor, arginine/serine-rich 10 (SFRS10), or transformer-2 protein homolog B, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. It contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. TRA2-beta specifically binds to two types of RNA sequences, the CAA and (GAA)2 sequences, through the RRMs in different RNA binding modes. . Length = 89

>gnl|CDD|241082 cd12638, RRM3_CELF1_2, RNA recognition motif 3 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 37.7 bits (87), Expect = 0.001
 Identities = 22/83 (26%), Positives = 39/83 (46%), Gaps = 1/83 (1%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           ++F+  L  +  D  L + F   + +V  AKV ID  T  +K +GFV + +      A+ 
Sbjct: 9   NLFIYHLPQEFGDQDLLQMFMP-FGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQ 67

Query: 270 EMNGVYCSSRPMRIDVATPKKAS 292
            MNG     + +++ +   K  S
Sbjct: 68  AMNGFQIGMKRLKVQLKRSKNDS 90

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|240851 cd12405, RRM3_NCL, RNA recognition motif 3 in vertebrate nucleolin

 Score = 37.2 bits (86), Expect = 0.001
 Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 7/73 (9%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG----KGCGFVQFANRKDAEVALQKLQ 384
            + V  L    S++ L+E F +     S++IP      KG  FV+F + +DA+ AL    
Sbjct: 3   VLVVNNLSYSASEDSLQEVFEK---ATSIRIPQNNGRPKGYAFVEFESAEDAKEALNSCN 59

Query: 385 GTAIGKQTVRLSW 397
            T I  +++RL +
Sbjct: 60  NTEIEGRSIRLEF 72

This subfamily corresponds to the RRM3 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 72

>gnl|CDD|241024 cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 37.7 bits (87), Expect = 0.001
 Identities = 19/73 (26%), Positives = 38/73 (52%), Gaps = 5/73 (6%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           IFVG +  D  +  L++ F  +Y  ++  +++ D  +G+ +G+ FV F D +   + + +
Sbjct: 3   IFVGGIKEDTEEHHLRDYFE-QYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 61

Query: 271 ----MNGVYCSSR 279
               +NG  C  R
Sbjct: 62  KYHTVNGHNCEVR 74

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|241024 cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 37.3 bits (86), Expect = 0.001
 Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 7/60 (11%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCG------FVQFANRKDAE-VALQK 382
           IFVG +  D  +  LR+ F Q+G+I  ++I   +G G      FV F +    + + +QK
Sbjct: 3   IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 62

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|240922 cd12478, RRM1_U2B, RNA recognition motif 1 in U2 small nuclear ribonucleoprotein B" (U2B") and similar proteins

 Score = 37.7 bits (87), Expect = 0.001
 Identities = 24/80 (30%), Positives = 42/80 (52%), Gaps = 7/80 (8%)

Query: 327 NATIFVGALDSDVSDEDLREP----FSQFG---EILSVKIPVGKGCGFVQFANRKDAEVA 379
           N TI++  L+  +  E+L+      FSQFG   +I+++K    +G  FV F     A  A
Sbjct: 1   NHTIYINNLNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELSSATNA 60

Query: 380 LQKLQGTAIGKQTVRLSWGR 399
           L++LQG     + +R+ + +
Sbjct: 61  LRQLQGFPFYGKPMRIQYAK 80

This subgroup corresponds to the RRM1 of U2B" (also termed U2 snRNP B") a unique protein that comprises the U2 snRNP. It was initially identified as binding to stem-loop IV (SLIV) at the 3' end of U2 snRNA. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B" does not require an auxiliary protein for binding to RNA. In addition, the nuclear transport of U2B" is independent of U2 snRNA binding. U2B" contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also contains a nuclear localization signal (NLS) in the central domain. However, nuclear import of U2B'' does not depend on this NLS. The N-terminal RRM is sufficient to direct U2B" to the nucleus. . Length = 91

>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 37.4 bits (87), Expect = 0.001
 Identities = 19/49 (38%), Positives = 29/49 (59%), Gaps = 7/49 (14%)

Query: 343 DLREPFSQFGEILSVKIP-------VGKGCGFVQFANRKDAEVALQKLQ 384
           +LRE FS FGE+ +V++P         +G GFV F  ++DA+ A + L 
Sbjct: 16  ELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAFKALC 64

This subgroup corresponds to the RRM6 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|240920 cd12476, RRM1_SNF, RNA recognition motif 1 found in Drosophila melanogaster sex determination protein SNF and similar proteins

 Score = 37.6 bits (87), Expect = 0.001
 Identities = 24/78 (30%), Positives = 42/78 (53%), Gaps = 7/78 (8%)

Query: 329 TIFVGALDSDVSDEDLREP----FSQFGEILSV---KIPVGKGCGFVQFANRKDAEVALQ 381
           TI++  L+  V  E+L++     FSQFG+IL +   K    +G  FV F +   A  AL+
Sbjct: 1   TIYINNLNEKVKKEELKKSLYAIFSQFGQILDIVALKTLKMRGQAFVVFKDISSATNALR 60

Query: 382 KLQGTAIGKQTVRLSWGR 399
            +QG     + +R+++ +
Sbjct: 61  SMQGFPFYDKPMRIAYSK 78

This subgroup corresponds to the RRM1 of SNF (Sans fille), also termed U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A), an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila. It is essential in Drosophila sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). SNF contains two RNA recognition motifs (RRMs); it can self-associate through RRM1, and each RRM can recognize poly(U) RNA binding independently. . Length = 78

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

 Score = 37.2 bits (86), Expect = 0.001
 Identities = 27/85 (31%), Positives = 37/85 (43%), Gaps = 13/85 (15%)

Query: 211 IFVGDLAPDVTDSILQETFSS----KYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSR 266
           IFV +L  D T  +L++ F+      Y  +K          G++KG G VRF       R
Sbjct: 2   IFVRNLPFDFTWKMLKDKFNECGHVLYADIK-------MENGKSKGCGVVRFESPEVAER 54

Query: 267 AMTEMNGVYCSSRPMRIDVATPKKA 291
           A   MNG   + R   IDV   + A
Sbjct: 55  ACRMMNGYKLNGR--EIDVRIDRNA 77

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

 Score = 37.3 bits (86), Expect = 0.001
 Identities = 21/59 (35%), Positives = 36/59 (61%), Gaps = 2/59 (3%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAM 268
           ++ V +L+P V++ +L++ FS   P V+ A VI+D + GR  G GFV F  +    +A+
Sbjct: 1   ALTVKNLSPVVSNELLEQAFSQFGP-VERAVVIVD-DRGRPTGKGFVEFAAKPAARKAL 57

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

>gnl|CDD|240917 cd12473, RRM2_MSSP1, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 37.4 bits (86), Expect = 0.001
 Identities = 20/65 (30%), Positives = 34/65 (52%), Gaps = 1/65 (1%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY 177
           ++I +L   MDE  L N     GQV++ +++R+  +G S G GF    S    E V+  +
Sbjct: 3   LYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVISHF 61

Query: 178 SGSLM 182
           +G  +
Sbjct: 62  NGKFI 66

This subgroup corresponds to the RRM2 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2). MSSP-1 is a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 85

>gnl|CDD|240915 cd12471, RRM1_MSSP2, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 37.4 bits (86), Expect = 0.001
 Identities = 17/41 (41%), Positives = 28/41 (68%)

Query: 140 GQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGS 180
           G++V+ K I +K T + +GYGFV+F S +AA+K + +   S
Sbjct: 26  GKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKAS 66

This subgroup corresponds to the RRM1 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 75

>gnl|CDD|240887 cd12441, RRM_Nup53_like, RNA recognition motif in nucleoporin Nup53 and similar proteins

 Score = 36.8 bits (86), Expect = 0.001
 Identities = 17/39 (43%), Positives = 24/39 (61%), Gaps = 1/39 (2%)

Query: 344 LREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQK 382
           LRE FS  G IL V+ P G     +++++R +AE AL K
Sbjct: 18  LRE-FSSCGTILEVRYPPGANWIHLKYSSRLEAERALSK 55

This subfamily corresponds to the RRM domain of nucleoporin Nup53, also termed mitotic phosphoprotein 44 (MP-44), or nuclear pore complex protein Nup53, required for normal cell growth and nuclear morphology in vertebrate. It tightly associates with the nuclear envelope membrane and the nuclear lamina where it interacts with lamin B. It may also interact with a group of nucleoporins including Nup93, Nup155, and Nup205 and play a role in the association of the mitotic checkpoint protein Mad1 with the nuclear pore complex (NPC). The family also includes Saccharomyces cerevisiae Nup53p, an ortholog of vertebrate nucleoporin Nup53. A unique property of yeast Nup53p is that it contains an additional Kap121p-binding domain and interacts specifically with the karyopherin Kap121p, which is involved in the assembly of Nup53p into NPCs. Both, vertebrate Nup35 and yeast Nup53p, contain an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a C-terminal amphipathic alpha-helix and several FG repeats. This family corresponds to the RRM domain which lacks the conserved residues that typically bind RNA in canonical RRM domains. Length = 73

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

 Score = 40.3 bits (94), Expect = 0.002
 Identities = 37/196 (18%), Positives = 67/196 (34%), Gaps = 37/196 (18%)

Query: 113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEK 172
           D    I+IG+L  ++ E  +       G +    +I++  TG S+GY F E+   +  + 
Sbjct: 293 DSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDV 352

Query: 173 VLQSYSGSLM--------------------------PNTDQPFRLNWATFSGSDRRTEA- 205
            + + +G                             P T     L+ +      + T+  
Sbjct: 353 AIAALNGKDTGDNKLHVQRACVGANQATIDTSNGMAPVTLLAKALSQSILQIGGKPTKVV 412

Query: 206 CSDLSIFVGDLAPD-----VTDSILQETFSSKYPSVKGAKV---IIDSNTGRTKGYGFVR 257
                +   DL  D     + + +  E   SKY  +    +     D N+    G  F+ 
Sbjct: 413 QLTNLVTGDDLMDDEEYEEIYEDVKTE--FSKYGPLINIVIPRPNGDRNSTPGVGKVFLE 470

Query: 258 FGDENERSRAMTEMNG 273
           + D     +AM  MNG
Sbjct: 471 YADVRSAEKAMEGMNG 486

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

 Score = 36.4 bits (85), Expect = 0.002
 Identities = 18/56 (32%), Positives = 33/56 (58%), Gaps = 1/56 (1%)

Query: 127 MDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLM 182
           +D+  L   FS  G + + KV+ +++ G+S+G+GFV F S   A K +   +G ++
Sbjct: 13  IDDERLREEFSPFGTITSAKVMTDEK-GRSKGFGFVCFSSPEEATKAVTEMNGRII 67

This subfamily corresponds to the RRM4 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in theThe CD corresponds to the RRM. regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 79

>gnl|CDD|240759 cd12313, RRM1_RRM2_RBM5_like, RNA recognition motif 1 and 2 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 36.8 bits (86), Expect = 0.002
 Identities = 17/70 (24%), Positives = 31/70 (44%), Gaps = 5/70 (7%)

Query: 216 LAPDVTDSILQETFSS-KYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGV 274
           L    T+  + +  S+     +K  ++I D  TG ++G+ FV F    +   A   M+ +
Sbjct: 10  LDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLED---ATQWMDAL 66

Query: 275 YCSSRPMRID 284
             +  P  ID
Sbjct: 67  N-NLDPFVID 75

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

 Score = 36.4 bits (85), Expect = 0.002
 Identities = 24/64 (37%), Positives = 34/64 (53%), Gaps = 10/64 (15%)

Query: 211 IFVGDLAPD-VTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           +FVG+L  D V+   L+E FS KY  + G  +         KGYGFV+F +E +   A+ 
Sbjct: 3   VFVGNLNTDKVSKEDLEEIFS-KYGKILGISL--------HKGYGFVQFDNEEDARAAVA 53

Query: 270 EMNG 273
             NG
Sbjct: 54  GENG 57

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

>gnl|CDD|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate Hu-antigen D (HuD)

 Score = 37.0 bits (85), Expect = 0.002
 Identities = 25/81 (30%), Positives = 40/81 (49%), Gaps = 6/81 (7%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKL 383
           IFV  L  D  +  L + F  FG + +VK+         KG GFV   N  +A +A+  L
Sbjct: 6   IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 384 QGTAIGKQTVRLSWGRNPGNK 404
            G  +G + +++S+  N  +K
Sbjct: 66  NGYRLGDRVLQVSFKTNKTHK 86

This subgroup corresponds to the RRM3 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells. And it also regulates the neurite elongation and morphological differentiation. HuD specifically bound poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 86

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

 Score = 36.9 bits (86), Expect = 0.002
 Identities = 14/71 (19%), Positives = 32/71 (45%), Gaps = 5/71 (7%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKI-----PVGKGCGFVQFANRKDAEVALQKLQ 384
           +++  L   + ++DL      +G+++S +I        +G GF +  +R+  E  + K  
Sbjct: 3   LYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKGQSRGVGFARMESREKCEDIISKFN 62

Query: 385 GTAIGKQTVRL 395
           G  +  +   L
Sbjct: 63  GKYLKGEGEPL 73

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

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

 Score = 36.6 bits (84), Expect = 0.002
 Identities = 22/80 (27%), Positives = 40/80 (50%), Gaps = 6/80 (7%)

Query: 326 NNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK------GCGFVQFANRKDAEVA 379
           +   + V  L  +++ E+ +  F   GEI S K+   K      G GFV + +  DA+ A
Sbjct: 2   SKTNLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKA 61

Query: 380 LQKLQGTAIGKQTVRLSWGR 399
           +  L G  +  +T+++S+ R
Sbjct: 62  INTLNGLKLQTKTIKVSYAR 81

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

>gnl|CDD|240939 cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 36.5 bits (84), Expect = 0.002
 Identities = 19/70 (27%), Positives = 37/70 (52%), Gaps = 2/70 (2%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIG 389
           +FV  L + V++E L + F QFG++  VK    K   F+ F  R  A  A++++ G  + 
Sbjct: 4   LFVRNLANTVTEEILEKAFGQFGKLERVKKL--KDYAFIHFDERDGAVKAMEEMNGKELE 61

Query: 390 KQTVRLSWGR 399
            + + + + +
Sbjct: 62  GENIEIVFAK 71

This subgroup corresponds to the RRM3 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP that is a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. . Length = 72

>gnl|CDD|241060 cd12616, RRM1_TIAR, RNA recognition motif 1 in nucleolysin TIAR and similar proteins

 Score = 37.0 bits (85), Expect = 0.002
 Identities = 22/78 (28%), Positives = 43/78 (55%), Gaps = 3/78 (3%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           +++VG+L+ DVT+ ++ + FS   P  K  K+I +  +     Y FV F +  + + A+ 
Sbjct: 1   TLYVGNLSRDVTEVLILQLFSQIGP-CKSCKMITEHTS--NDPYCFVEFYEHRDAAAALA 57

Query: 270 EMNGVYCSSRPMRIDVAT 287
            MNG     + ++++ AT
Sbjct: 58  AMNGRKILGKEVKVNWAT 75

This subgroup corresponds to the RRM1 of nucleolysin TIAR, also termed TIA-1-related protein, and a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 81

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

 Score = 37.0 bits (86), Expect = 0.002
 Identities = 17/51 (33%), Positives = 28/51 (54%), Gaps = 1/51 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDE 261
           +FVG+L  D+T+  L+E F  ++ +V   ++      GR   +GFV F D 
Sbjct: 6   LFVGNLPHDITEDELKEFF-KEFGNVLEVRINSKGGGGRLPNFGFVVFDDP 55

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

 Score = 36.8 bits (86), Expect = 0.002
 Identities = 17/55 (30%), Positives = 31/55 (56%), Gaps = 1/55 (1%)

Query: 128 DETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLM 182
            E  L   F   G+V +VKV+R +  G+S  +GFV F S   A++ ++ ++ + +
Sbjct: 13  TEDRLREHFESKGEVTDVKVMRTRD-GKSRRFGFVGFKSEEDAQQAVKYFNKTFI 66

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

 Score = 36.5 bits (84), Expect = 0.002
 Identities = 19/51 (37%), Positives = 30/51 (58%), Gaps = 1/51 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDE 261
           +F+G L+   T   L+E F  ++  VK   V+ D  T R++G+GFV F D+
Sbjct: 3   MFIGGLSWQTTQEGLREYFG-QFGEVKECLVMRDPLTKRSRGFGFVTFMDQ 52

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|241059 cd12615, RRM1_TIA1, RNA recognition motif 1 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 36.9 bits (85), Expect = 0.002
 Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 4/74 (5%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCG----FVQFANRKDAEVALQKLQ 384
           T++VG L  DV++  + + FSQ G   S K+ +         FV+F   + A  +L  + 
Sbjct: 1   TLYVGNLSRDVTEALILQLFSQIGPCKSCKMIMDTAGNDPYCFVEFFEHRHAAASLAAMN 60

Query: 385 GTAIGKQTVRLSWG 398
           G  I  + V+++W 
Sbjct: 61  GRKIMGKEVKVNWA 74

This subgroup corresponds to the RRM1 of TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1) and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and functions as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 74

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

 Score = 37.0 bits (86), Expect = 0.002
 Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 1/63 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +F+ +LA   T+  L++ FS KY  +    + ID  T + KG+ FV +       +A  E
Sbjct: 5   LFIRNLAYTCTEEDLEKLFS-KYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAE 63

Query: 271 MNG 273
           ++G
Sbjct: 64  LDG 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|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 37.0 bits (85), Expect = 0.002
 Identities = 25/83 (30%), Positives = 43/83 (51%), Gaps = 11/83 (13%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +F+G L+ + T+  L+  +  ++  +    V+ D  + R++G+GFV F   NE   AM  
Sbjct: 5   LFIGGLSFETTEESLR-NYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAM-- 61

Query: 271 MNGVYCSSRPMRID--VATPKKA 291
                 ++RP  ID  V  PK+A
Sbjct: 62  ------AARPHTIDGRVVEPKRA 78

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|240855 cd12409, RRM1_RRT5, RNA recognition motif 1 in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins

 Score = 37.0 bits (86), Expect = 0.002
 Identities = 18/79 (22%), Positives = 33/79 (41%), Gaps = 13/79 (16%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK------------GCGFVQFANRKDA 376
            +++  L    S+EDL E    F E +SV IP               G  + +F++ + A
Sbjct: 1   RVYISNLSYSSSEEDLEEFLKDF-EPVSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQA 59

Query: 377 EVALQKLQGTAIGKQTVRL 395
           E  ++ L G     + + +
Sbjct: 60  EKVVKDLNGKVFKNRKLFV 78

This subfamily corresponds to the RRM1 of the lineage specific family containing a group of uncharacterized yeast regulators of rDNA transcription protein 5 (RRT5), which may play roles in the modulation of rDNA transcription. RRT5 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 84

>gnl|CDD|240866 cd12420, RRM_RBPMS_like, RNA recognition motif in RNA-binding protein with multiple splicing (RBP-MS)-like proteins

 Score = 36.9 bits (86), Expect = 0.002
 Identities = 24/77 (31%), Positives = 32/77 (41%), Gaps = 10/77 (12%)

Query: 329 TIFVGALDSDVSDEDLREPFSQF----GEILSVKIPVGKGC---GFVQFANRKDAEVALQ 381
           T+FV  L SDV + +L   F  F       L  K   G      GFV F++ + A  A+ 
Sbjct: 2   TLFVSGLPSDVKERELAHLFRPFPGYEASRLVFKEKKGGEKQPVGFVDFSSAQCAAAAMD 61

Query: 382 KLQG---TAIGKQTVRL 395
            LQG          +RL
Sbjct: 62  ALQGYRFDPDTSSVLRL 78

This subfamily corresponds to the RRM of RNA-binding proteins with multiple splicing (RBP-MS)-like proteins, including protein products of RBPMS genes (RBP-MS and its paralogue RBP-MS2), the Drosophila couch potato (cpo), and Caenorhabditis elegans Mec-8 genes. RBP-MS may be involved in regulation of mRNA translation and localization during Xenopus laevis development. It has also been shown to physically interact with Smad2, Smad3 and Smad4, and stimulates Smad-mediated transactivation. Cpo may play an important role in regulating normal function of the nervous system, whereas mutations in Mec-8 affect mechanosensory and chemosensory neuronal function. All members contain a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Some uncharacterized family members contain two RRMs; this subfamily includes their RRM1. Their RRM2 shows high sequence homology to the RRM of yeast proteins scw1, Whi3, and Whi4. Length = 79

>gnl|CDD|241004 cd12560, RRM_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor 12 (SRSF12) and similar proteins

 Score = 37.3 bits (86), Expect = 0.002
 Identities = 20/61 (32%), Positives = 33/61 (54%), Gaps = 6/61 (9%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQK 382
           ++FV  +      EDLR  F ++G I+ V +P+       +G  ++QF + +DAE AL  
Sbjct: 2   SLFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYN 61

Query: 383 L 383
           L
Sbjct: 62  L 62

This subgroup corresponds to the RRM of SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19). SRSF12 is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. SRSF12 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|240684 cd12238, RRM1_RBM40_like, RNA recognition motif 1 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 36.8 bits (86), Expect = 0.002
 Identities = 20/72 (27%), Positives = 32/72 (44%), Gaps = 7/72 (9%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKG----CGFVQFANRKDAEVALQKLQ 384
           T+ V  L  ++S++D  +    FG   SV++   +G      F  F N + A  AL +L 
Sbjct: 1   TLLVRHLPPELSEDDKEDLLKHFG-ASSVRVMSRRGKLKNTAFATFDNEQAASQALSRLH 59

Query: 385 GTAIGKQTVRLS 396
              I  +  RL 
Sbjct: 60  QLKILGK--RLV 69

This subfamily corresponds to the RRM1 of RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein), It serves as a bridging factor between the U11 and U12 snRNPs. It contains two repeats of RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. . Length = 73

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

 Score = 36.6 bits (85), Expect = 0.002
 Identities = 16/56 (28%), Positives = 27/56 (48%), Gaps = 2/56 (3%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQG 385
           ++V     D S+  +RE FS +G +  VK+       FV+F + + A  A   + G
Sbjct: 2   LYVRPFPPDTSESAIREIFSPYGAVKEVKMI--SNFAFVEFESLESAIRAKDSVHG 55

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

>gnl|CDD|241123 cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), and similar proteins

 Score = 37.0 bits (85), Expect = 0.002
 Identities = 19/59 (32%), Positives = 29/59 (49%)

Query: 116 KTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVL 174
           + +W+  L      T L N FS  G+VV  KV+ N ++  +  YGFV   +   A K +
Sbjct: 2   RNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCI 60

This subgroup corresponds to RRM of SAFB1, also termed scaffold attachment factor B (SAF-B), heat-shock protein 27 estrogen response element ERE and TATA-box-binding protein (HET), or heterogeneous nuclear ribonucleoprotein hnRNP A1- associated protein (HAP), a large multi-domain protein with well-described functions in transcriptional repression, RNA splicing and metabolism, and a proposed role in chromatin organization. Based on the numerous functions, SAFB1 has been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. SAFB1 specifically binds to AT-rich scaffold or matrix attachment region DNA elements (S/MAR DNA) by using its N-terminal scaffold attachment factor-box (SAF-box, also known as SAP domain), a homeodomain-like DNA binding motif. The central region of SAFB1 is composed of an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a nuclear localization signal (NLS). The C-terminus of SAFB1 contains Glu/Arg- and Gly-rich regions that might be involved in protein-protein interaction. Additional studies indicate that the C-terminal region contains a potent and transferable transcriptional repression domain. Another family member is SAFB2, a homolog of SAFB1. Both SAFB1 and SAFB2 are ubiquitously coexpressed and share very high sequence similarity, suggesting that they might function in a similar manner. However, unlike SAFB1, exclusively existing in the nucleus, SAFB2 is also present in the cytoplasm. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1. Length = 76

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

 Score = 36.8 bits (86), Expect = 0.002
 Identities = 22/72 (30%), Positives = 34/72 (47%), Gaps = 9/72 (12%)

Query: 210 SIFVGDLAPDVTD-------SILQETFSSKYPSVKGAKVII-DSNTGRTKGYGFVRFGDE 261
           ++ V D  P V +        +L++ FS K+   K   + +    TG+TKGY FV F   
Sbjct: 2   NVVVVDGLPVVGEEKLEKLKKVLRKIFS-KFGVGKIVGIYMPVDETGKTKGYAFVEFATP 60

Query: 262 NERSRAMTEMNG 273
            E   A+  +NG
Sbjct: 61  EEAKEAVKALNG 72

This subfamily corresponds to the RRM domain in eukaryotic translation initiation factor 3 (eIF-3), a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3B, also termed eIF-3 subunit 9, or Prt1 homolog, eIF-3-eta, eIF-3 p110, or eIF-3 p116, is the major scaffolding subunit of eIF-3. It interacts with eIF-3 subunits A, G, I, and J. eIF-3B contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is involved in the interaction with eIF-3J. The interaction between eIF-3B and eIF-3J is crucial for the eIF-3 recruitment to the 40 S ribosomal subunit. eIF-3B also binds directly to domain III of the internal ribosome-entry site (IRES) element of hepatitis-C virus (HCV) RNA through its N-terminal RRM, which may play a critical role in both cap-dependent and cap-independent translation. Additional research has shown that eIF-3B may function as an oncogene in glioma cells and can be served as a potential therapeutic target for anti-glioma therapy. This family also includes the yeast homolog of eIF-3 subunit B (eIF-3B, also termed PRT1 or eIF-3 p90) that interacts with the yeast homologs of eIF-3 subunits A(TIF32), G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In yeast, eIF-3B (PRT1) contains an N-terminal RRM that is directly involved in the interaction with eIF-3A (TIF32) and eIF-3J (HCR1). In contrast to its human homolog, yeast eIF-3B (PRT1) may have potential to bind its total RNA through its RRM domain. . Length = 84

>gnl|CDD|240868 cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition motif in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins

 Score = 36.8 bits (86), Expect = 0.002
 Identities = 14/43 (32%), Positives = 20/43 (46%), Gaps = 2/43 (4%)

Query: 348 FSQFGEILSVKI-PVGKG-CGFVQFANRKDAEVALQKLQGTAI 388
           FS +G +  + I     G    VQF + + AE A + L G  I
Sbjct: 22  FSPYGAVEKILIFEKNTGVQALVQFDSVESAENAKKALNGRNI 64

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

>gnl|CDD|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 4 (SRSF4)

 Score = 36.5 bits (84), Expect = 0.002
 Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 2/72 (2%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIG 389
           +++G L     + D+   F  +G+IL V +    G GFV+F + +DA+ A+ +L G  + 
Sbjct: 2   VYIGRLSYQARERDVERFFKGYGKILEVDLK--NGYGFVEFDDLRDADDAVYELNGKDLC 59

Query: 390 KQTVRLSWGRNP 401
            + V +   R P
Sbjct: 60  GERVIVEHARGP 71

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

 Score = 36.5 bits (84), Expect = 0.002
 Identities = 18/52 (34%), Positives = 30/52 (57%), Gaps = 1/52 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDEN 262
           IFVG L+ + T   +++ F  ++  V  A ++ D  T R +G+GFV F  E+
Sbjct: 2   IFVGGLSVNTTVEDVKQYFE-QFGKVDDAMLMFDKTTNRHRGFGFVTFESED 52

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|240738 cd12292, RRM2_La_like, RNA recognition motif 2 in La autoantigen (La or SS-B or LARP3), La-related protein 7 (LARP7 or PIP7S) and similar proteins

 Score = 36.1 bits (84), Expect = 0.002
 Identities = 14/45 (31%), Positives = 24/45 (53%)

Query: 336 DSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVAL 380
              V+ ED++  F+QFGE+  V    G   G+++F   + A+ A 
Sbjct: 10  GPGVTREDIKAVFAQFGEVKYVDFTEGADTGYIRFKTPEAAQKAR 54

This subfamily corresponds to the RRM2 of La and LARP7. La is 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. LARP7 is an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. It is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP), 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. LARP7 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. Both La and LARP7 contain an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 75

>gnl|CDD|240788 cd12342, RRM_Nab3p, RNA recognition motif in yeast nuclear polyadenylated RNA-binding protein 3 (Nab3p) and similar proteins

 Score = 36.3 bits (84), Expect = 0.002
 Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 3/67 (4%)

Query: 330 IFVGALDSD-VSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAI 388
           +F+G L +  VS EDL   FS +GE+  + +      GFVQF + +    A+   QG  I
Sbjct: 2   LFIGNLPTKRVSKEDLFRIFSTYGELAQIVLK--NAYGFVQFDSPESCANAINCEQGKMI 59

Query: 389 GKQTVRL 395
             + + L
Sbjct: 60  RGRKLHL 66

This subfamily corresponds to the RRM of Nab3p, an acidic nuclear polyadenylated RNA-binding protein encoded by Saccharomyces cerevisiae NAB3 gene that is essential for cell viability. Nab3p is predominantly localized within the nucleoplasm and essential for growth in yeast. It may play an important role in packaging pre-mRNAs into ribonucleoprotein structures amenable to efficient nuclear RNA processing. Nab3p contains an N-terminal aspartic/glutamic acid-rich region, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal region rich in glutamine and proline residues. . Length = 71

>gnl|CDD|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins

 Score = 35.7 bits (83), Expect = 0.003
 Identities = 19/68 (27%), Positives = 33/68 (48%), Gaps = 6/68 (8%)

Query: 117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQS 176
           T+++G L   + E  L + F   G++ ++ V+  +Q        FV F +R AAEK  + 
Sbjct: 3   TLYVGGLGERVTEKDLRDHFYQFGEIRSITVVPRQQ------CAFVTFTTREAAEKAAER 56

Query: 177 YSGSLMPN 184
               L+ N
Sbjct: 57  LFNKLIIN 64

This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines. Length = 74

>gnl|CDD|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 = 0.003
 Identities = 25/74 (33%), Positives = 43/74 (58%), Gaps = 8/74 (10%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQK 382
           T+++G L  D++++D+RE F    EI SV++         KG G V FA+ +  + AL K
Sbjct: 1   TVYIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLDAAL-K 58

Query: 383 LQGTAIGKQTVRLS 396
           L GT +  + +R++
Sbjct: 59  LDGTVLCGRPIRIA 72

The CD corresponds to the RRM2 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

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

 Score = 37.2 bits (86), Expect = 0.003
 Identities = 20/70 (28%), Positives = 30/70 (42%), Gaps = 8/70 (11%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK------GCGFVQFANRKDAEVALQK 382
           T+FV  L  D ++E L   FS+FG +      + K      G GFV F ++      L+ 
Sbjct: 3   TLFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACLK- 61

Query: 383 LQGTAIGKQT 392
               A G  +
Sbjct: 62  -NAPAAGSTS 70

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|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end) protein family

 Score = 36.0 bits (84), Expect = 0.003
 Identities = 17/78 (21%), Positives = 35/78 (44%), Gaps = 9/78 (11%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           ++VG L P  + + L+  F  ++ +++     ID + GR   Y ++ +        A   
Sbjct: 1   LWVGGLGPWTSLAELEREF-DRFGAIRR----IDYDPGRN--YAYIEYESIEAAQAAKEA 53

Query: 271 MNG--VYCSSRPMRIDVA 286
           + G  +    R +R+D A
Sbjct: 54  LRGFPLGGPGRRLRVDFA 71

This subfamily corresponds to the RRM3 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B) and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and is a novel component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 72

>gnl|CDD|240677 cd12231, RRM2_U2AF65, RNA recognition motif 2 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 36.1 bits (84), Expect = 0.003
 Identities = 18/66 (27%), Positives = 34/66 (51%), Gaps = 6/66 (9%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILS---VK-IPVG--KGCGFVQFANRKDAEVALQKL 383
           IF+G L + +S++ ++E    FG++ +   VK    G  KG  F ++ +    + A+  L
Sbjct: 3   IFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAGL 62

Query: 384 QGTAIG 389
            G  +G
Sbjct: 63  NGMQLG 68

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

 Score = 36.1 bits (83), Expect = 0.003
 Identities = 18/58 (31%), Positives = 31/58 (53%), Gaps = 1/58 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAM 268
           +F+G L+ D +   L E + S++  V    +  D  TGR++G+GFV F D     + +
Sbjct: 2   MFIGGLSWDTSKKDLTE-YLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVL 58

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

 Score = 36.6 bits (84), Expect = 0.003
 Identities = 16/52 (30%), Positives = 30/52 (57%), Gaps = 1/52 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDEN 262
           +FVG +  D  +  L++ F  +Y  +   ++I D  +G+ +G+GFV F D +
Sbjct: 3   LFVGGIKEDTEEHHLRDYFE-EYGKIDTIEIITDRQSGKKRGFGFVTFDDHD 53

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

 Score = 36.1 bits (83), Expect = 0.003
 Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 4/75 (5%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPV----GKGCGFVQFANRKDAEVALQKLQG 385
           IFV  L  D + + L++ F++ G +L   I +     KGCG V+F + + AE A + + G
Sbjct: 2   IFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVRFESPEVAERACRMMNG 61

Query: 386 TAIGKQTVRLSWGRN 400
             +  + + +   RN
Sbjct: 62  YKLNGREIDVRIDRN 76

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

 Score = 36.2 bits (84), Expect = 0.003
 Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 6/64 (9%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKL 383
           +F+  L    ++EDL + FS++G +  V +P+       KG  FV +   + A  A  +L
Sbjct: 5   LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAEL 64

Query: 384 QGTA 387
            GT 
Sbjct: 65  DGTV 68

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|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 = 36.0 bits (84), Expect = 0.003
 Identities = 18/68 (26%), Positives = 33/68 (48%), Gaps = 7/68 (10%)

Query: 335 LDSDVSDEDLREPFSQFG-EILSVKI---PVGK--GCGFVQFANRKDAEVALQKLQGTAI 388
           L    ++ED+R+ FS        + I     G+  G  +V+FA+ +DA  AL+K     +
Sbjct: 7   LPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRALRKHNNK-M 65

Query: 389 GKQTVRLS 396
           G + + + 
Sbjct: 66  GGRYIEVF 73

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|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 36.5 bits (84), Expect = 0.003
 Identities = 20/73 (27%), Positives = 38/73 (52%), Gaps = 5/73 (6%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           IFVG +  D  +  L++ F  KY  ++  +V+ D  +G+ +G+ FV F D +   + + +
Sbjct: 3   IFVGGIKEDTEEYHLRDYFE-KYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVVQ 61

Query: 271 ----MNGVYCSSR 279
               +NG  C  +
Sbjct: 62  KYHTINGHNCEVK 74

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|240964 cd12520, RRM1_MRN1, RNA recognition motif 1 of RNA-binding protein MRN1 and similar proteins

 Score = 36.3 bits (84), Expect = 0.003
 Identities = 18/77 (23%), Positives = 36/77 (46%), Gaps = 7/77 (9%)

Query: 327 NATIFVGALDSDVSDEDLREPFSQ--FGEILSVKIPVGKGCGFVQFANRKDAEVALQK-- 382
           + T+++G L  + + ++L    S    G I +V+I   K C F+ F +   A        
Sbjct: 1   SRTVYLGNLPPNTTVKEL---LSHVRSGPIENVRILPEKNCAFISFLDPSAATAFHSDAI 57

Query: 383 LQGTAIGKQTVRLSWGR 399
           L+  +I    +++ WG+
Sbjct: 58  LKRLSIKGVELKIGWGK 74

This subgroup corresponds to the RRM1 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa,which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 74

>gnl|CDD|240870 cd12424, RRM3_hnRNPL_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and similar proteins

 Score = 36.0 bits (84), Expect = 0.003
 Identities = 20/69 (28%), Positives = 33/69 (47%), Gaps = 2/69 (2%)

Query: 330 IFVGALDSDVSDED-LREPFSQFGEILSVKIPVGK-GCGFVQFANRKDAEVALQKLQGTA 387
           + V  LD D  + D L   F  +G +L +K    K G   VQ  + + AE A++ L G  
Sbjct: 2   LMVYGLDKDKMNCDKLFNLFCLYGNVLRIKFLKSKPGTAMVQMGDPQAAERAIEYLNGVV 61

Query: 388 IGKQTVRLS 396
           +  Q + ++
Sbjct: 62  LFGQKLEVN 70

This subfamily corresponds to the RRM3 of heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), and similar proteins. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. It is closely related in domain structure and sequence to hnRNP-L, which contains three RNA-recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. Like PTB, PTBPH3 contains four RRMs. Length = 71

>gnl|CDD|241199 cd12755, RRM2_RBM5, RNA recognition motif 2 in vertebrate RNA-binding protein 5 (RBM5)

 Score = 36.5 bits (84), Expect = 0.003
 Identities = 14/34 (41%), Positives = 24/34 (70%)

Query: 142 VVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQ 175
           V N+++I++KQT Q+ G+ FV+  S   A ++LQ
Sbjct: 31  VNNIRLIKDKQTQQNRGFAFVQLSSALEASQLLQ 64

This subgroup corresponds to the RRM2 of RBM5, also termed protein G15, or putative tumor suppressor LUCA15, or renal carcinoma antigen NY-REN-9, a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM5 shows high sequence similarity to RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). Both, RBM5 and RBM6, specifically bind poly(G) RNA. They contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain. . Length = 86

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

 Score = 36.2 bits (83), Expect = 0.003
 Identities = 24/78 (30%), Positives = 44/78 (56%), Gaps = 4/78 (5%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           ++ V +L+P V++ +L+E F S++  V+ A VI+D + GR+ G G V F  +    +A  
Sbjct: 1   ALSVRNLSPYVSNELLEEAF-SQFGPVERAVVIVD-DRGRSTGKGIVEFASKPAARKAFE 58

Query: 270 E-MNGVY-CSSRPMRIDV 285
               GV+  ++ P  + V
Sbjct: 59  RCTEGVFLLTTTPRPVIV 76

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

>gnl|CDD|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding protein Musashi homolog 2 (Musashi-2 ) and similar proteins

 Score = 36.2 bits (83), Expect = 0.003
 Identities = 23/71 (32%), Positives = 34/71 (47%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY 177
           ++IG L        L + FS  G++    V+R+  T +S G+GFV F   A+ +KVL   
Sbjct: 2   MFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLAQP 61

Query: 178 SGSLMPNTDQP 188
              L   T  P
Sbjct: 62  HHELDSKTIDP 72

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|241208 cd12764, RRM2_SRSF4, RNA recognition motif 2 in vertebrate serine/arginine-rich splicing factor 4 (SRSF4)

 Score = 35.8 bits (82), Expect = 0.003
 Identities = 22/67 (32%), Positives = 35/67 (52%), Gaps = 1/67 (1%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-KGCGFVQFANRKDAEVALQKLQGTAI 388
           + V  L S  S +DL++   Q GE+       G K  G ++F +  D + AL+KL GT +
Sbjct: 3   LIVENLSSRCSWQDLKDYMRQAGEVTYADAHKGRKNEGVIEFRSYSDMKRALEKLDGTEV 62

Query: 389 GKQTVRL 395
             + +RL
Sbjct: 63  NGRKIRL 69

This subgroup corresponds to the RRM2 of SRSF4, also termed pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing factor, arginine/serine-rich 4 (SFRS4), 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. SFRS4 also induces production of HIV-1 vpr mRNA through the inhibition of the 5'-splice site of exon 3. In addition, SRSF4 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 RS domains rich in serine-arginine dipeptides. . Length = 72

>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 = 35.7 bits (83), Expect = 0.004
 Identities = 14/45 (31%), Positives = 22/45 (48%)

Query: 136 FSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGS 180
           F   G++  V +  +K+T +S+G+ FV F     A K      GS
Sbjct: 20  FEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSELDGS 64

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|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 35.6 bits (82), Expect = 0.004
 Identities = 20/73 (27%), Positives = 38/73 (52%), Gaps = 7/73 (9%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +FVG+L PD+T+  +++ F  KY   K  ++ I  +    KG+GF+R         A  E
Sbjct: 4   LFVGNLPPDITEEEMRKLF-EKYG--KAGEIFIHKD----KGFGFIRLETRTLAEIAKAE 56

Query: 271 MNGVYCSSRPMRI 283
           ++ +    + +R+
Sbjct: 57  LDNMPLRGKQLRV 69

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|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering time control protein FCA and similar proteins

 Score = 35.7 bits (82), Expect = 0.004
 Identities = 18/78 (23%), Positives = 42/78 (53%), Gaps = 1/78 (1%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY 177
           +++G +   + E  +   F   G V+ V +I++K+TG  +G  FV++ +R  A++ +++ 
Sbjct: 2   LFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRAL 61

Query: 178 SGSL-MPNTDQPFRLNWA 194
                +P    P ++ +A
Sbjct: 62  HNQRTLPGGASPVQVRYA 79

This subgroup corresponds to the RRM1 of FCA, a gene controlling flowering time in Arabidopsis, encoding a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain. . Length = 80

>gnl|CDD|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 35.7 bits (82), Expect = 0.004
 Identities = 15/44 (34%), Positives = 27/44 (61%)

Query: 132 LHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQ 175
           L + F+  G+V +  +  +  TG+S G+GF+ F   ++ EKVL+
Sbjct: 16  LKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLE 59

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|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 = 36.0 bits (83), Expect = 0.004
 Identities = 17/48 (35%), Positives = 29/48 (60%)

Query: 132 LHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSG 179
           L   F   G V++ KV  ++ T QS+ +GFV F + A+A+  +Q+ +G
Sbjct: 21  LMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNG 68

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

>gnl|CDD|240818 cd12372, RRM_CFIm68_CFIm59, RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6), pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7), and similar proteins

 Score = 35.7 bits (83), Expect = 0.004
 Identities = 21/83 (25%), Positives = 35/83 (42%), Gaps = 16/83 (19%)

Query: 330 IFVGALDSDVSDEDLREPFSQFG--EILSVKI----PVG--KGCGFVQFANRKDAEVALQ 381
           ++VG L    +DEDL    ++ G  ++ S+K       G  KG  +V+FA+   A    +
Sbjct: 1   LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKE 60

Query: 382 KLQGTAIGKQTVRLSWGRNPGNK 404
           KL+G            G+     
Sbjct: 61  KLEGREFN--------GKKCVVT 75

This subfamily corresponds to the RRM of cleavage factor Im (CFIm) subunits. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. Two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. Structurally related CFIm68 and CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59), are functionally redundant. Both contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. Their N-terminal RRM mediates the interaction with CFIm25, and also serves to enhance RNA binding and facilitate RNA looping. . Length = 76

>gnl|CDD|240915 cd12471, RRM1_MSSP2, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 35.5 bits (81), Expect = 0.004
 Identities = 26/92 (28%), Positives = 39/92 (42%), Gaps = 19/92 (20%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           ++++  L P  TD  L +     Y  +   K I+D  T + KGYGFV F   +   +A+T
Sbjct: 3   NLYIRGLHPGTTDQDLVK-LCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 61

Query: 270 EMNGVYCSSRPMRIDVATPKKASGYQQQYSSQ 301
            +                  KASG Q Q + Q
Sbjct: 62  AL------------------KASGVQAQMAKQ 75

This subgroup corresponds to the RRM1 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 75

>gnl|CDD|240737 cd12291, RRM1_La, RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins

 Score = 35.6 bits (83), Expect = 0.004
 Identities = 17/59 (28%), Positives = 34/59 (57%), Gaps = 5/59 (8%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-----KGCGFVQFANRKDAEVALQK 382
           T++V     D + +D++E F +FG++ ++++        KG  FV+F   +DA+  L+K
Sbjct: 1   TVYVKGFPKDATLDDIQEFFEKFGKVNNIRMRRDLDKKFKGSVFVEFKTEEDAKKFLEK 59

This subfamily corresponds to the RRM1 of La autoantigen, also termed Lupus La protein, or La ribonucleoprotein, or Sjoegren syndrome type B antigen (SS-B), a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. La contains an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also possesses a short basic motif (SBM) and a nuclear localization signal (NLS) at the C-terminus. . Length = 72

>gnl|CDD|241017 cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA-binding protein Musashi homolog 2 (Musashi-2) and similar proteins

 Score = 35.8 bits (82), Expect = 0.004
 Identities = 17/52 (32%), Positives = 31/52 (59%), Gaps = 1/52 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDEN 262
           IFVG L+ +     +++ F  ++  V+ A ++ D  T R +G+GFV F +E+
Sbjct: 6   IFVGGLSANTVVEDVKQYFE-QFGKVEDAMLMFDKTTNRHRGFGFVTFENED 56

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|241006 cd12562, RRM2_RBM5_like, RNA recognition motif 2 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 36.0 bits (83), Expect = 0.004
 Identities = 13/32 (40%), Positives = 23/32 (71%)

Query: 144 NVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQ 175
           N+++I++KQT Q+ G+ FV+  S   A ++LQ
Sbjct: 33  NIRLIKDKQTQQNRGFAFVQLSSALEASQLLQ 64

This subgroup corresponds to the RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37), RNA-binding protein 10 (RBM10 or S1-1) and similar proteins. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. Both, RBM5 and RBM10, contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. . Length = 86

>gnl|CDD|240802 cd12356, RRM_PPARGC1B, RNA recognition motif in peroxisome proliferator-activated receptor gamma coactivator 1-beta (PGC-1-beta) and similar proteins

 Score = 36.0 bits (83), Expect = 0.004
 Identities = 22/75 (29%), Positives = 41/75 (54%), Gaps = 8/75 (10%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPV---GKGCGFVQFANRKDAEVALQKLQGT 386
           I++  L S +S  +L++ F  FGEI   K+ +   G+  GF+ + + + A ++L K  G 
Sbjct: 5   IYIRNLSSSMSSTELKKRFEVFGEIEECKVLIKSRGEKYGFITYRHSEHAALSLGK--GA 62

Query: 387 AIGKQTVR---LSWG 398
           ++ K+      LS+G
Sbjct: 63  SLRKRNEPSFQLSYG 77

This subfamily corresponds to the RRM of PGC-1beta, also termed PPAR-gamma coactivator 1-beta, or PPARGC-1-beta, or PGC-1-related estrogen receptor alpha coactivator, which is one of the members of PGC-1 transcriptional coactivators family, including PGC-1alpha and PGC-1-related coactivator (PRC). PGC-1beta plays a nonredundant role in controlling mitochondrial oxidative energy metabolism and affects both, insulin sensitivity and mitochondrial biogenesis, and functions in a number of oxidative tissues. It is involved in maintaining baseline mitochondrial function and cardiac contractile function following pressure overload hypertrophy by preserving glucose metabolism and preventing oxidative stress. PGC-1beta induces hypertriglyceridemia in response to dietary fats through activating hepatic lipogenesis and lipoprotein secretion. It can stimulate apolipoprotein C3 (APOC3) expression, further mediating hypolipidemic effect of nicotinic acid. PGC-1beta also drives nuclear respiratory factor 1 (NRF-1) target gene expression and NRF-1 and estrogen related receptor alpha (ERRalpha)-dependent mitochondrial biogenesis. The modulation of the expression of PGC-1beta can trigger ERRalpha-induced adipogenesis. PGC-1beta is also a potent regulator inducing angiogenesis in skeletal muscle. The transcriptional activity of PGC-1beta can be increased through binding to host cell factor (HCF), a cellular protein involved in herpes simplex virus (HSV) infection and cell cycle regulation. PGC-1beta is a multi-domain protein containing an N-terminal activation domain, an LXXLL coactivator signature, a tetrapeptide motif (DHDY) responsible for HCF binding, two glutamic/aspartic acid-rich acidic domains, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In contrast to PGC-1alpha, PGC-1beta lacks most of the arginine/serine (SR)-rich domain that is responsible for the regulation of RNA processing. . Length = 79

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	449
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	100.0
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	100.0
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	100.0
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	100.0
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	100.0
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	100.0
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	100.0
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	100.0
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	100.0
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	100.0
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	100.0
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	100.0
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	100.0
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	100.0
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	100.0
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	100.0
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.97
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.97
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.97
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.97
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.96
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.96
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.96
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.96
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.96
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.95
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.95
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.94
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.94
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.94
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.93
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.93
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.93
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.93
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.91
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.91
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.91
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.9
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.9
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.9
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.89
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.86
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.86
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.86
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.85
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.84
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.82
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.82
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.8
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.8
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	99.79
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.77
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.75
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.75
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.72
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.72
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.68
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.68
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.68
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.67
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.63
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.63
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.62
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.61
KOG0122	270	consensus Translation initiation factor 3, subunit	99.6
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.59
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.58
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.56
KOG0122	270	consensus Translation initiation factor 3, subunit	99.53
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.53
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.53
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.52
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.5
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.48
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.47
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.46
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.46
PLN03120	260	nucleic acid binding protein; Provisional	99.46
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.45
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.43
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.42
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.42
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.41
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.41
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	99.4
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.4
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.4
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	99.39
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.39
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	99.39
PLN03120	260	nucleic acid binding protein; Provisional	99.37
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.37
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.36
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.36
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.35
PLN03213	759	repressor of silencing 3; Provisional	99.34
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.34
smart00362	72	RRM_2 RNA recognition motif.	99.33
PLN03121	243	nucleic acid binding protein; Provisional	99.32
PLN03213	759	repressor of silencing 3; Provisional	99.29
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.29
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.28
PLN03121	243	nucleic acid binding protein; Provisional	99.27
smart00362	72	RRM_2 RNA recognition motif.	99.26
smart00360	71	RRM RNA recognition motif.	99.24
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.24
KOG4660	549	consensus Protein Mei2, essential for commitment t	99.24
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	99.24
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.24
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.23
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	99.23
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	99.22
smart00360	71	RRM RNA recognition motif.	99.22
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.21
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.15
smart00361	70	RRM_1 RNA recognition motif.	99.12
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	99.08
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.07
KOG0226	290	consensus RNA-binding proteins [General function p	99.05
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	99.05
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	99.04
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.02
smart00361	70	RRM_1 RNA recognition motif.	99.02
KOG4210	285	consensus Nuclear localization sequence binding pr	99.0
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.97
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	98.96
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	98.95
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.94
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.93
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.9
KOG4210	285	consensus Nuclear localization sequence binding pr	98.89
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.89
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	98.85
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.84
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.75
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.73
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.69
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.66
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	98.63
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.61
KOG0226	290	consensus RNA-binding proteins [General function p	98.57
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.54
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.5
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.47
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.46
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.41
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.41
KOG0151	877	consensus Predicted splicing regulator, contains R	98.38
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.33
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.32
KOG0151	877	consensus Predicted splicing regulator, contains R	98.3
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	98.12
KOG1995	351	consensus Conserved Zn-finger protein [General fun	98.12
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.94
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.92
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	97.81
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.79
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.79
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.72
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.67
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.67
KOG1995	351	consensus Conserved Zn-finger protein [General fun	97.64
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	97.62
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.53
KOG1996	378	consensus mRNA splicing factor [RNA processing and	97.49
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	97.48
KOG3152	278	consensus TBP-binding protein, activator of basal	97.45
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.44
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	97.3
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	97.28
KOG3152	278	consensus TBP-binding protein, activator of basal	97.26
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	97.09
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.09
KOG2314	698	consensus Translation initiation factor 3, subunit	97.04
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	97.01
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	96.94
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	96.89
KOG2314	698	consensus Translation initiation factor 3, subunit	96.76
KOG2135	526	consensus Proteins containing the RNA recognition	96.71
KOG2591	684	consensus c-Mpl binding protein, contains La domai	96.7
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	96.69
KOG1996	378	consensus mRNA splicing factor [RNA processing and	96.57
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	96.42
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	96.33
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	96.12
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	96.0
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	95.96
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	95.91
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	95.88
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	95.79
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	95.62
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	95.45
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	95.44
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	95.44
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	95.4
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	95.23
KOG2068	327	consensus MOT2 transcription factor [Transcription	94.85
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	94.82
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	94.81
KOG2591	684	consensus c-Mpl binding protein, contains La domai	94.79
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	94.13
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	93.91
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	93.9
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	93.87
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	93.84
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	93.6
KOG0921	1282	consensus Dosage compensation complex, subunit MLE	93.52
KOG2068	327	consensus MOT2 transcription factor [Transcription	93.19
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	92.9
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	92.26
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	90.8
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	90.27
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	90.05
TIGR02542	145	B_forsyth_147 Bacteroides forsythus 147-residue re	88.49
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	88.04
KOG2135	526	consensus Proteins containing the RNA recognition	87.71
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	87.58
KOG2318	650	consensus Uncharacterized conserved protein [Funct	87.49
KOG2318	650	consensus Uncharacterized conserved protein [Funct	87.21
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	86.96
KOG4019	193	consensus Calcineurin-mediated signaling pathway i	86.51
KOG4274	742	consensus Positive cofactor 2 (PC2), subunit of a	86.16
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	84.89
PF14111	153	DUF4283: Domain of unknown function (DUF4283)	81.15
KOG3648	1179	consensus Golgi apparatus protein (cysteine-rich f	81.04

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=100.00  E-value=6.4e-46  Score=360.31  Aligned_cols=282  Identities=26%  Similarity=0.457  Sum_probs=227.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccccc
Q 013141          114 ETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNW  193 (449)
Q Consensus       114 ~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~  193 (449)
                      ...+|||+|||+++++++|+++|+.||+|.+|+|++++.+|+++|||||+|.+.++|++||+.|++..+.  ++.+++.|
T Consensus         2 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~--g~~i~v~~   79 (352)
T TIGR01661         2 SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQ--NKTIKVSY   79 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEEC--CeeEEEEe
Confidence            4679999999999999999999999999999999999999999999999999999999999999999885  46778877


Q ss_pred             cccCCCCCccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCC
Q 013141          194 ATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNG  273 (449)
Q Consensus       194 ~~~~~~~~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g  273 (449)
                      +.+...     ....++|||+|||.++++++|+++|+ .||.|..+.++.+..++.++|+|||+|.+.++|++|++.|+|
T Consensus        80 a~~~~~-----~~~~~~l~v~~l~~~~~~~~l~~~f~-~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g  153 (352)
T TIGR01661        80 ARPSSD-----SIKGANLYVSGLPKTMTQHELESIFS-PFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNG  153 (352)
T ss_pred             eccccc-----ccccceEEECCccccCCHHHHHHHHh-ccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCC
Confidence            764432     23456899999999999999999995 999999999999988889999999999999999999999999


Q ss_pred             ceecC--cceEEeecCCCCCCchhhcchhhhh------hhc-C-------------------------------------
Q 013141          274 VYCSS--RPMRIDVATPKKASGYQQQYSSQAL------VLA-G-------------------------------------  307 (449)
Q Consensus       274 ~~~~g--~~i~v~~~~~~~~~~~~~~~~~~~~------~~~-~-------------------------------------  307 (449)
                      ..+.+  ..|.|.++.................      ... .                                     
T Consensus       154 ~~~~g~~~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  233 (352)
T TIGR01661       154 TTPSGCTEPITVKFANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQH  233 (352)
T ss_pred             CccCCCceeEEEEECCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhhhhhhhc
Confidence            98876  5688888765542211100000000      000 0                                     


Q ss_pred             -----------CCCCCCCC-----cCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC------CcE
Q 013141          308 -----------GPGSNGAR-----VQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGC  365 (449)
Q Consensus       308 -----------~~~~~~~~-----~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~------~g~  365 (449)
                                 ........     ...........+.+|||+|||+++++++|+++|++||.|.+|+|+++      +|+
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                       00000000     00001111233457999999999999999999999999999999864      799


Q ss_pred             EEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCCC
Q 013141          366 GFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGN  403 (449)
Q Consensus       366 afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~~  403 (449)
                      |||+|.+.++|.+|++.|||..|+|+.|+|.|..++..
T Consensus       314 aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~~~~~  351 (352)
T TIGR01661       314 GFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTNKAY  351 (352)
T ss_pred             EEEEECCHHHHHHHHHHhCCCEECCeEEEEEEccCCCC
Confidence            99999999999999999999999999999999988653

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

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

Probab=100.00  E-value=5.5e-45  Score=360.59  Aligned_cols=248  Identities=19%  Similarity=0.374  Sum_probs=209.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      ...++|||+|||++++|++|+++|+.||.|.+|+|++| .+|+++|||||+|.+.++|++||+.||+..+.. ++.+.+.
T Consensus        56 ~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~-Gr~l~V~  133 (578)
T TIGR01648        56 GRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRP-GRLLGVC  133 (578)
T ss_pred             CCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecC-Ccccccc
Confidence            35689999999999999999999999999999999999 789999999999999999999999999987742 2334443


Q ss_pred             ccccCCCCCccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCC-eeEEEEe-ecCCCCCcceEEEEEeCCHHHHHHHHHH
Q 013141          193 WATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPS-VKGAKVI-IDSNTGRTKGYGFVRFGDENERSRAMTE  270 (449)
Q Consensus       193 ~~~~~~~~~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~-v~~i~~~-~~~~~~~~~g~afV~f~~~~~A~~A~~~  270 (449)
                      ++           ...++|||+|||.++++++|.++|+ .+++ +.++.+. .....++++|||||+|.+.++|..|++.
T Consensus       134 ~S-----------~~~~rLFVgNLP~~~TeeeL~eeFs-kv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~Airk  201 (578)
T TIGR01648       134 IS-----------VDNCRLFVGGIPKNKKREEILEEFS-KVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRK  201 (578)
T ss_pred             cc-----------ccCceeEeecCCcchhhHHHHHHhh-cccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHH
Confidence            32           2457999999999999999999996 6653 4444443 3334567899999999999999999998


Q ss_pred             hCC--ceecCcceEEeecCCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhc
Q 013141          271 MNG--VYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPF  348 (449)
Q Consensus       271 l~g--~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f  348 (449)
                      |+.  ..++++.|.|+|+.++....                           .......++|||+||+.++++++|+++|
T Consensus       202 L~~gki~l~Gr~I~VdwA~p~~~~d---------------------------~~~~~~~k~LfVgNL~~~~tee~L~~~F  254 (578)
T TIGR01648       202 LMPGRIQLWGHVIAVDWAEPEEEVD---------------------------EDVMAKVKILYVRNLMTTTTEEIIEKSF  254 (578)
T ss_pred             hhccceEecCceEEEEeeccccccc---------------------------ccccccccEEEEeCCCCCCCHHHHHHHH
Confidence            864  45799999999998764321                           1122335789999999999999999999


Q ss_pred             ccc--CceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCCC
Q 013141          349 SQF--GEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGN  403 (449)
Q Consensus       349 ~~~--G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~~  403 (449)
                      +.|  |.|++|.++  +++|||+|.+.++|.+|++.||+..|.|+.|+|+|+++...
T Consensus       255 ~~f~~G~I~rV~~~--rgfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~Akp~~~  309 (578)
T TIGR01648       255 SEFKPGKVERVKKI--RDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKPVDK  309 (578)
T ss_pred             HhcCCCceEEEEee--cCeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEccCCCc
Confidence            999  999999887  57999999999999999999999999999999999987543

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

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

Probab=100.00  E-value=6.2e-45  Score=332.49  Aligned_cols=252  Identities=18%  Similarity=0.373  Sum_probs=220.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      ...+.|||+.||.++.|+||..+|++.|.|-++++++|+.+|.+||||||.|++.++|.+|++.||+..|. .++.|.|.
T Consensus        81 ~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir-~GK~igvc  159 (506)
T KOG0117|consen   81 PRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIR-PGKLLGVC  159 (506)
T ss_pred             CCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCcccc-CCCEeEEE
Confidence            35678999999999999999999999999999999999999999999999999999999999999999884 34555554


Q ss_pred             ccccCCCCCccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecC-CCCCcceEEEEEeCCHHHHHHHHHHh
Q 013141          193 WATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDS-NTGRTKGYGFVRFGDENERSRAMTEM  271 (449)
Q Consensus       193 ~~~~~~~~~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~-~~~~~~g~afV~f~~~~~A~~A~~~l  271 (449)
                      .+           ..+++|||+|||.++++++|++.|.+..--|.+|.+...+ +..+.||||||+|.+...|..|.++|
T Consensus       160 ~S-----------van~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl  228 (506)
T KOG0117|consen  160 VS-----------VANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKL  228 (506)
T ss_pred             Ee-----------eecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhc
Confidence            33           3678999999999999999999996444447888777664 35678999999999999999998877


Q ss_pred             CC--ceecCcceEEeecCCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhcc
Q 013141          272 NG--VYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFS  349 (449)
Q Consensus       272 ~g--~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~  349 (449)
                      -.  ..++|..+.|+|+.+.....                           .+.....+.|||+||+.++|+|.|+++|+
T Consensus       229 ~~g~~klwgn~~tVdWAep~~e~d---------------------------ed~ms~VKvLYVRNL~~~tTeE~lk~~F~  281 (506)
T KOG0117|consen  229 MPGKIKLWGNAITVDWAEPEEEPD---------------------------EDTMSKVKVLYVRNLMESTTEETLKKLFN  281 (506)
T ss_pred             cCCceeecCCcceeeccCcccCCC---------------------------hhhhhheeeeeeeccchhhhHHHHHHHHH
Confidence            54  55799999999999986642                           22344568899999999999999999999


Q ss_pred             ccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCCCCC
Q 013141          350 QFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQ  405 (449)
Q Consensus       350 ~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~~~~  405 (449)
                      +||.|++|+.+++  +|||+|.++++|.+|++.+||++|+|..|.|+++|+...+.
T Consensus       282 ~~G~veRVkk~rD--YaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP~~k~k  335 (506)
T KOG0117|consen  282 EFGKVERVKKPRD--YAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKPVDKKK  335 (506)
T ss_pred             hccceEEeecccc--eeEEeecchHHHHHHHHHhcCceecCceEEEEecCChhhhc
Confidence            9999999999855  99999999999999999999999999999999999865444

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=2.3e-42  Score=296.22  Aligned_cols=239  Identities=33%  Similarity=0.632  Sum_probs=206.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccc
Q 013141          112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRL  191 (449)
Q Consensus       112 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~  191 (449)
                      ++..|||||+||..++||+-|..+|++.|+|.+++|+.|                                     .+++
T Consensus         3 ~~~prtlyvgnld~~vte~~i~~lf~qig~v~~~k~i~~-------------------------------------e~~v   45 (321)
T KOG0148|consen    3 SDEPRTLYVGNLDSTVTEDFIATLFNQIGSVTKTKVIFD-------------------------------------ELKV   45 (321)
T ss_pred             CCCCceEEeeccChhhHHHHHHHHHHhccccccceeehh-------------------------------------hhcc
Confidence            467899999999999999999999999999999999886                                     3455


Q ss_pred             cccccCCCCCccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh
Q 013141          192 NWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEM  271 (449)
Q Consensus       192 ~~~~~~~~~~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l  271 (449)
                      .|+.......+.....--.+||+.|...++.++|++.|. +||+|.+.++++|..|+++|||+||.|...++|+.||..|
T Consensus        46 ~wa~~p~nQsk~t~~~hfhvfvgdls~eI~~e~lr~aF~-pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~M  124 (321)
T KOG0148|consen   46 NWATAPGNQSKPTSNQHFHVFVGDLSPEIDNEKLREAFA-PFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQM  124 (321)
T ss_pred             ccccCcccCCCCccccceeEEehhcchhcchHHHHHHhc-cccccccceEeecccCCcccceeEEeccchHHHHHHHHHh
Confidence            555544333333333345799999999999999999995 9999999999999999999999999999999999999999


Q ss_pred             CCceecCcceEEeecCCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhcccc
Q 013141          272 NGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQF  351 (449)
Q Consensus       272 ~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~  351 (449)
                      ||.-|++|.|+..|++.+......+.                ...........++.++|||+||+..++|++|++.|+.|
T Consensus       125 nGqWlG~R~IRTNWATRKp~e~n~~~----------------ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~f  188 (321)
T KOG0148|consen  125 NGQWLGRRTIRTNWATRKPSEMNGKP----------------LTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPF  188 (321)
T ss_pred             CCeeeccceeeccccccCccccCCCC----------------ccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccC
Confidence            99999999999999998863321111                11112234456778999999999999999999999999


Q ss_pred             CceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCCCC
Q 013141          352 GEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNK  404 (449)
Q Consensus       352 G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~~~  404 (449)
                      |.|.+|++.+++|++||+|++.|+|.+||..+|+.+++|..+++.|.|.....
T Consensus       189 G~I~EVRvFk~qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCsWGKe~~~~  241 (321)
T KOG0148|consen  189 GPIQEVRVFKDQGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGKEGDDG  241 (321)
T ss_pred             CcceEEEEecccceEEEEecchhhHHHHHHHhcCceeCceEEEEeccccCCCC
Confidence            99999999999999999999999999999999999999999999999975543

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

Probab=100.00  E-value=7.6e-42  Score=291.11  Aligned_cols=283  Identities=27%  Similarity=0.471  Sum_probs=235.7

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      ..+..+.|.|.-||..+|+|||+.+|...|+|++|++++|+.+|.+-||+||.|.++++|++|+..|||..+  ..+.|+
T Consensus        37 t~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrL--Q~KTIK  114 (360)
T KOG0145|consen   37 TDESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRL--QNKTIK  114 (360)
T ss_pred             cCcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceee--ccceEE
Confidence            345567799999999999999999999999999999999999999999999999999999999999999888  678899


Q ss_pred             ccccccCCCCCccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHH
Q 013141          191 LNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE  270 (449)
Q Consensus       191 ~~~~~~~~~~~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~  270 (449)
                      |+++.++....     ....|||++||..+|..||+.+|+ .||.|...+++.|..++.+||.+||.|+..++|++||+.
T Consensus       115 VSyARPSs~~I-----k~aNLYvSGlPktMtqkelE~iFs-~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~  188 (360)
T KOG0145|consen  115 VSYARPSSDSI-----KDANLYVSGLPKTMTQKELEQIFS-PFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKG  188 (360)
T ss_pred             EEeccCChhhh-----cccceEEecCCccchHHHHHHHHH-HhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHh
Confidence            99998765433     456899999999999999999997 999999999999999999999999999999999999999


Q ss_pred             hCCceec--CcceEEeecCCCCCCchhhcc----hhhhhhhcCCC----------------------------CCCCCCc
Q 013141          271 MNGVYCS--SRPMRIDVATPKKASGYQQQY----SSQALVLAGGP----------------------------GSNGARV  316 (449)
Q Consensus       271 l~g~~~~--g~~i~v~~~~~~~~~~~~~~~----~~~~~~~~~~~----------------------------~~~~~~~  316 (449)
                      |||..-.  ..+|.|+++............    .... ...+++                            ..-....
T Consensus       189 lNG~~P~g~tepItVKFannPsq~t~~a~ls~ly~sp~-rr~~Gp~hh~~~r~r~~~~~~~~~~~~rfsP~~~d~m~~l~  267 (360)
T KOG0145|consen  189 LNGQKPSGCTEPITVKFANNPSQKTNQALLSQLYQSPA-RRYGGPMHHQAQRFRLDNLLNPHAAQARFSPMTIDGMSGLA  267 (360)
T ss_pred             ccCCCCCCCCCCeEEEecCCcccccchhhhHHhhcCcc-ccCCCcccchhhhhccccccchhhhhccCCCccccccceee
Confidence            9998864  467999998765432211100    0000 000000                            0000001


Q ss_pred             CCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC------CcEEEEEecCHHHHHHHHHHhcCCeeCC
Q 013141          317 QGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKLQGTAIGK  390 (449)
Q Consensus       317 ~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~------~g~afV~F~~~~~A~~A~~~l~g~~~~g  390 (449)
                      ....+......++|||.||.++.+|.-|+.+|.+||.|..|+|+++      +||+||++.+-++|..|+..|||..+++
T Consensus       268 ~~~lp~~~~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~  347 (360)
T KOG0145|consen  268 GVNLPGGPGGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGD  347 (360)
T ss_pred             eeccCCCCCCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccc
Confidence            1122334456899999999999999999999999999999999986      7999999999999999999999999999


Q ss_pred             eEEEEEecCCCC
Q 013141          391 QTVRLSWGRNPG  402 (449)
Q Consensus       391 ~~l~v~~~~~~~  402 (449)
                      +.|.|.|..+..
T Consensus       348 rvLQVsFKtnk~  359 (360)
T KOG0145|consen  348 RVLQVSFKTNKA  359 (360)
T ss_pred             eEEEEEEecCCC
Confidence            999999988753

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

Probab=100.00  E-value=7.1e-41  Score=343.44  Aligned_cols=270  Identities=26%  Similarity=0.485  Sum_probs=223.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      ....+|||+|||+++++++|+++|+.||.|.+|+++.+. +|+++|||||+|.+.++|.+|++.+++..+.+  +.+.+.
T Consensus        86 ~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~-~g~skg~afV~F~~~e~A~~Ai~~lng~~~~~--~~i~v~  162 (562)
T TIGR01628        86 SGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDE-NGKSRGYGFVHFEKEESAKAAIQKVNGMLLND--KEVYVG  162 (562)
T ss_pred             cCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecC-CCCcccEEEEEECCHHHHHHHHHHhcccEecC--ceEEEe
Confidence            345689999999999999999999999999999999985 68899999999999999999999999998854  455554


Q ss_pred             ccccCCCCCccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC
Q 013141          193 WATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMN  272 (449)
Q Consensus       193 ~~~~~~~~~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~  272 (449)
                      ................++|||+||+.++|+++|+++|+ .||.|.++.++++. ++.++|||||+|.+.++|.+|++.|+
T Consensus       163 ~~~~~~~~~~~~~~~~~~l~V~nl~~~~tee~L~~~F~-~fG~i~~~~i~~~~-~g~~~G~afV~F~~~e~A~~Av~~l~  240 (562)
T TIGR01628       163 RFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFA-KFGEITSAAVMKDG-SGRSRGFAFVNFEKHEDAAKAVEEMN  240 (562)
T ss_pred             ccccccccccccccCCCeEEEeCCCCcCCHHHHHHHHH-hcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhC
Confidence            33322222122334457899999999999999999995 99999999999884 68899999999999999999999999


Q ss_pred             Cceec----CcceEEeecCCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhc
Q 013141          273 GVYCS----SRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPF  348 (449)
Q Consensus       273 g~~~~----g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f  348 (449)
                      +..+.    ++.+.|.++..+..+............              .........++|||+||++++++++|+++|
T Consensus       241 g~~i~~~~~g~~l~v~~a~~k~er~~~~~~~~~~~~--------------~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F  306 (562)
T TIGR01628       241 GKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQ--------------QERKMKAQGVNLYVKNLDDTVTDEKLRELF  306 (562)
T ss_pred             CcEecccccceeeEeecccChhhhHHHHHhhHHhhh--------------hhhhcccCCCEEEEeCCCCccCHHHHHHHH
Confidence            99999    999999988776543211111000000              001123456789999999999999999999


Q ss_pred             cccCceEEEEEeCC-----CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCC
Q 013141          349 SQFGEILSVKIPVG-----KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNP  401 (449)
Q Consensus       349 ~~~G~v~~v~i~~~-----~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~  401 (449)
                      +.||.|.+|+++.+     +|+|||+|.+.++|.+|++.|||+.|+|+.|.|.|+...
T Consensus       307 ~~~G~i~~~~i~~d~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a~~k  364 (562)
T TIGR01628       307 SECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRK  364 (562)
T ss_pred             HhcCCeEEEEEEECCCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEeccCc
Confidence            99999999999863     699999999999999999999999999999999999864

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=6.1e-41  Score=343.90  Aligned_cols=252  Identities=30%  Similarity=0.523  Sum_probs=222.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccccccc
Q 013141          117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATF  196 (449)
Q Consensus       117 ~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~~~~  196 (449)
                      +|||+|||+++||++|+++|+.||.|.+|+|++|+.+++++|||||+|.+.++|++|++.+++..+.  ++.|++.|+..
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~--gk~i~i~~s~~   79 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLG--GKPIRIMWSQR   79 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEEC--CeeEEeecccc
Confidence            7999999999999999999999999999999999999999999999999999999999999998884  57788888764


Q ss_pred             CCCCCccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee
Q 013141          197 SGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYC  276 (449)
Q Consensus       197 ~~~~~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~  276 (449)
                      ....+   .....+|||+||+.++++++|+++|+ .||.|.+++++.+ .+++++|||||+|.+.++|++|++.+++..+
T Consensus        80 ~~~~~---~~~~~~vfV~nLp~~~~~~~L~~~F~-~~G~i~~~~i~~~-~~g~skg~afV~F~~~e~A~~Ai~~lng~~~  154 (562)
T TIGR01628        80 DPSLR---RSGVGNIFVKNLDKSVDNKALFDTFS-KFGNILSCKVATD-ENGKSRGYGFVHFEKEESAKAAIQKVNGMLL  154 (562)
T ss_pred             ccccc---ccCCCceEEcCCCccCCHHHHHHHHH-hcCCcceeEeeec-CCCCcccEEEEEECCHHHHHHHHHHhcccEe
Confidence            33222   23356899999999999999999995 9999999999988 4688999999999999999999999999999


Q ss_pred             cCcceEEeecCCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEE
Q 013141          277 SSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILS  356 (449)
Q Consensus       277 ~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~  356 (449)
                      .++.|.|.....+..+.                           .......++|||+||+.++|+++|+++|+.||.|.+
T Consensus       155 ~~~~i~v~~~~~~~~~~---------------------------~~~~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~  207 (562)
T TIGR01628       155 NDKEVYVGRFIKKHERE---------------------------AAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITS  207 (562)
T ss_pred             cCceEEEeccccccccc---------------------------cccccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEE
Confidence            99999997765543321                           012234568999999999999999999999999999


Q ss_pred             EEEeCC-----CcEEEEEecCHHHHHHHHHHhcCCeeC----CeEEEEEecCCCC
Q 013141          357 VKIPVG-----KGCGFVQFANRKDAEVALQKLQGTAIG----KQTVRLSWGRNPG  402 (449)
Q Consensus       357 v~i~~~-----~g~afV~F~~~~~A~~A~~~l~g~~~~----g~~l~v~~~~~~~  402 (449)
                      +.+.++     +|+|||+|.+.++|.+|++.|++..|.    |+.|.|.++....
T Consensus       208 ~~i~~~~~g~~~G~afV~F~~~e~A~~Av~~l~g~~i~~~~~g~~l~v~~a~~k~  262 (562)
T TIGR01628       208 AAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRA  262 (562)
T ss_pred             EEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCcEecccccceeeEeecccChh
Confidence            999863     689999999999999999999999999    9999999876543

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

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

Probab=100.00  E-value=2.4e-39  Score=323.80  Aligned_cols=278  Identities=19%  Similarity=0.234  Sum_probs=211.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccccc
Q 013141          114 ETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNW  193 (449)
Q Consensus       114 ~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~  193 (449)
                      ++++|||+|||+++++++|+++|+.||.|.+|.++++      ++||||+|.+.++|++|++.++...+...+++|+|.|
T Consensus         1 ps~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~------k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~   74 (481)
T TIGR01649         1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPG------KRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNY   74 (481)
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECC------CCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEe
Confidence            4789999999999999999999999999999999875      3799999999999999998764433333667888888


Q ss_pred             cccCCCCCcc-------ccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHH
Q 013141          194 ATFSGSDRRT-------EACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSR  266 (449)
Q Consensus       194 ~~~~~~~~~~-------~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~  266 (449)
                      +.........       ......+|||+||++.+|+++|+++|+ .||.|.+|.++++..    +++|||+|.+.++|.+
T Consensus        75 s~~~~~~~~~~~~~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~-~~G~V~~v~i~~~~~----~~~afVef~~~~~A~~  149 (481)
T TIGR01649        75 STSQEIKRDGNSDFDSAGPNKVLRVIVENPMYPITLDVLYQIFN-PYGKVLRIVTFTKNN----VFQALVEFESVNSAQH  149 (481)
T ss_pred             cCCcccccCCCCcccCCCCCceEEEEEcCCCCCCCHHHHHHHHh-ccCCEEEEEEEecCC----ceEEEEEECCHHHHHH
Confidence            7644322211       112234799999999999999999996 999999999987643    4689999999999999


Q ss_pred             HHHHhCCceecC--cceEEeecCCCCCCc------h---hhc-c-------------hhhhhh--------hcCCCCCC-
Q 013141          267 AMTEMNGVYCSS--RPMRIDVATPKKASG------Y---QQQ-Y-------------SSQALV--------LAGGPGSN-  312 (449)
Q Consensus       267 A~~~l~g~~~~g--~~i~v~~~~~~~~~~------~---~~~-~-------------~~~~~~--------~~~~~~~~-  312 (449)
                      |++.|||..|.+  +.|+|+|++.....-      .   ... .             ......        ...+.+.. 
T Consensus       150 A~~~Lng~~i~~~~~~l~v~~sk~~~l~v~~~~~~s~dyt~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~  229 (481)
T TIGR01649       150 AKAALNGADIYNGCCTLKIEYAKPTRLNVKYNDDDSRDYTNPDLPGRRDPGLDQTHRQRQPALLGQHPSSYGHDGYSSHG  229 (481)
T ss_pred             HHHHhcCCcccCCceEEEEEEecCCCceeEecccCCCCCcCCCCCCCCCCCcCccccccccccccCCCccCCCcccccCC
Confidence            999999999964  578888887633110      0   000 0             000000        00000000 


Q ss_pred             -----------CC--------------------CcCCCCCCCCCCCcEEEEcCCCC-CCCHhHHHhhccccCceEEEEEe
Q 013141          313 -----------GA--------------------RVQGSQSDGESNNATIFVGALDS-DVSDEDLREPFSQFGEILSVKIP  360 (449)
Q Consensus       313 -----------~~--------------------~~~~~~~~~~~~~~~l~V~nlp~-~~t~~~L~~~f~~~G~v~~v~i~  360 (449)
                                 ..                    ............+++|||+||++ .+++++|+++|+.||.|.+|+|+
T Consensus       230 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~  309 (481)
T TIGR01649       230 GPLAPLAGGDRMGPPHGPPSRYRPAYEAAPLAPAISSYGPAGGGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFM  309 (481)
T ss_pred             CCCCcccccccCCCcccCCCCCcccccccccCccccccCCCCCCCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEE
Confidence                       00                    00000011134678999999998 69999999999999999999998


Q ss_pred             CC-CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCC
Q 013141          361 VG-KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPG  402 (449)
Q Consensus       361 ~~-~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~  402 (449)
                      ++ +++|||+|.+.++|.+|++.|||..|.|+.|+|.+++...
T Consensus       310 ~~~~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~~  352 (481)
T TIGR01649       310 KNKKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQN  352 (481)
T ss_pred             eCCCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccccc
Confidence            76 6999999999999999999999999999999999997643

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

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

Probab=100.00  E-value=1.2e-38  Score=319.94  Aligned_cols=285  Identities=21%  Similarity=0.398  Sum_probs=219.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccc
Q 013141          112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRL  191 (449)
Q Consensus       112 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~  191 (449)
                      ....++|||+|||+.+++++|+++|+.||.|.+|++++++.+++++|||||+|.+.++|.+|| .|++..+.+  .+|.+
T Consensus        86 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al-~l~g~~~~g--~~i~v  162 (457)
T TIGR01622        86 ERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKAL-ALTGQMLLG--RPIIV  162 (457)
T ss_pred             ccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHH-HhCCCEECC--eeeEE
Confidence            456789999999999999999999999999999999999999999999999999999999999 489988855  44554


Q ss_pred             cccccCCCCC-------ccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHH
Q 013141          192 NWATFSGSDR-------RTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENER  264 (449)
Q Consensus       192 ~~~~~~~~~~-------~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A  264 (449)
                      .+........       .......++|||+|||.++|+++|+++|. .||.|..|.++.+..++.++|||||+|.+.++|
T Consensus       163 ~~~~~~~~~~~~~~~~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~-~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A  241 (457)
T TIGR01622       163 QSSQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFE-PFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEA  241 (457)
T ss_pred             eecchhhhhhhhcccccCCCCCCCCEEEEcCCCCCCCHHHHHHHHH-hcCCeEEEEEEEcCCCCccceEEEEEECCHHHH
Confidence            4433211110       01112358999999999999999999995 999999999999999899999999999999999


Q ss_pred             HHHHHHhCCceecCcceEEeecCCCCCCchhhcc--------------------hhhhhh-hcC---CC---CCCC----
Q 013141          265 SRAMTEMNGVYCSSRPMRIDVATPKKASGYQQQY--------------------SSQALV-LAG---GP---GSNG----  313 (449)
Q Consensus       265 ~~A~~~l~g~~~~g~~i~v~~~~~~~~~~~~~~~--------------------~~~~~~-~~~---~~---~~~~----  313 (449)
                      .+|++.|+|..|.|+.|+|.++............                    ...... ...   +.   ....    
T Consensus       242 ~~A~~~l~g~~i~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  321 (457)
T TIGR01622       242 KEALEVMNGFELAGRPIKVGYAQDSTYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIPGTGSKIAL  321 (457)
T ss_pred             HHHHHhcCCcEECCEEEEEEEccCCCccccchhhhccccccccCCcCCCccchHHHHHhhccCCCCccccCCCccchhhh
Confidence            9999999999999999999997643211100000                    000000 000   00   0000    


Q ss_pred             -------------CC----------cC-C---CCCCCCCCCcEEEEcCCCCCCC----------HhHHHhhccccCceEE
Q 013141          314 -------------AR----------VQ-G---SQSDGESNNATIFVGALDSDVS----------DEDLREPFSQFGEILS  356 (449)
Q Consensus       314 -------------~~----------~~-~---~~~~~~~~~~~l~V~nlp~~~t----------~~~L~~~f~~~G~v~~  356 (449)
                                   ..          .. .   ..........+|+|.||....+          .+||++.|++||.|+.
T Consensus       322 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~l~n~~~~~~~~~~~~~~~~~~dv~~e~~k~G~v~~  401 (457)
T TIGR01622       322 MQKLQRDGIIDPNIPSRYATGALAIMARNSFVPSTNNNLATTCLVLSNMFDPATEEEPNFDNEILDDVKEECSKYGGVVH  401 (457)
T ss_pred             hccccccccccccccccccccccccccCCCCCCcccCCCCCcEEEEecCCCCcccccchHHHHHHHHHHHHHHhcCCeeE
Confidence                         00          00 0   0001235678999999955443          3789999999999999


Q ss_pred             EEEeC--CCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCC
Q 013141          357 VKIPV--GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRN  400 (449)
Q Consensus       357 v~i~~--~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  400 (449)
                      |.|..  ..|++||+|.+.++|.+|++.|||+.|+|+.|.|.|...
T Consensus       402 v~v~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~f~gr~i~~~~~~~  447 (457)
T TIGR01622       402 IYVDTKNSAGKIYLKFSSVDAALAAFQALNGRYFGGKMITAAFVVN  447 (457)
T ss_pred             EEEeCCCCceeEEEEECCHHHHHHHHHHhcCcccCCeEEEEEEEcH
Confidence            99974  479999999999999999999999999999999998764

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.

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

Probab=100.00  E-value=2.1e-38  Score=314.03  Aligned_cols=174  Identities=18%  Similarity=0.363  Sum_probs=153.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      ...++|||+|||+++++++|+++|..||.|.+|+++.|+.+++++|||||+|.+.++|++|++.||+..+.+  +.|++.
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~G--R~IkV~  182 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGG--RNIKVG  182 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEec--ceeeec
Confidence            467899999999999999999999999999999999999999999999999999999999999999999865  455555


Q ss_pred             ccccCCCC------CccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHH
Q 013141          193 WATFSGSD------RRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSR  266 (449)
Q Consensus       193 ~~~~~~~~------~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~  266 (449)
                      +.......      ........++|||+||++++++++|+++|+ .||.|.++++.+++.+++++|||||+|.+.++|.+
T Consensus       183 rp~~~p~a~~~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs-~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~k  261 (612)
T TIGR01645       183 RPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFE-AFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSE  261 (612)
T ss_pred             ccccccccccccccccccccccceEEeecCCCCCCHHHHHHHHh-hcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHH
Confidence            43321111      112223457999999999999999999995 99999999999999999999999999999999999


Q ss_pred             HHHHhCCceecCcceEEeecCCC
Q 013141          267 AMTEMNGVYCSSRPMRIDVATPK  289 (449)
Q Consensus       267 A~~~l~g~~~~g~~i~v~~~~~~  289 (449)
                      |++.||+..|+|+.|+|.++...
T Consensus       262 AI~amNg~elgGr~LrV~kAi~p  284 (612)
T TIGR01645       262 AIASMNLFDLGGQYLRVGKCVTP  284 (612)
T ss_pred             HHHHhCCCeeCCeEEEEEecCCC
Confidence            99999999999999999998764

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.

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

Probab=100.00  E-value=1.2e-37  Score=311.54  Aligned_cols=278  Identities=17%  Similarity=0.245  Sum_probs=215.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccccc
Q 013141          114 ETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNW  193 (449)
Q Consensus       114 ~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~  193 (449)
                      ...+|+|+||++.+|+++|+++|+.||.|.+|.++++..    +++|||+|.+.++|.+|++.||+..|.+..+.+++.|
T Consensus        95 ~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~~----~~~afVef~~~~~A~~A~~~Lng~~i~~~~~~l~v~~  170 (481)
T TIGR01649        95 KVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNN----VFQALVEFESVNSAQHAKAALNGADIYNGCCTLKIEY  170 (481)
T ss_pred             ceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecCC----ceEEEEEECCHHHHHHHHHHhcCCcccCCceEEEEEE
Confidence            345799999999999999999999999999999988642    3689999999999999999999999977666777777


Q ss_pred             cccCCCC-------------------Cc----------------------------------------------------
Q 013141          194 ATFSGSD-------------------RR----------------------------------------------------  202 (449)
Q Consensus       194 ~~~~~~~-------------------~~----------------------------------------------------  202 (449)
                      ++.....                   ..                                                    
T Consensus       171 sk~~~l~v~~~~~~s~dyt~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~  250 (481)
T TIGR01649       171 AKPTRLNVKYNDDDSRDYTNPDLPGRRDPGLDQTHRQRQPALLGQHPSSYGHDGYSSHGGPLAPLAGGDRMGPPHGPPSR  250 (481)
T ss_pred             ecCCCceeEecccCCCCCcCCCCCCCCCCCcCccccccccccccCCCccCCCcccccCCCCCCcccccccCCCcccCCCC
Confidence            6531100                   00                                                    


Q ss_pred             -------------------cccCCCceEEEcCCCC-CCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHH
Q 013141          203 -------------------TEACSDLSIFVGDLAP-DVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDEN  262 (449)
Q Consensus       203 -------------------~~~~~~~~l~v~~lp~-~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~  262 (449)
                                         ....++++|||+||++ .+|+++|+++|+ .||.|.+|++++++     +|+|||+|.+.+
T Consensus       251 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nL~~~~vt~~~L~~lF~-~yG~V~~vki~~~~-----~g~afV~f~~~~  324 (481)
T TIGR01649       251 YRPAYEAAPLAPAISSYGPAGGGPGSVLMVSGLHQEKVNCDRLFNLFC-VYGNVERVKFMKNK-----KETALIEMADPY  324 (481)
T ss_pred             CcccccccccCccccccCCCCCCCCCEEEEeCCCCCCCCHHHHHHHHH-hcCCeEEEEEEeCC-----CCEEEEEECCHH
Confidence                               0012456999999998 699999999995 99999999999863     689999999999


Q ss_pred             HHHHHHHHhCCceecCcceEEeecCCCCCCchhhcc-hhh-h--hhhcCCCCCC-CCCcCCCCCCCCCCCcEEEEcCCCC
Q 013141          263 ERSRAMTEMNGVYCSSRPMRIDVATPKKASGYQQQY-SSQ-A--LVLAGGPGSN-GARVQGSQSDGESNNATIFVGALDS  337 (449)
Q Consensus       263 ~A~~A~~~l~g~~~~g~~i~v~~~~~~~~~~~~~~~-~~~-~--~~~~~~~~~~-~~~~~~~~~~~~~~~~~l~V~nlp~  337 (449)
                      +|.+|+..||+..|.|+.|+|.+++........... ... .  .......... ............+++.+|||.|||.
T Consensus       325 ~A~~Ai~~lng~~l~g~~l~v~~s~~~~~~~~~~~~~~~~~~~~~d~~~~~~~r~~~~~~~~~~~~~~ps~~L~v~NLp~  404 (481)
T TIGR01649       325 QAQLALTHLNGVKLFGKPLRVCPSKQQNVQPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNNIQPPSATLHLSNIPL  404 (481)
T ss_pred             HHHHHHHHhCCCEECCceEEEEEcccccccCCCCCcCcCCCcccccccCCccccCCCcccccccccCCCCcEEEEecCCC
Confidence            999999999999999999999998665321110000 000 0  0000000000 0000000111235678999999999


Q ss_pred             CCCHhHHHhhccccCc--eEEEEEeCC----CcEEEEEecCHHHHHHHHHHhcCCeeCCeE------EEEEecCCC
Q 013141          338 DVSDEDLREPFSQFGE--ILSVKIPVG----KGCGFVQFANRKDAEVALQKLQGTAIGKQT------VRLSWGRNP  401 (449)
Q Consensus       338 ~~t~~~L~~~f~~~G~--v~~v~i~~~----~g~afV~F~~~~~A~~A~~~l~g~~~~g~~------l~v~~~~~~  401 (449)
                      ++++++|+++|+.||.  |..|++...    +++|||+|++.++|.+|+..||++.|.++.      |+|+|++++
T Consensus       405 ~~tee~L~~lF~~~G~~~i~~ik~~~~~~~~~~~gfVeF~~~e~A~~Al~~ln~~~l~~~~~~~~~~lkv~fs~~~  480 (481)
T TIGR01649       405 SVSEEDLKELFAENGVHKVKKFKFFPKDNERSKMGLLEWESVEDAVEALIALNHHQLNEPNGSAPYHLKVSFSTSR  480 (481)
T ss_pred             CCCHHHHHHHHHhcCCccceEEEEecCCCCcceeEEEEcCCHHHHHHHHHHhcCCccCCCCCCccceEEEEeccCC
Confidence            9999999999999998  888988654    589999999999999999999999999885      999999874

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).

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

Probab=100.00  E-value=9.2e-38  Score=284.21  Aligned_cols=288  Identities=25%  Similarity=0.494  Sum_probs=235.2

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCC-CCCCCCCcc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGS-LMPNTDQPF  189 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~-~~~~~~~~~  189 (449)
                      .+.+.-+|||+-||..++|+||+++|++||.|.+|.|++|+.++.++|||||.|.+.++|.+|+..|++. .|.+...+|
T Consensus        30 ~d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pv  109 (510)
T KOG0144|consen   30 PDGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPV  109 (510)
T ss_pred             CCchhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcce
Confidence            3467778999999999999999999999999999999999999999999999999999999999999885 588999999


Q ss_pred             cccccccCCCCCccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH
Q 013141          190 RLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT  269 (449)
Q Consensus       190 ~~~~~~~~~~~~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~  269 (449)
                      .+++++.+....    ..+++|||+-|+..+||.||+++|+ +||.|+++.|++|.. +.+||+|||+|.+.+.|..||+
T Consensus       110 qvk~Ad~E~er~----~~e~KLFvg~lsK~~te~evr~iFs-~fG~Ied~~ilrd~~-~~sRGcaFV~fstke~A~~Aik  183 (510)
T KOG0144|consen  110 QVKYADGERERI----VEERKLFVGMLSKQCTENEVREIFS-RFGHIEDCYILRDPD-GLSRGCAFVKFSTKEMAVAAIK  183 (510)
T ss_pred             eecccchhhhcc----ccchhhhhhhccccccHHHHHHHHH-hhCccchhhheeccc-ccccceeEEEEehHHHHHHHHH
Confidence            999987543322    4578999999999999999999997 999999999999965 8999999999999999999999


Q ss_pred             HhCCcee---cCcceEEeecCCCCCCchhhcchhhh---hhhcCC-----------------------------------
Q 013141          270 EMNGVYC---SSRPMRIDVATPKKASGYQQQYSSQA---LVLAGG-----------------------------------  308 (449)
Q Consensus       270 ~l~g~~~---~g~~i~v~~~~~~~~~~~~~~~~~~~---~~~~~~-----------------------------------  308 (449)
                      .||+..-   +..+|.|+|+++++.+..+.......   ....++                                   
T Consensus       184 a~ng~~tmeGcs~PLVVkFADtqkdk~~~~lqq~~~~~~qql~~~~~~~n~~~~~~l~~~~~~~~Qq~~~sqn~g~l~g~  263 (510)
T KOG0144|consen  184 ALNGTQTMEGCSQPLVVKFADTQKDKDGKRLQQLNPALLQQLGNGQNPQNLASLGALSNGYQGPQQQTQQSQNVGTLGGL  263 (510)
T ss_pred             hhccceeeccCCCceEEEecccCCCchHHHHHhhhHHHHHHhcCCCCccchhhhhccCcccCchhhhccccCCCcccccc
Confidence            9999653   66789999999887554222200000   000000                                   


Q ss_pred             ------------------------------------------CCCCCC---------C----------------------
Q 013141          309 ------------------------------------------PGSNGA---------R----------------------  315 (449)
Q Consensus       309 ------------------------------------------~~~~~~---------~----------------------  315 (449)
                                                                .+....         .                      
T Consensus       264 ~~L~~l~a~~~qq~~~~~~~~ta~q~~~~s~q~~pl~~qts~~~~~~~~~~~~~~ss~~~~s~~~~aq~~~~q~~p~t~~  343 (510)
T KOG0144|consen  264 PPLGPLNATQLQQAAALAAAATAAQKTASSTQGLPLRTQTSFPGSQTSPQSASAPSSSLSTSQNPLAQLGARQTFPGTPA  343 (510)
T ss_pred             cCCCCcchhHHHHHHHhhhhcccccCCCCCcccCccccccCCccccCCCccccCccccCcccccchhhhhHhhcCCCCch
Confidence                                                      000000         0                      


Q ss_pred             ---------------------------------------------------------------------cCCCCCCCCCC
Q 013141          316 ---------------------------------------------------------------------VQGSQSDGESN  326 (449)
Q Consensus       316 ---------------------------------------------------------------------~~~~~~~~~~~  326 (449)
                                                                                           .........+.
T Consensus       344 ~~n~~~~~a~a~~~sp~aa~~~~lq~~~ltp~~~~~~~~~tQa~q~~~q~a~~a~~~l~~q~~~~qq~~~~~~~q~eGpe  423 (510)
T KOG0144|consen  344 NYNLAGGMAGAGTTSPVAASLANLQQIGLTPFAGAAALDHTQAMQQYAQSANLAAPGLVGQQATTQQAQMVGNGQVEGPE  423 (510)
T ss_pred             hcccccccccccccCcccccccccccccCCChhhhhhHhHHHhhhHhhhhhhhcccchhhhhHhhhhhhcccCccccCCC
Confidence                                                                                 00011123356


Q ss_pred             CcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCC
Q 013141          327 NATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRN  400 (449)
Q Consensus       327 ~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~------~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  400 (449)
                      +..+||.+||-+.-+.||...|..||.|++.++.-      ++.|+||.|++..+|..||..|||..++.++|+|...+.
T Consensus       424 GanlfiyhlPqefgdq~l~~~f~pfG~Vlsakvfidk~tnlskcfgfvSyen~~sa~~aI~amngfQig~KrlkVQlk~~  503 (510)
T KOG0144|consen  424 GANLFIYHLPQEFGDQDLIATFQPFGGVLSAKVFIDKVTNLSKCFGFVSYENAQSAQNAISAMNGFQIGSKRLKVQLKRD  503 (510)
T ss_pred             ccceeeeeCchhhhhHHHHHHhccccceeEEEEEEecccCHhhhcCcccccchhhhHHHHHHhcchhhccccceEEeeec
Confidence            67899999999999999999999999999977654      368999999999999999999999999999999999887


Q ss_pred             CCCC
Q 013141          401 PGNK  404 (449)
Q Consensus       401 ~~~~  404 (449)
                      +.+.
T Consensus       504 ~~np  507 (510)
T KOG0144|consen  504 RNNP  507 (510)
T ss_pred             cCCC
Confidence            6543

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

Probab=100.00  E-value=8.8e-37  Score=310.59  Aligned_cols=277  Identities=18%  Similarity=0.296  Sum_probs=208.5

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhhcc------------CCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHh
Q 013141          110 FTNDETKTIWIGDLFHWMDETFLHNCFSHT------------GQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY  177 (449)
Q Consensus       110 ~~~~~~~~l~v~nLp~~~t~~~l~~~f~~~------------G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l  177 (449)
                      ......++|||+|||+.+|+++|+++|..+            +.|.++.+      ++.+|||||+|.+.++|..|| .|
T Consensus       170 ~~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~------~~~kg~afVeF~~~e~A~~Al-~l  242 (509)
T TIGR01642       170 QATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI------NKEKNFAFLEFRTVEEATFAM-AL  242 (509)
T ss_pred             cCCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEE------CCCCCEEEEEeCCHHHHhhhh-cC
Confidence            345678999999999999999999999975            23444444      345689999999999999999 59


Q ss_pred             cCCCCCCCCCcccccccccCCC------------------------CCccccCCCceEEEcCCCCCCCHHHHHHHHhhhC
Q 013141          178 SGSLMPNTDQPFRLNWATFSGS------------------------DRRTEACSDLSIFVGDLAPDVTDSILQETFSSKY  233 (449)
Q Consensus       178 ~~~~~~~~~~~~~~~~~~~~~~------------------------~~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~  233 (449)
                      ++..+.+  ..|+|.+......                        .........++|||+|||..+++++|+++|. .|
T Consensus       243 ~g~~~~g--~~l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~-~~  319 (509)
T TIGR01642       243 DSIIYSN--VFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLE-SF  319 (509)
T ss_pred             CCeEeeC--ceeEecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHH-hc
Confidence            9988855  4555543221110                        0001123457899999999999999999995 99


Q ss_pred             CCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecCCCCCCchhhcchhhhhhhcCCCCCCC
Q 013141          234 PSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNG  313 (449)
Q Consensus       234 g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  313 (449)
                      |.|..+.++++..++.++|||||+|.+.++|..||+.|+|..|.++.|.|.++.................. ..   ...
T Consensus       320 G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~~~~~~~~~~~~~~~~-~~---~~~  395 (509)
T TIGR01642       320 GDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVGANQATIDTSNGMAPV-TL---LAK  395 (509)
T ss_pred             CCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccCCCCCCcccccccccc-cc---ccc
Confidence            99999999999999999999999999999999999999999999999999998754332111100000000 00   000


Q ss_pred             CCcCCCCCCCCCCCcEEEEcCCCCC--C--------CHhHHHhhccccCceEEEEEeCC---------CcEEEEEecCHH
Q 013141          314 ARVQGSQSDGESNNATIFVGALDSD--V--------SDEDLREPFSQFGEILSVKIPVG---------KGCGFVQFANRK  374 (449)
Q Consensus       314 ~~~~~~~~~~~~~~~~l~V~nlp~~--~--------t~~~L~~~f~~~G~v~~v~i~~~---------~g~afV~F~~~~  374 (449)
                      .............+.+|+|.||...  +        ..++|+++|+.||.|++|.|++.         .|+|||+|.+.+
T Consensus       396 ~~~~~~~~~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e  475 (509)
T TIGR01642       396 ALSQSILQIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVR  475 (509)
T ss_pred             cchhhhccccCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeeccCcCCCcCCCcceEEEEECCHH
Confidence            0000000112345788999999642  1        23689999999999999999863         489999999999


Q ss_pred             HHHHHHHHhcCCeeCCeEEEEEecCC
Q 013141          375 DAEVALQKLQGTAIGKQTVRLSWGRN  400 (449)
Q Consensus       375 ~A~~A~~~l~g~~~~g~~l~v~~~~~  400 (449)
                      +|.+|+..|||+.|.|+.|.|.|...
T Consensus       476 ~A~~A~~~lnGr~~~gr~v~~~~~~~  501 (509)
T TIGR01642       476 SAEKAMEGMNGRKFNDRVVVAAFYGE  501 (509)
T ss_pred             HHHHHHHHcCCCEECCeEEEEEEeCH
Confidence            99999999999999999999999764

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

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

Probab=100.00  E-value=5.9e-36  Score=279.73  Aligned_cols=281  Identities=20%  Similarity=0.325  Sum_probs=219.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccccccc
Q 013141          116 KTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWAT  195 (449)
Q Consensus       116 ~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~~~  195 (449)
                      .||||++||++++.++|.++|+.+|+|..|.++.++.++.++||+||.|.-.|++++|++..++..+.+  +.+++..+.
T Consensus         6 ~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~G--r~l~v~~A~   83 (678)
T KOG0127|consen    6 ATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEG--RILNVDPAK   83 (678)
T ss_pred             ceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccc--eeccccccc
Confidence            799999999999999999999999999999999999999999999999999999999999999988855  445554444


Q ss_pred             cCCCCC---------------------ccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEE
Q 013141          196 FSGSDR---------------------RTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYG  254 (449)
Q Consensus       196 ~~~~~~---------------------~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~a  254 (449)
                      ......                     .....+..+|.|+|||+.+.+++|+.+|+ .||.|.+|.|++....+.+ |||
T Consensus        84 ~R~r~e~~~~~e~~~veK~~~q~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs-~~G~V~Ei~IP~k~dgklc-GFa  161 (678)
T KOG0127|consen   84 KRARSEEVEKGENKAVEKPIEQKRPTKAKVDLPKWRLIIRNLPFKCKKPDLKNVFS-NFGKVVEIVIPRKKDGKLC-GFA  161 (678)
T ss_pred             ccccchhcccccchhhhcccccCCcchhhccCccceEEeecCCcccCcHHHHHHHh-hcceEEEEEcccCCCCCcc-ceE
Confidence            221111                     01123367899999999999999999997 9999999999988775555 999


Q ss_pred             EEEeCCHHHHHHHHHHhCCceecCcceEEeecCCCCCCchhhc------chh---hh-hh----------------hcCC
Q 013141          255 FVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKASGYQQQ------YSS---QA-LV----------------LAGG  308 (449)
Q Consensus       255 fV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~~~~~~~~~~~------~~~---~~-~~----------------~~~~  308 (449)
                      ||.|....+|..|++.+|+..|+||+|-|+|+.++........      ...   .. ..                .+.+
T Consensus       162 FV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed~e~d~ed  241 (678)
T KOG0127|consen  162 FVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDKDTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEEDGEEDSED  241 (678)
T ss_pred             EEEEeeHHHHHHHHHhccCceecCceeEEeeecccccccccchhhhhhhhhccchhhhcccccccccccchhcccccccc
Confidence            9999999999999999999999999999999988764322110      000   00 00                0000


Q ss_pred             CC----------------------CCCC-C---cCC------CCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEE
Q 013141          309 PG----------------------SNGA-R---VQG------SQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILS  356 (449)
Q Consensus       309 ~~----------------------~~~~-~---~~~------~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~  356 (449)
                      ..                      .... +   ...      ..........+|||.|||+++|+++|.++|++||.|.+
T Consensus       242 eEe~D~~se~~ee~~~~Eee~~~vDd~e~S~~~~~~k~~q~k~~~en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~y  321 (678)
T KOG0127|consen  242 EEETDGNSEAFEEGEESEEEEDDVDDEESSGKKESDKKAQNKTTRENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKY  321 (678)
T ss_pred             cccccccchhhhccccccccccccccccccccCcccchhccccccccccccceEEEecCCccccHHHHHHHHHhhcccee
Confidence            00                      0000 0   000      00122234579999999999999999999999999999


Q ss_pred             EEEeC------CCcEEEEEecCHHHHHHHHHHh-----cC-CeeCCeEEEEEecCC
Q 013141          357 VKIPV------GKGCGFVQFANRKDAEVALQKL-----QG-TAIGKQTVRLSWGRN  400 (449)
Q Consensus       357 v~i~~------~~g~afV~F~~~~~A~~A~~~l-----~g-~~~~g~~l~v~~~~~  400 (449)
                      +.|+.      ++|+|||.|.+..+|..||+..     .| ..|+||.|.|+.+-.
T Consensus       322 a~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR~Lkv~~Av~  377 (678)
T KOG0127|consen  322 AIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGRLLKVTLAVT  377 (678)
T ss_pred             EEEEeccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEeccEEeeeeccc
Confidence            98875      4799999999999999999887     23 678999999998764

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=100.00  E-value=5e-35  Score=276.56  Aligned_cols=169  Identities=25%  Similarity=0.489  Sum_probs=151.8

Q ss_pred             ccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEE
Q 013141          204 EACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRI  283 (449)
Q Consensus       204 ~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  283 (449)
                      .....++|||++||+++|+++|+++|+ .||.|.+|+|++|..+++++|||||+|.++++|++||+.|++..+.+++|+|
T Consensus       103 ~~~~~~~LfVgnLp~~~te~~L~~lF~-~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V  181 (346)
T TIGR01659       103 TNNSGTNLIVNYLPQDMTDRELYALFR-TIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKV  181 (346)
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHH-hcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeee
Confidence            345678999999999999999999995 9999999999999999999999999999999999999999999999999999


Q ss_pred             eecCCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC-
Q 013141          284 DVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-  362 (449)
Q Consensus       284 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~-  362 (449)
                      .++++...                                ....++|||.|||.++++++|+++|++||.|++|+|+++ 
T Consensus       182 ~~a~p~~~--------------------------------~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~  229 (346)
T TIGR01659       182 SYARPGGE--------------------------------SIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDK  229 (346)
T ss_pred             eccccccc--------------------------------ccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecC
Confidence            99865321                                112467999999999999999999999999999999865 


Q ss_pred             -----CcEEEEEecCHHHHHHHHHHhcCCeeCC--eEEEEEecCCCCCCC
Q 013141          363 -----KGCGFVQFANRKDAEVALQKLQGTAIGK--QTVRLSWGRNPGNKQ  405 (449)
Q Consensus       363 -----~g~afV~F~~~~~A~~A~~~l~g~~~~g--~~l~v~~~~~~~~~~  405 (449)
                           +++|||+|.+.++|++||+.||+..|.+  +.|+|.|++......
T Consensus       230 ~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~a~~~~~~~  279 (346)
T TIGR01659       230 LTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAEEHGKAK  279 (346)
T ss_pred             CCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCcccccc
Confidence                 4899999999999999999999999876  789999998765443

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

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=100.00  E-value=7.7e-33  Score=261.69  Aligned_cols=174  Identities=26%  Similarity=0.473  Sum_probs=156.1

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcc
Q 013141          110 FTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPF  189 (449)
Q Consensus       110 ~~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~  189 (449)
                      ......++|||+|||+++|+++|+++|+.||+|++|+|++|+.+++++|||||+|.++++|++||+.|++..+.  .+.|
T Consensus       102 ~~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~--gr~i  179 (346)
T TIGR01659       102 DTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVR--NKRL  179 (346)
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccC--Ccee
Confidence            45567889999999999999999999999999999999999999999999999999999999999999999884  5678


Q ss_pred             cccccccCCCCCccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH
Q 013141          190 RLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT  269 (449)
Q Consensus       190 ~~~~~~~~~~~~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~  269 (449)
                      +|.++....     .....++|||+|||.++|+++|+++|+ .||+|..+++++++.+++++|+|||+|.+.++|++||+
T Consensus       180 ~V~~a~p~~-----~~~~~~~lfV~nLp~~vtee~L~~~F~-~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~  253 (346)
T TIGR01659       180 KVSYARPGG-----ESIKDTNLYVTNLPRTITDDQLDTIFG-KYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAIS  253 (346)
T ss_pred             eeecccccc-----cccccceeEEeCCCCcccHHHHHHHHH-hcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHH
Confidence            888776432     123456899999999999999999995 99999999999999999999999999999999999999


Q ss_pred             HhCCceecC--cceEEeecCCCCC
Q 013141          270 EMNGVYCSS--RPMRIDVATPKKA  291 (449)
Q Consensus       270 ~l~g~~~~g--~~i~v~~~~~~~~  291 (449)
                      .||+..+.+  ++|+|.++.....
T Consensus       254 ~lng~~~~g~~~~l~V~~a~~~~~  277 (346)
T TIGR01659       254 ALNNVIPEGGSQPLTVRLAEEHGK  277 (346)
T ss_pred             HhCCCccCCCceeEEEEECCcccc
Confidence            999998866  6888888876543

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

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

Probab=99.97  E-value=9e-31  Score=248.74  Aligned_cols=239  Identities=29%  Similarity=0.564  Sum_probs=213.8

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccccccc
Q 013141          116 KTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWAT  195 (449)
Q Consensus       116 ~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~~~  195 (449)
                      .+|||+   +++||..|.++|+++|+|+++++.+|. |  +-|||||.|.++++|++||..+|...+  .++++++.|+.
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t--slgy~yvnf~~~~da~~A~~~~n~~~~--~~~~~rim~s~   73 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T--SLGYAYVNFQQPADAERALDTMNFDVL--KGKPIRIMWSQ   73 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecC-C--ccceEEEecCCHHHHHHHHHHcCCccc--CCcEEEeehhc
Confidence            468999   999999999999999999999999997 6  999999999999999999999999999  66899999987


Q ss_pred             cCCCCCccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCce
Q 013141          196 FSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVY  275 (449)
Q Consensus       196 ~~~~~~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~  275 (449)
                      .....          |||.||+++++..+|.++|+ .||.|.++++..+.. | ++|| ||+|+++++|.+||+.+||..
T Consensus        74 rd~~~----------~~i~nl~~~~~~~~~~d~f~-~~g~ilS~kv~~~~~-g-~kg~-FV~f~~e~~a~~ai~~~ng~l  139 (369)
T KOG0123|consen   74 RDPSL----------VFIKNLDESIDNKSLYDTFS-EFGNILSCKVATDEN-G-SKGY-FVQFESEESAKKAIEKLNGML  139 (369)
T ss_pred             cCCce----------eeecCCCcccCcHHHHHHHH-hhcCeeEEEEEEcCC-C-ceee-EEEeCCHHHHHHHHHHhcCcc
Confidence            44322          99999999999999999996 999999999999965 5 8999 999999999999999999999


Q ss_pred             ecCcceEEeecCCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceE
Q 013141          276 CSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEIL  355 (449)
Q Consensus       276 ~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~  355 (449)
                      +.++.|.|.....+..+.....                       . ....-+.++|.+++.+++++.|.++|..+|.|.
T Consensus       140 l~~kki~vg~~~~~~er~~~~~-----------------------~-~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~  195 (369)
T KOG0123|consen  140 LNGKKIYVGLFERKEEREAPLG-----------------------E-YKKRFTNVYVKNLEEDSTDEELKDLFSAYGSIT  195 (369)
T ss_pred             cCCCeeEEeeccchhhhccccc-----------------------c-hhhhhhhhheeccccccchHHHHHhhcccCcce
Confidence            9999999999888766532111                       1 223356789999999999999999999999999


Q ss_pred             EEEEeC-----CCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCC
Q 013141          356 SVKIPV-----GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRN  400 (449)
Q Consensus       356 ~v~i~~-----~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  400 (449)
                      ++.+++     .++++||.|.+.++|..|++.||+..+.+..+.|.-+..
T Consensus       196 s~~v~~~~~g~~~~~gfv~f~~~e~a~~av~~l~~~~~~~~~~~V~~aqk  245 (369)
T KOG0123|consen  196 SVAVMRDSIGKSKGFGFVNFENPEDAKKAVETLNGKIFGDKELYVGRAQK  245 (369)
T ss_pred             EEEEeecCCCCCCCccceeecChhHHHHHHHhccCCcCCccceeeccccc
Confidence            999987     379999999999999999999999999999999987765

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

Probab=99.97  E-value=3.3e-30  Score=230.03  Aligned_cols=281  Identities=20%  Similarity=0.338  Sum_probs=214.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccccc
Q 013141          114 ETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNW  193 (449)
Q Consensus       114 ~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~  193 (449)
                      --|+|||+.|.+++.|+.|+..|.+||+|++|.+..|+.|++++|||||||+-+|.|..|++.+|+..+.+  +.|++..
T Consensus       112 iMcRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGG--RNiKVgr  189 (544)
T KOG0124|consen  112 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGG--RNIKVGR  189 (544)
T ss_pred             HhHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccC--ccccccC
Confidence            56899999999999999999999999999999999999999999999999999999999999999999966  4555543


Q ss_pred             cccCCCCC------ccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHH
Q 013141          194 ATFSGSDR------RTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRA  267 (449)
Q Consensus       194 ~~~~~~~~------~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A  267 (449)
                      ...-....      ..+...-++|||..+.++++++||+..| +.||+|..+.+-+++..+..|||+|++|.+..+-..|
T Consensus       190 PsNmpQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVF-EAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eA  268 (544)
T KOG0124|consen  190 PSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVF-EAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEA  268 (544)
T ss_pred             CCCCcccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHH-HhhcceeeEEeeccCCCCCccceeeEEeccccchHHH
Confidence            32111111      1223445789999999999999999999 6999999999999999899999999999999999999


Q ss_pred             HHHhCCceecCcceEEeecCCCCCCchhhcch----h-------------hh-hhhc--------CCCC-----------
Q 013141          268 MTEMNGVYCSSRPMRIDVATPKKASGYQQQYS----S-------------QA-LVLA--------GGPG-----------  310 (449)
Q Consensus       268 ~~~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~----~-------------~~-~~~~--------~~~~-----------  310 (449)
                      |..||-..++|..|+|-.+.............    .             .. ....        +.++           
T Consensus       269 iasMNlFDLGGQyLRVGk~vTPP~aLl~Pat~s~~P~aaaVAaAAaTAKi~A~eAvAg~avlg~~G~~~~vSpA~~aa~p  348 (544)
T KOG0124|consen  269 IASMNLFDLGGQYLRVGKCVTPPDALLQPATVSAIPAAAAVAAAAATAKIMAAEAVAGSAVLGTVGAPGLVSPAPRAAQP  348 (544)
T ss_pred             hhhcchhhcccceEecccccCCCchhcCCCCcccCchHHHHHHHHHHHHHHHHHHhccCCcccccCCccccCccccccCC
Confidence            99999999999999998775433211000000    0             00 0000        0000           


Q ss_pred             ---------------------CCC-------------------CCcCC---------------C----------------
Q 013141          311 ---------------------SNG-------------------ARVQG---------------S----------------  319 (449)
Q Consensus       311 ---------------------~~~-------------------~~~~~---------------~----------------  319 (449)
                                           ...                   ....+               .                
T Consensus       349 ~~~l~qa~~a~~~pgvi~~vtP~~P~iP~~i~p~g~v~P~LA~ppT~g~L~kkkeKe~eelqpkl~~~~~L~~QE~msI~  428 (544)
T KOG0124|consen  349 LGTLPQAVMAAQAPGVITGVTPARPPIPVTIPPVGVVNPILASPPTLGLLEKKKEKEEEELQPKLERPEMLSEQEHMSIS  428 (544)
T ss_pred             CCCccccchhccCCceeccCCCCCCCCCccCCCcceechhhcCCCchhhcchhhhhhHhhhcccccCHHHhhhhhCcccc
Confidence                                 000                   00000               0                


Q ss_pred             ----------CCCCCCCCcEEEEcCC--CCCCC---HhHHHhhccccCceEEEEEeCCC----------cEEEEEecCHH
Q 013141          320 ----------QSDGESNNATIFVGAL--DSDVS---DEDLREPFSQFGEILSVKIPVGK----------GCGFVQFANRK  374 (449)
Q Consensus       320 ----------~~~~~~~~~~l~V~nl--p~~~t---~~~L~~~f~~~G~v~~v~i~~~~----------g~afV~F~~~~  374 (449)
                                ..-....+++|.++|+  |.+++   +.+|.+.|.+||.|.+|.|...+          -..||+|+...
T Consensus       429 G~sARhlvMqkLmR~~~S~VivLRNMV~P~DiDe~LegEi~EECgKfG~V~rViI~nekq~e~edaeiiVKIFVefS~~~  508 (544)
T KOG0124|consen  429 GSSARHLVMQKLMRKQESTVIVLRNMVDPKDIDEDLEGEITEECGKFGAVNRVIIYNEKQGEEEDAEIIVKIFVEFSIAS  508 (544)
T ss_pred             CccHHHHHHHHHhccccCcEEEEeccCChhhhhhHHHHHHHHHHhcccceeEEEEEecccccccchhhhheeeeeechhh
Confidence                      0001234567888887  44444   47899999999999999987532          35799999999


Q ss_pred             HHHHHHHHhcCCeeCCeEEEEEe
Q 013141          375 DAEVALQKLQGTAIGKQTVRLSW  397 (449)
Q Consensus       375 ~A~~A~~~l~g~~~~g~~l~v~~  397 (449)
                      ++.+|.++|+|+.|+|+++..+.
T Consensus       509 e~~rak~ALdGRfFgGr~VvAE~  531 (544)
T KOG0124|consen  509 ETHRAKQALDGRFFGGRKVVAEV  531 (544)
T ss_pred             HHHHHHHhhccceecCceeehhh
Confidence            99999999999999999987664

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

Probab=99.97  E-value=1.6e-29  Score=240.16  Aligned_cols=265  Identities=29%  Similarity=0.460  Sum_probs=216.1

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccccccccC
Q 013141          118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATFS  197 (449)
Q Consensus       118 l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~~~~~  197 (449)
                      |||.||+++++.++|.++|+.||.|++|++.++.+ | ++|| ||+|+++++|.+|++.+|+..+.+..+.+-+...+..
T Consensus        79 ~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~-g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~e  155 (369)
T KOG0123|consen   79 VFIKNLDESIDNKSLYDTFSEFGNILSCKVATDEN-G-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKEE  155 (369)
T ss_pred             eeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCC-C-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchhh
Confidence            99999999999999999999999999999999964 5 9999 9999999999999999999999654443333222211


Q ss_pred             CCCCc-cccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee
Q 013141          198 GSDRR-TEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYC  276 (449)
Q Consensus       198 ~~~~~-~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~  276 (449)
                      ..... .....-..+++.+++.+.+.+.|.++|. .+|.|..+.++.+.. +.+++|+||.|.+.++|..|++.|++..+
T Consensus       156 r~~~~~~~~~~~t~v~vk~~~~~~~~~~l~~~f~-~~g~i~s~~v~~~~~-g~~~~~gfv~f~~~e~a~~av~~l~~~~~  233 (369)
T KOG0123|consen  156 REAPLGEYKKRFTNVYVKNLEEDSTDEELKDLFS-AYGSITSVAVMRDSI-GKSKGFGFVNFENPEDAKKAVETLNGKIF  233 (369)
T ss_pred             hcccccchhhhhhhhheeccccccchHHHHHhhc-ccCcceEEEEeecCC-CCCCCccceeecChhHHHHHHHhccCCcC
Confidence            11111 1223345789999999999999999995 999999999999855 66999999999999999999999999999


Q ss_pred             cCcceEEeecCCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEE
Q 013141          277 SSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILS  356 (449)
Q Consensus       277 ~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~  356 (449)
                      .+..+.|..+..+..+...........              ............|||.||+..++++.|+++|+.||.|.+
T Consensus       234 ~~~~~~V~~aqkk~e~~~~l~~~~~~~--------------~~~~~~~~~~~nl~vknld~~~~~e~L~~~f~~~GeI~s  299 (369)
T KOG0123|consen  234 GDKELYVGRAQKKSEREAELKRKFEQE--------------FAKRSVSLQGANLYVKNLDETLSDEKLRKIFSSFGEITS  299 (369)
T ss_pred             CccceeecccccchhhHHHHhhhhHhh--------------hhhccccccccccccccCccccchhHHHHHHhcccceee
Confidence            999999998887433321111100000              001222445678999999999999999999999999999


Q ss_pred             EEEeC-----CCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCC
Q 013141          357 VKIPV-----GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNP  401 (449)
Q Consensus       357 v~i~~-----~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~  401 (449)
                      ++|+.     .+|++||.|.+.++|.+|+..+|+..+.++.|.|.++...
T Consensus       300 ~kv~~~~~g~skG~gfV~fs~~eeA~~A~~~~n~~~i~~k~l~vav~qr~  349 (369)
T KOG0123|consen  300 AKVMVDENGKSKGFGFVEFSSPEEAKKAMTEMNGRLIGGKPLYVAVAQRK  349 (369)
T ss_pred             EEEEeccCCCccceEEEEcCCHHHHHHHHHhhChhhhcCCchhhhHHhhh
Confidence            99886     3799999999999999999999999999999999988743

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

Probab=99.97  E-value=2.9e-30  Score=243.27  Aligned_cols=285  Identities=18%  Similarity=0.346  Sum_probs=217.4

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      .+...++||+--|+-.+++.||.+||+.+|.|.+|.+|.|+.+++++|.|||+|.+.+.+-.|+ .|.|..+.+  .+|.
T Consensus       175 eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~ai-aLsGqrllg--~pv~  251 (549)
T KOG0147|consen  175 EERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAI-ALSGQRLLG--VPVI  251 (549)
T ss_pred             hHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHh-hhcCCcccC--ceeE
Confidence            3456789999999999999999999999999999999999999999999999999999999999 789988855  4444


Q ss_pred             ccccccCCCCC---------ccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCH
Q 013141          191 LNWATFSGSDR---------RTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDE  261 (449)
Q Consensus       191 ~~~~~~~~~~~---------~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~  261 (449)
                      +..........         .....+-..|||+||.++++++.|+.+| +.||.|..|.+.+|..||.++||+||+|.+.
T Consensus       252 vq~sEaeknr~a~~s~a~~~k~~~~p~~rl~vgnLHfNite~~lr~if-epfg~Ie~v~l~~d~~tG~skgfGfi~f~~~  330 (549)
T KOG0147|consen  252 VQLSEAEKNRAANASPALQGKGFTGPMRRLYVGNLHFNITEDMLRGIF-EPFGKIENVQLTKDSETGRSKGFGFITFVNK  330 (549)
T ss_pred             ecccHHHHHHHHhccccccccccccchhhhhhcccccCchHHHHhhhc-cCcccceeeeeccccccccccCcceEEEecH
Confidence            43332111100         0111222339999999999999999999 6999999999999998999999999999999


Q ss_pred             HHHHHHHHHhCCceecCcceEEeecCCCCCCchh-----hc---------------chhhhhhhcCCC------------
Q 013141          262 NERSRAMTEMNGVYCSSRPMRIDVATPKKASGYQ-----QQ---------------YSSQALVLAGGP------------  309 (449)
Q Consensus       262 ~~A~~A~~~l~g~~~~g~~i~v~~~~~~~~~~~~-----~~---------------~~~~~~~~~~~~------------  309 (449)
                      ++|.+|++.|||.++.|+.|+|.....+......     ..               .........+..            
T Consensus       331 ~~ar~a~e~lngfelAGr~ikV~~v~~r~~~~~a~~~~~d~D~~d~~gl~~~~~g~~Ql~~kla~~~~~~~~s~~~~~l~  410 (549)
T KOG0147|consen  331 EDARKALEQLNGFELAGRLIKVSVVTERVDTKEAAVTQFDFDEDDRQGLSLGSGGRNQLMAKLAEGKGRSLPSTAISALL  410 (549)
T ss_pred             HHHHHHHHHhccceecCceEEEEEeeeecccccccccccccchhhccccccccccHHHHHHHHhccCCccccchhhhHHH
Confidence            9999999999999999999999876554322211     00               000000000000            


Q ss_pred             -----------C--C--CCCCcCCCCCCCCCCCcEEEEcCCCCC--CC--------HhHHHhhccccCceEEEEEeCCC-
Q 013141          310 -----------G--S--NGARVQGSQSDGESNNATIFVGALDSD--VS--------DEDLREPFSQFGEILSVKIPVGK-  363 (449)
Q Consensus       310 -----------~--~--~~~~~~~~~~~~~~~~~~l~V~nlp~~--~t--------~~~L~~~f~~~G~v~~v~i~~~~-  363 (449)
                                 .  .  .........+.-...+.|+.|.|+=..  .|        .+||.+.|.+||.|..|.+.++. 
T Consensus       411 ~~~~~~~~~~~~~~~~~~~~~p~~~~p~~~i~t~C~lL~nMFdpstete~n~d~eI~edV~Eec~k~g~v~hi~vd~ns~  490 (549)
T KOG0147|consen  411 LLAKLASAAQFNGVVRVRSVDPADASPAFDIPTQCLLLSNMFDPSTETEPNWDQEIREDVIEECGKHGKVCHIFVDKNSA  490 (549)
T ss_pred             hccccchHHhhcCCcCccccCccccccccCCccHHHHHhhcCCcccccCcchhhHHHHHHHHHHHhcCCeeEEEEccCCC
Confidence                       0  0  000000001111256678888888332  22        38899999999999999998865 


Q ss_pred             cEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 013141          364 GCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGR  399 (449)
Q Consensus       364 g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  399 (449)
                      |++||.|.+.++|..|+.+|||.+|.|+.|..+|-.
T Consensus       491 g~VYvrc~s~~~A~~a~~alhgrWF~gr~Ita~~~~  526 (549)
T KOG0147|consen  491 GCVYVRCPSAEAAGTAVKALHGRWFAGRMITAKYLP  526 (549)
T ss_pred             ceEEEecCcHHHHHHHHHHHhhhhhccceeEEEEee
Confidence            999999999999999999999999999999999854

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

Probab=99.96  E-value=3.1e-28  Score=241.60  Aligned_cols=227  Identities=19%  Similarity=0.248  Sum_probs=173.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCC-cEEEEEEe-cCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccc
Q 013141          114 ETKTIWIGDLFHWMDETFLHNCFSHTGQ-VVNVKVIR-NKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRL  191 (449)
Q Consensus       114 ~~~~l~v~nLp~~~t~~~l~~~f~~~G~-v~~v~~~~-~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~  191 (449)
                      ..++|||+|||+++++++|.++|+.++. ++++.++. ....++++|||||+|.+.++|.+|++.|+...+...++.|.|
T Consensus       137 ~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~V  216 (578)
T TIGR01648       137 DNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAV  216 (578)
T ss_pred             cCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccceEecCceEEE
Confidence            4688999999999999999999999864 55554443 234567899999999999999999998876554445678999


Q ss_pred             cccccCCCCCccccCCCceEEEcCCCCCCCHHHHHHHHhhhC--CCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH
Q 013141          192 NWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKY--PSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT  269 (449)
Q Consensus       192 ~~~~~~~~~~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~--g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~  269 (449)
                      +|+.+............++|||+||+.++|+++|+++|+ .|  |+|++|.+++        +||||+|.+.++|++|++
T Consensus       217 dwA~p~~~~d~~~~~~~k~LfVgNL~~~~tee~L~~~F~-~f~~G~I~rV~~~r--------gfAFVeF~s~e~A~kAi~  287 (578)
T TIGR01648       217 DWAEPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFS-EFKPGKVERVKKIR--------DYAFVHFEDREDAVKAMD  287 (578)
T ss_pred             EeecccccccccccccccEEEEeCCCCCCCHHHHHHHHH-hcCCCceEEEEeec--------CeEEEEeCCHHHHHHHHH
Confidence            998876554444444567899999999999999999995 99  9999998763        499999999999999999


Q ss_pred             HhCCceecCcceEEeecCCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhcc
Q 013141          270 EMNGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFS  349 (449)
Q Consensus       270 ~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~  349 (449)
                      .||+..|+|+.|+|+++.+............    ..+.................+.+.++++.|+++..+++.|.++|.
T Consensus       288 ~lnG~~i~Gr~I~V~~Akp~~~~~~~~~~rg----~gg~~~~~~~~~~~~g~~~sp~s~~~~~g~~~~~~~~~~~~~~f~  363 (578)
T TIGR01648       288 ELNGKELEGSEIEVTLAKPVDKKSYVRYTRG----TGGRGKERQAARQSLGQVYDPASRSLAYEDYYYHPPYAPSLHFPR  363 (578)
T ss_pred             HhCCCEECCEEEEEEEccCCCcccccccccc----cCCCcccccccccccCcccCccccccccccccccccccchhhccc
Confidence            9999999999999999988654321110000    000000000111112223445688999999999999999999999


Q ss_pred             ccCc
Q 013141          350 QFGE  353 (449)
Q Consensus       350 ~~G~  353 (449)
                      .+|.
T Consensus       364 ~~g~  367 (578)
T TIGR01648       364 MPGP  367 (578)
T ss_pred             cCcc
Confidence            8875

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.

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

Probab=99.96  E-value=1.1e-28  Score=244.95  Aligned_cols=176  Identities=20%  Similarity=0.431  Sum_probs=151.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeec
Q 013141          207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVA  286 (449)
Q Consensus       207 ~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~  286 (449)
                      ..++|||+||++++++++|+++|. .||.|.+|++++|+.+++++|||||+|.+.++|.+|++.|||..|.|+.|+|.+.
T Consensus       106 ~~~rLfVGnLp~~~tEe~Lr~lF~-~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp  184 (612)
T TIGR01645       106 IMCRVYVGSISFELREDTIRRAFD-PFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  184 (612)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHH-ccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeeccc
Confidence            457899999999999999999995 9999999999999999999999999999999999999999999999999999864


Q ss_pred             CCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeC-----
Q 013141          287 TPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV-----  361 (449)
Q Consensus       287 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~-----  361 (449)
                      ........                     ............++|||+||+.++++++|+++|+.||.|.+++|.+     
T Consensus       185 ~~~p~a~~---------------------~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tg  243 (612)
T TIGR01645       185 SNMPQAQP---------------------IIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGR  243 (612)
T ss_pred             cccccccc---------------------ccccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCC
Confidence            33211100                     0000011122457899999999999999999999999999999986     


Q ss_pred             -CCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCCCC
Q 013141          362 -GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNK  404 (449)
Q Consensus       362 -~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~~~  404 (449)
                       .+|||||+|.+.++|.+|++.||+..|+|+.|+|.++..+...
T Consensus       244 ksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi~pP~~  287 (612)
T TIGR01645       244 GHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTPPDA  287 (612)
T ss_pred             CcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecCCCccc
Confidence             3689999999999999999999999999999999999976544

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.96  E-value=7.3e-29  Score=213.36  Aligned_cols=169  Identities=30%  Similarity=0.570  Sum_probs=155.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccccc
Q 013141          114 ETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNW  193 (449)
Q Consensus       114 ~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~  193 (449)
                      .+--|||+.|..+++.++|++.|.+||+|.+++|++|.+|+++|||+||.|.+.++|++||..|+|.-|  ..|.||-.|
T Consensus        61 ~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWl--G~R~IRTNW  138 (321)
T KOG0148|consen   61 QHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWL--GRRTIRTNW  138 (321)
T ss_pred             cceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeee--ccceeeccc
Confidence            356799999999999999999999999999999999999999999999999999999999999999998  568899999


Q ss_pred             cccCCCCCc-----------cccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHH
Q 013141          194 ATFSGSDRR-----------TEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDEN  262 (449)
Q Consensus       194 ~~~~~~~~~-----------~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~  262 (449)
                      +..+..+..           ....++++||++||+.-+|+++|++.|+ .||.|.+|++.++      +||+||.|.+.|
T Consensus       139 ATRKp~e~n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs-~fG~I~EVRvFk~------qGYaFVrF~tkE  211 (321)
T KOG0148|consen  139 ATRKPSEMNGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFS-PFGPIQEVRVFKD------QGYAFVRFETKE  211 (321)
T ss_pred             cccCccccCCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcc-cCCcceEEEEecc------cceEEEEecchh
Confidence            987764432           3456788999999999999999999996 9999999999988      679999999999


Q ss_pred             HHHHHHHHhCCceecCcceEEeecCCCCC
Q 013141          263 ERSRAMTEMNGVYCSSRPMRIDVATPKKA  291 (449)
Q Consensus       263 ~A~~A~~~l~g~~~~g~~i~v~~~~~~~~  291 (449)
                      .|..||..+|+.+|.|..+++.|.+....
T Consensus       212 aAahAIv~mNntei~G~~VkCsWGKe~~~  240 (321)
T KOG0148|consen  212 AAAHAIVQMNNTEIGGQLVRCSWGKEGDD  240 (321)
T ss_pred             hHHHHHHHhcCceeCceEEEEeccccCCC
Confidence            99999999999999999999999987654

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.96  E-value=2e-28  Score=237.67  Aligned_cols=177  Identities=26%  Similarity=0.494  Sum_probs=156.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccccc
Q 013141          114 ETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNW  193 (449)
Q Consensus       114 ~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~  193 (449)
                      ..++|||+|||+++++++|+++|+.||.|..+.++.+..++.++|||||+|.+.++|++|++.|++..+.+....+++.|
T Consensus        88 ~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~i~v~~  167 (352)
T TIGR01661        88 KGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKF  167 (352)
T ss_pred             ccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEE
Confidence            45689999999999999999999999999999999998889999999999999999999999999999988777888877


Q ss_pred             cccCCCCCc-----------------------------------------------------------------------
Q 013141          194 ATFSGSDRR-----------------------------------------------------------------------  202 (449)
Q Consensus       194 ~~~~~~~~~-----------------------------------------------------------------------  202 (449)
                      +........                                                                       
T Consensus       168 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  247 (352)
T TIGR01661       168 ANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAAQRASPP  247 (352)
T ss_pred             CCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhhhhhhhcccccccccccCCCc
Confidence            643220000                                                                       


Q ss_pred             ----------------cccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHH
Q 013141          203 ----------------TEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSR  266 (449)
Q Consensus       203 ----------------~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~  266 (449)
                                      .......+|||+|||+++++++|+++|+ .||.|.++++++|..++.++|||||+|.+.++|.+
T Consensus       248 ~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~~e~~L~~~F~-~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~  326 (352)
T TIGR01661       248 ATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFG-PFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAM  326 (352)
T ss_pred             cccccccccccCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHH-hCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHH
Confidence                            0011123699999999999999999995 99999999999999899999999999999999999


Q ss_pred             HHHHhCCceecCcceEEeecCCCCC
Q 013141          267 AMTEMNGVYCSSRPMRIDVATPKKA  291 (449)
Q Consensus       267 A~~~l~g~~~~g~~i~v~~~~~~~~  291 (449)
                      ||+.|||..|+|+.|+|.|...+..
T Consensus       327 Ai~~lnG~~~~gr~i~V~~~~~~~~  351 (352)
T TIGR01661       327 AILSLNGYTLGNRVLQVSFKTNKAY  351 (352)
T ss_pred             HHHHhCCCEECCeEEEEEEccCCCC
Confidence            9999999999999999999988753

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

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

Probab=99.96  E-value=5.2e-28  Score=234.08  Aligned_cols=257  Identities=23%  Similarity=0.389  Sum_probs=206.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      ...+.|+|+|||..+..++|..+|..||.|..|.+.+.   |.   -++|+|.+..+|..|++.|....+  ...++.+.
T Consensus       383 rs~~vil~kNlpa~t~~~elt~~F~~fG~i~rvllp~~---G~---~aiv~fl~p~eAr~Afrklaysr~--k~~plyle  454 (725)
T KOG0110|consen  383 RSDTVILVKNLPAGTLSEELTEAFLRFGEIGRVLLPPG---GT---GAIVEFLNPLEARKAFRKLAYSRF--KSAPLYLE  454 (725)
T ss_pred             hhcceeeeccCccccccHHHHHHhhcccccceeecCcc---cc---eeeeeecCccchHHHHHHhchhhh--ccCccccc
Confidence            44578999999999999999999999999999955432   21   499999999999999999887766  33445454


Q ss_pred             ccccCCCC----------------------C------------c-----------cccCCCceEEEcCCCCCCCHHHHHH
Q 013141          193 WATFSGSD----------------------R------------R-----------TEACSDLSIFVGDLAPDVTDSILQE  227 (449)
Q Consensus       193 ~~~~~~~~----------------------~------------~-----------~~~~~~~~l~v~~lp~~~t~~~l~~  227 (449)
                      |+....-.                      +            .           ......++|||.||++++|.++|..
T Consensus       455 ~aP~dvf~~~pka~~~~~e~~~~~ee~~~Er~s~~d~~v~eD~d~te~ss~a~~a~~~~~~t~lfvkNlnf~Tt~e~l~~  534 (725)
T KOG0110|consen  455 WAPEDVFTEDPKADDLSAESRSKMEENPSERVSAEDGQVEEDKDPTEESSLARVAEDEETETKLFVKNLNFDTTLEDLED  534 (725)
T ss_pred             cChhhhccCCccccccccccccccccCcceecccccccccccCCccccccchhhhhccccchhhhhhcCCcccchhHHHH
Confidence            44311000                      0            0           0001123499999999999999999


Q ss_pred             HHhhhCCCeeEEEEeecCCC---CCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecCCCCCCchhhcchhhhhh
Q 013141          228 TFSSKYPSVKGAKVIIDSNT---GRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKASGYQQQYSSQALV  304 (449)
Q Consensus       228 ~f~~~~g~v~~i~~~~~~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~  304 (449)
                      .|. ..|.|.++.|.+.+..   -.+.||+||+|.+.++|.+|++.|+|..++|+.|.|+++..+....           
T Consensus       535 ~F~-k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~~k~~~~-----------  602 (725)
T KOG0110|consen  535 LFS-KQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISENKPAST-----------  602 (725)
T ss_pred             HHH-hcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEeccCccccc-----------
Confidence            996 8999999988765432   1356999999999999999999999999999999999998332210           


Q ss_pred             hcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC------CcEEEEEecCHHHHHH
Q 013141          305 LAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEV  378 (449)
Q Consensus       305 ~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~------~g~afV~F~~~~~A~~  378 (449)
                                  .+.........+.|+|.|||+..+..+|+++|..||.|.+|+|+..      +|||||+|-++++|.+
T Consensus       603 ------------~gK~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~n  670 (725)
T KOG0110|consen  603 ------------VGKKKSKKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKN  670 (725)
T ss_pred             ------------cccccccccccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHH
Confidence                        0112223344789999999999999999999999999999999873      7999999999999999


Q ss_pred             HHHHhcCCeeCCeEEEEEecCCC
Q 013141          379 ALQKLQGTAIGKQTVRLSWGRNP  401 (449)
Q Consensus       379 A~~~l~g~~~~g~~l~v~~~~~~  401 (449)
                      |+.+|..+.|.||+|.++|+++.
T Consensus       671 A~~al~STHlyGRrLVLEwA~~d  693 (725)
T KOG0110|consen  671 AFDALGSTHLYGRRLVLEWAKSD  693 (725)
T ss_pred             HHHhhcccceechhhheehhccc
Confidence            99999999999999999999964

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

Probab=99.95  E-value=5.3e-28  Score=220.71  Aligned_cols=173  Identities=27%  Similarity=0.498  Sum_probs=153.0

Q ss_pred             ccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee---cCcc
Q 013141          204 EACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYC---SSRP  280 (449)
Q Consensus       204 ~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~---~g~~  280 (449)
                      .+.+..++||+-||..++|.||+++| |+||.|.+|.|++|+.++.++|+|||+|.+.++|.+|+.+|++...   ...+
T Consensus        30 ~d~~~vKlfVgqIprt~sE~dlr~lF-e~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~p  108 (510)
T KOG0144|consen   30 PDGSAVKLFVGQIPRTASEKDLRELF-EKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHP  108 (510)
T ss_pred             CCchhhhheeccCCccccHHHHHHHH-HHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcc
Confidence            34566789999999999999999999 6999999999999999999999999999999999999999998664   4567


Q ss_pred             eEEeecCCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEe
Q 013141          281 MRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIP  360 (449)
Q Consensus       281 i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~  360 (449)
                      |.|++++.+.++                               -...++|||+-|+..++|+||+++|++||.|++|.|+
T Consensus       109 vqvk~Ad~E~er-------------------------------~~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~il  157 (510)
T KOG0144|consen  109 VQVKYADGERER-------------------------------IVEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYIL  157 (510)
T ss_pred             eeecccchhhhc-------------------------------cccchhhhhhhccccccHHHHHHHHHhhCccchhhhe
Confidence            889998877554                               1346789999999999999999999999999999999


Q ss_pred             C-----CCcEEEEEecCHHHHHHHHHHhcCCe-eCC--eEEEEEecCCCCCCCCCC
Q 013141          361 V-----GKGCGFVQFANRKDAEVALQKLQGTA-IGK--QTVRLSWGRNPGNKQWRG  408 (449)
Q Consensus       361 ~-----~~g~afV~F~~~~~A~~A~~~l~g~~-~~g--~~l~v~~~~~~~~~~~~~  408 (449)
                      +     +||||||+|++++.|..||+.|||.. ++|  ..|.|+|+...+.+..+.
T Consensus       158 rd~~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkFADtqkdk~~~~  213 (510)
T KOG0144|consen  158 RDPDGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKFADTQKDKDGKR  213 (510)
T ss_pred             ecccccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEecccCCCchHHH
Confidence            8     48999999999999999999999984 555  579999999876655433

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

Probab=99.95  E-value=6.7e-27  Score=219.28  Aligned_cols=279  Identities=24%  Similarity=0.430  Sum_probs=202.5

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccccc
Q 013141          115 TKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWA  194 (449)
Q Consensus       115 ~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~~  194 (449)
                      .-+|+|+||||.+.+.+|..+|+.||.|++|.|.+.+ .|+..|||||.|....+|..||+.+|+..|.  +++|-++|+
T Consensus       117 k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~-dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~--gR~VAVDWA  193 (678)
T KOG0127|consen  117 KWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKK-DGKLCGFAFVQFKEKKDAEKALEFFNGNKID--GRPVAVDWA  193 (678)
T ss_pred             cceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCC-CCCccceEEEEEeeHHHHHHHHHhccCceec--CceeEEeee
Confidence            5689999999999999999999999999999999765 5777799999999999999999999999994  578888887


Q ss_pred             ccCCC-------------------------------------------CC--c---------------------c-----
Q 013141          195 TFSGS-------------------------------------------DR--R---------------------T-----  203 (449)
Q Consensus       195 ~~~~~-------------------------------------------~~--~---------------------~-----  203 (449)
                      -....                                           +.  .                     .     
T Consensus       194 V~Kd~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed~e~d~edeEe~D~~se~~ee~~~~Eee~~~vDd~e~S~~  273 (678)
T KOG0127|consen  194 VDKDTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEEDGEEDSEDEEETDGNSEAFEEGEESEEEEDDVDDEESSGK  273 (678)
T ss_pred             cccccccccchhhhhhhhhccchhhhcccccccccccchhcccccccccccccccchhhhcccccccccccccccccccc
Confidence            42100                                           00  0                     0     


Q ss_pred             --------------ccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH
Q 013141          204 --------------EACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT  269 (449)
Q Consensus       204 --------------~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~  269 (449)
                                    ......+|||+|||+++|+++|.+.|+ .||+|..+.++.++.|++++|.|||.|.+..+|..||+
T Consensus       274 ~~~~k~~q~k~~~en~~~~~tVFvRNL~fD~tEEel~~~fs-kFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~  352 (678)
T KOG0127|consen  274 KESDKKAQNKTTRENITEGKTVFVRNLPFDTTEEELKEHFS-KFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIE  352 (678)
T ss_pred             CcccchhccccccccccccceEEEecCCccccHHHHHHHHH-hhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHH
Confidence                          001125899999999999999999996 99999999999999999999999999999999999998


Q ss_pred             Hh-----CC-ceecCcceEEeecCCCCCCchhhcch-------hhhhhhcCC-------CCCCCCCc-------------
Q 013141          270 EM-----NG-VYCSSRPMRIDVATPKKASGYQQQYS-------SQALVLAGG-------PGSNGARV-------------  316 (449)
Q Consensus       270 ~l-----~g-~~~~g~~i~v~~~~~~~~~~~~~~~~-------~~~~~~~~~-------~~~~~~~~-------------  316 (449)
                      ..     .| ..+.||.|.|..+..+..........       ...++....       +.......             
T Consensus       353 ~Aspa~e~g~~ll~GR~Lkv~~Av~RkeA~dmeqkk~~Kk~~gkrNLyLa~EG~I~~gt~aAeglS~~Dm~kRer~~~~k  432 (678)
T KOG0127|consen  353 AASPASEDGSVLLDGRLLKVTLAVTRKEAADMEQKKKRKKPKGKRNLYLAREGLIRDGTPAAEGLSATDMAKRERIAERK  432 (678)
T ss_pred             hcCccCCCceEEEeccEEeeeeccchHHHHHHHHHhhhhccCCccceeeeccCccccCChhhcccchhhHHHHHHHHHHH
Confidence            76     23 67899999999998775432111110       011111110       00000000             


Q ss_pred             --CCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccc----c-CceEE-EEEeC---------CCcEEEEEecCHHHHHHH
Q 013141          317 --QGSQSDGESNNATIFVGALDSDVSDEDLREPFSQ----F-GEILS-VKIPV---------GKGCGFVQFANRKDAEVA  379 (449)
Q Consensus       317 --~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~----~-G~v~~-v~i~~---------~~g~afV~F~~~~~A~~A  379 (449)
                        .-..+......+.|.|.|||..++...|..++..    | +.|.. ++.+.         +.+++||.|...+.|.+|
T Consensus       433 ~k~lknpnlhlSrtRL~i~Nlpramn~KqL~~Ll~~Av~~~at~~kk~~R~~~~le~~~k~~s~g~aF~~f~EhEhalka  512 (678)
T KOG0127|consen  433 RKKLKNPNLHLSRTRLVIRNLPRAMNPKQLNRLLRDAVTGFATKVKKCIRQIKFLEEEKKNYSEGYAFVGFTEHEHALKA  512 (678)
T ss_pred             HHhhcCCceeeehhhhhhhcCccccCHHHHHHHHHHHHhhhhhhcchhhhhhhhHHhhhhcccccccccCccHHHHHHHh
Confidence              0011222334567999999999999998877654    2 22222 22221         379999999999999999


Q ss_pred             HHHhcCCeeCCeEEEEEecCCC
Q 013141          380 LQKLQGTAIGKQTVRLSWGRNP  401 (449)
Q Consensus       380 ~~~l~g~~~~g~~l~v~~~~~~  401 (449)
                      +..+ |. +  +.-.|.|+...
T Consensus       513 lk~~-G~-l--kq~~Vefev~~  530 (678)
T KOG0127|consen  513 LKVL-GV-L--KQAKVEFEVDG  530 (678)
T ss_pred             hhcc-cc-c--ccceEEEEecc
Confidence            9866 22 1  34455665543

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

Probab=99.94  E-value=7.9e-26  Score=227.07  Aligned_cols=174  Identities=27%  Similarity=0.488  Sum_probs=149.1

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEe
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRID  284 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  284 (449)
                      ....++|||+|||.++++++|+++|+ .||.|.+|.++++..+++++|||||+|.+.++|.+|| .|+|..+.|++|.|.
T Consensus        86 ~~~~~~l~V~nlp~~~~~~~l~~~F~-~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al-~l~g~~~~g~~i~v~  163 (457)
T TIGR01622        86 ERDDRTVFVLQLALKARERDLYEFFS-KVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKAL-ALTGQMLLGRPIIVQ  163 (457)
T ss_pred             ccCCcEEEEeCCCCCCCHHHHHHHHH-hcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHH-HhCCCEECCeeeEEe
Confidence            34567999999999999999999995 9999999999999999999999999999999999999 599999999999998


Q ss_pred             ecCCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeC---
Q 013141          285 VATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV---  361 (449)
Q Consensus       285 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~---  361 (449)
                      ++...........          .          ......+..++|||+|||..+++++|+++|+.||.|.+|.|..   
T Consensus       164 ~~~~~~~~~~~~~----------~----------~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~  223 (457)
T TIGR01622       164 SSQAEKNRAAKAA----------T----------HQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPE  223 (457)
T ss_pred             ecchhhhhhhhcc----------c----------ccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCC
Confidence            8654432210000          0          0000122378999999999999999999999999999999984   


Q ss_pred             ---CCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCC
Q 013141          362 ---GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRN  400 (449)
Q Consensus       362 ---~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  400 (449)
                         .+++|||+|.+.++|.+|++.|+|..|.|+.|+|.|+..
T Consensus       224 ~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~  265 (457)
T TIGR01622       224 TGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQD  265 (457)
T ss_pred             CCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccC
Confidence               368999999999999999999999999999999999774

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.

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

Probab=99.94  E-value=9.6e-25  Score=203.41  Aligned_cols=274  Identities=21%  Similarity=0.282  Sum_probs=185.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      .....|.+++|||++|++||.+||+.| .|.++.+.+.  +|+..|.|||+|.++|++++||++ +...+..  +-|.|-
T Consensus         8 ~~~~~vr~rGLPwsat~~ei~~Ff~~~-~I~~~~~~r~--~Gr~sGeA~Ve~~seedv~~Alkk-dR~~mg~--RYIEVf   81 (510)
T KOG4211|consen    8 STAFEVRLRGLPWSATEKEILDFFSNC-GIENLEIPRR--NGRPSGEAYVEFTSEEDVEKALKK-DRESMGH--RYIEVF   81 (510)
T ss_pred             CcceEEEecCCCccccHHHHHHHHhcC-ceeEEEEecc--CCCcCcceEEEeechHHHHHHHHh-hHHHhCC--ceEEEE
Confidence            456679999999999999999999999 5788766664  699999999999999999999964 5544432  333332


Q ss_pred             ccccCCC---CCc---cccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeE-EEEeecCCCCCcceEEEEEeCCHHHHH
Q 013141          193 WATFSGS---DRR---TEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKG-AKVIIDSNTGRTKGYGFVRFGDENERS  265 (449)
Q Consensus       193 ~~~~~~~---~~~---~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~-i~~~~~~~~~~~~g~afV~f~~~~~A~  265 (449)
                      .+...+.   .++   ........|.+++||+.||++||.++|+ -.-.|.. |.++.+ ..+++.|-|||.|++.+.|+
T Consensus        82 ~~~~~e~d~~~~~~g~~s~~~d~vVRLRGLPfscte~dI~~FFa-GL~Iv~~gi~l~~d-~rgR~tGEAfVqF~sqe~ae  159 (510)
T KOG4211|consen   82 TAGGAEADWVMRPGGPNSSANDGVVRLRGLPFSCTEEDIVEFFA-GLEIVPDGILLPMD-QRGRPTGEAFVQFESQESAE  159 (510)
T ss_pred             ccCCccccccccCCCCCCCCCCceEEecCCCccCcHHHHHHHhc-CCcccccceeeecc-CCCCcccceEEEecCHHHHH
Confidence            2221111   111   1224567899999999999999999995 5554544 445555 44779999999999999999


Q ss_pred             HHHHHhCCceecCcceEEeecCCCCCCchh----------hcchh----hh-hhhcCCC---------------------
Q 013141          266 RAMTEMNGVYCSSRPMRIDVATPKKASGYQ----------QQYSS----QA-LVLAGGP---------------------  309 (449)
Q Consensus       266 ~A~~~l~g~~~~g~~i~v~~~~~~~~~~~~----------~~~~~----~~-~~~~~~~---------------------  309 (449)
                      .|+ .-+...|+.+.|+|..+.....+...          .....    .. .......                     
T Consensus       160 ~Al-~rhre~iGhRYIEvF~Ss~~e~~~~~~~~~~~~~rpGpy~~~~a~Rg~~d~~~~~~~~~~~~r~g~~~~g~~g~~~  238 (510)
T KOG4211|consen  160 IAL-GRHRENIGHRYIEVFRSSRAEVKRAAGPGDGRVGRPGPYDRPGAPRGGYDYGQGRDPGRNATRYGAGGEGYYGFSR  238 (510)
T ss_pred             HHH-HHHHHhhccceEEeehhHHHHHHhhccccccccCCCCccccccCCccccccccccCCCccccccccccCCcccccc
Confidence            998 46667788889988776543211110          00000    00 0000000                     


Q ss_pred             ---------------------CCC-CCCcC---CCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeC---
Q 013141          310 ---------------------GSN-GARVQ---GSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV---  361 (449)
Q Consensus       310 ---------------------~~~-~~~~~---~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~---  361 (449)
                                           ... .....   ............++..+||+..++.+|.++|+.. ....|+|..   
T Consensus       239 ~~~~~d~~~~gs~~~~~~~~~~~~~g~~~~g~~g~~~~~~~~g~fv~MRGlpy~a~~~di~nfFspl-~p~~v~i~ig~d  317 (510)
T KOG4211|consen  239 YPSLQDYGNFGSYGGGRDPNYPVSSGPHRQGGAGDYGNGGPGGHFVHMRGLPYDATENDIANFFSPL-NPYRVHIEIGPD  317 (510)
T ss_pred             CccccccccccccccccccccCCCCCcccCCCcccccCCCCCCceeeecCCCccCCCcchhhhcCCC-CceeEEEEeCCC
Confidence                                 000 00000   0001111223788999999999999999999875 334555543   


Q ss_pred             --CCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 013141          362 --GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSW  397 (449)
Q Consensus       362 --~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  397 (449)
                        ..+.|+|+|.|.++|..|+.. ++..+..+.|.+-.
T Consensus       318 Gr~TGEAdveF~t~edav~Amsk-d~anm~hrYVElFl  354 (510)
T KOG4211|consen  318 GRATGEADVEFATGEDAVGAMGK-DGANMGHRYVELFL  354 (510)
T ss_pred             CccCCcceeecccchhhHhhhcc-CCcccCcceeeecc
Confidence              368999999999999999864 77778777776644

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

Probab=99.94  E-value=2.2e-25  Score=204.70  Aligned_cols=203  Identities=20%  Similarity=0.353  Sum_probs=163.6

Q ss_pred             EEEccHHHHHHHHHHhcCCCCCCCCCcccccccccCCCCCccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEE
Q 013141          162 VEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKV  241 (449)
Q Consensus       162 V~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~  241 (449)
                      -...+.++|.++|.+-.+..|....-  ..++..+............+.|||+.||.++.|++|.-+| ++.|+|.+++|
T Consensus        39 ~~~~~~eaal~al~E~tgy~l~ve~g--qrk~ggPpP~weg~~p~~G~EVfvGkIPrD~~EdeLvplf-EkiG~I~elRL  115 (506)
T KOG0117|consen   39 AGVQSEEAALKALLERTGYTLVVENG--QRKYGGPPPGWEGPPPPRGCEVFVGKIPRDVFEDELVPLF-EKIGKIYELRL  115 (506)
T ss_pred             cccccHHHHHHHHHHhcCceEEEecc--ccccCCCCCcccCCCCCCCceEEecCCCccccchhhHHHH-HhccceeeEEE
Confidence            33445788888887656554422111  1111222222333444667899999999999999999999 69999999999


Q ss_pred             eecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee-cCcceEEeecCCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCC
Q 013141          242 IIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYC-SSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQ  320 (449)
Q Consensus       242 ~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~-~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  320 (449)
                      ++|+.+|.+||||||+|.+.++|.+||+.||+.+| .|+.|.|+.+...                               
T Consensus       116 MmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~Svan-------------------------------  164 (506)
T KOG0117|consen  116 MMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCVSVAN-------------------------------  164 (506)
T ss_pred             eecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEEeeec-------------------------------
Confidence            99999999999999999999999999999999998 8899999888664                               


Q ss_pred             CCCCCCCcEEEEcCCCCCCCHhHHHhhccccCc-eEEEEEeC-------CCcEEEEEecCHHHHHHHHHHhc--CCeeCC
Q 013141          321 SDGESNNATIFVGALDSDVSDEDLREPFSQFGE-ILSVKIPV-------GKGCGFVQFANRKDAEVALQKLQ--GTAIGK  390 (449)
Q Consensus       321 ~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~-v~~v~i~~-------~~g~afV~F~~~~~A~~A~~~l~--g~~~~g  390 (449)
                             ++|||+|||...++++|++.|++.++ |++|.+..       ++|||||+|.|...|..|..+|-  ...+-|
T Consensus       165 -------~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwg  237 (506)
T KOG0117|consen  165 -------CRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIKLWG  237 (506)
T ss_pred             -------ceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCCceeecC
Confidence                   67999999999999999999999874 77777653       58999999999999999998883  335779


Q ss_pred             eEEEEEecCCCCCCC
Q 013141          391 QTVRLSWGRNPGNKQ  405 (449)
Q Consensus       391 ~~l~v~~~~~~~~~~  405 (449)
                      ..+.|+|+.+.....
T Consensus       238 n~~tVdWAep~~e~d  252 (506)
T KOG0117|consen  238 NAITVDWAEPEEEPD  252 (506)
T ss_pred             CcceeeccCcccCCC
Confidence            999999999754443

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

Probab=99.93  E-value=3.6e-24  Score=195.76  Aligned_cols=170  Identities=17%  Similarity=0.289  Sum_probs=135.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhh-ccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFS-HTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRL  191 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~-~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~  191 (449)
                      ...|.+||.|||+++...+|+++|. +.|+|+-|.++.|. +|+++|||.|||+++|.+++|++.|+...+.++...++-
T Consensus        42 ~r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~-~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKE  120 (608)
T KOG4212|consen   42 ARDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDE-SGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKE  120 (608)
T ss_pred             cccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeeccc-CCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEec
Confidence            3456799999999999999999996 57899999999996 699999999999999999999999999988655444332


Q ss_pred             cccc----------------------------cC---------------CC-CCc-------------------------
Q 013141          192 NWAT----------------------------FS---------------GS-DRR-------------------------  202 (449)
Q Consensus       192 ~~~~----------------------------~~---------------~~-~~~-------------------------  202 (449)
                      +...                            -+               .+ ...                         
T Consensus       121 d~d~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~~~lfgl~  200 (608)
T KOG4212|consen  121 DHDEQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSNYNLFGLS  200 (608)
T ss_pred             cCchhhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCccccccccccchhhhcccch
Confidence            2210                            00               00 000                         


Q ss_pred             ---------cccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCC
Q 013141          203 ---------TEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNG  273 (449)
Q Consensus       203 ---------~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g  273 (449)
                               ..+....++||.||...+....|++.|. -.|.|..|.+-.|+. +.++|++.++|.++-+|..||..|++
T Consensus       201 ~~Flr~~h~f~pPl~~k~fvanl~~~vg~~kL~qvfg-mAGkv~~vdf~idKe-G~s~G~~vi~y~hpveavqaIsml~~  278 (608)
T KOG4212|consen  201 ASFLRSLHIFSPPLHNKVFVANLDYKVGNKKLKQVFG-MAGKVQSVDFSIDKE-GNSRGFAVIEYDHPVEAVQAISMLDR  278 (608)
T ss_pred             hhhhhhccCCCCCccceeeeeccccccchHHHHHHhc-cceeeeeeceeeccc-cccCCeeEEEecchHHHHHHHHhhcc
Confidence                     0112345799999999999999999995 899999999998866 68999999999999999999999987


Q ss_pred             ceecCcceEEee
Q 013141          274 VYCSSRPMRIDV  285 (449)
Q Consensus       274 ~~~~g~~i~v~~  285 (449)
                      .-+.+++..+..
T Consensus       279 ~g~~~~~~~~Rl  290 (608)
T KOG4212|consen  279 QGLFDRRMTVRL  290 (608)
T ss_pred             CCCccccceeec
Confidence            666666655554

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

Probab=99.93  E-value=6.1e-26  Score=184.42  Aligned_cols=174  Identities=29%  Similarity=0.568  Sum_probs=155.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      ....||||+||+..++++-|.++|-+.|+|+++.+.+|+.+...+|||||+|.++|+|+-|++-||...|  .+++|++.
T Consensus         7 nqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkL--YgrpIrv~   84 (203)
T KOG0131|consen    7 NQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKL--YGRPIRVN   84 (203)
T ss_pred             CCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHh--cCceeEEE
Confidence            4567999999999999999999999999999999999999999999999999999999999999997777  56888887


Q ss_pred             ccccCCCCCccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeE-EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh
Q 013141          193 WATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKG-AKVIIDSNTGRTKGYGFVRFGDENERSRAMTEM  271 (449)
Q Consensus       193 ~~~~~~~~~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~-i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l  271 (449)
                      .+...    ........+|||+||.+.+++..|.+.|+ .||.+.. -.+++++.|+.+++++||-|++.+.+.+|+..+
T Consensus        85 kas~~----~~nl~vganlfvgNLd~~vDe~~L~dtFs-afG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~  159 (203)
T KOG0131|consen   85 KASAH----QKNLDVGANLFVGNLDPEVDEKLLYDTFS-AFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSM  159 (203)
T ss_pred             ecccc----cccccccccccccccCcchhHHHHHHHHH-hccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHh
Confidence            76621    12223447899999999999999999997 9998766 378899999999999999999999999999999


Q ss_pred             CCceecCcceEEeecCCCCCCc
Q 013141          272 NGVYCSSRPMRIDVATPKKASG  293 (449)
Q Consensus       272 ~g~~~~g~~i~v~~~~~~~~~~  293 (449)
                      |+..++.++++|+++..+...+
T Consensus       160 ngq~l~nr~itv~ya~k~~~kg  181 (203)
T KOG0131|consen  160 NGQYLCNRPITVSYAFKKDTKG  181 (203)
T ss_pred             ccchhcCCceEEEEEEecCCCc
Confidence            9999999999999998887665

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

Probab=99.93  E-value=2.3e-25  Score=190.58  Aligned_cols=166  Identities=27%  Similarity=0.553  Sum_probs=150.2

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEe
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRID  284 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  284 (449)
                      ....+.|.|.-||..+|.|||+.+|+ ..|+|+++++++|+.+|.+-||+||.|.+++||++|+..|||..+..+.|+|+
T Consensus        38 ~~skTNLIvNYLPQ~MTqdE~rSLF~-SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVS  116 (360)
T KOG0145|consen   38 DESKTNLIVNYLPQNMTQDELRSLFG-SIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVS  116 (360)
T ss_pred             CcccceeeeeecccccCHHHHHHHhh-cccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEE
Confidence            34566788989999999999999996 99999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeC---
Q 013141          285 VATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV---  361 (449)
Q Consensus       285 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~---  361 (449)
                      ++++....                                .....|||++||..+|..||.++|++||.|.--+|+.   
T Consensus       117 yARPSs~~--------------------------------Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqv  164 (360)
T KOG0145|consen  117 YARPSSDS--------------------------------IKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQV  164 (360)
T ss_pred             eccCChhh--------------------------------hcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcc
Confidence            99987542                                3356799999999999999999999999987777764   


Q ss_pred             ---CCcEEEEEecCHHHHHHHHHHhcCCeeCC--eEEEEEecCCCCC
Q 013141          362 ---GKGCGFVQFANRKDAEVALQKLQGTAIGK--QTVRLSWGRNPGN  403 (449)
Q Consensus       362 ---~~g~afV~F~~~~~A~~A~~~l~g~~~~g--~~l~v~~~~~~~~  403 (449)
                         ++|.+||+|+.+++|+.||+.|||..=-|  ..|.|.|+.++..
T Consensus       165 tg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepItVKFannPsq  211 (360)
T KOG0145|consen  165 TGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPITVKFANNPSQ  211 (360)
T ss_pred             cceecceeEEEecchhHHHHHHHhccCCCCCCCCCCeEEEecCCccc
Confidence               48999999999999999999999998665  5799999998743

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

Probab=99.93  E-value=2.2e-24  Score=195.82  Aligned_cols=281  Identities=19%  Similarity=0.294  Sum_probs=198.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccc
Q 013141          112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRL  191 (449)
Q Consensus       112 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~  191 (449)
                      ..+++.|.+||||++++|+||.+++.+||.|..+.+++.++      .||++|.|+++|...+.......-.-++.++.+
T Consensus        25 ~~pSkV~HlRnlp~e~tE~elI~Lg~pFG~vtn~~~lkGkn------QAflem~d~~sAvtmv~~y~~~~p~lr~~~~yi   98 (492)
T KOG1190|consen   25 AEPSKVVHLRNLPWEVTEEELISLGLPFGKVTNLLMLKGKN------QAFLEMADEESAVTMVNYYTSVTPVLRGQPIYI   98 (492)
T ss_pred             cCCcceeEeccCCccccHHHHHHhcccccceeeeeeeccch------hhhhhhcchhhhhheeecccccCccccCcceee
Confidence            35789999999999999999999999999999999998765      799999999999986654444333334444444


Q ss_pred             cccccCC---------------------------------CC--CccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCe
Q 013141          192 NWATFSG---------------------------------SD--RRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSV  236 (449)
Q Consensus       192 ~~~~~~~---------------------------------~~--~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v  236 (449)
                      .++....                                 ..  ......+-.+++|.++-+.+|.|-|..+|+ +||.|
T Consensus        99 q~sn~~~lkt~s~p~q~r~~~vy~~~s~~q~~~~~~s~~~~~~G~~~~~n~vLr~iie~m~ypVslDVLHqvFS-~fG~V  177 (492)
T KOG1190|consen   99 QYSNHSELKTDSQPNQIRGQAVYQAVSSVQEIVLPLSASAVVVGNEDGPNPVLRTIIENMFYPVSLDVLHQVFS-KFGFV  177 (492)
T ss_pred             hhhhHHHHhccCchhhhhhhhHHhhhhcccccccccccccccccccCCCceeEEEEeccceeeeEHHHHHHHHh-hccee
Confidence            3332110                                 00  001112234577899999999999999996 99999


Q ss_pred             eEEEEeecCCCCCcceE-EEEEeCCHHHHHHHHHHhCCcee--cCcceEEeecCCCCCCchhhcchhhh-----hhhc--
Q 013141          237 KGAKVIIDSNTGRTKGY-GFVRFGDENERSRAMTEMNGVYC--SSRPMRIDVATPKKASGYQQQYSSQA-----LVLA--  306 (449)
Q Consensus       237 ~~i~~~~~~~~~~~~g~-afV~f~~~~~A~~A~~~l~g~~~--~g~~i~v~~~~~~~~~~~~~~~~~~~-----~~~~--  306 (449)
                      ..|......     .+| |+|+|.+.+.|..|...|+|..|  +-+.|+|+++.-....-.-...+++.     .-.+  
T Consensus       178 lKIiTF~Kn-----n~FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~Sklt~LnvKynndkSRDyTnp~LP~gd~  252 (492)
T KOG1190|consen  178 LKIITFTKN-----NGFQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFSKLTDLNVKYNNDKSRDYTNPDLPVGDG  252 (492)
T ss_pred             EEEEEEecc-----cchhhhhhccchhhHHHHHHhccCCcccCceeEEEeehhhcccceeeccccccccccCCCCCCCcc
Confidence            998766442     233 89999999999999999999888  44567777765432111000000000     0000  


Q ss_pred             -------------------CCCCCCC-----CCcCCCCCCCCCCCcEEEEcCCCC-CCCHhHHHhhccccCceEEEEEeC
Q 013141          307 -------------------GGPGSNG-----ARVQGSQSDGESNNATIFVGALDS-DVSDEDLREPFSQFGEILSVKIPV  361 (449)
Q Consensus       307 -------------------~~~~~~~-----~~~~~~~~~~~~~~~~l~V~nlp~-~~t~~~L~~~f~~~G~v~~v~i~~  361 (449)
                                         +.+....     ..............++|.|.||.. .+|.+.|..+|.-||+|.+|+|+.
T Consensus       253 ~p~l~~~~~aa~~~~~~~~g~p~aip~~~~~a~~a~~~~~~~~~n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~  332 (492)
T KOG1190|consen  253 QPSLDQLMAAAFGSVPAVHGAPLAIPSGAAGANAADGKIESPSANVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILY  332 (492)
T ss_pred             ccccchhhhccccccccccCCcccCCccchhhcccccccccCCCceEEEEecCchhccchhHHHHHHhhhcceEEEEeee
Confidence                               0000000     000000111111257888888866 589999999999999999999998


Q ss_pred             C-CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCCCC
Q 013141          362 G-KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNK  404 (449)
Q Consensus       362 ~-~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~~~  404 (449)
                      + +..|+|.|.|...|..|++.|+|.++.|+.|+|+++|...-.
T Consensus       333 nkkd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~~vq  376 (492)
T KOG1190|consen  333 NKKDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHTNVQ  376 (492)
T ss_pred             cCCcceeeeecchhHHHHHHHHhhcceecCceEEEeeccCcccc
Confidence            6 568999999999999999999999999999999999975433

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

Probab=99.91  E-value=3.8e-24  Score=173.99  Aligned_cols=167  Identities=29%  Similarity=0.514  Sum_probs=148.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEee
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV  285 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  285 (449)
                      ....+|||+||+..++++.|+++|- ..|+|.++.+.+|..+...+|||||+|.++|+|+-||+-||...+.|++|+|..
T Consensus         7 nqd~tiyvgnld~kvs~~~l~EL~i-qagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~k   85 (203)
T KOG0131|consen    7 NQDATLYVGNLDEKVSEELLYELFI-QAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNK   85 (203)
T ss_pred             CCCceEEEecCCHHHHHHHHHHHHH-hcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEe
Confidence            4567999999999999999999996 999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEE-EEeC---
Q 013141          286 ATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSV-KIPV---  361 (449)
Q Consensus       286 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v-~i~~---  361 (449)
                      +.....                               ....+..|||+||.+++++..|.+.|+.||.+.+. ++++   
T Consensus        86 as~~~~-------------------------------nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~  134 (203)
T KOG0131|consen   86 ASAHQK-------------------------------NLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPD  134 (203)
T ss_pred             cccccc-------------------------------cccccccccccccCcchhHHHHHHHHHhccccccCCccccccc
Confidence            873322                               23345789999999999999999999999987662 3333   


Q ss_pred             ---CCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCCCC
Q 013141          362 ---GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNK  404 (449)
Q Consensus       362 ---~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~~~  404 (449)
                         .++++||.|.+.+.+.+|+..|||..++++.|+|+|+.....+
T Consensus       135 tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~ya~k~~~k  180 (203)
T KOG0131|consen  135 TGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVSYAFKKDTK  180 (203)
T ss_pred             CCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEEEEEecCCC
Confidence               3689999999999999999999999999999999999876544

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

Probab=99.91  E-value=1.2e-22  Score=184.49  Aligned_cols=276  Identities=18%  Similarity=0.289  Sum_probs=210.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccE-EEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          114 ETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGY-GFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       114 ~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~-afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      .--+++|.|+-+.+|-+.|..+|++||.|..|.-+...+     +| |+|.|.+.+.|..|...|+|..|...++.++++
T Consensus       149 ~vLr~iie~m~ypVslDVLHqvFS~fG~VlKIiTF~Knn-----~FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId  223 (492)
T KOG1190|consen  149 PVLRTIIENMFYPVSLDVLHQVFSKFGFVLKIITFTKNN-----GFQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRID  223 (492)
T ss_pred             eeEEEEeccceeeeEHHHHHHHHhhcceeEEEEEEeccc-----chhhhhhccchhhHHHHHHhccCCcccCceeEEEee
Confidence            445688999999999999999999999998887766543     34 999999999999999999999999889999998


Q ss_pred             ccccCCCCC--------------------------------------------------------ccccC--CCceEEEc
Q 013141          193 WATFSGSDR--------------------------------------------------------RTEAC--SDLSIFVG  214 (449)
Q Consensus       193 ~~~~~~~~~--------------------------------------------------------~~~~~--~~~~l~v~  214 (449)
                      +++-.....                                                        .....  .+..|.|.
T Consensus       224 ~Sklt~LnvKynndkSRDyTnp~LP~gd~~p~l~~~~~aa~~~~~~~~g~p~aip~~~~~a~~a~~~~~~~~~n~vllvs  303 (492)
T KOG1190|consen  224 FSKLTDLNVKYNNDKSRDYTNPDLPVGDGQPSLDQLMAAAFGSVPAVHGAPLAIPSGAAGANAADGKIESPSANVVLLVS  303 (492)
T ss_pred             hhhcccceeeccccccccccCCCCCCCccccccchhhhccccccccccCCcccCCccchhhcccccccccCCCceEEEEe
Confidence            875220000                                                        00001  14678888


Q ss_pred             CCCC-CCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecCCCCCCc
Q 013141          215 DLAP-DVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKASG  293 (449)
Q Consensus       215 ~lp~-~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~~~~~~~  293 (449)
                      ||.. .+|.+.|..+|+ .||+|.+|+|+.++.     -.|+|++.+...|..|++.|+|..+.|+.|+|.+++......
T Consensus       304 nln~~~VT~d~LftlFg-vYGdVqRVkil~nkk-----d~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~~vql  377 (492)
T KOG1190|consen  304 NLNEEAVTPDVLFTLFG-VYGDVQRVKILYNKK-----DNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHTNVQL  377 (492)
T ss_pred             cCchhccchhHHHHHHh-hhcceEEEEeeecCC-----cceeeeecchhHHHHHHHHhhcceecCceEEEeeccCccccC
Confidence            8875 589999999997 999999999998753     369999999999999999999999999999999998765432


Q ss_pred             hhhcchhhhhhhcCCCCCCCCC---cCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEE-EEEe-CCCcEEEE
Q 013141          294 YQQQYSSQALVLAGGPGSNGAR---VQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILS-VKIP-VGKGCGFV  368 (449)
Q Consensus       294 ~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~-v~i~-~~~g~afV  368 (449)
                      ..................-...   .........+++.+|++.|+|.++++|+|++.|..-|...+ .++. +++..|++
T Consensus       378 p~egq~d~glT~dy~~spLhrfkkpgsKN~~ni~PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff~kd~kmal~  457 (492)
T KOG1190|consen  378 PREGQEDQGLTKDYGNSPLHRFKKPGSKNYQNIFPPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFFQKDRKMALP  457 (492)
T ss_pred             CCCCCccccccccCCCCchhhccCcccccccccCCchhheeeccCCcccchhHHHHhhhcCCceEEeeeecCCCcceeec
Confidence            2222111111111111000000   00011223466789999999999999999999988776544 4443 47899999


Q ss_pred             EecCHHHHHHHHHHhcCCeeCC-eEEEEEecCC
Q 013141          369 QFANRKDAEVALQKLQGTAIGK-QTVRLSWGRN  400 (449)
Q Consensus       369 ~F~~~~~A~~A~~~l~g~~~~g-~~l~v~~~~~  400 (449)
                      .+.+.|+|..|+..+|...++. ..|||+|+|.
T Consensus       458 q~~sveeA~~ali~~hnh~lgen~hlRvSFSks  490 (492)
T KOG1190|consen  458 QLESVEEAIQALIDLHNHYLGENHHLRVSFSKS  490 (492)
T ss_pred             ccCChhHhhhhccccccccCCCCceEEEEeecc
Confidence            9999999999999999999985 4999999985

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

Probab=99.91  E-value=9.3e-24  Score=183.78  Aligned_cols=148  Identities=22%  Similarity=0.493  Sum_probs=139.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecCC
Q 013141          209 LSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATP  288 (449)
Q Consensus       209 ~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~~  288 (449)
                      .+|||+|||..+++.+|+.+| +.||.|.++.|+++        |+||..++...++.||.+|++..|+|..|.|+-++.
T Consensus         3 ~KLFIGNLp~~~~~~elr~lF-e~ygkVlECDIvKN--------YgFVHiEdktaaedairNLhgYtLhg~nInVeaSks   73 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLF-EQYGKVLECDIVKN--------YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKS   73 (346)
T ss_pred             cchhccCCCcccchHHHHHHH-HhhCceEeeeeecc--------cceEEeecccccHHHHhhcccceecceEEEEEeccc
Confidence            379999999999999999999 69999999999965        999999999999999999999999999999999988


Q ss_pred             CCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEE
Q 013141          289 KKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFV  368 (449)
Q Consensus       289 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV  368 (449)
                      +..                                  .+++|+|+||.+.++.++|+..|++||.|.+++|.  ++++||
T Consensus        74 Ksk----------------------------------~stkl~vgNis~tctn~ElRa~fe~ygpviecdiv--kdy~fv  117 (346)
T KOG0109|consen   74 KSK----------------------------------ASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIV--KDYAFV  117 (346)
T ss_pred             cCC----------------------------------CccccccCCCCccccCHHHhhhhcccCCceeeeee--cceeEE
Confidence            743                                  36889999999999999999999999999999999  679999


Q ss_pred             EecCHHHHHHHHHHhcCCeeCCeEEEEEecCCC
Q 013141          369 QFANRKDAEVALQKLQGTAIGKQTVRLSWGRNP  401 (449)
Q Consensus       369 ~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~  401 (449)
                      .|+-.++|..|++.|++++|.|++++|..+..+
T Consensus       118 h~d~~eda~~air~l~~~~~~gk~m~vq~stsr  150 (346)
T KOG0109|consen  118 HFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTSR  150 (346)
T ss_pred             EEeeccchHHHHhcccccccccceeeeeeeccc
Confidence            999999999999999999999999999998864

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

Probab=99.90  E-value=7.2e-23  Score=208.55  Aligned_cols=174  Identities=18%  Similarity=0.308  Sum_probs=143.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      ...++|||+|||+.+++++|+++|+.||.|..+.++++..+|.++|||||+|.+.++|..|++.|++..+.+  ..|.|.
T Consensus       293 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~--~~l~v~  370 (509)
T TIGR01642       293 DSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGD--NKLHVQ  370 (509)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECC--eEEEEE
Confidence            456899999999999999999999999999999999999999999999999999999999999999999855  455665


Q ss_pred             ccccCCCCCc-----------------------cccCCCceEEEcCCCCC--C--------CHHHHHHHHhhhCCCeeEE
Q 013141          193 WATFSGSDRR-----------------------TEACSDLSIFVGDLAPD--V--------TDSILQETFSSKYPSVKGA  239 (449)
Q Consensus       193 ~~~~~~~~~~-----------------------~~~~~~~~l~v~~lp~~--~--------t~~~l~~~f~~~~g~v~~i  239 (449)
                      ++........                       ....++.+|+|.|+...  +        ..++|+++|. .||.|..|
T Consensus       371 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~-~~G~v~~v  449 (509)
T TIGR01642       371 RACVGANQATIDTSNGMAPVTLLAKALSQSILQIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFS-KYGPLINI  449 (509)
T ss_pred             ECccCCCCCCccccccccccccccccchhhhccccCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHH-hcCCeeEE
Confidence            5532211000                       01235678899998632  1        2367899995 99999999


Q ss_pred             EEeecC---CCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecCCC
Q 013141          240 KVIIDS---NTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPK  289 (449)
Q Consensus       240 ~~~~~~---~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~~~  289 (449)
                      .|+++.   .++...|++||+|.+.++|.+|+..|||..|.|+.|.|.|....
T Consensus       450 ~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~~~gr~v~~~~~~~~  502 (509)
T TIGR01642       450 VIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKFNDRVVVAAFYGED  502 (509)
T ss_pred             EeeccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEeCHH
Confidence            998753   34556799999999999999999999999999999999998654

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

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

Probab=99.90  E-value=4.4e-23  Score=189.04  Aligned_cols=174  Identities=26%  Similarity=0.454  Sum_probs=148.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccccc
Q 013141          114 ETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNW  193 (449)
Q Consensus       114 ~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~  193 (449)
                      ..++|||++|+|+++++.|+++|..||.|.+|.+++|+.+++++||+||+|++.+.+.++|.. ....|++  +.|....
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~-~~h~~dg--r~ve~k~   81 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNA-RTHKLDG--RSVEPKR   81 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecc-cccccCC--cccccee
Confidence            788999999999999999999999999999999999999999999999999999999999954 3344433  3444433


Q ss_pred             cccCCCCCc-cccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC
Q 013141          194 ATFSGSDRR-TEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMN  272 (449)
Q Consensus       194 ~~~~~~~~~-~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~  272 (449)
                      +.+...... .......+|||++||.+++++++++.| +.||.|..+.++.|..+.+++||+||.|.+++.+++++ ...
T Consensus        82 av~r~~~~~~~~~~~tkkiFvGG~~~~~~e~~~r~yf-e~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~-~~~  159 (311)
T KOG4205|consen   82 AVSREDQTKVGRHLRTKKIFVGGLPPDTTEEDFKDYF-EQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVT-LQK  159 (311)
T ss_pred             ccCcccccccccccceeEEEecCcCCCCchHHHhhhh-hccceeEeeEEeecccccccccceeeEeccccccceec-ccc
Confidence            332222111 122256799999999999999999999 69999999999999999999999999999999999998 577


Q ss_pred             CceecCcceEEeecCCCCCC
Q 013141          273 GVYCSSRPMRIDVATPKKAS  292 (449)
Q Consensus       273 g~~~~g~~i~v~~~~~~~~~  292 (449)
                      -+.|+++.++|..+.++...
T Consensus       160 f~~~~gk~vevkrA~pk~~~  179 (311)
T KOG4205|consen  160 FHDFNGKKVEVKRAIPKEVM  179 (311)
T ss_pred             eeeecCceeeEeeccchhhc
Confidence            78899999999999998765

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

Probab=99.90  E-value=9.4e-24  Score=183.78  Aligned_cols=150  Identities=23%  Similarity=0.459  Sum_probs=135.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccccccc
Q 013141          116 KTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWAT  195 (449)
Q Consensus       116 ~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~~~  195 (449)
                      -+|||+|||..+++.+|+.+|++||.|++|.|+++        |+||..++...|+.|+..|++..|.+  ..|.|+.++
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN--------YgFVHiEdktaaedairNLhgYtLhg--~nInVeaSk   72 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKN--------YGFVHIEDKTAAEDAIRNLHGYTLHG--VNINVEASK   72 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeecc--------cceEEeecccccHHHHhhcccceecc--eEEEEEecc
Confidence            37999999999999999999999999999999996        99999999999999999999999955  555555444


Q ss_pred             cCCCCCccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCce
Q 013141          196 FSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVY  275 (449)
Q Consensus       196 ~~~~~~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~  275 (449)
                      .+       ...+++|+|+||.+.++.+||++.| ++||.|.++.|++|        |+||.|...++|..||+.|++.+
T Consensus        73 sK-------sk~stkl~vgNis~tctn~ElRa~f-e~ygpviecdivkd--------y~fvh~d~~eda~~air~l~~~~  136 (346)
T KOG0109|consen   73 SK-------SKASTKLHVGNISPTCTNQELRAKF-EKYGPVIECDIVKD--------YAFVHFDRAEDAVEAIRGLDNTE  136 (346)
T ss_pred             cc-------CCCccccccCCCCccccCHHHhhhh-cccCCceeeeeecc--------eeEEEEeeccchHHHHhcccccc
Confidence            22       4567899999999999999999999 69999999999965        99999999999999999999999


Q ss_pred             ecCcceEEeecCCCCC
Q 013141          276 CSSRPMRIDVATPKKA  291 (449)
Q Consensus       276 ~~g~~i~v~~~~~~~~  291 (449)
                      |.|++++|..++.+-.
T Consensus       137 ~~gk~m~vq~stsrlr  152 (346)
T KOG0109|consen  137 FQGKRMHVQLSTSRLR  152 (346)
T ss_pred             cccceeeeeeeccccc
Confidence            9999999999887643

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

Probab=99.89  E-value=1.1e-20  Score=169.97  Aligned_cols=279  Identities=16%  Similarity=0.181  Sum_probs=202.3

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      ....+..|.||+|-..++|.||.+.++.||+|.-|.++..+      ..|.|+|++.+.|+.|+..--...+...+...-
T Consensus        27 k~~~spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~~P~~------r~alvefedi~~akn~Vnfaa~n~i~i~gq~Al  100 (494)
T KOG1456|consen   27 KPNPSPVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMPHK------RQALVEFEDIEGAKNCVNFAADNQIYIAGQQAL  100 (494)
T ss_pred             CCCCCceEEEeccccccchhHHHHHHhcCCceEEEEecccc------ceeeeeeccccchhhheehhccCcccccCchhh
Confidence            44578899999999999999999999999999888887765      379999999999999995433333333444444


Q ss_pred             ccccccCCCCCc--cccCCCceEEEc--CCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHH
Q 013141          191 LNWATFSGSDRR--TEACSDLSIFVG--DLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSR  266 (449)
Q Consensus       191 ~~~~~~~~~~~~--~~~~~~~~l~v~--~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~  266 (449)
                      +.++.....+++  ....++..|.+.  |--+.+|.|-|..+. ...|.|.+|.|++..     ---|+|+|++.+.|.+
T Consensus       101 ~NyStsq~i~R~g~es~~pN~VLl~TIlNp~YpItvDVly~Ic-np~GkVlRIvIfkkn-----gVQAmVEFdsv~~Aqr  174 (494)
T KOG1456|consen  101 FNYSTSQCIERPGDESATPNKVLLFTILNPQYPITVDVLYTIC-NPQGKVLRIVIFKKN-----GVQAMVEFDSVEVAQR  174 (494)
T ss_pred             cccchhhhhccCCCCCCCCCeEEEEEeecCccccchhhhhhhc-CCCCceEEEEEEecc-----ceeeEEeechhHHHHH
Confidence            444432222222  222334444443  444578999999999 599999999998752     2369999999999999


Q ss_pred             HHHHhCCcee--cCcceEEeecCCCCCCchhhcchhh-------------------------------hhhhcCCC--CC
Q 013141          267 AMTEMNGVYC--SSRPMRIDVATPKKASGYQQQYSSQ-------------------------------ALVLAGGP--GS  311 (449)
Q Consensus       267 A~~~l~g~~~--~g~~i~v~~~~~~~~~~~~~~~~~~-------------------------------~~~~~~~~--~~  311 (449)
                      |.+.|||..|  +-.+|+|+++++.+.+-.+......                               ..+..+..  .+
T Consensus       175 Ak~alNGADIYsGCCTLKIeyAkP~rlnV~knd~DtwDyTlp~~~~~~~~g~~~~~r~~~p~~~~~~pss~~G~h~~y~s  254 (494)
T KOG1456|consen  175 AKAALNGADIYSGCCTLKIEYAKPTRLNVQKNDKDTWDYTLPDLRGPYDPGRNHYDRQRQPAPLGYHPSSRGGGHSGYYS  254 (494)
T ss_pred             HHhhcccccccccceeEEEEecCcceeeeeecCCccccccCCCCCCCCCCCCCCCccccCCCccCCChhhcCCCCCCCcc
Confidence            9999999887  5578999999886532211110000                               00000000  00


Q ss_pred             ------CCCC-----------cCCCCCCCCCCCcEEEEcCCCCC-CCHhHHHhhccccCceEEEEEeCC-CcEEEEEecC
Q 013141          312 ------NGAR-----------VQGSQSDGESNNATIFVGALDSD-VSDEDLREPFSQFGEILSVKIPVG-KGCGFVQFAN  372 (449)
Q Consensus       312 ------~~~~-----------~~~~~~~~~~~~~~l~V~nlp~~-~t~~~L~~~f~~~G~v~~v~i~~~-~g~afV~F~~  372 (449)
                            ....           .....+.....++++.|.+|... ++.+.|.++|..||.|++|++++. .+.|.|++.|
T Consensus       255 g~~~~p~~~~P~r~~~~~~~~~g~a~p~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk~gtamVemgd  334 (494)
T KOG1456|consen  255 GDRHGPPHPPPSRYRDGYRDGRGYASPGGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTKPGTAMVEMGD  334 (494)
T ss_pred             cccCCCCCCCCCCCccccccCCCCCCCCCCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecccceeEEEcCc
Confidence                  0000           00112244567889999999875 678999999999999999999986 5999999999


Q ss_pred             HHHHHHHHHHhcCCeeCCeEEEEEecCCC
Q 013141          373 RKDAEVALQKLQGTAIGKQTVRLSWGRNP  401 (449)
Q Consensus       373 ~~~A~~A~~~l~g~~~~g~~l~v~~~~~~  401 (449)
                      ..+.++|+..||+..+-|.+|.|.+++-.
T Consensus       335 ~~aver~v~hLnn~~lfG~kl~v~~SkQ~  363 (494)
T KOG1456|consen  335 AYAVERAVTHLNNIPLFGGKLNVCVSKQN  363 (494)
T ss_pred             HHHHHHHHHHhccCccccceEEEeecccc
Confidence            99999999999999999999999999843

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

Probab=99.86  E-value=2.8e-21  Score=185.57  Aligned_cols=274  Identities=21%  Similarity=0.325  Sum_probs=201.3

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhcc-----------C-CcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHT-----------G-QVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYS  178 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~-----------G-~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~  178 (449)
                      .....+.++|+++|+.++++.+..+|..-           | .|+.+.+-..+      .|||++|.+.++|..|+ .++
T Consensus       171 ~t~q~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~n~~~------nfa~ie~~s~~~at~~~-~~~  243 (500)
T KOG0120|consen  171 ATRQARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQLNLEK------NFAFIEFRSISEATEAM-ALD  243 (500)
T ss_pred             hhhhhhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeeecccc------cceeEEecCCCchhhhh-ccc
Confidence            34566789999999999999999999763           2 36666665554      59999999999999999 567


Q ss_pred             CCCCCCCCCcccccccc----------------cCCCCCccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEe
Q 013141          179 GSLMPNTDQPFRLNWAT----------------FSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVI  242 (449)
Q Consensus       179 ~~~~~~~~~~~~~~~~~----------------~~~~~~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~  242 (449)
                      +..+.+....+......                .............+++||++||..++++.++|++ +.||.+....++
T Consensus       244 ~~~f~g~~~~~~r~~d~~~~p~~~~~~~~~~~~~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell-~~fg~lk~f~lv  322 (500)
T KOG0120|consen  244 GIIFEGRPLKIRRPHDYQPVPGITLSPSQLGKVGLLPASTDVPDSPNKIFVGGLPLYLTEDQVKELL-DSFGPLKAFRLV  322 (500)
T ss_pred             chhhCCCCceecccccccCCccchhhhccccccCCcccccCcccccchhhhccCcCccCHHHHHHHH-Hhcccchhheee
Confidence            76664433333221111                0111122344566789999999999999999999 599999999999


Q ss_pred             ecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecCCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCC
Q 013141          243 IDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSD  322 (449)
Q Consensus       243 ~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  322 (449)
                      .+..++.++||||.+|.+......|++.|||..++++.+.|..+................        ............
T Consensus       323 ~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~~~~~~~~~~~~~--------~~~~i~~~~~q~  394 (500)
T KOG0120|consen  323 KDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGASNANVNFNISQS--------QVPGIPLLMTQM  394 (500)
T ss_pred             cccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhccchhccccCCcccc--------ccccchhhhccc
Confidence            999999999999999999999999999999999999999999987765432221110000        000000000011


Q ss_pred             CCCCCcEEEEcCCCC--C--------CCHhHHHhhccccCceEEEEEeCC---------CcEEEEEecCHHHHHHHHHHh
Q 013141          323 GESNNATIFVGALDS--D--------VSDEDLREPFSQFGEILSVKIPVG---------KGCGFVQFANRKDAEVALQKL  383 (449)
Q Consensus       323 ~~~~~~~l~V~nlp~--~--------~t~~~L~~~f~~~G~v~~v~i~~~---------~g~afV~F~~~~~A~~A~~~l  383 (449)
                      ......+|.+.|+=.  +        ...|+|+..|.+||.|.+|.|.++         .|.+||+|.+.++|++|++.|
T Consensus       395 ~g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L  474 (500)
T KOG0120|consen  395 AGIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEEL  474 (500)
T ss_pred             CCCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHc
Confidence            223344444444411  1        123677788999999999999874         489999999999999999999


Q ss_pred             cCCeeCCeEEEEEecCC
Q 013141          384 QGTAIGKQTVRLSWGRN  400 (449)
Q Consensus       384 ~g~~~~g~~l~v~~~~~  400 (449)
                      +|++|.|+++..+|-..
T Consensus       475 ~GrKF~nRtVvtsYyde  491 (500)
T KOG0120|consen  475 TGRKFANRTVVASYYDE  491 (500)
T ss_pred             cCceeCCcEEEEEecCH
Confidence            99999999999998764

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

Probab=99.86  E-value=1.1e-21  Score=168.71  Aligned_cols=180  Identities=24%  Similarity=0.456  Sum_probs=156.0

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCC-CCCCCCcc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSL-MPNTDQPF  189 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~-~~~~~~~~  189 (449)
                      +..+.|+|||+-|...-+|||++.+|..||.|.+|.+.+.. +|.+||||||+|.+..+|..||..|++.. +.+-...+
T Consensus        15 rg~~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~-dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSL   93 (371)
T KOG0146|consen   15 RGGDDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGP-DGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSL   93 (371)
T ss_pred             CCccchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCC-CCCCCCceEEEeccchHHHHHHHHhcccccCCCCccce
Confidence            33478899999999999999999999999999999999986 69999999999999999999999999864 66666666


Q ss_pred             cccccccCCCCC--------------------------------------------------------------------
Q 013141          190 RLNWATFSGSDR--------------------------------------------------------------------  201 (449)
Q Consensus       190 ~~~~~~~~~~~~--------------------------------------------------------------------  201 (449)
                      .|++++.+.+..                                                                    
T Consensus        94 VVK~ADTdkER~lRRMQQma~qlGm~~Pl~l~~g~~~ay~qalmQqQa~~~at~~~~~L~p~~~~~~~~mQ~~aA~~ang  173 (371)
T KOG0146|consen   94 VVKFADTDKERTLRRMQQMAGQLGMFNPLALPFGAYGAYAQALMQQQAALLATVAGPYLSPMAAFAAAQMQQMAALNANG  173 (371)
T ss_pred             EEEeccchHHHHHHHHHHHHHHhcccCccccccchhHHHHHHHHHHHHHHHHhhcccccChhhhhHHHHHHHHHHHhhcc
Confidence            666665210000                                                                    


Q ss_pred             --------------------------------------------------------------------------------
Q 013141          202 --------------------------------------------------------------------------------  201 (449)
Q Consensus       202 --------------------------------------------------------------------------------  201 (449)
                                                                                                      
T Consensus       174 l~A~Pv~p~s~~~~pp~~~a~~~~~~~A~~g~ng~~~l~~q~~gqpa~~~vy~ng~~pypaQsp~va~~lq~a~~g~~~Y  253 (371)
T KOG0146|consen  174 LAAAPVTPASGGSTPPGIGATAVPGIPAPIGVNGFTGLPPQPNGQPAAEAVYANGLHPYPAQSPTVADPLQQAYAGVQQY  253 (371)
T ss_pred             cccCCcCccccCCCCCcccccccCCcccccccccccCCCCCCCCCcchhHHhhcCCccCCCCCccccchhhhhhhhHHHH
Confidence                                                                                            


Q ss_pred             -------------------------ccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEE
Q 013141          202 -------------------------RTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFV  256 (449)
Q Consensus       202 -------------------------~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV  256 (449)
                                               ..+....+.|||..||.+..+.||...|. .||.|.+.++..|+.|+.+|+|+||
T Consensus       254 ~Aaypaays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHLPQEFgDaEliQmF~-PFGhivSaKVFvDRATNQSKCFGFV  332 (371)
T KOG0146|consen  254 AAAYPAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHLPQEFGDAELIQMFL-PFGHIVSAKVFVDRATNQSKCFGFV  332 (371)
T ss_pred             hhhcchhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeCchhhccHHHHHHhc-cccceeeeeeeehhccccccceeeE
Confidence                                     00115568899999999999999999996 9999999999999999999999999


Q ss_pred             EeCCHHHHHHHHHHhCCceecCcceEEeecCCCCCC
Q 013141          257 RFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKAS  292 (449)
Q Consensus       257 ~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~~~~~~  292 (449)
                      .|++..+|.+||..|||..|+=++|+|...++++..
T Consensus       333 SfDNp~SaQaAIqAMNGFQIGMKRLKVQLKRPkdan  368 (371)
T KOG0146|consen  333 SFDNPASAQAAIQAMNGFQIGMKRLKVQLKRPKDAN  368 (371)
T ss_pred             ecCCchhHHHHHHHhcchhhhhhhhhhhhcCccccC
Confidence            999999999999999999999999999998888653

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

Probab=99.86  E-value=2.4e-21  Score=173.50  Aligned_cols=172  Identities=22%  Similarity=0.456  Sum_probs=146.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecCC
Q 013141          209 LSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATP  288 (449)
Q Consensus       209 ~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~~  288 (449)
                      ++|||+.|.+++.|+.|+..| ..||+|++|.+..|+.|++.+|||||+|+-+|.|..|++.|||..++||.|+|.+...
T Consensus       114 cRvYVGSIsfEl~EDtiR~AF-~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPsN  192 (544)
T KOG0124|consen  114 CRVYVGSISFELREDTIRRAF-DPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSN  192 (544)
T ss_pred             HheeeeeeEEEechHHHHhhc-cCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCCC
Confidence            589999999999999999999 5999999999999999999999999999999999999999999999999999984432


Q ss_pred             CCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC------
Q 013141          289 KKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------  362 (449)
Q Consensus       289 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~------  362 (449)
                      -...  +.....-                   ......-.+|||..+.++++++||+.+|+.||+|.+|.+.+.      
T Consensus       193 mpQA--QpiID~v-------------------qeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~H  251 (544)
T KOG0124|consen  193 MPQA--QPIIDMV-------------------QEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGH  251 (544)
T ss_pred             Cccc--chHHHHH-------------------HHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCc
Confidence            2110  0000000                   001122468999999999999999999999999999999873      


Q ss_pred             CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCC
Q 013141          363 KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPG  402 (449)
Q Consensus       363 ~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~  402 (449)
                      +|++||+|.+..+-..|+..||-..++|..|||-.+-.+.
T Consensus       252 kGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~vTPP  291 (544)
T KOG0124|consen  252 KGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTPP  291 (544)
T ss_pred             cceeeEEeccccchHHHhhhcchhhcccceEecccccCCC
Confidence            7999999999999999999999999999999998766443

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

Probab=99.85  E-value=1e-20  Score=162.85  Aligned_cols=209  Identities=25%  Similarity=0.443  Sum_probs=158.7

Q ss_pred             CcccccccccCCCCCccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHH
Q 013141          187 QPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSR  266 (449)
Q Consensus       187 ~~~~~~~~~~~~~~~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~  266 (449)
                      ++|.|+.+..+     ......++|||+-|.+.-+|||++.+|. .||+|+++.+++.+. |.+||++||.|.+..+|..
T Consensus         3 rpiqvkpadse-----srg~~drklfvgml~kqq~e~dvrrlf~-pfG~~~e~tvlrg~d-g~sKGCAFVKf~s~~eAqa   75 (371)
T KOG0146|consen    3 RPIQVKPADSE-----SRGGDDRKLFVGMLNKQQSEDDVRRLFQ-PFGNIEECTVLRGPD-GNSKGCAFVKFSSHAEAQA   75 (371)
T ss_pred             CCccccccccc-----cCCccchhhhhhhhcccccHHHHHHHhc-ccCCcceeEEecCCC-CCCCCceEEEeccchHHHH
Confidence            45555544322     2233678999999999999999999995 999999999999865 8999999999999999999


Q ss_pred             HHHHhCCcee---cCcceEEeecCCCCCCchhhcchhhhh-----------------------------------h----
Q 013141          267 AMTEMNGVYC---SSRPMRIDVATPKKASGYQQQYSSQAL-----------------------------------V----  304 (449)
Q Consensus       267 A~~~l~g~~~---~g~~i~v~~~~~~~~~~~~~~~~~~~~-----------------------------------~----  304 (449)
                      ||..|+|...   ....|.|++++..+++..++.......                                   +    
T Consensus        76 AI~aLHgSqTmpGASSSLVVK~ADTdkER~lRRMQQma~qlGm~~Pl~l~~g~~~ay~qalmQqQa~~~at~~~~~L~p~  155 (371)
T KOG0146|consen   76 AINALHGSQTMPGASSSLVVKFADTDKERTLRRMQQMAGQLGMFNPLALPFGAYGAYAQALMQQQAALLATVAGPYLSPM  155 (371)
T ss_pred             HHHHhcccccCCCCccceEEEeccchHHHHHHHHHHHHHHhcccCccccccchhHHHHHHHHHHHHHHHHhhcccccChh
Confidence            9999999664   456799999988776543332110000                                   0    


Q ss_pred             --------------hcCC----C-------------------------CC---------------------CC-------
Q 013141          305 --------------LAGG----P-------------------------GS---------------------NG-------  313 (449)
Q Consensus       305 --------------~~~~----~-------------------------~~---------------------~~-------  313 (449)
                                    ...+    +                         +.                     +.       
T Consensus       156 ~~~~~~~mQ~~aA~~angl~A~Pv~p~s~~~~pp~~~a~~~~~~~A~~g~ng~~~l~~q~~gqpa~~~vy~ng~~pypaQ  235 (371)
T KOG0146|consen  156 AAFAAAQMQQMAALNANGLAAAPVTPASGGSTPPGIGATAVPGIPAPIGVNGFTGLPPQPNGQPAAEAVYANGLHPYPAQ  235 (371)
T ss_pred             hhhHHHHHHHHHHHhhcccccCCcCccccCCCCCcccccccCCcccccccccccCCCCCCCCCcchhHHhhcCCccCCCC
Confidence                          0000    0                         00                     00       


Q ss_pred             -----CC----------------------cCC---------CCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEE
Q 013141          314 -----AR----------------------VQG---------SQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSV  357 (449)
Q Consensus       314 -----~~----------------------~~~---------~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v  357 (449)
                           ..                      ...         -.....++.|.|||..||-+..+.||...|-.||.|.+.
T Consensus       236 sp~va~~lq~a~~g~~~Y~Aaypaays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSa  315 (371)
T KOG0146|consen  236 SPTVADPLQQAYAGVQQYAAAYPAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSA  315 (371)
T ss_pred             CccccchhhhhhhhHHHHhhhcchhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeCchhhccHHHHHHhccccceeee
Confidence                 00                      000         001234678999999999999999999999999999998


Q ss_pred             EEeC------CCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCC
Q 013141          358 KIPV------GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPG  402 (449)
Q Consensus       358 ~i~~------~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~  402 (449)
                      ++..      +|.|+||.|+++.+|..||.+|||..|+-++|+|...+++.
T Consensus       316 KVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQLKRPkd  366 (371)
T KOG0146|consen  316 KVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQLKRPKD  366 (371)
T ss_pred             eeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhhhcCccc
Confidence            7764      47999999999999999999999999999999999998864

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

Probab=99.84  E-value=1.2e-20  Score=183.34  Aligned_cols=175  Identities=18%  Similarity=0.357  Sum_probs=145.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCC---CcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          116 KTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTG---QSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       116 ~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g---~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      ++|||.||++++|.++|..+|...|.|.++.|.+.+...   .+.|||||+|.+.++|.+|++.|+++.+.+....+++.
T Consensus       516 t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S  595 (725)
T KOG0110|consen  516 TKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKIS  595 (725)
T ss_pred             hhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEec
Confidence            349999999999999999999999999999888765321   25599999999999999999999999997765555554


Q ss_pred             ccccCCCCCc--cccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHH
Q 013141          193 WATFSGSDRR--TEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE  270 (449)
Q Consensus       193 ~~~~~~~~~~--~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~  270 (449)
                      -..+.....+  .....-++|+|+|||+..+..+++++|. .||.|.+|++++....+.++|||||+|.+..+|.+|++.
T Consensus       596 ~~k~~~~~gK~~~~kk~~tKIlVRNipFeAt~rEVr~LF~-aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~a  674 (725)
T KOG0110|consen  596 ENKPASTVGKKKSKKKKGTKILVRNIPFEATKREVRKLFT-AFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDA  674 (725)
T ss_pred             cCccccccccccccccccceeeeeccchHHHHHHHHHHHh-cccceeeeccchhhcchhhccceeeeccCcHHHHHHHHh
Confidence            4111111111  1222246899999999999999999996 999999999998866667899999999999999999999


Q ss_pred             hCCceecCcceEEeecCCCCC
Q 013141          271 MNGVYCSSRPMRIDVATPKKA  291 (449)
Q Consensus       271 l~g~~~~g~~i~v~~~~~~~~  291 (449)
                      |....+.||.|.++|+.....
T Consensus       675 l~STHlyGRrLVLEwA~~d~~  695 (725)
T KOG0110|consen  675 LGSTHLYGRRLVLEWAKSDNT  695 (725)
T ss_pred             hcccceechhhheehhccchH
Confidence            999999999999999987654

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

Probab=99.82  E-value=1.1e-19  Score=166.82  Aligned_cols=167  Identities=25%  Similarity=0.423  Sum_probs=145.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeec
Q 013141          207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVA  286 (449)
Q Consensus       207 ~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~  286 (449)
                      ..++|||++|+++++++.|++.|+ .||+|.++.+++|+.+++++||+||+|++.+...+++ ......|+++.|.++.+
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~-~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl-~~~~h~~dgr~ve~k~a   82 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFS-QFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVL-NARTHKLDGRSVEPKRA   82 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhc-ccCceeeEEEeccCCCCCcccccceecCCCcchheee-cccccccCCccccceec
Confidence            568999999999999999999995 9999999999999999999999999999999999888 45567789999999999


Q ss_pred             CCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeC-----
Q 013141          287 TPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV-----  361 (449)
Q Consensus       287 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~-----  361 (449)
                      .++.....                          ........+|||++||.++++++++++|++||.|..+.++.     
T Consensus        83 v~r~~~~~--------------------------~~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~  136 (311)
T KOG4205|consen   83 VSREDQTK--------------------------VGRHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTS  136 (311)
T ss_pred             cCcccccc--------------------------cccccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeeccccc
Confidence            88875421                          11122578999999999999999999999999999988875     


Q ss_pred             -CCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCC
Q 013141          362 -GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPG  402 (449)
Q Consensus       362 -~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~  402 (449)
                       .++|+||+|.+.+++.+++. ..-+.|+++.+.|.-+.++.
T Consensus       137 ~~rgFgfv~~~~e~sVdkv~~-~~f~~~~gk~vevkrA~pk~  177 (311)
T KOG4205|consen  137 RPRGFGFVTFDSEDSVDKVTL-QKFHDFNGKKVEVKRAIPKE  177 (311)
T ss_pred             ccccceeeEeccccccceecc-cceeeecCceeeEeeccchh
Confidence             37999999999999888875 57788999999999887644

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

Probab=99.82  E-value=1.2e-17  Score=150.57  Aligned_cols=271  Identities=18%  Similarity=0.178  Sum_probs=206.9

Q ss_pred             EcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccccccccCCC
Q 013141          120 IGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATFSGS  199 (449)
Q Consensus       120 v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~~~~~~~  199 (449)
                      |-|--+.+|.+.|..++...|.|.+|.|++..  |.   .|.|||++.+.|++|.+.|||..|......++++++++...
T Consensus       127 IlNp~YpItvDVly~Icnp~GkVlRIvIfkkn--gV---QAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIeyAkP~rl  201 (494)
T KOG1456|consen  127 ILNPQYPITVDVLYTICNPQGKVLRIVIFKKN--GV---QAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIEYAKPTRL  201 (494)
T ss_pred             eecCccccchhhhhhhcCCCCceEEEEEEecc--ce---eeEEeechhHHHHHHHhhcccccccccceeEEEEecCccee
Confidence            44545799999999999999999999998863  33   69999999999999999999999988889999988874310


Q ss_pred             CC----------------c-------------------------------------------------------------
Q 013141          200 DR----------------R-------------------------------------------------------------  202 (449)
Q Consensus       200 ~~----------------~-------------------------------------------------------------  202 (449)
                      ..                .                                                             
T Consensus       202 nV~knd~DtwDyTlp~~~~~~~~g~~~~~r~~~p~~~~~~pss~~G~h~~y~sg~~~~p~~~~P~r~~~~~~~~~g~a~p  281 (494)
T KOG1456|consen  202 NVQKNDKDTWDYTLPDLRGPYDPGRNHYDRQRQPAPLGYHPSSRGGGHSGYYSGDRHGPPHPPPSRYRDGYRDGRGYASP  281 (494)
T ss_pred             eeeecCCccccccCCCCCCCCCCCCCCCccccCCCccCCChhhcCCCCCCCcccccCCCCCCCCCCCccccccCCCCCCC
Confidence            00                0                                                             


Q ss_pred             cccCCCceEEEcCCCCC-CCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcce
Q 013141          203 TEACSDLSIFVGDLAPD-VTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPM  281 (449)
Q Consensus       203 ~~~~~~~~l~v~~lp~~-~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i  281 (449)
                      ....+...++|.+|... +.-+.|.++|. .||.|++|++++.+     .|.|+|++.|..+.++|+..||+..+.|.+|
T Consensus       282 ~g~~~g~VmMVyGLdh~k~N~drlFNl~C-lYGNV~rvkFmkTk-----~gtamVemgd~~aver~v~hLnn~~lfG~kl  355 (494)
T KOG1456|consen  282 GGGAPGCVMMVYGLDHGKMNCDRLFNLFC-LYGNVERVKFMKTK-----PGTAMVEMGDAYAVERAVTHLNNIPLFGGKL  355 (494)
T ss_pred             CCCCCCcEEEEEeccccccchhhhhhhhh-hcCceeeEEEeecc-----cceeEEEcCcHHHHHHHHHHhccCccccceE
Confidence            00123457888899864 55678999996 99999999999874     4689999999999999999999999999999


Q ss_pred             EEeecCCCCCCc-----hhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCc-eE
Q 013141          282 RIDVATPKKASG-----YQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGE-IL  355 (449)
Q Consensus       282 ~v~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~-v~  355 (449)
                      .|.+++-.....     +.....+...+.......-..+..........++++|+.-|.|..+||+.|.++|...+. ..
T Consensus       356 ~v~~SkQ~~v~~~~pflLpDgSpSfKdys~SkNnRFssp~qAsKNrIq~Ps~vLHffNaP~~vtEe~l~~i~nek~v~~~  435 (494)
T KOG1456|consen  356 NVCVSKQNFVSPVQPFLLPDGSPSFKDYSGSKNNRFSSPEQASKNRIQPPSNVLHFFNAPLGVTEEQLIGICNEKDVPPT  435 (494)
T ss_pred             EEeeccccccccCCceecCCCCcchhhcccccccccCChhHhhcccccCCcceeEEecCCCccCHHHHHHHhhhcCCCcc
Confidence            999987654322     111122222222222223333334445566778999999999999999999999976643 45


Q ss_pred             EEEEeCC----CcEEEEEecCHHHHHHHHHHhcCCeeCC------eEEEEEecCCC
Q 013141          356 SVKIPVG----KGCGFVQFANRKDAEVALQKLQGTAIGK------QTVRLSWGRNP  401 (449)
Q Consensus       356 ~v~i~~~----~g~afV~F~~~~~A~~A~~~l~g~~~~g------~~l~v~~~~~~  401 (449)
                      +|+|...    ...+.++|++.++|..||..||...+.+      -.|++-|+...
T Consensus       436 svkvFp~kserSssGllEfe~~s~Aveal~~~NH~pi~~p~gs~PfilKlcfsts~  491 (494)
T KOG1456|consen  436 SVKVFPLKSERSSSGLLEFENKSDAVEALMKLNHYPIEGPNGSFPFILKLCFSTSK  491 (494)
T ss_pred             eEEeecccccccccceeeeehHHHHHHHHHHhccccccCCCCCCCeeeeeeecccc
Confidence            6666653    3578999999999999999999999875      35677776653

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

Probab=99.80  E-value=6.1e-18  Score=138.00  Aligned_cols=173  Identities=19%  Similarity=0.356  Sum_probs=135.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEee
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV  285 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  285 (449)
                      ..+++|||+|||.++.+.+|.++|. +||.|..|.+...   .....||||+|++..+|+.||..-+|..+++..|+|++
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFy-Kyg~i~~ieLK~r---~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEf   79 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFY-KYGRIREIELKNR---PGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEF   79 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHh-hhcceEEEEeccC---CCCCCeeEEEecCccchhhhhhcccccccCcceEEEEe
Confidence            3567999999999999999999996 9999999988643   23467999999999999999999999999999999999


Q ss_pred             cCCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcE
Q 013141          286 ATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGC  365 (449)
Q Consensus       286 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~  365 (449)
                      ..........     ...+...+.+ ..................|.|.+||.+-++.||++++.+-|+|....+.++ +.
T Consensus        80 prggr~s~~~-----~G~y~gggrg-Ggg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD-g~  152 (241)
T KOG0105|consen   80 PRGGRSSSDR-----RGSYSGGGRG-GGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD-GV  152 (241)
T ss_pred             ccCCCccccc-----ccccCCCCCC-CCCCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc-cc
Confidence            8766422111     0111111111 111111112333445678999999999999999999999999999998875 59


Q ss_pred             EEEEecCHHHHHHHHHHhcCCeeC
Q 013141          366 GFVQFANRKDAEVALQKLQGTAIG  389 (449)
Q Consensus       366 afV~F~~~~~A~~A~~~l~g~~~~  389 (449)
                      +.|+|...++.+-|+..|+...+.
T Consensus       153 GvV~~~r~eDMkYAvr~ld~~~~~  176 (241)
T KOG0105|consen  153 GVVEYLRKEDMKYAVRKLDDQKFR  176 (241)
T ss_pred             eeeeeeehhhHHHHHHhhcccccc
Confidence            999999999999999999888775

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

Probab=99.80  E-value=2.5e-18  Score=142.63  Aligned_cols=82  Identities=24%  Similarity=0.544  Sum_probs=75.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC------CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEE
Q 013141          323 GESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLS  396 (449)
Q Consensus       323 ~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~------~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~  396 (449)
                      .....++|||+|||+.+++++|+++|++||.|.+|.|+.+      +++|||+|.+.++|++|++.||+..|+|+.|+|+
T Consensus        30 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~  109 (144)
T PLN03134         30 LRLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVN  109 (144)
T ss_pred             ccCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            3456789999999999999999999999999999999753      6999999999999999999999999999999999


Q ss_pred             ecCCCCCC
Q 013141          397 WGRNPGNK  404 (449)
Q Consensus       397 ~~~~~~~~  404 (449)
                      |++.+...
T Consensus       110 ~a~~~~~~  117 (144)
T PLN03134        110 PANDRPSA  117 (144)
T ss_pred             eCCcCCCC
Confidence            99876544

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

Probab=99.79  E-value=7.4e-19  Score=158.70  Aligned_cols=282  Identities=16%  Similarity=0.155  Sum_probs=192.5

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      ..++...|..|+|||..++.+|..+|.-.-...-...+.....|+..|++.|.|.|.|.-+.|++. +...+  ..+.+.
T Consensus        56 ~~~~~vvvRaRglpwq~Sd~~ia~ff~gl~ia~gg~aKOG~~qgrRnge~lvrf~d~e~RdlalkR-hkhh~--g~ryie  132 (508)
T KOG1365|consen   56 SADDNVVVRARGLPWQSSDQDIARFFKGLNIANGGRALCLNAQGRRNGEALVRFVDPEGRDLALKR-HKHHM--GTRYIE  132 (508)
T ss_pred             ccCcceEEEecCCCCCcccCCHHHHHhhhhccccceeeeehhhhccccceEEEecCchhhhhhhHh-hhhhc--cCCcee
Confidence            345667788999999999999999998764444445555556688889999999999999999965 33333  233443


Q ss_pred             ccccccC---------CCCCc--cccCCCceEEEcCCCCCCCHHHHHHHHhh---hCCCeeEEEEeecCCCCCcceEEEE
Q 013141          191 LNWATFS---------GSDRR--TEACSDLSIFVGDLAPDVTDSILQETFSS---KYPSVKGAKVIIDSNTGRTKGYGFV  256 (449)
Q Consensus       191 ~~~~~~~---------~~~~~--~~~~~~~~l~v~~lp~~~t~~~l~~~f~~---~~g~v~~i~~~~~~~~~~~~g~afV  256 (449)
                      +-.+..+         ..+..  .....-..|.+++||+++++.++.++|..   ..+..+.|.+++.+ .|+..|-|||
T Consensus       133 vYka~ge~f~~iagg~s~e~~~flsk~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rp-dgrpTGdAFv  211 (508)
T KOG1365|consen  133 VYKATGEEFLKIAGGTSNEAAPFLSKENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRP-DGRPTGDAFV  211 (508)
T ss_pred             eeccCchhheEecCCccccCCCCCCcccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECC-CCCcccceEE
Confidence            3222211         11111  22233446778999999999999999941   13456677777764 4899999999


Q ss_pred             EeCCHHHHHHHHHHhCCceecCcceEEeecCCCCCCchhhcchhhhhhhcCCCCCCCCC-cCCCCCCCCCCCcEEEEcCC
Q 013141          257 RFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGAR-VQGSQSDGESNNATIFVGAL  335 (449)
Q Consensus       257 ~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~l~V~nl  335 (449)
                      .|..+++|..|+. -|...++-|.|++..++..+....-.........  +...+.... .............+|.+++|
T Consensus       212 lfa~ee~aq~aL~-khrq~iGqRYIElFRSTaaEvqqvlnr~~s~pLi--~~~~sp~~p~~p~~~~p~~~~kdcvRLRGL  288 (508)
T KOG1365|consen  212 LFACEEDAQFALR-KHRQNIGQRYIELFRSTAAEVQQVLNREVSEPLI--PGLTSPLLPGGPARLVPPTRSKDCVRLRGL  288 (508)
T ss_pred             EecCHHHHHHHHH-HHHHHHhHHHHHHHHHhHHHHHHHHHhhcccccc--CCCCCCCCCCCccccCCCCCCCCeeEecCC
Confidence            9999999999994 5556677788888777654322111111110000  000111111 01111222333779999999


Q ss_pred             CCCCCHhHHHhhccccCc-eEE--EEEeC-----CCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 013141          336 DSDVSDEDLREPFSQFGE-ILS--VKIPV-----GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGR  399 (449)
Q Consensus       336 p~~~t~~~L~~~f~~~G~-v~~--v~i~~-----~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  399 (449)
                      |++.+.|||.++|..|-. |..  |++..     ..|.|||+|.+.++|..|..+-|.+.++.+.|.|--+.
T Consensus       289 Py~AtvEdIL~FlgdFa~~i~f~gVHmv~N~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp~S  360 (508)
T KOG1365|consen  289 PYEATVEDILDFLGDFATDIRFQGVHMVLNGQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFPCS  360 (508)
T ss_pred             ChhhhHHHHHHHHHHHhhhcccceeEEEEcCCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEeecc
Confidence            999999999999998853 333  55543     36999999999999999999989888889999987655

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

Probab=99.77  E-value=2e-17  Score=140.73  Aligned_cols=190  Identities=22%  Similarity=0.355  Sum_probs=147.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHH----HHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcce
Q 013141          206 CSDLSIFVGDLAPDVTDSILQE----TFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPM  281 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~----~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i  281 (449)
                      .++.+|||.||+..+..++|++    +|+ .||.|.+|...+   +.+.+|-|||.|.+.+.|-.|++.|+|..+.|+++
T Consensus         7 ~pn~TlYInnLnekI~~~elkrsL~~LFs-qfG~ildI~a~k---t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~m   82 (221)
T KOG4206|consen    7 NPNGTLYINNLNEKIKKDELKRSLYLLFS-QFGKILDISAFK---TPKMRGQAFVVFKETEAASAALRALQGFPFYGKPM   82 (221)
T ss_pred             CCCceEeehhccccccHHHHHHHHHHHHH-hhCCeEEEEecC---CCCccCceEEEecChhHHHHHHHHhcCCcccCchh
Confidence            3445999999999999999988    996 999999998884   46789999999999999999999999999999999


Q ss_pred             EEeecCCCCCCchhhcc-------h--hhhhhh------cCCCCC--CCCCcCCC-CCCCCCCCcEEEEcCCCCCCCHhH
Q 013141          282 RIDVATPKKASGYQQQY-------S--SQALVL------AGGPGS--NGARVQGS-QSDGESNNATIFVGALDSDVSDED  343 (449)
Q Consensus       282 ~v~~~~~~~~~~~~~~~-------~--~~~~~~------~~~~~~--~~~~~~~~-~~~~~~~~~~l~V~nlp~~~t~~~  343 (449)
                      +|.++..+.....+...       .  ......      ..+...  ........ .....+...++++.|||.+++.+.
T Consensus        83 riqyA~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~~~~~ppn~ilf~~niP~es~~e~  162 (221)
T KOG4206|consen   83 RIQYAKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFLAQMAPPNNILFLTNIPSESESEM  162 (221)
T ss_pred             heecccCccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCccccCCCCceEEEEecCCcchhHHH
Confidence            99999876432222110       0  000000      000000  00000000 133356778999999999999999


Q ss_pred             HHhhccccCceEEEEEeCC-CcEEEEEecCHHHHHHHHHHhcCCeeC-CeEEEEEecC
Q 013141          344 LREPFSQFGEILSVKIPVG-KGCGFVQFANRKDAEVALQKLQGTAIG-KQTVRLSWGR  399 (449)
Q Consensus       344 L~~~f~~~G~v~~v~i~~~-~g~afV~F~~~~~A~~A~~~l~g~~~~-g~~l~v~~~~  399 (449)
                      |..+|.+|.....|+++.. ++.|||+|.+...|..|...|.+..+- ...++|.|++
T Consensus       163 l~~lf~qf~g~keir~i~~~~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~a~  220 (221)
T KOG4206|consen  163 LSDLFEQFPGFKEIRLIPPRSGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITFAK  220 (221)
T ss_pred             HHHHHhhCcccceeEeccCCCceeEEecchhhhhHHHhhhhccceeccCceEEecccC
Confidence            9999999999999999885 689999999999999999999999887 8899998876

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

Probab=99.75  E-value=2.3e-18  Score=163.28  Aligned_cols=175  Identities=27%  Similarity=0.447  Sum_probs=144.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEee
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV  285 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  285 (449)
                      ...+++|+--|....+..+|.++|+ .+|.|.+|.++.|..+++++|.+||+|.|.+....|| .|.|..+.|.+|.|..
T Consensus       177 Rd~Rtvf~~qla~r~~pRdL~efFs-~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~ai-aLsGqrllg~pv~vq~  254 (549)
T KOG0147|consen  177 RDQRTVFCMQLARRNPPRDLEEFFS-IVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAI-ALSGQRLLGVPVIVQL  254 (549)
T ss_pred             HhHHHHHHHHHhhcCCchhHHHHHH-hhcCcceeEeeccccchhhcceeEEEEecccchhhHh-hhcCCcccCceeEecc
Confidence            4456788888888899999999996 9999999999999999999999999999999999999 7999999999999987


Q ss_pred             cCCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC---
Q 013141          286 ATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG---  362 (449)
Q Consensus       286 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~---  362 (449)
                      ........   .  .....           ...  .....+...|||+||...+++++|+.+|+.||.|..|.+..+   
T Consensus       255 sEaeknr~---a--~~s~a-----------~~~--k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~t  316 (549)
T KOG0147|consen  255 SEAEKNRA---A--NASPA-----------LQG--KGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSET  316 (549)
T ss_pred             cHHHHHHH---H--hcccc-----------ccc--cccccchhhhhhcccccCchHHHHhhhccCcccceeeeecccccc
Confidence            75543320   0  00000           000  000111223999999999999999999999999999999864   


Q ss_pred             ---CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCC
Q 013141          363 ---KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRN  400 (449)
Q Consensus       363 ---~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  400 (449)
                         +||+||+|.+.++|++|++.|||.+|.|+.|+|.....
T Consensus       317 G~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~  357 (549)
T KOG0147|consen  317 GRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTE  357 (549)
T ss_pred             ccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeee
Confidence               79999999999999999999999999999999986553

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

Probab=99.75  E-value=2.3e-17  Score=134.59  Aligned_cols=151  Identities=19%  Similarity=0.261  Sum_probs=125.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      ..+++|||+|||.++-+.||.++|-+||.|.+|.+...+   ....||||+|++..+|+.||..-++..+++  ..++|+
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~---g~ppfafVeFEd~RDAeDAiygRdGYdydg--~rLRVE   78 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRP---GPPPFAFVEFEDPRDAEDAIYGRDGYDYDG--CRLRVE   78 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCC---CCCCeeEEEecCccchhhhhhcccccccCc--ceEEEE
Confidence            568999999999999999999999999999999886543   346799999999999999999889988865  456666


Q ss_pred             ccccCCCC---------------------CccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcc
Q 013141          193 WATFSGSD---------------------RRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTK  251 (449)
Q Consensus       193 ~~~~~~~~---------------------~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~  251 (449)
                      ++......                     -.....+...|.|.+||++-++.+|++... +.|+|-...+.+|       
T Consensus        79 fprggr~s~~~~G~y~gggrgGgg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmR-eaGdvCfadv~rD-------  150 (241)
T KOG0105|consen   79 FPRGGRSSSDRRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMR-EAGDVCFADVQRD-------  150 (241)
T ss_pred             eccCCCcccccccccCCCCCCCCCCCcccCCcccccceeEEEecCCCCCchHHHHHHHH-hhCCeeeeeeecc-------
Confidence            65432110                     012334567899999999999999999996 8999998888876       


Q ss_pred             eEEEEEeCCHHHHHHHHHHhCCcee
Q 013141          252 GYGFVRFGDENERSRAMTEMNGVYC  276 (449)
Q Consensus       252 g~afV~f~~~~~A~~A~~~l~g~~~  276 (449)
                      |++.|+|...|+.+-|++.|+...+
T Consensus       151 g~GvV~~~r~eDMkYAvr~ld~~~~  175 (241)
T KOG0105|consen  151 GVGVVEYLRKEDMKYAVRKLDDQKF  175 (241)
T ss_pred             cceeeeeeehhhHHHHHHhhccccc
Confidence            3789999999999999999988766

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

Probab=99.72  E-value=2.1e-16  Score=134.57  Aligned_cols=163  Identities=21%  Similarity=0.398  Sum_probs=135.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHH----HhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcc
Q 013141          114 ETKTIWIGDLFHWMDETFLHN----CFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPF  189 (449)
Q Consensus       114 ~~~~l~v~nLp~~~t~~~l~~----~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~  189 (449)
                      +..||||+||+..+..++|+.    +|++||.|++|...+.   .+.+|-|||.|.+.+.|..|+..|+|..+  .+.++
T Consensus         8 pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt---~KmRGQA~VvFk~~~~As~A~r~l~gfpF--ygK~m   82 (221)
T KOG4206|consen    8 PNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKT---PKMRGQAFVVFKETEAASAALRALQGFPF--YGKPM   82 (221)
T ss_pred             CCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCC---CCccCceEEEecChhHHHHHHHHhcCCcc--cCchh
Confidence            344999999999999999988    9999999999988764   67899999999999999999999999998  45677


Q ss_pred             cccccccCCCCC---------------------------------------------ccccCCCceEEEcCCCCCCCHHH
Q 013141          190 RLNWATFSGSDR---------------------------------------------RTEACSDLSIFVGDLAPDVTDSI  224 (449)
Q Consensus       190 ~~~~~~~~~~~~---------------------------------------------~~~~~~~~~l~v~~lp~~~t~~~  224 (449)
                      ++.+++.+....                                             .....++..+|+.|||..++.+.
T Consensus        83 riqyA~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~~~~~ppn~ilf~~niP~es~~e~  162 (221)
T KOG4206|consen   83 RIQYAKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFLAQMAPPNNILFLTNIPSESESEM  162 (221)
T ss_pred             heecccCccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCccccCCCCceEEEEecCCcchhHHH
Confidence            776665332110                                             01135667899999999999999


Q ss_pred             HHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceec-CcceEEeecC
Q 013141          225 LQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCS-SRPMRIDVAT  287 (449)
Q Consensus       225 l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~-g~~i~v~~~~  287 (449)
                      +..+| +.|....+|+++...     ++.|||+|.++..|..|...+.+..|. ...+.|.+++
T Consensus       163 l~~lf-~qf~g~keir~i~~~-----~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~a~  220 (221)
T KOG4206|consen  163 LSDLF-EQFPGFKEIRLIPPR-----SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITFAK  220 (221)
T ss_pred             HHHHH-hhCcccceeEeccCC-----CceeEEecchhhhhHHHhhhhccceeccCceEEecccC
Confidence            99999 499999999998653     569999999999999999999998885 7777777654

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

Probab=99.72  E-value=2.9e-16  Score=144.31  Aligned_cols=196  Identities=18%  Similarity=0.330  Sum_probs=149.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEee
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV  285 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  285 (449)
                      ...+.+||.|||+++.+.+|+++|.++.|+|+.|.++.| .++++||+|.|+|+++|.+++|++.||...+.||+|.|+.
T Consensus        42 ~r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D-~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKE  120 (608)
T KOG4212|consen   42 ARDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFD-ESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKE  120 (608)
T ss_pred             cccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecc-cCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEec
Confidence            344569999999999999999999999999999999999 5699999999999999999999999999999999999987


Q ss_pred             cCCCCCCchhhcchhhh---------------hhhcC---CCC-----------------------------------CC
Q 013141          286 ATPKKASGYQQQYSSQA---------------LVLAG---GPG-----------------------------------SN  312 (449)
Q Consensus       286 ~~~~~~~~~~~~~~~~~---------------~~~~~---~~~-----------------------------------~~  312 (449)
                      ........+...-....               .....   +..                                   ..
T Consensus       121 d~d~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~~~lfgl~  200 (608)
T KOG4212|consen  121 DHDEQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSNYNLFGLS  200 (608)
T ss_pred             cCchhhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCccccccccccchhhhcccch
Confidence            76533211110000000               00000   000                                   00


Q ss_pred             CCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhcCCe
Q 013141          313 GARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV-----GKGCGFVQFANRKDAEVALQKLQGTA  387 (449)
Q Consensus       313 ~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~-----~~g~afV~F~~~~~A~~A~~~l~g~~  387 (449)
                      ............+....+||.||.+.+..+.|++.|.-.|.|..|.+.-     ++++|.++|+++-+|..||..|++.-
T Consensus       201 ~~Flr~~h~f~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idKeG~s~G~~vi~y~hpveavqaIsml~~~g  280 (608)
T KOG4212|consen  201 ASFLRSLHIFSPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDKEGNSRGFAVIEYDHPVEAVQAISMLDRQG  280 (608)
T ss_pred             hhhhhhccCCCCCccceeeeeccccccchHHHHHHhccceeeeeeceeeccccccCCeeEEEecchHHHHHHHHhhccCC
Confidence            0000000112345567899999999999999999999999999998764     46999999999999999999999888


Q ss_pred             eCCeEEEEEecCCCC
Q 013141          388 IGKQTVRLSWGRNPG  402 (449)
Q Consensus       388 ~~g~~l~v~~~~~~~  402 (449)
                      +.+++..++..+...
T Consensus       281 ~~~~~~~~Rl~~~~D  295 (608)
T KOG4212|consen  281 LFDRRMTVRLDRIPD  295 (608)
T ss_pred             Cccccceeecccccc
Confidence            888888888866543

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

Probab=99.68  E-value=1.1e-16  Score=137.87  Aligned_cols=165  Identities=23%  Similarity=0.419  Sum_probs=135.1

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecCC
Q 013141          209 LSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATP  288 (449)
Q Consensus       209 ~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~~  288 (449)
                      ..+||++||+.+.+.+|.++|. .||.|.++.+.        .||+||+|.+..+|..|+..|++..+++..+.|+++..
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~-~yg~~~d~~mk--------~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~   72 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFK-GYGKIPDADMK--------NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARG   72 (216)
T ss_pred             CceeecccCCccchhHHHHHHh-hccccccceee--------cccceeccCchhhhhcccchhcCceecceeeeeecccc
Confidence            3689999999999999999995 99999999875        45899999999999999999999999999899998886


Q ss_pred             CCCCchhhcchhhhhhhcCCCCCCCCC-cCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEE
Q 013141          289 KKASGYQQQYSSQALVLAGGPGSNGAR-VQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGF  367 (449)
Q Consensus       289 ~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~af  367 (449)
                      .....             +.+...... ..........+.+.+.|.++...+.+.+|.++|+++|.+....+  ..+++|
T Consensus        73 ~~~~~-------------g~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--~~~~~~  137 (216)
T KOG0106|consen   73 KRRGR-------------GRPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--RRNFAF  137 (216)
T ss_pred             ccccc-------------CCCCCCCccchhhccCCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhh--hccccc
Confidence            43221             000000000 11222334566788999999999999999999999999966655  578999


Q ss_pred             EEecCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 013141          368 VQFANRKDAEVALQKLQGTAIGKQTVRLSW  397 (449)
Q Consensus       368 V~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  397 (449)
                      |+|++.++|.+|++.|++..+.++.|.+..
T Consensus       138 v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~  167 (216)
T KOG0106|consen  138 VEFSEQEDAKRALEKLDGKKLNGRRISVEK  167 (216)
T ss_pred             eeehhhhhhhhcchhccchhhcCceeeecc
Confidence            999999999999999999999999999943

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

Probab=99.68  E-value=4.9e-15  Score=139.02  Aligned_cols=167  Identities=19%  Similarity=0.328  Sum_probs=128.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEee
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV  285 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  285 (449)
                      .....|-+.+||+++|++||.++|+ ..+ |+++.+.+  .+|+..|-|||+|.+++++++|+ +.+...+..+.|+|-.
T Consensus         8 ~~~~~vr~rGLPwsat~~ei~~Ff~-~~~-I~~~~~~r--~~Gr~sGeA~Ve~~seedv~~Al-kkdR~~mg~RYIEVf~   82 (510)
T KOG4211|consen    8 STAFEVRLRGLPWSATEKEILDFFS-NCG-IENLEIPR--RNGRPSGEAYVEFTSEEDVEKAL-KKDRESMGHRYIEVFT   82 (510)
T ss_pred             CcceEEEecCCCccccHHHHHHHHh-cCc-eeEEEEec--cCCCcCcceEEEeechHHHHHHH-HhhHHHhCCceEEEEc
Confidence            3445688899999999999999996 554 77755554  46899999999999999999999 5777889999999999


Q ss_pred             cCCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEE-EEEeC---
Q 013141          286 ATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILS-VKIPV---  361 (449)
Q Consensus       286 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~-v~i~~---  361 (449)
                      +......-..+.                     .......+..+|.+.+||+.+|++||.+||+..-.|.. |.++.   
T Consensus        83 ~~~~e~d~~~~~---------------------~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~r  141 (510)
T KOG4211|consen   83 AGGAEADWVMRP---------------------GGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQR  141 (510)
T ss_pred             cCCccccccccC---------------------CCCCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCC
Confidence            877655321111                     00111145678999999999999999999997644444 22322   


Q ss_pred             --CCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 013141          362 --GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGR  399 (449)
Q Consensus       362 --~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  399 (449)
                        ..+.|||.|++.+.|++|+.. |...|+.+.|.|--+.
T Consensus       142 gR~tGEAfVqF~sqe~ae~Al~r-hre~iGhRYIEvF~Ss  180 (510)
T KOG4211|consen  142 GRPTGEAFVQFESQESAEIALGR-HRENIGHRYIEVFRSS  180 (510)
T ss_pred             CCcccceEEEecCHHHHHHHHHH-HHHhhccceEEeehhH
Confidence              368999999999999999975 7778888888886443

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

Probab=99.68  E-value=4.5e-16  Score=129.09  Aligned_cols=86  Identities=34%  Similarity=0.644  Sum_probs=80.4

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEe
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRID  284 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  284 (449)
                      ...+++|||+||++++|+++|+++|. .||.|.++.+++|..+++++|||||+|.+.++|++|++.|++..|.++.|+|+
T Consensus        31 ~~~~~~lfVgnL~~~~te~~L~~~F~-~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~  109 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDDASLRDAFA-HFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVN  109 (144)
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHh-cCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            45677999999999999999999995 99999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 013141          285 VATPKKA  291 (449)
Q Consensus       285 ~~~~~~~  291 (449)
                      ++..+..
T Consensus       110 ~a~~~~~  116 (144)
T PLN03134        110 PANDRPS  116 (144)
T ss_pred             eCCcCCC
Confidence            9977543

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

Probab=99.67  E-value=5.2e-15  Score=132.70  Aligned_cols=193  Identities=18%  Similarity=0.220  Sum_probs=141.5

Q ss_pred             ccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeE--------EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCce
Q 013141          204 EACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKG--------AKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVY  275 (449)
Q Consensus       204 ~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~--------i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~  275 (449)
                      ....++.|||.|||.++|.+++.++|+ ++|.|..        |++.++.. |..+|-|+|.|...+++..||+.|++..
T Consensus       130 ~~~~Nt~VYVsgLP~DiT~dE~~~~~s-KcGiI~~d~~t~epk~KlYrd~~-G~lKGDaLc~y~K~ESVeLA~~ilDe~~  207 (382)
T KOG1548|consen  130 EPKVNTSVYVSGLPLDITVDEFAEVMS-KCGIIMRDPQTGEPKVKLYRDNQ-GKLKGDALCCYIKRESVELAIKILDEDE  207 (382)
T ss_pred             ccccCceEEecCCCCcccHHHHHHHHH-hcceEeccCCCCCeeEEEEecCC-CCccCceEEEeecccHHHHHHHHhCccc
Confidence            345667899999999999999999997 8887754        67888754 9999999999999999999999999999


Q ss_pred             ecCcceEEeecCCCCCCchh--------hcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCC----CCC---
Q 013141          276 CSSRPMRIDVATPKKASGYQ--------QQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDS----DVS---  340 (449)
Q Consensus       276 ~~g~~i~v~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~----~~t---  340 (449)
                      +.|+.|+|+.+.....-...        .............. -...+. ..........++|.|.|+=.    ..+   
T Consensus       208 ~rg~~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~-~dw~pd-~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l  285 (382)
T KOG1548|consen  208 LRGKKLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKL-LDWRPD-RDDPSKARADRTVILKNMFTPEDFEKNPDL  285 (382)
T ss_pred             ccCcEEEEehhhhhhccCcCcccccccccccHHHHHHHHHhh-cccCCC-ccccccccCCcEEEeeecCCHHHhccCHHH
Confidence            99999999988653211000        00000000000000 000000 01122334567888888832    112   


Q ss_pred             ----HhHHHhhccccCceEEEEEeC--CCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCC
Q 013141          341 ----DEDLREPFSQFGEILSVKIPV--GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRN  400 (449)
Q Consensus       341 ----~~~L~~~f~~~G~v~~v~i~~--~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  400 (449)
                          .++|++.+++||.|.+|.|..  ..|.+-|.|.|.++|..||+.|+|+.|+|+.|..+....
T Consensus       286 ~~dlkedl~eec~K~G~v~~vvv~d~hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~DG  351 (382)
T KOG1548|consen  286 LNDLKEDLTEECEKFGQVRKVVVYDRHPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWDG  351 (382)
T ss_pred             HHHHHHHHHHHHHHhCCcceEEEeccCCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeCC
Confidence                477888899999999999883  579999999999999999999999999999998876543

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

Probab=99.63  E-value=4.9e-15  Score=124.79  Aligned_cols=183  Identities=21%  Similarity=0.365  Sum_probs=126.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecC-CCCCcceEEEEEeCCHHHHHHHHHHhCCcee---cCcce
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDS-NTGRTKGYGFVRFGDENERSRAMTEMNGVYC---SSRPM  281 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~-~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~---~g~~i  281 (449)
                      ..-++|||.+||.++...||..+|+ .|-..+...+.... ...-.+-+|||+|.+..+|.+|++.|||..|   .+..|
T Consensus        32 ~~VRTLFVSGLP~DvKpREiynLFR-~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stL  110 (284)
T KOG1457|consen   32 GAVRTLFVSGLPNDVKPREIYNLFR-RFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTL  110 (284)
T ss_pred             cccceeeeccCCcccCHHHHHHHhc-cCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCcee
Confidence            4467999999999999999999997 66666666554432 2223457999999999999999999999998   56788


Q ss_pred             EEeecCCCCCCchhhcchhhh----hh--------h-------cC---CCC-----CCCCCc------------------
Q 013141          282 RIDVATPKKASGYQQQYSSQA----LV--------L-------AG---GPG-----SNGARV------------------  316 (449)
Q Consensus       282 ~v~~~~~~~~~~~~~~~~~~~----~~--------~-------~~---~~~-----~~~~~~------------------  316 (449)
                      ++++++........+......    ..        .       ..   ++.     ......                  
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            998887644332221111000    00        0       00   000     000000                  


Q ss_pred             -------C--CCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeC--CCcEEEEEecCHHHHHHHHHHhcC
Q 013141          317 -------Q--GSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV--GKGCGFVQFANRKDAEVALQKLQG  385 (449)
Q Consensus       317 -------~--~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~--~~g~afV~F~~~~~A~~A~~~l~g  385 (449)
                             .  .........+.+|||-||...++||+|+.+|+.|-....++|..  +...|||+|++.+.|..|+..|.|
T Consensus       191 P~a~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~~g~~vaf~~~~~~~~at~am~~lqg  270 (284)
T KOG1457|consen  191 PSANAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRARGGMPVAFADFEEIEQATDAMNHLQG  270 (284)
T ss_pred             CcccchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecCCCcceEeecHHHHHHHHHHHHHhhc
Confidence                   0  00011223456899999999999999999999997766666654  356899999999999999999998


Q ss_pred             CeeC
Q 013141          386 TAIG  389 (449)
Q Consensus       386 ~~~~  389 (449)
                      ..|-
T Consensus       271 ~~~s  274 (284)
T KOG1457|consen  271 NLLS  274 (284)
T ss_pred             ceec
Confidence            7653

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

Probab=99.63  E-value=1.9e-15  Score=122.77  Aligned_cols=84  Identities=30%  Similarity=0.537  Sum_probs=76.1

Q ss_pred             CCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC-CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCCC
Q 013141          325 SNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGN  403 (449)
Q Consensus       325 ~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~-~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~~  403 (449)
                      ...++|||+||+..+++.||..+|..||.|.+|.|.+. .|||||+|+|+.+|..|+..|+|+.|+|..|+|++++....
T Consensus         8 ~~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnPPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G~~r   87 (195)
T KOG0107|consen    8 NGNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTGRPR   87 (195)
T ss_pred             CCCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecCCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecCCcc
Confidence            34789999999999999999999999999999999874 79999999999999999999999999999999999998765


Q ss_pred             CCCCC
Q 013141          404 KQWRG  408 (449)
Q Consensus       404 ~~~~~  408 (449)
                      ...++
T Consensus        88 ~~r~g   92 (195)
T KOG0107|consen   88 GSRRG   92 (195)
T ss_pred             ccccC
Confidence            44333

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

Probab=99.62  E-value=2.5e-14  Score=128.32  Aligned_cols=172  Identities=17%  Similarity=0.289  Sum_probs=137.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCcEE--------EEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCC
Q 013141          112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVN--------VKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMP  183 (449)
Q Consensus       112 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~--------v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~  183 (449)
                      ....+.|||.|||.++|.+++.++|+.||.|.+        |++.++.. |..+|-|+|.|.-.++++.|+..|++..+.
T Consensus       131 ~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~-G~lKGDaLc~y~K~ESVeLA~~ilDe~~~r  209 (382)
T KOG1548|consen  131 PKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQ-GKLKGDALCCYIKRESVELAIKILDEDELR  209 (382)
T ss_pred             cccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCC-CCccCceEEEeecccHHHHHHHHhCccccc
Confidence            445567999999999999999999999997653        89999964 999999999999999999999999999994


Q ss_pred             CCCCcccccccccCCC---------------------------------CCccccCCCceEEEcCCC----CCCC-----
Q 013141          184 NTDQPFRLNWATFSGS---------------------------------DRRTEACSDLSIFVGDLA----PDVT-----  221 (449)
Q Consensus       184 ~~~~~~~~~~~~~~~~---------------------------------~~~~~~~~~~~l~v~~lp----~~~t-----  221 (449)
                        ++.|+|..++....                                 .........++|.+.|+=    ...+     
T Consensus       210 --g~~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~  287 (382)
T KOG1548|consen  210 --GKKLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARADRTVILKNMFTPEDFEKNPDLLN  287 (382)
T ss_pred             --CcEEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccccccccCCcEEEeeecCCHHHhccCHHHHH
Confidence              67777776653210                                 111233456788888862    1222     


Q ss_pred             --HHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecCCCCC
Q 013141          222 --DSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKA  291 (449)
Q Consensus       222 --~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~~~~~  291 (449)
                        .++|++.. ++||.|..|.|.-.    .+.|.+.|.|.+.++|..||+.|+|+.|+||.|..+.++.+..
T Consensus       288 dlkedl~eec-~K~G~v~~vvv~d~----hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~DG~t~  354 (382)
T KOG1548|consen  288 DLKEDLTEEC-EKFGQVRKVVVYDR----HPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWDGKTK  354 (382)
T ss_pred             HHHHHHHHHH-HHhCCcceEEEecc----CCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeCCcce
Confidence              35667778 49999999988643    3578999999999999999999999999999999999877643

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

Probab=99.61  E-value=6.8e-16  Score=133.01  Aligned_cols=152  Identities=19%  Similarity=0.352  Sum_probs=127.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccccccc
Q 013141          116 KTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWAT  195 (449)
Q Consensus       116 ~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~~~  195 (449)
                      ..|||++||+.+.+.+|..||..||.+.+|.+..        ||+||+|.+..+|..|+..+++..+.+..  +.++|+.
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~--------gf~fv~fed~rda~Dav~~l~~~~l~~e~--~vve~~r   71 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMKN--------GFGFVEFEDPRDADDAVHDLDGKELCGER--LVVEHAR   71 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceeec--------ccceeccCchhhhhcccchhcCceeccee--eeeeccc
Confidence            4799999999999999999999999999998855        58999999999999999999999997755  6777776


Q ss_pred             cCC---------------CCCccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCC
Q 013141          196 FSG---------------SDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGD  260 (449)
Q Consensus       196 ~~~---------------~~~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~  260 (449)
                      ...               ..........+.+.|.+++..+.+.+|.+.|+ .+|.+....+        ..+++||+|.+
T Consensus        72 ~~~~~~g~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~-~~g~~~~~~~--------~~~~~~v~Fs~  142 (216)
T KOG0106|consen   72 GKRRGRGRPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFR-PAGEVTYVDA--------RRNFAFVEFSE  142 (216)
T ss_pred             ccccccCCCCCCCccchhhccCCcccccceeeeccchhhhhHHHHhhhhc-ccCCCchhhh--------hccccceeehh
Confidence            321               01112345567899999999999999999996 9999854444        24589999999


Q ss_pred             HHHHHHHHHHhCCceecCcceEEeec
Q 013141          261 ENERSRAMTEMNGVYCSSRPMRIDVA  286 (449)
Q Consensus       261 ~~~A~~A~~~l~g~~~~g~~i~v~~~  286 (449)
                      .+++.+|+..|++..+.++.|++...
T Consensus       143 ~~da~ra~~~l~~~~~~~~~l~~~~~  168 (216)
T KOG0106|consen  143 QEDAKRALEKLDGKKLNGRRISVEKN  168 (216)
T ss_pred             hhhhhhcchhccchhhcCceeeeccc
Confidence            99999999999999999999999433

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

Probab=99.60  E-value=3.6e-15  Score=127.58  Aligned_cols=84  Identities=30%  Similarity=0.480  Sum_probs=78.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccc
Q 013141          112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRL  191 (449)
Q Consensus       112 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~  191 (449)
                      ..+..+|.|.||+.+++|++|+++|.+||.|.+|.+.+|++||.++|||||.|.+.++|.+||+.|||.-+  ....++|
T Consensus       186 R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gy--d~LILrv  263 (270)
T KOG0122|consen  186 RDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGY--DNLILRV  263 (270)
T ss_pred             CCccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCccc--ceEEEEE
Confidence            34788999999999999999999999999999999999999999999999999999999999999999888  4578999


Q ss_pred             cccccC
Q 013141          192 NWATFS  197 (449)
Q Consensus       192 ~~~~~~  197 (449)
                      +|+++.
T Consensus       264 EwskP~  269 (270)
T KOG0122|consen  264 EWSKPS  269 (270)
T ss_pred             EecCCC
Confidence            998764

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

Probab=99.59  E-value=3.3e-15  Score=127.42  Aligned_cols=80  Identities=28%  Similarity=0.488  Sum_probs=69.3

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      .+..-++|||++|+|+++.|+|+++|++||+|++..|+.|+.+||+|||+||+|+|.++|++|++. -.-.|+++...+.
T Consensus         8 ~DT~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcn   86 (247)
T KOG0149|consen    8 GDTTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCN   86 (247)
T ss_pred             CCceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccc
Confidence            445667899999999999999999999999999999999999999999999999999999999965 4445655544444


Q ss_pred             c
Q 013141          191 L  191 (449)
Q Consensus       191 ~  191 (449)
                      +
T Consensus        87 l   87 (247)
T KOG0149|consen   87 L   87 (247)
T ss_pred             h
Confidence            4

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

Probab=99.58  E-value=3.2e-14  Score=119.94  Aligned_cols=160  Identities=18%  Similarity=0.255  Sum_probs=120.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEe-cCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCC-CCCcc
Q 013141          112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIR-NKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPN-TDQPF  189 (449)
Q Consensus       112 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~-~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~-~~~~~  189 (449)
                      ....|||||.+||.++...||..+|..|--.+.+.+.. ++....++-+|||.|.+..+|.+|+..|||..++- ....+
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            45689999999999999999999999987666655544 33333456899999999999999999999988753 34556


Q ss_pred             cccccccCCCCCcc------------------------------------------------------------------
Q 013141          190 RLNWATFSGSDRRT------------------------------------------------------------------  203 (449)
Q Consensus       190 ~~~~~~~~~~~~~~------------------------------------------------------------------  203 (449)
                      +++.++......+.                                                                  
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            66655422100000                                                                  


Q ss_pred             ---------------ccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH
Q 013141          204 ---------------EACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAM  268 (449)
Q Consensus       204 ---------------~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~  268 (449)
                                     ....-.+|||.||.++++|++|+.+|+ .|.....++|...    .....||++|++.+.|..|+
T Consensus       191 P~a~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~-~~~gf~~l~~~~~----~g~~vaf~~~~~~~~at~am  265 (284)
T KOG1457|consen  191 PSANAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLS-RYPGFHILKIRAR----GGMPVAFADFEEIEQATDAM  265 (284)
T ss_pred             CcccchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHH-hCCCceEEEEecC----CCcceEeecHHHHHHHHHHH
Confidence                           001113699999999999999999995 9988776666432    12458999999999999999


Q ss_pred             HHhCCcee
Q 013141          269 TEMNGVYC  276 (449)
Q Consensus       269 ~~l~g~~~  276 (449)
                      ..|.|..|
T Consensus       266 ~~lqg~~~  273 (284)
T KOG1457|consen  266 NHLQGNLL  273 (284)
T ss_pred             HHhhccee
Confidence            99999776

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

Probab=99.56  E-value=6.2e-15  Score=113.23  Aligned_cols=82  Identities=28%  Similarity=0.565  Sum_probs=76.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccc
Q 013141          112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRL  191 (449)
Q Consensus       112 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~  191 (449)
                      ...+++|||+||++.++||.|.++|+.+|+|..|.|--|+.+..+-|||||+|.+.++|+.||+.+++..+  ..++|++
T Consensus        33 ~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrL--ddr~ir~  110 (153)
T KOG0121|consen   33 LRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRL--DDRPIRI  110 (153)
T ss_pred             HhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcc--cccceee
Confidence            35789999999999999999999999999999999999999999999999999999999999999999999  4577887


Q ss_pred             cccc
Q 013141          192 NWAT  195 (449)
Q Consensus       192 ~~~~  195 (449)
                      +|..
T Consensus       111 D~D~  114 (153)
T KOG0121|consen  111 DWDA  114 (153)
T ss_pred             eccc
Confidence            7764

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

Probab=99.53  E-value=3.7e-14  Score=121.49  Aligned_cols=84  Identities=24%  Similarity=0.477  Sum_probs=80.4

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEe
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRID  284 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  284 (449)
                      ..+.++|-|.||+.++++++|+++|. +||.|.++.|.+|+.||.+||||||.|.+.++|.+||+.|||.-++.--|+|+
T Consensus       186 R~D~~tvRvtNLsed~~E~dL~eLf~-~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvE  264 (270)
T KOG0122|consen  186 RDDEATVRVTNLSEDMREDDLEELFR-PFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVE  264 (270)
T ss_pred             CCccceeEEecCccccChhHHHHHhh-ccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEE
Confidence            34678999999999999999999996 99999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCC
Q 013141          285 VATPK  289 (449)
Q Consensus       285 ~~~~~  289 (449)
                      |++++
T Consensus       265 wskP~  269 (270)
T KOG0122|consen  265 WSKPS  269 (270)
T ss_pred             ecCCC
Confidence            99886

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

Probab=99.53  E-value=2.2e-14  Score=119.52  Aligned_cols=77  Identities=30%  Similarity=0.543  Sum_probs=71.9

Q ss_pred             CCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC------CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 013141          324 ESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSW  397 (449)
Q Consensus       324 ~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~------~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  397 (449)
                      -+....|.|.||.+-++.++|+.+|++||.|-+|.|+++      +|||||.|.+..+|++|+++|+|..|+|+.|+|.+
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            344678999999999999999999999999999999974      69999999999999999999999999999999998


Q ss_pred             cCC
Q 013141          398 GRN  400 (449)
Q Consensus       398 ~~~  400 (449)
                      ++=
T Consensus        90 ary   92 (256)
T KOG4207|consen   90 ARY   92 (256)
T ss_pred             hhc
Confidence            874

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

Probab=99.53  E-value=2.1e-14  Score=127.85  Aligned_cols=81  Identities=28%  Similarity=0.471  Sum_probs=74.6

Q ss_pred             CCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeC----CCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 013141          322 DGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV----GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSW  397 (449)
Q Consensus       322 ~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~----~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  397 (449)
                      ......++|+|+|||+...+-||+.+|.+||+|.+|+|+.    +|||+||+|++.+||++|.++|||..++||+|.|..
T Consensus        91 ~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~  170 (376)
T KOG0125|consen   91 SSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNN  170 (376)
T ss_pred             CCCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCCCCccceEEecChhhHHHHHHHhhcceeeceEEEEec
Confidence            3455678999999999999999999999999999999986    489999999999999999999999999999999999


Q ss_pred             cCCCC
Q 013141          398 GRNPG  402 (449)
Q Consensus       398 ~~~~~  402 (449)
                      ++.+-
T Consensus       171 ATarV  175 (376)
T KOG0125|consen  171 ATARV  175 (376)
T ss_pred             cchhh
Confidence            88643

>PF00076 RRM_1: RNA recognition motif

Probab=99.52  E-value=4.1e-14  Score=102.93  Aligned_cols=66  Identities=38%  Similarity=0.659  Sum_probs=62.5

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCC
Q 013141          118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPN  184 (449)
Q Consensus       118 l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~  184 (449)
                      |||+|||+++|+++|+++|+.||.|..+.+..+ .++..+++|||+|.+.++|++|++.+++..+.+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~   66 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNGKKING   66 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCCCEECc
Confidence            799999999999999999999999999999998 578999999999999999999999999988754

(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 ....

>PF00076 RRM_1: RNA recognition motif

Probab=99.50  E-value=1.5e-13  Score=99.97  Aligned_cols=70  Identities=37%  Similarity=0.780  Sum_probs=66.5

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceE
Q 013141          211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMR  282 (449)
Q Consensus       211 l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  282 (449)
                      |||+|||.++|+++|+++|+ .||.|..+.+..+ .++..+++|||+|.+.++|++|++.|++..+.++.|+
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 LYVGNLPPDVTEEELRDFFS-QFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHH-TTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHH-Hhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            79999999999999999995 8999999999998 6788999999999999999999999999999999885

(a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....

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

Probab=99.48  E-value=1.2e-13  Score=123.14  Aligned_cols=98  Identities=21%  Similarity=0.380  Sum_probs=80.8

Q ss_pred             CCCCCCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCC
Q 013141          107 NNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTD  186 (449)
Q Consensus       107 ~~~~~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~  186 (449)
                      .+.......++|+|+|||+..-|.||+.+|.+||.|++|.||-+.  -.+|||+||+|++.++|++|-++||++.+.+  
T Consensus        88 t~s~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE--RGSKGFGFVTmen~~dadRARa~LHgt~VEG--  163 (376)
T KOG0125|consen   88 TNSSSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE--RGSKGFGFVTMENPADADRARAELHGTVVEG--  163 (376)
T ss_pred             CcCCCCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEecc--CCCCccceEEecChhhHHHHHHHhhcceeec--
Confidence            344455678899999999999999999999999999999999974  4689999999999999999999999999955  


Q ss_pred             CcccccccccCCCCCccccCCC
Q 013141          187 QPFRLNWATFSGSDRRTEACSD  208 (449)
Q Consensus       187 ~~~~~~~~~~~~~~~~~~~~~~  208 (449)
                      +.|+|+.+...-..++.+..+.
T Consensus       164 RkIEVn~ATarV~n~K~~v~p~  185 (376)
T KOG0125|consen  164 RKIEVNNATARVHNKKKKVLPY  185 (376)
T ss_pred             eEEEEeccchhhccCCcccCCC
Confidence            6777777765544444444333

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

Probab=99.47  E-value=6e-13  Score=124.95  Aligned_cols=150  Identities=23%  Similarity=0.364  Sum_probs=113.4

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccccc
Q 013141          115 TKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWA  194 (449)
Q Consensus       115 ~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~~  194 (449)
                      .++|||+|||+++++++|+++|..||.|..+.+..++.+++++|||||+|.+.++|..|+..+++..+.+  +.+++.+.
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~--~~~~v~~~  192 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEG--RPLRVQKA  192 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECC--ceeEeecc
Confidence            6999999999999999999999999999999999998899999999999999999999999999998855  55555553


Q ss_pred             c----cCCCCC---------------ccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEE
Q 013141          195 T----FSGSDR---------------RTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGF  255 (449)
Q Consensus       195 ~----~~~~~~---------------~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~af  255 (449)
                      .    ......               .........+++.+++..++..++...|. .++.+....+.............+
T Consensus       193 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~  271 (306)
T COG0724         193 QPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFK-SRGDIVRASLPPSKDGKIPKSRSF  271 (306)
T ss_pred             ccccccccccccccchhhhccccccccccccccceeeccccccccchhHHHHhcc-ccccceeeeccCCCCCcccccccc
Confidence            2    111111               12234456799999999999999999995 999996666655443333333333


Q ss_pred             EEeCCHHHHHHH
Q 013141          256 VRFGDENERSRA  267 (449)
Q Consensus       256 V~f~~~~~A~~A  267 (449)
                      +.+.....+...
T Consensus       272 ~~~~~~~~~~~~  283 (306)
T COG0724         272 VGNEASKDALES  283 (306)
T ss_pred             cchhHHHhhhhh
Confidence            333333333333

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

Probab=99.46  E-value=1.3e-13  Score=117.87  Aligned_cols=81  Identities=36%  Similarity=0.542  Sum_probs=73.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEee
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV  285 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  285 (449)
                      ..-++|||++|++.++.|+|++.| |.||+|.+..|+.|+.++++|||+||+|.|.++|.+||+.-+ -.|+||+..++.
T Consensus        10 T~~TKifVggL~w~T~~~~l~~yF-eqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~-piIdGR~aNcnl   87 (247)
T KOG0149|consen   10 TTFTKIFVGGLAWETHKETLRRYF-EQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPN-PIIDGRKANCNL   87 (247)
T ss_pred             ceEEEEEEcCcccccchHHHHHHH-HHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCC-Ccccccccccch
Confidence            345689999999999999999999 699999999999999999999999999999999999996444 568999999888


Q ss_pred             cCC
Q 013141          286 ATP  288 (449)
Q Consensus       286 ~~~  288 (449)
                      +.-
T Consensus        88 A~l   90 (247)
T KOG0149|consen   88 ASL   90 (247)
T ss_pred             hhh
Confidence            765

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

Probab=99.46  E-value=1.8e-13  Score=111.31  Aligned_cols=79  Identities=24%  Similarity=0.492  Sum_probs=73.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeec
Q 013141          207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVA  286 (449)
Q Consensus       207 ~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~  286 (449)
                      ..++|||+||+..+++.||+.+|. .||.|..|+|-+++     .|||||+|++..||+.|+..|+|..|+|..|+|+.+
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~-~yG~lrsvWvArnP-----PGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S   82 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFS-KYGPLRSVWVARNP-----PGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELS   82 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHH-hcCcceeEEEeecC-----CCceEEeccCcccHHHHHhhcCCccccCceEEEEee
Confidence            467999999999999999999996 99999999998753     689999999999999999999999999999999999


Q ss_pred             CCCCC
Q 013141          287 TPKKA  291 (449)
Q Consensus       287 ~~~~~  291 (449)
                      .-...
T Consensus        83 ~G~~r   87 (195)
T KOG0107|consen   83 TGRPR   87 (195)
T ss_pred             cCCcc
Confidence            87654

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.46  E-value=3e-13  Score=119.93  Aligned_cols=74  Identities=27%  Similarity=0.376  Sum_probs=69.3

Q ss_pred             CcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC---CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCC
Q 013141          327 NATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG---KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNP  401 (449)
Q Consensus       327 ~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~---~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~  401 (449)
                      .++|||+||++.+++++|+++|+.||.|.+|+|+++   +++|||+|.+.++|..|+. |+|..|.|+.|+|+++.+-
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~~   80 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENERSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAEDY   80 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccCC
Confidence            578999999999999999999999999999999875   5899999999999999995 9999999999999998753

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

Probab=99.45  E-value=5e-13  Score=98.86  Aligned_cols=79  Identities=19%  Similarity=0.367  Sum_probs=72.3

Q ss_pred             CCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeC---CCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 013141          322 DGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV---GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWG  398 (449)
Q Consensus       322 ~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~---~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~  398 (449)
                      .+.+..+.|||.|||+++|.|++.++|.+||.|..|+|-.   .+|.|||.|+|..+|++|+++|+|..+.++.|.|-|.
T Consensus        13 lppevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyy   92 (124)
T KOG0114|consen   13 LPPEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYY   92 (124)
T ss_pred             CChhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEec
Confidence            3455678999999999999999999999999999999965   3799999999999999999999999999999999886


Q ss_pred             CC
Q 013141          399 RN  400 (449)
Q Consensus       399 ~~  400 (449)
                      .+
T Consensus        93 q~   94 (124)
T KOG0114|consen   93 QP   94 (124)
T ss_pred             CH
Confidence            64

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.43  E-value=7.1e-13  Score=96.37  Aligned_cols=65  Identities=34%  Similarity=0.665  Sum_probs=59.9

Q ss_pred             EEEcCCCCCCCHhHHHhhccccCceEEEEEeCC-----CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEE
Q 013141          330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-----KGCGFVQFANRKDAEVALQKLQGTAIGKQTVR  394 (449)
Q Consensus       330 l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~-----~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~  394 (449)
                      |+|+|||+.+++++|+++|+.||.|..+.+..+     +++|||+|.+.++|.+|++.+++..|+|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            799999999999999999999999999999876     59999999999999999999999999999985

k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....

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

Probab=99.42  E-value=4.7e-13  Score=103.01  Aligned_cols=82  Identities=23%  Similarity=0.389  Sum_probs=77.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEee
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV  285 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  285 (449)
                      ..+++|||+||+..++||.|.++|+ +.|+|..|.+=.|+.+..+=|||||+|-+.++|+.|++-+++..++.+.|+++|
T Consensus        34 r~S~tvyVgNlSfyttEEqiyELFs-~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~  112 (153)
T KOG0121|consen   34 RKSCTVYVGNLSFYTTEEQIYELFS-KCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDW  112 (153)
T ss_pred             hhcceEEEeeeeeeecHHHHHHHHH-hccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeec
Confidence            4578999999999999999999997 999999999999999889999999999999999999999999999999999998


Q ss_pred             cCC
Q 013141          286 ATP  288 (449)
Q Consensus       286 ~~~  288 (449)
                      .--
T Consensus       113 D~G  115 (153)
T KOG0121|consen  113 DAG  115 (153)
T ss_pred             ccc
Confidence            744

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.42  E-value=1.2e-12  Score=95.14  Aligned_cols=70  Identities=29%  Similarity=0.665  Sum_probs=64.3

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceE
Q 013141          211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMR  282 (449)
Q Consensus       211 l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  282 (449)
                      |||+|||+++++++|+++|+ .+|.|..+.+..++. +.++++|||+|.+.++|.+|++.+++..+.|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~-~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFS-RFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCT-TSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHH-hcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            79999999999999999995 999999999999977 89999999999999999999999999999999875

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 ....

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

Probab=99.41  E-value=1.6e-12  Score=114.60  Aligned_cols=89  Identities=26%  Similarity=0.494  Sum_probs=82.4

Q ss_pred             cccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceE
Q 013141          203 TEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMR  282 (449)
Q Consensus       203 ~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  282 (449)
                      ....+-+||||+-|+.+++|.+|++.| +.||+|+.|.|++|..||+++|||||+|.++.+...|.+..+|..|+++.|.
T Consensus        96 a~gDPy~TLFv~RLnydT~EskLrreF-~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~  174 (335)
T KOG0113|consen   96 AIGDPYKTLFVARLNYDTSESKLRREF-EKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRIL  174 (335)
T ss_pred             ccCCccceeeeeeccccccHHHHHHHH-HhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEE
Confidence            344677899999999999999999999 5999999999999999999999999999999999999999999999999999


Q ss_pred             EeecCCCCCC
Q 013141          283 IDVATPKKAS  292 (449)
Q Consensus       283 v~~~~~~~~~  292 (449)
                      |++.......
T Consensus       175 VDvERgRTvk  184 (335)
T KOG0113|consen  175 VDVERGRTVK  184 (335)
T ss_pred             EEeccccccc
Confidence            9988766543

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

Probab=99.41  E-value=1.3e-11  Score=115.80  Aligned_cols=145  Identities=28%  Similarity=0.521  Sum_probs=114.7

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecC
Q 013141          208 DLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVAT  287 (449)
Q Consensus       208 ~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~  287 (449)
                      ..+|||+|||.++++++|.++|. .||.|..+.+..+..++.++|+|||+|.+.++|..|++.+++..|.++.|.|.+..
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~-~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~  193 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFK-KFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQ  193 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHH-hcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeeccc
Confidence            68999999999999999999995 99999999999998899999999999999999999999999999999999999976


Q ss_pred             C-CCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC
Q 013141          288 P-KKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG  362 (449)
Q Consensus       288 ~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~  362 (449)
                      . ...+...... .        .....................+++.+++..++..++...|..+|.+..+.+...
T Consensus       194 ~~~~~~~~~~~~-~--------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  260 (306)
T COG0724         194 PASQPRSELSNN-L--------DASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPS  260 (306)
T ss_pred             cccccccccccc-c--------chhhhccccccccccccccceeeccccccccchhHHHHhccccccceeeeccCC
Confidence            4 1111000000 0        000000001222344566788999999999999999999999999977777653

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

Probab=99.40  E-value=4.2e-12  Score=123.54  Aligned_cols=179  Identities=13%  Similarity=0.052  Sum_probs=124.8

Q ss_pred             CCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCC
Q 013141          104 NGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMP  183 (449)
Q Consensus       104 ~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~  183 (449)
                      .+.+...-..+.+.+-+.+++++.++.|+++||... .|.++.|..+...+...|-++|+|....++.+|+.. +...+ 
T Consensus       300 sggstpqvv~d~~y~~~~gm~fn~~~nd~rkfF~g~-~~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~~r-n~~~~-  376 (944)
T KOG4307|consen  300 SGGSTPQVVSDKYYNNYKGMEFNNDFNDGRKFFPGR-NAQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAFTR-NPSDD-  376 (944)
T ss_pred             CCCCCCcccchhheeeecccccccccchhhhhcCcc-cccccchhhhhcCCCcCCceEEEecCcchHHHHHhc-Cchhh-
Confidence            333444455677889999999999999999999764 466677777766555589999999999999999964 33322 


Q ss_pred             CCCCcccccccccC---------------------------------CC-CCccccCCCceEEEcCCCCCCCHHHHHHHH
Q 013141          184 NTDQPFRLNWATFS---------------------------------GS-DRRTEACSDLSIFVGDLAPDVTDSILQETF  229 (449)
Q Consensus       184 ~~~~~~~~~~~~~~---------------------------------~~-~~~~~~~~~~~l~v~~lp~~~t~~~l~~~f  229 (449)
                       ..+.+.+......                                 .. ..+..-.....|||..||..+++..+.++|
T Consensus       377 -~~R~~q~~P~g~~~~~~a~~~~~~~~~~~~~~~hg~p~~~pr~~~~~gq~vp~P~~ag~~lyv~~lP~~t~~~~~v~~f  455 (944)
T KOG4307|consen  377 -VNRPFQTGPPGNLGRNGAPPFQAGVPPPVIQNNHGRPIAPPRAMVRPGQNVPFPGGAGGALYVFQLPVMTPIVPPVNKF  455 (944)
T ss_pred             -hhcceeecCCCccccccCccccccCCCCcccccCCCCCCCcccccCCCCCCCCCCCccceEEeccCCccccccchhhhh
Confidence             1223332211100                                 00 000112335689999999999999999999


Q ss_pred             hhhCCCeeE-EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecCC
Q 013141          230 SSKYPSVKG-AKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATP  288 (449)
Q Consensus       230 ~~~~g~v~~-i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~~  288 (449)
                      . .--.|++ |.|.+. .+++.++.|||+|..++++..|...-+...++.+-|+|+....
T Consensus       456 ~-~~~~Ved~I~lt~~-P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si~~  513 (944)
T KOG4307|consen  456 M-GAAAVEDFIELTRL-PTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSIAD  513 (944)
T ss_pred             h-hhhhhhheeEeccC-CcccccchhhheeccccccchhhhcccccccCceEEEeechhh
Confidence            6 5556666 555554 4578889999999998888888766666667777777765543

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

Probab=99.40  E-value=2e-12  Score=95.66  Aligned_cols=84  Identities=18%  Similarity=0.329  Sum_probs=75.7

Q ss_pred             ccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEE
Q 013141          204 EACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRI  283 (449)
Q Consensus       204 ~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  283 (449)
                      .+..++.|||.|||+++|.|++.++|+ +||.|..|++=.++   ..+|.|||.|++..+|++|++.|+|..++++.+.|
T Consensus        14 ppevnriLyirNLp~~ITseemydlFG-kyg~IrQIRiG~~k---~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~v   89 (124)
T KOG0114|consen   14 PPEVNRILYIRNLPFKITSEEMYDLFG-KYGTIRQIRIGNTK---ETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVV   89 (124)
T ss_pred             ChhhheeEEEecCCccccHHHHHHHhh-cccceEEEEecCcc---CcCceEEEEehHhhhHHHHHHHhcccccCCceEEE
Confidence            345678999999999999999999997 99999999997554   45899999999999999999999999999999999


Q ss_pred             eecCCCCC
Q 013141          284 DVATPKKA  291 (449)
Q Consensus       284 ~~~~~~~~  291 (449)
                      -+..+.+.
T Consensus        90 lyyq~~~~   97 (124)
T KOG0114|consen   90 LYYQPEDA   97 (124)
T ss_pred             EecCHHHH
Confidence            99887654

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

Probab=99.40  E-value=1.5e-12  Score=125.72  Aligned_cols=177  Identities=16%  Similarity=0.320  Sum_probs=131.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccc
Q 013141          112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRL  191 (449)
Q Consensus       112 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~  191 (449)
                      .....+++|++||..+++..++++...||++....++.+..+|-++||||.+|.++.....|++.|||..+......+..
T Consensus       286 ~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~  365 (500)
T KOG0120|consen  286 PDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQR  365 (500)
T ss_pred             ccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeeh
Confidence            34567899999999999999999999999999999999999999999999999999999999999999988654444433


Q ss_pred             cccccCCCCC-----------------ccccCCCceEEEcCCC--CCC-CH-------HHHHHHHhhhCCCeeEEEEeec
Q 013141          192 NWATFSGSDR-----------------RTEACSDLSIFVGDLA--PDV-TD-------SILQETFSSKYPSVKGAKVIID  244 (449)
Q Consensus       192 ~~~~~~~~~~-----------------~~~~~~~~~l~v~~lp--~~~-t~-------~~l~~~f~~~~g~v~~i~~~~~  244 (449)
                      ..........                 .....+...|.+.|+=  .++ ++       |+++..++ +||.|..|.+.++
T Consensus       366 A~~g~~~~~~~~~~~~~~~~~i~~~~~q~~g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~-k~g~v~~v~ipr~  444 (500)
T KOG0120|consen  366 AIVGASNANVNFNISQSQVPGIPLLMTQMAGIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTECA-KFGAVRSVEIPRP  444 (500)
T ss_pred             hhccchhccccCCccccccccchhhhcccCCCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHhc-ccCceeEEecCCC
Confidence            2222111000                 0111222333333321  011 11       34445564 8999999999877


Q ss_pred             CC---CCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecCCC
Q 013141          245 SN---TGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPK  289 (449)
Q Consensus       245 ~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~~~  289 (449)
                      ..   .....|..||+|.+.+++++|+++|+|++|.++.|...|.+..
T Consensus       445 ~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYydeD  492 (500)
T KOG0120|consen  445 YPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYDED  492 (500)
T ss_pred             CCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecCHH
Confidence            22   2234577899999999999999999999999999999887654

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

Probab=99.39  E-value=1.7e-12  Score=117.89  Aligned_cols=170  Identities=14%  Similarity=0.157  Sum_probs=123.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhc---c-CCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcc
Q 013141          114 ETKTIWIGDLFHWMDETFLHNCFSH---T-GQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPF  189 (449)
Q Consensus       114 ~~~~l~v~nLp~~~t~~~l~~~f~~---~-G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~  189 (449)
                      ..-.|.+|+||+++++.|+.+||.+   . |.++.|-+++.. +|+..|-|||.|..+++|..||.+. ...|..  +-|
T Consensus       160 ~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rp-dgrpTGdAFvlfa~ee~aq~aL~kh-rq~iGq--RYI  235 (508)
T KOG1365|consen  160 NQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRP-DGRPTGDAFVLFACEEDAQFALRKH-RQNIGQ--RYI  235 (508)
T ss_pred             cceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECC-CCCcccceEEEecCHHHHHHHHHHH-HHHHhH--HHH
Confidence            3457899999999999999999963   2 245566666654 6999999999999999999999652 222211  111


Q ss_pred             cccccc----------------------cC-C---CCCccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCC-eeE--EE
Q 013141          190 RLNWAT----------------------FS-G---SDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPS-VKG--AK  240 (449)
Q Consensus       190 ~~~~~~----------------------~~-~---~~~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~-v~~--i~  240 (449)
                      .+-.+.                      +. .   ...-....+...|.+++||++.+.|+|.++|. .|.. |..  |.
T Consensus       236 ElFRSTaaEvqqvlnr~~s~pLi~~~~sp~~p~~p~~~~p~~~~kdcvRLRGLPy~AtvEdIL~Flg-dFa~~i~f~gVH  314 (508)
T KOG1365|consen  236 ELFRSTAAEVQQVLNREVSEPLIPGLTSPLLPGGPARLVPPTRSKDCVRLRGLPYEATVEDILDFLG-DFATDIRFQGVH  314 (508)
T ss_pred             HHHHHhHHHHHHHHHhhccccccCCCCCCCCCCCccccCCCCCCCCeeEecCCChhhhHHHHHHHHH-HHhhhcccceeE
Confidence            111110                      00 0   00001223366899999999999999999996 5543 444  67


Q ss_pred             EeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecCCC
Q 013141          241 VIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPK  289 (449)
Q Consensus       241 ~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~~~  289 (449)
                      ++.+ ..|++.|-|||+|.+.++|.+|...++++....|.|+|-.+...
T Consensus       315 mv~N-~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp~S~e  362 (508)
T KOG1365|consen  315 MVLN-GQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFPCSVE  362 (508)
T ss_pred             EEEc-CCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEeeccHH
Confidence            7777 45899999999999999999999999988888999999776554

>PF13893 RRM_5: RNA recognition motif

Probab=99.39  E-value=2.1e-12  Score=89.15  Aligned_cols=55  Identities=36%  Similarity=0.645  Sum_probs=52.0

Q ss_pred             HHhhccccCceEEEEEeCCC-cEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 013141          344 LREPFSQFGEILSVKIPVGK-GCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWG  398 (449)
Q Consensus       344 L~~~f~~~G~v~~v~i~~~~-g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~  398 (449)
                      |+++|++||+|.++.+.+++ ++|||+|.+.++|.+|++.||+..|.|+.|+|.|+
T Consensus         1 L~~~f~~fG~V~~i~~~~~~~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKKRGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTSTTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            68999999999999999887 99999999999999999999999999999999986

(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 ....

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

Probab=99.39  E-value=8.3e-12  Score=118.42  Aligned_cols=156  Identities=19%  Similarity=0.277  Sum_probs=116.7

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCC--Cccc---EEEEEEccHHHHHHHHHHhcCCCCCCC
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTG--QSEG---YGFVEFYSRAAAEKVLQSYSGSLMPNT  185 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g--~~~g---~afV~f~~~~~A~~Al~~l~~~~~~~~  185 (449)
                      ...-+++|||++||++++|+.|...|..||.+.-=.-.+....+  -.+|   |+|+.|+++.++..-|..+....   .
T Consensus       255 ~~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~~~---~  331 (520)
T KOG0129|consen  255 SPRYSRKVFVGGLPWDITEAQINASFGQFGSVKVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSEGE---G  331 (520)
T ss_pred             ccccccceeecCCCccccHHHHHhhcccccceEeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhhcc---c
Confidence            34567889999999999999999999999975332221211111  2456   99999999999998887654411   1


Q ss_pred             CCcccccccccCC----------------CCCccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCC
Q 013141          186 DQPFRLNWATFSG----------------SDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGR  249 (449)
Q Consensus       186 ~~~~~~~~~~~~~----------------~~~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~  249 (449)
                      ..-+++.....+.                ........+.+||||++||.-++.++|..+|...||.|..+-|-.|++-+.
T Consensus       332 ~~yf~vss~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KY  411 (520)
T KOG0129|consen  332 NYYFKVSSPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKY  411 (520)
T ss_pred             ceEEEEecCcccccceeEEeeEeccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCC
Confidence            1111111111110                112234577899999999999999999999977999999999999988899


Q ss_pred             cceEEEEEeCCHHHHHHHHH
Q 013141          250 TKGYGFVRFGDENERSRAMT  269 (449)
Q Consensus       250 ~~g~afV~f~~~~~A~~A~~  269 (449)
                      ++|.+=|+|.+..+-.+||.
T Consensus       412 PkGaGRVtFsnqqsYi~AIs  431 (520)
T KOG0129|consen  412 PKGAGRVTFSNQQAYIKAIS  431 (520)
T ss_pred             CCCcceeeecccHHHHHHHh
Confidence            99999999999999999985

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.37  E-value=3e-12  Score=113.65  Aligned_cols=78  Identities=15%  Similarity=0.213  Sum_probs=71.5

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecC
Q 013141          208 DLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVAT  287 (449)
Q Consensus       208 ~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~  287 (449)
                      .++|||+||++++|+++|+++|+ .||.|.+|.|+++..   ++|||||+|.+.++|+.|+ .|+|..|.|+.|+|.++.
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS-~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~Al-lLnG~~l~gr~V~Vt~a~   78 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFS-FSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETAL-LLSGATIVDQSVTITPAE   78 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHH-hcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHH-HhcCCeeCCceEEEEecc
Confidence            46999999999999999999996 999999999998853   4789999999999999999 599999999999999987


Q ss_pred             CCC
Q 013141          288 PKK  290 (449)
Q Consensus       288 ~~~  290 (449)
                      ...
T Consensus        79 ~~~   81 (260)
T PLN03120         79 DYQ   81 (260)
T ss_pred             CCC
Confidence            553

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

Probab=99.37  E-value=7e-13  Score=127.53  Aligned_cols=84  Identities=31%  Similarity=0.577  Sum_probs=80.1

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecCC
Q 013141          209 LSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATP  288 (449)
Q Consensus       209 ~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~~  288 (449)
                      +.|||+|+|+++++++|.++|+ ..|.|.+++++.|+.+|+++||+|++|.+.++|..|++.|||.++.|++|+|.|+..
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~-~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~   97 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFS-GVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASN   97 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHh-ccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeecccc
Confidence            7899999999999999999996 999999999999999999999999999999999999999999999999999999987


Q ss_pred             CCCCc
Q 013141          289 KKASG  293 (449)
Q Consensus       289 ~~~~~  293 (449)
                      ...+.
T Consensus        98 ~~~~~  102 (435)
T KOG0108|consen   98 RKNAE  102 (435)
T ss_pred             cchhH
Confidence            76543

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

Probab=99.36  E-value=3e-13  Score=110.58  Aligned_cols=87  Identities=25%  Similarity=0.478  Sum_probs=80.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEee
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV  285 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  285 (449)
                      ..+.-|||+|||+++||.||.-+|+ .||+|.+|.+++|+.||+++||||+.|++-.+...|+..|||..|.||.|+|+.
T Consensus        33 kdsA~Iyiggl~~~LtEgDil~VFS-qyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDH  111 (219)
T KOG0126|consen   33 KDSAYIYIGGLPYELTEGDILCVFS-QYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDH  111 (219)
T ss_pred             ccceEEEECCCcccccCCcEEEEee-ccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeee
Confidence            3566899999999999999999997 999999999999999999999999999999999999999999999999999998


Q ss_pred             cCCCCCCc
Q 013141          286 ATPKKASG  293 (449)
Q Consensus       286 ~~~~~~~~  293 (449)
                      ........
T Consensus       112 v~~Yk~pk  119 (219)
T KOG0126|consen  112 VSNYKKPK  119 (219)
T ss_pred             cccccCCc
Confidence            76655443

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

Probab=99.36  E-value=2.3e-12  Score=113.63  Aligned_cols=84  Identities=21%  Similarity=0.364  Sum_probs=75.7

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcc
Q 013141          110 FTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPF  189 (449)
Q Consensus       110 ~~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~  189 (449)
                      ...++-+||||.-|+++++|.+|+..|+.||+|+.|.|++|+.||+++|||||+|+++.+...|.+..++..|++..+.|
T Consensus        96 a~gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~V  175 (335)
T KOG0113|consen   96 AIGDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILV  175 (335)
T ss_pred             ccCCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEE
Confidence            34478899999999999999999999999999999999999999999999999999999999999999999997655554


Q ss_pred             cccc
Q 013141          190 RLNW  193 (449)
Q Consensus       190 ~~~~  193 (449)
                      -++.
T Consensus       176 DvER  179 (335)
T KOG0113|consen  176 DVER  179 (335)
T ss_pred             Eecc
Confidence            4443

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

Probab=99.35  E-value=7.2e-14  Score=114.16  Aligned_cols=79  Identities=24%  Similarity=0.473  Sum_probs=73.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccc
Q 013141          112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRL  191 (449)
Q Consensus       112 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~  191 (449)
                      -.++.-|||+|||++.||.||.-+|++||+|++|.+++|+.||+++||||+.|++..+...|+..|||..|.  ++.|+|
T Consensus        32 YkdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~--gRtirV  109 (219)
T KOG0126|consen   32 YKDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKIL--GRTIRV  109 (219)
T ss_pred             cccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceec--ceeEEe
Confidence            457889999999999999999999999999999999999999999999999999999999999999999884  466666


Q ss_pred             c
Q 013141          192 N  192 (449)
Q Consensus       192 ~  192 (449)
                      +
T Consensus       110 D  110 (219)
T KOG0126|consen  110 D  110 (219)
T ss_pred             e
Confidence            4

>PLN03213 repressor of silencing 3; Provisional

Probab=99.34  E-value=3.4e-12  Score=119.57  Aligned_cols=77  Identities=19%  Similarity=0.376  Sum_probs=71.0

Q ss_pred             CCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeC--CCcEEEEEecCH--HHHHHHHHHhcCCeeCCeEEEEEecC
Q 013141          324 ESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV--GKGCGFVQFANR--KDAEVALQKLQGTAIGKQTVRLSWGR  399 (449)
Q Consensus       324 ~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~--~~g~afV~F~~~--~~A~~A~~~l~g~~~~g~~l~v~~~~  399 (449)
                      .....+|||+||.+.+++++|+.+|..||.|.+|.|++  .||||||+|.+.  .++.+||..|||..+.|+.|+|.-++
T Consensus         7 ~~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRETGRGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAK   86 (759)
T PLN03213          7 GGGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTKGRSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAK   86 (759)
T ss_pred             CCcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecccCCceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeecc
Confidence            34468999999999999999999999999999999997  479999999987  68999999999999999999999888


Q ss_pred             C
Q 013141          400 N  400 (449)
Q Consensus       400 ~  400 (449)
                      +
T Consensus        87 P   87 (759)
T PLN03213         87 E   87 (759)
T ss_pred             H
Confidence            3

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

Probab=99.34  E-value=2e-12  Score=107.97  Aligned_cols=84  Identities=26%  Similarity=0.422  Sum_probs=78.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEee
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV  285 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  285 (449)
                      ..-..|.|-||.+-++.++|+.+| ++||.|-+|.|.+|..|..++|||||.|.+..+|+.|+++|+|..++|+.|+|.+
T Consensus        11 ~gm~SLkVdNLTyRTspd~LrrvF-ekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~   89 (256)
T KOG4207|consen   11 EGMTSLKVDNLTYRTSPDDLRRVF-EKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQM   89 (256)
T ss_pred             ccceeEEecceeccCCHHHHHHHH-HHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehh
Confidence            344689999999999999999999 6999999999999999999999999999999999999999999999999999998


Q ss_pred             cCCCC
Q 013141          286 ATPKK  290 (449)
Q Consensus       286 ~~~~~  290 (449)
                      +.-..
T Consensus        90 arygr   94 (256)
T KOG4207|consen   90 ARYGR   94 (256)
T ss_pred             hhcCC
Confidence            86543

>smart00362 RRM_2 RNA recognition motif

Probab=99.33  E-value=7.6e-12  Score=90.98  Aligned_cols=68  Identities=50%  Similarity=0.850  Sum_probs=64.2

Q ss_pred             EEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCC----cEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEE
Q 013141          329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK----GCGFVQFANRKDAEVALQKLQGTAIGKQTVRLS  396 (449)
Q Consensus       329 ~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~----g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~  396 (449)
                      +|+|.|||..+++++|+++|+.||.|.++.+..++    ++|||+|.+.++|.+|++.|++..+.|+.|+|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDTGKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            48999999999999999999999999999998865    999999999999999999999999999999873

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.32  E-value=8.4e-12  Score=108.86  Aligned_cols=74  Identities=26%  Similarity=0.300  Sum_probs=68.5

Q ss_pred             CCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC---CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCC
Q 013141          326 NNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG---KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRN  400 (449)
Q Consensus       326 ~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~---~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  400 (449)
                      ...+|+|+||++.+|+++|+++|+.||.|.+|+|.++   +++|||+|.++++|..|+ .|+|..|.++.|.|+....
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~et~gfAfVtF~d~~aaetAl-lLnGa~l~d~~I~It~~~~   80 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGEYACTAYVTFKDAYALETAV-LLSGATIVDQRVCITRWGQ   80 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCCcceEEEEEECCHHHHHHHH-hcCCCeeCCceEEEEeCcc
Confidence            4689999999999999999999999999999999985   479999999999999998 5999999999999997664

>PLN03213 repressor of silencing 3; Provisional

Probab=99.29  E-value=1.5e-11  Score=115.44  Aligned_cols=80  Identities=19%  Similarity=0.380  Sum_probs=72.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCH--HHHHHHHHHhCCceecCcceEE
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDE--NERSRAMTEMNGVYCSSRPMRI  283 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~--~~A~~A~~~l~g~~~~g~~i~v  283 (449)
                      ....+|||+||++++++++|+.+|+ .||.|.+|.|++  .+|  ||||||+|.+.  .++.+||..|||..+.|+.|+|
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFS-eFGsVkdVEIpR--ETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKV   82 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFS-PMGTVDAVEFVR--TKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRL   82 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHH-hcCCeeEEEEec--ccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEE
Confidence            3457999999999999999999996 999999999994  456  89999999987  6899999999999999999999


Q ss_pred             eecCCCC
Q 013141          284 DVATPKK  290 (449)
Q Consensus       284 ~~~~~~~  290 (449)
                      ..+++.-
T Consensus        83 NKAKP~Y   89 (759)
T PLN03213         83 EKAKEHY   89 (759)
T ss_pred             eeccHHH
Confidence            9998764

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

Probab=99.29  E-value=2e-12  Score=108.82  Aligned_cols=86  Identities=27%  Similarity=0.583  Sum_probs=81.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEee
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV  285 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  285 (449)
                      ...++|||++|..++++.-|...|- +||+|.+|.+..|..+.+.|||+||+|.-.|||.+||..||+.++.||.|+|.+
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFI-PFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~   86 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFI-PFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNL   86 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccc-cccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEee
Confidence            3567999999999999999999995 999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 013141          286 ATPKKAS  292 (449)
Q Consensus       286 ~~~~~~~  292 (449)
                      +.+.+..
T Consensus        87 AkP~kik   93 (298)
T KOG0111|consen   87 AKPEKIK   93 (298)
T ss_pred             cCCcccc
Confidence            9987643

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

Probab=99.28  E-value=8.1e-12  Score=97.06  Aligned_cols=88  Identities=23%  Similarity=0.406  Sum_probs=81.3

Q ss_pred             cccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceE
Q 013141          203 TEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMR  282 (449)
Q Consensus       203 ~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  282 (449)
                      ..+.....|||.++....++++|.+.|. .||+|+.|.+..|..||..+|||+|+|.+.++|.+|+..+||..+.+..|.
T Consensus        67 qrSVEGwIi~VtgvHeEatEedi~d~F~-dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~  145 (170)
T KOG0130|consen   67 QRSVEGWIIFVTGVHEEATEEDIHDKFA-DYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVS  145 (170)
T ss_pred             ccceeeEEEEEeccCcchhHHHHHHHHh-hcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCcee
Confidence            3345567899999999999999999997 999999999999999999999999999999999999999999999999999


Q ss_pred             EeecCCCCC
Q 013141          283 IDVATPKKA  291 (449)
Q Consensus       283 v~~~~~~~~  291 (449)
                      |.|+..+..
T Consensus       146 VDw~Fv~gp  154 (170)
T KOG0130|consen  146 VDWCFVKGP  154 (170)
T ss_pred             EEEEEecCC
Confidence            999876644

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.27  E-value=3.5e-11  Score=105.05  Aligned_cols=79  Identities=16%  Similarity=0.213  Sum_probs=71.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeec
Q 013141          207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVA  286 (449)
Q Consensus       207 ~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~  286 (449)
                      ...+|||+||++.+|+++|+++|+ .||+|.+|.|+++.   ..+++|||+|.++++++.|+ .|+|..|.++.|.|..+
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS-~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAl-lLnGa~l~d~~I~It~~   78 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFS-HCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAV-LLSGATIVDQRVCITRW   78 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHH-hcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHH-hcCCCeeCCceEEEEeC
Confidence            357999999999999999999996 99999999999884   45689999999999999999 79999999999999987


Q ss_pred             CCCC
Q 013141          287 TPKK  290 (449)
Q Consensus       287 ~~~~  290 (449)
                      ....
T Consensus        79 ~~y~   82 (243)
T PLN03121         79 GQYE   82 (243)
T ss_pred             cccc
Confidence            6543

>smart00362 RRM_2 RNA recognition motif

Probab=99.26  E-value=4.6e-11  Score=86.77  Aligned_cols=72  Identities=39%  Similarity=0.814  Sum_probs=66.5

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEe
Q 013141          210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRID  284 (449)
Q Consensus       210 ~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  284 (449)
                      +|+|+|||..+++++|+++|. .||.|..+.+..+.  +.++++|||+|.+.++|++|++.+++..+.++.++|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~-~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFS-KFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHH-hcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            589999999999999999995 99999999998876  6788999999999999999999999999999998874

>smart00360 RRM RNA recognition motif

Probab=99.24  E-value=2.7e-11  Score=87.74  Aligned_cols=65  Identities=37%  Similarity=0.621  Sum_probs=60.5

Q ss_pred             EcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCC
Q 013141          120 IGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPN  184 (449)
Q Consensus       120 v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~  184 (449)
                      |+|||+.+++++|+++|..||.|..+.+..++.+++++|+|||+|.+.++|.+|++.+++..+.+
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~   65 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDG   65 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCC
Confidence            68999999999999999999999999999988788999999999999999999999999877743

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

Probab=99.24  E-value=7.3e-12  Score=105.50  Aligned_cols=80  Identities=29%  Similarity=0.615  Sum_probs=74.5

Q ss_pred             CCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC------CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 013141          325 SNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWG  398 (449)
Q Consensus       325 ~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~------~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~  398 (449)
                      ...++|||++|..++++..|...|-+||+|.+|.++-+      ++|+||+|.-.++|..||..||+.+|.||+|+|.|+
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~A   87 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLA   87 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeec
Confidence            45689999999999999999999999999999999853      799999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 013141          399 RNPGNK  404 (449)
Q Consensus       399 ~~~~~~  404 (449)
                      ++.+-+
T Consensus        88 kP~kik   93 (298)
T KOG0111|consen   88 KPEKIK   93 (298)
T ss_pred             CCcccc
Confidence            986544

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

Probab=99.24  E-value=1.5e-10  Score=110.98  Aligned_cols=166  Identities=20%  Similarity=0.228  Sum_probs=108.2

Q ss_pred             CCCCCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCC
Q 013141          108 NNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQ  187 (449)
Q Consensus       108 ~~~~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~  187 (449)
                      ....+-..++|+|-|||.+|++++|+.+|+.||+|..|+.-+.     .+|.+||+|.|..+|++|+++|+...+.++.+
T Consensus        68 p~~~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~-----~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~  142 (549)
T KOG4660|consen   68 PSEKDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPN-----KRGIVFVEFYDVRDAERALKALNRREIAGKRI  142 (549)
T ss_pred             CCcccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccc-----cCceEEEEEeehHhHHHHHHHHHHHHhhhhhh
Confidence            3344567899999999999999999999999999999776554     35899999999999999999999988855433


Q ss_pred             cccccccc--------------cCCC--CCccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcc
Q 013141          188 PFRLNWAT--------------FSGS--DRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTK  251 (449)
Q Consensus       188 ~~~~~~~~--------------~~~~--~~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~  251 (449)
                      . +-.-+.              ....  .......+...++. .|++..+..-++.++ ..+|.+.. +..     +.-+
T Consensus       143 k-~~~~~~~~~~~~~~~~~~~~~~~p~a~s~pgg~~~~~~~g-~l~P~~s~~~~~~~~-~~~~~~~~-~~~-----~~~~  213 (549)
T KOG4660|consen  143 K-RPGGARRAMGLQSGTSFLNHFGSPLANSPPGGWPRGQLFG-MLSPTRSSILLEHIS-SVDGSSPG-RET-----PLLN  213 (549)
T ss_pred             c-CCCcccccchhcccchhhhhccchhhcCCCCCCcCCccee-eeccchhhhhhhcch-hccCcccc-ccc-----cchh
Confidence            3 100000              0000  00011111223333 388877775556666 37776655 221     2112


Q ss_pred             eEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecCC
Q 013141          252 GYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATP  288 (449)
Q Consensus       252 g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~~  288 (449)
                      ---|++|.+..++..+.... |..+.+....+.++.+
T Consensus       214 hq~~~~~~~~~s~a~~~~~~-G~~~s~~~~v~t~S~~  249 (549)
T KOG4660|consen  214 HQRFVEFADNRSYAFSEPRG-GFLISNSSGVITFSGP  249 (549)
T ss_pred             hhhhhhhccccchhhcccCC-ceecCCCCceEEecCC
Confidence            24578888888886655433 6666666666666554

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

Probab=99.24  E-value=1.1e-10  Score=113.86  Aligned_cols=186  Identities=11%  Similarity=0.011  Sum_probs=130.1

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecCC
Q 013141          209 LSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATP  288 (449)
Q Consensus       209 ~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~~  288 (449)
                      +.+-+.+.+++.++.+++++|-  --.|..+.|..+...+...|.++|+|....++.+|+ +-|...+-.|.+.+.....
T Consensus       312 ~y~~~~gm~fn~~~nd~rkfF~--g~~~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~-~rn~~~~~~R~~q~~P~g~  388 (944)
T KOG4307|consen  312 YYNNYKGMEFNNDFNDGRKFFP--GRNAQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAF-TRNPSDDVNRPFQTGPPGN  388 (944)
T ss_pred             heeeecccccccccchhhhhcC--cccccccchhhhhcCCCcCCceEEEecCcchHHHHH-hcCchhhhhcceeecCCCc
Confidence            4466678999999999999993  445667777777665556889999999999999998 4566667788888877666


Q ss_pred             CCCCchhhcchhhh-hhhcCCC------CCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEE-EEEe
Q 013141          289 KKASGYQQQYSSQA-LVLAGGP------GSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILS-VKIP  360 (449)
Q Consensus       289 ~~~~~~~~~~~~~~-~~~~~~~------~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~-v~i~  360 (449)
                      .............. .......      ...................+|||..||..+++.++.++|+..-.|++ |.|.
T Consensus       389 ~~~~~a~~~~~~~~~~~~~~~hg~p~~~pr~~~~~gq~vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt  468 (944)
T KOG4307|consen  389 LGRNGAPPFQAGVPPPVIQNNHGRPIAPPRAMVRPGQNVPFPGGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELT  468 (944)
T ss_pred             cccccCccccccCCCCcccccCCCCCCCcccccCCCCCCCCCCCccceEEeccCCccccccchhhhhhhhhhhhheeEec
Confidence            54432221111111 0000000      00111111123345667889999999999999999999988777777 6665


Q ss_pred             CC-----CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 013141          361 VG-----KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSW  397 (449)
Q Consensus       361 ~~-----~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  397 (449)
                      +.     ++.|||.|..++++.+|..--+...++.+.|+|.-
T Consensus       469 ~~P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~s  510 (944)
T KOG4307|consen  469 RLPTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDS  510 (944)
T ss_pred             cCCcccccchhhheeccccccchhhhcccccccCceEEEeec
Confidence            42     58999999999999998876677778889999974

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

Probab=99.24  E-value=1.5e-11  Score=95.60  Aligned_cols=84  Identities=21%  Similarity=0.452  Sum_probs=76.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccccc
Q 013141          114 ETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNW  193 (449)
Q Consensus       114 ~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~  193 (449)
                      ..-.|||.++...++|++|.+.|..||+|+.+.+.-|+.||-.+|||+|+|++.+.|.+|+..+|+..|  .+..+.|+|
T Consensus        71 EGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~l--l~q~v~VDw  148 (170)
T KOG0130|consen   71 EGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAEL--LGQNVSVDW  148 (170)
T ss_pred             eeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhh--hCCceeEEE
Confidence            344699999999999999999999999999999999999999999999999999999999999999988  457788888


Q ss_pred             cccCCC
Q 013141          194 ATFSGS  199 (449)
Q Consensus       194 ~~~~~~  199 (449)
                      .-.+..
T Consensus       149 ~Fv~gp  154 (170)
T KOG0130|consen  149 CFVKGP  154 (170)
T ss_pred             EEecCC
Confidence            765433

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

Probab=99.23  E-value=2.2e-11  Score=117.23  Aligned_cols=80  Identities=25%  Similarity=0.554  Sum_probs=76.1

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccccccc
Q 013141          116 KTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWAT  195 (449)
Q Consensus       116 ~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~~~  195 (449)
                      +.|||+|||++++|++|.++|+..|.|.+++++.|+.+|+++||+|++|.+.++|.+|++.||+..+  .++.+++.|+.
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~--~gr~l~v~~~~   96 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEF--NGRKLRVNYAS   96 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCccc--CCceEEeeccc
Confidence            8999999999999999999999999999999999999999999999999999999999999999999  56888888886


Q ss_pred             cC
Q 013141          196 FS  197 (449)
Q Consensus       196 ~~  197 (449)
                      ..
T Consensus        97 ~~   98 (435)
T KOG0108|consen   97 NR   98 (435)
T ss_pred             cc
Confidence            44

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

Probab=99.23  E-value=1.4e-12  Score=130.16  Aligned_cols=239  Identities=15%  Similarity=0.210  Sum_probs=183.2

Q ss_pred             CCceEEEcCCCCCCCHH-HHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          114 ETKTIWIGDLFHWMDET-FLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       114 ~~~~l~v~nLp~~~t~~-~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      ..+...+.++.+..... ..+..|..++.|+.|.+......-..--+.++.+....+++.|... .+..+.+....+-+.
T Consensus       570 ~~~e~~s~~v~p~~~~ke~~~~~~k~~~~vekv~~p~~g~k~h~q~~~~~~~s~~~~~esat~p-a~~~~a~~~~av~~a  648 (881)
T KOG0128|consen  570 ERREKESTNVYPEQQKKEIQRRQFKGEGNVEKVNGPKRGFKAHEQPQQQKVQSKHGSAESATVP-AGGALANRSAAVGLA  648 (881)
T ss_pred             hhhhhcccCCCcchhhHHhhHHHhhcccccccccCccccccccccchhhhhhccccchhhcccc-cccccCCccccCCCC
Confidence            44567788888777666 6788999999999998877332122222889999999999999954 555554444343333


Q ss_pred             ccccCCCCCccc---cCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH
Q 013141          193 WATFSGSDRRTE---ACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT  269 (449)
Q Consensus       193 ~~~~~~~~~~~~---~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~  269 (449)
                      .+..+....+..   .....++|++||+..+.+++|...|+ .++.+..+.+......++.+|.|+|+|.+.+++.+|+.
T Consensus       649 d~~~~~~~~kvs~n~~R~~~~~fvsnl~~~~~~~dl~~~~~-~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~  727 (881)
T KOG0128|consen  649 DAEEKEENFKVSPNEIRDLIKIFVSNLSPKMSEEDLSERFS-PSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVA  727 (881)
T ss_pred             CchhhhhccCcCchHHHHHHHHHHhhcchhhcCchhhhhcC-ccchhhhHHHHHHhhccccccceeeEeecCCchhhhhh
Confidence            333322222211   12346799999999999999999996 99999888877566778999999999999999999996


Q ss_pred             HhCCceecCcceEEeecCCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhcc
Q 013141          270 EMNGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFS  349 (449)
Q Consensus       270 ~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~  349 (449)
                      -..++.++                                                 ...|+|.|.|+..|.++|+.+|+
T Consensus       728 f~d~~~~g-------------------------------------------------K~~v~i~g~pf~gt~e~~k~l~~  758 (881)
T KOG0128|consen  728 FRDSCFFG-------------------------------------------------KISVAISGPPFQGTKEELKSLAS  758 (881)
T ss_pred             hhhhhhhh-------------------------------------------------hhhhheeCCCCCCchHHHHhhcc
Confidence            44433332                                                 24589999999999999999999


Q ss_pred             ccCceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCCC
Q 013141          350 QFGEILSVKIPV-----GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGN  403 (449)
Q Consensus       350 ~~G~v~~v~i~~-----~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~~  403 (449)
                      .+|.+.++.++.     .+|.++|.|.+..++.+++...+...+.-+.+.|..+.+...
T Consensus       759 ~~gn~~~~~~vt~r~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp~~~  817 (881)
T KOG0128|consen  759 KTGNVTSLRLVTVRAGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNPERD  817 (881)
T ss_pred             ccCCccccchhhhhccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCCccc
Confidence            999999988764     368999999999999999999999888888888888776433

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

Probab=99.22  E-value=3.1e-10  Score=107.91  Aligned_cols=167  Identities=23%  Similarity=0.315  Sum_probs=113.5

Q ss_pred             cccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCC--Ccce---EEEEEeCCHHHHHHHHHHhCCceec
Q 013141          203 TEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTG--RTKG---YGFVRFGDENERSRAMTEMNGVYCS  277 (449)
Q Consensus       203 ~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~--~~~g---~afV~f~~~~~A~~A~~~l~g~~~~  277 (449)
                      ....-+++|||++||++++|++|...|. .||.+.--.-.+....+  -++|   |+|+.|+++..+..-+.++.- .-.
T Consensus       254 ~~~~~S~KVFvGGlp~dise~~i~~~F~-~FGs~~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~-~~~  331 (520)
T KOG0129|consen  254 RSPRYSRKVFVGGLPWDITEAQINASFG-QFGSVKVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSE-GEG  331 (520)
T ss_pred             CccccccceeecCCCccccHHHHHhhcc-cccceEeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhh-ccc
Confidence            4445678999999999999999999996 99986543332221111  2466   999999999998887766543 111


Q ss_pred             CcceEEeecCCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhcc-ccCceEE
Q 013141          278 SRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFS-QFGEILS  356 (449)
Q Consensus       278 g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~-~~G~v~~  356 (449)
                      .-.+.|+..+.+...-.-..+...      +     ...........++.+||||++||..++.++|-.+|+ -||.|.+
T Consensus       332 ~~yf~vss~~~k~k~VQIrPW~la------D-----s~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~y  400 (520)
T KOG0129|consen  332 NYYFKVSSPTIKDKEVQIRPWVLA------D-----SDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLY  400 (520)
T ss_pred             ceEEEEecCcccccceeEEeeEec------c-----chhhhccCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEE
Confidence            222233333332221000000000      0     000011234566789999999999999999999998 7999999


Q ss_pred             EEEeCC------CcEEEEEecCHHHHHHHHHH
Q 013141          357 VKIPVG------KGCGFVQFANRKDAEVALQK  382 (449)
Q Consensus       357 v~i~~~------~g~afV~F~~~~~A~~A~~~  382 (449)
                      +-|..+      +|.+-|+|.+..+-.+||.+
T Consensus       401 aGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  401 VGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             EEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            988765      79999999999999999975

>smart00360 RRM RNA recognition motif

Probab=99.22  E-value=7.2e-11  Score=85.42  Aligned_cols=71  Identities=37%  Similarity=0.780  Sum_probs=66.2

Q ss_pred             EcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEe
Q 013141          213 VGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRID  284 (449)
Q Consensus       213 v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  284 (449)
                      |+|||..+++++|+++|. .||.|..+.+..++.++.++++|||+|.+.++|.+|++.+++..+.++.|+|+
T Consensus         1 i~~l~~~~~~~~l~~~f~-~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFS-KFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHH-hhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            578999999999999995 99999999999988788999999999999999999999999999999998874

>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=99.21  E-value=7.8e-11  Score=86.07  Aligned_cols=69  Identities=48%  Similarity=0.836  Sum_probs=64.9

Q ss_pred             EEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC-----CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 013141          329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-----KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSW  397 (449)
Q Consensus       329 ~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~-----~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  397 (449)
                      +|+|+|||..+++++|+++|+.||.|..+.+..+     +++|||+|.+.++|..|++.+++..+.|+.|.|.|
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            4899999999999999999999999999999874     58999999999999999999999999999999875

This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).

>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability

Probab=99.15  E-value=4.3e-10  Score=82.06  Aligned_cols=74  Identities=39%  Similarity=0.809  Sum_probs=67.9

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEee
Q 013141          210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV  285 (449)
Q Consensus       210 ~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  285 (449)
                      +|+|++||..+++++|+++|. .+|.|..+.+..+..+ .+++++||+|.+.++|..|++.+++..+.++.+.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~-~~g~i~~~~~~~~~~~-~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFS-KFGKVESVRIVRDKDT-KSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHH-hcCCEEEEEEeeCCCC-CcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            489999999999999999995 8999999999988654 6789999999999999999999999999999998864

This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).

>smart00361 RRM_1 RNA recognition motif

Probab=99.12  E-value=3.9e-10  Score=81.58  Aligned_cols=62  Identities=23%  Similarity=0.496  Sum_probs=54.1

Q ss_pred             HHHHHHHHhh----hCCCeeEEE-EeecCCC--CCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEe
Q 013141          222 DSILQETFSS----KYPSVKGAK-VIIDSNT--GRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRID  284 (449)
Q Consensus       222 ~~~l~~~f~~----~~g~v~~i~-~~~~~~~--~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  284 (449)
                      +++|+++| .    .||.|.++. ++.++.+  +.++|++||+|.+.++|.+|++.|||..+.|+.|++.
T Consensus         2 ~~~l~~~~-~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~~   70 (70)
T smart00361        2 DEDFEREF-SEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKAE   70 (70)
T ss_pred             chhHHHHH-HHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEeC
Confidence            45677777 5    899999996 7777666  8899999999999999999999999999999999863

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

Probab=99.08  E-value=3.1e-11  Score=101.81  Aligned_cols=146  Identities=20%  Similarity=0.366  Sum_probs=119.1

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      ..+..++|||.||...|+|+-|.++|-+.|+|..|.|..++ +++.+ ||||+|.++-++.-|++-+|+..+.+.  +++
T Consensus         5 aae~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~-d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~--e~q   80 (267)
T KOG4454|consen    5 AAEMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQ-DQEQK-FAYVFFPNENSVQLAGQLENGDDLEED--EEQ   80 (267)
T ss_pred             CcchhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCc-cCCCc-eeeeecccccchhhhhhhcccchhccc--hhh
Confidence            34678999999999999999999999999999999988876 46777 999999999999999999999888553  333


Q ss_pred             ccccccCCCCCccccCCCceEEEcC----CCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHH
Q 013141          191 LNWATFSGSDRRTEACSDLSIFVGD----LAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSR  266 (449)
Q Consensus       191 ~~~~~~~~~~~~~~~~~~~~l~v~~----lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~  266 (449)
                      +                  +++.++    |...++++.+.+.|+ .-+.++.+++..+.. ++.+.++|+++......-.
T Consensus        81 ~------------------~~r~G~shapld~r~~~ei~~~v~s-~a~p~~~~R~~~~~d-~rnrn~~~~~~qr~~~~P~  140 (267)
T KOG4454|consen   81 R------------------TLRCGNSHAPLDERVTEEILYEVFS-QAGPIEGVRIPTDND-GRNRNFGFVTYQRLCAVPF  140 (267)
T ss_pred             c------------------ccccCCCcchhhhhcchhhheeeec-ccCCCCCcccccccc-CCccCccchhhhhhhcCcH
Confidence            2                  333344    666788999999996 899999999988855 8889999999988888888


Q ss_pred             HHHHhCCceecCcc
Q 013141          267 AMTEMNGVYCSSRP  280 (449)
Q Consensus       267 A~~~l~g~~~~g~~  280 (449)
                      ++....+....-++
T Consensus       141 ~~~~y~~l~~~~~~  154 (267)
T KOG4454|consen  141 ALDLYQGLELFQKK  154 (267)
T ss_pred             HhhhhcccCcCCCC
Confidence            87766665443333

>PF13893 RRM_5: RNA recognition motif

Probab=99.07  E-value=7.5e-10  Score=76.32  Aligned_cols=56  Identities=30%  Similarity=0.629  Sum_probs=50.2

Q ss_pred             HHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeec
Q 013141          225 LQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVA  286 (449)
Q Consensus       225 l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~  286 (449)
                      |+++|+ +||+|..+.+..+.     +++|||+|.+.++|..|++.||+..+.|++|+|+|+
T Consensus         1 L~~~f~-~fG~V~~i~~~~~~-----~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFS-KFGEVKKIKIFKKK-----RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHT-TTS-EEEEEEETTS-----TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhC-CcccEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            678995 99999999998653     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 ....

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

Probab=99.05  E-value=1.8e-10  Score=99.56  Aligned_cols=171  Identities=32%  Similarity=0.437  Sum_probs=130.9

Q ss_pred             ceEEEcCCCCCCCHHH-H--HHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          116 KTIWIGDLFHWMDETF-L--HNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       116 ~~l~v~nLp~~~t~~~-l--~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      -.+++.++-..+..+- |  ...|+.+-.++..+++++.. +..++++|+.|.....-.++-..-+++.+.  ..++++.
T Consensus        97 f~p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~~p-~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~--~~~VR~a  173 (290)
T KOG0226|consen   97 FRPFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRDRP-QPIRPEAFESFKASDALLKAETEKEKKKIG--KPPVRLA  173 (290)
T ss_pred             ccccccccccccCCCCCCcchhhhccchhhhhhhhhhcCC-CccCcccccCcchhhhhhhhcccccccccc--Ccceeec
Confidence            3455666655555544 3  66777777777778888764 778899999999888777777655666553  2335554


Q ss_pred             ccccCCCCCc-cccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh
Q 013141          193 WATFSGSDRR-TEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEM  271 (449)
Q Consensus       193 ~~~~~~~~~~-~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l  271 (449)
                      .....++... .-.....+||.+.|..+++.+-|...|. +|-....-++++|+.|++++||+||-|.+..++.+|+++|
T Consensus       174 ~gtswedPsl~ew~~~DfRIfcgdlgNevnd~vl~raf~-Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem  252 (290)
T KOG0226|consen  174 AGTSWEDPSLAEWDEDDFRIFCGDLGNEVNDDVLARAFK-KFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREM  252 (290)
T ss_pred             cccccCCcccccCccccceeecccccccccHHHHHHHHH-hccchhhccccccccccccccceeeeecCHHHHHHHHHhh
Confidence            3332222221 3345567899999999999999999995 9999999999999999999999999999999999999999


Q ss_pred             CCceecCcceEEeecCCCC
Q 013141          272 NGVYCSSRPMRIDVATPKK  290 (449)
Q Consensus       272 ~g~~~~g~~i~v~~~~~~~  290 (449)
                      +|+.++.+.|++..+.-+.
T Consensus       253 ~gkyVgsrpiklRkS~wke  271 (290)
T KOG0226|consen  253 NGKYVGSRPIKLRKSEWKE  271 (290)
T ss_pred             cccccccchhHhhhhhHHh
Confidence            9999999999887665443

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

Probab=99.05  E-value=6.8e-10  Score=100.29  Aligned_cols=81  Identities=35%  Similarity=0.695  Sum_probs=73.3

Q ss_pred             CCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHh-cCCeeCCeEEEEEec
Q 013141          320 QSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKL-QGTAIGKQTVRLSWG  398 (449)
Q Consensus       320 ~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l-~g~~~~g~~l~v~~~  398 (449)
                      .+.......+|||++|...+++.+|+++|.+||+|.+|.+...+++|||+|.+.++|+.|.+.+ +...|+|.+|.|.|+
T Consensus       221 epPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg  300 (377)
T KOG0153|consen  221 EPPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPRKGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWG  300 (377)
T ss_pred             CCCcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecccccceeeehhhHHHHHHHHhhcceeeecceEEEEEeC
Confidence            3445566789999999999999999999999999999999999999999999999999988776 666789999999999


Q ss_pred             CC
Q 013141          399 RN  400 (449)
Q Consensus       399 ~~  400 (449)
                      ++
T Consensus       301 ~~  302 (377)
T KOG0153|consen  301 RP  302 (377)
T ss_pred             CC
Confidence            98

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=99.04  E-value=1.1e-09  Score=104.92  Aligned_cols=78  Identities=29%  Similarity=0.397  Sum_probs=66.8

Q ss_pred             CCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC------CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 013141          326 NNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGR  399 (449)
Q Consensus       326 ~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~------~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  399 (449)
                      ....|||.|||.+++.++|+++|+.||.|+...|...      ..|+||+|.+.+++..||++ +-..+++++|.|+-.+
T Consensus       287 ~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek~  365 (419)
T KOG0116|consen  287 DGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEKR  365 (419)
T ss_pred             cccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEecc
Confidence            3445999999999999999999999999999877642      28999999999999999986 5778899999999888


Q ss_pred             CCCCC
Q 013141          400 NPGNK  404 (449)
Q Consensus       400 ~~~~~  404 (449)
                      ...+.
T Consensus       366 ~~~~g  370 (419)
T KOG0116|consen  366 PGFRG  370 (419)
T ss_pred             ccccc
Confidence            64433

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

Probab=99.02  E-value=5.6e-10  Score=110.55  Aligned_cols=80  Identities=35%  Similarity=0.720  Sum_probs=75.2

Q ss_pred             CCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCCCCC
Q 013141          326 NNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQ  405 (449)
Q Consensus       326 ~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~~~~  405 (449)
                      -+++|||+.|+..+++.||+++|+.||.|.+|.++.+++||||.+....+|.+|+.+|++..+.++.|+|.|+...+-+.
T Consensus       420 ~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~G~ks  499 (894)
T KOG0132|consen  420 CSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPPRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGKGPKS  499 (894)
T ss_pred             eeeeeeeccccchhhHHHHHHHHHhcccceeEeeccCCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccCCcch
Confidence            46799999999999999999999999999999999999999999999999999999999999999999999998755443

>smart00361 RRM_1 RNA recognition motif

Probab=99.02  E-value=7.6e-10  Score=80.04  Aligned_cols=57  Identities=14%  Similarity=0.278  Sum_probs=50.7

Q ss_pred             HHHHHHHhh----ccCCcEEEE-EEecCCC--CCcccEEEEEEccHHHHHHHHHHhcCCCCCCC
Q 013141          129 ETFLHNCFS----HTGQVVNVK-VIRNKQT--GQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNT  185 (449)
Q Consensus       129 ~~~l~~~f~----~~G~v~~v~-~~~~~~~--g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~  185 (449)
                      +++|+++|+    .||.|.+|. ++.++.+  ++++||+||+|.+.++|.+|++.||+..+.++
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr   65 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGR   65 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            678999998    999999995 7777766  89999999999999999999999999988553

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=99.00  E-value=7.4e-10  Score=102.09  Aligned_cols=178  Identities=21%  Similarity=0.311  Sum_probs=141.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      ...+++|++++.+.+.+.++..++...|.+..+.+........++|+++|.|...+.+..||.......+..+....-+.
T Consensus        86 ~~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~  165 (285)
T KOG4210|consen   86 GSSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLN  165 (285)
T ss_pred             cccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCccc
Confidence            46789999999999999999999999999888888887778899999999999999999999653333443322222222


Q ss_pred             cccc---CCCCCccccCCCceEE-EcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH
Q 013141          193 WATF---SGSDRRTEACSDLSIF-VGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAM  268 (449)
Q Consensus       193 ~~~~---~~~~~~~~~~~~~~l~-v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~  268 (449)
                      ....   .............+++ |++|+.++++++|++.|. .+|.|..+++..+..++..+|+++|.|.+...+..++
T Consensus       166 ~~~~~~~~n~~~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~-~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~  244 (285)
T KOG4210|consen  166 TRRGLRPKNKLSRLSSGPSDTIFFVGELDFSLTRDDLKEHFV-SSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLAL  244 (285)
T ss_pred             ccccccccchhcccccCccccceeecccccccchHHHhhhcc-CcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHh
Confidence            2111   1111122333444555 999999999999999995 9999999999999999999999999999999999998


Q ss_pred             HHhCCceecCcceEEeecCCCCCC
Q 013141          269 TEMNGVYCSSRPMRIDVATPKKAS  292 (449)
Q Consensus       269 ~~l~g~~~~g~~i~v~~~~~~~~~  292 (449)
                      .. ....+.++++.+.+..+....
T Consensus       245 ~~-~~~~~~~~~~~~~~~~~~~~~  267 (285)
T KOG4210|consen  245 ND-QTRSIGGRPLRLEEDEPRPKS  267 (285)
T ss_pred             hc-ccCcccCcccccccCCCCccc
Confidence            76 788899999999999887543

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

Probab=98.97  E-value=9.3e-10  Score=109.00  Aligned_cols=107  Identities=23%  Similarity=0.395  Sum_probs=82.8

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccccc
Q 013141          115 TKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWA  194 (449)
Q Consensus       115 ~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~~  194 (449)
                      ++||||++|+..++|.||..+|+.||.|.+|.++..+      |||||.+....+|.+||.+|+...+  ..+.|++.|+
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~R------~cAfI~M~~RqdA~kalqkl~n~kv--~~k~Iki~Wa  492 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPPR------GCAFIKMVRRQDAEKALQKLSNVKV--ADKTIKIAWA  492 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeeccCC------ceeEEEEeehhHHHHHHHHHhcccc--cceeeEEeee
Confidence            4789999999999999999999999999999998764      7999999999999999999998777  6688889998


Q ss_pred             ccCCCCCccccCCCceEEEcCCCCCCCHHHHHHHH
Q 013141          195 TFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETF  229 (449)
Q Consensus       195 ~~~~~~~~~~~~~~~~l~v~~lp~~~t~~~l~~~f  229 (449)
                      --......-...-...+=|.-||++.-.++|+.++
T Consensus       493 ~g~G~kse~k~~wD~~lGVt~IP~~kLt~dl~~~~  527 (894)
T KOG0132|consen  493 VGKGPKSEYKDYWDVELGVTYIPWEKLTDDLEAWC  527 (894)
T ss_pred             ccCCcchhhhhhhhcccCeeEeehHhcCHHHHHhh
Confidence            75544432222223333444567654444555555

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

Probab=98.96  E-value=5.2e-11  Score=119.13  Aligned_cols=150  Identities=20%  Similarity=0.281  Sum_probs=129.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccccc
Q 013141          114 ETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNW  193 (449)
Q Consensus       114 ~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~  193 (449)
                      ...++||+||+..+.+++|...|..+|.+..+.+....+.++.+|+|||+|..++++.+|+...+.+.+.          
T Consensus       666 ~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~g----------  735 (881)
T KOG0128|consen  666 DLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFG----------  735 (881)
T ss_pred             HHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhh----------
Confidence            4567999999999999999999999999888887766678999999999999999999999765554442          


Q ss_pred             cccCCCCCccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCC
Q 013141          194 ATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNG  273 (449)
Q Consensus       194 ~~~~~~~~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g  273 (449)
                                    ...|+|.|.|+..|.++++.++. .+|.+.+++++..+ .|+++|.++|.|.++.++.++....+.
T Consensus       736 --------------K~~v~i~g~pf~gt~e~~k~l~~-~~gn~~~~~~vt~r-~gkpkg~a~v~y~~ea~~s~~~~s~d~  799 (881)
T KOG0128|consen  736 --------------KISVAISGPPFQGTKEELKSLAS-KTGNVTSLRLVTVR-AGKPKGKARVDYNTEADASRKVASVDV  799 (881)
T ss_pred             --------------hhhhheeCCCCCCchHHHHhhcc-ccCCccccchhhhh-ccccccceeccCCCcchhhhhcccchh
Confidence                          34789999999999999999995 99999999877664 489999999999999999999888877


Q ss_pred             ceecCcceEEeecCCC
Q 013141          274 VYCSSRPMRIDVATPK  289 (449)
Q Consensus       274 ~~~~g~~i~v~~~~~~  289 (449)
                      ..+....+.|..+.+.
T Consensus       800 ~~~rE~~~~v~vsnp~  815 (881)
T KOG0128|consen  800 AGKRENNGEVQVSNPE  815 (881)
T ss_pred             hhhhhcCccccccCCc
Confidence            7777777777776653

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

Probab=98.95  E-value=1.2e-09  Score=110.09  Aligned_cols=166  Identities=20%  Similarity=0.348  Sum_probs=137.7

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcc
Q 013141          110 FTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPF  189 (449)
Q Consensus       110 ~~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~  189 (449)
                      .+...+++||++||...+++.+|+..|..+|.|.+|.|-..+. +.-.-|+||.|.+...+-.|+..+.+..|......+
T Consensus       367 DD~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~-~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~  445 (975)
T KOG0112|consen  367 DDFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHI-KTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRI  445 (975)
T ss_pred             cchhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCC-CcccchhhhhhhccccCcccchhhcCCccccCcccc
Confidence            4556789999999999999999999999999999999877643 455569999999999999999999888886554444


Q ss_pred             cccccccCCCCCccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH
Q 013141          190 RLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT  269 (449)
Q Consensus       190 ~~~~~~~~~~~~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~  269 (449)
                      .+...         .....+.+++++|.+.+....|...| ..||.|..|.+-.    +  ..|++|.|.+...+..|+.
T Consensus       446 glG~~---------kst~ttr~~sgglg~w~p~~~l~r~f-d~fGpir~Idy~h----g--q~yayi~yes~~~aq~a~~  509 (975)
T KOG0112|consen  446 GLGQP---------KSTPTTRLQSGGLGPWSPVSRLNREF-DRFGPIRIIDYRH----G--QPYAYIQYESPPAAQAATH  509 (975)
T ss_pred             ccccc---------ccccceeeccCCCCCCChHHHHHHHh-hccCcceeeeccc----C--CcceeeecccCccchhhHH
Confidence            43322         35577899999999999999999999 5999999887643    3  3399999999999999999


Q ss_pred             HhCCceecC--cceEEeecCCCCCC
Q 013141          270 EMNGVYCSS--RPMRIDVATPKKAS  292 (449)
Q Consensus       270 ~l~g~~~~g--~~i~v~~~~~~~~~  292 (449)
                      .|.+..|++  +.++|.++.+....
T Consensus       510 ~~rgap~G~P~~r~rvdla~~~~~~  534 (975)
T KOG0112|consen  510 DMRGAPLGGPPRRLRVDLASPPGAT  534 (975)
T ss_pred             HHhcCcCCCCCcccccccccCCCCC
Confidence            999999855  66888888776544

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

Probab=98.94  E-value=1.5e-09  Score=98.00  Aligned_cols=84  Identities=25%  Similarity=0.472  Sum_probs=76.1

Q ss_pred             CCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCC------cEEEEEecCHHHHHHHHHHhcCCeeCCeEEEE
Q 013141          322 DGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK------GCGFVQFANRKDAEVALQKLQGTAIGKQTVRL  395 (449)
Q Consensus       322 ~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~------g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v  395 (449)
                      ...++.++|||--|.+-++++||.-+|+.||.|.++.|++++      .+|||+|++.+++.+|.-.|++..|++++|+|
T Consensus       234 d~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHV  313 (479)
T KOG0415|consen  234 DVKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHV  313 (479)
T ss_pred             ccCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEe
Confidence            445678999999999999999999999999999999999863      68999999999999999999999999999999


Q ss_pred             EecCCCCCCC
Q 013141          396 SWGRNPGNKQ  405 (449)
Q Consensus       396 ~~~~~~~~~~  405 (449)
                      .|+-......
T Consensus       314 DFSQSVsk~k  323 (479)
T KOG0415|consen  314 DFSQSVSKVK  323 (479)
T ss_pred             ehhhhhhhhh
Confidence            9988655433

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

Probab=98.93  E-value=1.9e-09  Score=97.48  Aligned_cols=86  Identities=26%  Similarity=0.433  Sum_probs=80.8

Q ss_pred             ccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEE
Q 013141          204 EACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRI  283 (449)
Q Consensus       204 ~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  283 (449)
                      ...+.+.|||-.|.+-++.++|.-+|+ .||.|.++.+++|..||.+-.||||+|.+.+++++|.-.|++..|+++.|+|
T Consensus       235 ~~PPeNVLFVCKLNPVTtDeDLeiIFS-rFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHV  313 (479)
T KOG0415|consen  235 VKPPENVLFVCKLNPVTTDEDLEIIFS-RFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHV  313 (479)
T ss_pred             cCCCcceEEEEecCCcccccchhhHHh-hcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEe
Confidence            346788999999999999999999997 9999999999999999999999999999999999999999999999999999


Q ss_pred             eecCCCC
Q 013141          284 DVATPKK  290 (449)
Q Consensus       284 ~~~~~~~  290 (449)
                      .++....
T Consensus       314 DFSQSVs  320 (479)
T KOG0415|consen  314 DFSQSVS  320 (479)
T ss_pred             ehhhhhh
Confidence            9986644

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

Probab=98.90  E-value=2.8e-09  Score=102.41  Aligned_cols=179  Identities=18%  Similarity=0.218  Sum_probs=118.4

Q ss_pred             ccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEE
Q 013141          204 EACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRI  283 (449)
Q Consensus       204 ~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  283 (449)
                      ...+..+|+|.|||.++++++|+++|+ .||+|+.|+.-     ...++..||+|-|..+|++|+++|++++|.++.|. 
T Consensus        71 ~~~~~~~L~v~nl~~~Vsn~~L~~~f~-~yGeir~ir~t-----~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k-  143 (549)
T KOG4660|consen   71 KDMNQGTLVVFNLPRSVSNDTLLRIFG-AYGEIREIRET-----PNKRGIVFVEFYDVRDAERALKALNRREIAGKRIK-  143 (549)
T ss_pred             ccCccceEEEEecCCcCCHHHHHHHHH-hhcchhhhhcc-----cccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc-
Confidence            356778999999999999999999995 99999997654     34578999999999999999999999999999998 


Q ss_pred             eecCCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCC
Q 013141          284 DVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK  363 (449)
Q Consensus       284 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~  363 (449)
                         .+...+...........+..-.......     ....-. ...+++ .|++..+..-++..+.-+|.+..-....-.
T Consensus       144 ---~~~~~~~~~~~~~~~~~~~~~~~p~a~s-----~pgg~~-~~~~~g-~l~P~~s~~~~~~~~~~~~~~~~~~~~~~~  213 (549)
T KOG4660|consen  144 ---RPGGARRAMGLQSGTSFLNHFGSPLANS-----PPGGWP-RGQLFG-MLSPTRSSILLEHISSVDGSSPGRETPLLN  213 (549)
T ss_pred             ---CCCcccccchhcccchhhhhccchhhcC-----CCCCCc-CCccee-eeccchhhhhhhcchhccCccccccccchh
Confidence               2222111111100000000000000000     000111 222332 288888776667777777877662222223


Q ss_pred             cEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCC
Q 013141          364 GCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRN  400 (449)
Q Consensus       364 g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  400 (449)
                      ..-|+.|.+..++..+...+ |..+.+....++++.+
T Consensus       214 hq~~~~~~~~~s~a~~~~~~-G~~~s~~~~v~t~S~~  249 (549)
T KOG4660|consen  214 HQRFVEFADNRSYAFSEPRG-GFLISNSSGVITFSGP  249 (549)
T ss_pred             hhhhhhhccccchhhcccCC-ceecCCCCceEEecCC
Confidence            47789999988887776644 7778888888888876

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.89  E-value=3.4e-09  Score=97.74  Aligned_cols=176  Identities=24%  Similarity=0.320  Sum_probs=135.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeec
Q 013141          207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVA  286 (449)
Q Consensus       207 ~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~  286 (449)
                      ...++|++++...+.+.++..++ ...|.+....+........+++++.+.|...+.+..++.......+.++.+.....
T Consensus        87 ~~~~~f~g~~s~~~e~~~~~~~~-~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~  165 (285)
T KOG4210|consen   87 SSSTFFVGELSENIEESEDDNFS-SEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLN  165 (285)
T ss_pred             ccccccccccccchhhccccccc-hhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCccc
Confidence            46789999999999888888888 48887777777766677888999999999999999999644444666666666555


Q ss_pred             CCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC----
Q 013141          287 TPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG----  362 (449)
Q Consensus       287 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~----  362 (449)
                      ..........                     .............+|.+++..+++++|+.+|..+|.|..++++..    
T Consensus       166 ~~~~~~~~n~---------------------~~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~  224 (285)
T KOG4210|consen  166 TRRGLRPKNK---------------------LSRLSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESG  224 (285)
T ss_pred             ccccccccch---------------------hcccccCccccceeecccccccchHHHhhhccCcCcceeeccCCCCCcc
Confidence            5444210000                     001112233344559999999999999999999999999999863    


Q ss_pred             --CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCCCCC
Q 013141          363 --KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQ  405 (449)
Q Consensus       363 --~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~~~~  405 (449)
                        ++++||.|.+...+..++.. ....+.++.+++.+.+......
T Consensus       225 ~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~  268 (285)
T KOG4210|consen  225 DSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEEDEPRPKSD  268 (285)
T ss_pred             chhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccCCCCcccc
Confidence              68999999999999999987 8889999999999999876553

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

Probab=98.89  E-value=3.2e-09  Score=89.39  Aligned_cols=77  Identities=29%  Similarity=0.418  Sum_probs=68.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhcc-CCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHT-GQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPF  189 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~-G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~  189 (449)
                      .....++|..+|.-+.+.+|..+|.++ |.|..+++.+++.||.++|||||+|++++.|+-|-+.||+.+|.+.-..+
T Consensus        47 ~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c  124 (214)
T KOG4208|consen   47 EIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLEC  124 (214)
T ss_pred             CCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeee
Confidence            456679999999999999999999999 78888888899999999999999999999999999999999985543333

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

Probab=98.85  E-value=2.9e-09  Score=107.32  Aligned_cols=162  Identities=20%  Similarity=0.379  Sum_probs=138.7

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEe
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRID  284 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  284 (449)
                      ...+.+||++||+..+++.+|+..|. .+|.|.+|.|-..+. +.-.-|+||.|.+.+.+-.|+..+.+..|....+++.
T Consensus       369 ~~atrTLf~Gnl~~kl~eseiR~af~-e~gkve~VDiKtP~~-~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~g  446 (975)
T KOG0112|consen  369 FRATRTLFLGNLDSKLTESEIRPAFD-ESGKVEEVDIKTPHI-KTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIG  446 (975)
T ss_pred             hhhhhhhhhcCcccchhhhhhhhhhh-hhccccccccccCCC-CcccchhhhhhhccccCcccchhhcCCccccCccccc
Confidence            35577999999999999999999995 999999998876532 3444589999999999999998999888866666665


Q ss_pred             ecCCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCc
Q 013141          285 VATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKG  364 (449)
Q Consensus       285 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g  364 (449)
                      +...+                                  ....+.+++++|...+....|...|..||.|..|.+.....
T Consensus       447 lG~~k----------------------------------st~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hgq~  492 (975)
T KOG0112|consen  447 LGQPK----------------------------------STPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHGQP  492 (975)
T ss_pred             ccccc----------------------------------cccceeeccCCCCCCChHHHHHHHhhccCcceeeecccCCc
Confidence            55432                                  22367899999999999999999999999999999988889


Q ss_pred             EEEEEecCHHHHHHHHHHhcCCeeCC--eEEEEEecCCCC
Q 013141          365 CGFVQFANRKDAEVALQKLQGTAIGK--QTVRLSWGRNPG  402 (449)
Q Consensus       365 ~afV~F~~~~~A~~A~~~l~g~~~~g--~~l~v~~~~~~~  402 (449)
                      +++|.|++...|..|+..|.|..|++  +.|+|.|+....
T Consensus       493 yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdla~~~~  532 (975)
T KOG0112|consen  493 YAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDLASPPG  532 (975)
T ss_pred             ceeeecccCccchhhHHHHhcCcCCCCCcccccccccCCC
Confidence            99999999999999999999999984  789999998653

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

Probab=98.84  E-value=1.4e-08  Score=85.70  Aligned_cols=87  Identities=21%  Similarity=0.298  Sum_probs=78.9

Q ss_pred             cccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceE
Q 013141          203 TEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMR  282 (449)
Q Consensus       203 ~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  282 (449)
                      ........+++..+|.-+.+.++..+|++.+|.|..+++.+++.||.++|||||+|++++.|+-|.+.||+..+.++-|.
T Consensus        44 p~~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~  123 (214)
T KOG4208|consen   44 PEQEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLE  123 (214)
T ss_pred             CccCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheee
Confidence            34455678999999999999999999974458899999999999999999999999999999999999999999999999


Q ss_pred             EeecCCC
Q 013141          283 IDVATPK  289 (449)
Q Consensus       283 v~~~~~~  289 (449)
                      +.+..+.
T Consensus       124 c~vmppe  130 (214)
T KOG4208|consen  124 CHVMPPE  130 (214)
T ss_pred             eEEeCch
Confidence            9998876

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

Probab=98.75  E-value=2.4e-08  Score=95.65  Aligned_cols=77  Identities=21%  Similarity=0.451  Sum_probs=71.2

Q ss_pred             CCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC------CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 013141          325 SNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWG  398 (449)
Q Consensus       325 ~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~------~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~  398 (449)
                      ...+.|||.+|...+...||+.+|++||+|+-.+|+.+      +.++||++.+.++|.++|+.||.++|+|+.|.|+-+
T Consensus       403 ~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEka  482 (940)
T KOG4661|consen  403 TLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKA  482 (940)
T ss_pred             ccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeec
Confidence            34678999999999999999999999999999998864      689999999999999999999999999999999998


Q ss_pred             CCC
Q 013141          399 RNP  401 (449)
Q Consensus       399 ~~~  401 (449)
                      |+.
T Consensus       483 KNE  485 (940)
T KOG4661|consen  483 KNE  485 (940)
T ss_pred             ccC
Confidence            863

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

Probab=98.73  E-value=2.2e-08  Score=90.71  Aligned_cols=83  Identities=23%  Similarity=0.377  Sum_probs=70.0

Q ss_pred             CCCCCCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCC
Q 013141          107 NNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTD  186 (449)
Q Consensus       107 ~~~~~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~  186 (449)
                      .....+...++|||++|-..++|.+|+++|.+||+|.++.++..+      ++|||+|.+.++|+.|.+++-. .+...+
T Consensus       220 lepPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~~------~CAFv~ftTR~aAE~Aae~~~n-~lvI~G  292 (377)
T KOG0153|consen  220 LEPPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPRK------GCAFVTFTTREAAEKAAEKSFN-KLVING  292 (377)
T ss_pred             cCCCcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeeccc------ccceeeehhhHHHHHHHHhhcc-eeeecc
Confidence            334456678899999999999999999999999999999998865      5999999999999999987655 344466


Q ss_pred             Cccccccccc
Q 013141          187 QPFRLNWATF  196 (449)
Q Consensus       187 ~~~~~~~~~~  196 (449)
                      ..+++.|...
T Consensus       293 ~Rl~i~Wg~~  302 (377)
T KOG0153|consen  293 FRLKIKWGRP  302 (377)
T ss_pred             eEEEEEeCCC
Confidence            7777889876

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

Probab=98.69  E-value=1.2e-08  Score=86.45  Aligned_cols=143  Identities=26%  Similarity=0.329  Sum_probs=113.6

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEe
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRID  284 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  284 (449)
                      ....++|||.|+...++++-|.|+|- ..|+|..|.|..+.. ++.+ ||||.|.++-...-|++.+||..+.++.+.+.
T Consensus         6 ae~drtl~v~n~~~~v~eelL~Elfi-qaGPV~kv~ip~~~d-~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~   82 (267)
T KOG4454|consen    6 AEMDRTLLVQNMYSGVSEELLSELFI-QAGPVYKVGIPSGQD-QEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRT   82 (267)
T ss_pred             cchhhHHHHHhhhhhhhHHHHHHHhh-ccCceEEEeCCCCcc-CCCc-eeeeecccccchhhhhhhcccchhccchhhcc
Confidence            34567999999999999999999995 999999999988765 5556 99999999999999999999999988888776


Q ss_pred             ecCCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeC---
Q 013141          285 VATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV---  361 (449)
Q Consensus       285 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~---  361 (449)
                      +..-....                                         -|...++++.+...|+.-|.+..+++.+   
T Consensus        83 ~r~G~sha-----------------------------------------pld~r~~~ei~~~v~s~a~p~~~~R~~~~~d  121 (267)
T KOG4454|consen   83 LRCGNSHA-----------------------------------------PLDERVTEEILYEVFSQAGPIEGVRIPTDND  121 (267)
T ss_pred             cccCCCcc-----------------------------------------hhhhhcchhhheeeecccCCCCCcccccccc
Confidence            54332111                                         1555678888888999989998888875   


Q ss_pred             --CCcEEEEEecCHHHHHHHHHHhcCCeeCCe
Q 013141          362 --GKGCGFVQFANRKDAEVALQKLQGTAIGKQ  391 (449)
Q Consensus       362 --~~g~afV~F~~~~~A~~A~~~l~g~~~~g~  391 (449)
                        ++.+.||++--..+.-.++....+...--+
T Consensus       122 ~rnrn~~~~~~qr~~~~P~~~~~y~~l~~~~~  153 (267)
T KOG4454|consen  122 GRNRNFGFVTYQRLCAVPFALDLYQGLELFQK  153 (267)
T ss_pred             CCccCccchhhhhhhcCcHHhhhhcccCcCCC
Confidence              357888888777777777776666654433

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.66  E-value=1.7e-07  Score=71.04  Aligned_cols=80  Identities=20%  Similarity=0.307  Sum_probs=66.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhcc--CCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCC--CCcccc
Q 013141          116 KTIWIGDLFHWMDETFLHNCFSHT--GQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNT--DQPFRL  191 (449)
Q Consensus       116 ~~l~v~nLp~~~t~~~l~~~f~~~--G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~--~~~~~~  191 (449)
                      +||+|+|||...|.++|.+++...  |...-+.+..|..++.+.|||||.|.+.++|.+..+.+++..+...  .+.+.+
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            689999999999999999998763  5666788899988999999999999999999999999999888532  334444


Q ss_pred             cccc
Q 013141          192 NWAT  195 (449)
Q Consensus       192 ~~~~  195 (449)
                      .||.
T Consensus        82 ~yAr   85 (97)
T PF04059_consen   82 SYAR   85 (97)
T ss_pred             ehhH
Confidence            4443

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=98.63  E-value=5.5e-09  Score=96.58  Aligned_cols=153  Identities=20%  Similarity=0.357  Sum_probs=126.0

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCce-ecCcceEEeecC
Q 013141          209 LSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVY-CSSRPMRIDVAT  287 (449)
Q Consensus       209 ~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~-~~g~~i~v~~~~  287 (449)
                      +++|++||.+.++.++|..+|.+.--....-.+++       .||+||...+...|.+|++.++++. +.|+.+.+..+.
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 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLVK-------SGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSV   74 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceeee-------cceeeccCCchhhhhhhHHhhchhhhhcCceeeccchh
Confidence            46899999999999999999964322222222332       4799999999999999999999855 789999999888


Q ss_pred             CCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeC-CC--c
Q 013141          288 PKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV-GK--G  364 (449)
Q Consensus       288 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~-~~--g  364 (449)
                      ++..+                                  ++.+-|.|+|....++.|..++..||.|+.+.... +.  -
T Consensus        75 ~kkqr----------------------------------srk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~eta  120 (584)
T KOG2193|consen   75 PKKQR----------------------------------SRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSETA  120 (584)
T ss_pred             hHHHH----------------------------------hhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchHHH
Confidence            87654                                  45588999999999999999999999999987653 22  3


Q ss_pred             EEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCC
Q 013141          365 CGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPG  402 (449)
Q Consensus       365 ~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~  402 (449)
                      ..-|+|.+.+.++.|+..|+|..|....++|.|--+..
T Consensus       121 vvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~YiPdeq  158 (584)
T KOG2193|consen  121 VVNVTYSAQQQHRQAIHKLNGPQLENQHLKVGYIPDEQ  158 (584)
T ss_pred             HHHHHHHHHHHHHHHHHhhcchHhhhhhhhcccCchhh
Confidence            44578999999999999999999999999999976543

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

Probab=98.61  E-value=1.3e-07  Score=90.70  Aligned_cols=83  Identities=23%  Similarity=0.419  Sum_probs=77.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEee
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV  285 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  285 (449)
                      ...+.|||.+|...+...+|+.+|+ +||.|.-.+++.+..+.-.++|+||++.+.++|.+||+.|+..++.|+.|.|+.
T Consensus       403 ~~gRNlWVSGLSstTRAtDLKnlFS-KyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEk  481 (940)
T KOG4661|consen  403 TLGRNLWVSGLSSTTRATDLKNLFS-KYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEK  481 (940)
T ss_pred             ccccceeeeccccchhhhHHHHHHH-HhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeee
Confidence            4467899999999999999999997 999999999999988888899999999999999999999999999999999999


Q ss_pred             cCCC
Q 013141          286 ATPK  289 (449)
Q Consensus       286 ~~~~  289 (449)
                      ++..
T Consensus       482 aKNE  485 (940)
T KOG4661|consen  482 AKNE  485 (940)
T ss_pred             cccC
Confidence            8764

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

Probab=98.57  E-value=4.8e-08  Score=84.78  Aligned_cols=146  Identities=25%  Similarity=0.424  Sum_probs=108.3

Q ss_pred             HHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecCCCCCCchhhcchhhhhhh
Q 013141          226 QETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKASGYQQQYSSQALVL  305 (449)
Q Consensus       226 ~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~  305 (449)
                      ...|+ .+-.+....++++.. +.-++++|+.|.....-.++-..-+++.+..+.|++...+.-...             
T Consensus       117 ~~~f~-~~p~L~ktk~v~~~p-~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a~gtswedP-------------  181 (290)
T KOG0226|consen  117 PVVFS-EYPSLVKTKLVRDRP-QPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLAAGTSWEDP-------------  181 (290)
T ss_pred             hhhhc-cchhhhhhhhhhcCC-CccCcccccCcchhhhhhhhccccccccccCcceeeccccccCCc-------------
Confidence            44553 566666666666643 566789999998877776666556667776666555443332221             


Q ss_pred             cCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeC------CCcEEEEEecCHHHHHHH
Q 013141          306 AGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVA  379 (449)
Q Consensus       306 ~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~------~~g~afV~F~~~~~A~~A  379 (449)
                                   ...+-.....+||.+.|..+++++.|-..|.+|-.....++++      ++|++||.|.+..++..|
T Consensus       182 -------------sl~ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rA  248 (290)
T KOG0226|consen  182 -------------SLAEWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRA  248 (290)
T ss_pred             -------------ccccCccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHH
Confidence                         1223345678899999999999999999999997766666665      469999999999999999


Q ss_pred             HHHhcCCeeCCeEEEEEecC
Q 013141          380 LQKLQGTAIGKQTVRLSWGR  399 (449)
Q Consensus       380 ~~~l~g~~~~g~~l~v~~~~  399 (449)
                      +..|+|+.++.+.|+++-+.
T Consensus       249 mrem~gkyVgsrpiklRkS~  268 (290)
T KOG0226|consen  249 MREMNGKYVGSRPIKLRKSE  268 (290)
T ss_pred             HHhhcccccccchhHhhhhh
Confidence            99999999999998876443

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation

Probab=98.54  E-value=1.9e-07  Score=72.70  Aligned_cols=69  Identities=35%  Similarity=0.541  Sum_probs=47.4

Q ss_pred             cEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCC-----eeCCeEEEEE
Q 013141          328 ATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGT-----AIGKQTVRLS  396 (449)
Q Consensus       328 ~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~-----~~~g~~l~v~  396 (449)
                      ++|+|.+++..++.++|++.|+.||.|.+|.+.++...|||+|.+.++|++|++.+...     .+.+..+.++
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~   75 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLE   75 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEE
Confidence            67999999999999999999999999999999999999999999999999999988544     5566666655

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

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

Probab=98.50  E-value=4.2e-07  Score=80.81  Aligned_cols=83  Identities=29%  Similarity=0.478  Sum_probs=74.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeec
Q 013141          207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVA  286 (449)
Q Consensus       207 ~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~  286 (449)
                      ...+|+|.||+..++.+||+++|. .|+.+..+.+..+ .+|.+.|.|-|.|...++|.+|++.+++..++|+.+++...
T Consensus        82 ~~~~v~v~NL~~~V~~~Dl~eLF~-~~~~~~r~~vhy~-~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i  159 (243)
T KOG0533|consen   82 RSTKVNVSNLPYGVIDADLKELFA-EFGELKRVAVHYD-RAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEII  159 (243)
T ss_pred             CcceeeeecCCcCcchHHHHHHHH-HhccceEEeeccC-CCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEe
Confidence            346899999999999999999995 9999999988888 45999999999999999999999999999999999999887


Q ss_pred             CCCCC
Q 013141          287 TPKKA  291 (449)
Q Consensus       287 ~~~~~  291 (449)
                      .....
T Consensus       160 ~~~~~  164 (243)
T KOG0533|consen  160 SSPSQ  164 (243)
T ss_pred             cCccc
Confidence            66543

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

Probab=98.47  E-value=4.5e-07  Score=80.64  Aligned_cols=80  Identities=20%  Similarity=0.337  Sum_probs=69.5

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      ....+.+|+|.|||+.|+++||+++|..||.+..+.+..++ .|++.|.|-|.|...++|++|++.+++..+++..  ++
T Consensus        79 ~~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~--mk  155 (243)
T KOG0533|consen   79 NETRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNGVALDGRP--MK  155 (243)
T ss_pred             cCCCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcCcccCCce--ee
Confidence            34456789999999999999999999999998888888886 6999999999999999999999999997776544  55


Q ss_pred             ccc
Q 013141          191 LNW  193 (449)
Q Consensus       191 ~~~  193 (449)
                      +..
T Consensus       156 ~~~  158 (243)
T KOG0533|consen  156 IEI  158 (243)
T ss_pred             eEE
Confidence            443

>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=98.46  E-value=6.1e-07  Score=64.49  Aligned_cols=69  Identities=20%  Similarity=0.424  Sum_probs=48.3

Q ss_pred             cEEEEcCCCCCCCHhHHH----hhccccC-ceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCC
Q 013141          328 ATIFVGALDSDVSDEDLR----EPFSQFG-EILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRN  400 (449)
Q Consensus       328 ~~l~V~nlp~~~t~~~L~----~~f~~~G-~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  400 (449)
                      ..|+|.|||...+...|+    .++..+| .|.+|    ..+.|+|.|.+.+.|.+|.++|+|..+.|+.|.|+|...
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v----~~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~~~   76 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV----SGGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFSPK   76 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS--
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE----eCCEEEEEeCCHHHHHHHHHhhcccccccceEEEEEcCC
Confidence            468999999998876655    5555775 67766    268999999999999999999999999999999999854

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.41  E-value=1.3e-06  Score=78.06  Aligned_cols=79  Identities=25%  Similarity=0.433  Sum_probs=71.8

Q ss_pred             CCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC------CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEE
Q 013141          322 DGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRL  395 (449)
Q Consensus       322 ~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~------~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v  395 (449)
                      ....+...+||+|+.+.+|.++|..+|+.||.|..|.++.+      ++++||+|.+.+.+..|+. |++..|.++.|.|
T Consensus        96 ~~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~v  174 (231)
T KOG4209|consen   96 QKEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEV  174 (231)
T ss_pred             hhccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCccccccccee
Confidence            34556789999999999999999999999999998888763      6899999999999999998 9999999999999


Q ss_pred             EecCCC
Q 013141          396 SWGRNP  401 (449)
Q Consensus       396 ~~~~~~  401 (449)
                      ++.+-+
T Consensus       175 t~~r~~  180 (231)
T KOG4209|consen  175 TLKRTN  180 (231)
T ss_pred             eeeeee
Confidence            998876

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.41  E-value=2.8e-06  Score=64.47  Aligned_cols=81  Identities=17%  Similarity=0.231  Sum_probs=68.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhh-CCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceec----CcceEE
Q 013141          209 LSIFVGDLAPDVTDSILQETFSSK-YPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCS----SRPMRI  283 (449)
Q Consensus       209 ~~l~v~~lp~~~t~~~l~~~f~~~-~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~----g~~i~v  283 (449)
                      +||+|+|||...|.++|.+++.+. .|...-+.++.|..++...|||||.|.+.+.|.+..+.++|..+.    .+...|
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            689999999999999999888543 355667888899888999999999999999999999999998873    556677


Q ss_pred             eecCCC
Q 013141          284 DVATPK  289 (449)
Q Consensus       284 ~~~~~~  289 (449)
                      .+|+..
T Consensus        82 ~yAriQ   87 (97)
T PF04059_consen   82 SYARIQ   87 (97)
T ss_pred             ehhHhh
Confidence            776543

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=98.38  E-value=8.9e-07  Score=87.46  Aligned_cols=81  Identities=40%  Similarity=0.751  Sum_probs=74.2

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeC---------CCcEEEEEecCHHHHHHHHHHhcCCeeCCe
Q 013141          321 SDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV---------GKGCGFVQFANRKDAEVALQKLQGTAIGKQ  391 (449)
Q Consensus       321 ~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~---------~~g~afV~F~~~~~A~~A~~~l~g~~~~g~  391 (449)
                      .+..+..+.|||+||+++++++.|...|..||.|.+|+|+-         .+.|+||-|-+..+|.+|++.|+|..+.+.
T Consensus       168 DdgDP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~  247 (877)
T KOG0151|consen  168 DDGDPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEY  247 (877)
T ss_pred             CCCCCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeee
Confidence            34567788999999999999999999999999999999973         368999999999999999999999999999


Q ss_pred             EEEEEecCCC
Q 013141          392 TVRLSWGRNP  401 (449)
Q Consensus       392 ~l~v~~~~~~  401 (449)
                      .+++.|++..
T Consensus       248 e~K~gWgk~V  257 (877)
T KOG0151|consen  248 EMKLGWGKAV  257 (877)
T ss_pred             eeeecccccc
Confidence            9999999853

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=98.33  E-value=9.4e-07  Score=85.10  Aligned_cols=78  Identities=18%  Similarity=0.291  Sum_probs=61.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccc
Q 013141          112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRL  191 (449)
Q Consensus       112 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~  191 (449)
                      .....+|||+|||.++++.+|+++|..||+|+...|......++...|+||+|.+.+++..||.+ +  .+....+.+.|
T Consensus       285 ~~~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-s--p~~ig~~kl~V  361 (419)
T KOG0116|consen  285 RADGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-S--PLEIGGRKLNV  361 (419)
T ss_pred             eecccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-C--ccccCCeeEEE
Confidence            34455699999999999999999999999999988877654455568999999999999999965 3  33333444444


Q ss_pred             c
Q 013141          192 N  192 (449)
Q Consensus       192 ~  192 (449)
                      +
T Consensus       362 e  362 (419)
T KOG0116|consen  362 E  362 (419)
T ss_pred             E
Confidence            3

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.32  E-value=7.6e-07  Score=79.47  Aligned_cols=82  Identities=22%  Similarity=0.455  Sum_probs=72.2

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      ..-+.+.|||+|+-+.+|.++|...|+.||.|..+.|.+|+..+.++||+||+|.+.+.++.++. |++..+.+  ..+.
T Consensus        97 ~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~--~~i~  173 (231)
T KOG4209|consen   97 KEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPG--PAIE  173 (231)
T ss_pred             hccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCccccc--ccce
Confidence            34577899999999999999999999999999999999999999999999999999999999997 99999854  4555


Q ss_pred             ccccc
Q 013141          191 LNWAT  195 (449)
Q Consensus       191 ~~~~~  195 (449)
                      +.+..
T Consensus       174 vt~~r  178 (231)
T KOG4209|consen  174 VTLKR  178 (231)
T ss_pred             eeeee
Confidence            54443

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.30  E-value=1.6e-06  Score=85.73  Aligned_cols=85  Identities=27%  Similarity=0.551  Sum_probs=72.7

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCC---CCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCC
Q 013141          110 FTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQ---TGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTD  186 (449)
Q Consensus       110 ~~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~---~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~  186 (449)
                      ..+..++.|||+||++.++++.|..-|..||+|.+|+|+..+.   ..+.+-|+||-|.+..+|++|++.|++.++  ..
T Consensus       169 dgDP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv--~~  246 (877)
T KOG0151|consen  169 DGDPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIV--ME  246 (877)
T ss_pred             CCCCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceee--ee
Confidence            3456788899999999999999999999999999999987542   334567999999999999999999999988  55


Q ss_pred             Cccccccccc
Q 013141          187 QPFRLNWATF  196 (449)
Q Consensus       187 ~~~~~~~~~~  196 (449)
                      ..+++.|.+.
T Consensus       247 ~e~K~gWgk~  256 (877)
T KOG0151|consen  247 YEMKLGWGKA  256 (877)
T ss_pred             eeeeeccccc
Confidence            7788888853

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=98.12  E-value=2.6e-06  Score=78.52  Aligned_cols=184  Identities=16%  Similarity=0.137  Sum_probs=122.6

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCC---CCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEee
Q 013141          209 LSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSN---TGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV  285 (449)
Q Consensus       209 ~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  285 (449)
                      ..|.|.||.+++|.+.+..+|. ..|.|.++.|+.+..   -......|||.|.+...+..|- .|.+..|-++.|.|-.
T Consensus         8 ~vIqvanispsat~dqm~tlFg-~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQ-hLtntvfvdraliv~p   85 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFG-NLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQ-HLTNTVFVDRALIVRP   85 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHh-hccccccccccCCCCCccCcceeeeEEEeccCCcceeHHh-hhccceeeeeeEEEEe
Confidence            4789999999999999999996 999999999886432   2234568999999999988885 7888888888877765


Q ss_pred             cCCCCCCchhhc---chhhh---hhhcCCC-----CC------CCCCcCCC-------CCCCCCCCcEEEEcCCCCCCCH
Q 013141          286 ATPKKASGYQQQ---YSSQA---LVLAGGP-----GS------NGARVQGS-------QSDGESNNATIFVGALDSDVSD  341 (449)
Q Consensus       286 ~~~~~~~~~~~~---~~~~~---~~~~~~~-----~~------~~~~~~~~-------~~~~~~~~~~l~V~nlp~~~t~  341 (449)
                      ............   .....   .....+.     ..      .......+       .....+...+|+|.+|+..+..
T Consensus        86 ~~~~~~p~r~af~~l~~~navprll~pdg~Lp~~~~lt~~nh~p~ailktP~Lp~~~~A~kleeirRt~~v~sl~~~~~l  165 (479)
T KOG4676|consen   86 YGDEVIPDRFAFVELADQNAVPRLLPPDGVLPGDRPLTKINHSPNAILKTPELPPQAAAKKLEEIRRTREVQSLISAAIL  165 (479)
T ss_pred             cCCCCCccHHHHHhcCcccccccccCCCCccCCCCccccccCCccceecCCCCChHhhhhhhHHHHhhhhhhcchhhhcc
Confidence            544322111000   00000   0000000     00      00000000       0011122367999999999999


Q ss_pred             hHHHhhccccCceEEEEEeC--CCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEE
Q 013141          342 EDLREPFSQFGEILSVKIPV--GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRL  395 (449)
Q Consensus       342 ~~L~~~f~~~G~v~~v~i~~--~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v  395 (449)
                      .++.+.|..+|.|.+.++..  ....|.|+|........|+. ++|..+.-...++
T Consensus       166 ~e~~e~f~r~Gev~ya~~ask~~s~~c~~sf~~qts~~halr-~~gre~k~qhsr~  220 (479)
T KOG4676|consen  166 PESGESFERKGEVSYAHTASKSRSSSCSHSFRKQTSSKHALR-SHGRERKRQHSRR  220 (479)
T ss_pred             hhhhhhhhhcchhhhhhhhccCCCcchhhhHhhhhhHHHHHH-hcchhhhhhhhhh
Confidence            99999999999999988764  35678899998888888875 6788776333333

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=98.12  E-value=8.7e-06  Score=74.83  Aligned_cols=82  Identities=27%  Similarity=0.354  Sum_probs=70.2

Q ss_pred             CCCCcEEEEcCCCCCCCHhHHHhhccccCceEE--------EEEeC------CCcEEEEEecCHHHHHHHHHHhcCCeeC
Q 013141          324 ESNNATIFVGALDSDVSDEDLREPFSQFGEILS--------VKIPV------GKGCGFVQFANRKDAEVALQKLQGTAIG  389 (449)
Q Consensus       324 ~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~--------v~i~~------~~g~afV~F~~~~~A~~A~~~l~g~~~~  389 (449)
                      .....+|||.+|+..+++++|.++|.++|.|..        |.|.+      .|+.|.|+|+|...|+.|+.-++++.|.
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            456678999999999999999999999988754        23322      3799999999999999999999999999


Q ss_pred             CeEEEEEecCCCCCCC
Q 013141          390 KQTVRLSWGRNPGNKQ  405 (449)
Q Consensus       390 g~~l~v~~~~~~~~~~  405 (449)
                      +..|+|.++....+..
T Consensus       143 gn~ikvs~a~~r~~ve  158 (351)
T KOG1995|consen  143 GNTIKVSLAERRTGVE  158 (351)
T ss_pred             CCCchhhhhhhccCcc
Confidence            9999999988765433

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=97.94  E-value=6.1e-05  Score=54.36  Aligned_cols=72  Identities=15%  Similarity=0.232  Sum_probs=46.5

Q ss_pred             ceEEEcCCCCCCCHHHHH----HHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEe
Q 013141          209 LSIFVGDLAPDVTDSILQ----ETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRID  284 (449)
Q Consensus       209 ~~l~v~~lp~~~t~~~l~----~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  284 (449)
                      ..|+|.|||.+.+...|+    .++..-.|.|..|.          .+.|+|.|.+.+.|.+|.+.|+|..+.|..|.|.
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~----------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~   72 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS----------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVS   72 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe----------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEE
Confidence            468999999999877665    44433345555552          3579999999999999999999999999999999


Q ss_pred             ecCCCC
Q 013141          285 VATPKK  290 (449)
Q Consensus       285 ~~~~~~  290 (449)
                      +.....
T Consensus        73 ~~~~~r   78 (90)
T PF11608_consen   73 FSPKNR   78 (90)
T ss_dssp             SS--S-
T ss_pred             EcCCcc
Confidence            985543

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.92  E-value=2.7e-05  Score=70.51  Aligned_cols=73  Identities=19%  Similarity=0.503  Sum_probs=62.5

Q ss_pred             CcEEEEcCCCCCCCHhH----HH--hhccccCceEEEEEeCCC---------cEEEEEecCHHHHHHHHHHhcCCeeCCe
Q 013141          327 NATIFVGALDSDVSDED----LR--EPFSQFGEILSVKIPVGK---------GCGFVQFANRKDAEVALQKLQGTAIGKQ  391 (449)
Q Consensus       327 ~~~l~V~nlp~~~t~~~----L~--~~f~~~G~v~~v~i~~~~---------g~afV~F~~~~~A~~A~~~l~g~~~~g~  391 (449)
                      ..-+||-+|++.+..|+    |+  ++|.+||.|..|.|-+..         --+||+|.+.++|.+||..++|..++|+
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr  193 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGR  193 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCc
Confidence            35689999999987766    33  789999999999987521         2359999999999999999999999999


Q ss_pred             EEEEEecC
Q 013141          392 TVRLSWGR  399 (449)
Q Consensus       392 ~l~v~~~~  399 (449)
                      .|+.+|..
T Consensus       194 ~lkatYGT  201 (480)
T COG5175         194 VLKATYGT  201 (480)
T ss_pred             eEeeecCc
Confidence            99999987

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=97.81  E-value=2.6e-06  Score=79.24  Aligned_cols=156  Identities=15%  Similarity=0.290  Sum_probs=115.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccccccc
Q 013141          116 KTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWAT  195 (449)
Q Consensus       116 ~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~~~  195 (449)
                      ..||++||.+.++..||..+|...-.-.+-.++..      .||+||...+..-|.+|++.+++..- ..+..+.+...-
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~k------~gyafvd~pdq~wa~kaie~~sgk~e-lqGkr~e~~~sv   74 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLVK------SGYAFVDCPDQQWANKAIETLSGKVE-LQGKRQEVEHSV   74 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceeee------cceeeccCCchhhhhhhHHhhchhhh-hcCceeeccchh
Confidence            36899999999999999999987532222222222      27999999999999999999888642 133334433322


Q ss_pred             cCCCCCccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEee-cCCCCCcceEEEEEeCCHHHHHHHHHHhCCc
Q 013141          196 FSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVII-DSNTGRTKGYGFVRFGDENERSRAMTEMNGV  274 (449)
Q Consensus       196 ~~~~~~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~-~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~  274 (449)
                      ..       ...++++-|.|+|+...++-|..++. .||.++.+..+. +..    .-..-|+|.+.+.+..||..|+|.
T Consensus        75 ~k-------kqrsrk~Qirnippql~wevld~Ll~-qyg~ve~~eqvnt~~e----tavvnvty~~~~~~~~ai~kl~g~  142 (584)
T KOG2193|consen   75 PK-------KQRSRKIQIRNIPPQLQWEVLDSLLA-QYGTVENCEQVNTDSE----TAVVNVTYSAQQQHRQAIHKLNGP  142 (584)
T ss_pred             hH-------HHHhhhhhHhcCCHHHHHHHHHHHHh-ccCCHhHhhhhccchH----HHHHHHHHHHHHHHHHHHHhhcch
Confidence            11       22345688999999999999999996 999999886542 222    223357899999999999999999


Q ss_pred             eecCcceEEeecCCCC
Q 013141          275 YCSSRPMRIDVATPKK  290 (449)
Q Consensus       275 ~~~g~~i~v~~~~~~~  290 (449)
                      .+....+++.|..+..
T Consensus       143 Q~en~~~k~~YiPdeq  158 (584)
T KOG2193|consen  143 QLENQHLKVGYIPDEQ  158 (584)
T ss_pred             HhhhhhhhcccCchhh
Confidence            9999999998876543

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=97.79  E-value=4.1e-05  Score=51.42  Aligned_cols=52  Identities=35%  Similarity=0.613  Sum_probs=44.7

Q ss_pred             cEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHH
Q 013141          328 ATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVAL  380 (449)
Q Consensus       328 ~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~  380 (449)
                      +.|.|.+.+.+.. ++|..+|..||+|.++.+.......+|+|.+..+|++|+
T Consensus         2 ~wI~V~Gf~~~~~-~~vl~~F~~fGeI~~~~~~~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLA-EEVLEHFASFGEIVDIYVPESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHH-HHHHHHHHhcCCEEEEEcCCCCcEEEEEECCHHHHHhhC
Confidence            4678888887766 556668889999999999978899999999999999985

>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=97.79  E-value=5.2e-05  Score=59.08  Aligned_cols=59  Identities=24%  Similarity=0.300  Sum_probs=40.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCC
Q 013141          116 KTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGS  180 (449)
Q Consensus       116 ~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~  180 (449)
                      +.|.|.++...++.++|++.|+.||.|.-|.+.+...      .|||.|.+.++|.+|++.+...
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~------~g~VRf~~~~~A~~a~~~~~~~   60 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDT------EGYVRFKTPEAAQKALEKLKEA   60 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-S------EEEEEESS---HHHHHHHHHHT
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCC------EEEEEECCcchHHHHHHHHHhc
Confidence            4689999999999999999999999999998877643      7999999999999999887654

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []

Probab=97.72  E-value=9.2e-05  Score=56.68  Aligned_cols=71  Identities=25%  Similarity=0.294  Sum_probs=54.0

Q ss_pred             CcEEEEcCCCCCCCHhHHHhhccccCceEEEE-------------EeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeE-
Q 013141          327 NATIFVGALDSDVSDEDLREPFSQFGEILSVK-------------IPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQT-  392 (449)
Q Consensus       327 ~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~-------------i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~-  392 (449)
                      .+-|.|-+.|.. ..+.|.++|++||+|.+..             +........|+|+++.+|.+||. -||+.|.|.. 
T Consensus         6 ~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~m   83 (100)
T PF05172_consen    6 ETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSLM   83 (100)
T ss_dssp             CCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCEE
T ss_pred             CeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcEE
Confidence            456888899888 5588889999999998885             55567899999999999999997 5999999864 


Q ss_pred             EEEEecC
Q 013141          393 VRLSWGR  399 (449)
Q Consensus       393 l~v~~~~  399 (449)
                      +-|.|.+
T Consensus        84 vGV~~~~   90 (100)
T PF05172_consen   84 VGVKPCD   90 (100)
T ss_dssp             EEEEE-H
T ss_pred             EEEEEcH
Confidence            4477764

This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A.

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=97.67  E-value=7.7e-05  Score=70.00  Aligned_cols=64  Identities=30%  Similarity=0.362  Sum_probs=56.5

Q ss_pred             CCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC-------------------CcEEEEEecCHHHHHHHHHHh
Q 013141          323 GESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-------------------KGCGFVQFANRKDAEVALQKL  383 (449)
Q Consensus       323 ~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~-------------------~g~afV~F~~~~~A~~A~~~l  383 (449)
                      .+..+++|.+.|||.+-..+.|.++|..+|.|+.|+|+..                   +-+|+|+|++.+.|.+|.+.|
T Consensus       227 eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~  306 (484)
T KOG1855|consen  227 EELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELL  306 (484)
T ss_pred             cccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhh
Confidence            3457899999999999999999999999999999999752                   468999999999999999988


Q ss_pred             cCC
Q 013141          384 QGT  386 (449)
Q Consensus       384 ~g~  386 (449)
                      +..
T Consensus       307 ~~e  309 (484)
T KOG1855|consen  307 NPE  309 (484)
T ss_pred             chh
Confidence            543

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=97.67  E-value=9.7e-05  Score=49.62  Aligned_cols=52  Identities=23%  Similarity=0.335  Sum_probs=42.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHH
Q 013141          116 KTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVL  174 (449)
Q Consensus       116 ~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al  174 (449)
                      +.|-|.+.+.+..+ +|..+|..||+|+++.+-...      -+.||+|.+..+|++||
T Consensus         2 ~wI~V~Gf~~~~~~-~vl~~F~~fGeI~~~~~~~~~------~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAE-EVLEHFASFGEIVDIYVPEST------NWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHH-HHHHHHHhcCCEEEEEcCCCC------cEEEEEECCHHHHHhhC
Confidence            57889999987665 455688899999998886433      38999999999999986

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=97.64  E-value=5.7e-05  Score=69.62  Aligned_cols=85  Identities=20%  Similarity=0.281  Sum_probs=76.0

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeE--------EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKG--------AKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYC  276 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~--------i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~  276 (449)
                      .....+|||-+|+..+++++|.++|. ..+.|..        |.|.+|++|+++|+-|.|.|.+...|+.||.-+++..|
T Consensus        63 ~s~~~ti~v~g~~d~~~~~~~~~~f~-qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf  141 (351)
T KOG1995|consen   63 KSDNETIFVWGCPDSVCENDNADFFL-QCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDF  141 (351)
T ss_pred             ccccccceeeccCccchHHHHHHHHh-hcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccc
Confidence            34556899999999999999999995 8888754        77888999999999999999999999999999999999


Q ss_pred             cCcceEEeecCCCC
Q 013141          277 SSRPMRIDVATPKK  290 (449)
Q Consensus       277 ~g~~i~v~~~~~~~  290 (449)
                      .+.+|+|..+..+.
T Consensus       142 ~gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  142 CGNTIKVSLAERRT  155 (351)
T ss_pred             cCCCchhhhhhhcc
Confidence            99999998887654

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=97.62  E-value=1.6e-05  Score=73.44  Aligned_cols=155  Identities=12%  Similarity=0.095  Sum_probs=105.5

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCC---CCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccc
Q 013141          115 TKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQ---TGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRL  191 (449)
Q Consensus       115 ~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~---~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~  191 (449)
                      ...|.|.||.+.+|.+.++.+|.-.|.|.++.++....   -......|||.|.|...+..|- .|..+.+-.+.+ |.+
T Consensus         7 ~~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQ-hLtntvfvdral-iv~   84 (479)
T KOG4676|consen    7 LGVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQ-HLTNTVFVDRAL-IVR   84 (479)
T ss_pred             CceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHh-hhccceeeeeeE-EEE
Confidence            34899999999999999999999999999999988432   2234568999999999999887 344433311111 111


Q ss_pred             cccccC-----------------------CC---CCc------------------------cccCCCceEEEcCCCCCCC
Q 013141          192 NWATFS-----------------------GS---DRR------------------------TEACSDLSIFVGDLAPDVT  221 (449)
Q Consensus       192 ~~~~~~-----------------------~~---~~~------------------------~~~~~~~~l~v~~lp~~~t  221 (449)
                      -+....                       ..   ...                        ......++++|.+|+..+.
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            111000                       00   000                        0112235789999999999


Q ss_pred             HHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceec
Q 013141          222 DSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCS  277 (449)
Q Consensus       222 ~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~  277 (449)
                      ..++.+.| +.+|+|....+-.    +...-+|.++|........|+ .++|..+.
T Consensus       165 l~e~~e~f-~r~Gev~ya~~as----k~~s~~c~~sf~~qts~~hal-r~~gre~k  214 (479)
T KOG4676|consen  165 LPESGESF-ERKGEVSYAHTAS----KSRSSSCSHSFRKQTSSKHAL-RSHGRERK  214 (479)
T ss_pred             chhhhhhh-hhcchhhhhhhhc----cCCCcchhhhHhhhhhHHHHH-Hhcchhhh
Confidence            99999999 5999988776543    223446779999888888887 46666654

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=97.53  E-value=9.1e-05  Score=69.54  Aligned_cols=79  Identities=15%  Similarity=0.136  Sum_probs=64.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEec---CCCCC----------cccEEEEEEccHHHHHHHHHHhcC
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRN---KQTGQ----------SEGYGFVEFYSRAAAEKVLQSYSG  179 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~---~~~g~----------~~g~afV~f~~~~~A~~Al~~l~~  179 (449)
                      -.+++|.+-|||.+-.-+.|.++|..+|.|..|+|+..   ..+.+          .+-+|+|+|...+.|.+|.+.++.
T Consensus       229 l~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~~  308 (484)
T KOG1855|consen  229 LPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLNP  308 (484)
T ss_pred             cccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhch
Confidence            38999999999999999999999999999999999886   33332          245799999999999999988766


Q ss_pred             CCCCCCCCcccc
Q 013141          180 SLMPNTDQPFRL  191 (449)
Q Consensus       180 ~~~~~~~~~~~~  191 (449)
                      ...+..+..+++
T Consensus       309 e~~wr~glkvkL  320 (484)
T KOG1855|consen  309 EQNWRMGLKVKL  320 (484)
T ss_pred             hhhhhhcchhhh
Confidence            555544444444

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

Probab=97.49  E-value=0.00019  Score=63.96  Aligned_cols=61  Identities=21%  Similarity=0.247  Sum_probs=52.9

Q ss_pred             CHhHHHhhccccCceEEEEEeCC-------CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCC
Q 013141          340 SDEDLREPFSQFGEILSVKIPVG-------KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRN  400 (449)
Q Consensus       340 t~~~L~~~f~~~G~v~~v~i~~~-------~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  400 (449)
                      -++++++.|++||.|..|.|...       ---.||+|+..++|.+|+-.|||+.|+|+.++..|..-
T Consensus       299 lede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn~  366 (378)
T KOG1996|consen  299 LEDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYNL  366 (378)
T ss_pred             HHHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheeccH
Confidence            35789999999999999888652       24579999999999999999999999999999888653

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=97.48  E-value=0.0001  Score=67.22  Aligned_cols=70  Identities=23%  Similarity=0.453  Sum_probs=63.1

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccC--CcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCC
Q 013141          116 KTIWIGDLFHWMDETFLHNCFSHTG--QVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNT  185 (449)
Q Consensus       116 ~~l~v~nLp~~~t~~~l~~~f~~~G--~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~  185 (449)
                      ..+||+||-|.+|++||.+.+...|  .+.+++++.++.+|.+||||+|...+..+.++.++.|-.+.|.+.
T Consensus        81 ~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ  152 (498)
T KOG4849|consen   81 YCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQ  152 (498)
T ss_pred             EEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCC
Confidence            4699999999999999999998877  578899999999999999999999999999999988887777554

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=97.45  E-value=6.2e-05  Score=65.97  Aligned_cols=67  Identities=24%  Similarity=0.404  Sum_probs=59.5

Q ss_pred             CCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC------------------CcEEEEEecCHHHHHHHHHHhcCCe
Q 013141          326 NNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------------------KGCGFVQFANRKDAEVALQKLQGTA  387 (449)
Q Consensus       326 ~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~------------------~g~afV~F~~~~~A~~A~~~l~g~~  387 (449)
                      ..-+||+++||+.+....|+++|+.||.|-+|.+-+.                  -..++|+|.+...|.++...||+..
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~  152 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTP  152 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCc
Confidence            4578999999999999999999999999999988652                  1357899999999999999999999


Q ss_pred             eCCeE
Q 013141          388 IGKQT  392 (449)
Q Consensus       388 ~~g~~  392 (449)
                      |+|+.
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99864

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.44  E-value=0.0005  Score=62.56  Aligned_cols=81  Identities=19%  Similarity=0.370  Sum_probs=64.5

Q ss_pred             CceEEEcCCCCCCCHHHH------HHHHhhhCCCeeEEEEeecCCCCCc-ceE--EEEEeCCHHHHHHHHHHhCCceecC
Q 013141          208 DLSIFVGDLAPDVTDSIL------QETFSSKYPSVKGAKVIIDSNTGRT-KGY--GFVRFGDENERSRAMTEMNGVYCSS  278 (449)
Q Consensus       208 ~~~l~v~~lp~~~t~~~l------~~~f~~~~g~v~~i~~~~~~~~~~~-~g~--afV~f~~~~~A~~A~~~l~g~~~~g  278 (449)
                      .+-+||-+|++.+..|++      .++|+ .||.|..|.+.+...+..+ .+.  .||+|.+.|+|.++|.+.+|..++|
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFG-QyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DG  192 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFG-QYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDG  192 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhh-hccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccC
Confidence            456899999998877663      37896 9999999988766422221 222  3999999999999999999999999


Q ss_pred             cceEEeecCCC
Q 013141          279 RPMRIDVATPK  289 (449)
Q Consensus       279 ~~i~v~~~~~~  289 (449)
                      |.|+..+.+.+
T Consensus       193 r~lkatYGTTK  203 (480)
T COG5175         193 RVLKATYGTTK  203 (480)
T ss_pred             ceEeeecCchH
Confidence            99999887754

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=97.30  E-value=9.4e-05  Score=65.07  Aligned_cols=58  Identities=24%  Similarity=0.391  Sum_probs=51.2

Q ss_pred             hHHHhhcc-ccCceEEEEEeCC-----CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 013141          342 EDLREPFS-QFGEILSVKIPVG-----KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGR  399 (449)
Q Consensus       342 ~~L~~~f~-~~G~v~~v~i~~~-----~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  399 (449)
                      ++|...|+ +||+|+.+.|..+     .|.+||.|...++|++|++.||+..|.|+.|...+..
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~p  146 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSP  146 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecC
Confidence            55666666 8999999988764     5899999999999999999999999999999998766

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=97.28  E-value=0.00058  Score=60.05  Aligned_cols=90  Identities=18%  Similarity=0.400  Sum_probs=75.2

Q ss_pred             HHHHHHHHHhcCCCCCCCCCcccccccccCCCCCccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCC
Q 013141          168 AAAEKVLQSYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNT  247 (449)
Q Consensus       168 ~~A~~Al~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~  247 (449)
                      .-|+.|..+|++...  ..+.+++.++.            ...|+|.||...++.|.+.+.|+ .||+|+.-.++.| ..
T Consensus         5 t~ae~ak~eLd~~~~--~~~~lr~rfa~------------~a~l~V~nl~~~~sndll~~~f~-~fg~~e~av~~vD-~r   68 (275)
T KOG0115|consen    5 TLAEIAKRELDGRFP--KGRSLRVRFAM------------HAELYVVNLMQGASNDLLEQAFR-RFGPIERAVAKVD-DR   68 (275)
T ss_pred             cHHHHHHHhcCCCCC--CCCceEEEeec------------cceEEEEecchhhhhHHHHHhhh-hcCccchheeeec-cc
Confidence            346667777899888  55778877775            25899999999999999999996 9999999888777 44


Q ss_pred             CCcceEEEEEeCCHHHHHHHHHHhCC
Q 013141          248 GRTKGYGFVRFGDENERSRAMTEMNG  273 (449)
Q Consensus       248 ~~~~g~afV~f~~~~~A~~A~~~l~g  273 (449)
                      ++..+-++|+|...-.|.+|+..+.-
T Consensus        69 ~k~t~eg~v~~~~k~~a~~a~rr~~~   94 (275)
T KOG0115|consen   69 GKPTREGIVEFAKKPNARKAARRCRE   94 (275)
T ss_pred             ccccccchhhhhcchhHHHHHHHhcc
Confidence            78888999999999999999988753

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=97.26  E-value=0.0002  Score=62.80  Aligned_cols=74  Identities=16%  Similarity=0.268  Sum_probs=62.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCC--------CCcc----eEEEEEeCCHHHHHHHHHHhCCc
Q 013141          207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNT--------GRTK----GYGFVRFGDENERSRAMTEMNGV  274 (449)
Q Consensus       207 ~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~--------~~~~----g~afV~f~~~~~A~~A~~~l~g~  274 (449)
                      ....||+++||+.+...-|+++|+ .||.|-+|.+-....+        +..+    .-++|+|.+...|.++...||+.
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~-~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~  151 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILS-QYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNT  151 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHH-hccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCC
Confidence            456899999999999999999996 9999999999876554        2221    23799999999999999999999


Q ss_pred             eecCcce
Q 013141          275 YCSSRPM  281 (449)
Q Consensus       275 ~~~g~~i  281 (449)
                      .|+|+.-
T Consensus       152 ~Iggkk~  158 (278)
T KOG3152|consen  152 PIGGKKK  158 (278)
T ss_pred             ccCCCCC
Confidence            9988753

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=97.09  E-value=0.00099  Score=58.65  Aligned_cols=87  Identities=25%  Similarity=0.386  Sum_probs=73.6

Q ss_pred             HHHHHHHHhCCceecCcceEEeecCCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHh
Q 013141          263 ERSRAMTEMNGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDE  342 (449)
Q Consensus       263 ~A~~A~~~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~  342 (449)
                      -|+.|..+|++....++.++|.|+..                                       ..|+|.||...++.|
T Consensus         6 ~ae~ak~eLd~~~~~~~~lr~rfa~~---------------------------------------a~l~V~nl~~~~snd   46 (275)
T KOG0115|consen    6 LAEIAKRELDGRFPKGRSLRVRFAMH---------------------------------------AELYVVNLMQGASND   46 (275)
T ss_pred             HHHHHHHhcCCCCCCCCceEEEeecc---------------------------------------ceEEEEecchhhhhH
Confidence            46677778999999999999999866                                       248999999999999


Q ss_pred             HHHhhccccCceEEEEEeCC-----CcEEEEEecCHHHHHHHHHHhcCCee
Q 013141          343 DLREPFSQFGEILSVKIPVG-----KGCGFVQFANRKDAEVALQKLQGTAI  388 (449)
Q Consensus       343 ~L~~~f~~~G~v~~v~i~~~-----~g~afV~F~~~~~A~~A~~~l~g~~~  388 (449)
                      .|...|+.||.|....+..+     .+..+|+|...-.|.+|+......-|
T Consensus        47 ll~~~f~~fg~~e~av~~vD~r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~   97 (275)
T KOG0115|consen   47 LLEQAFRRFGPIERAVAKVDDRGKPTREGIVEFAKKPNARKAARRCREGGF   97 (275)
T ss_pred             HHHHhhhhcCccchheeeecccccccccchhhhhcchhHHHHHHHhccCcc
Confidence            99999999999988665542     57899999999999999988754433

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=97.09  E-value=0.0027  Score=51.63  Aligned_cols=56  Identities=25%  Similarity=0.474  Sum_probs=46.1

Q ss_pred             hHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCC
Q 013141          342 EDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRN  400 (449)
Q Consensus       342 ~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  400 (449)
                      .+|.+.|..||+|.=|++..  +.-+|+|.+-+.|.+|+. |+|..++|+.|+|+...+
T Consensus        51 ~~ll~~~~~~GevvLvRfv~--~~mwVTF~dg~sALaals-~dg~~v~g~~l~i~LKtp  106 (146)
T PF08952_consen   51 DELLQKFAQYGEVVLVRFVG--DTMWVTFRDGQSALAALS-LDGIQVNGRTLKIRLKTP  106 (146)
T ss_dssp             HHHHHHHHCCS-ECEEEEET--TCEEEEESSCHHHHHHHH-GCCSEETTEEEEEEE---
T ss_pred             HHHHHHHHhCCceEEEEEeC--CeEEEEECccHHHHHHHc-cCCcEECCEEEEEEeCCc
Confidence            36778889999998888874  589999999999999985 899999999999998765

; PDB: 1UFW_A 2DNR_A.

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=97.04  E-value=0.0014  Score=63.95  Aligned_cols=72  Identities=24%  Similarity=0.355  Sum_probs=59.5

Q ss_pred             CCCceEEEcCCCC--CCC----HHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCC
Q 013141          113 DETKTIWIGDLFH--WMD----ETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNT  185 (449)
Q Consensus       113 ~~~~~l~v~nLp~--~~t----~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~  185 (449)
                      .....|+|.|+|-  ...    ..-|.++|+++|.++.+.+..+.. |.++||.|++|.+..+|+.|++.|||+.++.+
T Consensus        56 g~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~-ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldkn  133 (698)
T KOG2314|consen   56 GFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEE-GGTKGYLFVEYASMRDAKKAVKSLNGKRLDKN  133 (698)
T ss_pred             CcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCcc-CCeeeEEEEEecChhhHHHHHHhcccceeccc
Confidence            3456799999994  222    334678999999999999998865 55999999999999999999999999988654

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=97.01  E-value=0.00055  Score=66.98  Aligned_cols=80  Identities=11%  Similarity=0.156  Sum_probs=69.3

Q ss_pred             CCCCCCcEEEEcCCCCCCCHhHHHhhcc-ccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCee---CCeEEEEEe
Q 013141          322 DGESNNATIFVGALDSDVSDEDLREPFS-QFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAI---GKQTVRLSW  397 (449)
Q Consensus       322 ~~~~~~~~l~V~nlp~~~t~~~L~~~f~-~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~---~g~~l~v~~  397 (449)
                      .....+++|+|.||-.-+|.-.|+.++. ..|.|....|.+=+..|||.|.+.++|...+.+|||..+   +.+.|.+.|
T Consensus       439 sR~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~WmDkIKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~adf  518 (718)
T KOG2416|consen  439 SRKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWMDKIKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIADF  518 (718)
T ss_pred             CCCCccceEeeecccccchHHHHHHHHhhccCchHHHHHHHhhcceeEecccHHHHHHHHHHHhccccCCCCCceeEeee
Confidence            3556789999999999999999999997 567788876655578999999999999999999999987   478999999


Q ss_pred             cCCC
Q 013141          398 GRNP  401 (449)
Q Consensus       398 ~~~~  401 (449)
                      ....
T Consensus       519 ~~~d  522 (718)
T KOG2416|consen  519 VRAD  522 (718)
T ss_pred             cchh
Confidence            8853

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=96.94  E-value=0.0031  Score=57.80  Aligned_cols=72  Identities=18%  Similarity=0.248  Sum_probs=58.6

Q ss_pred             CCCcEEEEcCCCCCCCHhHHHhhccccC--ceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEE
Q 013141          325 SNNATIFVGALDSDVSDEDLREPFSQFG--EILSVKIPV------GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLS  396 (449)
Q Consensus       325 ~~~~~l~V~nlp~~~t~~~L~~~f~~~G--~v~~v~i~~------~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~  396 (449)
                      ....++||+||-+.+|++||.+.+..-|  .+.++++..      +||||+|...+..+.++.++.|--++|+|..-.|.
T Consensus        78 Grk~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~  157 (498)
T KOG4849|consen   78 GRKYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVL  157 (498)
T ss_pred             CceEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeee
Confidence            3456899999999999999999887766  345555554      48999999999999999999999999998655443

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=96.89  E-value=0.00052  Score=60.51  Aligned_cols=67  Identities=16%  Similarity=0.343  Sum_probs=55.6

Q ss_pred             HHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecCCCC
Q 013141          223 SILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKK  290 (449)
Q Consensus       223 ~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~~~~  290 (449)
                      ++|...|.++||+|+++.+..+- ...-.|.++|.|..+++|++|++.||+..+.|++|..++.....
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl-~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pvT~  149 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNL-GDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPVTD  149 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhccc-chhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCcCc
Confidence            56666676699999999776553 24557889999999999999999999999999999999886543

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=96.76  E-value=0.0039  Score=60.92  Aligned_cols=73  Identities=25%  Similarity=0.405  Sum_probs=60.1

Q ss_pred             CCCcEEEEcCCCCCCC------HhHHHhhccccCceEEEEEeCC-----CcEEEEEecCHHHHHHHHHHhcCCeeC-CeE
Q 013141          325 SNNATIFVGALDSDVS------DEDLREPFSQFGEILSVKIPVG-----KGCGFVQFANRKDAEVALQKLQGTAIG-KQT  392 (449)
Q Consensus       325 ~~~~~l~V~nlp~~~t------~~~L~~~f~~~G~v~~v~i~~~-----~g~afV~F~~~~~A~~A~~~l~g~~~~-g~~  392 (449)
                      .-..+|+|.|+|---.      ...|..+|+++|+|..+.++.+     +|+.|++|.+..+|+.|++.|||+.|+ +++
T Consensus        56 g~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHt  135 (698)
T KOG2314|consen   56 GFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHT  135 (698)
T ss_pred             CcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccce
Confidence            3457899999986432      2446688999999999998853     699999999999999999999999987 677


Q ss_pred             EEEEe
Q 013141          393 VRLSW  397 (449)
Q Consensus       393 l~v~~  397 (449)
                      ..|..
T Consensus       136 f~v~~  140 (698)
T KOG2314|consen  136 FFVRL  140 (698)
T ss_pred             EEeeh
Confidence            77764

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=96.71  E-value=0.0012  Score=62.93  Aligned_cols=75  Identities=21%  Similarity=0.383  Sum_probs=63.6

Q ss_pred             CCCcEEEEcCCCCCC-CHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCC
Q 013141          325 SNNATIFVGALDSDV-SDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRN  400 (449)
Q Consensus       325 ~~~~~l~V~nlp~~~-t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  400 (449)
                      ...+.|-+.-++... +.++|..+|.+||.|..|.+..+.--|.|+|.+..+|-+|.. .++..|+++.|+|.|-++
T Consensus       370 ~dhs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~~~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~whnp  445 (526)
T KOG2135|consen  370 VDHSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYSSLHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWHNP  445 (526)
T ss_pred             cccchhhhhccCCCCchHhhhhhhhhhcCccccccccCchhhheeeeeccccccchhc-cccceecCceeEEEEecC
Confidence            344556666666664 668999999999999999998877889999999999988864 799999999999999887

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=96.70  E-value=0.0046  Score=60.30  Aligned_cols=70  Identities=11%  Similarity=0.224  Sum_probs=56.7

Q ss_pred             CCcEEEEcCCCCCCCHhHHHhhccc--cCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCC--eeCCeEEEEE
Q 013141          326 NNATIFVGALDSDVSDEDLREPFSQ--FGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGT--AIGKQTVRLS  396 (449)
Q Consensus       326 ~~~~l~V~nlp~~~t~~~L~~~f~~--~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~--~~~g~~l~v~  396 (449)
                      ..|+|.|+-||..+.+|+|+.+|+.  +-.+.+|.+-.+ ..+||+|++..||+.|.+.|...  +|.|+.|-.+
T Consensus       174 kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N-~nWyITfesd~DAQqAykylreevk~fqgKpImAR  247 (684)
T KOG2591|consen  174 KRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHN-DNWYITFESDTDAQQAYKYLREEVKTFQGKPIMAR  247 (684)
T ss_pred             ceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeec-CceEEEeecchhHHHHHHHHHHHHHhhcCcchhhh
Confidence            3578899999999999999999964  678899988764 46899999999999999988543  4666655433

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=96.69  E-value=0.01  Score=40.79  Aligned_cols=54  Identities=17%  Similarity=0.199  Sum_probs=45.5

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhcc----CCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHh
Q 013141          115 TKTIWIGDLFHWMDETFLHNCFSHT----GQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY  177 (449)
Q Consensus       115 ~~~l~v~nLp~~~t~~~l~~~f~~~----G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l  177 (449)
                      ...|+|+++. +++.++|+.+|..|    + ...|.-+-|.       .|-|.|.+.+.|.+||..|
T Consensus         5 peavhirGvd-~lsT~dI~~y~~~y~~~~~-~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    5 PEAVHIRGVD-ELSTDDIKAYFSEYFDEEG-PFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eceEEEEcCC-CCCHHHHHHHHHHhcccCC-CceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            3479999984 58889999999999    4 4678888885       4999999999999999754

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

Probab=96.57  E-value=0.0069  Score=54.34  Aligned_cols=67  Identities=18%  Similarity=0.206  Sum_probs=54.8

Q ss_pred             HHHHHHHHhhhCCCeeEEEEeecCCCCCc-ceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecCCC
Q 013141          222 DSILQETFSSKYPSVKGAKVIIDSNTGRT-KGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPK  289 (449)
Q Consensus       222 ~~~l~~~f~~~~g~v~~i~~~~~~~~~~~-~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~~~  289 (449)
                      ++++++.+ ++||.|..|.|..++..... .--.||+|...++|.+|+-.|||+.|+|+.++..|....
T Consensus       300 ede~keEc-eKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn~e  367 (378)
T KOG1996|consen  300 EDETKEEC-EKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYNLE  367 (378)
T ss_pred             HHHHHHHH-HhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheeccHH
Confidence            45788889 59999999988877543222 234799999999999999999999999999998887554

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=96.42  E-value=0.014  Score=40.24  Aligned_cols=55  Identities=20%  Similarity=0.329  Sum_probs=44.6

Q ss_pred             CcEEEEcCCCCCCCHhHHHhhcccc---CceEEEEEeCCCcEEEEEecCHHHHHHHHHHh
Q 013141          327 NATIFVGALDSDVSDEDLREPFSQF---GEILSVKIPVGKGCGFVQFANRKDAEVALQKL  383 (449)
Q Consensus       327 ~~~l~V~nlp~~~t~~~L~~~f~~~---G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l  383 (449)
                      ...|+|.+++ .++.++|+.+|..|   ....+|+.+.+ ..|-|.|.+.+.|.+|+.+|
T Consensus         5 peavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdD-tScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    5 PEAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDD-TSCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecC-CcEEEEECCHHHHHHHHHcC
Confidence            4679999985 47789999999988   23567887765 57889999999999999765

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=96.33  E-value=0.0047  Score=60.73  Aligned_cols=81  Identities=14%  Similarity=0.158  Sum_probs=66.3

Q ss_pred             ccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee---cCcc
Q 013141          204 EACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYC---SSRP  280 (449)
Q Consensus       204 ~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~---~g~~  280 (449)
                      ....++.|+|.||-.-+|.-.|++++....|.|.+.+|  |+.    +..|||.|.+.++|.+.+.+|||..+   +.+.
T Consensus       440 R~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~Wm--DkI----KShCyV~yss~eEA~atr~AlhnV~WP~sNPK~  513 (718)
T KOG2416|consen  440 RKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWM--DKI----KSHCYVSYSSVEEAAATREALHNVQWPPSNPKH  513 (718)
T ss_pred             CCCccceEeeecccccchHHHHHHHHhhccCchHHHHH--HHh----hcceeEecccHHHHHHHHHHHhccccCCCCCce
Confidence            34567899999999999999999999767777777733  322    55799999999999999999999887   6788


Q ss_pred             eEEeecCCCC
Q 013141          281 MRIDVATPKK  290 (449)
Q Consensus       281 i~v~~~~~~~  290 (449)
                      |.+.|.....
T Consensus       514 L~adf~~~de  523 (718)
T KOG2416|consen  514 LIADFVRADE  523 (718)
T ss_pred             eEeeecchhH
Confidence            8888876543

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []

Probab=96.12  E-value=0.028  Score=43.11  Aligned_cols=78  Identities=15%  Similarity=0.207  Sum_probs=50.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEe-ecC------CCCCcceEEEEEeCCHHHHHHHHHHhCCceecCc
Q 013141          207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVI-IDS------NTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSR  279 (449)
Q Consensus       207 ~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~-~~~------~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~  279 (449)
                      ..+-|.|.+.|+. ....|.+.|+ +||+|.+..-. ++.      ..........|+|.+..+|.+|+ ..||..+.|.
T Consensus         5 ~~~wVtVFGfp~~-~~~~Vl~~F~-~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL-~~NG~i~~g~   81 (100)
T PF05172_consen    5 SETWVTVFGFPPS-ASNQVLRHFS-SFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRAL-QKNGTIFSGS   81 (100)
T ss_dssp             GCCEEEEE---GG-GHHHHHHHHH-CCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHH-TTTTEEETTC
T ss_pred             CCeEEEEEccCHH-HHHHHHHHHH-hcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHH-HhCCeEEcCc
Confidence            3456889999997 5667888895 99998877511 100      00122457899999999999999 6899999876


Q ss_pred             ce-EEeecC
Q 013141          280 PM-RIDVAT  287 (449)
Q Consensus       280 ~i-~v~~~~  287 (449)
                      .+ -|.+.+
T Consensus        82 ~mvGV~~~~   90 (100)
T PF05172_consen   82 LMVGVKPCD   90 (100)
T ss_dssp             EEEEEEE-H
T ss_pred             EEEEEEEcH
Confidence            54 466653

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.

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=96.00  E-value=0.038  Score=40.21  Aligned_cols=54  Identities=26%  Similarity=0.432  Sum_probs=40.7

Q ss_pred             cEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhc
Q 013141          328 ATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQ  384 (449)
Q Consensus       328 ~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~  384 (449)
                      .+.+|. .|...-..||.++|+.||.|.=-.| . ...|||...+.+.|..|+..+.
T Consensus        10 HVFhlt-FPkeWK~~DI~qlFspfG~I~VsWi-~-dTSAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen   10 HVFHLT-FPKEWKTSDIYQLFSPFGQIYVSWI-N-DTSAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             CEEEEE---TT--HHHHHHHCCCCCCEEEEEE-C-TTEEEEEECCCHHHHHHHHHHT
T ss_pred             eEEEEe-CchHhhhhhHHHHhccCCcEEEEEE-c-CCcEEEEeecHHHHHHHHHHhc
Confidence            445554 9999999999999999998654433 3 5789999999999999998885

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=95.96  E-value=0.033  Score=44.77  Aligned_cols=75  Identities=28%  Similarity=0.375  Sum_probs=56.9

Q ss_pred             CCCCCcEEEEcCCCCCC-CHhH---HHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 013141          323 GESNNATIFVGALDSDV-SDED---LREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWG  398 (449)
Q Consensus       323 ~~~~~~~l~V~nlp~~~-t~~~---L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~  398 (449)
                      .+++..+|.|.=|...+ ..+|   |...++.||.|.+|.+. ++-.|.|.|.|..+|=+|+.++.. ...|..+++.|-
T Consensus        82 kepPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c-GrqsavVvF~d~~SAC~Av~Af~s-~~pgtm~qCsWq  159 (166)
T PF15023_consen   82 KEPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC-GRQSAVVVFKDITSACKAVSAFQS-RAPGTMFQCSWQ  159 (166)
T ss_pred             CCCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec-CCceEEEEehhhHHHHHHHHhhcC-CCCCceEEeecc
Confidence            35556778777665554 2344   44567889999999865 578999999999999999999876 557888888874


Q ss_pred             C
Q 013141          399 R  399 (449)
Q Consensus       399 ~  399 (449)
                      .
T Consensus       160 q  160 (166)
T PF15023_consen  160 Q  160 (166)
T ss_pred             c
Confidence            3

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=95.91  E-value=0.0067  Score=60.64  Aligned_cols=70  Identities=14%  Similarity=0.276  Sum_probs=59.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRL  191 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~  191 (449)
                      ...-+|||+|+...++.+-++.+...||-|.+++...         |+|.+|.....+.+|+..++...+.+......+
T Consensus        38 ~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~~  107 (668)
T KOG2253|consen   38 PPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---------FGFCEFLKHIGDLRASRLLTELNIDDQKLIENV  107 (668)
T ss_pred             CCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---------hcccchhhHHHHHHHHHHhcccCCCcchhhccc
Confidence            3567999999999999999999999999988877644         899999999999999988888777665555555

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=95.88  E-value=0.019  Score=49.44  Aligned_cols=62  Identities=23%  Similarity=0.250  Sum_probs=49.6

Q ss_pred             CHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhc--CCeeCCeEEEEEecCCC
Q 013141          340 SDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQ--GTAIGKQTVRLSWGRNP  401 (449)
Q Consensus       340 t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~--g~~~~g~~l~v~~~~~~  401 (449)
                      ..+.|+++|..|+.+..+.++++-+-..|.|.+.++|.+|...|+  +..|.|..|+|-|+...
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~sFrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~   71 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKSFRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPT   71 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETTTTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----S
T ss_pred             hHHHHHHHHHhcCCceEEEEcCCCCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcccc
Confidence            458899999999999999999988889999999999999999999  99999999999998643

Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=95.79  E-value=0.024  Score=51.25  Aligned_cols=72  Identities=19%  Similarity=0.262  Sum_probs=56.5

Q ss_pred             CcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeE-EEEEecCC
Q 013141          327 NATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQT-VRLSWGRN  400 (449)
Q Consensus       327 ~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~-l~v~~~~~  400 (449)
                      ..=|.|.+.++.-. .-|..+|++||.|++.....+...-+|+|.++.+|.+||.+ ||+.|+|.. |-|.-..+
T Consensus       197 D~WVTVfGFppg~~-s~vL~~F~~cG~Vvkhv~~~ngNwMhirYssr~~A~KALsk-ng~ii~g~vmiGVkpCtD  269 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQV-SIVLNLFSRCGEVVKHVTPSNGNWMHIRYSSRTHAQKALSK-NGTIIDGDVMIGVKPCTD  269 (350)
T ss_pred             cceEEEeccCccch-hHHHHHHHhhCeeeeeecCCCCceEEEEecchhHHHHhhhh-cCeeeccceEEeeeecCC
Confidence            34466777776644 56788999999999988887778899999999999999975 999998765 44555444

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=95.62  E-value=0.038  Score=47.51  Aligned_cols=75  Identities=12%  Similarity=0.242  Sum_probs=51.6

Q ss_pred             CCcEEEEcCCCCCCCHhHHHhhccc-cCce---EEEEEeCC--------CcEEEEEecCHHHHHHHHHHhcCCeeCC---
Q 013141          326 NNATIFVGALDSDVSDEDLREPFSQ-FGEI---LSVKIPVG--------KGCGFVQFANRKDAEVALQKLQGTAIGK---  390 (449)
Q Consensus       326 ~~~~l~V~nlp~~~t~~~L~~~f~~-~G~v---~~v~i~~~--------~g~afV~F~~~~~A~~A~~~l~g~~~~g---  390 (449)
                      ...+|.|++||+.+|++++.+.++. ++.-   .++....+        ..-|||.|.+.++.......++|..|.+   
T Consensus         6 ~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~kg   85 (176)
T PF03467_consen    6 EGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSKG   85 (176)
T ss_dssp             ---EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TTS
T ss_pred             cCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCCC
Confidence            4568999999999999999998887 6655   33432111        2579999999999999999999988753   


Q ss_pred             --eEEEEEecCC
Q 013141          391 --QTVRLSWGRN  400 (449)
Q Consensus       391 --~~l~v~~~~~  400 (449)
                        ....|+|+--
T Consensus        86 ~~~~~~VE~Apy   97 (176)
T PF03467_consen   86 NEYPAVVEFAPY   97 (176)
T ss_dssp             -EEEEEEEE-SS
T ss_pred             CCcceeEEEcch
Confidence              3556666553

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.

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=95.45  E-value=0.087  Score=50.50  Aligned_cols=69  Identities=14%  Similarity=0.190  Sum_probs=59.3

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecC
Q 013141          208 DLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSS  278 (449)
Q Consensus       208 ~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g  278 (449)
                      ++.|+|-.+|..++..||..|+....-.|.++++++|....  +=..+|+|.+-++|....+.+||+.|..
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~pn--rymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMPN--RYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCCc--eEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            78899999999999999999997566679999999975433  3368999999999999999999988744

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=95.44  E-value=0.06  Score=43.96  Aligned_cols=56  Identities=25%  Similarity=0.451  Sum_probs=44.4

Q ss_pred             HHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecCCC
Q 013141          224 ILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPK  289 (449)
Q Consensus       224 ~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~~~  289 (449)
                      +|.+.|. .||++.=|+++.+        .-+|+|.+-+.|.+|+ .++|..++|+.|+|+.-.+.
T Consensus        52 ~ll~~~~-~~GevvLvRfv~~--------~mwVTF~dg~sALaal-s~dg~~v~g~~l~i~LKtpd  107 (146)
T PF08952_consen   52 ELLQKFA-QYGEVVLVRFVGD--------TMWVTFRDGQSALAAL-SLDGIQVNGRTLKIRLKTPD  107 (146)
T ss_dssp             HHHHHHH-CCS-ECEEEEETT--------CEEEEESSCHHHHHHH-HGCCSEETTEEEEEEE----
T ss_pred             HHHHHHH-hCCceEEEEEeCC--------eEEEEECccHHHHHHH-ccCCcEECCEEEEEEeCCcc
Confidence            6778885 8999887777754        4699999999999998 79999999999999987765

; PDB: 1UFW_A 2DNR_A.

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=95.44  E-value=0.22  Score=39.03  Aligned_cols=67  Identities=13%  Similarity=0.101  Sum_probs=48.2

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecC
Q 013141          210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSS  278 (449)
Q Consensus       210 ~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g  278 (449)
                      .+.+...|..++.++|..+.+..-..|..+++++|...  .+-.++++|.+.++|++..+.+||+.+..
T Consensus        15 ~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~p--nrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   15 LCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGTP--NRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             EEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCCC--ceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            44444455556666777666533445778888887442  45579999999999999999999998744

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=95.40  E-value=0.2  Score=39.19  Aligned_cols=69  Identities=10%  Similarity=0.170  Sum_probs=51.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccC-CcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCC
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTG-QVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMP  183 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G-~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~  183 (449)
                      ..+..+.+-..|+.++.++|..+.+.+- .|..++|++|..  .++-.++++|.+.++|......+||+.+.
T Consensus        11 ~~~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~--pnrymVLikF~~~~~Ad~Fy~~fNGk~Fn   80 (110)
T PF07576_consen   11 RRSTLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGT--PNRYMVLIKFRDQESADEFYEEFNGKPFN   80 (110)
T ss_pred             CCceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCC--CceEEEEEEECCHHHHHHHHHHhCCCccC
Confidence            3444555655666677777877766654 467888888753  34557999999999999999999998874

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=95.23  E-value=0.1  Score=37.97  Aligned_cols=57  Identities=14%  Similarity=0.217  Sum_probs=41.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCC
Q 013141          207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNG  273 (449)
Q Consensus       207 ~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g  273 (449)
                      .....+|+ +|..+...||.++|+ .||.|.-..|- |       ..|||...+.+.|..++..+..
T Consensus         8 RdHVFhlt-FPkeWK~~DI~qlFs-pfG~I~VsWi~-d-------TSAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen    8 RDHVFHLT-FPKEWKTSDIYQLFS-PFGQIYVSWIN-D-------TSAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             GCCEEEEE---TT--HHHHHHHCC-CCCCEEEEEEC-T-------TEEEEEECCCHHHHHHHHHHTT
T ss_pred             cceEEEEe-CchHhhhhhHHHHhc-cCCcEEEEEEc-C-------CcEEEEeecHHHHHHHHHHhcc
Confidence            34556665 999999999999996 99987655543 2       2799999999999999987763

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=94.85  E-value=0.011  Score=54.44  Aligned_cols=73  Identities=21%  Similarity=0.387  Sum_probs=59.6

Q ss_pred             cEEEEcCCCCCCCHhHHH---hhccccCceEEEEEeCCC---------cEEEEEecCHHHHHHHHHHhcCCeeCCeEEEE
Q 013141          328 ATIFVGALDSDVSDEDLR---EPFSQFGEILSVKIPVGK---------GCGFVQFANRKDAEVALQKLQGTAIGKQTVRL  395 (449)
Q Consensus       328 ~~l~V~nlp~~~t~~~L~---~~f~~~G~v~~v~i~~~~---------g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v  395 (449)
                      ..+||-+|+..+..+.+.   +.|.+||.|.+|.+.++.         ..++|+|...++|..||...+|..++|+.|+.
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            457888888876555554   578999999999887632         35899999999999999999999999999888


Q ss_pred             EecCC
Q 013141          396 SWGRN  400 (449)
Q Consensus       396 ~~~~~  400 (449)
                      .+...
T Consensus       158 ~~gtt  162 (327)
T KOG2068|consen  158 SLGTT  162 (327)
T ss_pred             hhCCC
Confidence            87663

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=94.82  E-value=0.014  Score=59.87  Aligned_cols=74  Identities=19%  Similarity=0.241  Sum_probs=64.2

Q ss_pred             EEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCee--CCeEEEEEecCCCCC
Q 013141          330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAI--GKQTVRLSWGRNPGN  403 (449)
Q Consensus       330 l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~--~g~~l~v~~~~~~~~  403 (449)
                      ..+.|.+-..+-..|-.+|++||.|.+++.+++-..|.|+|.+.+.|..|+++|+|+++  -|...+|.|++.-..
T Consensus       301 ~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~~~~  376 (1007)
T KOG4574|consen  301 QSLENNAVNLTSSSLATLCSDYGSVASAWTLRDLNMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKTLPM  376 (1007)
T ss_pred             hhhhcccccchHHHHHHHHHhhcchhhheecccccchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEecccccc
Confidence            34555566667788999999999999999999999999999999999999999999985  488899999997543

>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes

Probab=94.81  E-value=0.12  Score=36.14  Aligned_cols=55  Identities=18%  Similarity=0.291  Sum_probs=45.6

Q ss_pred             CCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEE
Q 013141          338 DVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRL  395 (449)
Q Consensus       338 ~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v  395 (449)
                      .++-++|+..++.|+-   .+|..++.--||.|.|.++|+++....+++.+...+|.+
T Consensus        11 ~~~v~d~K~~Lr~y~~---~~I~~d~tGfYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRW---DRIRDDRTGFYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCCc---ceEEecCCEEEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            4678999999999953   334455666799999999999999999999998888765

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=94.79  E-value=0.059  Score=52.87  Aligned_cols=61  Identities=11%  Similarity=0.186  Sum_probs=51.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhc--cCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcC
Q 013141          112 NDETKTIWIGDLFHWMDETFLHNCFSH--TGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSG  179 (449)
Q Consensus       112 ~~~~~~l~v~nLp~~~t~~~l~~~f~~--~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~  179 (449)
                      ....|.|+||.||..+..|+|+.+|+.  |-.+.+|.+-.+..       =||+|++..+|..|.+.|..
T Consensus       172 ~~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~n-------WyITfesd~DAQqAykylre  234 (684)
T KOG2591|consen  172 NHKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHNDN-------WYITFESDTDAQQAYKYLRE  234 (684)
T ss_pred             CcceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecCc-------eEEEeecchhHHHHHHHHHH
Confidence            345567999999999999999999975  66788998877643       69999999999999987655

>PF10567 Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IPR018885 This conserved domain is found in fungal proteins and appears to be involved in RNA-processing

Probab=94.13  E-value=1.3  Score=40.54  Aligned_cols=173  Identities=9%  Similarity=0.060  Sum_probs=102.9

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCC-------CCCcceEEEEEeCCHHHHHHHHH----HhCC
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSN-------TGRTKGYGFVRFGDENERSRAMT----EMNG  273 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~-------~~~~~g~afV~f~~~~~A~~A~~----~l~g  273 (449)
                      ....+.|.+.|+..+++-..+.+.|- +||.|++|.++.+..       .........+-|-+.+.|-....    .|..
T Consensus        12 ~YrTRSLLfeNv~~sidLh~Fl~~fv-~~~pIESiYL~~~~~~~~d~~~~d~~~~SilLSFlsr~~CLdFYNnvLQrLsE   90 (309)
T PF10567_consen   12 EYRTRSLLFENVNNSIDLHSFLTKFV-KFGPIESIYLIKSNDKPSDDYNDDKNNQSILLSFLSREICLDFYNNVLQRLSE   90 (309)
T ss_pred             cceeHHHHHhhccccccHHHHHHHhh-ccCceeEEEEecCCCcccccccccccceEEEEeeechHHHHHHHHHHHHHHHH
Confidence            34456788999999999888888884 999999999997751       12234568899999998876543    2322


Q ss_pred             --ceecCcceEEeecCCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHh---hc
Q 013141          274 --VYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLRE---PF  348 (449)
Q Consensus       274 --~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~---~f  348 (449)
                        ..+....+.+.+..-+............  +.    .................++.|.|.--.....++-|.+   ++
T Consensus        91 fK~~L~S~~L~lsFV~l~y~~~~~~~~~~~--~~----~~~~~~~L~~~i~~~gATRSl~IeF~~~~~~~dl~~~kL~fL  164 (309)
T PF10567_consen   91 FKTKLKSESLTLSFVSLNYQKKTDPNDEEA--DF----SDYLVASLQYNIINRGATRSLAIEFKDPVDKDDLIEKKLPFL  164 (309)
T ss_pred             HHHhcCCcceeEEEEEEecccccccccccc--ch----hhHHhhhhhheeecCCcceEEEEEecCccchhHHHHHhhhhh
Confidence              3356777777776542221110000000  00    0000000111122334567777765533333333333   22


Q ss_pred             cccC----ceEEEEEeC--------CCcEEEEEecCHHHHHHHHHHhc
Q 013141          349 SQFG----EILSVKIPV--------GKGCGFVQFANRKDAEVALQKLQ  384 (449)
Q Consensus       349 ~~~G----~v~~v~i~~--------~~g~afV~F~~~~~A~~A~~~l~  384 (449)
                      ..-+    .|++|.++.        ++.+|.++|-+..-|...+.-|.
T Consensus       165 ~~~~n~RYVlEsIDlVna~~~~~~Fp~~YaILtFlnIsMAiEV~dYlk  212 (309)
T PF10567_consen  165 KNSNNKRYVLESIDLVNADEPSKHFPKNYAILTFLNISMAIEVLDYLK  212 (309)
T ss_pred             ccCCCceEEEEEEEEeccCcccccCCcceEEEeehhHHhHHHHHHHHH
Confidence            2222    477788874        36899999999999999888875

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.

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=93.91  E-value=0.096  Score=45.05  Aligned_cols=71  Identities=13%  Similarity=0.185  Sum_probs=45.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhh-CCCe---eEEEEeecCCC--CCcceEEEEEeCCHHHHHHHHHHhCCceecC
Q 013141          207 SDLSIFVGDLAPDVTDSILQETFSSK-YPSV---KGAKVIIDSNT--GRTKGYGFVRFGDENERSRAMTEMNGVYCSS  278 (449)
Q Consensus       207 ~~~~l~v~~lp~~~t~~~l~~~f~~~-~g~v---~~i~~~~~~~~--~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g  278 (449)
                      ...+|.|+.||+++|++++.+.++ . +++.   ..+.-......  .....-|+|.|.+.+++...+..++|..|.+
T Consensus         6 ~~~KvVIR~LPP~LteeeF~~~i~-~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D   82 (176)
T PF03467_consen    6 EGTKVVIRRLPPNLTEEEFWEQIS-PWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVD   82 (176)
T ss_dssp             ---EEEEEEE-TTS-HHHHCCCCS-S--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-
T ss_pred             cCceEEEeCCCCCCCHHHHHHHhh-hhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEEC
Confidence            456899999999999999999774 4 5555   23331122111  1123469999999999999999999988743

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=93.90  E-value=0.036  Score=57.07  Aligned_cols=75  Identities=20%  Similarity=0.199  Sum_probs=65.0

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccccccc
Q 013141          117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATF  196 (449)
Q Consensus       117 ~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~~~~  196 (449)
                      +.++.|.+-..+-.-|..+|..||.|.+.+.+++-+      .|.|+|.+.+.|..|++.++|+.+...+.+.+|.+++.
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            345555566778888999999999999999999865      79999999999999999999999888888999988874


Q ss_pred             C
Q 013141          197 S  197 (449)
Q Consensus       197 ~  197 (449)
                      .
T Consensus       374 ~  374 (1007)
T KOG4574|consen  374 L  374 (1007)
T ss_pred             c
Confidence            4

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=93.87  E-value=0.3  Score=39.40  Aligned_cols=73  Identities=18%  Similarity=0.195  Sum_probs=52.4

Q ss_pred             CCCCceEEEcCCCCCCC-HHH---HHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCC
Q 013141          112 NDETKTIWIGDLFHWMD-ETF---LHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQ  187 (449)
Q Consensus       112 ~~~~~~l~v~nLp~~~t-~~~---l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~  187 (449)
                      +.+-.+|.|+=|..++. .+|   |...++.||+|.+|.+.-..       .|.|.|.|..+|.+|+.++.....   +.
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cGrq-------savVvF~d~~SAC~Av~Af~s~~p---gt  152 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCGRQ-------SAVVVFKDITSACKAVSAFQSRAP---GT  152 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecCCc-------eEEEEehhhHHHHHHHHhhcCCCC---Cc
Confidence            45667899988776554 334   45566889999999875432       599999999999999999877433   23


Q ss_pred             ccccccc
Q 013141          188 PFRLNWA  194 (449)
Q Consensus       188 ~~~~~~~  194 (449)
                      -+.+.|.
T Consensus       153 m~qCsWq  159 (166)
T PF15023_consen  153 MFQCSWQ  159 (166)
T ss_pred             eEEeecc
Confidence            4455554

>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=93.84  E-value=1.2  Score=40.56  Aligned_cols=160  Identities=10%  Similarity=0.168  Sum_probs=97.0

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecC-------CCCCcccEEEEEEccHHHHHHHHH----HhcC
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNK-------QTGQSEGYGFVEFYSRAAAEKVLQ----SYSG  179 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~-------~~g~~~g~afV~f~~~~~A~~Al~----~l~~  179 (449)
                      +...+|.|...|+..+++-.++...|-.||+|++|.++.+.       ...+......+-|-+.+.+-....    .|..
T Consensus        11 D~YrTRSLLfeNv~~sidLh~Fl~~fv~~~pIESiYL~~~~~~~~d~~~~d~~~~SilLSFlsr~~CLdFYNnvLQrLsE   90 (309)
T PF10567_consen   11 DEYRTRSLLFENVNNSIDLHSFLTKFVKFGPIESIYLIKSNDKPSDDYNDDKNNQSILLSFLSREICLDFYNNVLQRLSE   90 (309)
T ss_pred             ccceeHHHHHhhccccccHHHHHHHhhccCceeEEEEecCCCcccccccccccceEEEEeeechHHHHHHHHHHHHHHHH
Confidence            44578899999999999999999999999999999999986       112234578899999988766552    2221


Q ss_pred             CCCCCCCCccccccccc-----C--CCCCc--------------cccCCCceEEEcCCCCCCCHHHHH-H---HHhhhCC
Q 013141          180 SLMPNTDQPFRLNWATF-----S--GSDRR--------------TEACSDLSIFVGDLAPDVTDSILQ-E---TFSSKYP  234 (449)
Q Consensus       180 ~~~~~~~~~~~~~~~~~-----~--~~~~~--------------~~~~~~~~l~v~~lp~~~t~~~l~-~---~f~~~~g  234 (449)
                      ..-.-+...+.+.+..-     .  ..+..              ......+.|.|. +...++++++. +   ++ ..-+
T Consensus        91 fK~~L~S~~L~lsFV~l~y~~~~~~~~~~~~~~~~~~~~L~~~i~~~gATRSl~Ie-F~~~~~~~dl~~~kL~fL-~~~~  168 (309)
T PF10567_consen   91 FKTKLKSESLTLSFVSLNYQKKTDPNDEEADFSDYLVASLQYNIINRGATRSLAIE-FKDPVDKDDLIEKKLPFL-KNSN  168 (309)
T ss_pred             HHHhcCCcceeEEEEEEeccccccccccccchhhHHhhhhhheeecCCcceEEEEE-ecCccchhHHHHHhhhhh-ccCC
Confidence            11111222233322221     0  00000              122344566664 33445444332 2   23 1222


Q ss_pred             C----eeEEEEeecC--CCCCcceEEEEEeCCHHHHHHHHHHhC
Q 013141          235 S----VKGAKVIIDS--NTGRTKGYGFVRFGDENERSRAMTEMN  272 (449)
Q Consensus       235 ~----v~~i~~~~~~--~~~~~~g~afV~f~~~~~A~~A~~~l~  272 (449)
                      .    +++|.++...  ....++.||.++|-+..-|.+.++-+.
T Consensus       169 n~RYVlEsIDlVna~~~~~~Fp~~YaILtFlnIsMAiEV~dYlk  212 (309)
T PF10567_consen  169 NKRYVLESIDLVNADEPSKHFPKNYAILTFLNISMAIEVLDYLK  212 (309)
T ss_pred             CceEEEEEEEEeccCcccccCCcceEEEeehhHHhHHHHHHHHH
Confidence            2    5666666442  234467899999999999999987665

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=93.60  E-value=0.11  Score=38.74  Aligned_cols=73  Identities=18%  Similarity=0.249  Sum_probs=47.3

Q ss_pred             EEEEeCCHHHHHHHHHHhC-CceecCcceEEeecCCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEE
Q 013141          254 GFVRFGDENERSRAMTEMN-GVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFV  332 (449)
Q Consensus       254 afV~f~~~~~A~~A~~~l~-g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V  332 (449)
                      |+|+|.++.-|.+.++.-. ...+++..+.|..........                       ...........++|.|
T Consensus         1 AlITF~e~~VA~~i~~~~~~~v~l~~~~~~V~v~P~~~~~~-----------------------~k~qv~~~vs~rtVlv   57 (88)
T PF07292_consen    1 ALITFEEEGVAQRILKKKKHPVPLEDCCVRVKVSPVTLGHL-----------------------QKFQVFSGVSKRTVLV   57 (88)
T ss_pred             CEEEeCcHHHHHHHHhCCEEEEEECCEEEEEEEEeEecCCc-----------------------eEEEEEEcccCCEEEE
Confidence            6899999999999985322 233466666665443222110                       0001223445788999


Q ss_pred             cCCCCCCCHhHHHhhcc
Q 013141          333 GALDSDVSDEDLREPFS  349 (449)
Q Consensus       333 ~nlp~~~t~~~L~~~f~  349 (449)
                      .|||...++|+|++.++
T Consensus        58 sgip~~l~ee~l~D~Le   74 (88)
T PF07292_consen   58 SGIPDVLDEEELRDKLE   74 (88)
T ss_pred             eCCCCCCChhhheeeEE
Confidence            99999999999998764

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]

Probab=93.52  E-value=0.11  Score=54.31  Aligned_cols=33  Identities=30%  Similarity=0.516  Sum_probs=22.1

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCccccccCCCCC
Q 013141          416 GAHYGGQGYSGNGYAFPPNQDPNMYAATAVPGA  448 (449)
Q Consensus       416 g~~~g~~g~~g~g~~~~~~~~~~~~~~~~~~g~  448 (449)
                      |++|+++|+|++|||+-.+.....||++...|+
T Consensus      1195 Gggys~gGygsGGYGgsa~~~~~~~Gagvg~Gy 1227 (1282)
T KOG0921|consen 1195 GGGYSGGGYGSGGYGGSAPSARANYGAGVGNGY 1227 (1282)
T ss_pred             CCCCCCCCcCCCCCCCCCCCCCCCccccccCCC
Confidence            445666777788888776666556776655554

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=93.19  E-value=0.039  Score=51.04  Aligned_cols=82  Identities=17%  Similarity=0.332  Sum_probs=63.0

Q ss_pred             CceEEEcCCCCCCCHHHHH---HHHhhhCCCeeEEEEeecCC--CC-CcceEEEEEeCCHHHHHHHHHHhCCceecCcce
Q 013141          208 DLSIFVGDLAPDVTDSILQ---ETFSSKYPSVKGAKVIIDSN--TG-RTKGYGFVRFGDENERSRAMTEMNGVYCSSRPM  281 (449)
Q Consensus       208 ~~~l~v~~lp~~~t~~~l~---~~f~~~~g~v~~i~~~~~~~--~~-~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i  281 (449)
                      .+-+||-+|+..+..+++.   +.|+ .||.|..|.+.++..  .+ .....++|+|..+++|..||...+|...+++.+
T Consensus        77 knlvyvvgl~~~~ade~~l~~~eyfg-qygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~l  155 (327)
T KOG2068|consen   77 KNLVYVVGLPLDLADESVLERTEYFG-QYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRAL  155 (327)
T ss_pred             hhhhhhhCCCccccchhhhhCccccc-ccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhh
Confidence            3567888888877655554   5785 889999998887752  11 112338999999999999999999999999998


Q ss_pred             EEeecCCCC
Q 013141          282 RIDVATPKK  290 (449)
Q Consensus       282 ~v~~~~~~~  290 (449)
                      +..+.+.+.
T Consensus       156 ka~~gttky  164 (327)
T KOG2068|consen  156 KASLGTTKY  164 (327)
T ss_pred             HHhhCCCcc
Confidence            888777654

>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=92.90  E-value=0.083  Score=39.31  Aligned_cols=69  Identities=13%  Similarity=0.257  Sum_probs=43.9

Q ss_pred             EEEEEccHHHHHHHHHHhcCCCCCCCCCcccccccccCCCCCc----cccCCCceEEEcCCCCCCCHHHHHHHH
Q 013141          160 GFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATFSGSDRR----TEACSDLSIFVGDLAPDVTDSILQETF  229 (449)
Q Consensus       160 afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~l~v~~lp~~~t~~~l~~~f  229 (449)
                      |+|+|.++.-|++.++. ....+......+++...........    ....+.++|.|.|||..+++++|++.+
T Consensus         1 AlITF~e~~VA~~i~~~-~~~~v~l~~~~~~V~v~P~~~~~~~k~qv~~~vs~rtVlvsgip~~l~ee~l~D~L   73 (88)
T PF07292_consen    1 ALITFEEEGVAQRILKK-KKHPVPLEDCCVRVKVSPVTLGHLQKFQVFSGVSKRTVLVSGIPDVLDEEELRDKL   73 (88)
T ss_pred             CEEEeCcHHHHHHHHhC-CEEEEEECCEEEEEEEEeEecCCceEEEEEEcccCCEEEEeCCCCCCChhhheeeE
Confidence            68999999999999954 3333222223333322221111111    344667899999999999999998776

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=92.26  E-value=0.6  Score=45.00  Aligned_cols=68  Identities=13%  Similarity=0.250  Sum_probs=58.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccC-CcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCC
Q 013141          114 ETKTIWIGDLFHWMDETFLHNCFSHTG-QVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMP  183 (449)
Q Consensus       114 ~~~~l~v~nLp~~~t~~~l~~~f~~~G-~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~  183 (449)
                      .++.|.|-.+|..+|-.||..|+..+- .|.++++++|...  .+=.++|+|.+.++|....+.+||+.+.
T Consensus        73 ~~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~p--nrymvLIkFr~q~da~~Fy~efNGk~Fn  141 (493)
T KOG0804|consen   73 SSTMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMP--NRYMVLIKFRDQADADTFYEEFNGKQFN  141 (493)
T ss_pred             CCcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCC--ceEEEEEEeccchhHHHHHHHcCCCcCC
Confidence            388999999999999999999998765 5889999997542  3346899999999999999999998874

>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=90.80  E-value=0.27  Score=35.59  Aligned_cols=59  Identities=22%  Similarity=0.330  Sum_probs=35.7

Q ss_pred             CCCCHhHHHhhccccC-----ceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 013141          337 SDVSDEDLREPFSQFG-----EILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWG  398 (449)
Q Consensus       337 ~~~t~~~L~~~f~~~G-----~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~  398 (449)
                      ..++..+|..++...+     .|-.|+|.  ..++||+-.. +.|..+++.|++..+.|+.|+|+.+
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 DGLTPRDIVGAICNEAGIPGRDIGRIDIF--DNFSFVEVPE-EVAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             GT--HHHHHHHHHTCTTB-GGGEEEEEE---SS-EEEEE-T-T-HHHHHHHHTT--SSS----EEE-
T ss_pred             cCCCHHHHHHHHHhccCCCHHhEEEEEEe--eeEEEEEECH-HHHHHHHHHhcCCCCCCeeEEEEEC
Confidence            3577788888876653     45667776  5688998864 5889999999999999999999864

; PDB: 2G0C_A 3MOJ_B.

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=90.27  E-value=1  Score=47.27  Aligned_cols=60  Identities=13%  Similarity=0.169  Sum_probs=46.3

Q ss_pred             CCCCHhHHHhhccccCceE-----EEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 013141          337 SDVSDEDLREPFSQFGEIL-----SVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGR  399 (449)
Q Consensus       337 ~~~t~~~L~~~f~~~G~v~-----~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  399 (449)
                      ..++..+|..++..-+.|.     .|+|.  ..+.||+.. .+.|...+..|++..+.|+.|.|+.++
T Consensus       497 ~~~~~~~~~~~i~~~~~~~~~~ig~i~i~--~~~s~v~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~  561 (629)
T PRK11634        497 DGVEVRHIVGAIANEGDISSRYIGNIKLF--ASHSTIELP-KGMPGEVLQHFTRTRILNKPMNMQLLG  561 (629)
T ss_pred             cCCCHHHHHHHHHhhcCCChhhCCcEEEe--CCceEEEcC-hhhHHHHHHHhccccccCCceEEEECC
Confidence            4577788887776655443     35555  468899986 467889999999999999999999875

>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=90.05  E-value=0.87  Score=39.35  Aligned_cols=63  Identities=19%  Similarity=0.192  Sum_probs=45.8

Q ss_pred             CHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC--CceecCcceEEeecCCCC
Q 013141          221 TDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMN--GVYCSSRPMRIDVATPKK  290 (449)
Q Consensus       221 t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~--g~~~~g~~i~v~~~~~~~  290 (449)
                      ..+.|+++|. .++.+..+..++.      -+-..|.|.+.++|.+|...|+  +..+.|..+++.++....
T Consensus         8 ~~~~l~~l~~-~~~~~~~~~~L~s------FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~~   72 (184)
T PF04847_consen    8 NLAELEELFS-TYDPPVQFSPLKS------FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPTP   72 (184)
T ss_dssp             -HHHHHHHHH-TT-SS-EEEEETT------TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----SS
T ss_pred             hHHHHHHHHH-hcCCceEEEEcCC------CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccccc
Confidence            4578999995 9999888877754      2357899999999999999999  899999999999985543

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.

>TIGR02542 B_forsyth_147 Bacteroides forsythus 147-residue repeat

Probab=88.49  E-value=1.1  Score=34.58  Aligned_cols=118  Identities=18%  Similarity=0.164  Sum_probs=60.5

Q ss_pred             CCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccccccccCCCCC
Q 013141          122 DLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATFSGSDR  201 (449)
Q Consensus       122 nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~~~~~~~~~  201 (449)
                      -||+.++  .|-++|+.-|.|.+|..+..-.+                 ..|+-.++|..-.. +-.+++..........
T Consensus        10 VlPPYTn--KLSDYfeSPGKI~svItvtqypd-----------------ndal~~~~G~lE~v-Dg~i~IGs~q~~~sV~   69 (145)
T TIGR02542        10 VLPPYTN--KLSDYFESPGKIQSVITVTQYPD-----------------NDALLYVHGTLEQV-DGNIRIGSGQTPASVR   69 (145)
T ss_pred             ecCCccc--hhhHHhcCCCceEEEEEEeccCC-----------------chhhheeeeehhhc-cCcEEEccCCCcccEE
Confidence            3777664  49999999999998876553211                 12232334432211 1123333222111111


Q ss_pred             ccccCCCceEEEcCCCCCCCHHHHHHHHhhh--CCCeeEEEEeecCCCCCcceEEEEEeCCH
Q 013141          202 RTEACSDLSIFVGDLAPDVTDSILQETFSSK--YPSVKGAKVIIDSNTGRTKGYGFVRFGDE  261 (449)
Q Consensus       202 ~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~--~g~v~~i~~~~~~~~~~~~g~afV~f~~~  261 (449)
                      -......+.+  .--|..+|..+++++|+|.  |-.|.+-.+.+|.-..-+-..||..|...
T Consensus        70 i~gTPsgnnv--~F~PYTlT~~e~r~iF~Epm~YQGITReQV~rdGLP~GsYRiCFrL~~~~  129 (145)
T TIGR02542        70 IQGTPSGNNV--IFPPYTLTYNELRQIFREPMVYQGITREQVQRDGLPEGSYRICFRLFNAT  129 (145)
T ss_pred             EecCCCCCce--ecCceeeeHHHHHHHHhhhhhhccccHHHHhhcCCCCCceEEEEEEeccc
Confidence            1111111222  2246788999999999753  33344444455532222345688888765

The longest predicted protein in Bacteroides forsythus ATCC 43037 is over 3000 residues long and lacks homology to other known proteins. Immediately after the signal sequence are four tandem repeats, approximately 147 residues long. This model describes that repeat. This model describes that repeat.

>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=88.04  E-value=2.4  Score=30.59  Aligned_cols=59  Identities=14%  Similarity=0.289  Sum_probs=34.7

Q ss_pred             CCCCHHHHHHHHhhhCCC-----eeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeec
Q 013141          218 PDVTDSILQETFSSKYPS-----VKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVA  286 (449)
Q Consensus       218 ~~~t~~~l~~~f~~~~g~-----v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~  286 (449)
                      ..++..+|..++. ..+.     |-.|.+..+        |+||+-... .|..+++.|++..+.|+.++|+.+
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 DGLTPRDIVGAIC-NEAGIPGRDIGRIDIFDN--------FSFVEVPEE-VAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             GT--HHHHHHHHH-TCTTB-GGGEEEEEE-SS---------EEEEE-TT--HHHHHHHHTT--SSS----EEE-
T ss_pred             cCCCHHHHHHHHH-hccCCCHHhEEEEEEeee--------EEEEEECHH-HHHHHHHHhcCCCCCCeeEEEEEC
Confidence            3578889999886 4433     445666533        789987764 788999999999999999999864

; PDB: 2G0C_A 3MOJ_B.

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=87.71  E-value=0.34  Score=46.88  Aligned_cols=70  Identities=17%  Similarity=0.199  Sum_probs=55.6

Q ss_pred             EcCCCCCC-CHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecCCCC
Q 013141          213 VGDLAPDV-TDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKK  290 (449)
Q Consensus       213 v~~lp~~~-t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~~~~  290 (449)
                      +.-.++.+ +.++|...|. .||+|..|.+-...      -.|.|+|.+..+|-+|. ..++-.|+++.|+|.|..+..
T Consensus       377 lek~~~glnt~a~ln~hfA-~fG~i~n~qv~~~~------~~a~vTF~t~aeag~a~-~s~~avlnnr~iKl~whnps~  447 (526)
T KOG2135|consen  377 LEKSPFGLNTIADLNPHFA-QFGEIENIQVDYSS------LHAVVTFKTRAEAGEAY-ASHGAVLNNRFIKLFWHNPSP  447 (526)
T ss_pred             hhccCCCCchHhhhhhhhh-hcCccccccccCch------hhheeeeeccccccchh-ccccceecCceeEEEEecCCc
Confidence            33344433 5678999996 99999999886542      25899999999997776 588899999999999998854

>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=87.58  E-value=4  Score=28.64  Aligned_cols=55  Identities=22%  Similarity=0.416  Sum_probs=41.7

Q ss_pred             CCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEE
Q 013141          219 DVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRI  283 (449)
Q Consensus       219 ~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  283 (449)
                      .++.++++..|. .|.- .  +++.++     .|| ||.|.+..+|+++....++..+....+.+
T Consensus        11 ~~~v~d~K~~Lr-~y~~-~--~I~~d~-----tGf-YIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLR-KYRW-D--RIRDDR-----TGF-YIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHh-cCCc-c--eEEecC-----CEE-EEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            467889999995 8862 3  333332     344 89999999999999999999887766654

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG2318 consensus Uncharacterized conserved protein [Function unknown]

Probab=87.49  E-value=2.6  Score=42.18  Aligned_cols=76  Identities=25%  Similarity=0.290  Sum_probs=61.4

Q ss_pred             CCCCCcEEEEcCCCCC-CCHhHHHhhcccc----CceEEEEEeCC--------------C--------------------
Q 013141          323 GESNNATIFVGALDSD-VSDEDLREPFSQF----GEILSVKIPVG--------------K--------------------  363 (449)
Q Consensus       323 ~~~~~~~l~V~nlp~~-~t~~~L~~~f~~~----G~v~~v~i~~~--------------~--------------------  363 (449)
                      ....+++|-|-||.++ +...||.-+|+.|    |.|.+|.|..+              .                    
T Consensus       170 ~~~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeFGkeRM~eEeV~GP~~el~~~~e~~~~s~sD~ee  249 (650)
T KOG2318|consen  170 LGEETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEFGKERMKEEEVHGPPKELFKPVEEYKESESDDEE  249 (650)
T ss_pred             cccccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhhhHHHhhhhcccCChhhhccccccCcccccchhh
Confidence            3566789999999997 7889999888766    68999988631              0                    


Q ss_pred             -------------------cEEEEEecCHHHHHHHHHHhcCCeeCC--eEEEEEec
Q 013141          364 -------------------GCGFVQFANRKDAEVALQKLQGTAIGK--QTVRLSWG  398 (449)
Q Consensus       364 -------------------g~afV~F~~~~~A~~A~~~l~g~~~~g--~~l~v~~~  398 (449)
                                         =+|.|+|.+.+.|....+..+|..|..  ..|-++|-
T Consensus       250 ~~~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~DLRFI  305 (650)
T KOG2318|consen  250 EEDVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSANKLDLRFI  305 (650)
T ss_pred             hhhHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccceeeeeec
Confidence                               268899999999999999999999984  55555553

>KOG2318 consensus Uncharacterized conserved protein [Function unknown]

Probab=87.21  E-value=5.4  Score=40.00  Aligned_cols=128  Identities=14%  Similarity=0.161  Sum_probs=72.8

Q ss_pred             CCCCceEEEcCCCC-CCCHHHHHHHhhcc----CCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCC
Q 013141          112 NDETKTIWIGDLFH-WMDETFLHNCFSHT----GQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTD  186 (449)
Q Consensus       112 ~~~~~~l~v~nLp~-~~t~~~l~~~f~~~----G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~  186 (449)
                      ...+++|-|-||-| .+..+||.-+|+.|    |.|.+|.|.+...            .-.   ..+-+..+|..+... 
T Consensus       171 ~~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeF------------Gke---RM~eEeV~GP~~el~-  234 (650)
T KOG2318|consen  171 GEETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEF------------GKE---RMKEEEVHGPPKELF-  234 (650)
T ss_pred             ccccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhh------------hHH---HhhhhcccCChhhhc-
Confidence            56788999999998 67889999998876    4788998877632            111   112222233322110 


Q ss_pred             CcccccccccCCCCCccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHH
Q 013141          187 QPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSR  266 (449)
Q Consensus       187 ~~~~~~~~~~~~~~~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~  266 (449)
                        -.+...            +...     .....-++-.++.++ .|+ +..++.          -||.|+|.+.+.|..
T Consensus       235 --~~~e~~------------~~s~-----sD~ee~~~~~~~kLR-~Yq-~~rLkY----------YyAVvecDsi~tA~~  283 (650)
T KOG2318|consen  235 --KPVEEY------------KESE-----SDDEEEEDVDREKLR-QYQ-LNRLKY----------YYAVVECDSIETAKA  283 (650)
T ss_pred             --cccccC------------cccc-----cchhhhhhHHHHHHH-HHH-hhhhee----------EEEEEEecCchHHHH
Confidence              000000            0000     011111112234443 333 122211          279999999999999


Q ss_pred             HHHHhCCceecCcceEEeec
Q 013141          267 AMTEMNGVYCSSRPMRIDVA  286 (449)
Q Consensus       267 A~~~l~g~~~~g~~i~v~~~  286 (449)
                      ..+.|+|..+......+...
T Consensus       284 vYe~CDG~EfEsS~~~~DLR  303 (650)
T KOG2318|consen  284 VYEECDGIEFESSANKLDLR  303 (650)
T ss_pred             HHHhcCcceeccccceeeee
Confidence            99999999996655554443

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=86.96  E-value=0.54  Score=47.55  Aligned_cols=74  Identities=23%  Similarity=0.180  Sum_probs=64.8

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 013141          321 SDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSW  397 (449)
Q Consensus       321 ~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  397 (449)
                      ....+...++||+|+-..+..+-++.++..+|.|.++....   |+|+.|.....+.+|+..|+-..++|..+.+.-
T Consensus        34 ~~~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~~  107 (668)
T KOG2253|consen   34 FQPLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---FGFCEFLKHIGDLRASRLLTELNIDDQKLIENV  107 (668)
T ss_pred             ccCCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---hcccchhhHHHHHHHHHHhcccCCCcchhhccc
Confidence            34556778999999999999999999999999988877664   999999999999999999999999888877654

>KOG4019 consensus Calcineurin-mediated signaling pathway inhibitor DSCR1 [Signal transduction mechanisms; General function prediction only]

Probab=86.51  E-value=0.67  Score=39.08  Aligned_cols=75  Identities=17%  Similarity=0.187  Sum_probs=58.0

Q ss_pred             CCcEEEEcCCCCCCC-----HhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCe-EEEEEecC
Q 013141          326 NNATIFVGALDSDVS-----DEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQ-TVRLSWGR  399 (449)
Q Consensus       326 ~~~~l~V~nlp~~~t-----~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~-~l~v~~~~  399 (449)
                      -...+.+-+++..+-     .....++|..|-+..-..++++.+...|.|.+.+.|..|...++.+.|.|+ .++.-|+.
T Consensus         9 lp~~~~~c~i~~~VF~~~~~k~~~~~lFrq~n~~~~fq~lrsfrrvRi~f~~p~~a~~a~i~~~~~~f~~~~~~k~yfaQ   88 (193)
T KOG4019|consen    9 LPTAIIACDIHEEVFVNREDKALFENLFRQINEDATFQLLRSFRRVRINFSNPEAAADARIKLHSTSFNGKNELKLYFAQ   88 (193)
T ss_pred             ccceeeeecccHHhhccHHHHHHHHhHHhhhCcchHHHHHHhhceeEEeccChhHHHHHHHHhhhcccCCCceEEEEEcc
Confidence            345566777766542     234456777777776677778888999999999999999999999999998 78777776


Q ss_pred             C
Q 013141          400 N  400 (449)
Q Consensus       400 ~  400 (449)
                      .
T Consensus        89 ~   89 (193)
T KOG4019|consen   89 P   89 (193)
T ss_pred             C
Confidence            5

>KOG4274 consensus Positive cofactor 2 (PC2), subunit of a multiprotein coactivator of RNA polymerase II [Transcription]

Probab=86.16  E-value=0.85  Score=45.24  Aligned_cols=17  Identities=24%  Similarity=0.153  Sum_probs=10.2

Q ss_pred             HHHHHHhhhCCCCCCCC
Q 013141           11 AAAAAAAAVSGGAGGGS   27 (449)
Q Consensus        11 ~~~~~~~~~~~~~~~~~   27 (449)
                      .+|+.++||..-+.++-
T Consensus       131 gtA~~~~av~s~~~P~t  147 (742)
T KOG4274|consen  131 GTAPHSMAVVSTATPQT  147 (742)
T ss_pred             ccchhHHHHhccCCCCc
Confidence            45556666666666663

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=84.89  E-value=3.4  Score=37.88  Aligned_cols=74  Identities=19%  Similarity=0.246  Sum_probs=53.5

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcc-eEEeec
Q 013141          208 DLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRP-MRIDVA  286 (449)
Q Consensus       208 ~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~-i~v~~~  286 (449)
                      +.=|-|.++++.- ..-|..+|. ++|+|.+.....+      -.+-.|.|.+..+|.+|| ..+|+.|++.. |-|+..
T Consensus       197 D~WVTVfGFppg~-~s~vL~~F~-~cG~Vvkhv~~~n------gNwMhirYssr~~A~KAL-skng~ii~g~vmiGVkpC  267 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQ-VSIVLNLFS-RCGEVVKHVTPSN------GNWMHIRYSSRTHAQKAL-SKNGTIIDGDVMIGVKPC  267 (350)
T ss_pred             cceEEEeccCccc-hhHHHHHHH-hhCeeeeeecCCC------CceEEEEecchhHHHHhh-hhcCeeeccceEEeeeec
Confidence            3456777888854 446777884 9999888765422      347899999999999999 57888887654 446655


Q ss_pred             CCCC
Q 013141          287 TPKK  290 (449)
Q Consensus       287 ~~~~  290 (449)
                      .++.
T Consensus       268 tDks  271 (350)
T KOG4285|consen  268 TDKS  271 (350)
T ss_pred             CCHH
Confidence            5543

>PF14111 DUF4283: Domain of unknown function (DUF4283)

Probab=81.15  E-value=1.1  Score=37.41  Aligned_cols=111  Identities=16%  Similarity=0.121  Sum_probs=75.1

Q ss_pred             CCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecCCCCCCchhhcc
Q 013141          219 DVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKASGYQQQY  298 (449)
Q Consensus       219 ~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~~~~~~~~~~~~  298 (449)
                      ..+...|.+.+...++....+.+..-     ..++..+.|.+++++.++++ .....+.+..+.+...++.....     
T Consensus        28 ~~~~~~l~~~l~~~W~~~~~~~i~~l-----~~~~fl~~F~~~~d~~~vl~-~~p~~~~~~~~~l~~W~~~~~~~-----   96 (153)
T PF14111_consen   28 PISLSALEQELAKIWKLKGGVKIRDL-----GDNLFLFQFESEEDRQRVLK-GGPWNFNGHFLILQRWSPDFNPS-----   96 (153)
T ss_pred             CCCHHHHHHHHHHHhCCCCcEEEEEe-----CCCeEEEEEEeccceeEEEe-cccccccccchhhhhhccccccc-----
Confidence            45677777777544454434444322     24588999999999999884 45556777778887776543211     


Q ss_pred             hhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCC-CCHhHHHhhccccCceEEEEEeC
Q 013141          299 SSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSD-VSDEDLREPFSQFGEILSVKIPV  361 (449)
Q Consensus       299 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~-~t~~~L~~~f~~~G~v~~v~i~~  361 (449)
                                           .........=|.|.+||.. .+++-|+.+.+.+|.+.+++...
T Consensus        97 ---------------------~~~~~~~~vWVri~glP~~~~~~~~~~~i~~~iG~~i~vD~~t  139 (153)
T PF14111_consen   97 ---------------------EVKFEHIPVWVRIYGLPLHLWSEEILKAIGSKIGEPIEVDENT  139 (153)
T ss_pred             ---------------------ccceeccchhhhhccCCHHHhhhHHHHHHHHhcCCeEEEEcCC
Confidence                                 0111122344788899988 67888999999999999998765

>KOG3648 consensus Golgi apparatus protein (cysteine-rich fibroblast growth factor receptor) [Intracellular trafficking, secretion, and vesicular transport]

Probab=81.04  E-value=0.29  Score=49.06  Aligned_cols=12  Identities=42%  Similarity=0.819  Sum_probs=5.2

Q ss_pred             CCCCCCCCCCCC
Q 013141           20 SGGAGGGSQPTP   31 (449)
Q Consensus        20 ~~~~~~~~q~~~   31 (449)
                      +||+||-.|+-+
T Consensus        53 ~~~~~~~~~~~~   64 (1179)
T KOG3648|consen   53 AGGGGPAGQQLP   64 (1179)
T ss_pred             cCCCCchhhhhH
Confidence            344444444433

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	449
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		2e-17
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		4e-11
2dhg_A	104	Solution Structure Of The C-Terminal Rna Recognitio		1e-16
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		6e-16
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		8e-15
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		2e-04
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		1e-15
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		9e-15
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		3e-04
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		6e-14
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		4e-09
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		2e-05
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		7e-14
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		4e-09
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		2e-05
2div_A	99	Solution Structure Of The Rrm Domain Of Trna Seleno		2e-13
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		3e-13
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		5e-11
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		1e-04
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		5e-12
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		3e-07
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		1e-11
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		2e-11
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		2e-06
1x5t_A	96	Solution Structure Of The Second Rrm Domain In Spli		1e-09
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		1e-09
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		6e-06
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		3e-09
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		2e-08
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		3e-09
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		1e-07
3md1_A	83	Crystal Structure Of The Second Rrm Domain Of Yeast		6e-09
3md1_A	83	Crystal Structure Of The Second Rrm Domain Of Yeast		7e-06
2ytc_A	85	Solution Structure Of Rna Binding Domain In Pre-Mrn		1e-08
1x4g_A	109	Solution Structure Of Rrm Domain In Nucleolysin Tia		1e-08
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		2e-08
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		4e-08
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		4e-08
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		5e-08
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		5e-08
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		5e-08
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		5e-08
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		9e-08
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		1e-05
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		1e-07
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		1e-07
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		3e-07
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		2e-04
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		4e-07
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		5e-07
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		1e-06
2d9p_A	103	Solution Structure Of Rna Binding Domain 4 In Polya		5e-07
2d9p_A	103	Solution Structure Of Rna Binding Domain 4 In Polya		4e-05
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		6e-07
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		2e-05
3bs9_A	87	X-Ray Structure Of Human Tia-1 Rrm2 Length = 87		1e-06
2dhs_A	187	Solution Structure Of Nucleic Acid Binding Protein		2e-06
2dhs_A	187	Solution Structure Of Nucleic Acid Binding Protein		5e-06
2xsf_A	89	Crystal Structure Of The Rrm Domain Of Mouse Delete		3e-06
3nnc_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		3e-06
3nnc_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		4e-06
1x5u_A	105	Solution Structure Of Rrm Domain In Splicing Factor		4e-06
1x5u_A	105	Solution Structure Of Rrm Domain In Splicing Factor		4e-05
1x5u_A	105	Solution Structure Of Rrm Domain In Splicing Factor		2e-04
3nmr_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		5e-06
2cq3_A	103	Solution Structure Of Rna Binding Domain In Rna Bin		7e-06
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		9e-06
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		5e-04
2xs5_A	87	Crystal Structure Of The Rrm Domain Of Mouse Delete		9e-06
2xs2_A	102	Crystal Structure Of The Rrm Domain Of Mouse Delete		9e-06
2krr_A	180	Solution Structure Of The Rbd1,2 Domains From Human		2e-05
1fje_B	175	Solution Structure Of Nucleolin Rbd12 In Complex Wi		2e-05
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		2e-05
2err_A	109	Nmr Structure Of The Rna Binding Domain Of Human Fo		2e-05
2fc8_A	102	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		3e-05
1h2t_Z	156	Structure Of The Human Nuclear Cap-Binding-Complex		3e-05
1h2t_Z	156	Structure Of The Human Nuclear Cap-Binding-Complex		4e-05
2k8g_A	95	Solution Structure Of Rrm2 Domain Of Pabp1 Length =		3e-05
4f25_A	115	Crystal Structure Of The Second Rrm Domain Of Human		4e-05
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		6e-05
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		4e-04
2ki2_A	90	Solution Structure Of Ss-Dna Binding Protein 12rnp2		6e-05
2cpz_A	115	Solution Structure Of Rna Binding Domain 3 In Cug T		7e-05
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		8e-05
2dnk_A	105	Solution Structure Of Rna Binding Domain In Bruno-L		8e-05
1h6k_Z	98	Nuclear Cap Binding Complex Length = 98		9e-05
3sde_B	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		1e-04
2cq0_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		1e-04
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		1e-04
2sxl_A	88	Sex-Lethal Rbd1, Nmr, Minimized Average Structure L		1e-04
2jvo_A	108	Segmental Isotope Labeling Of Npl3 Length = 108		1e-04
2khc_A	118	Bruno Rrm3+ Length = 118		1e-04
2km8_B	84	Interdomain Rrm Packing Contributes To Rna Recognit		2e-04
4fxv_A	99	Crystal Structure Of An Elav-Like Protein 1 (Elavl1		2e-04
1x5o_A	114	Solution Structure Of Rrm Domain In Rna Binding Mot		2e-04
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		2e-04
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		2e-04
1sxl_A	97	Resonance Assignments And Solution Structure Of The		3e-04
2cpj_A	99	Solution Structure Of The N-Terminal Rna Recognitio		3e-04
3nnh_A	88	Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuug		3e-04
2x1a_A	97	Structure Of Rna15 Rrm With Rna Bound (G) Length =		3e-04
2x1a_A	97	Structure Of Rna15 Rrm With Rna Bound (G) Length =		6e-04
3vaf_A	174	Structure Of U2af65 Variant With Bru3 Dna Length =		4e-04
2g4b_A	172	Structure Of U2af65 Variant With Polyuridine Tract		4e-04
2ywk_A	95	Crystal Structure Of Rrm-Domain Derived From Human		4e-04
2dnh_A	105	Solution Structure Of Rna Binding Domain In Bruno-L		6e-04
1d9a_A	85	Solution Structure Of The Second Rna-Binding Domain		7e-04
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		7e-04
2x1f_A	96	Structure Of Rna15 Rrm With Bound Rna (Gu) Length =		7e-04
3mdf_A	85	Crystal Structure Of The Rrm Domain Of Cyclophilin		8e-04

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 87.0 bits (214), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 52/171 (30%), Positives = 90/171 (52%), Gaps = 7/171 (4%)
Query: 116 KTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQ 175
           + +++G+L   + E  L   F   G + N+K++ +K   ++  Y FVE++    A   LQ
Sbjct: 1   RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQ 59
Query: 176 SYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPS 235
           + +G  + N     ++NWA  S   +++ +    ++FVGDL  +V D  L+  F   +PS
Sbjct: 60  TLNGKQIENN--IVKINWAFQS---QQSSSDDTFNLFVGDLNVNVDDETLRNAFKD-FPS 113
Query: 236 VKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVA 286
                V+ D  TG ++GYGFV F  +++   AM  M G   + RP+RI+ A
Sbjct: 114 YLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 164

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 65.9 bits (159), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 50/194 (25%), Positives = 87/194 (44%), Gaps = 38/194 (19%)
Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           ++VG+L   +T+ IL++ F    P +   K++ID N  +   Y FV +   ++ + A+  
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGP-IANIKIMIDKNN-KNVNYAFVEYHQSHDANIALQT 60
Query: 271 MNGVYCSSRPMRIDVATPKKASGXXXXXXXXALVLAGGPGSNGARVQGSQSDGESNNATI 330
           +NG    +  ++I+ A                              Q S SD   N   +
Sbjct: 61  LNGKQIENNIVKINWAFQS---------------------------QQSSSDDTFN---L 90
Query: 331 FVGALDSDVSDEDLREPFSQFGEILS------VKIPVGKGCGFVQFANRKDAEVALQKLQ 384
           FVG L+ +V DE LR  F  F   LS      ++    +G GFV F ++ DA+ A+  +Q
Sbjct: 91  FVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQ 150
Query: 385 GTAIGKQTVRLSWG 398
           G  +  + +R++W 
Sbjct: 151 GQDLNGRPLRINWA 164

>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif In Trna Selenocysteine Associated Protein Length = 104

Iteration: 1
 Score = 84.7 bits (208), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 45/85 (52%), Positives = 59/85 (69%), Gaps = 2/85 (2%)
Query: 208 DLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRA 267
           + S+FVGDL PDV D +L E F   YPS +G KV++D  TG +KGYGFV+F DE E+ RA
Sbjct: 9   EYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLD-QTGVSKGYGFVKFTDELEQKRA 67
Query: 268 MTEMNG-VYCSSRPMRIDVATPKKA 291
           +TE  G V   S+P+R+ VA PK +
Sbjct: 68  LTECQGAVGLGSKPVRLSVAIPKAS 92

>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In Complex With Rrm1-2 Of Pabp And Poly(A) Length = 213

Iteration: 1
 Score = 82.0 bits (201), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 49/163 (30%), Positives = 90/163 (55%), Gaps = 8/163 (4%)
Query: 117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQS 176
           ++++GDL   + E  L+  FS  G +++++V R+  T +S GY +V F   A AE+ L +
Sbjct: 17  SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 76
Query: 177 YSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSV 236
            +  ++    +P R+ W+    S R++      +IF+ +L   + +  L +TFS+ + ++
Sbjct: 77  MNFDVIKG--KPVRIMWSQRDPSLRKSGVG---NIFIKNLDKSIDNKALYDTFSA-FGNI 130
Query: 237 KGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSR 279
              KV+ D N   +KGYGFV F  +    RA+ +MNG+  + R
Sbjct: 131 LSCKVVCDENG--SKGYGFVHFETQEAAERAIEKMNGMLLNDR 171

>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In Complex With Rrm1-2 Of Pabp And Poly(A) Length = 213

Iteration: 1
 Score = 78.2 bits (191), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 57/188 (30%), Positives = 85/188 (45%), Gaps = 35/188 (18%)
Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           S++VGDL PDVT+++L E FS   P +   +V  D  T R+ GY +V F    +  RA+ 
Sbjct: 17  SLYVGDLHPDVTEAMLYEKFSPAGP-ILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 75
Query: 270 EMNGVYCSSRPMRIDVATPKKASGXXXXXXXXALVLAGGPGSNGARVQGSQSDGESNNAT 329
            MN      +P+RI  +                              Q   S  +S    
Sbjct: 76  TMNFDVIKGKPVRIMWS------------------------------QRDPSLRKSGVGN 105
Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPV----GKGCGFVQFANRKDAEVALQKLQG 385
           IF+  LD  + ++ L + FS FG ILS K+       KG GFV F  ++ AE A++K+ G
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 165
Query: 386 TAIGKQTV 393
             +  + V
Sbjct: 166 MLLNDRKV 173

>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In Complex With Rrm1-2 Of Pabp And Poly(A) Length = 213

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 28/85 (32%), Positives = 43/85 (50%), Gaps = 7/85 (8%)
Query: 328 ATIFVGALDSDVSDEDLREPFSQFGEILSVKI------PVGKGCGFVQFANRKDAEVALQ 381
           A+++VG L  DV++  L E FS  G ILS+++          G  +V F    DAE AL 
Sbjct: 16  ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 75
Query: 382 KLQGTAIGKQTVRLSWG-RNPGNKQ 405
            +    I  + VR+ W  R+P  ++
Sbjct: 76  TMNFDVIKGKPVRIMWSQRDPSLRK 100

>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In Complex With Polyadenylate Rna Length = 190

Iteration: 1
 Score = 81.3 bits (199), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 49/163 (30%), Positives = 90/163 (55%), Gaps = 8/163 (4%)
Query: 117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQS 176
           ++++GDL   + E  L+  FS  G +++++V R+  T +S GY +V F   A AE+ L +
Sbjct: 12  SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 71
Query: 177 YSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSV 236
            +  ++    +P R+ W+    S R++      +IF+ +L   + +  L +TFS+ + ++
Sbjct: 72  MNFDVIKG--KPVRIMWSQRDPSLRKSGVG---NIFIKNLDKSIDNKALYDTFSA-FGNI 125
Query: 237 KGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSR 279
              KV+ D N   +KGYGFV F  +    RA+ +MNG+  + R
Sbjct: 126 LSCKVVCDENG--SKGYGFVHFETQEAAERAIEKMNGMLLNDR 166

>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In Complex With Polyadenylate Rna Length = 190

Iteration: 1
 Score = 78.2 bits (191), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 57/188 (30%), Positives = 85/188 (45%), Gaps = 35/188 (18%)
Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           S++VGDL PDVT+++L E FS   P +   +V  D  T R+ GY +V F    +  RA+ 
Sbjct: 12  SLYVGDLHPDVTEAMLYEKFSPAGP-ILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 70
Query: 270 EMNGVYCSSRPMRIDVATPKKASGXXXXXXXXALVLAGGPGSNGARVQGSQSDGESNNAT 329
            MN      +P+RI  +                              Q   S  +S    
Sbjct: 71  TMNFDVIKGKPVRIMWS------------------------------QRDPSLRKSGVGN 100
Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPV----GKGCGFVQFANRKDAEVALQKLQG 385
           IF+  LD  + ++ L + FS FG ILS K+       KG GFV F  ++ AE A++K+ G
Sbjct: 101 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 160
Query: 386 TAIGKQTV 393
             +  + V
Sbjct: 161 MLLNDRKV 168

>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In Complex With Polyadenylate Rna Length = 190

Iteration: 1
 Score = 43.1 bits (100), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 28/85 (32%), Positives = 43/85 (50%), Gaps = 7/85 (8%)
Query: 328 ATIFVGALDSDVSDEDLREPFSQFGEILSVKI------PVGKGCGFVQFANRKDAEVALQ 381
           A+++VG L  DV++  L E FS  G ILS+++          G  +V F    DAE AL 
Sbjct: 11  ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 70
Query: 382 KLQGTAIGKQTVRLSWG-RNPGNKQ 405
            +    I  + VR+ W  R+P  ++
Sbjct: 71  TMNFDVIKGKPVRIMWSQRDPSLRK 95

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 75.5 bits (184), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 44/149 (29%), Positives = 77/149 (51%), Gaps = 12/149 (8%)
Query: 127 MDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTD 186
           M +  L + FS  G+V + K+IR+K  G S GYGFV + +   AE+ + + +G       
Sbjct: 14  MTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNG------- 66
Query: 187 QPFRLNWATFSGSDRR--TEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIID 244
              RL   T   S  R  +E   D ++++  L   +T   +++ F S++  +  ++V++D
Sbjct: 67  --LRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMF-SRFGRIINSRVLVD 123
Query: 245 SNTGRTKGYGFVRFGDENERSRAMTEMNG 273
             TG ++G  F+RF   +E   A+T  NG
Sbjct: 124 QTTGLSRGVAFIRFDKRSEAEEAITSFNG 152

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 59.3 bits (142), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 43/181 (23%), Positives = 78/181 (43%), Gaps = 39/181 (21%)
Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           + V  L  ++T   L+  FSS    V+ AK+I D   G + GYGFV +    +  RA+  
Sbjct: 5   LIVNYLPQNMTQDELRSLFSS-IGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 271 MNGVYCSSRPMRIDVATPKKASGXXXXXXXXALVLAGGPGSNGARVQGSQSDGESNNATI 330
           +NG+   S+ +++  A P                                S     +A +
Sbjct: 64  LNGLRLQSKTIKVSYARP--------------------------------SSEVIKDANL 91
Query: 331 FVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVALQKLQ 384
           ++  L   ++ +D+ + FS+FG I++ ++ V       +G  F++F  R +AE A+    
Sbjct: 92  YISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFN 151
Query: 385 G 385
           G
Sbjct: 152 G 152

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/76 (32%), Positives = 41/76 (53%), Gaps = 6/76 (7%)
Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK------GCGFVQFANRKDAEVALQKL 383
           + V  L  +++ ++LR  FS  GE+ S K+   K      G GFV +   KDAE A+  L
Sbjct: 5   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 384 QGTAIGKQTVRLSWGR 399
            G  +  +T+++S+ R
Sbjct: 65  NGLRLQSKTIKVSYAR 80

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 75.1 bits (183), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 44/149 (29%), Positives = 77/149 (51%), Gaps = 12/149 (8%)
Query: 127 MDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTD 186
           M +  L + FS  G+V + K+IR+K  G S GYGFV + +   AE+ + + +G       
Sbjct: 14  MTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNG------- 66
Query: 187 QPFRLNWATFSGSDRR--TEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIID 244
              RL   T   S  R  +E   D ++++  L   +T   +++ F S++  +  ++V++D
Sbjct: 67  --LRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMF-SRFGRIINSRVLVD 123
Query: 245 SNTGRTKGYGFVRFGDENERSRAMTEMNG 273
             TG ++G  F+RF   +E   A+T  NG
Sbjct: 124 QTTGLSRGVAFIRFDKRSEAEEAITSFNG 152

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 59.3 bits (142), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 43/181 (23%), Positives = 78/181 (43%), Gaps = 39/181 (21%)
Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           + V  L  ++T   L+  FSS    V+ AK+I D   G + GYGFV +    +  RA+  
Sbjct: 5   LIVNYLPQNMTQDELRSLFSS-IGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 271 MNGVYCSSRPMRIDVATPKKASGXXXXXXXXALVLAGGPGSNGARVQGSQSDGESNNATI 330
           +NG+   S+ +++  A P                                S     +A +
Sbjct: 64  LNGLRLQSKTIKVSYARP--------------------------------SSEVIKDANL 91
Query: 331 FVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVALQKLQ 384
           ++  L   ++ +D+ + FS+FG I++ ++ V       +G  F++F  R +AE A+    
Sbjct: 92  YISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFN 151
Query: 385 G 385
           G
Sbjct: 152 G 152

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/76 (32%), Positives = 41/76 (53%), Gaps = 6/76 (7%)
Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK------GCGFVQFANRKDAEVALQKL 383
           + V  L  +++ ++LR  FS  GE+ S K+   K      G GFV +   KDAE A+  L
Sbjct: 5   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 384 QGTAIGKQTVRLSWGR 399
            G  +  +T+++S+ R
Sbjct: 65  NGLRLQSKTIKVSYAR 80

>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna Selenocysteine Associated Protein Length = 99

Iteration: 1
 Score = 73.9 bits (180), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 38/85 (44%), Positives = 55/85 (64%), Gaps = 3/85 (3%)
Query: 117 TIWIGDLFHWMDETFLHNCFSHTGQ-VVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQ 175
           ++W+GDL  +MDE F+   F+  G+ V++VK+IRN+ TG   GY FVEF   A AEK L 
Sbjct: 11  SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH 70
Query: 176 SYSGSLMPNTD--QPFRLNWATFSG 198
             +G  +P     + F+LN+AT+SG
Sbjct: 71  KINGKPLPGATPAKRFKLNYATYSG 95

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 72.8 bits (177), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 45/149 (30%), Positives = 76/149 (51%), Gaps = 12/149 (8%)
Query: 127 MDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTD 186
           M +    + F   G++ + K++R+K TGQS GYGFV +     AEK + + +G       
Sbjct: 14  MTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNG------- 66
Query: 187 QPFRLNWATFSGSDRRTEACS--DLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIID 244
              RL   T   S  R  + S  D +++V  L   +T   L++ F S+Y  +  +++++D
Sbjct: 67  --LRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLF-SQYGRIITSRILVD 123
Query: 245 SNTGRTKGYGFVRFGDENERSRAMTEMNG 273
             TG ++G GF+RF    E   A+  +NG
Sbjct: 124 QVTGVSRGVGFIRFDKRIEAEEAIKGLNG 152

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 65.9 bits (159), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 43/169 (25%), Positives = 79/169 (46%), Gaps = 41/169 (24%)
Query: 226 QETFSSKYPSV---KGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMR 282
           QE F S + S+   +  K++ D  TG++ GYGFV + D  +  +A+  +NG+   ++ ++
Sbjct: 16  QEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIK 75
Query: 283 IDVATPKKASGXXXXXXXXALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDE 342
           +  A P  AS                                  +A ++V  L   ++ +
Sbjct: 76  VSYARPSSAS--------------------------------IRDANLYVSGLPKTMTQK 103
Query: 343 DLREPFSQFGEILSVKIP------VGKGCGFVQFANRKDAEVALQKLQG 385
           +L + FSQ+G I++ +I       V +G GF++F  R +AE A++ L G
Sbjct: 104 ELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNG 152

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/76 (32%), Positives = 40/76 (52%), Gaps = 6/76 (7%)
Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK------GCGFVQFANRKDAEVALQKL 383
           + V  L  +++ E+ R  F   GEI S K+   K      G GFV + + KDAE A+  L
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 384 QGTAIGKQTVRLSWGR 399
            G  +  +T+++S+ R
Sbjct: 65  NGLRLQTKTIKVSYAR 80

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 68.9 bits (167), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 44/162 (27%), Positives = 83/162 (51%), Gaps = 10/162 (6%)
Query: 127 MDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTD 186
           M +  L+  F   G +   +++R+ +TG S GY FV+F S   +++ ++  +G  + N  
Sbjct: 15  MTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRN-- 72
Query: 187 QPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSN 246
           +  ++++A   G     E+  D +++V +L   +TD  L   F  KY S+    ++ D  
Sbjct: 73  KRLKVSYARPGG-----ESIKDTNLYVTNLPRTITDDQLDTIFG-KYGSIVQKNILRDKL 126
Query: 247 TGRTKGYGFVRFGDENERSRAMTEMNGVYCS--SRPMRIDVA 286
           TGR +G  FVR+    E   A++ +N V     S+P+ + +A
Sbjct: 127 TGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 168

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 53.1 bits (126), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 43/184 (23%), Positives = 79/184 (42%), Gaps = 39/184 (21%)
Query: 206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERS 265
            S+ ++ V  L  D+TD  L   F +  P +   +++ D  TG + GY FV F  E +  
Sbjct: 1   ASNTNLIVNYLPQDMTDRELYALFRAIGP-INTCRIMRDYKTGYSYGYAFVDFTSEMDSQ 59
Query: 266 RAMTEMNGVYCSSRPMRIDVATPKKASGXXXXXXXXALVLAGGPGSNGARVQGSQSDGES 325
           RA+  +NG+   ++ +++  A P                             G +S  ++
Sbjct: 60  RAIKVLNGITVRNKRLKVSYARP-----------------------------GGESIKDT 90
Query: 326 NNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK------GCGFVQFANRKDAEVA 379
           N   ++V  L   ++D+ L   F ++G I+   I   K      G  FV++  R++A+ A
Sbjct: 91  N---LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 147
Query: 380 LQKL 383
           +  L
Sbjct: 148 ISAL 151

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 67.8 bits (164), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 43/169 (25%), Positives = 80/169 (47%), Gaps = 41/169 (24%)
Query: 226 QETFSSKYPSV---KGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMR 282
           Q+ F S + S+   +  K++ D  TG++ GYGFV + D N+  +A+  +NG+   ++ ++
Sbjct: 18  QDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIK 77
Query: 283 IDVATPKKASGXXXXXXXXALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDE 342
           +  A P  AS                                  +A ++V  L   +S +
Sbjct: 78  VSYARPSSAS--------------------------------IRDANLYVSGLPKTMSQK 105
Query: 343 DLREPFSQFGEILSVKIP------VGKGCGFVQFANRKDAEVALQKLQG 385
           ++ + FSQ+G I++ +I       V +G GF++F  R +AE A++ L G
Sbjct: 106 EMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNG 154

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 67.4 bits (163), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 43/157 (27%), Positives = 80/157 (50%), Gaps = 10/157 (6%)
Query: 132 LHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRL 191
           L+  F   G +   ++ R+ +TG S GY FV+F S   +++ ++  +G  + N  +  ++
Sbjct: 31  LYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVLNGITVRN--KRLKV 88
Query: 192 NWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTK 251
           ++A   G     E+  D +++V +L   +TD  L   F  KY S+    ++ D  TGR +
Sbjct: 89  SYARPGG-----ESIKDTNLYVTNLPRTITDDQLDTIFG-KYGSIVQKNILRDKLTGRPR 142
Query: 252 GYGFVRFGDENERSRAMTEMNGVYCS--SRPMRIDVA 286
           G  FVR+    E   A++ +N V     S+P+ + +A
Sbjct: 143 GVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 179

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 43/184 (23%), Positives = 77/184 (41%), Gaps = 39/184 (21%)
Query: 206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERS 265
            S+ ++ V  L  D TD  L   F +  P +   ++  D  TG + GY FV F  E +  
Sbjct: 12  ASNTNLIVNYLPQDXTDRELYALFRAIGP-INTCRIXRDYKTGYSFGYAFVDFTSEXDSQ 70
Query: 266 RAMTEMNGVYCSSRPMRIDVATPKKASGXXXXXXXXALVLAGGPGSNGARVQGSQSDGES 325
           RA+  +NG+   ++ +++  A P                             G +S  ++
Sbjct: 71  RAIKVLNGITVRNKRLKVSYARP-----------------------------GGESIKDT 101
Query: 326 NNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK------GCGFVQFANRKDAEVA 379
           N   ++V  L   ++D+ L   F ++G I+   I   K      G  FV++  R++A+ A
Sbjct: 102 N---LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 158
Query: 380 LQKL 383
           +  L
Sbjct: 159 ISAL 162

>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing Factor 3b Length = 96

Iteration: 1
 Score = 60.8 bits (146), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 28/83 (33%), Positives = 49/83 (59%)
Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           IF+G+L P++ + +L +TFS+    ++  K++ D +TG +KGY F+ F   +    A+  
Sbjct: 8   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 271 MNGVYCSSRPMRIDVATPKKASG 293
           MNG Y  +RP+ +  A  K + G
Sbjct: 68  MNGQYLCNRPITVSYAFKKDSKG 90

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 60.8 bits (146), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 46/180 (25%), Positives = 89/180 (49%), Gaps = 19/180 (10%)
Query: 114 ETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKV 173
           E+  ++IG L     E  L   F   G V ++K++++  TG+S G+GF+ F   ++ ++V
Sbjct: 2   ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61
Query: 174 LQS---YSGSLM-PNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETF 229
           +++     G ++ P    P             R E      IFVG + PDV     +E F
Sbjct: 62  VKTQHILDGKVIDPKRAIP-------------RDEQDKTGKIFVGGIGPDVRPKEFEEFF 108
Query: 230 SSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPK 289
            S++ ++  A++++D +TG+++G+GFV +   +   R + +   +    R + I  A P+
Sbjct: 109 -SQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDR-VCQNKFIDFKDRKIEIKRAEPR 166

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 48.9 bits (115), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 47/173 (27%), Positives = 75/173 (43%), Gaps = 44/173 (25%)
Query: 204 EACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENE 263
           E+C    +F+G L  D T+  L+E F  KY +V   K++ D  TGR++G+GF+ F    E
Sbjct: 2   ESCK---MFIGGLNWDTTEDNLREYFG-KYGTVTDLKIMKDPATGRSRGFGFLSF----E 53
Query: 264 RSRAMTEMNGVYCSSRPMRIDVATPKKASGXXXXXXXXALVLAGGPGSNGARVQGSQSDG 323
           +  ++ E   V  +   +   V  PK+A                              D 
Sbjct: 54  KPSSVDE---VVKTQHILDGKVIDPKRAI---------------------------PRDE 83
Query: 324 ESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK------GCGFVQF 370
           +     IFVG +  DV  ++  E FSQ+G I+  ++ + K      G GFV +
Sbjct: 84  QDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTY 136

>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 = 60.1 bits (144), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 29/91 (31%), Positives = 54/91 (59%), Gaps = 1/91 (1%)
Query: 199 SDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRF 258
           S ++ +  +   +FVGDL+P++T   ++  F+  +  +  A+V+ D  TG++KGYGFV F
Sbjct: 6   SGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAP-FGRISDARVVKDMATGKSKGYGFVSF 64
Query: 259 GDENERSRAMTEMNGVYCSSRPMRIDVATPK 289
            ++ +   A+ +M G +   R +R + AT K
Sbjct: 65  FNKWDAENAIQQMGGQWLGGRQIRTNWATRK 95

>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic Granule-Associated Rna Binding Protein 1 Length = 115

Iteration: 1
 Score = 57.0 bits (136), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 31/89 (34%), Positives = 49/89 (55%), Gaps = 7/89 (7%)
Query: 320 QSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANR 373
           Q    SN+  +FVG L  +++ ED++  F+ FG I   ++         KG GFV F N+
Sbjct: 8   QKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNK 67
Query: 374 KDAEVALQKLQGTAIGKQTVRLSWG-RNP 401
            DAE A+Q++ G  +G + +R +W  R P
Sbjct: 68  WDAENAIQQMGGQWLGGRQIRTNWATRKP 96

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 59.7 bits (143), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 29/91 (31%), Positives = 53/91 (58%), Gaps = 1/91 (1%)
Query: 199 SDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRF 258
           S ++ +  +   +FVGDL+P++T   ++  F+  +  +  A+V+ D  TG++KGYGFV F
Sbjct: 6   SGQKKDTSNHFHVFVGDLSPEITTEDIKSAFAP-FGKISDARVVKDMATGKSKGYGFVSF 64
Query: 259 GDENERSRAMTEMNGVYCSSRPMRIDVATPK 289
            ++ +   A+  M G +   R +R + AT K
Sbjct: 65  YNKLDAENAIVHMGGQWLGGRQIRTNWATRK 95

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 54.3 bits (129), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 30/89 (33%), Positives = 48/89 (53%), Gaps = 7/89 (7%)
Query: 320 QSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIP------VGKGCGFVQFANR 373
           Q    SN+  +FVG L  +++ ED++  F+ FG+I   ++         KG GFV F N+
Sbjct: 8   QKKDTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNK 67
Query: 374 KDAEVALQKLQGTAIGKQTVRLSWG-RNP 401
            DAE A+  + G  +G + +R +W  R P
Sbjct: 68  LDAENAIVHMGGQWLGGRQIRTNWATRKP 96

>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast Poly(U)-Binding Protein (Pub1) Length = 83

Iteration: 1
 Score = 58.9 bits (141), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 30/78 (38%), Positives = 44/78 (56%), Gaps = 1/78 (1%)
Query: 209 LSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAM 268
            ++FVGDL  +V D  L+  F   +PS     V+ D  TG ++GYGFV F  +++   AM
Sbjct: 2   FNLFVGDLNVNVDDETLRNAFKD-FPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 60
Query: 269 TEMNGVYCSSRPMRIDVA 286
             M G   + RP+RI+ A
Sbjct: 61  DSMQGQDLNGRPLRINWA 78

>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast Poly(U)-Binding Protein (Pub1) Length = 83

Iteration: 1
 Score = 48.5 bits (114), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 6/75 (8%)
Query: 330 IFVGALDSDVSDEDLREPFSQFGEILS------VKIPVGKGCGFVQFANRKDAEVALQKL 383
           +FVG L+ +V DE LR  F  F   LS      ++    +G GFV F ++ DA+ A+  +
Sbjct: 4   LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 384 QGTAIGKQTVRLSWG 398
           QG  +  + +R++W 
Sbjct: 64  QGQDLNGRPLRINWA 78

>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna- Splicing Factor Rbm22 Length = 85

Iteration: 1
 Score = 57.8 bits (138), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 31/83 (37%), Positives = 47/83 (56%), Gaps = 2/83 (2%)
Query: 319 SQSDGESNN-ATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAE 377
           S S GE     T++VG L   +++ DLR  F QFGEI ++ +   + C F+QFA R+ AE
Sbjct: 3   SGSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAE 62
Query: 378 VALQK-LQGTAIGKQTVRLSWGR 399
           VA +K      +  + + + WGR
Sbjct: 63  VAAEKSFNKLIVNGRRLNVKWGR 85

>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar Length = 109

Iteration: 1
 Score = 57.8 bits (138), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 24/73 (32%), Positives = 44/73 (60%)
Query: 327 NATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGT 386
           N T++ G + S ++D+ +R+ FS FG+I+ +++   KG  FV+F+  + A  A+  + GT
Sbjct: 25  NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGT 84
Query: 387 AIGKQTVRLSWGR 399
            I    V+  WG+
Sbjct: 85  TIEGHVVKCYWGK 97

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 57.0 bits (136), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 25/81 (30%), Positives = 50/81 (61%), Gaps = 1/81 (1%)
Query: 209 LSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAM 268
           + ++VG L  ++T+ +L+  F   +  ++  ++++DS TGR+KGYGF+ F D     +A+
Sbjct: 27  MRLYVGSLHFNITEDMLRGIFEP-FGRIESIQLMMDSETGRSKGYGFITFSDSECAKKAL 85
Query: 269 TEMNGVYCSSRPMRIDVATPK 289
            ++NG   + RPM++   T +
Sbjct: 86  EQLNGFELAGRPMKVGHVTER 106

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 55.8 bits (133), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 47/181 (25%), Positives = 80/181 (44%), Gaps = 39/181 (21%)
Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +F+G L+ + TD  L+  F  ++ ++    V+ D NT R++G+GFV +    E   AM  
Sbjct: 9   LFIGGLSFETTDESLRSHFE-QWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-- 65
Query: 271 MNGVYCSSRPMRID--VATPKKASGXXXXXXXXALVLAGGPGSNGARVQGSQSDGESNNA 328
                 ++RP ++D  V  PK+A                 PG++                
Sbjct: 66  ------NARPHKVDGRVVEPKRAVSREDSQR---------PGAH------------LTVK 98
Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCG------FVQFANRKDAE-VALQ 381
            IFVG +  D  +  LR+ F Q+G+I  ++I   +G G      FV F +    + + +Q
Sbjct: 99  KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 158
Query: 382 K 382
           K
Sbjct: 159 K 159

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 55.8 bits (133), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 47/181 (25%), Positives = 80/181 (44%), Gaps = 39/181 (21%)
Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +F+G L+ + TD  L+  F  ++ ++    V+ D NT R++G+GFV +    E   AM  
Sbjct: 16  LFIGGLSFETTDESLRSHFE-QWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-- 72
Query: 271 MNGVYCSSRPMRID--VATPKKASGXXXXXXXXALVLAGGPGSNGARVQGSQSDGESNNA 328
                 ++RP ++D  V  PK+A                 PG++                
Sbjct: 73  ------NARPHKVDGRVVEPKRAVSREDSQR---------PGAH------------LTVK 105
Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCG------FVQFANRKDAE-VALQ 381
            IFVG +  D  +  LR+ F Q+G+I  ++I   +G G      FV F +    + + +Q
Sbjct: 106 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 165
Query: 382 K 382
           K
Sbjct: 166 K 166

>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 = 55.8 bits (133), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 47/181 (25%), Positives = 80/181 (44%), Gaps = 39/181 (21%)
Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +F+G L+ + TD  L+  F  ++ ++    V+ D NT R++G+GFV +    E   AM  
Sbjct: 17  LFIGGLSFETTDESLRSHFE-QWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-- 73
Query: 271 MNGVYCSSRPMRID--VATPKKASGXXXXXXXXALVLAGGPGSNGARVQGSQSDGESNNA 328
                 ++RP ++D  V  PK+A                 PG++                
Sbjct: 74  ------NARPHKVDGRVVEPKRAVSREDSQR---------PGAH------------LTVK 106
Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCG------FVQFANRKDAE-VALQ 381
            IFVG +  D  +  LR+ F Q+G+I  ++I   +G G      FV F +    + + +Q
Sbjct: 107 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 166
Query: 382 K 382
           K
Sbjct: 167 K 167

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 55.8 bits (133), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 47/181 (25%), Positives = 80/181 (44%), Gaps = 39/181 (21%)
Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +F+G L+ + TD  L+  F  ++ ++    V+ D NT R++G+GFV +    E   AM  
Sbjct: 16  LFIGGLSFETTDESLRSHFE-QWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-- 72
Query: 271 MNGVYCSSRPMRID--VATPKKASGXXXXXXXXALVLAGGPGSNGARVQGSQSDGESNNA 328
                 ++RP ++D  V  PK+A                 PG++                
Sbjct: 73  ------NARPHKVDGRVVEPKRAVSREDSQR---------PGAH------------LTVK 105
Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCG------FVQFANRKDAE-VALQ 381
            IFVG +  D  +  LR+ F Q+G+I  ++I   +G G      FV F +    + + +Q
Sbjct: 106 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 165
Query: 382 K 382
           K
Sbjct: 166 K 166

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 55.8 bits (133), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 47/181 (25%), Positives = 80/181 (44%), Gaps = 39/181 (21%)
Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +F+G L+ + TD  L+  F  ++ ++    V+ D NT R++G+GFV +    E   AM  
Sbjct: 14  LFIGGLSFETTDESLRSHFE-QWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-- 70
Query: 271 MNGVYCSSRPMRID--VATPKKASGXXXXXXXXALVLAGGPGSNGARVQGSQSDGESNNA 328
                 ++RP ++D  V  PK+A                 PG++                
Sbjct: 71  ------NARPHKVDGRVVEPKRAVSREDSQR---------PGAH------------LTVK 103
Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCG------FVQFANRKDAE-VALQ 381
            IFVG +  D  +  LR+ F Q+G+I  ++I   +G G      FV F +    + + +Q
Sbjct: 104 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 163
Query: 382 K 382
           K
Sbjct: 164 K 164

>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 = 55.8 bits (133), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 47/181 (25%), Positives = 80/181 (44%), Gaps = 39/181 (21%)
Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +F+G L+ + TD  L+  F  ++ ++    V+ D NT R++G+GFV +    E   AM  
Sbjct: 15  LFIGGLSFETTDESLRSHFE-QWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-- 71
Query: 271 MNGVYCSSRPMRID--VATPKKASGXXXXXXXXALVLAGGPGSNGARVQGSQSDGESNNA 328
                 ++RP ++D  V  PK+A                 PG++                
Sbjct: 72  ------NARPHKVDGRVVEPKRAVSREDSQR---------PGAH------------LTVK 104
Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCG------FVQFANRKDAE-VALQ 381
            IFVG +  D  +  LR+ F Q+G+I  ++I   +G G      FV F +    + + +Q
Sbjct: 105 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 164
Query: 382 K 382
           K
Sbjct: 165 K 165

>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 = 54.7 bits (130), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 36/174 (20%), Positives = 80/174 (45%), Gaps = 5/174 (2%)
Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY 177
           +++G +++ + E  +   F+  G + ++ +  +  T + +G+ FVE+    AA+  L+  
Sbjct: 31  VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 178 SGSLM----PNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKY 233
           +  ++        +P  +  A         EA +   I+V  +  D++D  ++  F + +
Sbjct: 91  NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEA-F 149
Query: 234 PSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVAT 287
             +K A +  D  TG+ KGYGF+ +        A++ MN      + +R+  A 
Sbjct: 150 GKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAV 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 = 47.8 bits (112), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 45/210 (21%), Positives = 89/210 (42%), Gaps = 33/210 (15%)
Query: 201 RRTEACSDLS-IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFG 259
           +R  A + +S ++VG +  ++ +  +++ F+   P +K   +  DS T + KG+ FV + 
Sbjct: 20  QRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGP-IKSIDMSWDSVTMKHKGFAFVEYE 78
Query: 260 DENERSRAMTEMNGVYCSSRPMRIDVATPKKASGXXXXXXXXALVLAGGPGSNGARVQGS 319
                  A+ +MN V    R +++                       G P + G      
Sbjct: 79  VPEAAQLALEQMNSVMLGGRNIKV-----------------------GRPSNIGQAQPII 115
Query: 320 QSDGESNNA--TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFA 371
               E   A   I+V ++  D+SD+D++  F  FG+I S  +         KG GF+++ 
Sbjct: 116 DQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYE 175
Query: 372 NRKDAEVALQKLQGTAIGKQTVRLSWGRNP 401
             + ++ A+  +    +G Q +R+     P
Sbjct: 176 KAQSSQDAVSSMNLFDLGGQYLRVGKAVTP 205

>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 = 54.7 bits (130), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 29/81 (35%), Positives = 46/81 (56%), Gaps = 1/81 (1%)
Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           S+FVG++  + T+  L++ FS   P V   +++ D  TG+ KGYGF  + D+     AM 
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVS-FRLVYDRETGKPKGYGFCEYQDQETALSAMR 68
Query: 270 EMNGVYCSSRPMRIDVATPKK 290
            +NG   S R +R+D A  +K
Sbjct: 69  NLNGREFSGRALRVDNAASEK 89

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 54.7 bits (130), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 28/83 (33%), Positives = 48/83 (57%), Gaps = 1/83 (1%)
Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           ++VG L  ++T+ +L+  F   +  +    ++ DS+TGR+KGYGF+ F D     RA+ +
Sbjct: 8   LYVGSLHFNITEDMLRGIFEP-FGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ 66
Query: 271 MNGVYCSSRPMRIDVATPKKASG 293
           +NG   + RPMR+   T +   G
Sbjct: 67  LNGFELAGRPMRVGHVTERLDGG 89

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 53.1 bits (126), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 29/82 (35%), Positives = 45/82 (54%), Gaps = 1/82 (1%)
Query: 205 ACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENER 264
           A  +  +FVG L+ D  +  L++ FS KY  +    V+ D  T R++G+GFV F + ++ 
Sbjct: 9   ASDEGKLFVGGLSFDTNEQSLEQVFS-KYGQISEVVVVKDRETQRSRGFGFVTFENIDDA 67
Query: 265 SRAMTEMNGVYCSSRPMRIDVA 286
             AM  MNG     R +R+D A
Sbjct: 68  KDAMMAMNGKSVDGRQIRVDQA 89

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/87 (28%), Positives = 47/87 (54%), Gaps = 7/87 (8%)
Query: 325 SNNATIFVGALDSDVSDEDLREPFSQFGEILSVKI------PVGKGCGFVQFANRKDAEV 378
           S+   +FVG L  D +++ L + FS++G+I  V +         +G GFV F N  DA+ 
Sbjct: 10  SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKD 69
Query: 379 ALQKLQGTAIGKQTVRLSW-GRNPGNK 404
           A+  + G ++  + +R+   G++  N+
Sbjct: 70  AMMAMNGKSVDGRQIRVDQAGKSSDNR 96

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 52.8 bits (125), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 37/142 (26%), Positives = 70/142 (49%), Gaps = 21/142 (14%)
Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY 177
           +++G+L   + E      F   G+   V + R++      G+GF+   SR  AE      
Sbjct: 25  LFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR------GFGFIRLESRTLAEIAKAEL 78
Query: 178 SGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVK 237
            G+++ +  +P R+ +AT   +           + V +L+P V++ +L++ F S++  V+
Sbjct: 79  DGTILKS--RPLRIRFATHGAA-----------LTVKNLSPVVSNELLEQAF-SQFGPVE 124
Query: 238 GAKVIIDSNTGRTKGYGFVRFG 259
            A V++D + GR  G GFV F 
Sbjct: 125 KAVVVVD-DRGRATGKGFVEFA 145

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 52.4 bits (124), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 54/203 (26%), Positives = 82/203 (40%), Gaps = 59/203 (29%)
Query: 189 FRLNWATF--SGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKY--PSVKGAKVIID 244
           F ++  +F   G    T+ C    +FVG+L  D+T+   +  F  +Y  PS    +V I+
Sbjct: 4   FTIDIKSFLKPGEKTYTQRCR---LFVGNLPTDITEEDFKRLFE-RYGEPS----EVFIN 55
Query: 245 SNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKASGXXXXXXXXALV 304
               R +G+GF+R         A  E++G    SRP+RI  AT                 
Sbjct: 56  ----RDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFAT----------------- 94
Query: 305 LAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV--- 361
                                + A + V  L   VS+E L + FSQFG +    + V   
Sbjct: 95  ---------------------HGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDR 133
Query: 362 --GKGCGFVQFANRKDAEVALQK 382
               G GFV+FA +  A  AL++
Sbjct: 134 GRATGKGFVEFAAKPPARKALER 156

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 51.2 bits (121), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 23/74 (31%), Positives = 43/74 (58%)
Query: 325 SNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQ 384
           +    +FVG L +D+++ED +  F ++GE   V I   +G GF++  +R  AE+A  +L 
Sbjct: 20  TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELD 79
Query: 385 GTAIGKQTVRLSWG 398
           GT +  + +R+ + 
Sbjct: 80  GTILKSRPLRIRFA 93

>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In Polyadenylation Binding Protein 3 Length = 103

Iteration: 1
 Score = 52.4 bits (124), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 27/82 (32%), Positives = 53/82 (64%), Gaps = 3/82 (3%)
Query: 209 LSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAM 268
           ++++V +L   + D  L++ FS  + ++  AKV+++   GR+KG+GFV F    E ++A+
Sbjct: 16  VNLYVKNLDDGIDDERLRKAFSP-FGTITSAKVMMEG--GRSKGFGFVCFSSPEEATKAV 72
Query: 269 TEMNGVYCSSRPMRIDVATPKK 290
           TEMNG   +++P+ + +A  K+
Sbjct: 73  TEMNGRIVATKPLYVALAQRKE 94

>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In Polyadenylation Binding Protein 3 Length = 103

Iteration: 1
 Score = 46.2 bits (108), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 30/103 (29%), Positives = 52/103 (50%), Gaps = 10/103 (9%)
Query: 307 GGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV----G 362
           G  GS+G R+   Q         ++V  LD  + DE LR+ FS FG I S K+ +     
Sbjct: 1   GSSGSSGDRITRYQV------VNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRS 54
Query: 363 KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQ 405
           KG GFV F++ ++A  A+ ++ G  +  + + ++  +    +Q
Sbjct: 55  KGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQ 97

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 52.4 bits (124), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 33/159 (20%), Positives = 74/159 (46%), Gaps = 5/159 (3%)
Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY 177
           +++G +++ + E  +   F+  G + ++ +  +  T + +G+ FVE+    AA+  L+  
Sbjct: 16  VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 178 SGSLM----PNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKY 233
           +  ++        +P  +  A         EA +   I+V  +  D++D  ++  F + +
Sbjct: 76  NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEA-F 134
Query: 234 PSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMN 272
             +K   +  D  TG+ KGYGF+ +        A++ MN
Sbjct: 135 GKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN 173

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 42/199 (21%), Positives = 83/199 (41%), Gaps = 32/199 (16%)
Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           ++VG +  ++ +  +++ F+   P +K   +  DS T + KG+ FV +        A+ +
Sbjct: 16  VYVGSIYYELGEDTIRQAFAPFGP-IKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 74
Query: 271 MNGVYCSSRPMRIDVATPKKASGXXXXXXXXALVLAGGPGSNGARVQGSQSDGESNNA-- 328
           MN V    R +++                       G P + G          E   A  
Sbjct: 75  MNSVMLGGRNIKV-----------------------GRPSNIGQAQPIIDQLAEEARAFN 111
Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQK 382
            I+V ++  D+SD+D++  F  FG+I S  +         KG GF+++   + ++ A+  
Sbjct: 112 RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 171
Query: 383 LQGTAIGKQTVRLSWGRNP 401
           +    +G Q +R+     P
Sbjct: 172 MNLFDLGGQYLRVGKAVTP 190

>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2 Length = 87

Iteration: 1
 Score = 50.8 bits (120), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 28/83 (33%), Positives = 49/83 (59%), Gaps = 1/83 (1%)
Query: 207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSR 266
           S   +FVGDL+P++T + +     + +  +  A+V+ D  TG++KGYGFV F ++ +   
Sbjct: 5   SHFHVFVGDLSPEITTAAIAAA-FAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAEN 63
Query: 267 AMTEMNGVYCSSRPMRIDVATPK 289
           A+ +M G +   R +R + AT K
Sbjct: 64  AIQQMGGQWLGGRQIRTNWATRK 86

>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein Cugbp1ab And Its Binding Study With Dna And Rna Length = 187

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 44/179 (24%), Positives = 83/179 (46%), Gaps = 20/179 (11%)
Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTG--QSEGYGFVEFYSRAAAEKVLQ 175
           +++G +     E  L   F   G V  + V+R++     QS+G  FV FY+R AA +   
Sbjct: 18  MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 77
Query: 176 S-YSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYP 234
           + ++  ++P    P ++  A       +  A  D  +F+G ++   T++ ++  FSS + 
Sbjct: 78  ALHNMKVLPGMHHPIQMKPA----DSEKNNAVEDRKLFIGMISKKCTENDIRVMFSS-FG 132
Query: 235 SVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVY-------CSSRPMRIDVA 286
            ++  + I+    G ++G  FV F     R+ A T +  ++       CSS PM +  A
Sbjct: 133 QIEECR-ILRGPDGLSRGCAFVTF---TTRAMAQTAIKAMHQAQTMEGCSS-PMVVKFA 186

>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein Cugbp1ab And Its Binding Study With Dna And Rna Length = 187

Iteration: 1
 Score = 48.9 bits (115), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 25/78 (32%), Positives = 40/78 (51%), Gaps = 9/78 (11%)
Query: 316 VQGSQSDGESNNAT----IFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-----KGCG 366
           +Q   +D E NNA     +F+G +    ++ D+R  FS FG+I   +I  G     +GC 
Sbjct: 92  IQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCA 151
Query: 367 FVQFANRKDAEVALQKLQ 384
           FV F  R  A+ A++ + 
Sbjct: 152 FVTFTTRAMAQTAIKAMH 169

>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like Length = 89

Iteration: 1
 Score = 50.1 bits (118), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 24/60 (40%), Positives = 40/60 (66%), Gaps = 1/60 (1%)
Query: 117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQS 176
           T+++G +   MDET + + F+  G V  VK+I ++ TG S+GYGFV FY+    +K+++S
Sbjct: 12  TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVES 70

>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 49.7 bits (117), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 44/179 (24%), Positives = 83/179 (46%), Gaps = 20/179 (11%)
Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTG--QSEGYGFVEFYSRAAAEKVLQ 175
           +++G +     E  L   F   G V  + V+R++     QS+G  FV FY+R AA +   
Sbjct: 6   MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 176 S-YSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYP 234
           + ++  ++P    P ++  A       +  A  D  +F+G ++   T++ ++  FSS + 
Sbjct: 66  ALHNMKVLPGMHHPIQMKPA----DSEKNNAVEDRKLFIGMISKKCTENDIRVMFSS-FG 120
Query: 235 SVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVY-------CSSRPMRIDVA 286
            ++  + I+    G ++G  FV F     R+ A T +  ++       CSS PM +  A
Sbjct: 121 QIEECR-ILRGPDGLSRGCAFVTF---TTRAMAQTAIKAMHQAQTMEGCSS-PMVVKFA 174

>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 49.3 bits (116), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 25/78 (32%), Positives = 40/78 (51%), Gaps = 9/78 (11%)
Query: 316 VQGSQSDGESNNAT----IFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-----KGCG 366
           +Q   +D E NNA     +F+G +    ++ D+R  FS FG+I   +I  G     +GC 
Sbjct: 80  IQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCA 139
Query: 367 FVQFANRKDAEVALQKLQ 384
           FV F  R  A+ A++ + 
Sbjct: 140 FVTFTTRAMAQTAIKAMH 157

>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b Length = 105

Iteration: 1
 Score = 49.7 bits (117), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 26/79 (32%), Positives = 43/79 (54%), Gaps = 2/79 (2%)
Query: 117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQS 176
           T+++G L   + E  L   F   G VVN  + +++ TGQ +GYGFVEF S   A+  ++ 
Sbjct: 17  TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI 76
Query: 177 YSGSLMPNTDQPFRLNWAT 195
               ++    +P R+N A+
Sbjct: 77  M--DMIKLYGKPIRVNKAS 93

>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b Length = 105

Iteration: 1
 Score = 46.2 bits (108), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 26/85 (30%), Positives = 45/85 (52%), Gaps = 1/85 (1%)
Query: 203 TEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDEN 262
           +E   D +++VG L   V++ +L E F    P V    +  D  TG+ +GYGFV F  E 
Sbjct: 10  SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVN-THMPKDRVTGQHQGYGFVEFLSEE 68
Query: 263 ERSRAMTEMNGVYCSSRPMRIDVAT 287
           +   A+  M+ +    +P+R++ A+
Sbjct: 69  DADYAIKIMDMIKLYGKPIRVNKAS 93

>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b Length = 105

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/76 (30%), Positives = 44/76 (57%), Gaps = 6/76 (7%)
Query: 327 NATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK------GCGFVQFANRKDAEVAL 380
           +AT++VG LD  VS+  L E F Q G +++  +P  +      G GFV+F + +DA+ A+
Sbjct: 15  DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 74
Query: 381 QKLQGTAIGKQTVRLS 396
           + +    +  + +R++
Sbjct: 75  KIMDMIKLYGKPIRVN 90

>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 49.3 bits (116), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 9/75 (12%)
Query: 316 VQGSQSDGESNNAT----IFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-----KGCG 366
           +Q   +D E NNA     +F+G +    ++ D+R  FS FG+I   +I  G     +GC 
Sbjct: 80  IQXKPADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQIEECRILRGPDGLSRGCA 139
Query: 367 FVQFANRKDAEVALQ 381
           FV F  R  A+ A++
Sbjct: 140 FVTFTTRAXAQTAIK 154

>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding Motif Protein 9 Length = 103

Iteration: 1
 Score = 48.5 bits (114), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 26/60 (43%), Positives = 36/60 (60%), Gaps = 4/60 (6%)
Query: 341 DEDLREPFSQFGEILSVKIPV----GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLS 396
           D DLR+ F QFG+IL V+I       KG GFV F N  DA+ A +KL GT +  + + ++
Sbjct: 29  DPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN 88

>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U Binding Splicing Factor 60kda (Puf60) From Homo Sapiens At 2.50 A Resolution Length = 200

Iteration: 1
 Score = 48.1 bits (113), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 32/159 (20%), Positives = 71/159 (44%), Gaps = 5/159 (3%)
Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY 177
           +++G +++ + E  +   F+  G + ++    +  T + +G+ FVE+    AA+  L+  
Sbjct: 15  VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 178 SGSLM----PNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKY 233
           +   +        +P  +  A         EA +   I+V  +  D++D  ++  F + +
Sbjct: 75  NSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEA-F 133
Query: 234 PSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMN 272
             +K   +  D  TG+ KGYGF+ +        A++  N
Sbjct: 134 GKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXN 172

>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 = 42.4 bits (98), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 44/213 (20%), Positives = 86/213 (40%), Gaps = 33/213 (15%)
Query: 198 GSDRRTEACS-DLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFV 256
           G+ +R  A +    ++VG +  ++ +  +++ F+   P +K      DS T + KG+ FV
Sbjct: 1   GAAQRQRALAIXCRVYVGSIYYELGEDTIRQAFAPFGP-IKSIDXSWDSVTXKHKGFAFV 59
Query: 257 RFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKASGXXXXXXXXALVLAGGPGSNGARV 316
            +        A+ + N V    R +++                       G P + G   
Sbjct: 60  EYEVPEAAQLALEQXNSVXLGGRNIKV-----------------------GRPSNIGQAQ 96
Query: 317 QGSQSDGESNNA--TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFV 368
                  E   A   I+V ++  D+SD+D++  F  FG+I S  +         KG GF+
Sbjct: 97  PIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFI 156
Query: 369 QFANRKDAEVALQKLQGTAIGKQTVRLSWGRNP 401
           ++   + ++ A+       +G Q +R+     P
Sbjct: 157 EYEKAQSSQDAVSSXNLFDLGGQYLRVGKAVTP 189

>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 = 48.1 bits (113), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 24/60 (40%), Positives = 40/60 (66%), Gaps = 1/60 (1%)
Query: 117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQS 176
           T+++G +   MDET + + F+  G V  VK+I ++ TG S+GYGFV FY+    +K+++S
Sbjct: 11  TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVES 69

>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like In Complex With Rna, Uuguucuu Length = 102

Iteration: 1
 Score = 48.1 bits (113), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 24/60 (40%), Positives = 40/60 (66%), Gaps = 1/60 (1%)
Query: 117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQS 176
           T+++G +   MDET + + F+  G V  VK+I ++ TG S+GYGFV FY+    +K+++S
Sbjct: 11  TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVES 69

>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human Nucleoli Length = 180

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 47/205 (22%), Positives = 84/205 (40%), Gaps = 44/205 (21%)
Query: 203 TEACSDLSIFVGDL-----APDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVR 257
           TE  +  ++FVG+L     AP++   I  + F+      K    ++D   G T+ +G+V 
Sbjct: 2   TEPTTAFNLFVGNLNFNKSAPELKTGI-SDVFA------KNDLAVVDVRIGMTRKFGYVD 54
Query: 258 FGDENERSRAMTEMNGVYCSSRPMRIDVATPKKASGXXXXXXXXALVLAGGPGSNGARVQ 317
           F    +  +A+ E+ G+      ++++   PK                            
Sbjct: 55  FESAEDLEKAL-ELTGLKVFGNEIKLE--KPK---------------------------- 83
Query: 318 GSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEI-LSVKIPVGKGCGFVQFANRKDA 376
           G  S  E +  T+    L   V+ ++L+E F    EI L  K    KG  +++F    DA
Sbjct: 84  GKDSKKERDARTLLAKNLPYKVTQDELKEVFEDAAEIRLVSKDGKSKGIAYIEFKTEADA 143
Query: 377 EVALQKLQGTAIGKQTVRLSWGRNP 401
           E   ++ QGT I  +++ L +   P
Sbjct: 144 EKTFEEKQGTEIDGRSISLYYTGEP 168

>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre Rna Length = 175

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 41/196 (20%), Positives = 90/196 (45%), Gaps = 34/196 (17%)
Query: 203 TEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDEN 262
           +E+ +  ++F+G+L P+ + + L+   S  +   K    ++D  TG  + +G+V F    
Sbjct: 8   SESTTPFNLFIGNLNPNKSVAELKVAISELFA--KNDLAVVDVRTGTNRKFGYVDFESAE 65
Query: 263 ERSRAMTEMNGVYCSSRPMRIDVATPKKASGXXXXXXXXALVLAGGPGSNGARVQGSQSD 322
           +  +A+ E+ G+      ++++   PK                    G +  +V+ ++  
Sbjct: 66  DLEKAL-ELTGLKVFGNEIKLE--KPK--------------------GRDSKKVRAAR-- 100
Query: 323 GESNNATIFVGALDSDVSDEDLREPFSQFGEI-LSVKIPVGKGCGFVQFANRKDAEVALQ 381
                 T+    L  ++++++L+E F    EI L  +    KG  +++F +  DAE  L+
Sbjct: 101 ------TLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLE 154
Query: 382 KLQGTAIGKQTVRLSW 397
           + QG  I  ++V L +
Sbjct: 155 EKQGAEIDGRSVSLYY 170

>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1) Of Hu Antigen C (Huc) Length = 89

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 22/73 (30%), Positives = 43/73 (58%), Gaps = 3/73 (4%)
Query: 223 SILQETFSSKYPSV---KGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSR 279
           ++ Q+ F S + S+   +  K++ D  TG++ GYGFV + D N+  +A+  +NG+   ++
Sbjct: 15  NMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTK 74
Query: 280 PMRIDVATPKKAS 292
            +++  A P  AS
Sbjct: 75  TIKVSYARPSSAS 87

>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In Complex With Ugcaugu Length = 109

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 26/60 (43%), Positives = 36/60 (60%), Gaps = 4/60 (6%)
Query: 341 DEDLREPFSQFGEILSVKIPV----GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLS 396
           D DLR+ F QFG+IL V+I       KG GFV F N  DA+ A +KL GT +  + + ++
Sbjct: 43  DPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN 102

>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 102

Iteration: 1
 Score = 46.2 bits (108), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 27/80 (33%), Positives = 42/80 (52%), Gaps = 4/80 (5%)
Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           ++FV  L+ D T+  L+E+F     SV+ A+++ D  TG +KG+GFV F  E +   A  
Sbjct: 17  TLFVKGLSEDTTEETLKESFDG---SVR-ARIVTDRETGSSKGFGFVDFNSEEDAKAAKE 72
Query: 270 EMNGVYCSSRPMRIDVATPK 289
            M         + +D A PK
Sbjct: 73  AMEDGEIDGNKVTLDWAKPK 92

>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc) In Complex With A Cap Analogue M7gpppg Length = 156

Iteration: 1
 Score = 46.2 bits (108), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 22/77 (28%), Positives = 44/77 (57%), Gaps = 2/77 (2%)
Query: 117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQS 176
           T+++G+L  +  E  ++  FS +G +  + +  +K    + G+ FVE+YSRA AE  ++ 
Sbjct: 41  TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 100
Query: 177 YSGSLMPNTDQPFRLNW 193
            +G+ +   D+  R +W
Sbjct: 101 INGTRLD--DRIIRTDW 115

>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc) In Complex With A Cap Analogue M7gpppg Length = 156

Iteration: 1
 Score = 46.2 bits (108), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 28/91 (30%), Positives = 49/91 (53%), Gaps = 8/91 (8%)
Query: 326 NNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK----GCGF--VQFANRKDAEVA 379
            + T++VG L    ++E + E FS+ G+I  + + + K     CGF  V++ +R DAE A
Sbjct: 38  KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENA 97
Query: 380 LQKLQGTAIGKQTVRLSW--GRNPGNKQWRG 408
           ++ + GT +  + +R  W  G   G +  RG
Sbjct: 98  MRYINGTRLDDRIIRTDWDAGFKEGRQYGRG 128

>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1 Length = 95

Iteration: 1
 Score = 46.2 bits (108), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 26/74 (35%), Positives = 40/74 (54%), Gaps = 4/74 (5%)
Query: 324 ESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV----GKGCGFVQFANRKDAEVA 379
           +S    IF+  LD  + ++ L + FS FG ILS K+       KG GFV F  ++ AE A
Sbjct: 8   KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERA 67
Query: 380 LQKLQGTAIGKQTV 393
           ++K+ G  +  + V
Sbjct: 68  IEKMNGMLLNDRKV 81

>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1 At Ph 6.0 Length = 115

Iteration: 1
 Score = 45.8 bits (107), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 26/75 (34%), Positives = 40/75 (53%), Gaps = 4/75 (5%)
Query: 323 GESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV----GKGCGFVQFANRKDAEV 378
           G   +  IF+  LD  + ++ L + FS FG ILS K+       KG GFV F  ++ AE 
Sbjct: 1   GPLGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAER 60
Query: 379 ALQKLQGTAIGKQTV 393
           A++K+ G  +  + V
Sbjct: 61  AIEKMNGMLLNDRKV 75

>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna- Binding Region Containing Protein 1 Length = 116

Iteration: 1
 Score = 45.4 bits (106), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 22/58 (37%), Positives = 32/58 (55%)
Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQ 175
           I++G L +   +  L   F   G +    VI ++QTG+S GYGFV    RAAAE+  +
Sbjct: 20  IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 77

>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna- Binding Region Containing Protein 1 Length = 116

Iteration: 1
 Score = 42.7 bits (99), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 24/64 (37%), Positives = 35/64 (54%), Gaps = 1/64 (1%)
Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           IFVG L    TD+ L++ F   +  ++ A VI D  TG+++GYGFV   D     RA  +
Sbjct: 20  IFVGGLPYHTTDASLRKYFEG-FGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 271 MNGV 274
            N +
Sbjct: 79  PNPI 82

>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 = 45.4 bits (106), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 27/82 (32%), Positives = 46/82 (56%), Gaps = 2/82 (2%)
Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           +I+VG+L    T   ++E FS ++  V   K+I D  T + KG+GFV   +E+  S A+ 
Sbjct: 3   NIYVGNLVYSATSEQVKELFS-QFGKVFNVKLIYDRETKKPKGFGFVEMQEESV-SEAIA 60
Query: 270 EMNGVYCSSRPMRIDVATPKKA 291
           +++      R +R+  A PKK+
Sbjct: 61  KLDNTDFMGRTIRVTEANPKKS 82

>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 = 45.4 bits (106), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 33/105 (31%), Positives = 53/105 (50%), Gaps = 12/105 (11%)
Query: 307 GGPGSNGARVQ-----GSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV 361
           G  GS+G   Q     GSQ +G    A +F+  L  +  D+DL + F  FG ++S K+ +
Sbjct: 1   GSSGSSGLTQQSIGAAGSQKEGP-EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFI 59
Query: 362 GK-----GC-GFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRN 400
            K      C GFV + N   A+ A+Q + G  IG + +++   R+
Sbjct: 60  DKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRS 104

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 45.1 bits (105), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 20/67 (29%), Positives = 39/67 (58%)
Query: 113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEK 172
           D  + + +  +   +DE  L   F   G + +VK++ +++T QS GYGFV+F S ++A++
Sbjct: 40  DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQ 99
Query: 173 VLQSYSG 179
            +   +G
Sbjct: 100 AIAGLNG 106

>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4 Rna Binding Protein Length = 105

Iteration: 1
 Score = 45.1 bits (105), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 22/62 (35%), Positives = 35/62 (56%), Gaps = 5/62 (8%)
Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-----KGCGFVQFANRKDAEVALQKLQ 384
           +FVG L+   S++D+R  F  FG I    I  G     KGC FV++++  +A+ A+  L 
Sbjct: 18  LFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAINALH 77
Query: 385 GT 386
           G+
Sbjct: 78  GS 79

>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex Length = 98

Iteration: 1
 Score = 45.1 bits (105), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 24/76 (31%), Positives = 44/76 (57%), Gaps = 5/76 (6%)
Query: 327 NATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK---GCGF--VQFANRKDAEVALQ 381
           + T++VG L    ++E + E FS+ G+I  + + + K    CGF  V++ +R DAE A++
Sbjct: 18  SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAMR 77
Query: 382 KLQGTAIGKQTVRLSW 397
            + GT +  + +R  W
Sbjct: 78  YINGTRLDDRIIRTDW 93

>pdb|3SDE|B Chain B, 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 = 21/74 (28%), Positives = 42/74 (56%)
Query: 325 SNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQ 384
           +  + +FVG L  D+++E++R+ F ++G+   V I   KG GF++   R  AE+A  +L 
Sbjct: 20  TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELD 79
Query: 385 GTAIGKQTVRLSWG 398
              +  + +R+ + 
Sbjct: 80  NMPLRGKQLRVRFA 93

>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 3 Subunit 4 Length = 103

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/67 (31%), Positives = 35/67 (52%)
Query: 113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEK 172
           D+  TI + +L     ET L   F   G +  + + ++K TGQS+G+ F+ F+ R  A +
Sbjct: 13  DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAAR 72
Query: 173 VLQSYSG 179
            +   SG
Sbjct: 73  AIAGVSG 79

>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 = 44.7 bits (104), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 25/76 (32%), Positives = 41/76 (53%), Gaps = 6/76 (7%)
Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK------GCGFVQFANRKDAEVALQKL 383
           + V  L  +++ ++LR  FS  GE+ S K+   K      G GFV +   KDAE A+  L
Sbjct: 7   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 66
Query: 384 QGTAIGKQTVRLSWGR 399
            G  +  +T+++S+ R
Sbjct: 67  NGLRLQSKTIKVSYAR 82

>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure Length = 88

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 24/82 (29%), Positives = 43/82 (52%), Gaps = 1/82 (1%)
Query: 207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSR 266
           S+ ++ V  L  D+TD  L   F +  P +   +++ D  TG + GY FV F  E +  R
Sbjct: 2   SNTNLIVNYLPQDMTDRELYALFRAIGP-INTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60
Query: 267 AMTEMNGVYCSSRPMRIDVATP 288
           A+  +NG+   ++ +++  A P
Sbjct: 61  AIKVLNGITVRNKRLKVSYARP 82

>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3 Length = 108

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 24/85 (28%), Positives = 43/85 (50%), Gaps = 2/85 (2%)
Query: 320 QSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVA 379
           + +GE +N  +FV     DV + +L E F  FG +  VKI    G  FV+F   + A  A
Sbjct: 24  RQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--NGFAFVEFEEAESAAKA 81
Query: 380 LQKLQGTAIGKQTVRLSWGRNPGNK 404
           ++++ G +   Q + + + + P  +
Sbjct: 82  IEEVHGKSFANQPLEVVYSKLPAKR 106

>pdb|2KHC|A Chain A, Bruno Rrm3+ Length = 118

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/85 (28%), Positives = 44/85 (51%), Gaps = 1/85 (1%)
Query: 201 RRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGD 260
           ++ E     ++F+  L  + TD+ L  TF   + +V  AKV ID  T  +K +GFV F +
Sbjct: 33  KQIEGPEGCNLFIYHLPQEFTDTDLASTFLP-FGNVISAKVFIDKQTSLSKCFGFVSFDN 91
Query: 261 ENERSRAMTEMNGVYCSSRPMRIDV 285
            +    A+  MNG    ++ +++ +
Sbjct: 92  PDSAQVAIKAMNGFQVGTKRLKVQL 116

>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 = 44.3 bits (103), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/70 (34%), Positives = 43/70 (61%), Gaps = 5/70 (7%)
Query: 112 NDETKTIWIGDL-FHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFY---SR 167
           N  ++ +++G + +   +E  L  C S+ G V+N+K++ + QTG+S+GY F+EF    S 
Sbjct: 1   NPPSRVVYLGSIPYDQTEEQILDLC-SNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESS 59
Query: 168 AAAEKVLQSY 177
           A+A + L  Y
Sbjct: 60  ASAVRNLNGY 69

>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 = 43.9 bits (102), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 25/76 (32%), Positives = 40/76 (52%), Gaps = 6/76 (7%)
Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK------GCGFVQFANRKDAEVALQKL 383
           + V  L  + + ++LR  FS  GE+ S K+   K      G GFV +   KDAE A+  L
Sbjct: 22  LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 81
Query: 384 QGTAIGKQTVRLSWGR 399
            G  +  +T+++S+ R
Sbjct: 82  NGLRLQSKTIKVSYAR 97

>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif, Single-Stranded Interacting Protein 1 Length = 114

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/84 (29%), Positives = 39/84 (46%), Gaps = 4/84 (4%)
Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY 177
           ++I +L   MDE  L N     GQV++ +++R+  +G S G GF    S    E V+  +
Sbjct: 28  LYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHF 86
Query: 178 SGSLM---PNTDQPFRLNWATFSG 198
           +G  +   P    P       FSG
Sbjct: 87  NGKFIKTPPGVSAPTEPLLCKFSG 110

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 22/83 (26%), Positives = 43/83 (51%), Gaps = 6/83 (7%)
Query: 323 GESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDA 376
           G +    ++VG L  +V D+ L   F  FG+I  ++IP+       +G  FV+F   +DA
Sbjct: 1   GSTTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 60
Query: 377 EVALQKLQGTAIGKQTVRLSWGR 399
             A+  +  + +  +T+R++  +
Sbjct: 61  AAAIDNMNESELFGRTIRVNLAK 83

>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/69 (33%), Positives = 37/69 (53%)
Query: 113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEK 172
           DE   +++G L     +  L + FS  G+VV+  ++++K T QS G+GFV+F        
Sbjct: 14  DEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGT 73
Query: 173 VLQSYSGSL 181
           VL S   +L
Sbjct: 74  VLASRPHTL 82

>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second Rna-Binding Domain Of Sex-Lethal Determined By Multidimensional Heteronuclear Magnetic Resonance Spectroscopy Length = 97

Iteration: 1
 Score = 43.1 bits (100), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 26/85 (30%), Positives = 44/85 (51%), Gaps = 3/85 (3%)
Query: 204 EACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENE 263
           E+  D +++V +L   +TD  L   F  KY S+    ++ D  TGR +G  FVR+    E
Sbjct: 9   ESIKDTNLYVTNLPRTITDDQLDTIFG-KYGSIVQKNILRDKLTGRPRGVAFVRYNKREE 67
Query: 264 RSRAMTEMNGVY--CSSRPMRIDVA 286
              A++ +N V     S+P+ + +A
Sbjct: 68  AQEAISALNNVIPEGGSQPLSVRLA 92

>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif Of Nono Length = 99

Iteration: 1
 Score = 43.1 bits (100), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 23/68 (33%), Positives = 40/68 (58%), Gaps = 1/68 (1%)
Query: 325 SNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQ 384
           +  + +FVG L  D+++E++R+ F ++G+   V I   KG GF++   R  AE+A  +L 
Sbjct: 13  TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELD 72
Query: 385 GTAI-GKQ 391
              + GKQ
Sbjct: 73  NMPLRGKQ 80

>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna Length = 88

Iteration: 1
 Score = 43.1 bits (100), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 24/72 (33%), Positives = 34/72 (47%), Gaps = 8/72 (11%)
Query: 325 SNNATIFVGALDSDVSDEDLREPFSQFGEILSVKI--------PVGKGCGFVQFANRKDA 376
           S+   +FVG +    S++DLRE F Q+G +  + +        P  KGC FV F  RK A
Sbjct: 1   SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 377 EVALQKLQGTAI 388
             A   L    +
Sbjct: 61  LEAQNALHNMKV 72

>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G) Length = 97

Iteration: 1
 Score = 43.1 bits (100), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 23/67 (34%), Positives = 42/67 (62%), Gaps = 5/67 (7%)
Query: 115 TKTIWIGDL-FHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFY---SRAAA 170
           ++ +++G + +   +E  L  C S+ G V+N+K++ + QTG+S+GY F+EF    S A+A
Sbjct: 3   SRVVYLGSIPYDQTEEQILDLC-SNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 61
Query: 171 EKVLQSY 177
            + L  Y
Sbjct: 62  VRNLNGY 68

>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G) Length = 97

Iteration: 1
 Score = 42.4 bits (98), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 24/83 (28%), Positives = 43/83 (51%), Gaps = 1/83 (1%)
Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +++G +  D T+  + +  S+  P V   K++ D  TGR+KGY F+ F D    + A+  
Sbjct: 6   VYLGSIPYDQTEEQILDLCSNVGP-VINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 64
Query: 271 MNGVYCSSRPMRIDVATPKKASG 293
           +NG    SR ++   ++    SG
Sbjct: 65  LNGYQLGSRFLKCGYSSNSDISG 87

>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna Length = 174

Iteration: 1
 Score = 42.7 bits (99), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 33/143 (23%), Positives = 58/143 (40%), Gaps = 23/143 (16%)
Query: 152 QTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDL-- 209
           Q  Q + + F+EF S               +  T Q    +   F G   +     D   
Sbjct: 48  QINQDKNFAFLEFRS---------------VDETTQAMAFDGIIFQGQSLKIRRPHDYQP 92
Query: 210 -----SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENER 264
                 +F+G L   + D  ++E  +S  P +K   ++ DS TG +KGY F  + D N  
Sbjct: 93  LPGAHKLFIGGLPNYLNDDQVKELLTSFGP-LKAFNLVKDSATGLSKGYAFCEYVDINVT 151
Query: 265 SRAMTEMNGVYCSSRPMRIDVAT 287
            +A+  +NG+    + + +  A+
Sbjct: 152 DQAIAGLNGMQLGDKKLLVQRAS 174

>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract Length = 172

Iteration: 1
 Score = 42.7 bits (99), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 33/143 (23%), Positives = 58/143 (40%), Gaps = 23/143 (16%)
Query: 152 QTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDL-- 209
           Q  Q + + F+EF S               +  T Q    +   F G   +     D   
Sbjct: 46  QINQDKNFAFLEFRS---------------VDETTQAMAFDGIIFQGQSLKIRRPHDYQP 90
Query: 210 -----SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENER 264
                 +F+G L   + D  ++E  +S  P +K   ++ DS TG +KGY F  + D N  
Sbjct: 91  LPGAHKLFIGGLPNYLNDDQVKELLTSFGP-LKAFNLVKDSATGLSKGYAFCEYVDINVT 149
Query: 265 SRAMTEMNGVYCSSRPMRIDVAT 287
            +A+  +NG+    + + +  A+
Sbjct: 150 DQAIAGLNGMQLGDKKLLVQRAS 172

>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human Putative Rna-Binding Protein 11 Length = 95

Iteration: 1
 Score = 42.7 bits (99), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 28/82 (34%), Positives = 40/82 (48%), Gaps = 4/82 (4%)
Query: 207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSR 266
           +D ++FVG+L   V + IL E F    P  K    I     G+ K +GFV F      S 
Sbjct: 15  ADRTVFVGNLEARVREEILYELFLQAGPLTK--VTICKDREGKPKSFGFVCFKHPESVSY 72
Query: 267 AMTEMNGVYCSSRPMRIDVATP 288
           A+  +NG+    RP  I+V+ P
Sbjct: 73  AIALLNGIRLYGRP--INVSGP 92

>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5 Rna Binding Protein Length = 105

Iteration: 1
 Score = 42.4 bits (98), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 22/62 (35%), Positives = 34/62 (54%), Gaps = 5/62 (8%)
Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-----KGCGFVQFANRKDAEVALQKLQ 384
           +FVG L+   S+ED+   F  FG I    +  G     KGC FV+F++  +A+ A+  L 
Sbjct: 18  LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALH 77
Query: 385 GT 386
           G+
Sbjct: 78  GS 79

>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2) Of Hu Antigen C (Huc) Length = 85

Iteration: 1
 Score = 42.0 bits (97), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 21/65 (32%), Positives = 39/65 (60%), Gaps = 6/65 (9%)
Query: 327 NATIFVGALDSDVSDEDLREPFSQFGEILSVKI------PVGKGCGFVQFANRKDAEVAL 380
           +A ++V  L   +S +++ + FSQ+G I++ +I       V +G GF++F  R +AE A+
Sbjct: 1   DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 60
Query: 381 QKLQG 385
           + L G
Sbjct: 61  KGLNG 65

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 42.0 bits (97), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 26/89 (29%), Positives = 46/89 (51%), Gaps = 10/89 (11%)
Query: 321 SDGESNNAT----IFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQF 370
           S G S  AT    ++VG L  +V D+ L   F  FG+I  ++IP+       +G  FV+F
Sbjct: 2   SSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 61
Query: 371 ANRKDAEVALQKLQGTAIGKQTVRLSWGR 399
              +DA  A+  +  + +  +T+R++  +
Sbjct: 62  ELAEDAAAAIDNMNESELFGRTIRVNLAK 90

>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu) Length = 96

Iteration: 1
 Score = 42.0 bits (97), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 23/83 (27%), Positives = 43/83 (51%), Gaps = 1/83 (1%)
Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +++G +  D T+  + +  S+  P +   K++ D  TGR+KGY F+ F D    + A+  
Sbjct: 5   VYLGSIPYDQTEEQILDLCSNVGPVIN-LKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63
Query: 271 MNGVYCSSRPMRIDVATPKKASG 293
           +NG    SR ++   ++    SG
Sbjct: 64  LNGYQLGSRFLKCGYSSNSDISG 86

>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33 Length = 85

Iteration: 1
 Score = 41.6 bits (96), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 21/76 (27%), Positives = 41/76 (53%), Gaps = 6/76 (7%)
Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKL 383
           ++VG L  +V D+ L   F  FG+I  ++IP+       +G  FV+F   +DA  A+  +
Sbjct: 10  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 384 QGTAIGKQTVRLSWGR 399
             + +  +T+R++  +
Sbjct: 70  NESELFGRTIRVNLAK 85

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	449
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-75
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-40
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-17
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-16
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	3e-68
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	9e-49
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	3e-19
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-64
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-39
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-33
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-18
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-62
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-34
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-33
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	3e-51
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	4e-40
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	1e-20
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	7e-46
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-41
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	3e-18
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	4e-44
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	5e-38
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	8e-20
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-39
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	6e-38
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	6e-17
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	7e-39
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-34
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	9e-15
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	6e-12
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-37
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	1e-36
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	1e-13
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	2e-37
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	9e-15
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	1e-11
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	2e-35
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	6e-19
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	2e-13
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	2e-35
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	3e-17
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	9e-16
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	7e-35
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	3e-22
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	2e-15
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-07
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	7e-35
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	3e-33
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	9e-18
2div_A	99	TRNA selenocysteine associated protein; structural	1e-34
2div_A	99	TRNA selenocysteine associated protein; structural	2e-20
2div_A	99	TRNA selenocysteine associated protein; structural	1e-14
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	3e-34
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	4e-13
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	2e-11
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-33
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-21
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-16
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	4e-08
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	3e-32
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	8e-32
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-10
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-32
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	9e-12
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-10
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	6e-32
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	7e-11
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	9e-11
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	6e-32
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-16
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-15
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	5e-31
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	4e-14
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	5e-08
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	6e-31
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-28
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	3e-11
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-09
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	2e-30
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	1e-16
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	2e-12
1x5p_A	97	Negative elongation factor E; structure genomics,	7e-30
1x5p_A	97	Negative elongation factor E; structure genomics,	2e-10
1x5p_A	97	Negative elongation factor E; structure genomics,	1e-09
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	4e-29
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	4e-14
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	1e-09
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	2e-28
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	6e-28
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	2e-09
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	2e-28
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	9e-20
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	5e-16
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	9e-28
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-18
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-15
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-10
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	2e-27
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	6e-13
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	1e-06
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	4e-27
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	2e-14
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	6e-09
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	6e-26
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	9e-16
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	9e-11
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	8e-26
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	4e-14
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	5e-09
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	1e-24
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	8e-13
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	1e-10
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-24
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	4e-08
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	4e-04
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	1e-23
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	7e-09
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	4e-07
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	2e-22
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	4e-17
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	5e-11
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	5e-22
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	2e-17
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	8e-14
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	1e-21
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	9e-17
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	9e-12
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	1e-21
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	2e-14
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	1e-11
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	2e-21
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	4e-15
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	3e-11
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	2e-21
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	3e-17
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	9e-14
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	2e-21
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	6e-16
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	1e-09
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	3e-21
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	3e-16
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	8e-12
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	4e-21
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	5e-14
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	9e-12
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	4e-21
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	2e-17
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	4e-13
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	5e-21
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	2e-15
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	5e-11
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	6e-21
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	4e-16
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	3e-14
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	6e-21
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	1e-14
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-12
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	8e-21
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	3e-17
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	2e-14
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	2e-20
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	1e-16
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	2e-12
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	2e-20
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	2e-16
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	5e-11
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-20
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	4e-16
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-10
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-20
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	1e-14
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	3e-20
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	2e-12
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	4e-20
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	7e-16
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	6e-12
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	6e-20
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	4e-16
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	1e-11
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	7e-20
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	3e-16
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	2e-10
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	1e-19
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	6e-16
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	6e-10
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	1e-19
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	4e-15
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	2e-12
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	1e-19
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	1e-05
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	2e-19
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	1e-14
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	7e-12
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	2e-19
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	9e-16
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	9e-12
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	3e-19
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	3e-16
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	6e-14
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	3e-19
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	3e-12
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	1e-10
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	4e-19
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	1e-16
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	4e-11
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	4e-19
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	4e-14
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	1e-11
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	5e-19
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	4e-16
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	6e-10
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	6e-19
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	2e-07
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	3e-06
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	6e-19
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	4e-12
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	4e-11
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	6e-19
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	3e-15
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	2e-06
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	8e-19
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	9e-16
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	6e-07
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	9e-19
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	2e-16
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	7e-11
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	1e-18
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	1e-16
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	3e-09
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	1e-18
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	7e-16
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	9e-09
1x4e_A	85	RNA binding motif, single-stranded interacting pro	1e-18
1x4e_A	85	RNA binding motif, single-stranded interacting pro	3e-16
1x4e_A	85	RNA binding motif, single-stranded interacting pro	2e-12
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	2e-18
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	4e-11
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	9e-05
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	2e-18
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	9e-18
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	3e-11
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	2e-18
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	1e-15
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	3e-08
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	5e-18
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	8e-16
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	6e-10
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	6e-18
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	5e-17
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	5e-05
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	7e-18
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	1e-14
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	1e-12
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	7e-18
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	4e-16
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	9e-10
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	8e-18
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	2e-17
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	6e-13
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	9e-18
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	2e-16
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	1e-09
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	1e-17
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	2e-14
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	3e-10
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	1e-17
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	1e-10
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	1e-04
1x5o_A	114	RNA binding motif, single-stranded interacting pro	1e-17
1x5o_A	114	RNA binding motif, single-stranded interacting pro	3e-15
1x5o_A	114	RNA binding motif, single-stranded interacting pro	3e-11
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	1e-17
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	3e-12
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	1e-05
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	1e-17
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	3e-14
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	1e-10
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	1e-17
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	1e-12
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	2e-05
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	2e-17
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	1e-10
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	2e-08
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	2e-17
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	1e-12
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	1e-05
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	2e-17
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	7e-12
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	5e-11
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	2e-17
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	3e-16
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	2e-09
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	3e-17
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	1e-14
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	2e-09
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	4e-17
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	1e-13
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	1e-11
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	4e-17
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-14
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	6e-09
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	5e-17
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	3e-13
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	5e-06
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	7e-17
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	5e-14
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	7e-12
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	8e-17
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	2e-15
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	4e-06
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	1e-16
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	1e-10
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	3e-05
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	2e-16
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	7e-13
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	1e-10
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	6e-16
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	6e-12
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	5e-08
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	6e-16
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	9e-12
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	4e-10
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	9e-16
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	1e-15
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	7e-13
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	1e-15
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	8e-14
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	4e-11
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	1e-15
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	2e-14
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	8e-12
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	2e-15
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	8e-11
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	1e-05
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	2e-15
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	7e-15
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	3e-07
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	2e-15
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	6e-08
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	5e-04
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	2e-15
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	2e-11
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	4e-08
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	4e-15
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	9e-09
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	4e-15
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	6e-08
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	7e-04
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	4e-15
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	9e-14
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	1e-13
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	6e-15
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	7e-13
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	1e-05
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	1e-14
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	1e-12
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	6e-05
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	1e-14
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	1e-11
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	2e-07
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	1e-14
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	5e-11
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	8e-11
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	2e-14
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	6e-11
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	4e-10
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	3e-14
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	5e-08
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	5e-07
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	3e-14
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	9e-09
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	5e-08
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	4e-14
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	4e-12
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	2e-05
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	4e-14
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	2e-12
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	4e-07
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	4e-14
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	2e-10
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	2e-10
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	5e-14
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	1e-08
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	2e-05
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	6e-14
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	2e-10
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	5e-09
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	1e-13
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	2e-10
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	2e-05
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	1e-13
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	7e-11
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	1e-10
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	1e-13
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	9e-11
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	2e-09
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	1e-13
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	1e-08
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	7e-07
2dis_A	109	Unnamed protein product; structural genomics, RRM	2e-13
2dis_A	109	Unnamed protein product; structural genomics, RRM	3e-10
2dis_A	109	Unnamed protein product; structural genomics, RRM	1e-08
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	2e-13
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	3e-07
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	3e-13
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	2e-11
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	3e-06
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	5e-13
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	4e-08
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	1e-04
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	8e-13
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	7e-07
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	4e-05
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	8e-13
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	2e-06
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	4e-05
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	9e-13
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	5e-06
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	3e-04
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	1e-12
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	3e-07
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	1e-04
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	2e-12
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	4e-11
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	4e-11
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-12
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-10
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	3e-08
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	2e-12
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	5e-10
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	3e-08
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	2e-12
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	2e-06
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	4e-12
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	5e-08
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	1e-04
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	5e-12
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	1e-11
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	1e-08
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	6e-12
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	2e-10
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	3e-09
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	6e-12
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	2e-08
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	2e-05
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	1e-11
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	1e-10
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	6e-05
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	5e-11
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	7e-07
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	1e-10
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	2e-10
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	4e-08
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	1e-10
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	4e-09
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	2e-10
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	9e-10
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	4e-05
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	3e-10
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	1e-09
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	4e-10
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	7e-10
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	5e-10
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	3e-07
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	3e-05
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	6e-10
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	1e-07
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	7e-10
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-09
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-04
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	9e-10
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	3e-08
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	4e-05
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	1e-09
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	1e-07
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	5e-04
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	6e-09
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	3e-06
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	6e-09
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	8e-07
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	2e-08
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	6e-06
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	2e-08
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	2e-08
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	3e-06
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	6e-04
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	5e-08
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	1e-05
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	5e-08
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	1e-05
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	5e-08
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	4e-06
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	8e-08
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	2e-07
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	5e-05
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	1e-04
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	2e-07
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	1e-04
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	2e-06
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	6e-06
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	9e-06
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	3e-04
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	2e-05
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	4e-04
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	2e-05
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	4e-05
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	6e-05
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	7e-05
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	2e-04
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	4e-04
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	8e-05
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	1e-04
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	5e-04

>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 =  231 bits (591), Expect = 4e-75
 Identities = 52/172 (30%), Positives = 86/172 (50%), Gaps = 7/172 (4%)

Query: 116 KTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQ 175
           + +++G+L   + E  L   F   G + N+K++ +K   ++  Y FVE++    A   LQ
Sbjct: 1   RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQ 59

Query: 176 SYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPS 235
           + +G  + N     ++NWA  S            ++FVGDL  +V D  L+  F   +PS
Sbjct: 60  TLNGKQIEN--NIVKINWAFQSQQSSSD---DTFNLFVGDLNVNVDDETLRNAFK-DFPS 113

Query: 236 VKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVAT 287
                V+ D  TG ++GYGFV F  +++   AM  M G   + RP+RI+ A 
Sbjct: 114 YLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAA 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 =  141 bits (357), Expect = 2e-40
 Identities = 46/194 (23%), Positives = 83/194 (42%), Gaps = 38/194 (19%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
            ++VG+L   +T+ IL++ F      +   K++ID    +   Y FV +   ++ + A+ 
Sbjct: 2   VLYVGNLDKAITEDILKQYFQV-GGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQ 59

Query: 270 EMNGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNAT 329
            +NG    +  ++I+ A                                SQ     +   
Sbjct: 60  TLNGKQIENNIVKINWAFQ------------------------------SQQSSSDDTFN 89

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPV----G--KGCGFVQFANRKDAEVALQKL 383
           +FVG L+ +V DE LR  F  F   LS  +      G  +G GFV F ++ DA+ A+  +
Sbjct: 90  LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 149

Query: 384 QGTAIGKQTVRLSW 397
           QG  +  + +R++W
Sbjct: 150 QGQDLNGRPLRINW 163

>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 = 78.3 bits (194), Expect = 2e-17
 Identities = 23/88 (26%), Positives = 41/88 (46%), Gaps = 5/88 (5%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK-----GCGFVQFANRKDAEVALQKL 383
            ++VG LD  ++++ L++ F   G I ++KI + K        FV++    DA +ALQ L
Sbjct: 2   VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTL 61

Query: 384 QGTAIGKQTVRLSWGRNPGNKQWRGDHS 411
            G  I    V+++W             +
Sbjct: 62  NGKQIENNIVKINWAFQSQQSSSDDTFN 89

>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 = 74.5 bits (184), Expect = 5e-16
 Identities = 29/84 (34%), Positives = 46/84 (54%), Gaps = 2/84 (2%)

Query: 112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAE 171
           +D+T  +++GDL   +D+  L N F      ++  V+ + QTG S GYGFV F S+  A+
Sbjct: 84  SDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQ 143

Query: 172 KVLQSYSGSLMPNTDQPFRLNWAT 195
             + S  G  +    +P R+NWA 
Sbjct: 144 NAMDSMQGQDLNG--RPLRINWAA 165

>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 =  215 bits (550), Expect = 3e-68
 Identities = 53/205 (25%), Positives = 101/205 (49%), Gaps = 11/205 (5%)

Query: 112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAE 171
           +    ++++GDL   + E  L+  FS  G +++++V R+  T +S GY +V F   A AE
Sbjct: 12  SYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAE 71

Query: 172 KVLQSYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSS 231
           + L + +  ++    +P R+ W+    S R++      +IF+ +L   + +  L +TF S
Sbjct: 72  RALDTMNFDVIKG--KPVRIMWSQRDPSLRKS---GVGNIFIKNLDKSIDNKALYDTF-S 125

Query: 232 KYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKA 291
            + ++   KV+ D     +KGYGFV F  +    RA+ +MNG+  + R + +     +K 
Sbjct: 126 AFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKE 183

Query: 292 SGYQQQYSSQALVLAGGP---GSNG 313
              +    ++       P   GS+G
Sbjct: 184 REAELGARAKEFYPYDVPDYAGSSG 208

>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 =  165 bits (419), Expect = 9e-49
 Identities = 55/216 (25%), Positives = 90/216 (41%), Gaps = 35/216 (16%)

Query: 194 ATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGY 253
                 +    +    S++VGDL PDVT+++L E FS     +   +V  D  T R+ GY
Sbjct: 1   GPLGSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSP-AGPILSIRVCRDMITRRSLGY 59

Query: 254 GFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNG 313
            +V F    +  RA+  MN      +P+RI  +                           
Sbjct: 60  AYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDP----------------------- 96

Query: 314 ARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV----GKGCGFVQ 369
                  S  +S    IF+  LD  + ++ L + FS FG ILS K+       KG GFV 
Sbjct: 97  -------SLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVH 149

Query: 370 FANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQ 405
           F  ++ AE A++K+ G  +  + V +   ++   ++
Sbjct: 150 FETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKERE 185

>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 = 85.0 bits (211), Expect = 3e-19
 Identities = 30/110 (27%), Positives = 47/110 (42%), Gaps = 11/110 (10%)

Query: 308 GPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------ 361
           GP         + S      A+++VG L  DV++  L E FS  G ILS+++        
Sbjct: 1   GPLG-----SMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRR 55

Query: 362 GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQWRGDHS 411
             G  +V F    DAE AL  +    I  + VR+ W +   + +  G  +
Sbjct: 56  SLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGN 105

>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 =  207 bits (529), Expect = 3e-64
 Identities = 48/296 (16%), Positives = 100/296 (33%), Gaps = 56/296 (18%)

Query: 116 KTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQ 175
           + I I  L   +    +H+  S    +    V + K      G  FV   +   AE  + 
Sbjct: 23  RKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYK------GTAFVTLLNGEQAEAAIN 75

Query: 176 SYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPS 235
           ++  S +    +   +               +D  + V +L P +T    +E     + S
Sbjct: 76  AFHQSRLRE--RELSVQLQP-----------TDALLCVANLPPSLTQQQFEELVR-PFGS 121

Query: 236 VKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKASGYQ 295
           ++   ++    TG++KGYGF  +  ++  +RA +++ G     R + +            
Sbjct: 122 LERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAG------ 175

Query: 296 QQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDED-LREPFSQFGEI 354
                                    +    ++  + V  L    +D D L    S     
Sbjct: 176 -----------------------QLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSP 212

Query: 355 LSVKIPVG-----KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQ 405
              ++  G     KG   +++   + AE A Q+  G ++G   +R+S+       +
Sbjct: 213 TFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPGR 268

>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 =  142 bits (361), Expect = 1e-39
 Identities = 31/189 (16%), Positives = 65/189 (34%), Gaps = 9/189 (4%)

Query: 117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQS 176
            + + +L   + +          G +    ++ +++TGQS+GYGF E+  + +A +    
Sbjct: 97  LLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSD 156

Query: 177 YSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDS-ILQETFSSKYPS 235
             G  +    +   ++W                 + V  L P   D   L    S    S
Sbjct: 157 LLGKPLGP--RTLYVHWTD--AGQLTPALLHSRCLCVDRLPPGFNDVDALCRALS-AVHS 211

Query: 236 VKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPK--KASG 293
               ++      G+ KG+  + +        A  + +G+      +R+    P     S 
Sbjct: 212 PTFCQLACG-QDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPGRSM 270

Query: 294 YQQQYSSQA 302
                ++QA
Sbjct: 271 LAALIAAQA 279

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score =  125 bits (317), Expect = 3e-33
 Identities = 30/217 (13%), Positives = 60/217 (27%), Gaps = 57/217 (26%)

Query: 187 QPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSN 246
           +  R             +  +   I +  L  DVT+  + +  S           +    
Sbjct: 6   EEIRKRL-----EHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDY-----E---LKYCF 52

Query: 247 TGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLA 306
             + KG  FV   +  +   A+   +      R + + +                     
Sbjct: 53  VDKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQP------------------- 93

Query: 307 GGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV----- 361
                               +A + V  L   ++ +   E    FG +    +       
Sbjct: 94  -------------------TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTG 134

Query: 362 -GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSW 397
             KG GF ++  +  A  A   L G  +G +T+ + W
Sbjct: 135 QSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHW 171

>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 = 84.6 bits (210), Expect = 1e-18
 Identities = 15/90 (16%), Positives = 37/90 (41%), Gaps = 2/90 (2%)

Query: 315 RVQGSQSDGE-SNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANR 373
           R +   ++ +  N   I +  L  DV+++++ +  S +  +    +   KG  FV   N 
Sbjct: 9   RKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYKGTAFVTLLNG 67

Query: 374 KDAEVALQKLQGTAIGKQTVRLSWGRNPGN 403
           + AE A+     + + ++ + +        
Sbjct: 68  EQAEAAINAFHQSRLRERELSVQLQPTDAL 97

>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 =  202 bits (516), Expect = 3e-62
 Identities = 46/294 (15%), Positives = 105/294 (35%), Gaps = 52/294 (17%)

Query: 112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAE 171
           N E  T+ + +L    ++  ++  F H G +++V V  +    ++  +  +EF     A 
Sbjct: 38  NRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFRFARIEFARYDGAL 95

Query: 172 KVLQSYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSS 231
             +      +         ++  T              ++++ +  P  T   +++    
Sbjct: 96  AAITKTHKVVG---QNEIIVSHLTEC------------TLWMTNFPPSYTQRNIRDLLQ- 139

Query: 232 KYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKA 291
               V  +  +       ++ + ++    + +    + ++NG+      +   V+ P + 
Sbjct: 140 DINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEK 199

Query: 292 SGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDED-LREPFSQ 350
           S      + +                            I +  L +++ DE+ LRE F  
Sbjct: 200 SKRTDSATLE-------------------------GREIMIRNLSTELLDENLLRESFEG 234

Query: 351 FGEILSVKIPVG-------KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSW 397
           FG I  + IP G         C F+ F N+  AE ALQ +  + +G + + +S 
Sbjct: 235 FGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSL 287

>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 =  129 bits (326), Expect = 2e-34
 Identities = 32/263 (12%), Positives = 77/263 (29%), Gaps = 68/263 (25%)

Query: 156 SEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATFSGSD---RRTEACSDLSIF 212
           S  YG    ++R  +++ L         +   P      +   ++   R  E  +   + 
Sbjct: 1   SMEYGH---HARPDSKRPL---------DEGSPAAAGLTSKKANEALTRNRELTT---VL 45

Query: 213 VGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMN 272
           V +L      + + + F      +    V       +   +  + F   +    A+T+ +
Sbjct: 46  VKNLPKSYNQNKVYKYFK-HCGPIIHVDVADS--LKKNFRFARIEFARYDGALAAITKTH 102

Query: 273 GVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFV 332
                   + +                                             T+++
Sbjct: 103 K-VVGQNEIIV---------------------------------------SHLTECTLWM 122

Query: 333 GALDSDVSDEDLREPFSQFGEI-LSVKIP---VG--KGCGFVQFANRKDAEVALQKLQGT 386
                  +  ++R+       + LS+++P       +   ++   +++DA   ++KL G 
Sbjct: 123 TNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGL 182

Query: 387 AIGKQTVRLSWGRNPGNKQWRGD 409
            I   T+      NP  K  R D
Sbjct: 183 KIEGYTLVTKV-SNPLEKSKRTD 204

>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 =  126 bits (319), Expect = 2e-33
 Identities = 25/194 (12%), Positives = 75/194 (38%), Gaps = 8/194 (4%)

Query: 100 NGKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGY 159
           +     +    ++    T+W+ +      +  + +       V     + + +   S  +
Sbjct: 102 HKVVGQNEIIVSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRF 161

Query: 160 GFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLS--IFVGDLA 217
            +++  S+  A   ++  +G  +           +      +RT++ +     I + +L+
Sbjct: 162 AYIDVTSKEDARYCVEKLNGLKIE--GYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLS 219

Query: 218 PDVTD-SILQETFSSKYPSVKGAKVIID-SNTGRTKGYGFVRFGDENERSRAMTEMNGVY 275
            ++ D ++L+E+F   + S++   +              F+ F +++   RA+ +MN   
Sbjct: 220 TELLDENLLRESFE-GFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSL 277

Query: 276 CSSRPMRIDVATPK 289
             +R + + +A  K
Sbjct: 278 LGNREISVSLADKK 291

>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 =  169 bits (431), Expect = 3e-51
 Identities = 44/172 (25%), Positives = 85/172 (49%), Gaps = 10/172 (5%)

Query: 117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQS 176
            + +  L   M +  L+  F   G +   +++R+ +TG S GY FV+F S   +++ ++ 
Sbjct: 5   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64

Query: 177 YSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSV 236
            +G  + N  +  ++++A         E+  D +++V +L   +TD  L   F  KY S+
Sbjct: 65  LNGITVRN--KRLKVSYA-----RPGGESIKDTNLYVTNLPRTITDDQLDTIF-GKYGSI 116

Query: 237 KGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVY--CSSRPMRIDVA 286
               ++ D  TGR +G  FVR+    E   A++ +N V     S+P+ + +A
Sbjct: 117 VQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 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 =  140 bits (355), Expect = 4e-40
 Identities = 41/195 (21%), Positives = 79/195 (40%), Gaps = 39/195 (20%)

Query: 207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSR 266
           S+ ++ V  L  D+TD  L   F +    +   +++ D  TG + GY FV F  E +  R
Sbjct: 2   SNTNLIVNYLPQDMTDRELYALFRA-IGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60

Query: 267 AMTEMNGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESN 326
           A+  +NG+   ++ +++  A P                               +S  ++N
Sbjct: 61  AIKVLNGITVRNKRLKVSYARPG-----------------------------GESIKDTN 91

Query: 327 NATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVAL 380
              ++V  L   ++D+ L   F ++G I+   I         +G  FV++  R++A+ A+
Sbjct: 92  ---LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 148

Query: 381 QKLQGTAIGKQTVRL 395
             L        +  L
Sbjct: 149 SALNNVIPEGGSQPL 163

>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 = 87.6 bits (218), Expect = 1e-20
 Identities = 21/87 (24%), Positives = 40/87 (45%), Gaps = 6/87 (6%)

Query: 325 SNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEV 378
           ++N  + V  L  D++D +L   F   G I + +I          G  FV F +  D++ 
Sbjct: 1   ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60

Query: 379 ALQKLQGTAIGKQTVRLSWGRNPGNKQ 405
           A++ L G  +  + +++S+ R  G   
Sbjct: 61  AIKVLNGITVRNKRLKVSYARPGGESI 87

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score =  157 bits (399), Expect = 7e-46
 Identities = 37/209 (17%), Positives = 85/209 (40%), Gaps = 15/209 (7%)

Query: 98  LSNGKQNGSN----NNFTNDETKTIWIGDLFHW-MDETFLHNCFSHTGQVVNVKVIRNKQ 152
           ++ G+Q G                +++G + ++ + E  +   F+  G + ++ +  +  
Sbjct: 7   MTGGQQMGRGSAAQRQGALAIMSRVYVGSI-YYELGEDTIRQAFAPFGPIKSIDMSWDSV 65

Query: 153 TGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWAT------FSGSDRRTEAC 206
           T + +G+ FVE+    AA+  L+  +  ++    +  ++   +              EA 
Sbjct: 66  TMKHKGFAFVEYEVPEAAQLALEQMNSVML--GGRNIKVGRPSNIGQAQPIIDQLAEEAR 123

Query: 207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSR 266
           +   I+V  +  D++D  ++  F   +  +K A +  D  TG+ KGYGF+ +        
Sbjct: 124 AFNRIYVASVHQDLSDDDIKSVFE-AFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQD 182

Query: 267 AMTEMNGVYCSSRPMRIDVATPKKASGYQ 295
           A++ MN      + +R+  A         
Sbjct: 183 AVSSMNLFDLGGQYLRVGKAVTPPMPLLT 211

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score =  145 bits (369), Expect = 2e-41
 Identities = 38/212 (17%), Positives = 87/212 (41%), Gaps = 29/212 (13%)

Query: 199 SDRRTEACSDL-SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVR 257
           + +R  A + +  ++VG +  ++ +  +++ F+  +  +K   +  DS T + KG+ FV 
Sbjct: 18  AAQRQGALAIMSRVYVGSIYYELGEDTIRQAFA-PFGPIKSIDMSWDSVTMKHKGFAFVE 76

Query: 258 FGDENERSRAMTEMNGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQ 317
           +        A+ +MN V    R +++   +                            + 
Sbjct: 77  YEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIG---------------------QAQPII 115

Query: 318 GSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFA 371
              ++       I+V ++  D+SD+D++  F  FG+I S  +         KG GF+++ 
Sbjct: 116 DQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYE 175

Query: 372 NRKDAEVALQKLQGTAIGKQTVRLSWGRNPGN 403
             + ++ A+  +    +G Q +R+     P  
Sbjct: 176 KAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPM 207

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 82.4 bits (204), Expect = 3e-18
 Identities = 25/119 (21%), Positives = 56/119 (47%), Gaps = 8/119 (6%)

Query: 299 SSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVK 358
           S  A +  G     G+  Q   +   +  + ++VG++  ++ ++ +R+ F+ FG I S+ 
Sbjct: 2   SHMASMTGGQQMGRGSAAQRQGA--LAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSID 59

Query: 359 IPV------GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQWRGDHS 411
           +         KG  FV++   + A++AL+++    +G + +++    N G  Q   D  
Sbjct: 60  MSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQL 118

>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 =  151 bits (383), Expect = 4e-44
 Identities = 43/172 (25%), Positives = 87/172 (50%), Gaps = 10/172 (5%)

Query: 117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQS 176
            + +  L   M +    + F   G++ + K++R+K TGQS GYGFV +     AEK + +
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 177 YSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSV 236
            +G  +    +  ++++A        + +  D +++V  L   +T   L++ F S+Y  +
Sbjct: 64  LNGLRLQT--KTIKVSYA-----RPSSASIRDANLYVSGLPKTMTQKELEQLF-SQYGRI 115

Query: 237 KGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVY--CSSRPMRIDVA 286
             +++++D  TG ++G GF+RF    E   A+  +NG     ++ P+ +  A
Sbjct: 116 ITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 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 =  135 bits (341), Expect = 5e-38
 Identities = 43/185 (23%), Positives = 84/185 (45%), Gaps = 39/185 (21%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           ++ V  L  ++T    +  F S    ++  K++ D  TG++ GYGFV + D  +  +A+ 
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGS-IGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

Query: 270 EMNGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNAT 329
            +NG+   ++ +++  A P                              S S  ++N   
Sbjct: 63  TLNGLRLQTKTIKVSYARPS-----------------------------SASIRDAN--- 90

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVALQKL 383
           ++V  L   ++ ++L + FSQ+G I++ +I V       +G GF++F  R +AE A++ L
Sbjct: 91  LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150

Query: 384 QGTAI 388
            G   
Sbjct: 151 NGQKP 155

>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 = 85.3 bits (212), Expect = 8e-20
 Identities = 24/86 (27%), Positives = 40/86 (46%), Gaps = 6/86 (6%)

Query: 326 NNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVA 379
           +   + V  L  +++ E+ R  F   GEI S K+          G GFV + + KDAE A
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 380 LQKLQGTAIGKQTVRLSWGRNPGNKQ 405
           +  L G  +  +T+++S+ R      
Sbjct: 61  INTLNGLRLQTKTIKVSYARPSSASI 86

>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 =  138 bits (351), Expect = 2e-39
 Identities = 32/177 (18%), Positives = 69/177 (38%), Gaps = 13/177 (7%)

Query: 113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEK 172
                ++IG+L        L    S      ++ V+  + TG +  +G+V+F S    EK
Sbjct: 11  TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFESAEDLEK 69

Query: 173 VLQSYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSK 232
            L+  +G  +       +L            +  +  ++   +L+ ++T+  L+E F   
Sbjct: 70  ALE-LTGLKV--FGNEIKLEKPK---GRDSKKVRAARTLLAKNLSFNITEDELKEVFEDA 123

Query: 233 YPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPK 289
                  ++ + S  G++KG  ++ F  E +  + + E  G     R + +     K
Sbjct: 124 ------LEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK 174

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score =  135 bits (341), Expect = 6e-38
 Identities = 40/203 (19%), Positives = 84/203 (41%), Gaps = 36/203 (17%)

Query: 197 SGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFV 256
           S     +E+ +  ++F+G+L P+ + + L+   S +  +     V+ D  TG  + +G+V
Sbjct: 2   SHMVEGSESTTPFNLFIGNLNPNKSVAELKVAIS-ELFAKNDLAVV-DVRTGTNRKFGYV 59

Query: 257 RFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARV 316
            F    +  +A+ E+ G+      ++++    +                           
Sbjct: 60  DFESAEDLEKAL-ELTGLKVFGNEIKLEKPKGRD-------------------------- 92

Query: 317 QGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG--KGCGFVQFANRK 374
               S       T+    L  ++++++L+E F    EI  V    G  KG  +++F +  
Sbjct: 93  ----SKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-QDGKSKGIAYIEFKSEA 147

Query: 375 DAEVALQKLQGTAIGKQTVRLSW 397
           DAE  L++ QG  I  ++V L +
Sbjct: 148 DAEKNLEEKQGAEIDGRSVSLYY 170

>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 = 77.3 bits (191), Expect = 6e-17
 Identities = 20/101 (19%), Positives = 41/101 (40%), Gaps = 9/101 (8%)

Query: 318 GSQSD---GESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIP-----VGKGCGFVQ 369
           GS        +    +F+G L+ + S  +L+   S+      + +        +  G+V 
Sbjct: 1   GSHMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVD 60

Query: 370 FANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQWRGDH 410
           F + +D E AL+ L G  +    ++L   +   +K+ R   
Sbjct: 61  FESAEDLEKALE-LTGLKVFGNEIKLEKPKGRDSKKVRAAR 100

>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 =  137 bits (347), Expect = 7e-39
 Identities = 32/180 (17%), Positives = 75/180 (41%), Gaps = 14/180 (7%)

Query: 113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVK-----VIRNKQTGQSEGYGFVEFYSR 167
              + +++G++   + E  + + F+   ++  +       +   Q  Q + + F+EF S 
Sbjct: 2   GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 61

Query: 168 AAAEKVLQSYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQE 227
               + +  + G +     Q  ++                   +F+G L   + D  ++E
Sbjct: 62  DETTQAMA-FDGIIFQG--QSLKIRRPH-----DYQPLPGAHKLFIGGLPNYLNDDQVKE 113

Query: 228 TFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVAT 287
             +S +  +K   ++ DS TG +KGY F  + D N   +A+  +NG+    + + +  A+
Sbjct: 114 LLTS-FGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS 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 =  125 bits (316), Expect = 2e-34
 Identities = 28/198 (14%), Positives = 76/198 (38%), Gaps = 43/198 (21%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYP----SVKGAKVIIDSNTGRTKGYGFVRFGDENERS 265
            ++VG++   +T+  + + F+++      +      ++     + K + F+ F   +E +
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 266 RAMTEMNGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGES 325
           +AM   +G+    + ++I     ++   YQ                              
Sbjct: 66  QAM-AFDGIIFQGQSLKI-----RRPHDYQPL---------------------------P 92

Query: 326 NNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVA 379
               +F+G L + ++D+ ++E  + FG + +  +         KG  F ++ +    + A
Sbjct: 93  GAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQA 152

Query: 380 LQKLQGTAIGKQTVRLSW 397
           +  L G  +G + + +  
Sbjct: 153 IAGLNGMQLGDKKLLVQR 170

>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 = 71.1 bits (175), Expect = 9e-15
 Identities = 14/92 (15%), Positives = 40/92 (43%), Gaps = 2/92 (2%)

Query: 104 NGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVE 163
              ++         ++IG L +++++  +    +  G +    ++++  TG S+GY F E
Sbjct: 83  RRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCE 142

Query: 164 FYSRAAAEKVLQSYSGSLMPNTDQPFRLNWAT 195
           +      ++ +   +G  +   D+   +  A+
Sbjct: 143 YVDINVTDQAIAGLNGMQL--GDKKLLVQRAS 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 = 63.0 bits (154), Expect = 6e-12
 Identities = 11/92 (11%), Positives = 33/92 (35%), Gaps = 12/92 (13%)

Query: 325 SNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-----------KGCGFVQFANR 373
            +   ++VG +   +++E + + F+    +  +    G           K   F++F + 
Sbjct: 2   GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 61

Query: 374 KDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQ 405
            +   A+    G     Q++++    +     
Sbjct: 62  DETTQAM-AFDGIIFQGQSLKIRRPHDYQPLP 92

>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 =  134 bits (339), Expect = 2e-37
 Identities = 34/197 (17%), Positives = 77/197 (39%), Gaps = 24/197 (12%)

Query: 113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVK-----VIRNKQTGQSEGYGFVEFYSR 167
              + +++G++   + E  + + F+   ++  +       +   Q  Q + + F+EF S 
Sbjct: 2   AMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 61

Query: 168 AAAEKVLQSYSGSLMPNTDQPFRLNWAT---------------FSGSDRRTEACSDLSIF 212
               + +  + G +     Q  ++                     G        S   +F
Sbjct: 62  DETTQAMA-FDGIIF--QGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLF 118

Query: 213 VGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMN 272
           +G L   + D  ++E  +S +  +K   ++ DS TG +KGY F  + D N   +A+  +N
Sbjct: 119 IGGLPNYLNDDQVKELLTS-FGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLN 177

Query: 273 GVYCSSRPMRIDVATPK 289
           G+    + + +  A+  
Sbjct: 178 GMQLGDKKLLVQRASVG 194

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score =  132 bits (333), Expect = 1e-36
 Identities = 34/206 (16%), Positives = 84/206 (40%), Gaps = 24/206 (11%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYP----SVKGAKVIIDSNTGRTKGYGFVRFGDENERS 265
            ++VG++   +T+  + + F+++      +      ++     + K + F+ F   +E +
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 266 RAMTEMNGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGES 325
           +AM   +G+    + ++I     ++   YQ             PG     V  S      
Sbjct: 66  QAM-AFDGIIFQGQSLKI-----RRPHDYQPLPGMSENPSVYVPGVVSTVVPDS------ 113

Query: 326 NNATIFVGALDSDVSDEDLREPFSQFGEILSVKIP------VGKGCGFVQFANRKDAEVA 379
               +F+G L + ++D+ ++E  + FG + +  +       + KG  F ++ +    + A
Sbjct: 114 -AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQA 172

Query: 380 LQKLQGTAIGKQTVRLSWGRNPGNKQ 405
           +  L G  +G + + +    + G K 
Sbjct: 173 IAGLNGMQLGDKKLLVQRA-SVGAKN 197

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 68.9 bits (169), Expect = 1e-13
 Identities = 17/107 (15%), Positives = 43/107 (40%), Gaps = 2/107 (1%)

Query: 89  KQQQQQQHGLSNGKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVI 148
            Q         +    G  +    D    ++IG L +++++  +    +  G +    ++
Sbjct: 88  YQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLV 147

Query: 149 RNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWAT 195
           ++  TG S+GY F E+      ++ +   +G  +   D+   +  A+
Sbjct: 148 KDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQL--GDKKLLVQRAS 192

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score =  131 bits (331), Expect = 2e-37
 Identities = 45/102 (44%), Positives = 62/102 (60%), Gaps = 2/102 (1%)

Query: 202 RTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDE 261
              +  + S+FVGDL PDV D +L E F   YPS +G KV++D  TG +KGYGFV+F DE
Sbjct: 3   SGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLD-QTGVSKGYGFVKFTDE 61

Query: 262 NERSRAMTEMNG-VYCSSRPMRIDVATPKKASGYQQQYSSQA 302
            E+ RA+TE  G V   S+P+R+ VA PK +     +    +
Sbjct: 62  LEQKRALTECQGAVGLGSKPVRLSVAIPKASRVKPVESGPSS 103

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 68.8 bits (169), Expect = 9e-15
 Identities = 29/87 (33%), Positives = 41/87 (47%), Gaps = 8/87 (9%)

Query: 318 GSQSDGESNNATIFVGALDSDVSDEDLREPFSQ-FGEILSVKI---PVG--KGCGFVQFA 371
           GS         ++FVG L  DV D  L E F + +      K+     G  KG GFV+F 
Sbjct: 1   GSSGS-SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFT 59

Query: 372 NRKDAEVALQKLQG-TAIGKQTVRLSW 397
           +  + + AL + QG   +G + VRLS 
Sbjct: 60  DELEQKRALTECQGAVGLGSKPVRLSV 86

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 60.4 bits (147), Expect = 1e-11
 Identities = 26/96 (27%), Positives = 45/96 (46%), Gaps = 9/96 (9%)

Query: 101 GKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHT-GQVVNVKVIRNKQTGQSEGY 159
           G    S   ++      +++GDL   +D+  L+  F          KV+ + QTG S+GY
Sbjct: 1   GSSGSSGPEYS------LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLD-QTGVSKGY 53

Query: 160 GFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWAT 195
           GFV+F      ++ L    G++   + +P RL+ A 
Sbjct: 54  GFVKFTDELEQKRALTECQGAVGLGS-KPVRLSVAI 88

>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 =  126 bits (318), Expect = 2e-35
 Identities = 32/120 (26%), Positives = 61/120 (50%), Gaps = 5/120 (4%)

Query: 194 ATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGY 253
            +   S ++ +  +   +FVGDL+P++T   ++  F+  +  +  A+V+ D  TG++KGY
Sbjct: 1   GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFA-PFGRISDARVVKDMATGKSKGY 59

Query: 254 GFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNG 313
           GFV F ++ +   A+ +M G +   R +R + AT K  +      S+          S+G
Sbjct: 60  GFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYESNT----KQSGPSSG 115

>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 = 81.2 bits (201), Expect = 6e-19
 Identities = 33/115 (28%), Positives = 52/115 (45%), Gaps = 6/115 (5%)

Query: 313 GARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCG 366
           G+     Q    SN+  +FVG L  +++ ED++  F+ FG I   ++         KG G
Sbjct: 1   GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYG 60

Query: 367 FVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQWRGDHSNHWNGAHYGG 421
           FV F N+ DAE A+Q++ G  +G + +R +W             SN        G
Sbjct: 61  FVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYESNTKQSGPSSG 115

>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 = 65.4 bits (160), Expect = 2e-13
 Identities = 25/91 (27%), Positives = 46/91 (50%), Gaps = 2/91 (2%)

Query: 105 GSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEF 164
            S           +++GDL   +    +   F+  G++ + +V+++  TG+S+GYGFV F
Sbjct: 5   SSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSF 64

Query: 165 YSRAAAEKVLQSYSGSLMPNTDQPFRLNWAT 195
           +++  AE  +Q   G  +    +  R NWAT
Sbjct: 65  FNKWDAENAIQQMGGQWLGG--RQIRTNWAT 93

>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 =  124 bits (315), Expect = 2e-35
 Identities = 29/83 (34%), Positives = 50/83 (60%), Gaps = 1/83 (1%)

Query: 207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSR 266
           S   +FVGDL+P++T + +   F+  +  +  A+V+ D  TG++KGYGFV F ++ +   
Sbjct: 5   SHFHVFVGDLSPEITTAAIAAAFA-PFGRISDARVVKDMATGKSKGYGFVSFFNKWDAEN 63

Query: 267 AMTEMNGVYCSSRPMRIDVATPK 289
           A+ +M G +   R +R + AT K
Sbjct: 64  AIQQMGGQWLGGRQIRTNWATRK 86

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 75.3 bits (186), Expect = 3e-17
 Identities = 24/80 (30%), Positives = 42/80 (52%), Gaps = 6/80 (7%)

Query: 324 ESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAE 377
             ++  +FVG L  +++   +   F+ FG I   ++         KG GFV F N+ DAE
Sbjct: 3   LGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAE 62

Query: 378 VALQKLQGTAIGKQTVRLSW 397
            A+Q++ G  +G + +R +W
Sbjct: 63  NAIQQMGGQWLGGRQIRTNW 82

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 71.4 bits (176), Expect = 9e-16
 Identities = 24/79 (30%), Positives = 45/79 (56%), Gaps = 4/79 (5%)

Query: 118 IWIGDLFHW-MDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQS 176
           +++GDL    +    +   F+  G++ + +V+++  TG+S+GYGFV F+++  AE  +Q 
Sbjct: 9   VFVGDL-SPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67

Query: 177 YSGSLMPNTDQPFRLNWAT 195
             G  +    +  R NWAT
Sbjct: 68  MGGQWLGG--RQIRTNWAT 84

>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 =  127 bits (321), Expect = 7e-35
 Identities = 44/198 (22%), Positives = 86/198 (43%), Gaps = 13/198 (6%)

Query: 211 IFVGDLAPD-VTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           + V +L P+ VT   L   F   Y  V+  K++ +      K    V+  D N+   AM+
Sbjct: 6   LLVSNLNPERVTPQSLFILFG-VYGDVQRVKILFNK-----KENALVQMADGNQAQLAMS 59

Query: 270 EMNGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLA-GGPGSNGARVQGSQSDGESN-- 326
            +NG     +P+RI ++  +     ++    Q L    G    +  +  GS++       
Sbjct: 60  HLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPP 119

Query: 327 NATIFVGALDSDVSDEDLREPFSQFGEILSVKI--PVGKGCGFVQFANRKDAEVALQKLQ 384
           +AT+ +  +   VS+EDL+  FS  G ++         +    +Q  + ++A  AL  L 
Sbjct: 120 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLH 179

Query: 385 GTAIGK-QTVRLSWGRNP 401
              +G+   +R+S+ ++ 
Sbjct: 180 NHDLGENHHLRVSFSKST 197

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 93.0 bits (231), Expect = 3e-22
 Identities = 28/207 (13%), Positives = 63/207 (30%), Gaps = 44/207 (21%)

Query: 115 TKTIWIGDLFHW-MDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKV 173
              + + +L    +    L   F   G V  VK++ NK+         V+      A+  
Sbjct: 3   NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKK-----ENALVQMADGNQAQLA 57

Query: 174 LQSYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLS----------------------- 210
           +   +G  +    +P R+  +         E   D                         
Sbjct: 58  MSHLNGHKLH--GKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQN 115

Query: 211 -------IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENE 263
                  + + ++ P V++  L+  FSS      G  V       + +    ++ G   E
Sbjct: 116 IFPPSATLHLSNIPPSVSEEDLKVLFSS-----NGGVVKGFKFFQKDRKMALIQMGSVEE 170

Query: 264 RSRAMTEMNGV-YCSSRPMRIDVATPK 289
             +A+ +++      +  +R+  +   
Sbjct: 171 AVQALIDLHNHDLGENHHLRVSFSKST 197

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 73.4 bits (180), Expect = 2e-15
 Identities = 25/117 (21%), Positives = 48/117 (41%), Gaps = 5/117 (4%)

Query: 326 NNATIFVGALDSD-VSDEDLREPFSQFGEILSVKI-PVGKGCGFVQFANRKDAEVALQKL 383
            N+ + V  L+ + V+ + L   F  +G++  VKI    K    VQ A+   A++A+  L
Sbjct: 2   GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHL 61

Query: 384 QGTAIGKQTVRLSWGRNPGNKQWRGDHSNHWNGAHYGGQ---GYSGNGYAFPPNQDP 437
            G  +  + +R++  ++   +  R    +      YG      +   G     N  P
Sbjct: 62  NGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFP 118

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 51.1 bits (122), Expect = 1e-07
 Identities = 17/113 (15%), Positives = 33/113 (29%), Gaps = 5/113 (4%)

Query: 83  QNGGGVKQQQQQQHGLSNGKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQV 142
           Q   G+ +           K    N       + T+ + ++   + E  L   FS  G V
Sbjct: 88  QEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGV 147

Query: 143 VNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWAT 195
           V       K          ++  S   A + L       +       R++++ 
Sbjct: 148 VKGFKFFQK----DRKMALIQMGSVEEAVQALIDLHNHDLGEN-HHLRVSFSK 195

>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 =  126 bits (320), Expect = 7e-35
 Identities = 41/197 (20%), Positives = 72/197 (36%), Gaps = 43/197 (21%)

Query: 199 SDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTG--RTKGYGFV 256
           SD          +FVG +    ++  L+E F  +Y +V    V+ D +    ++KG  FV
Sbjct: 1   SDAIK-------MFVGQVPRTWSEKDLRELFE-QYGAVYEINVLRDRSQNPPQSKGCCFV 52

Query: 257 RFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARV 316
            F        A   ++ +                             VL G       + 
Sbjct: 53  TFYTRKAALEAQNALHNMK----------------------------VLPGMHHPIQMKP 84

Query: 317 QGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-----KGCGFVQFA 371
             S+ +    +  +F+G +    ++ D+R  FS FG+I   +I  G     +GC FV F 
Sbjct: 85  ADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFT 144

Query: 372 NRKDAEVALQKLQGTAI 388
            R  A+ A++ +     
Sbjct: 145 TRAMAQTAIKAMHQAQT 161

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score =  122 bits (309), Expect = 3e-33
 Identities = 41/181 (22%), Positives = 78/181 (43%), Gaps = 13/181 (7%)

Query: 112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTG--QSEGYGFVEFYSRAA 169
           +D  K +++G +     E  L   F   G V  + V+R++     QS+G  FV FY+R A
Sbjct: 1   SDAIK-MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKA 59

Query: 170 AEKVLQSYSGS-LMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQET 228
           A +   +     ++P    P ++  A       +  A  D  +F+G ++   T++ ++  
Sbjct: 60  ALEAQNALHNMKVLPGMHHPIQMKPA----DSEKNNAVEDRKLFIGMISKKCTENDIRVM 115

Query: 229 FSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVY---CSSRPMRIDV 285
           FS  +  ++  +++     G ++G  FV F        A+  M+        S PM +  
Sbjct: 116 FS-SFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKF 173

Query: 286 A 286
           A
Sbjct: 174 A 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 = 79.6 bits (197), Expect = 9e-18
 Identities = 24/83 (28%), Positives = 35/83 (42%), Gaps = 8/83 (9%)

Query: 325 SNNATIFVGALDSDVSDEDLREPFSQFGEILSVKI--------PVGKGCGFVQFANRKDA 376
           S+   +FVG +    S++DLRE F Q+G +  + +        P  KGC FV F  RK A
Sbjct: 1   SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60

Query: 377 EVALQKLQGTAIGKQTVRLSWGR 399
             A   L    +          +
Sbjct: 61  LEAQNALHNMKVLPGMHHPIQMK 83

>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 =  123 bits (311), Expect = 1e-34
 Identities = 40/99 (40%), Positives = 60/99 (60%), Gaps = 5/99 (5%)

Query: 105 GSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQ-VVNVKVIRNKQTGQSEGYGFVE 163
           GS+ +  +    ++W+GDL  +MDE F+   F+  G+ V++VK+IRN+ TG   GY FVE
Sbjct: 1   GSSGS--SGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVE 58

Query: 164 FYSRAAAEKVLQSYSGSLMPNTD--QPFRLNWATFSGSD 200
           F   A AEK L   +G  +P     + F+LN+AT+SG  
Sbjct: 59  FADLATAEKCLHKINGKPLPGATPAKRFKLNYATYSGPS 97

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 84.7 bits (210), Expect = 2e-20
 Identities = 22/87 (25%), Positives = 43/87 (49%), Gaps = 4/87 (4%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           S+++GDL P + ++ +   F++   +V   K+I +  TG   GY FV F D     + + 
Sbjct: 11  SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH 70

Query: 270 EMNGVY----CSSRPMRIDVATPKKAS 292
           ++NG        ++  +++ AT    S
Sbjct: 71  KINGKPLPGATPAKRFKLNYATYSGPS 97

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 68.5 bits (168), Expect = 1e-14
 Identities = 23/94 (24%), Positives = 43/94 (45%), Gaps = 11/94 (11%)

Query: 321 SDGESNNATIFVGALDSDVSDEDLREPFSQFGE-ILSVKIP------VGKGCGFVQFANR 373
           S      A++++G L+  + +  +   F+  GE ++SVKI       +  G  FV+FA+ 
Sbjct: 3   SGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADL 62

Query: 374 KDAEVALQKLQGTAIG----KQTVRLSWGRNPGN 403
             AE  L K+ G  +      +  +L++    G 
Sbjct: 63  ATAEKCLHKINGKPLPGATPAKRFKLNYATYSGP 96

>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 =  122 bits (309), Expect = 3e-34
 Identities = 29/107 (27%), Positives = 53/107 (49%), Gaps = 4/107 (3%)

Query: 307 GGPGSNG----ARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG 362
           G  GS+G     R +   +     N T++ G + S ++D+ +R+ FS FG+I+ +++   
Sbjct: 1   GSSGSSGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE 60

Query: 363 KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQWRGD 409
           KG  FV+F+  + A  A+  + GT I    V+  WG+   +      
Sbjct: 61  KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPDMTSGPS 107

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 64.7 bits (158), Expect = 4e-13
 Identities = 18/88 (20%), Positives = 36/88 (40%), Gaps = 7/88 (7%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           +++ G +A  +TD ++++TFS  +  +   +V  +      KGY FVRF      + A+ 
Sbjct: 27  TVYCGGIASGLTDQLMRQTFS-PFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIV 79

Query: 270 EMNGVYCSSRPMRIDVATPKKASGYQQQ 297
            +NG       ++               
Sbjct: 80  SVNGTTIEGHVVKCYWGKESPDMTSGPS 107

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 59.7 bits (145), Expect = 2e-11
 Identities = 21/108 (19%), Positives = 41/108 (37%), Gaps = 11/108 (10%)

Query: 97  GLSNGKQNGSNNNFTNDETK---TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQT 153
           G S   +     +  N  +    T++ G +   + +  +   FS  GQ++ ++V   K  
Sbjct: 4   GSSGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK-- 61

Query: 154 GQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATFSGSDR 201
               GY FV F +  +A   + S +G+ +       +  W   S    
Sbjct: 62  ----GYSFVRFSTHESAAHAIVSVNGTTIEG--HVVKCYWGKESPDMT 103

>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 =  124 bits (313), Expect = 2e-33
 Identities = 49/231 (21%), Positives = 94/231 (40%), Gaps = 20/231 (8%)

Query: 178 SGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPD-VTDSILQETFSSKYPSV 236
           S  L+P      R+     +G+           + V +L P+ VT   L   F   Y  V
Sbjct: 11  SSGLVPRGSHMGRIAIPGLAGAGNSV-------LLVSNLNPERVTPQSLFILFG-VYGDV 62

Query: 237 KGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKASGYQQ 296
           +  K++ +      K    V+  D N+   AM+ +NG     +P+RI ++  +     ++
Sbjct: 63  QRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPRE 117

Query: 297 QYSSQALV-LAGGPGSNGARVQGSQSDGESN--NATIFVGALDSDVSDEDLREPFSQFGE 353
               Q L    G    +  +  GS++       +AT+ +  +   VS+EDL+  FS  G 
Sbjct: 118 GQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGG 177

Query: 354 ILSVKI--PVGKGCGFVQFANRKDAEVALQKLQGTAIG-KQTVRLSWGRNP 401
           ++         +    +Q  + ++A  AL  L    +G    +R+S+ ++ 
Sbjct: 178 VVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST 228

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 91.2 bits (226), Expect = 3e-21
 Identities = 34/247 (13%), Positives = 74/247 (29%), Gaps = 52/247 (21%)

Query: 75  GGGGHPYYQNGGGVKQQQQQQHGLSNGKQNGSNNNFTNDETKTIWIGDLFHW-MDETFLH 133
           G   H ++ + G V +          G     N+         + + +L    +    L 
Sbjct: 2   GSSHHHHHHSSGLVPRGSHMGRIAIPGLAGAGNS--------VLLVSNLNPERVTPQSLF 53

Query: 134 NCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNW 193
             F   G V  VK++ NK+         V+      A+  +   +G  +    +P R+  
Sbjct: 54  ILFGVYGDVQRVKILFNKK-----ENALVQMADGNQAQLAMSHLNGHKLH--GKPIRITL 106

Query: 194 ATFSGSDRRTEACSDLS------------------------------IFVGDLAPDVTDS 223
           +         E   D                                + + ++ P V++ 
Sbjct: 107 SKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEE 166

Query: 224 ILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGV-YCSSRPMR 282
            L+  FSS      G  V       + +    ++ G   E  +A+ +++      +  +R
Sbjct: 167 DLKVLFSS-----NGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLR 221

Query: 283 IDVATPK 289
           +  +   
Sbjct: 222 VSFSKST 228

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 77.0 bits (189), Expect = 2e-16
 Identities = 27/148 (18%), Positives = 53/148 (35%), Gaps = 6/148 (4%)

Query: 291 ASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSD-VSDEDLREPFS 349
            S +   + S  L     P  +            + N+ + V  L+ + V+ + L   F 
Sbjct: 2   GSSHHHHHHSSGL----VPRGSHMGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFG 57

Query: 350 QFGEILSVKI-PVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQWRG 408
            +G++  VKI    K    VQ A+   A++A+  L G  +  + +R++  ++   +  R 
Sbjct: 58  VYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPRE 117

Query: 409 DHSNHWNGAHYGGQGYSGNGYAFPPNQD 436
              +      YG             N  
Sbjct: 118 GQEDQGLTKDYGNSPLHRFKKPGSKNFQ 145

>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 = 53.1 bits (127), Expect = 4e-08
 Identities = 21/156 (13%), Positives = 40/156 (25%), Gaps = 11/156 (7%)

Query: 46  MAMMQYPAAAMAMMQQQQMMMYPHHYMPYGGGGHPYYQNGGGVKQQQQQQHGLSNGKQN- 104
           +  M     A   M            +      H   Q     ++ Q       N   + 
Sbjct: 76  LVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHR 135

Query: 105 -----GSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGY 159
                  N       + T+ + ++   + E  L   FS  G VV       K        
Sbjct: 136 FKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK----DRKM 191

Query: 160 GFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWAT 195
             ++  S   A + L       +       R++++ 
Sbjct: 192 ALIQMGSVEEAVQALIDLHNHDLGEN-HHLRVSFSK 226

>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 =  122 bits (308), Expect = 3e-32
 Identities = 41/188 (21%), Positives = 84/188 (44%), Gaps = 22/188 (11%)

Query: 117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQS 176
            +++G+L   + E      F   G+   V + R++      G+GF+   SR  AE     
Sbjct: 24  RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR------GFGFIRLESRTLAEIAKAE 77

Query: 177 YSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSV 236
             G+++ +  +P R+ +AT              ++ V +L+P V++ +L++ FS ++  V
Sbjct: 78  LDGTILKS--RPLRIRFAT-----------HGAALTVKNLSPVVSNELLEQAFS-QFGPV 123

Query: 237 KGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMN-GVYCSSRPMRIDVATPKKASGYQ 295
           + A V++D + GR  G GFV F  +    +A+     G +  +   R  +  P +    +
Sbjct: 124 EKAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFDDE 182

Query: 296 QQYSSQAL 303
                + +
Sbjct: 183 DGLPEKLM 190

>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 =  121 bits (305), Expect = 8e-32
 Identities = 53/266 (19%), Positives = 79/266 (29%), Gaps = 54/266 (20%)

Query: 188 PFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNT 247
              +      G    T+ C    +FVG+L  D+T+   +  F  +Y       +  D   
Sbjct: 5   TIDIKSFLKPGEKTYTQRCR---LFVGNLPTDITEEDFKRLFE-RYGEPSEVFINRD--- 57

Query: 248 GRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAG 307
              +G+GF+R         A  E++G    SRP+RI  AT                    
Sbjct: 58  ---RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATH------------------- 95

Query: 308 GPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKI---PVG-- 362
                               A + V  L   VS+E L + FSQFG +    +     G  
Sbjct: 96  -------------------GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRA 136

Query: 363 KGCGFVQFANRKDAEVALQKLQGTA-IGKQTVRLSWGRNPGNKQWRGDHSNHWNGAHYGG 421
            G GFV+FA +  A  AL++    A +   T R                           
Sbjct: 137 TGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLMQKTQQY 196

Query: 422 QGYSGNGYAFPPNQDPNMYAATAVPG 447
                    F          A+    
Sbjct: 197 HKEREQPPRFAQPGTFEFEYASRWKA 222

>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 = 60.5 bits (147), Expect = 2e-10
 Identities = 20/82 (24%), Positives = 34/82 (41%), Gaps = 3/82 (3%)

Query: 115 TKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVL 174
              + + +L   +    L   FS  G V    V+ +   G++ G GFVEF ++  A K L
Sbjct: 96  GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKAL 154

Query: 175 QSYSGS--LMPNTDQPFRLNWA 194
           +       L+  T +P  +   
Sbjct: 155 ERCGDGAFLLTTTPRPVIVEPM 176

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score =  116 bits (293), Expect = 5e-32
 Identities = 23/91 (25%), Positives = 36/91 (39%)

Query: 309 PGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFV 368
           P  N   V            T ++G +    ++ DL   F  FG IL  K    KGC F+
Sbjct: 9   PQVNPQAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCFI 68

Query: 369 QFANRKDAEVALQKLQGTAIGKQTVRLSWGR 399
           ++   + A V +  L       + +R  WG+
Sbjct: 69  KYDTHEQAAVCIVALANFPFQGRNLRTGWGK 99

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 60.4 bits (147), Expect = 9e-12
 Identities = 15/78 (19%), Positives = 31/78 (39%), Gaps = 8/78 (10%)

Query: 117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQS 176
           T +IG++ H+  E  L   F + G +++ K    K      G  F+++ +   A   + +
Sbjct: 29  TAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEK------GCCFIKYDTHEQAAVCIVA 82

Query: 177 YSGSLMPNTDQPFRLNWA 194
            +        +  R  W 
Sbjct: 83  LANFPF--QGRNLRTGWG 98

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 57.3 bits (139), Expect = 1e-10
 Identities = 10/80 (12%), Positives = 29/80 (36%), Gaps = 7/80 (8%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           + ++G++    T++ L   F   +  +   K   +      KG  F+++    + +  + 
Sbjct: 29  TAYIGNIPHFATEADLIPLFQ-NFGFILDFKHYPE------KGCCFIKYDTHEQAAVCIV 81

Query: 270 EMNGVYCSSRPMRIDVATPK 289
            +       R +R      +
Sbjct: 82  ALANFPFQGRNLRTGWGKER 101

>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 =  115 bits (291), Expect = 6e-32
 Identities = 30/80 (37%), Positives = 44/80 (55%), Gaps = 1/80 (1%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           ++FVGDL  +V D  L+  F   +PS     V+ D  TG ++GYGFV F  +++   AM 
Sbjct: 3   NLFVGDLNVNVDDETLRNAFK-DFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61

Query: 270 EMNGVYCSSRPMRIDVATPK 289
            M G   + RP+RI+ A   
Sbjct: 62  SMQGQDLNGRPLRINWAAKL 81

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 73.3 bits (181), Expect = 1e-16
 Identities = 25/76 (32%), Positives = 40/76 (52%), Gaps = 6/76 (7%)

Query: 328 ATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVALQ 381
             +FVG L+ +V DE LR  F  F   LS  +         +G GFV F ++ DA+ A+ 
Sbjct: 2   FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61

Query: 382 KLQGTAIGKQTVRLSW 397
            +QG  +  + +R++W
Sbjct: 62  SMQGQDLNGRPLRINW 77

>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 = 69.8 bits (172), Expect = 3e-15
 Identities = 28/82 (34%), Positives = 44/82 (53%), Gaps = 4/82 (4%)

Query: 115 TKTIWIGDLFHW-MDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKV 173
           T  +++GDL +  +D+  L N F      ++  V+ + QTG S GYGFV F S+  A+  
Sbjct: 1   TFNLFVGDL-NVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNA 59

Query: 174 LQSYSGSLMPNTDQPFRLNWAT 195
           + S  G  +    +P R+NWA 
Sbjct: 60  MDSMQGQDLNG--RPLRINWAA 79

>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 =  113 bits (285), Expect = 5e-31
 Identities = 31/91 (34%), Positives = 49/91 (53%), Gaps = 7/91 (7%)

Query: 310 GSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQ 369
           GS+G       S  +    T++VG L   +++ DLR  F QFGEI ++ +   + C F+Q
Sbjct: 1   GSSG------SSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQ 54

Query: 370 FANRKDAEVALQK-LQGTAIGKQTVRLSWGR 399
           FA R+ AEVA +K      +  + + + WGR
Sbjct: 55  FATRQAAEVAAEKSFNKLIVNGRRLNVKWGR 85

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 66.5 bits (163), Expect = 4e-14
 Identities = 23/91 (25%), Positives = 43/91 (47%), Gaps = 8/91 (8%)

Query: 105 GSNNNFTNDET-KTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVE 163
           GS+ +   D+T  T+++G L   + ET L N F   G++  + V++ +         F++
Sbjct: 1   GSSGSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQ------QCAFIQ 54

Query: 164 FYSRAAAEKVLQSYSGSLMPNTDQPFRLNWA 194
           F +R AAE   +     L+ N  +   + W 
Sbjct: 55  FATRQAAEVAAEKSFNKLIVN-GRRLNVKWG 84

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 49.2 bits (118), Expect = 5e-08
 Identities = 12/75 (16%), Positives = 32/75 (42%), Gaps = 8/75 (10%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           +++VG L   +T++ L+  F  ++  ++   V+        +   F++F        A  
Sbjct: 14  TLYVGGLGDTITETDLRNHF-YQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAE 66

Query: 270 EM-NGVYCSSRPMRI 283
           +  N +  + R + +
Sbjct: 67  KSFNKLIVNGRRLNV 81

>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 =  116 bits (292), Expect = 6e-31
 Identities = 45/179 (25%), Positives = 88/179 (49%), Gaps = 17/179 (9%)

Query: 114 ETKTIWIGDLFHW-MDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEK 172
           E+  ++IG L +W   E  L   F   G V ++K++++  TG+S G+GF+ F   ++ ++
Sbjct: 2   ESCKMFIGGL-NWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDE 60

Query: 173 VLQSYSGSLMPNT--DQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFS 230
           V+++       +    +      A       R E      IFVG + PDV     +E FS
Sbjct: 61  VVKT------QHILDGKVIDPKRAI-----PRDEQDKTGKIFVGGIGPDVRPKEFEEFFS 109

Query: 231 SKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPK 289
            ++ ++  A++++D +TG+++G+GFV +   +   R   +   +    R + I  A P+
Sbjct: 110 -QWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVC-QNKFIDFKDRKIEIKRAEPR 166

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score =  109 bits (276), Expect = 1e-28
 Identities = 39/178 (21%), Positives = 69/178 (38%), Gaps = 41/178 (23%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +F+G L  D T+  L+E F  KY +V   K++ D  TGR++G+GF+ F   +     +  
Sbjct: 6   MFIGGLNWDTTEDNLREYFG-KYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64

Query: 271 MNGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATI 330
            + +    + +    A P+                                        I
Sbjct: 65  QHIL--DGKVIDPKRAIPRDEQ--------------------------------DKTGKI 90

Query: 331 FVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVALQK 382
           FVG +  DV  ++  E FSQ+G I+  ++ +       +G GFV + +    +   Q 
Sbjct: 91  FVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQN 148

>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 = 60.6 bits (148), Expect = 3e-11
 Identities = 15/61 (24%), Positives = 30/61 (49%), Gaps = 6/61 (9%)

Query: 328 ATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK------GCGFVQFANRKDAEVALQ 381
             +F+G L+ D ++++LRE F ++G +  +KI          G GF+ F      +  ++
Sbjct: 4   CKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK 63

Query: 382 K 382
            
Sbjct: 64  T 64

>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 = 56.0 bits (136), Expect = 1e-09
 Identities = 20/64 (31%), Positives = 36/64 (56%)

Query: 112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAE 171
            D+T  I++G +   +        FS  G +++ +++ +K TGQS G+GFV + S  A +
Sbjct: 84  QDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVD 143

Query: 172 KVLQ 175
           +V Q
Sbjct: 144 RVCQ 147

>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 =  111 bits (281), Expect = 2e-30
 Identities = 28/88 (31%), Positives = 49/88 (55%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
            IF+G+L P++ + +L +TFS+    ++  K++ D +TG +KGY F+ F   +    A+ 
Sbjct: 7   GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66

Query: 270 EMNGVYCSSRPMRIDVATPKKASGYQQQ 297
            MNG Y  +RP+ +  A  K + G    
Sbjct: 67  AMNGQYLCNRPITVSYAFKKDSKGSGPS 94

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 74.2 bits (183), Expect = 1e-16
 Identities = 26/98 (26%), Positives = 48/98 (48%), Gaps = 10/98 (10%)

Query: 323 GESNNATIFVGALDSDVSDEDLREPFSQFGEILSV-KIPV------GKGCGFVQFANRKD 375
           G S ++ IF+G LD ++ ++ L + FS FG IL   KI         KG  F+ FA+   
Sbjct: 1   GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA 60

Query: 376 AEVALQKLQGTAIGKQTVRLSWGRNPGNKQWRGDHSNH 413
           ++ A++ + G  +  + + +S+      K  +G   + 
Sbjct: 61  SDAAIEAMNGQYLCNRPITVSYAF---KKDSKGSGPSS 95

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 62.2 bits (152), Expect = 2e-12
 Identities = 25/80 (31%), Positives = 48/80 (60%), Gaps = 3/80 (3%)

Query: 117 TIWIGDLFHWMDETFLHNCFSHTGQVVNV-KVIRNKQTGQSEGYGFVEFYSRAAAEKVLQ 175
            I+IG+L   +DE  L++ FS  G ++   K++R+  TG S+GY F+ F S  A++  ++
Sbjct: 7   GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66

Query: 176 SYSGSLMPNTDQPFRLNWAT 195
           + +G  + N  +P  +++A 
Sbjct: 67  AMNGQYLCN--RPITVSYAF 84

>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 =  110 bits (278), Expect = 7e-30
 Identities = 22/96 (22%), Positives = 43/96 (44%), Gaps = 5/96 (5%)

Query: 310 GSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQ 369
           GS+G+     +        T++V   D  ++   LR  FS FG I+ + +   + C FV 
Sbjct: 1   GSSGS---SGERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVT 55

Query: 370 FANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQ 405
           +   + A+ A+ +L GT +    ++++  R      
Sbjct: 56  YEKMESADQAVAELNGTQVESVQLKVNIARKQPMLD 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 = 56.5 bits (137), Expect = 2e-10
 Identities = 20/97 (20%), Positives = 41/97 (42%), Gaps = 9/97 (9%)

Query: 194 ATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGY 253
            +   S  R       +++V     D+T ++L+  FS  +    G   IID +    +  
Sbjct: 1   GSSGSSGERRAPRKGNTLYVYGE--DMTPTLLRGAFS-PF----GN--IIDLSMDPPRNC 51

Query: 254 GFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKK 290
            FV +       +A+ E+NG    S  +++++A  + 
Sbjct: 52  AFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQP 88

>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 = 54.2 bits (131), Expect = 1e-09
 Identities = 15/95 (15%), Positives = 37/95 (38%), Gaps = 14/95 (14%)

Query: 105 GSNNNFTNDETK----TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYG 160
           GS+ +           T+++      M  T L   FS  G ++++ +   +         
Sbjct: 1   GSSGSSGERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPR------NCA 52

Query: 161 FVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWAT 195
           FV +    +A++ +   +G+ + +     ++N A 
Sbjct: 53  FVTYEKMESADQAVAELNGTQVES--VQLKVNIAR 85

>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 =  108 bits (273), Expect = 4e-29
 Identities = 25/104 (24%), Positives = 49/104 (47%), Gaps = 6/104 (5%)

Query: 307 GGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCG 366
           G  GS+G           +  + +FVG L  D+++E++R+ F ++G+   V I   KG G
Sbjct: 1   GSSGSSG------GEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFG 54

Query: 367 FVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQWRGDH 410
           F++   R  AE+A  +L    +  + +R+ +  +  +       
Sbjct: 55  FIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSASLTSGPSS 98

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 67.3 bits (165), Expect = 4e-14
 Identities = 24/96 (25%), Positives = 43/96 (44%), Gaps = 8/96 (8%)

Query: 197 SGSDRRTEACSDLS-IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGF 255
           SGS    +  +  S +FVG+L PD+T+  +++ F  KY       +  D      KG+GF
Sbjct: 3   SGSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFE-KYGKAGEVFIHKD------KGFGF 55

Query: 256 VRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKA 291
           +R         A  E++ +    + +R+  A    +
Sbjct: 56  IRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSAS 91

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 54.6 bits (132), Expect = 1e-09
 Identities = 18/95 (18%), Positives = 36/95 (37%), Gaps = 8/95 (8%)

Query: 101 GKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYG 160
           G    S    T  +   +++G+L   + E  +   F   G+   V + ++K      G+G
Sbjct: 1   GSSGSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFG 54

Query: 161 FVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWAT 195
           F+   +R  AE          +    +  R+ +A 
Sbjct: 55  FIRLETRTLAEIAKVELDNMPLRG--KQLRVRFAC 87

>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 =  110 bits (276), Expect = 2e-28
 Identities = 35/185 (18%), Positives = 77/185 (41%), Gaps = 4/185 (2%)

Query: 113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEK 172
           ++ + ++IG L     +  L + F   G + +  V+R+  T +S G+GFV + +    + 
Sbjct: 11  EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 70

Query: 173 VLQSYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSK 232
            + +    +     +P R    +   S R     +   IFVG +  D  +  L++ F  +
Sbjct: 71  AMNARPHKVDGRVVEPKR--AVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYF-EQ 127

Query: 233 YPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKAS 292
           Y  ++  +++ D  +G+ +G+ FV F D +   + +        +     +  A  K+  
Sbjct: 128 YGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNCEVRKALSKQEM 186

Query: 293 GYQQQ 297
                
Sbjct: 187 ASASS 191

>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 =  108 bits (273), Expect = 6e-28
 Identities = 43/180 (23%), Positives = 76/180 (42%), Gaps = 38/180 (21%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +F+G L+ + TD  L+  F  ++ ++    V+ D NT R++G+GFV +    E   AM  
Sbjct: 16  LFIGGLSFETTDESLRSHFE-QWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-- 72

Query: 271 MNGVYCSSRPMRID--VATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNA 328
                 ++RP ++D  V  PK+A                      +R    +        
Sbjct: 73  ------NARPHKVDGRVVEPKRAV---------------------SREDSQRPGAHLTVK 105

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK------GCGFVQFANRKDAEVALQK 382
            IFVG +  D  +  LR+ F Q+G+I  ++I   +      G  FV F +    +  + +
Sbjct: 106 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 165

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 56.5 bits (137), Expect = 2e-09
 Identities = 14/71 (19%), Positives = 35/71 (49%)

Query: 105 GSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEF 164
            S     +   K I++G +    +E  L + F   G++  ++++ ++ +G+  G+ FV F
Sbjct: 94  DSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153

Query: 165 YSRAAAEKVLQ 175
               + +K++ 
Sbjct: 154 DDHDSVDKIVI 164

>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 =  106 bits (268), Expect = 2e-28
 Identities = 27/100 (27%), Positives = 48/100 (48%), Gaps = 7/100 (7%)

Query: 310 GSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV----GKGC 365
           GS+G+       + +    T++VG L  DV++  + + FSQ G   S K+          
Sbjct: 1   GSSGS---SGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPY 57

Query: 366 GFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQ 405
            FV+F   +DA  AL  + G  I  + V+++W   P +++
Sbjct: 58  CFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQK 97

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 83.1 bits (206), Expect = 9e-20
 Identities = 22/92 (23%), Positives = 45/92 (48%), Gaps = 3/92 (3%)

Query: 199 SDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRF 258
           S    +     +++VG+L+ DVT+ ++ + FS +    K  K+I +  +     Y FV F
Sbjct: 6   SGMMEDDGQPRTLYVGNLSRDVTEVLILQLFS-QIGPCKSCKMITEHTSND--PYCFVEF 62

Query: 259 GDENERSRAMTEMNGVYCSSRPMRIDVATPKK 290
            +  + + A+  MNG     + ++++ AT   
Sbjct: 63  YEHRDAAAALAAMNGRKILGKEVKVNWATTPS 94

>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 = 72.3 bits (178), Expect = 5e-16
 Identities = 26/107 (24%), Positives = 48/107 (44%), Gaps = 5/107 (4%)

Query: 101 GKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYG 160
           G    S     + + +T+++G+L   + E  +   FS  G   + K+I    +     Y 
Sbjct: 1   GSSGSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YC 58

Query: 161 FVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATFSGSDRRTEACS 207
           FVEFY    A   L + +G  +    +  ++NWAT + S +++   S
Sbjct: 59  FVEFYEHRDAAAALAAMNGRKI--LGKEVKVNWAT-TPSSQKSGPSS 102

>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 =  108 bits (271), Expect = 9e-28
 Identities = 31/211 (14%), Positives = 65/211 (30%), Gaps = 25/211 (11%)

Query: 198 GSDRRTEACSDLSIFVGDLAPD-VTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFV 256
           G+D          + V  L    +    +   F   Y +V+  K +         G   V
Sbjct: 1   GADSPV-------LMVYGLDQSKMNCDRVFNVFC-LYGNVEKVKFMKSK-----PGAAMV 47

Query: 257 RFGDENERSRAMTEMNGVYCSSRPMRIDVA-----TPKKASGYQQQYSSQALVLAGGPGS 311
              D     RA+T +N  +   + M + V+      P ++ G +    S           
Sbjct: 48  EMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNR 107

Query: 312 NGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGC 365
                Q +++  +  +  +       +V++E+  E   + G      + V          
Sbjct: 108 FSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSS 167

Query: 366 GFVQFANRKDAEVALQKLQGTAIGKQTVRLS 396
           G +++ ++ DA   L  L    +        
Sbjct: 168 GLLEWDSKSDALETLGFLNHYQMKNPNGPYP 198

>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 = 82.4 bits (203), Expect = 2e-18
 Identities = 25/202 (12%), Positives = 56/202 (27%), Gaps = 37/202 (18%)

Query: 114 ETKTIWIGDLFHW-MDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEK 172
           ++  + +  L    M+   + N F   G V  VK +++K      G   VE     A ++
Sbjct: 3   DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKP-----GAAMVEMADGYAVDR 57

Query: 173 VLQSYSGSLM--------------PNTDQPFRLNWATFSGSDRRTE-------------- 204
            +   + + M                  Q + L   + S  D                  
Sbjct: 58  AITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKN 117

Query: 205 --ACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDEN 262
                   +   +   +VT+    E    +    +   V + S        G + +  ++
Sbjct: 118 RIQHPSNVLHFFNAPLEVTEENFFEICD-ELGVKRPTSVKVFSGKSERSSSGLLEWDSKS 176

Query: 263 ERSRAMTEMNGVYCSSRPMRID 284
           +    +  +N     +      
Sbjct: 177 DALETLGFLNHYQMKNPNGPYP 198

>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 = 73.6 bits (180), Expect = 2e-15
 Identities = 19/116 (16%), Positives = 41/116 (35%), Gaps = 2/116 (1%)

Query: 325 SNNATIFVGALDSDVSDED-LREPFSQFGEILSVKIPVGK-GCGFVQFANRKDAEVALQK 382
           +++  + V  LD    + D +   F  +G +  VK    K G   V+ A+    + A+  
Sbjct: 2   ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITH 61

Query: 383 LQGTAIGKQTVRLSWGRNPGNKQWRGDHSNHWNGAHYGGQGYSGNGYAFPPNQDPN 438
           L    +  Q + +   + P     +       + ++        N ++ P     N
Sbjct: 62  LNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKN 117

>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 = 2e-10
 Identities = 22/159 (13%), Positives = 43/159 (27%), Gaps = 9/159 (5%)

Query: 45  WMAMMQYPAAAMAM-------MQQQQMMMYPHHYMPYGGGGHPYYQNGGGVKQQQQQQHG 97
            + M    A   A+       M  Q+M +          G     ++G    +   +   
Sbjct: 46  MVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRN 105

Query: 98  LSNGKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSE 157
                   +  N     +  +   +    + E          G      V       +  
Sbjct: 106 NRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERS 165

Query: 158 GYGFVEFYSRAAAEKVLQSYSGSLM--PNTDQPFRLNWA 194
             G +E+ S++ A + L   +   M  PN   P+ L   
Sbjct: 166 SSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC 204

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score =  104 bits (261), Expect = 2e-27
 Identities = 29/115 (25%), Positives = 50/115 (43%), Gaps = 9/115 (7%)

Query: 291 ASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQ 350
            S +   + S  LV  G            + +GE +N  +FV     DV + +L E F  
Sbjct: 2   GSSHHHHHHSSGLVPRGSH-------MHHRQEGELSNTRLFVRPFPLDVQESELNEIFGP 54

Query: 351 FGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQ 405
           FG +  VKI    G  FV+F   + A  A++++ G +   Q + + + + P  + 
Sbjct: 55  FGPMKEVKIL--NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAKRY 107

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 63.9 bits (156), Expect = 6e-13
 Identities = 23/116 (19%), Positives = 46/116 (39%), Gaps = 19/116 (16%)

Query: 175 QSYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYP 234
             +S  L+P                 R+    S+  +FV     DV +S L E F   + 
Sbjct: 8   HHHSSGLVPRGSHM----------HHRQEGELSNTRLFVRPFPLDVQESELNEIFG-PFG 56

Query: 235 SVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKK 290
            +K  K++         G+ FV F +    ++A+ E++G   +++P+ +  +    
Sbjct: 57  PMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPA 104

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 46.1 bits (110), Expect = 1e-06
 Identities = 20/114 (17%), Positives = 39/114 (34%), Gaps = 16/114 (14%)

Query: 89  KQQQQQQHGLSNGKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVI 148
                   G     +     + T      +++      + E+ L+  F   G +  VK++
Sbjct: 10  HSSGLVPRGSHMHHRQEGELSNTR-----LFVRPFPLDVQESELNEIFGPFGPMKEVKIL 64

Query: 149 RNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATFSGSDRR 202
                    G+ FVEF    +A K ++   G    N  QP  + ++    + R 
Sbjct: 65  N--------GFAFVEFEEAESAAKAIEEVHGKSFAN--QPLEVVYSK-LPAKRY 107

>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 =  103 bits (258), Expect = 4e-27
 Identities = 22/99 (22%), Positives = 43/99 (43%), Gaps = 1/99 (1%)

Query: 313 GARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFAN 372
           G+       D  S+   ++V  L    S+E + + F+        ++   +   FV F+N
Sbjct: 1   GSSGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSN 60

Query: 373 RKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQWRGDHS 411
           R+DA  A++ L G  +    + ++  + P +K   G  S
Sbjct: 61  REDAVEAMKALNGKVLDGSPIEVTLAK-PVDKDSSGPSS 98

>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 = 68.1 bits (167), Expect = 2e-14
 Identities = 15/81 (18%), Positives = 34/81 (41%), Gaps = 7/81 (8%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
            ++V +L    ++ ++++ F+         +V       + + Y FV F +  +   AM 
Sbjct: 17  ILYVRNLMLSTSEEMIEKEFN-NIKPGAVERV------KKIRDYAFVHFSNREDAVEAMK 69

Query: 270 EMNGVYCSSRPMRIDVATPKK 290
            +NG      P+ + +A P  
Sbjct: 70  ALNGKVLDGSPIEVTLAKPVD 90

>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 = 52.3 bits (126), Expect = 6e-09
 Identities = 17/94 (18%), Positives = 37/94 (39%), Gaps = 8/94 (8%)

Query: 101 GKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYG 160
           G    S +  T    K +++ +L     E  +   F++       +V + +       Y 
Sbjct: 1   GSSGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIR------DYA 54

Query: 161 FVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWA 194
           FV F +R  A + +++ +G ++     P  +  A
Sbjct: 55  FVHFSNREDAVEAMKALNGKVL--DGSPIEVTLA 86

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A Length = 103

 Score =  100 bits (250), Expect = 6e-26
 Identities = 26/103 (25%), Positives = 46/103 (44%), Gaps = 2/103 (1%)

Query: 319 SQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEV 378
           S S G +    +FV  L + V++E L + FSQFG++  VK    K   F+ F  R  A  
Sbjct: 3   SGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--KDYAFIHFDERDGAVK 60

Query: 379 ALQKLQGTAIGKQTVRLSWGRNPGNKQWRGDHSNHWNGAHYGG 421
           A++++ G  +  + + + + + P  K+               G
Sbjct: 61  AMEEMNGKDLEGENIEIVFAKPPDQKRKERKAQRQAASGPSSG 103

>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 = 71.9 bits (177), Expect = 9e-16
 Identities = 30/102 (29%), Positives = 48/102 (47%), Gaps = 12/102 (11%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
            +FV +LA  VT+ IL++ FS ++  ++  K +        K Y F+ F + +   +AM 
Sbjct: 13  VLFVRNLANTVTEEILEKAFS-QFGKLERVKKL--------KDYAFIHFDERDGAVKAME 63

Query: 270 EMNGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGS 311
           EMNG       + I  A P      +++   QA   A GP S
Sbjct: 64  EMNGKDLEGENIEIVFAKPPDQKRKERKAQRQA---ASGPSS 102

>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 = 57.7 bits (140), Expect = 9e-11
 Identities = 21/100 (21%), Positives = 43/100 (43%), Gaps = 11/100 (11%)

Query: 105 GSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEF 164
           GS+ +    + K +++ +L + + E  L   FS  G++  VK ++         Y F+ F
Sbjct: 1   GSSGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK--------DYAFIHF 52

Query: 165 YSRAAAEKVLQSYSGSLMPNTDQPFRLNWATFSGSDRRTE 204
             R  A K ++  +G  +    +   + +A      +R E
Sbjct: 53  DERDGAVKAMEEMNGKDL--EGENIEIVFAK-PPDQKRKE 89

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score =  100 bits (250), Expect = 8e-26
 Identities = 15/86 (17%), Positives = 42/86 (48%), Gaps = 3/86 (3%)

Query: 207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSR 266
           +  ++F+G+L P+ + + L+   S +  +      ++D  TG  + +G+V F    +  +
Sbjct: 16  TPFNLFIGNLNPNKSVAELKVAIS-ELFAKNDL-AVVDVRTGTNRKFGYVDFESAEDLEK 73

Query: 267 AMTEMNGVYCSSRPMRIDVATPKKAS 292
           A+ E+ G+      ++++    +  +
Sbjct: 74  AL-ELTGLKVFGNEIKLEKPKGRDGT 98

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 66.9 bits (164), Expect = 4e-14
 Identities = 17/92 (18%), Positives = 38/92 (41%), Gaps = 6/92 (6%)

Query: 319 SQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKI---PVG--KGCGFVQFANR 373
            +    +    +F+G L+ + S  +L+   S+      + +     G  +  G+V F + 
Sbjct: 9   VEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESA 68

Query: 374 KDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQ 405
           +D E AL+ L G  +    ++L   +     +
Sbjct: 69  EDLEKALE-LTGLKVFGNEIKLEKPKGRDGTR 99

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 52.6 bits (127), Expect = 5e-09
 Identities = 17/98 (17%), Positives = 33/98 (33%), Gaps = 15/98 (15%)

Query: 113 DETKTIWIGDLFHW-MDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAE 171
                ++IG+L +       L    S      ++  + + +TG +  +G+V+F S    E
Sbjct: 15  TTPFNLFIGNL-NPNKSVAELKVAISELFAKNDL-AVVDVRTGTNRKFGYVDFESAEDLE 72

Query: 172 KVLQSYSGSLMPNTD---QPFRLNWATFSGSDRRTEAC 206
           K L+      +          +L           T  C
Sbjct: 73  KALE------LTGLKVFGNEIKLEKPK---GRDGTRGC 101

>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 = 96.5 bits (241), Expect = 1e-24
 Identities = 22/95 (23%), Positives = 43/95 (45%), Gaps = 5/95 (5%)

Query: 310 GSNGARVQGSQSDGES-NNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFV 368
           GS+G+        G++     ++VG L  + S   L   F +FG I ++    G    ++
Sbjct: 1   GSSGSSG--KIGYGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYI 58

Query: 369 QFANRKDAEVALQKLQGTAIGKQTVRL--SWGRNP 401
           Q+ +   A+ A  K++G  +G    RL   + ++ 
Sbjct: 59  QYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSG 93

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97

 Score = 63.4 bits (155), Expect = 8e-13
 Identities = 14/80 (17%), Positives = 31/80 (38%), Gaps = 6/80 (7%)

Query: 115 TKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVL 174
           T  +W+G L        L   F   G +  +  ++         + ++++ S  AA+   
Sbjct: 17  TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD------SFAYIQYESLDAAQAAC 70

Query: 175 QSYSGSLMPNTDQPFRLNWA 194
               G  +   D+  R+++A
Sbjct: 71  AKMRGFPLGGPDRRLRVDFA 90

>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 = 57.3 bits (139), Expect = 1e-10
 Identities = 16/85 (18%), Positives = 37/85 (43%), Gaps = 9/85 (10%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           ++VG L P+ + + L   F  ++ S++    +      +   + ++++   +    A  +
Sbjct: 20  LWVGGLGPNTSLAALAREFD-RFGSIRTIDHV------KGDSFAYIQYESLDAAQAACAK 72

Query: 271 MNGVY--CSSRPMRIDVATPKKASG 293
           M G       R +R+D A    +SG
Sbjct: 73  MRGFPLGGPDRRLRVDFAKSGPSSG 97

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 96.8 bits (241), Expect = 1e-24
 Identities = 19/81 (23%), Positives = 32/81 (39%)

Query: 318 GSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAE 377
           GS      +   I    L +     +++E FS+FG +  V +P G     V+F    +A 
Sbjct: 1   GSSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEAR 60

Query: 378 VALQKLQGTAIGKQTVRLSWG 398
            A + L  +      + L W 
Sbjct: 61  KAFRHLAYSKFHHVPLYLEWA 81

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 50.2 bits (120), Expect = 4e-08
 Identities = 18/93 (19%), Positives = 34/93 (36%), Gaps = 12/93 (12%)

Query: 194 ATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGY 253
            +   S R     S   I   +L      + +QETFS ++ S+   +V++          
Sbjct: 1   GSSGSSGR-----SKTVILAKNLPAGTLAAEIQETFS-RFGSLG--RVLLPE----GGIT 48

Query: 254 GFVRFGDENERSRAMTEMNGVYCSSRPMRIDVA 286
             V F +  E  +A   +        P+ ++ A
Sbjct: 49  AIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWA 81

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 39.0 bits (91), Expect = 4e-04
 Identities = 19/90 (21%), Positives = 28/90 (31%), Gaps = 9/90 (10%)

Query: 105 GSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEF 164
           GS+ +    +T  I   +L        +   FS  G +  V +              VEF
Sbjct: 1   GSSGSSGRSKT-VILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGG------ITAIVEF 53

Query: 165 YSRAAAEKVLQSYSGSLMPNTDQPFRLNWA 194
                A K  +  + S       P  L WA
Sbjct: 54  LEPLEARKAFRHLAYSKF--HHVPLYLEWA 81

>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 = 94.4 bits (235), Expect = 1e-23
 Identities = 27/106 (25%), Positives = 53/106 (50%), Gaps = 9/106 (8%)

Query: 307 GGPGSNGARVQG------SQSDGESNNATIFVGALDSD-VSDEDLREPFSQFGEILSVKI 359
           G  GS+G  ++       +++D +S N+ +F+G L++  V   D+   FS++G +    +
Sbjct: 1   GSSGSSGMSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV 60

Query: 360 PVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQ 405
              KG  FVQ++N + A  A+    G  +  QT+ ++    P   +
Sbjct: 61  H--KGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEPKPDR 104

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110

 Score = 52.4 bits (126), Expect = 7e-09
 Identities = 24/81 (29%), Positives = 38/81 (46%), Gaps = 10/81 (12%)

Query: 211 IFVGDLAPD-VTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           +F+G+L    V  S ++  FS KY  V G  V         KGY FV++ +E     A+ 
Sbjct: 30  VFIGNLNTALVKKSDVETIFS-KYGRVAGCSVH--------KGYAFVQYSNERHARAAVL 80

Query: 270 EMNGVYCSSRPMRIDVATPKK 290
             NG   + + + I++A   K
Sbjct: 81  GENGRVLAGQTLDINMAGEPK 101

>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 = 23/108 (21%), Positives = 41/108 (37%), Gaps = 11/108 (10%)

Query: 96  HGLSNGKQNGSNNNFTNDETKTIWIGDL-FHWMDETFLHNCFSHTGQVVNVKVIRNKQTG 154
             L     N +N N        ++IG+L    + ++ +   FS  G+V    V +     
Sbjct: 8   MSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHK----- 62

Query: 155 QSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATFSGSDRR 202
              GY FV++ +   A   +   +G ++    Q   +N A     DR 
Sbjct: 63  ---GYAFVQYSNERHARAAVLGENGRVLAG--QTLDINMAGEPKPDRS 105

>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 = 90.7 bits (226), Expect = 2e-22
 Identities = 29/94 (30%), Positives = 54/94 (57%), Gaps = 3/94 (3%)

Query: 196 FSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGF 255
              S  R      ++++V +L   + D  L++ FS  + ++  AKV+++   GR+KG+GF
Sbjct: 3   SGSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFS-PFGTITSAKVMME--GGRSKGFGF 59

Query: 256 VRFGDENERSRAMTEMNGVYCSSRPMRIDVATPK 289
           V F    E ++A+TEMNG   +++P+ + +A  K
Sbjct: 60  VCFSSPEEATKAVTEMNGRIVATKPLYVALAQRK 93

>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 = 75.7 bits (187), Expect = 4e-17
 Identities = 27/92 (29%), Positives = 47/92 (51%), Gaps = 7/92 (7%)

Query: 310 GSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV----GKGC 365
           GS+G+           N   ++V  LD  + DE LR+ FS FG I S K+ +     KG 
Sbjct: 1   GSSGSSGDRITRYQVVN---LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGF 57

Query: 366 GFVQFANRKDAEVALQKLQGTAIGKQTVRLSW 397
           GFV F++ ++A  A+ ++ G  +  + + ++ 
Sbjct: 58  GFVCFSSPEEATKAVTEMNGRIVATKPLYVAL 89

>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 = 58.4 bits (142), Expect = 5e-11
 Identities = 24/95 (25%), Positives = 44/95 (46%), Gaps = 4/95 (4%)

Query: 101 GKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYG 160
           G    S +  T  +   +++ +L   +D+  L   FS  G + + KV+     G+S+G+G
Sbjct: 1   GSSGSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFG 58

Query: 161 FVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWAT 195
           FV F S   A K +   +G ++    +P  +  A 
Sbjct: 59  FVCFSSPEEATKAVTEMNGRIVAT--KPLYVALAQ 91

>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 = 89.2 bits (222), Expect = 5e-22
 Identities = 25/91 (27%), Positives = 45/91 (49%), Gaps = 1/91 (1%)

Query: 203 TEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDEN 262
           +E   D +++VG L   V++ +L E F      V    +  D  TG+ +GYGFV F  E 
Sbjct: 10  SERNQDATVYVGGLDEKVSEPLLWELFLQ-AGPVVNTHMPKDRVTGQHQGYGFVEFLSEE 68

Query: 263 ERSRAMTEMNGVYCSSRPMRIDVATPKKASG 293
           +   A+  M+ +    +P+R++ A+    + 
Sbjct: 69  DADYAIKIMDMIKLYGKPIRVNKASAHNKNL 99

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 76.5 bits (189), Expect = 2e-17
 Identities = 27/107 (25%), Positives = 52/107 (48%), Gaps = 9/107 (8%)

Query: 310 GSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GK 363
           GS+G+    S+    + +AT++VG LD  VS+  L E F Q G +++  +P        +
Sbjct: 1   GSSGSSGPISER---NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQ 57

Query: 364 GCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQWRGDH 410
           G GFV+F + +DA+ A++ +    +  + +R++              
Sbjct: 58  GYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKNLSGPSS 104

>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 = 66.5 bits (163), Expect = 8e-14
 Identities = 28/95 (29%), Positives = 46/95 (48%), Gaps = 2/95 (2%)

Query: 101 GKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYG 160
           G    S      ++  T+++G L   + E  L   F   G VVN  + +++ TGQ +GYG
Sbjct: 1   GSSGSSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYG 60

Query: 161 FVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWAT 195
           FVEF S   A+  ++      +    +P R+N A+
Sbjct: 61  FVEFLSEEDADYAIKIMDMIKLYG--KPIRVNKAS 93

>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 = 88.4 bits (220), Expect = 1e-21
 Identities = 23/93 (24%), Positives = 44/93 (47%), Gaps = 1/93 (1%)

Query: 198 GSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVR 257
            S     A +   ++VG LA +V D +L   F   +  +   ++ +D  T + +G+ FV 
Sbjct: 2   SSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFI-PFGDITDIQIPLDYETEKHRGFAFVE 60

Query: 258 FGDENERSRAMTEMNGVYCSSRPMRIDVATPKK 290
           F    + + A+  MN      R +R+++A P +
Sbjct: 61  FELAEDAAAAIDNMNESELFGRTIRVNLAKPMR 93

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 74.6 bits (184), Expect = 9e-17
 Identities = 23/97 (23%), Positives = 45/97 (46%), Gaps = 6/97 (6%)

Query: 320 QSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANR 373
            S   +    ++VG L  +V D+ L   F  FG+I  ++IP+       +G  FV+F   
Sbjct: 5   SSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELA 64

Query: 374 KDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQWRGDH 410
           +DA  A+  +  + +  +T+R++  +    K+     
Sbjct: 65  EDAAAAIDNMNESELFGRTIRVNLAKPMRIKESGPSS 101

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 60.3 bits (147), Expect = 9e-12
 Identities = 14/60 (23%), Positives = 29/60 (48%)

Query: 113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEK 172
              + +++G L   +D+  LH  F   G + ++++  + +T +  G+ FVEF     A  
Sbjct: 10  TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 69

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 88.5 bits (220), Expect = 1e-21
 Identities = 26/99 (26%), Positives = 56/99 (56%), Gaps = 1/99 (1%)

Query: 192 NWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTK 251
           + A    ++ +  +   + ++VG L  ++T+ +L+  F   +  ++  ++++DS TGR+K
Sbjct: 10  HMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFE-PFGRIESIQLMMDSETGRSK 68

Query: 252 GYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKK 290
           GYGF+ F D     +A+ ++NG   + RPM++   T + 
Sbjct: 69  GYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERT 107

>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 = 68.5 bits (168), Expect = 2e-14
 Identities = 22/93 (23%), Positives = 49/93 (52%), Gaps = 6/93 (6%)

Query: 313 GARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCG 366
            A +  +   G +    ++VG+L  +++++ LR  F  FG I S+++ +       KG G
Sbjct: 12  AAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYG 71

Query: 367 FVQFANRKDAEVALQKLQGTAIGKQTVRLSWGR 399
           F+ F++ + A+ AL++L G  +  + +++    
Sbjct: 72  FITFSDSECAKKALEQLNGFELAGRPMKVGHVT 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 = 60.4 bits (147), Expect = 1e-11
 Identities = 21/89 (23%), Positives = 43/89 (48%), Gaps = 2/89 (2%)

Query: 92  QQQQHGLSNGKQNGSNNNFTNDETKTIWIGDLFHW-MDETFLHNCFSHTGQVVNVKVIRN 150
               H         +N    +     +++G L H+ + E  L   F   G++ +++++ +
Sbjct: 3   HHHHHHSHMAAAMANNLQKGSAGPMRLYVGSL-HFNITEDMLRGIFEPFGRIESIQLMMD 61

Query: 151 KQTGQSEGYGFVEFYSRAAAEKVLQSYSG 179
            +TG+S+GYGF+ F     A+K L+  +G
Sbjct: 62  SETGRSKGYGFITFSDSECAKKALEQLNG 90

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 87.6 bits (218), Expect = 2e-21
 Identities = 28/84 (33%), Positives = 48/84 (57%), Gaps = 1/84 (1%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
            ++VG L  ++T+ +L+  F   +  +    ++ DS+TGR+KGYGF+ F D     RA+ 
Sbjct: 7   GLYVGSLHFNITEDMLRGIFE-PFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65

Query: 270 EMNGVYCSSRPMRIDVATPKKASG 293
           ++NG   + RPMR+   T +   G
Sbjct: 66  QLNGFELAGRPMRVGHVTERLDGG 89

>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 = 69.9 bits (172), Expect = 4e-15
 Identities = 22/83 (26%), Positives = 46/83 (55%), Gaps = 6/83 (7%)

Query: 323 GESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDA 376
           G S ++ ++VG+L  +++++ LR  F  FG+I ++ +         KG GF+ F++ + A
Sbjct: 1   GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60

Query: 377 EVALQKLQGTAIGKQTVRLSWGR 399
             AL++L G  +  + +R+    
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 = 58.7 bits (143), Expect = 3e-11
 Identities = 19/70 (27%), Positives = 39/70 (55%), Gaps = 2/70 (2%)

Query: 112 NDETKTIWIGDLFHW-MDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAA 170
           +  +  +++G L H+ + E  L   F   G++ N+ ++++  TG+S+GYGF+ F     A
Sbjct: 2   SSGSSGLYVGSL-HFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60

Query: 171 EKVLQSYSGS 180
            + L+  +G 
Sbjct: 61  RRALEQLNGF 70

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 89.1 bits (221), Expect = 2e-21
 Identities = 21/97 (21%), Positives = 44/97 (45%), Gaps = 1/97 (1%)

Query: 190 RLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGR 249
            ++  +         A +   ++VG LA +V D +L   F   +  +   ++ +D  T +
Sbjct: 45  HVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFI-PFGDITDIQIPLDYETEK 103

Query: 250 TKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVA 286
            +G+ FV F    + + A+  MN      R +R+++A
Sbjct: 104 HRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 140

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 77.1 bits (190), Expect = 3e-17
 Identities = 23/93 (24%), Positives = 44/93 (47%), Gaps = 6/93 (6%)

Query: 311 SNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKG 364
             G+   G      +    ++VG L  +V D+ L   F  FG+I  ++IP+       +G
Sbjct: 47  DGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRG 106

Query: 365 CGFVQFANRKDAEVALQKLQGTAIGKQTVRLSW 397
             FV+F   +DA  A+  +  + +  +T+R++ 
Sbjct: 107 FAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 139

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 67.1 bits (164), Expect = 9e-14
 Identities = 16/91 (17%), Positives = 38/91 (41%)

Query: 90  QQQQQQHGLSNGKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIR 149
                +  +  G      +  +    + +++G L   +D+  LH  F   G + ++++  
Sbjct: 38  CVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPL 97

Query: 150 NKQTGQSEGYGFVEFYSRAAAEKVLQSYSGS 180
           + +T +  G+ FVEF     A   + + + S
Sbjct: 98  DYETEKHRGFAFVEFELAEDAAAAIDNMNES 128

>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 = 88.1 bits (219), Expect = 2e-21
 Identities = 20/81 (24%), Positives = 40/81 (49%), Gaps = 1/81 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +++ +L+P VT+  L   F+ ++   KG  +     TGR +G  F+ F ++    +A+  
Sbjct: 28  LYLKNLSPRVTERDLVSLFA-RFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 86

Query: 271 MNGVYCSSRPMRIDVATPKKA 291
           +NG     + + I+    KK 
Sbjct: 87  VNGYKLYGKILVIEFGKNKKQ 107

>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 = 72.7 bits (179), Expect = 6e-16
 Identities = 19/85 (22%), Positives = 38/85 (44%), Gaps = 6/85 (7%)

Query: 327 NATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVAL 380
           N  +++  L   V++ DL   F++F E     I         +G  F+ F N++ A  AL
Sbjct: 25  NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQAL 84

Query: 381 QKLQGTAIGKQTVRLSWGRNPGNKQ 405
             + G  +  + + + +G+N   + 
Sbjct: 85  HLVNGYKLYGKILVIEFGKNKKQRS 109

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 55.0 bits (133), Expect = 1e-09
 Identities = 13/90 (14%), Positives = 35/90 (38%), Gaps = 2/90 (2%)

Query: 106 SNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFY 165
            ++    +  K +++ +L   + E  L + F+   +     +     TG+  G  F+ F 
Sbjct: 16  FSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFP 75

Query: 166 SRAAAEKVLQSYSGSLMPNTDQPFRLNWAT 195
           ++  A + L   +G  +    +   + +  
Sbjct: 76  NKEIAWQALHLVNGYKL--YGKILVIEFGK 103

>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 = 87.3 bits (217), Expect = 3e-21
 Identities = 23/92 (25%), Positives = 43/92 (46%), Gaps = 1/92 (1%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
            +++G +  D T+  + +  S     V   K++ D  TGR+KGY F+ F D    + A+ 
Sbjct: 4   VVYLGSIPYDQTEEQILDLCS-NVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62

Query: 270 EMNGVYCSSRPMRIDVATPKKASGYQQQYSSQ 301
            +NG    SR ++   ++    SG   ++   
Sbjct: 63  NLNGYQLGSRFLKCGYSSNSDISGVSLEHHHH 94

>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 = 73.0 bits (180), Expect = 3e-16
 Identities = 17/94 (18%), Positives = 46/94 (48%), Gaps = 6/94 (6%)

Query: 328 ATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVALQ 381
             +++G++  D ++E + +  S  G ++++K+         KG  F++F + + +  A++
Sbjct: 3   RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62

Query: 382 KLQGTAIGKQTVRLSWGRNPGNKQWRGDHSNHWN 415
            L G  +G + ++  +  N        +H +H +
Sbjct: 63  NLNGYQLGSRFLKCGYSSNSDISGVSLEHHHHHH 96

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 60.3 bits (147), Expect = 8e-12
 Identities = 17/81 (20%), Positives = 47/81 (58%), Gaps = 2/81 (2%)

Query: 115 TKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVL 174
           ++ +++G + +   E  + +  S+ G V+N+K++ + QTG+S+GY F+EF    ++   +
Sbjct: 2   SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 61

Query: 175 QSYSGSLMPNTDQPFRLNWAT 195
           ++ +G  +    +  +  +++
Sbjct: 62  RNLNGYQL--GSRFLKCGYSS 80

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 86.9 bits (216), Expect = 4e-21
 Identities = 27/97 (27%), Positives = 42/97 (43%), Gaps = 4/97 (4%)

Query: 197 SGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFV 256
             S     +    ++FV  L+ D T+  L+E+F         A+++ D  TG +KG+GFV
Sbjct: 4   GSSGPNARSQPSKTLFVKGLSEDTTEETLKESFDG----SVRARIVTDRETGSSKGFGFV 59

Query: 257 RFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKASG 293
            F  E +   A   M         + +D A PK   G
Sbjct: 60  DFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGEGG 96

>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 = 66.9 bits (164), Expect = 5e-14
 Identities = 25/102 (24%), Positives = 41/102 (40%), Gaps = 9/102 (8%)

Query: 313 GARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCG 366
           G+      +     + T+FV  L  D ++E L+E    F   +  +I         KG G
Sbjct: 1   GSSGSSGPNARSQPSKTLFVKGLSEDTTEETLKE---SFDGSVRARIVTDRETGSSKGFG 57

Query: 367 FVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQWRG 408
           FV F + +DA+ A + ++   I    V L W +  G      
Sbjct: 58  FVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGEGGSGP 99

>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 = 60.3 bits (147), Expect = 9e-12
 Identities = 20/80 (25%), Positives = 37/80 (46%), Gaps = 3/80 (3%)

Query: 101 GKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYG 160
           G    S  N  +  +KT+++  L     E  L   F      V  +++ +++TG S+G+G
Sbjct: 1   GSSGSSGPNARSQPSKTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFG 57

Query: 161 FVEFYSRAAAEKVLQSYSGS 180
           FV+F S   A+   ++    
Sbjct: 58  FVDFNSEEDAKAAKEAMEDG 77

>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 = 87.3 bits (217), Expect = 4e-21
 Identities = 24/132 (18%), Positives = 47/132 (35%), Gaps = 27/132 (20%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           IF+ +L   + +  L +TFS  + ++   KV+ D     +KGYGFV F  +    RA+ +
Sbjct: 8   IFIKNLDKSIDNKALYDTFS-AFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEK 64

Query: 271 MNGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATI 330
           MNG+  + R + +     +K                          +            +
Sbjct: 65  MNGMLLNDRKVFVGRFKSRKER------------------------EAELGARAKEFTNV 100

Query: 331 FVGALDSDVSDE 342
           ++       +  
Sbjct: 101 YIKNFGPGSTRA 112

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score = 76.9 bits (190), Expect = 2e-17
 Identities = 26/79 (32%), Positives = 41/79 (51%), Gaps = 4/79 (5%)

Query: 323 GESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV----GKGCGFVQFANRKDAEV 378
           G   +  IF+  LD  + ++ L + FS FG ILS K+       KG GFV F  ++ AE 
Sbjct: 1   GPLGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAER 60

Query: 379 ALQKLQGTAIGKQTVRLSW 397
           A++K+ G  +  + V +  
Sbjct: 61  AIEKMNGMLLNDRKVFVGR 79

>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 = 65.0 bits (159), Expect = 4e-13
 Identities = 26/111 (23%), Positives = 54/111 (48%), Gaps = 7/111 (6%)

Query: 115 TKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVL 174
           +  I+I +L   +D   L++ FS  G +++ KV+ +     S+GYGFV F ++ AAE+ +
Sbjct: 5   SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAI 62

Query: 175 QSYSGSLMPNTDQPFRLNWATF---SGSDRRTEACSDLSIFVGDLAPDVTD 222
           +  +G L+   D+   +          ++    A    ++++ +  P  T 
Sbjct: 63  EKMNGMLL--NDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGPGSTR 111

>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 = 88.4 bits (219), Expect = 5e-21
 Identities = 37/151 (24%), Positives = 64/151 (42%), Gaps = 9/151 (5%)

Query: 146 KVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATFSGSDRRTEA 205
           K+I N +T + E     E    A AEKV + Y+     + +  +     TF+ ++     
Sbjct: 4   KLILNGKTLKGETTT--EAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHH 61

Query: 206 CSDL------SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFG 259
              +      S+ V +L    +   L+  F  KY  V    +  D  T  ++G+ FVRF 
Sbjct: 62  HHHMDVEGMTSLKVDNLTYRTSPDTLRRVFE-KYGRVGDVYIPRDRYTKESRGFAFVRFH 120

Query: 260 DENERSRAMTEMNGVYCSSRPMRIDVATPKK 290
           D+ +   AM  M+G     R +R+ +A   +
Sbjct: 121 DKRDAEDAMDAMDGAVLDGRELRVQMARYGR 151

>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 = 72.6 bits (178), Expect = 2e-15
 Identities = 30/139 (21%), Positives = 53/139 (38%), Gaps = 16/139 (11%)

Query: 282 RIDVATPKKASGYQQQYSSQALVLA------GGPGSNGARVQGSQSDGESNNATIFVGAL 335
            +D AT +K        +                 + G+       D E    ++ V  L
Sbjct: 20  AVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGM-TSLKVDNL 78

Query: 336 DSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVALQKLQGTAIG 389
               S + LR  F ++G +  V IP        +G  FV+F +++DAE A+  + G  + 
Sbjct: 79  TYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLD 138

Query: 390 KQTVRLSW---GRNPGNKQ 405
            + +R+     GR P +  
Sbjct: 139 GRELRVQMARYGRPPDSHH 157

>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 = 59.9 bits (145), Expect = 5e-11
 Identities = 17/97 (17%), Positives = 40/97 (41%)

Query: 84  NGGGVKQQQQQQHGLSNGKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVV 143
             G        +        +  +++   +   ++ + +L +      L   F   G+V 
Sbjct: 39  VDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVG 98

Query: 144 NVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGS 180
           +V + R++ T +S G+ FV F+ +  AE  + +  G+
Sbjct: 99  DVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGA 135

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 87.0 bits (216), Expect = 6e-21
 Identities = 28/112 (25%), Positives = 50/112 (44%), Gaps = 3/112 (2%)

Query: 175 QSYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYP 234
            + + S  P          A  +G   + E     ++F+  L  + TD+ L  TF   + 
Sbjct: 9   SASALSTSPLASVALSAAAAAAAGK--QIEGPEGCNLFIYHLPQEFTDTDLASTFLP-FG 65

Query: 235 SVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVA 286
           +V  AKV ID  T  +K +GFV F + +    A+  MNG    ++ +++ + 
Sbjct: 66  NVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLK 117

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 73.2 bits (180), Expect = 4e-16
 Identities = 31/119 (26%), Positives = 54/119 (45%), Gaps = 11/119 (9%)

Query: 291 ASGYQQQYSSQALVLAGGPG----SNGARVQGSQSDGESNNATIFVGALDSDVSDEDLRE 346
           A+G  Q  S+ AL  +        +  A   G Q +G      +F+  L  + +D DL  
Sbjct: 1   AAGLPQFGSASALSTSPLASVALSAAAAAAAGKQIEG-PEGCNLFIYHLPQEFTDTDLAS 59

Query: 347 PFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGR 399
            F  FG ++S K+ +       K  GFV F N   A+VA++ + G  +G + +++   +
Sbjct: 60  TFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLKK 118

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 68.2 bits (167), Expect = 3e-14
 Identities = 24/103 (23%), Positives = 44/103 (42%)

Query: 77  GGHPYYQNGGGVKQQQQQQHGLSNGKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCF 136
            G P + +   +         LS      +       E   ++I  L     +T L + F
Sbjct: 2   AGLPQFGSASALSTSPLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTF 61

Query: 137 SHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSG 179
              G V++ KV  +KQT  S+ +GFV F +  +A+  +++ +G
Sbjct: 62  LPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNG 104

>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 = 86.1 bits (214), Expect = 6e-21
 Identities = 30/94 (31%), Positives = 47/94 (50%), Gaps = 1/94 (1%)

Query: 199 SDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRF 258
           S     A  +  +FVG L+ D  +  L++ FS KY  +    V+ D  T R++G+GFV F
Sbjct: 3   SGSSGMASDEGKLFVGGLSFDTNEQSLEQVFS-KYGQISEVVVVKDRETQRSRGFGFVTF 61

Query: 259 GDENERSRAMTEMNGVYCSSRPMRIDVATPKKAS 292
            + ++   AM  MNG     R +R+D A     +
Sbjct: 62  ENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDN 95

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 68.8 bits (169), Expect = 1e-14
 Identities = 24/96 (25%), Positives = 45/96 (46%), Gaps = 6/96 (6%)

Query: 319 SQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFAN 372
             S   S+   +FVG L  D +++ L + FS++G+I  V +         +G GFV F N
Sbjct: 4   GSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFEN 63

Query: 373 RKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQWRG 408
             DA+ A+  + G ++  + +R+       + +   
Sbjct: 64  IDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDNRSGP 99

>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 = 61.9 bits (151), Expect = 2e-12
 Identities = 21/77 (27%), Positives = 41/77 (53%), Gaps = 1/77 (1%)

Query: 105 GSNNNFTN-DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVE 163
           GS+ +     +   +++G L    +E  L   FS  GQ+  V V+++++T +S G+GFV 
Sbjct: 1   GSSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVT 60

Query: 164 FYSRAAAEKVLQSYSGS 180
           F +   A+  + + +G 
Sbjct: 61  FENIDDAKDAMMAMNGK 77

>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 = 86.1 bits (214), Expect = 8e-21
 Identities = 27/98 (27%), Positives = 47/98 (47%), Gaps = 2/98 (2%)

Query: 197 SGSDRRTEACSDL-SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGF 255
           SGS        D  +I V +L+ D  ++ LQE F   + S+    +  D  TG++KG+ F
Sbjct: 3   SGSSGPNRRADDNATIRVTNLSEDTRETDLQELFR-PFGSISRIYLAKDKTTGQSKGFAF 61

Query: 256 VRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKASG 293
           + F    + +RA+  ++G       + ++ A P   SG
Sbjct: 62  ISFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTNSG 99

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 75.7 bits (187), Expect = 3e-17
 Identities = 29/101 (28%), Positives = 45/101 (44%), Gaps = 9/101 (8%)

Query: 310 GSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GK 363
           GS+G+     ++D   +NATI V  L  D  + DL+E F  FG I  + +         K
Sbjct: 1   GSSGSSGPNRRAD---DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSK 57

Query: 364 GCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNK 404
           G  F+ F  R+DA  A+  + G       + + W +   N 
Sbjct: 58  GFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTNS 98

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 68.0 bits (167), Expect = 2e-14
 Identities = 26/95 (27%), Positives = 42/95 (44%), Gaps = 2/95 (2%)

Query: 101 GKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYG 160
           G    S  N   D+  TI + +L     ET L   F   G +  + + ++K TGQS+G+ 
Sbjct: 1   GSSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFA 60

Query: 161 FVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWAT 195
           F+ F+ R  A + +   SG    +      + WA 
Sbjct: 61  FISFHRREDAARAIAGVSGFGYDH--LILNVEWAK 93

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 84.1 bits (209), Expect = 2e-20
 Identities = 21/82 (25%), Positives = 41/82 (50%), Gaps = 1/82 (1%)

Query: 205 ACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENER 264
           A +   ++VG LA +V D +L   F   +  +   ++ +D  T + +G+ FV F    + 
Sbjct: 4   ATTKRVLYVGGLAEEVDDKVLHAAFI-PFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 62

Query: 265 SRAMTEMNGVYCSSRPMRIDVA 286
           + A+  MN      R +R+++A
Sbjct: 63  AAAIDNMNESELFGRTIRVNLA 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 = 73.7 bits (182), Expect = 1e-16
 Identities = 21/82 (25%), Positives = 42/82 (51%), Gaps = 6/82 (7%)

Query: 324 ESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAE 377
            +    ++VG L  +V D+ L   F  FG+I  ++IP+       +G  FV+F   +DA 
Sbjct: 4   ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 63

Query: 378 VALQKLQGTAIGKQTVRLSWGR 399
            A+  +  + +  +T+R++  +
Sbjct: 64  AAIDNMNESELFGRTIRVNLAK 85

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 61.8 bits (151), Expect = 2e-12
 Identities = 15/65 (23%), Positives = 33/65 (50%)

Query: 116 KTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQ 175
           + +++G L   +D+  LH  F   G + ++++  + +T +  G+ FVEF     A   + 
Sbjct: 8   RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67

Query: 176 SYSGS 180
           + + S
Sbjct: 68  NMNES 72

>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 = 85.5 bits (212), Expect = 2e-20
 Identities = 23/95 (24%), Positives = 43/95 (45%), Gaps = 1/95 (1%)

Query: 197 SGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFV 256
                R     +  + V  L+   T+  L+E FS KY  +    ++ D  + R++G+ FV
Sbjct: 35  RHVGNRANPDPNCCLGVFGLSLYTTERDLREVFS-KYGPIADVSIVYDQQSRRSRGFAFV 93

Query: 257 RFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKA 291
            F + ++   A    NG+    R +R+D +  K+ 
Sbjct: 94  YFENVDDAKEAKERANGMELDGRRIRVDFSITKRP 128

>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 = 74.4 bits (183), Expect = 2e-16
 Identities = 31/115 (26%), Positives = 54/115 (46%), Gaps = 7/115 (6%)

Query: 289 KKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPF 348
             +SG   + S  A +  G     G+R  G++++ + N   + V  L    ++ DLRE F
Sbjct: 9   HHSSGLVPRGSHMASMTGGQQMGRGSRHVGNRANPDPNC-CLGVFGLSLYTTERDLREVF 67

Query: 349 SQFGEILSVKIPV------GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSW 397
           S++G I  V I         +G  FV F N  DA+ A ++  G  +  + +R+ +
Sbjct: 68  SKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF 122

>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 = 59.4 bits (144), Expect = 5e-11
 Identities = 24/116 (20%), Positives = 47/116 (40%), Gaps = 5/116 (4%)

Query: 65  MMYPHHYMPYGGGGHPYYQNGGGVKQQQQQQHGLSNGKQNGSNNNFTNDETKTIWIGDLF 124
           M   HH+  +  G  P   +   +   QQ   G  +     +      D    + +  L 
Sbjct: 1   MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSRHVGNRANP-----DPNCCLGVFGLS 55

Query: 125 HWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGS 180
            +  E  L   FS  G + +V ++ ++Q+ +S G+ FV F +   A++  +  +G 
Sbjct: 56  LYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGM 111

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 84.6 bits (210), Expect = 3e-20
 Identities = 23/83 (27%), Positives = 40/83 (48%), Gaps = 1/83 (1%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
            +FV +L+   ++  L++ FS  Y  +      IDS T + KG+ FV F       +A  
Sbjct: 10  RLFVRNLSYTSSEEDLEKLFS-AYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 270 EMNGVYCSSRPMRIDVATPKKAS 292
           E++G     R + +  +T KK +
Sbjct: 69  EVDGQVFQGRMLHVLPSTIKKEA 91

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 72.6 bits (179), Expect = 4e-16
 Identities = 24/100 (24%), Positives = 37/100 (37%), Gaps = 8/100 (8%)

Query: 318 GSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFA 371
           GS     S    +FV  L    S+EDL + FS +G +  +  P+       KG  FV F 
Sbjct: 1   GSSGSSGSG--RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFM 58

Query: 372 NRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQWRGDHS 411
             + A  A  ++ G     + + +            G  S
Sbjct: 59  FPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEASQSGPSS 98

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 56.1 bits (136), Expect = 3e-10
 Identities = 14/70 (20%), Positives = 27/70 (38%)

Query: 111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAA 170
            +  +  +++ +L +   E  L   FS  G +  +    +  T + +G+ FV F     A
Sbjct: 4   GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHA 63

Query: 171 EKVLQSYSGS 180
            K      G 
Sbjct: 64  VKAYAEVDGQ 73

>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 = 89.6 bits (221), Expect = 3e-20
 Identities = 54/297 (18%), Positives = 96/297 (32%), Gaps = 38/297 (12%)

Query: 116 KTIWIGDLFHWMDE----TFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAE 171
            TI+I +L   + +      L+  FS  GQ++++ V R   + +  G  FV F   ++A 
Sbjct: 10  HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSAT 66

Query: 172 KVLQSYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSS 231
             L+S  G   P  D+P R+ +A    SD   +                           
Sbjct: 67  NALRSMQG--FPFYDKPMRIQYAKTD-SDIIAKMKGTFV-------------------ER 104

Query: 232 KYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKA 291
                K      ++   +    G             +  M  +  + R M      P   
Sbjct: 105 DRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYM 164

Query: 292 SGYQQQYSSQALVLAGGPGSNGARVQGSQSDGES-------NNATIFVGALDSDVSDEDL 344
                            PG+   +         +        N  +F+  L  + ++  L
Sbjct: 165 PPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELML 224

Query: 345 REPFSQFGEILSVKI-PVGKGCGFVQFANRKDAEVALQKLQGTAIGK-QTVRLSWGR 399
              F+QF     V++ P      FV+F N   A  A   LQG  I +   +++S+ +
Sbjct: 225 SMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK 281

>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 = 73.4 bits (179), Expect = 1e-14
 Identities = 24/129 (18%), Positives = 47/129 (36%), Gaps = 7/129 (5%)

Query: 327 NATIFVGALDSDVSDEDLREP----FSQFGEILSVKIPVG---KGCGFVQFANRKDAEVA 379
           N TI++  L+  +  ++L++     FSQFG+IL + +      +G  FV F     A  A
Sbjct: 9   NHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 68

Query: 380 LQKLQGTAIGKQTVRLSWGRNPGNKQWRGDHSNHWNGAHYGGQGYSGNGYAFPPNQDPNM 439
           L+ +QG     + +R+ + +   +   +   +          +                 
Sbjct: 69  LRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGG 128

Query: 440 YAATAVPGA 448
            A   V   
Sbjct: 129 GATPVVGAV 137

>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 = 84.7 bits (210), Expect = 3e-20
 Identities = 24/102 (23%), Positives = 44/102 (43%), Gaps = 1/102 (0%)

Query: 191 LNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRT 250
           L   +   +  + E     ++F+  L  +  D  L + F   + +V  AKV ID  T  +
Sbjct: 8   LTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMP-FGNVVSAKVFIDKQTNLS 66

Query: 251 KGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKAS 292
           K +GFV + +      A+  MNG     + +++ +   K  S
Sbjct: 67  KCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDS 108

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score = 72.0 bits (177), Expect = 1e-15
 Identities = 28/103 (27%), Positives = 47/103 (45%), Gaps = 10/103 (9%)

Query: 307 GGPGSNGARVQGSQSDGESNNAT----IFVGALDSDVSDEDLREPFSQFGEILSVKIPVG 362
           G  GS+G   Q   + G          +F+  L  +  D+DL + F  FG ++S K+ + 
Sbjct: 1   GSSGSSGLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFID 60

Query: 363 ------KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGR 399
                 K  GFV + N   A+ A+Q + G  IG + +++   R
Sbjct: 61  KQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKR 103

>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 = 62.7 bits (153), Expect = 2e-12
 Identities = 26/96 (27%), Positives = 41/96 (42%), Gaps = 10/96 (10%)

Query: 84  NGGGVKQQQQQQHGLSNGKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVV 143
              G+ QQ     G       G+N          ++I  L     +  L   F   G VV
Sbjct: 4   GSSGLTQQSIGAAGSQKEGPEGAN----------LFIYHLPQEFGDQDLLQMFMPFGNVV 53

Query: 144 NVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSG 179
           + KV  +KQT  S+ +GFV + +  +A+  +QS +G
Sbjct: 54  SAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNG 89

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 84.2 bits (209), Expect = 4e-20
 Identities = 20/81 (24%), Positives = 37/81 (45%), Gaps = 1/81 (1%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
            +FV  +  + T+  + + F+ +Y  +K   + +D  TG  KGY  V +    E   AM 
Sbjct: 25  ILFVTGVHEEATEEDIHDKFA-EYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 83

Query: 270 EMNGVYCSSRPMRIDVATPKK 290
            +NG     +P+ +D    + 
Sbjct: 84  GLNGQDLMGQPISVDWCFVRG 104

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 72.3 bits (178), Expect = 7e-16
 Identities = 22/95 (23%), Positives = 45/95 (47%), Gaps = 8/95 (8%)

Query: 311 SNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV----G--KG 364
                  G Q   E     +FV  +  + ++ED+ + F+++GEI ++ + +    G  KG
Sbjct: 9   EQDGDEPGPQRSVEGWI--LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKG 66

Query: 365 CGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGR 399
              V++   K+A+ A++ L G  +  Q + + W  
Sbjct: 67  YTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCF 101

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 61.1 bits (149), Expect = 6e-12
 Identities = 20/85 (23%), Positives = 43/85 (50%), Gaps = 6/85 (7%)

Query: 113 DETKTIWIGDLFHW-MDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAE 171
            E   +++  + H    E  +H+ F+  G++ N+ +  +++TG  +GY  VE+ +   A+
Sbjct: 21  VEGWILFVTGV-HEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 79

Query: 172 KVLQSYSGS-LMPNTDQPFRLNWAT 195
             ++  +G  LM    QP  ++W  
Sbjct: 80  AAMEGLNGQDLM---GQPISVDWCF 101

>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 = 84.3 bits (209), Expect = 6e-20
 Identities = 20/81 (24%), Positives = 37/81 (45%), Gaps = 1/81 (1%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
            +FV  +  + T+  + + F+ +Y  +K   + +D  TG  KGY  V +    E   AM 
Sbjct: 24  ILFVTGVHEEATEEDIHDKFA-EYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 82

Query: 270 EMNGVYCSSRPMRIDVATPKK 290
            +NG     +P+ +D    + 
Sbjct: 83  GLNGQDLMGQPISVDWCFVRG 103

>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 = 73.6 bits (181), Expect = 4e-16
 Identities = 24/112 (21%), Positives = 49/112 (43%), Gaps = 12/112 (10%)

Query: 311 SNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKG 364
                  G Q   E     +FV  +  + ++ED+ + F+++GEI ++ + +       KG
Sbjct: 8   EQDGDEPGPQRSVEGWI--LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKG 65

Query: 365 CGFVQFANRKDAEVALQKLQGTAIGKQTVRLSW----GRNPGNKQWRGDHSN 412
              V++   K+A+ A++ L G  +  Q + + W    G   G ++     S 
Sbjct: 66  YTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPPKGKRRGGRRRSR 117

>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 = 60.8 bits (148), Expect = 1e-11
 Identities = 20/85 (23%), Positives = 43/85 (50%), Gaps = 6/85 (7%)

Query: 113 DETKTIWIGDLFHW-MDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAE 171
            E   +++  + H    E  +H+ F+  G++ N+ +  +++TG  +GY  VE+ +   A+
Sbjct: 20  VEGWILFVTGV-HEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 78

Query: 172 KVLQSYSGS-LMPNTDQPFRLNWAT 195
             ++  +G  LM    QP  ++W  
Sbjct: 79  AAMEGLNGQDLM---GQPISVDWCF 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 = 83.4 bits (207), Expect = 7e-20
 Identities = 22/97 (22%), Positives = 39/97 (40%), Gaps = 1/97 (1%)

Query: 197 SGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFV 256
           S      +    +++ V +L    +   L+  F  KY  V    +  + +T   +G+ FV
Sbjct: 2   SSGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFE-KYGRVGDVYIPREPHTKAPRGFAFV 60

Query: 257 RFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKASG 293
           RF D  +   A   M+G     R +R+ VA   +   
Sbjct: 61  RFHDRRDAQDAEAAMDGAELDGRELRVQVARYGRRDL 97

>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 = 73.0 bits (180), Expect = 3e-16
 Identities = 24/97 (24%), Positives = 39/97 (40%), Gaps = 6/97 (6%)

Query: 318 GSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFA 371
           GS         T+ V  L    S + LR  F ++G +  V IP        +G  FV+F 
Sbjct: 4   GSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFH 63

Query: 372 NRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQWRG 408
           +R+DA+ A   + G  +  + +R+   R         
Sbjct: 64  DRRDAQDAEAAMDGAELDGRELRVQVARYGRRDLSGP 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 = 56.8 bits (138), Expect = 2e-10
 Identities = 16/60 (26%), Positives = 26/60 (43%)

Query: 113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEK 172
           D   T+ + +L +      L   F   G+V +V + R   T    G+ FV F+ R  A+ 
Sbjct: 11  DGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQD 70

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 82.7 bits (205), Expect = 1e-19
 Identities = 21/97 (21%), Positives = 49/97 (50%), Gaps = 2/97 (2%)

Query: 197 SGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFV 256
           SG  R + +     +F+  L    T   L+E     + +VK  +++ +   G+ KG  +V
Sbjct: 6   SGVFRYSTSLEKHKLFISGLPFSCTKEELEEICK-AHGTVKDLRLVTN-RAGKPKGLAYV 63

Query: 257 RFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKASG 293
            + +E++ S+A+ +M+G+      +++ ++    +SG
Sbjct: 64  EYENESQASQAVMKMDGMTIKENIIKVAISNSGPSSG 100

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 72.3 bits (178), Expect = 6e-16
 Identities = 18/100 (18%), Positives = 41/100 (41%), Gaps = 7/100 (7%)

Query: 310 GSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-----KG 364
            S  + V    +  E +   +F+  L    + E+L E     G +  +++        KG
Sbjct: 2   SSGSSGVFRYSTSLEKHK--LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKG 59

Query: 365 CGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNK 404
             +V++ N   A  A+ K+ G  I +  ++++   +  + 
Sbjct: 60  LAYVEYENESQASQAVMKMDGMTIKENIIKVAISNSGPSS 99

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 55.4 bits (134), Expect = 6e-10
 Identities = 14/69 (20%), Positives = 32/69 (46%), Gaps = 1/69 (1%)

Query: 111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAA 170
           T+ E   ++I  L     +  L       G V +++++ N+  G+ +G  +VE+ + + A
Sbjct: 13  TSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQA 71

Query: 171 EKVLQSYSG 179
            + +    G
Sbjct: 72  SQAVMKMDG 80

>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 = 82.2 bits (204), Expect = 1e-19
 Identities = 22/93 (23%), Positives = 42/93 (45%), Gaps = 1/93 (1%)

Query: 195 TFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYG 254
           +   S  R     +  + V  L+   T+  L+E FS KY  +    ++ D  + R++G+ 
Sbjct: 2   SSGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFS-KYGPIADVSIVYDQQSRRSRGFA 60

Query: 255 FVRFGDENERSRAMTEMNGVYCSSRPMRIDVAT 287
           FV F + ++   A    NG+    R +R+   +
Sbjct: 61  FVYFENVDDAKEAKERANGMELDGRRIRVSGPS 93

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 69.5 bits (171), Expect = 4e-15
 Identities = 25/93 (26%), Positives = 39/93 (41%), Gaps = 6/93 (6%)

Query: 313 GARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCG 366
           G+            N  + V  L    ++ DLRE FS++G I  V I         +G  
Sbjct: 1   GSSGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFA 60

Query: 367 FVQFANRKDAEVALQKLQGTAIGKQTVRLSWGR 399
           FV F N  DA+ A ++  G  +  + +R+S   
Sbjct: 61  FVYFENVDDAKEAKERANGMELDGRRIRVSGPS 93

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 62.2 bits (152), Expect = 2e-12
 Identities = 19/80 (23%), Positives = 36/80 (45%)

Query: 101 GKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYG 160
           G    S N    D    + +  L  +  E  L   FS  G + +V ++ ++Q+ +S G+ 
Sbjct: 1   GSSGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFA 60

Query: 161 FVEFYSRAAAEKVLQSYSGS 180
           FV F +   A++  +  +G 
Sbjct: 61  FVYFENVDDAKEAKERANGM 80

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 86.8 bits (214), Expect = 1e-19
 Identities = 23/108 (21%), Positives = 45/108 (41%), Gaps = 12/108 (11%)

Query: 317 QGSQSDGESNNATIFVGALDSDVS---------DEDLREPFSQFGEILSVKIPVGKGCGF 367
            G        N T++VG +D  ++         +  +R  FS+ G+I  ++    K CGF
Sbjct: 124 MGGIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGF 183

Query: 368 VQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNK---QWRGDHSN 412
           V+F  + +AE A + +    +   + +    R  G     +W  +  +
Sbjct: 184 VKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRREGTGLLVKWANEDPD 231

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 45.5 bits (107), Expect = 1e-05
 Identities = 22/152 (14%), Positives = 47/152 (30%), Gaps = 28/152 (18%)

Query: 63  QMMMYPHHYMPYGGGGHPYYQNGGGVKQQQQQQHGLSNGKQNGSNNNFTNDETKTIWIGD 122
               Y HH +P                     +   ++ +++         + KT+++G 
Sbjct: 85  PKCEYLHH-IP--DEEDIGKLALRTEVLDCFGREKFADYREDMGGIGSFRKKNKTLYVGG 141

Query: 123 L---------FHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKV 173
           +              E+ +   FS  G +  ++ + +K        GFV+F  +A AE  
Sbjct: 142 IDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESK------NCGFVKFKYQANAEFA 195

Query: 174 LQSYSGSLM----------PNTDQPFRLNWAT 195
            ++ S   +                  + WA 
Sbjct: 196 KEAMSNQTLLLPSDKEWDDRREGTGLLVKWAN 227

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 81.9 bits (203), Expect = 2e-19
 Identities = 28/81 (34%), Positives = 46/81 (56%), Gaps = 1/81 (1%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           S+FVG++  + T+  L++ FS +   V   +++ D  TG+ KGYGF  + D+     AM 
Sbjct: 10  SVFVGNIPYEATEEQLKDIFS-EVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68

Query: 270 EMNGVYCSSRPMRIDVATPKK 290
            +NG   S R +R+D A  +K
Sbjct: 69  NLNGREFSGRALRVDNAASEK 89

>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 = 68.4 bits (168), Expect = 1e-14
 Identities = 20/95 (21%), Positives = 47/95 (49%), Gaps = 6/95 (6%)

Query: 324 ESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAE 377
           + +  ++FVG +  + ++E L++ FS+ G ++S ++         KG GF ++ +++ A 
Sbjct: 5   DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETAL 64

Query: 378 VALQKLQGTAIGKQTVRLSWGRNPGNKQWRGDHSN 412
            A++ L G     + +R+    +  NK+       
Sbjct: 65  SAMRNLNGREFSGRALRVDNAASEKNKEELKSLGT 99

>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 = 60.7 bits (148), Expect = 7e-12
 Identities = 17/67 (25%), Positives = 41/67 (61%)

Query: 113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEK 172
              +++++G++ +   E  L + FS  G VV+ +++ +++TG+ +GYGF E+  +  A  
Sbjct: 6   RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALS 65

Query: 173 VLQSYSG 179
            +++ +G
Sbjct: 66  AMRNLNG 72

>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 = 82.0 bits (203), Expect = 2e-19
 Identities = 19/81 (23%), Positives = 35/81 (43%), Gaps = 1/81 (1%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
            +FV  +  +  +  +QE F   Y  +K   + +D  TG +KGY  V +    +   A  
Sbjct: 28  ILFVTSIHEEAQEDEIQEKFC-DYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 86

Query: 270 EMNGVYCSSRPMRIDVATPKK 290
            +NG     + +++D    K 
Sbjct: 87  ALNGAEIMGQTIQVDWCFVKG 107

>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 = 71.9 bits (177), Expect = 9e-16
 Identities = 25/101 (24%), Positives = 47/101 (46%), Gaps = 8/101 (7%)

Query: 311 SNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV----G--KG 364
            +     G Q   E     +FV ++  +  +++++E F  +GEI ++ + +    G  KG
Sbjct: 12  DDDELEPGPQRSVEG--WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKG 69

Query: 365 CGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQ 405
              V++   K A  A + L G  I  QT+++ W    G K+
Sbjct: 70  YALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKR 110

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 60.8 bits (148), Expect = 9e-12
 Identities = 18/84 (21%), Positives = 41/84 (48%), Gaps = 6/84 (7%)

Query: 114 ETKTIWIGDLFHW-MDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEK 172
           E   +++  + H    E  +   F   G++ N+ +  +++TG S+GY  VE+ +   A  
Sbjct: 25  EGWILFVTSI-HEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALA 83

Query: 173 VLQSYSGS-LMPNTDQPFRLNWAT 195
             ++ +G+ +M    Q  +++W  
Sbjct: 84  AKEALNGAEIM---GQTIQVDWCF 104

>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 = 82.9 bits (205), Expect = 3e-19
 Identities = 19/97 (19%), Positives = 44/97 (45%), Gaps = 1/97 (1%)

Query: 194 ATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGY 253
                +    E     ++ V  +   V +  L++ F   Y  ++  K++ D  T +++GY
Sbjct: 28  QHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFER-YGPIESVKIVCDRETRQSRGY 86

Query: 254 GFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKK 290
           GFV+F   +   +A+  +NG    ++ +++ +A    
Sbjct: 87  GFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGH 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 = 74.4 bits (183), Expect = 3e-16
 Identities = 30/107 (28%), Positives = 52/107 (48%), Gaps = 5/107 (4%)

Query: 73  PYGGGGHPYYQNGGGVKQQQQQQHGLSNGKQNGSNNNFTNDETKTIWIGDLFHWMDETFL 132
           P      PY Q     + QQQQQ  +   + N   +   N     + +  +   +DE  L
Sbjct: 5   PLVSQYDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRN-----LMVNYIPTTVDEVQL 59

Query: 133 HNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSG 179
              F   G + +VK++ +++T QS GYGFV+F S ++A++ +   +G
Sbjct: 60  RQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNG 106

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score = 67.8 bits (166), Expect = 6e-14
 Identities = 29/133 (21%), Positives = 52/133 (39%), Gaps = 9/133 (6%)

Query: 293 GYQQQYSS--QALVLAGGPGSNGARVQGSQSDGESNNAT-IFVGALDSDVSDEDLREPFS 349
               QY    Q   L          +  +Q + E +    + V  + + V +  LR+ F 
Sbjct: 5   PLVSQYDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFE 64

Query: 350 QFGEILSVKIPV------GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGN 403
           ++G I SVKI         +G GFV+F +   A+ A+  L G  I  + ++++   +   
Sbjct: 65  RYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQ 124

Query: 404 KQWRGDHSNHWNG 416
           +          NG
Sbjct: 125 RPGIAGAVGDGNG 137

>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 = 81.1 bits (201), Expect = 3e-19
 Identities = 26/81 (32%), Positives = 44/81 (54%), Gaps = 2/81 (2%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           +I+VG+L    T   ++E FS ++  V   K+I D  T + KG+GFV   +E+    A+ 
Sbjct: 3   NIYVGNLVYSATSEQVKELFS-QFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSE-AIA 60

Query: 270 EMNGVYCSSRPMRIDVATPKK 290
           +++      R +R+  A PKK
Sbjct: 61  KLDNTDFMGRTIRVTEANPKK 81

>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 = 61.4 bits (150), Expect = 3e-12
 Identities = 25/88 (28%), Positives = 42/88 (47%), Gaps = 7/88 (7%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVALQK 382
            I+VG L    + E ++E FSQFG++ +VK+         KG GFV+    +    A+ K
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAK 61

Query: 383 LQGTAIGKQTVRLSWGRNPGNKQWRGDH 410
           L  T    +T+R++      + +    H
Sbjct: 62  LDNTDFMGRTIRVTEANPKKSLEHHHHH 89

>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 = 56.8 bits (138), Expect = 1e-10
 Identities = 18/56 (32%), Positives = 34/56 (60%)

Query: 116 KTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAE 171
           + I++G+L +      +   FS  G+V NVK+I +++T + +G+GFVE    + +E
Sbjct: 2   RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSE 57

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 81.1 bits (201), Expect = 4e-19
 Identities = 24/94 (25%), Positives = 43/94 (45%), Gaps = 2/94 (2%)

Query: 194 ATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGY 253
           ++ S      +  +D ++FVG+L   V + IL E F  +   +    +  D   G+ K +
Sbjct: 2   SSGSSGMFPAQEEADRTVFVGNLEARVREEILYELFL-QAGPLTKVTICKD-REGKPKSF 59

Query: 254 GFVRFGDENERSRAMTEMNGVYCSSRPMRIDVAT 287
           GFV F      S A+  +NG+    RP+ +   +
Sbjct: 60  GFVCFKHPESVSYAIALLNGIRLYGRPINVSGPS 93

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 74.2 bits (183), Expect = 1e-16
 Identities = 28/93 (30%), Positives = 43/93 (46%), Gaps = 7/93 (7%)

Query: 310 GSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV-----GKG 364
           GS+G+   G     E  + T+FVG L++ V +E L E F Q G +  V I        K 
Sbjct: 1   GSSGS--SGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKS 58

Query: 365 CGFVQFANRKDAEVALQKLQGTAIGKQTVRLSW 397
            GFV F + +    A+  L G  +  + + +S 
Sbjct: 59  FGFVCFKHPESVSYAIALLNGIRLYGRPINVSG 91

>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 = 58.4 bits (142), Expect = 4e-11
 Identities = 15/83 (18%), Positives = 39/83 (46%), Gaps = 3/83 (3%)

Query: 113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEK 172
           +  +T+++G+L   + E  L+  F   G +  V + +++  G+ + +GFV F    +   
Sbjct: 14  EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESVSY 72

Query: 173 VLQSYSGSLMPNTDQPFRLNWAT 195
            +   +G  +    +P  ++  +
Sbjct: 73  AIALLNGIRL--YGRPINVSGPS 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 = 80.7 bits (200), Expect = 4e-19
 Identities = 22/93 (23%), Positives = 43/93 (46%), Gaps = 1/93 (1%)

Query: 194 ATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGY 253
           ++ S       A S  +++V +L   +T++ L   FS KY  V    ++ D +T ++KG 
Sbjct: 2   SSGSSGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFS-KYGKVVKVTIMKDKDTRKSKGV 60

Query: 254 GFVRFGDENERSRAMTEMNGVYCSSRPMRIDVA 286
            F+ F D++        +N      R ++  +A
Sbjct: 61  AFILFLDKDSAQNCTRAINNKQLFGRVIKASIA 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 = 66.9 bits (164), Expect = 4e-14
 Identities = 20/93 (21%), Positives = 44/93 (47%), Gaps = 8/93 (8%)

Query: 310 GSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GK 363
           GS+G+   G       + +T++V  L   +++ DL   FS++G+++ V I         K
Sbjct: 1   GSSGSS--GMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSK 58

Query: 364 GCGFVQFANRKDAEVALQKLQGTAIGKQTVRLS 396
           G  F+ F ++  A+   + +    +  + ++ S
Sbjct: 59  GVAFILFLDKDSAQNCTRAINNKQLFGRVIKAS 91

>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 = 59.9 bits (146), Expect = 1e-11
 Identities = 16/64 (25%), Positives = 36/64 (56%)

Query: 116 KTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQ 175
            T+++ +L   +    L+  FS  G+VV V ++++K T +S+G  F+ F  + +A+   +
Sbjct: 17  STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76

Query: 176 SYSG 179
           + + 
Sbjct: 77  AINN 80

>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 = 81.6 bits (202), Expect = 5e-19
 Identities = 19/93 (20%), Positives = 46/93 (49%), Gaps = 4/93 (4%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +F+G L  +  + +L+  F  K+  +    +I D  T +++G+ F+ F +  +   A  +
Sbjct: 10  LFIGGLNRETNEKMLKAVFG-KHGPISEVLLIKD-RTSKSRGFAFITFENPADAKNAAKD 67

Query: 271 MNGVYCSSRPMRIDVATPK--KASGYQQQYSSQ 301
           MNG     + ++++ A     ++ G ++  +S 
Sbjct: 68  MNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASS 100

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score = 73.5 bits (181), Expect = 4e-16
 Identities = 20/107 (18%), Positives = 48/107 (44%), Gaps = 7/107 (6%)

Query: 325 SNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV-----GKGCGFVQFANRKDAEVA 379
            +   +F+G L+ + +++ L+  F + G I  V +        +G  F+ F N  DA+ A
Sbjct: 5   DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNA 64

Query: 380 LQKLQGTAIGKQTVRLSWGRNPGNKQ--WRGDHSNHWNGAHYGGQGY 424
            + + G ++  + +++   + P  +    R   ++  N +  G   +
Sbjct: 65  AKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSRNRSPSGSLEH 111

>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 = 55.4 bits (134), Expect = 6e-10
 Identities = 18/67 (26%), Positives = 33/67 (49%), Gaps = 1/67 (1%)

Query: 113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEK 172
           D    ++IG L    +E  L   F   G +  V +I+++ T +S G+ F+ F + A A+ 
Sbjct: 5   DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKN 63

Query: 173 VLQSYSG 179
             +  +G
Sbjct: 64  AAKDMNG 70

>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 = 81.1 bits (200), Expect = 6e-19
 Identities = 18/91 (19%), Positives = 38/91 (41%), Gaps = 6/91 (6%)

Query: 307 GGPGSNGARVQGSQSDGE------SNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIP 360
           G  GS+GA+    + +G       + +  +  G L + VS   L     + G + ++ +P
Sbjct: 1   GSSGSSGAKHTLLRHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMP 60

Query: 361 VGKGCGFVQFANRKDAEVALQKLQGTAIGKQ 391
             K   F ++   ++++ A   L G  +   
Sbjct: 61  PNKPYSFARYRTTEESKRAYVTLNGKEVVDD 91

>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 = 48.4 bits (115), Expect = 2e-07
 Identities = 13/85 (15%), Positives = 31/85 (36%), Gaps = 11/85 (12%)

Query: 115 TKTIWI--GDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEK 172
           T+++ +  G L + +    L       G V  + +  NK       Y F  + +   +++
Sbjct: 25  TQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK------PYSFARYRTTEESKR 78

Query: 173 VLQSYSGSLMPNT---DQPFRLNWA 194
              + +G  + +         LN+ 
Sbjct: 79  AYVTLNGKEVVDDLGQKITLYLNFV 103

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 44.9 bits (106), Expect = 3e-06
 Identities = 17/65 (26%), Positives = 25/65 (38%), Gaps = 7/65 (10%)

Query: 209 LSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAM 268
           L +  G L   V+ + L      K   V    +++  N    K Y F R+    E  RA 
Sbjct: 28  LVVANGGLGNGVSRNQLLPVLE-KCGLVD--ALLMPPN----KPYSFARYRTTEESKRAY 80

Query: 269 TEMNG 273
             +NG
Sbjct: 81  VTLNG 85

>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 = 80.3 bits (199), Expect = 6e-19
 Identities = 15/82 (18%), Positives = 31/82 (37%), Gaps = 1/82 (1%)

Query: 209 LSIFVGDLAPDVTDSILQETFSSK-YPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRA 267
           +++++G+L    TD  L E   S     +   K   +   G++KG+  V  G E    + 
Sbjct: 2   IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKL 61

Query: 268 MTEMNGVYCSSRPMRIDVATPK 289
           M  +       +   +  +   
Sbjct: 62  MDLLPKRELHGQNPVVTPSNKL 83

>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 = 61.1 bits (149), Expect = 4e-12
 Identities = 16/65 (24%), Positives = 31/65 (47%), Gaps = 2/65 (3%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTG--QVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQ 175
           ++IG+L  W  +  L       G   ++ +K   N+  GQS+G+  V   S A+++K++ 
Sbjct: 4   LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63

Query: 176 SYSGS 180
                
Sbjct: 64  LLPKR 68

>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 = 58.0 bits (141), Expect = 4e-11
 Identities = 17/73 (23%), Positives = 28/73 (38%), Gaps = 8/73 (10%)

Query: 330 IFVGALDSDVSDEDLREPFSQFG--EILSVKIPV----G--KGCGFVQFANRKDAEVALQ 381
           +++G L    +DEDL E     G  +IL +K       G  KG   V   +   ++  + 
Sbjct: 4   LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63

Query: 382 KLQGTAIGKQTVR 394
            L    +  Q   
Sbjct: 64  LLPKRELHGQNPV 76

>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 = 80.4 bits (199), Expect = 6e-19
 Identities = 18/86 (20%), Positives = 40/86 (46%), Gaps = 1/86 (1%)

Query: 321 SDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVAL 380
           S G S    +++G L   V+ +DLR+ F      L+ ++ +  G  FV + ++  A  A+
Sbjct: 2   SSGSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAI 61

Query: 381 QKLQGTA-IGKQTVRLSWGRNPGNKQ 405
           + L G   +  + + + +  +   + 
Sbjct: 62  ETLSGKVELHGKIMEVDYSVSKKLRS 87

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 70.0 bits (172), Expect = 3e-15
 Identities = 21/82 (25%), Positives = 38/82 (46%), Gaps = 8/82 (9%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
            +++G+L+P VT   L++ F          K+ +        GY FV + D+N   RA+ 
Sbjct: 10  KLYIGNLSPAVTADDLRQLFGD-------RKLPLAGQVLLKSGYAFVDYPDQNWAIRAIE 62

Query: 270 EMNGVY-CSSRPMRIDVATPKK 290
            ++G      + M +D +  KK
Sbjct: 63  TLSGKVELHGKIMEVDYSVSKK 84

>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 = 44.9 bits (107), Expect = 2e-06
 Identities = 13/80 (16%), Positives = 34/80 (42%), Gaps = 7/80 (8%)

Query: 116 KTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQ 175
             ++IG+L   +    L   F      +  +V+         GY FV++  +  A + ++
Sbjct: 9   NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKS------GYAFVDYPDQNWAIRAIE 62

Query: 176 SYSGSLMPNTDQPFRLNWAT 195
           + SG +  +  +   ++++ 
Sbjct: 63  TLSGKVELH-GKIMEVDYSV 81

>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 = 80.8 bits (200), Expect = 8e-19
 Identities = 26/111 (23%), Positives = 45/111 (40%), Gaps = 4/111 (3%)

Query: 194 ATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGY 253
            +   S          ++FV +L   V    L+E FS     V  A ++ D + G+++G 
Sbjct: 1   GSSGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFS-MAGVVVRADILEDKD-GKSRGI 58

Query: 254 GFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPK--KASGYQQQYSSQA 302
           G V F    E  +A++  NG     RPM + +      K   +  +   Q+
Sbjct: 59  GTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERALPKGDFFPPERPQQS 109

>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 = 72.0 bits (177), Expect = 9e-16
 Identities = 23/101 (22%), Positives = 38/101 (37%), Gaps = 8/101 (7%)

Query: 310 GSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-----KG 364
           GS+G+             +T+FV  LD  V  + L+E FS  G ++   I        +G
Sbjct: 1   GSSGSS---GALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRG 57

Query: 365 CGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQ 405
            G V F    +A  A+    G  +  + + +        K 
Sbjct: 58  IGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERALPKG 98

>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 = 46.9 bits (112), Expect = 6e-07
 Identities = 19/79 (24%), Positives = 33/79 (41%), Gaps = 1/79 (1%)

Query: 101 GKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYG 160
           G    S          T+++ +L + +    L   FS  G VV   ++ +K  G+S G G
Sbjct: 1   GSSGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIG 59

Query: 161 FVEFYSRAAAEKVLQSYSG 179
            V F     A + +  ++G
Sbjct: 60  TVTFEQSIEAVQAISMFNG 78

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A Length = 165

 Score = 82.2 bits (203), Expect = 9e-19
 Identities = 19/81 (23%), Positives = 35/81 (43%), Gaps = 1/81 (1%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
            +FV  +  +  +  +QE F   Y  +K   + +D  TG +KGY  V +    +   A  
Sbjct: 74  ILFVTSIHEEAQEDEIQEKFC-DYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 132

Query: 270 EMNGVYCSSRPMRIDVATPKK 290
            +NG     + +++D    K 
Sbjct: 133 ALNGAEIMGQTIQVDWCFVKG 153

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A Length = 165

 Score = 75.3 bits (185), Expect = 2e-16
 Identities = 30/159 (18%), Positives = 63/159 (39%), Gaps = 20/159 (12%)

Query: 258 FGDENERSRAMTEMN--GVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGAR 315
           F  + +  + +  +     +   R    D  T +    Y++  +            +   
Sbjct: 13  FEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNE----------DDDEL 62

Query: 316 VQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV----G--KGCGFVQ 369
             G Q   E     +FV ++  +  +++++E F  +GEI ++ + +    G  KG   V+
Sbjct: 63  EPGPQRSVEG--WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVE 120

Query: 370 FANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQWRG 408
           +   K A  A + L G  I  QT+++ W    G K+ + 
Sbjct: 121 YETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKRVKK 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 = 59.8 bits (145), Expect = 7e-11
 Identities = 18/119 (15%), Positives = 47/119 (39%), Gaps = 4/119 (3%)

Query: 78  GHPYYQNGGGVKQQQQQQHGLSNGKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFS 137
           G  +  +    +     +   +            + E   +++  +     E  +   F 
Sbjct: 35  GRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFC 94

Query: 138 HTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGS-LMPNTDQPFRLNWAT 195
             G++ N+ +  +++TG S+GY  VE+ +   A    ++ +G+ +M    Q  +++W  
Sbjct: 95  DYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIM---GQTIQVDWCF 150

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 80.0 bits (198), Expect = 1e-18
 Identities = 15/83 (18%), Positives = 35/83 (42%), Gaps = 4/83 (4%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTG---RTKGYGFVRFGDENERSR 266
            +F+ +L    T+  L+  FS K  ++K   +    N      + G+GFV +    +  +
Sbjct: 7   GLFIKNLNFSTTEETLKGVFS-KVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65

Query: 267 AMTEMNGVYCSSRPMRIDVATPK 289
           A+ ++ G       + + ++   
Sbjct: 66  ALKQLQGHTVDGHKLEVRISERA 88

>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 = 74.2 bits (183), Expect = 1e-16
 Identities = 22/86 (25%), Positives = 41/86 (47%), Gaps = 9/86 (10%)

Query: 323 GESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKI---------PVGKGCGFVQFANR 373
           G S ++ +F+  L+   ++E L+  FS+ G I S  I          +  G GFV++   
Sbjct: 1   GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60

Query: 374 KDAEVALQKLQGTAIGKQTVRLSWGR 399
           + A+ AL++LQG  +    + +    
Sbjct: 61  EQAQKALKQLQGHTVDGHKLEVRISE 86

>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 = 53.0 bits (128), Expect = 3e-09
 Identities = 18/70 (25%), Positives = 30/70 (42%), Gaps = 3/70 (4%)

Query: 114 ETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQ---SEGYGFVEFYSRAAA 170
            +  ++I +L     E  L   FS  G + +  + + K       S G+GFVE+     A
Sbjct: 4   GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQA 63

Query: 171 EKVLQSYSGS 180
           +K L+   G 
Sbjct: 64  QKALKQLQGH 73

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 80.0 bits (198), Expect = 1e-18
 Identities = 28/91 (30%), Positives = 46/91 (50%), Gaps = 2/91 (2%)

Query: 197 SGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFV 256
           SG        +   + V +L   V+D+ +QE F+ ++ ++K A V  D  +GR+ G   V
Sbjct: 18  SGFGGGAGVETGGKLLVSNLDFGVSDADIQELFA-EFGTLKKAAVHYDR-SGRSLGTADV 75

Query: 257 RFGDENERSRAMTEMNGVYCSSRPMRIDVAT 287
            F  + +  +AM + NGV    RPM I + T
Sbjct: 76  HFERKADALKAMKQYNGVPLDGRPMNIQLVT 106

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 72.3 bits (178), Expect = 7e-16
 Identities = 19/81 (23%), Positives = 34/81 (41%), Gaps = 5/81 (6%)

Query: 321 SDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-----KGCGFVQFANRKD 375
             G      + V  LD  VSD D++E F++FG +    +         G   V F  + D
Sbjct: 23  GAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKAD 82

Query: 376 AEVALQKLQGTAIGKQTVRLS 396
           A  A+++  G  +  + + + 
Sbjct: 83  ALKAMKQYNGVPLDGRPMNIQ 103

>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 = 51.9 bits (125), Expect = 9e-09
 Identities = 21/104 (20%), Positives = 43/104 (41%), Gaps = 8/104 (7%)

Query: 93  QQQHGLSNGKQNGSNNNFTNDETKTIWIGDLFHW-MDETFLHNCFSHTGQVVNVKVIRNK 151
           + QH L +    G     T      + + +L  + + +  +   F+  G +    V  ++
Sbjct: 10  KWQHDLFDSGFGGGAGVETG---GKLLVSNL-DFGVSDADIQELFAEFGTLKKAAVHYDR 65

Query: 152 QTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWAT 195
            +G+S G   V F  +A A K ++ Y+G  +    +P  +   T
Sbjct: 66  -SGRSLGTADVHFERKADALKAMKQYNGVPLDG--RPMNIQLVT 106

>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 = 79.1 bits (196), Expect = 1e-18
 Identities = 20/81 (24%), Positives = 35/81 (43%), Gaps = 3/81 (3%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +++  L P  TD  L +     Y  +   K I+D  T + KGYGFV F   +   +A+T 
Sbjct: 8   LYIRGLQPGTTDQDLVKLCQ-PYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTA 66

Query: 271 MNGVYCSSRPMRIDVATPKKA 291
           +      ++  +   + P   
Sbjct: 67  LKASGVQAQMAK--QSGPSSG 85

>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 = 72.6 bits (179), Expect = 3e-16
 Identities = 21/80 (26%), Positives = 40/80 (50%), Gaps = 6/80 (7%)

Query: 323 GESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDA 376
           G S ++ +++  L    +D+DL +    +G+I+S K  +       KG GFV F +   A
Sbjct: 1   GSSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAA 60

Query: 377 EVALQKLQGTAIGKQTVRLS 396
           + A+  L+ + +  Q  + S
Sbjct: 61  QKAVTALKASGVQAQMAKQS 80

>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 = 61.4 bits (150), Expect = 2e-12
 Identities = 20/69 (28%), Positives = 36/69 (52%)

Query: 112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAE 171
           +  +  ++I  L     +  L       G++V+ K I +K T + +GYGFV+F S +AA+
Sbjct: 2   SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQ 61

Query: 172 KVLQSYSGS 180
           K + +   S
Sbjct: 62  KAVTALKAS 70

>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 = 79.7 bits (197), Expect = 2e-18
 Identities = 26/102 (25%), Positives = 47/102 (46%), Gaps = 4/102 (3%)

Query: 307 GGPGSNGARVQGS-QSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV---G 362
           G  GS+G    G  +    +N+  I+VG L  D+  +D+ + F ++G I  + +     G
Sbjct: 1   GSSGSSGMSGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGG 60

Query: 363 KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNK 404
               FV+F + +DAE A+    G       +R+ + R+    
Sbjct: 61  PPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGT 102

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 58.9 bits (143), Expect = 4e-11
 Identities = 21/97 (21%), Positives = 41/97 (42%), Gaps = 4/97 (4%)

Query: 197 SGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFV 256
            G  R     +D  I+VG+L PD+    +++ F  KY +++   +    N      + FV
Sbjct: 11  GGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFY-KYGAIRDIDLK---NRRGGPPFAFV 66

Query: 257 RFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKASG 293
            F D  +   A+   +G       +R++     + +G
Sbjct: 67  EFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGTG 103

>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 = 40.8 bits (96), Expect = 9e-05
 Identities = 16/85 (18%), Positives = 29/85 (34%), Gaps = 3/85 (3%)

Query: 96  HGLSNGKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQ 155
            G S     G       +    I++G+L   +    + + F   G + ++ +   K    
Sbjct: 3   SGSSGMSGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL---KNRRG 59

Query: 156 SEGYGFVEFYSRAAAEKVLQSYSGS 180
              + FVEF     AE  +    G 
Sbjct: 60  GPPFAFVEFEDPRDAEDAVYGRDGY 84

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 80.2 bits (198), Expect = 2e-18
 Identities = 27/112 (24%), Positives = 47/112 (41%), Gaps = 1/112 (0%)

Query: 179 GSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKG 238
           GS M +     ++   + S      +     S+ V +L    +   L+  F  KY  V  
Sbjct: 18  GSHMASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFE-KYGRVGD 76

Query: 239 AKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKK 290
             +  D  T  ++G+ FVRF D+ +   AM  M+G     R +R+ +A   +
Sbjct: 77  VYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGR 128

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 78.6 bits (194), Expect = 9e-18
 Identities = 28/118 (23%), Positives = 49/118 (41%), Gaps = 6/118 (5%)

Query: 288 PKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREP 347
              +SG   + S  A +  G     G+   G          ++ V  L    S + LR  
Sbjct: 8   HHHSSGLVPRGSHMASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRV 67

Query: 348 FSQFGEILSVKIPV------GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGR 399
           F ++G +  V IP        +G  FV+F +++DAE A+  + G  +  + +R+   R
Sbjct: 68  FEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMAR 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 = 59.8 bits (145), Expect = 3e-11
 Identities = 20/103 (19%), Positives = 41/103 (39%), Gaps = 5/103 (4%)

Query: 75  GGGGHPYYQNGGGVKQQQQQ-----QHGLSNGKQNGSNNNFTNDETKTIWIGDLFHWMDE 129
           G   H ++ + G V +            +  G  +        +   ++ + +L +    
Sbjct: 2   GSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSP 61

Query: 130 TFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEK 172
             L   F   G+V +V + R++ T +S G+ FV F+ +  AE 
Sbjct: 62  DTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAED 104

>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 = 79.7 bits (197), Expect = 2e-18
 Identities = 29/116 (25%), Positives = 50/116 (43%), Gaps = 2/116 (1%)

Query: 174 LQSYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKY 233
           + S +G      D     +    SG        +   + V +L   V+D+ +QE F+ ++
Sbjct: 1   MASMTGGQQMGRDPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFA-EF 59

Query: 234 PSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPK 289
            ++K A V  D  +GR+ G   V F    +  +AM +  GV    RPM I +   +
Sbjct: 60  GTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQ 114

>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 = 72.4 bits (178), Expect = 1e-15
 Identities = 21/81 (25%), Positives = 37/81 (45%), Gaps = 5/81 (6%)

Query: 321 SDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-----KGCGFVQFANRKD 375
            +G    A + V  LD  VSD D++E F++FG +    +         G   V F  R D
Sbjct: 29  GEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRAD 88

Query: 376 AEVALQKLQGTAIGKQTVRLS 396
           A  A+++ +G  +  + + + 
Sbjct: 89  ALKAMKQYKGVPLDGRPMDIQ 109

>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 = 51.2 bits (123), Expect = 3e-08
 Identities = 21/102 (20%), Positives = 41/102 (40%), Gaps = 10/102 (9%)

Query: 83  QNGGGVKQQQQQ----QHGLSNGKQNGSNNNFTNDETKTIWIGDLFHW-MDETFLHNCFS 137
            +  G +Q  +     QH L +    G       +    + + +L  + + +  +   F+
Sbjct: 2   ASMTGGQQMGRDPDKWQHDLFDSGCGGGEGV---ETGAKLLVSNL-DFGVSDADIQELFA 57

Query: 138 HTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSG 179
             G +    V  ++ +G+S G   V F  RA A K ++ Y G
Sbjct: 58  EFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKG 98

>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 = 78.1 bits (193), Expect = 5e-18
 Identities = 21/100 (21%), Positives = 43/100 (43%), Gaps = 5/100 (5%)

Query: 194 ATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGY 253
            +   S   T +    ++ + +L+   T+  LQE F  K   +K    +  +  G++KGY
Sbjct: 1   GSSGSSGNSTWSGESKTLVLSNLSYSATEETLQEVFE-KATFIK----VPQNQNGKSKGY 55

Query: 254 GFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKASG 293
            F+ F    +   A+   N      R +R+++  P+ +  
Sbjct: 56  AFIEFASFEDAKEALNSCNKREIEGRAIRLELQGPRGSPN 95

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 71.9 bits (177), Expect = 8e-16
 Identities = 23/98 (23%), Positives = 40/98 (40%), Gaps = 2/98 (2%)

Query: 313 GARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG--KGCGFVQF 370
           G+      S     + T+ +  L    ++E L+E F +   I   +   G  KG  F++F
Sbjct: 1   GSSGSSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEF 60

Query: 371 ANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQWRG 408
           A+ +DA+ AL       I  + +RL      G+     
Sbjct: 61  ASFEDAKEALNSCNKREIEGRAIRLELQGPRGSPNSGP 98

>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 = 55.4 bits (134), Expect = 6e-10
 Identities = 22/79 (27%), Positives = 37/79 (46%), Gaps = 4/79 (5%)

Query: 101 GKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYG 160
           G    S N+  + E+KT+ + +L +   E  L   F     +     +   Q G+S+GY 
Sbjct: 1   GSSGSSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFIK----VPQNQNGKSKGYA 56

Query: 161 FVEFYSRAAAEKVLQSYSG 179
           F+EF S   A++ L S + 
Sbjct: 57  FIEFASFEDAKEALNSCNK 75

>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 = 79.5 bits (196), Expect = 6e-18
 Identities = 33/157 (21%), Positives = 63/157 (40%), Gaps = 17/157 (10%)

Query: 143 VNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATF------ 196
           +  K+I N +T + E     E    A AEKV + Y+     + +  +     TF      
Sbjct: 1   MQYKLILNGKTLKGET--TTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGS 58

Query: 197 ---SGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGY 253
                   R     D  ++VG+L  +   + L+  F   Y  ++   V  +       G+
Sbjct: 59  HHHHHHMHRDSCPLDCKVYVGNLGNNGNKTELERAFG-YYGPLRSVWVARNP-----PGF 112

Query: 254 GFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKK 290
            FV F D  + + A+ E++G       +R++++  +K
Sbjct: 113 AFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGEK 149

>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 = 76.8 bits (189), Expect = 5e-17
 Identities = 20/86 (23%), Positives = 38/86 (44%), Gaps = 1/86 (1%)

Query: 317 QGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIP-VGKGCGFVQFANRKD 375
                D    +  ++VG L ++ +  +L   F  +G + SV +     G  FV+F + +D
Sbjct: 63  HHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRD 122

Query: 376 AEVALQKLQGTAIGKQTVRLSWGRNP 401
           A  A+++L G  +    VR+      
Sbjct: 123 AADAVRELDGRTLCGCRVRVELSNGE 148

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 42.2 bits (99), Expect = 5e-05
 Identities = 17/63 (26%), Positives = 30/63 (47%), Gaps = 5/63 (7%)

Query: 117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQS 176
            +++G+L +  ++T L   F + G + +V V RN       G+ FVEF     A   ++ 
Sbjct: 75  KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRE 129

Query: 177 YSG 179
             G
Sbjct: 130 LDG 132

>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 = 78.2 bits (193), Expect = 7e-18
 Identities = 18/104 (17%), Positives = 45/104 (43%), Gaps = 8/104 (7%)

Query: 197 SGSDRRTEACSDL-SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGF 255
           SGS       ++  ++F+ +L+ D  +  L E    ++  +K  +V++  +T  +KG  F
Sbjct: 3   SGSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQ-QFGDLKYVRVVLHPDTEHSKGCAF 61

Query: 256 VRFGDENERSRAMTEMNGVYCSS------RPMRIDVATPKKASG 293
            +F  +    + +   +            R +++D+A  +  + 
Sbjct: 62  AQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAA 105

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 68.9 bits (169), Expect = 1e-14
 Identities = 21/81 (25%), Positives = 34/81 (41%), Gaps = 6/81 (7%)

Query: 313 GARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCG 366
           G+          +   T+F+  L  D  +E L E   QFG++  V++ +       KGC 
Sbjct: 1   GSSGSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCA 60

Query: 367 FVQFANRKDAEVALQKLQGTA 387
           F QF  ++ A+  L      A
Sbjct: 61  FAQFMTQEAAQKCLAAASLEA 81

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 63.1 bits (154), Expect = 1e-12
 Identities = 21/76 (27%), Positives = 35/76 (46%)

Query: 101 GKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYG 160
           G    S       E KT++I +L    +E  L       G +  V+V+ +  T  S+G  
Sbjct: 1   GSSGSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCA 60

Query: 161 FVEFYSRAAAEKVLQS 176
           F +F ++ AA+K L +
Sbjct: 61  FAQFMTQEAAQKCLAA 76

>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 = 77.2 bits (191), Expect = 7e-18
 Identities = 18/81 (22%), Positives = 36/81 (44%), Gaps = 2/81 (2%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIID-SNTGRTKGYGFVRFGDENERSRAMT 269
           + +G L  +VT   + E FS  Y  +K   + ++  +   +KGY +V F + +E  +A+ 
Sbjct: 7   VHIGRLTRNVTKDHIMEIFS-TYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65

Query: 270 EMNGVYCSSRPMRIDVATPKK 290
            M+G     + +         
Sbjct: 66  HMDGGQIDGQEITATAVLAPW 86

>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 = 72.6 bits (179), Expect = 4e-16
 Identities = 22/74 (29%), Positives = 38/74 (51%), Gaps = 7/74 (9%)

Query: 328 ATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV-------GKGCGFVQFANRKDAEVAL 380
             + +G L  +V+ + + E FS +G+I  + +PV        KG  +V+F N  +AE AL
Sbjct: 5   TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64

Query: 381 QKLQGTAIGKQTVR 394
           + + G  I  Q + 
Sbjct: 65  KHMDGGQIDGQEIT 78

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score = 54.5 bits (132), Expect = 9e-10
 Identities = 15/58 (25%), Positives = 27/58 (46%), Gaps = 3/58 (5%)

Query: 117 TIWIGDLFHW-MDETFLHNCFSHTGQVVNVKVIRNKQ-TGQSEGYGFVEFYSRAAAEK 172
            + IG L    + +  +   FS  G++  + +   +     S+GY +VEF +   AEK
Sbjct: 6   KVHIGRL-TRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEK 62

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score = 79.5 bits (196), Expect = 8e-18
 Identities = 25/99 (25%), Positives = 40/99 (40%), Gaps = 3/99 (3%)

Query: 196 FSGSDRRTEACSDLS--IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGY 253
           F G +   E     S  ++VG+L+   T+  + E FS K   +K   + +D       G+
Sbjct: 25  FRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFS-KSGDIKKIIMGLDKMKKTACGF 83

Query: 254 GFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKAS 292
            FV +    +   AM  +NG     R +R D     K  
Sbjct: 84  CFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEG 122

>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 = 78.3 bits (193), Expect = 2e-17
 Identities = 29/122 (23%), Positives = 51/122 (41%), Gaps = 8/122 (6%)

Query: 317 QGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQF 370
              Q      + T++VG L    ++E + E FS+ G+I  + + +        G  FV++
Sbjct: 29  NEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEY 88

Query: 371 ANRKDAEVALQKLQGTAIGKQTVRLSW--GRNPGNKQWRGDHSNHWNGAHYGGQGYSGNG 428
            +R DAE A++ + GT +  + +R  W  G   G +  RG         +         G
Sbjct: 89  YSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQYGRGRSGGQVRDEYRQDYDAGRGG 148

Query: 429 YA 430
           Y 
Sbjct: 149 YG 150

>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 = 65.6 bits (160), Expect = 6e-13
 Identities = 23/91 (25%), Positives = 48/91 (52%), Gaps = 2/91 (2%)

Query: 113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEK 172
            ++ T+++G+L  +  E  ++  FS +G +  + +  +K    + G+ FVE+YSRA AE 
Sbjct: 37  KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAEN 96

Query: 173 VLQSYSGSLMPNTDQPFRLNWATFSGSDRRT 203
            ++  +G+ +   D+  R +W       R+ 
Sbjct: 97  AMRYINGTRL--DDRIIRTDWDAGFKEGRQY 125

>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 = 77.3 bits (191), Expect = 9e-18
 Identities = 18/91 (19%), Positives = 41/91 (45%), Gaps = 3/91 (3%)

Query: 199 SDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRF 258
           S       +   + V ++     D  L++ F  ++  +   ++I +     +KG+GFV F
Sbjct: 6   SGNSESKSTPKRLHVSNIPFRFRDPDLRQMFG-QFGKILDVEIIFN--ERGSKGFGFVTF 62

Query: 259 GDENERSRAMTEMNGVYCSSRPMRIDVATPK 289
            +  +  RA  +++G     R + ++ AT +
Sbjct: 63  ENSADADRAREKLHGTVVEGRKIEVNNATAR 93

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 73.9 bits (182), Expect = 2e-16
 Identities = 30/94 (31%), Positives = 44/94 (46%), Gaps = 7/94 (7%)

Query: 310 GSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV----GKGC 365
           GS+G+               + V  +     D DLR+ F QFG+IL V+I       KG 
Sbjct: 1   GSSGSSGNSESKSTPKR---LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGF 57

Query: 366 GFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGR 399
           GFV F N  DA+ A +KL GT +  + + ++   
Sbjct: 58  GFVTFENSADADRAREKLHGTVVEGRKIEVNNAT 91

>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 = 54.2 bits (131), Expect = 1e-09
 Identities = 19/80 (23%), Positives = 41/80 (51%), Gaps = 2/80 (2%)

Query: 101 GKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYG 160
           G    S N+ +    K + + ++     +  L   F   G++++V++I N++   S+G+G
Sbjct: 1   GSSGSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFG 58

Query: 161 FVEFYSRAAAEKVLQSYSGS 180
           FV F + A A++  +   G+
Sbjct: 59  FVTFENSADADRAREKLHGT 78

>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 = 77.3 bits (191), Expect = 1e-17
 Identities = 27/87 (31%), Positives = 44/87 (50%), Gaps = 11/87 (12%)

Query: 307 GGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG---- 362
           G  GS+G+  +G +      +  +FVG L+   S+ED+   F  FG I    +  G    
Sbjct: 1   GSSGSSGSESRGGR------DRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGS 54

Query: 363 -KGCGFVQFANRKDAEVALQKLQGTAI 388
            KGC FV+F++  +A+ A+  L G+  
Sbjct: 55  SKGCAFVKFSSHTEAQAAIHALHGSQT 81

>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 = 67.7 bits (166), Expect = 2e-14
 Identities = 22/100 (22%), Positives = 39/100 (39%), Gaps = 5/100 (5%)

Query: 197 SGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFV 256
             S   +    D  +FVG L    ++  +   F   +  +    V+   + G +KG  FV
Sbjct: 4   GSSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQ-PFGVIDECTVLRGPD-GSSKGCAFV 61

Query: 257 RFGDENERSRAMTEMNGVY---CSSRPMRIDVATPKKASG 293
           +F    E   A+  ++G      +S  + +  A   K SG
Sbjct: 62  KFSSHTEAQAAIHALHGSQTMPGASSSLVVKFADTDKESG 101

>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 = 56.5 bits (137), Expect = 3e-10
 Identities = 21/83 (25%), Positives = 35/83 (42%), Gaps = 3/83 (3%)

Query: 113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEK 172
            + K +++G L     E  +   F   G +    V+R    G S+G  FV+F S   A+ 
Sbjct: 14  RDRK-LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQA 71

Query: 173 VLQSYSGS-LMPNTDQPFRLNWA 194
            + +  GS  MP       + +A
Sbjct: 72  AIHALHGSQTMPGASSSLVVKFA 94

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 77.2 bits (190), Expect = 1e-17
 Identities = 22/96 (22%), Positives = 41/96 (42%), Gaps = 1/96 (1%)

Query: 310 GSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEI-LSVKIPVGKGCGFV 368
            S  +       +G    A ++VG L  D    DL+    + G + L +     +   F+
Sbjct: 2   SSGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFL 61

Query: 369 QFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNK 404
            + +   A+ A+  LQG  +G  T+R++  R   +K
Sbjct: 62  HYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQRDK 97

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 57.1 bits (138), Expect = 1e-10
 Identities = 16/94 (17%), Positives = 36/94 (38%), Gaps = 6/94 (6%)

Query: 197 SGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFV 256
            GS     A     ++VG+L  D   S L+          +   V +       +   F+
Sbjct: 8   PGSPPGEGAPLAADVYVGNLPRDARVSDLKRALR------ELGSVPLRLTWQGPRRRAFL 61

Query: 257 RFGDENERSRAMTEMNGVYCSSRPMRIDVATPKK 290
            + D     +A++ + G+   +  +R+ +A  ++
Sbjct: 62  HYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQR 95

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 40.2 bits (94), Expect = 1e-04
 Identities = 16/98 (16%), Positives = 30/98 (30%), Gaps = 7/98 (7%)

Query: 97  GLSNGKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQS 156
           G S     GS           +++G+L      + L       G V      +  +    
Sbjct: 1   GSSGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPR---- 56

Query: 157 EGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWA 194
               F+ +   AAA++ +    G  +       R+  A
Sbjct: 57  -RRAFLHYPDSAAAQQAVSCLQGLRL--GTDTLRVALA 91

>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 = 77.7 bits (192), Expect = 1e-17
 Identities = 13/79 (16%), Positives = 32/79 (40%), Gaps = 2/79 (2%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +++ +L   + +  L+      +  V   +++ D ++G ++G GF R     +    +  
Sbjct: 28  LYISNLPLSMDEQELENMLK-PFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGH 85

Query: 271 MNGVYCSSRPMRIDVATPK 289
            NG +  + P       P 
Sbjct: 86  FNGKFIKTPPGVSAPTEPL 104

>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 = 70.7 bits (174), Expect = 3e-15
 Identities = 14/71 (19%), Positives = 31/71 (43%), Gaps = 5/71 (7%)

Query: 324 ESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKI---PVG--KGCGFVQFANRKDAEV 378
           E +   +++  L   + +++L      FG+++S +I     G  +G GF +  + +  E 
Sbjct: 22  EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEA 81

Query: 379 ALQKLQGTAIG 389
            +    G  I 
Sbjct: 82  VIGHFNGKFIK 92

>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 = 59.6 bits (145), Expect = 3e-11
 Identities = 25/96 (26%), Positives = 43/96 (44%), Gaps = 11/96 (11%)

Query: 87  GVKQQQQQQHGLSNGKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVK 146
           G+K    Q       +Q+ +N          ++I +L   MDE  L N     GQV++ +
Sbjct: 7   GLKASGVQAQMAKQQEQDPTN----------LYISNLPLSMDEQELENMLKPFGQVISTR 56

Query: 147 VIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLM 182
           ++R+  +G S G GF    S    E V+  ++G  +
Sbjct: 57  ILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFI 91

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 76.9 bits (190), Expect = 1e-17
 Identities = 21/81 (25%), Positives = 40/81 (49%), Gaps = 2/81 (2%)

Query: 321 SDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVAL 380
           S G S    +F+G L  + +++++R  F Q+G++L   I   K  GFV   ++  AE A+
Sbjct: 2   SSGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--KNYGFVHIEDKTAAEDAI 59

Query: 381 QKLQGTAIGKQTVRLSWGRNP 401
           + L    +    + +   +N 
Sbjct: 60  RNLHHYKLHGVNINVEASKNK 80

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 61.4 bits (150), Expect = 3e-12
 Identities = 18/93 (19%), Positives = 36/93 (38%), Gaps = 12/93 (12%)

Query: 198 GSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVR 257
           GS   +       +F+G+L  + T+  ++  F  +Y  V    +I        K YGFV 
Sbjct: 1   GSSGSSGMVK---LFIGNLPREATEQEIRSLFE-QYGKVLECDII--------KNYGFVH 48

Query: 258 FGDENERSRAMTEMNGVYCSSRPMRIDVATPKK 290
             D+     A+  ++        + ++ +  K 
Sbjct: 49  IEDKTAAEDAIRNLHHYKLHGVNINVEASKNKS 81

>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 = 43.0 bits (102), Expect = 1e-05
 Identities = 15/59 (25%), Positives = 25/59 (42%), Gaps = 8/59 (13%)

Query: 114 ETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEK 172
               ++IG+L     E  + + F   G+V+   +I+         YGFV    + AAE 
Sbjct: 7   GMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIK--------NYGFVHIEDKTAAED 57

>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 = 77.0 bits (190), Expect = 1e-17
 Identities = 26/101 (25%), Positives = 45/101 (44%), Gaps = 8/101 (7%)

Query: 313 GARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV-------GKGC 365
           G+     Q   +   + I V  +    +  ++RE FS FGE+ +V++P         +G 
Sbjct: 1   GSSGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGF 60

Query: 366 GFVQFANRKDAEVALQKL-QGTAIGKQTVRLSWGRNPGNKQ 405
           GFV F  ++DA+ A   L   T +  + + L W  +    Q
Sbjct: 61  GFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQ 101

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 67.7 bits (166), Expect = 3e-14
 Identities = 16/82 (19%), Positives = 37/82 (45%), Gaps = 3/82 (3%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIID-SNTGRTKGYGFVRFGDENERSRAMT 269
           I V ++        ++E FS  +  +K  ++    + TG  +G+GFV F  + +  +A  
Sbjct: 18  ILVRNIPFQANQREIRELFS-TFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFN 76

Query: 270 EM-NGVYCSSRPMRIDVATPKK 290
            + +  +   R + ++ A  + 
Sbjct: 77  ALCHSTHLYGRRLVLEWADSEV 98

>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 = 57.3 bits (139), Expect = 1e-10
 Identities = 22/99 (22%), Positives = 41/99 (41%), Gaps = 8/99 (8%)

Query: 101 GKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNK-QTGQSEGY 159
           G    S        T  I + ++    ++  +   FS  G++  V++ +    TG   G+
Sbjct: 1   GSSGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGF 60

Query: 160 GFVEFYSRAAAEKVLQSYSGSLMPNTD---QPFRLNWAT 195
           GFV+F ++  A+K       +L  +T    +   L WA 
Sbjct: 61  GFVDFITKQDAKKAFN----ALCHSTHLYGRRLVLEWAD 95

>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 = 76.9 bits (190), Expect = 1e-17
 Identities = 21/82 (25%), Positives = 41/82 (50%), Gaps = 7/82 (8%)

Query: 327 NATIFVGALDSDVSDEDLREP----FSQFGEILSVKIPVG---KGCGFVQFANRKDAEVA 379
           N TI++  L+  +  ++L++     FS+FG+IL + +      +G  FV F     A  A
Sbjct: 8   NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 67

Query: 380 LQKLQGTAIGKQTVRLSWGRNP 401
           L+ +QG     + +R+ + +  
Sbjct: 68  LRSMQGFPFYDKPMRIQYAKTD 89

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 62.6 bits (153), Expect = 1e-12
 Identities = 18/83 (21%), Positives = 37/83 (44%), Gaps = 6/83 (7%)

Query: 210 SIFVGDLAPDVTDSILQETFS---SKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSR 266
           +I++ +L   +    L+++     S++  +    V   S + + +G  FV F + +  + 
Sbjct: 10  TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILV---SRSLKMRGQAFVIFKEVSSATN 66

Query: 267 AMTEMNGVYCSSRPMRIDVATPK 289
           A+  M G     +PMRI  A   
Sbjct: 67  ALRSMQGFPFYDKPMRIQYAKTD 89

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 42.2 bits (100), Expect = 2e-05
 Identities = 27/94 (28%), Positives = 45/94 (47%), Gaps = 10/94 (10%)

Query: 115 TKTIWIGDLFHWMDE----TFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAA 170
             TI+I +L   + +      LH  FS  GQ++++ V R   + +  G  FV F   ++A
Sbjct: 8   NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSA 64

Query: 171 EKVLQSYSGSLMPNTDQPFRLNWATFSGSDRRTE 204
              L+S  G   P  D+P R+ +A  + SD   +
Sbjct: 65  TNALRSMQG--FPFYDKPMRIQYAK-TDSDIIAK 95

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 76.5 bits (189), Expect = 2e-17
 Identities = 18/81 (22%), Positives = 40/81 (49%), Gaps = 3/81 (3%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           + +VG+L  +     +   F     S++  +++ D +T + KG+ +V F + +    A+ 
Sbjct: 17  TAYVGNLPFNTVQGDIDAIFKD--LSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL- 73

Query: 270 EMNGVYCSSRPMRIDVATPKK 290
             +G     R +R+D+A  +K
Sbjct: 74  TYDGALLGDRSLRVDIAEGRK 94

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 56.9 bits (138), Expect = 1e-10
 Identities = 18/104 (17%), Positives = 33/104 (31%), Gaps = 10/104 (9%)

Query: 312 NGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGC 365
           +                T +VG L  +    D+   F     I SV++         KG 
Sbjct: 2   SSGSSGKELPTEPPY--TAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGF 58

Query: 366 GFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQWRGD 409
            +V+F      + AL    G  +G +++R+         +    
Sbjct: 59  CYVEFDEVDSLKEAL-TYDGALLGDRSLRVDIAEGRKQDKSGPS 101

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 51.1 bits (123), Expect = 2e-08
 Identities = 20/87 (22%), Positives = 45/87 (51%), Gaps = 4/87 (4%)

Query: 116 KTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQ 175
            T ++G+L     +  +   F     + +V+++R+K T + +G+ +VEF    + ++ L 
Sbjct: 16  YTAYVGNLPFNTVQGDIDAIFK-DLSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL- 73

Query: 176 SYSGSLMPNTDQPFRLNWATFSGSDRR 202
           +Y G+L+   D+  R++ A     D+ 
Sbjct: 74  TYDGALL--GDRSLRVDIAEGRKQDKS 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 = 76.1 bits (188), Expect = 2e-17
 Identities = 17/84 (20%), Positives = 35/84 (41%), Gaps = 2/84 (2%)

Query: 318 GSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAE 377
           GS       +  + VG +    ++++LR  F ++G ++   I   K   FV     +DA 
Sbjct: 1   GSSGSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--KDYAFVHMERAEDAV 58

Query: 378 VALQKLQGTAIGKQTVRLSWGRNP 401
            A++ L  T    + + +    + 
Sbjct: 59  EAIRGLDNTEFQGKRMHVQLSTSR 82

>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 = 62.3 bits (152), Expect = 1e-12
 Identities = 15/90 (16%), Positives = 35/90 (38%), Gaps = 9/90 (10%)

Query: 201 RRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGD 260
             +   +   + VG+++P  T+  L+  F  +Y  V    ++        K Y FV    
Sbjct: 3   SGSSGKASTKLHVGNISPTCTNQELRAKFE-EYGPVIECDIV--------KDYAFVHMER 53

Query: 261 ENERSRAMTEMNGVYCSSRPMRIDVATPKK 290
             +   A+  ++      + M + ++T + 
Sbjct: 54  AEDAVEAIRGLDNTEFQGKRMHVQLSTSRL 83

>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 = 42.6 bits (101), Expect = 1e-05
 Identities = 9/61 (14%), Positives = 19/61 (31%), Gaps = 8/61 (13%)

Query: 112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAE 171
              +  + +G++        L   F   G V+   +++         Y FV       A 
Sbjct: 7   GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAV 58

Query: 172 K 172
           +
Sbjct: 59  E 59

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 78.4 bits (193), Expect = 2e-17
 Identities = 22/117 (18%), Positives = 40/117 (34%), Gaps = 1/117 (0%)

Query: 182 MPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSK-YPSVKGAK 240
           +     P   N                 +++VG  +   TD  L +   S     V   K
Sbjct: 29  VRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELK 88

Query: 241 VIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKASGYQQQ 297
              +   G++KGY  V    EN   + +  + G   +   + +  AT +  S ++ Q
Sbjct: 89  FAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLSQFEAQ 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 = 62.2 bits (151), Expect = 7e-12
 Identities = 27/140 (19%), Positives = 47/140 (33%), Gaps = 15/140 (10%)

Query: 66  MYPHHYMPYG--GGGHPYYQNGGGVKQQQQQQHGLSNGKQN---GSNNNFTNDETKTIWI 120
           M+ HH+   G   G    Y          +Q+       +        +   +    +++
Sbjct: 1   MHHHHHHSSGVDLGTENLYFQSMEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYV 60

Query: 121 GDLFHWMDETFLHNCFSHTG--QVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYS 178
           G    W  +  L       G   VV +K   N+  GQS+GY  V   S  +  K+L+   
Sbjct: 61  GSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLEL-- 118

Query: 179 GSLMPNTD---QPFRLNWAT 195
              +P      +   +  AT
Sbjct: 119 ---LPGKVLNGEKVDVRPAT 135

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 59.9 bits (145), Expect = 5e-11
 Identities = 18/108 (16%), Positives = 38/108 (35%), Gaps = 8/108 (7%)

Query: 309 PGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFG--EILSVKIPV----- 361
           P +    +  + S   +  A ++VG+     +D+ L +     G  +++ +K        
Sbjct: 37  PNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANG 96

Query: 362 -GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQWRG 408
             KG   V  A+       L+ L G  +  + V +         Q+  
Sbjct: 97  QSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLSQFEA 144

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 76.6 bits (189), Expect = 2e-17
 Identities = 17/79 (21%), Positives = 39/79 (49%), Gaps = 3/79 (3%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           + V ++     D  L++ F  ++  +   ++I +     +KG+GFV F +  +  RA  +
Sbjct: 32  LHVSNIPFRFRDPDLRQMFG-QFGKILDVEIIFN--ERGSKGFGFVTFENSADADRAREK 88

Query: 271 MNGVYCSSRPMRIDVATPK 289
           ++G     R + ++ AT +
Sbjct: 89  LHGTVVEGRKIEVNNATAR 107

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 73.5 bits (181), Expect = 3e-16
 Identities = 29/89 (32%), Positives = 42/89 (47%), Gaps = 4/89 (4%)

Query: 310 GSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV----GKGC 365
                R     ++ +S    + V  +     D DLR+ F QFG+IL V+I       KG 
Sbjct: 12  SGLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGF 71

Query: 366 GFVQFANRKDAEVALQKLQGTAIGKQTVR 394
           GFV F N  DA+ A +KL GT +  + + 
Sbjct: 72  GFVTFENSADADRAREKLHGTVVEGRKIE 100

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 54.2 bits (131), Expect = 2e-09
 Identities = 18/92 (19%), Positives = 39/92 (42%), Gaps = 2/92 (2%)

Query: 89  KQQQQQQHGLSNGKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVI 148
                  H      +    N     + K + + ++     +  L   F   G++++V++I
Sbjct: 3   SSHHHHHHSSGLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEII 62

Query: 149 RNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGS 180
            N+    S+G+GFV F + A A++  +   G+
Sbjct: 63  FNE--RGSKGFGFVTFENSADADRAREKLHGT 92

>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 = 75.8 bits (187), Expect = 3e-17
 Identities = 15/83 (18%), Positives = 36/83 (43%), Gaps = 6/83 (7%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           ++   +L+ ++T+  L+E F          ++ + S  G++KG  ++ F  E +  + + 
Sbjct: 18  TLLAKNLSFNITEDELKEVFE------DALEIRLVSQDGKSKGIAYIEFKSEADAEKNLE 71

Query: 270 EMNGVYCSSRPMRIDVATPKKAS 292
           E  G     R + +     K  +
Sbjct: 72  EKQGAEIDGRSVSLYYTGEKGGT 94

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 68.4 bits (168), Expect = 1e-14
 Identities = 23/91 (25%), Positives = 43/91 (47%), Gaps = 5/91 (5%)

Query: 317 QGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG--KGCGFVQFANRK 374
             S+    +   T+    L  ++++++L+E F    EI  V    G  KG  +++F +  
Sbjct: 8   CTSKKVRAAR--TLLAKNLSFNITEDELKEVFEDALEIRLVS-QDGKSKGIAYIEFKSEA 64

Query: 375 DAEVALQKLQGTAIGKQTVRLSWGRNPGNKQ 405
           DAE  L++ QG  I  ++V L +    G  +
Sbjct: 65  DAEKNLEEKQGAEIDGRSVSLYYTGEKGGTR 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 = 53.4 bits (129), Expect = 2e-09
 Identities = 19/71 (26%), Positives = 32/71 (45%), Gaps = 7/71 (9%)

Query: 111 TNDETKTIWIGDLFHW-MDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAA 169
                +T+   +L  + + E  L   F    ++  V      Q G+S+G  ++EF S A 
Sbjct: 12  KVRAARTLLAKNL-SFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEAD 65

Query: 170 AEKVLQSYSGS 180
           AEK L+   G+
Sbjct: 66  AEKNLEEKQGA 76

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 75.2 bits (186), Expect = 4e-17
 Identities = 16/81 (19%), Positives = 35/81 (43%), Gaps = 2/81 (2%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           SI+VG++    T   L+  F     SV    ++ D  +G  KG+ ++ F D+     ++ 
Sbjct: 8   SIYVGNVDYGATAEELEAHFH-GCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL- 65

Query: 270 EMNGVYCSSRPMRIDVATPKK 290
            ++      R +++      +
Sbjct: 66  ALDESLFRGRQIKVIPKRTNR 86

>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 = 65.2 bits (160), Expect = 1e-13
 Identities = 19/87 (21%), Positives = 40/87 (45%), Gaps = 9/87 (10%)

Query: 324 ESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAE 377
           E++  +I+VG +D   + E+L   F   G +  V I         KG  +++F++++   
Sbjct: 3   EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 62

Query: 378 VALQKLQGTAIGKQTVRLSWGRN--PG 402
            +L  L  +    + +++   R   PG
Sbjct: 63  TSL-ALDESLFRGRQIKVIPKRTNRPG 88

>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 = 59.4 bits (145), Expect = 1e-11
 Identities = 13/62 (20%), Positives = 31/62 (50%)

Query: 114 ETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKV 173
           + ++I++G++ +      L   F   G V  V ++ +K +G  +G+ ++EF  + +    
Sbjct: 5   DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS 64

Query: 174 LQ 175
           L 
Sbjct: 65  LA 66

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 75.3 bits (186), Expect = 4e-17
 Identities = 25/84 (29%), Positives = 42/84 (50%), Gaps = 4/84 (4%)

Query: 321 SDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG----KGCGFVQFANRKDA 376
           S G S    IFV  L  D + + L++ F++ G +L   I +     KGCG V+F + + A
Sbjct: 2   SSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVA 61

Query: 377 EVALQKLQGTAIGKQTVRLSWGRN 400
           E A + + G  +  + + +   RN
Sbjct: 62  ERACRMMNGMKLSGREIDVRIDRN 85

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 68.0 bits (167), Expect = 1e-14
 Identities = 32/98 (32%), Positives = 48/98 (48%), Gaps = 8/98 (8%)

Query: 198 GSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVR 257
           GS   + AC    IFV +L  D T  +L++ F+ +   V  A + ++   G++KG G V+
Sbjct: 1   GSSGSSGACQ---IFVRNLPFDFTWKMLKDKFN-ECGHVLYADIKME--NGKSKGCGVVK 54

Query: 258 FGDENERSRAMTEMNGVYCSSRPM--RIDVATPKKASG 293
           F       RA   MNG+  S R +  RID      +SG
Sbjct: 55  FESPEVAERACRMMNGMKLSGREIDVRIDRNASGPSSG 92

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 52.2 bits (126), Expect = 6e-09
 Identities = 16/68 (23%), Positives = 31/68 (45%), Gaps = 4/68 (5%)

Query: 116 KTIWIGDLFHW-MDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVL 174
             I++ +L  +      L + F+  G V+   +      G+S+G G V+F S   AE+  
Sbjct: 9   CQIFVRNL-PFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERAC 65

Query: 175 QSYSGSLM 182
           +  +G  +
Sbjct: 66  RMMNGMKL 73

>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 = 74.9 bits (185), Expect = 5e-17
 Identities = 18/80 (22%), Positives = 34/80 (42%), Gaps = 2/80 (2%)

Query: 325 SNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQ 384
            N   IFVG + +  + ++LR  F + G ++   +   K   FV      DA+ A+ +L 
Sbjct: 7   GNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--KDYAFVHMEKEADAKAAIAQLN 64

Query: 385 GTAIGKQTVRLSWGRNPGNK 404
           G  +  + + +        K
Sbjct: 65  GKEVKGKRINVELSTKGQKK 84

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 64.2 bits (157), Expect = 3e-13
 Identities = 18/80 (22%), Positives = 35/80 (43%), Gaps = 9/80 (11%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           IFVG+++   T   L+  F  +   V    V+        K Y FV    E +   A+ +
Sbjct: 12  IFVGNVSAACTSQELRSLFE-RRGRVIECDVV--------KDYAFVHMEKEADAKAAIAQ 62

Query: 271 MNGVYCSSRPMRIDVATPKK 290
           +NG     + + ++++T  +
Sbjct: 63  LNGKEVKGKRINVELSTKGQ 82

>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 = 43.7 bits (104), Expect = 5e-06
 Identities = 15/68 (22%), Positives = 28/68 (41%), Gaps = 10/68 (14%)

Query: 105 GSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEF 164
           GS+ +  +  T  I++G++        L + F   G+V+   V++         Y FV  
Sbjct: 1   GSSGS--SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHM 50

Query: 165 YSRAAAEK 172
              A A+ 
Sbjct: 51  EKEADAKA 58

>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 = 75.0 bits (185), Expect = 7e-17
 Identities = 19/81 (23%), Positives = 37/81 (45%), Gaps = 2/81 (2%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           ++F   LA  +    L++ FS     V+  ++I D N+ R+KG  +V F +      A+ 
Sbjct: 27  TVFCMQLAARIRPRDLEDFFS-AVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI- 84

Query: 270 EMNGVYCSSRPMRIDVATPKK 290
            + G      P+ +  +  +K
Sbjct: 85  GLTGQRLLGVPIIVQASQAEK 105

>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 = 67.3 bits (165), Expect = 5e-14
 Identities = 22/109 (20%), Positives = 44/109 (40%), Gaps = 14/109 (12%)

Query: 310 GSNGARVQGSQSDG-------ESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV- 361
           GS+G+  +    +        E +  T+F   L + +   DL + FS  G++  V+I   
Sbjct: 1   GSSGSSGKSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISD 60

Query: 362 -----GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQ 405
                 KG  +V+F   +   +A+  L G  +    + +   +   N+ 
Sbjct: 61  RNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQAEKNRL 108

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 61.2 bits (149), Expect = 7e-12
 Identities = 14/62 (22%), Positives = 32/62 (51%)

Query: 114 ETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKV 173
           + +T++   L   +    L + FS  G+V +V++I ++ + +S+G  +VEF    +    
Sbjct: 24  DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLA 83

Query: 174 LQ 175
           + 
Sbjct: 84  IG 85

>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 = 75.1 bits (185), Expect = 8e-17
 Identities = 13/74 (17%), Positives = 37/74 (50%), Gaps = 3/74 (4%)

Query: 327 NATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV---GKGCGFVQFANRKDAEVALQKL 383
           N  +++  L   ++ E++ + F ++G I  +++      +G  +V + +  DA+ A+  L
Sbjct: 8   NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHL 67

Query: 384 QGTAIGKQTVRLSW 397
            G  +  + + + +
Sbjct: 68  SGFNVSNRYLVVLY 81

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 70.9 bits (174), Expect = 2e-15
 Identities = 17/82 (20%), Positives = 38/82 (46%), Gaps = 4/82 (4%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
            +++ +L   +T   + + F  KY  ++  +V    NT  T+G  +V + D  +   A+ 
Sbjct: 10  ILYIRNLPYKITAEEMYDIFG-KYGPIRQIRV---GNTPETRGTAYVVYEDIFDAKNAVD 65

Query: 270 EMNGVYCSSRPMRIDVATPKKA 291
            ++G   S+R + +      +A
Sbjct: 66  HLSGFNVSNRYLVVLYYNANRA 87

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 44.7 bits (106), Expect = 4e-06
 Identities = 11/92 (11%), Positives = 40/92 (43%), Gaps = 5/92 (5%)

Query: 113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEK 172
           +  + ++I +L + +    +++ F   G +  ++V     T ++ G  +V +     A+ 
Sbjct: 6   EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYEDIFDAKN 62

Query: 173 VLQSYSGSLMPNTDQPFRLNWATFSGSDRRTE 204
            +   SG     +++   + +   + + ++ +
Sbjct: 63  AVDHLSG--FNVSNRYLVVLYYNANRAFQKMD 92

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 74.6 bits (184), Expect = 1e-16
 Identities = 22/80 (27%), Positives = 36/80 (45%), Gaps = 1/80 (1%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPV-GKGCGFVQFANRKDAEVALQKLQGTAI 388
           ++VG L +     +L   FS +G + +V I     G  FV+F + +DAE A++ L G  I
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVI 62

Query: 389 GKQTVRLSWGRNPGNKQWRG 408
               VR+        +    
Sbjct: 63  CGSRVRVELSTGMPRRSRFD 82

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 57.3 bits (139), Expect = 1e-10
 Identities = 16/81 (19%), Positives = 35/81 (43%), Gaps = 6/81 (7%)

Query: 209 LSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAM 268
           + ++VG+L        L+  FS  Y  ++   +  +       G+ FV F D  +   A+
Sbjct: 1   MKVYVGNLGTGAGKGELERAFS-YYGPLRTVWIARNP-----PGFAFVEFEDPRDAEDAV 54

Query: 269 TEMNGVYCSSRPMRIDVATPK 289
             ++G       +R++++T  
Sbjct: 55  RGLDGKVICGSRVRVELSTGM 75

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 41.9 bits (99), Expect = 3e-05
 Identities = 17/62 (27%), Positives = 28/62 (45%), Gaps = 5/62 (8%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY 177
           +++G+L     +  L   FS+ G +  V + RN       G+ FVEF     AE  ++  
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGL 57

Query: 178 SG 179
            G
Sbjct: 58  DG 59

>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 = 74.4 bits (183), Expect = 2e-16
 Identities = 24/125 (19%), Positives = 46/125 (36%), Gaps = 9/125 (7%)

Query: 166 SRAAAEKVLQSYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSIL 225
           + A   +   S   +       P  L+       D+R       S++VG++    T   L
Sbjct: 1   AIAPCMQTTHSKMTAGAYTEGPPQPLSAEEKKEIDKR-------SVYVGNVDYGSTAQDL 53

Query: 226 QETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV 285
           +  FS    S+    ++ D  +G  KGY ++ F + N    A+  M+      R +++  
Sbjct: 54  EAHFS-SCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLP 111

Query: 286 ATPKK 290
                
Sbjct: 112 KRTNM 116

>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 = 64.4 bits (157), Expect = 7e-13
 Identities = 22/107 (20%), Positives = 47/107 (43%), Gaps = 7/107 (6%)

Query: 299 SSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVK 358
           ++ + + AG       +   ++   E +  +++VG +D   + +DL   FS  G I  + 
Sbjct: 8   TTHSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRIT 67

Query: 359 IPV------GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGR 399
           I         KG  +++FA R   + A+  +  T    +T+++   R
Sbjct: 68  ILCDKFSGHPKGYAYIEFAERNSVDAAVA-MDETVFRGRTIKVLPKR 113

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 58.2 bits (141), Expect = 1e-10
 Identities = 14/87 (16%), Positives = 36/87 (41%)

Query: 89  KQQQQQQHGLSNGKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVI 148
             +           Q  S       + +++++G++ +      L   FS  G +  + ++
Sbjct: 10  HSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITIL 69

Query: 149 RNKQTGQSEGYGFVEFYSRAAAEKVLQ 175
            +K +G  +GY ++EF  R + +  + 
Sbjct: 70  CDKFSGHPKGYAYIEFAERNSVDAAVA 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 = 72.3 bits (178), Expect = 6e-16
 Identities = 21/82 (25%), Positives = 42/82 (51%), Gaps = 4/82 (4%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNT-GRTKGYGFVRFGDENERSRAM 268
           + F+G+L  DVT+  ++E F     ++   ++  + +   R KG+G+  F D +    A+
Sbjct: 21  TAFLGNLPYDVTEESIKEFFRGL--NISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL 78

Query: 269 TEMNGVYCSSRPMRIDVATPKK 290
             +N     +R +R+DVA   +
Sbjct: 79  -SLNEESLGNRRIRVDVADQAQ 99

>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 = 60.7 bits (148), Expect = 6e-12
 Identities = 21/82 (25%), Positives = 38/82 (46%), Gaps = 9/82 (10%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPV-------GKGCGFVQFANRKDAEVALQ 381
           T F+G L  DV++E ++E F     I +V++P         KG G+ +F +      AL 
Sbjct: 21  TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL- 78

Query: 382 KLQGTAIGKQTVRLSWGRNPGN 403
            L   ++G + +R+       +
Sbjct: 79  SLNEESLGNRRIRVDVADQAQD 100

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 49.9 bits (120), Expect = 5e-08
 Identities = 16/81 (19%), Positives = 34/81 (41%), Gaps = 5/81 (6%)

Query: 116 KTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQT-GQSEGYGFVEFYSRAAAEKVL 174
            T ++G+L + + E  +   F     +  V++ R      + +G+G+ EF    +    L
Sbjct: 20  YTAFLGNLPYDVTEESIKEFFRG-LNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL 78

Query: 175 QSYSGSLMPNTDQPFRLNWAT 195
                SL    ++  R++ A 
Sbjct: 79  SLNEESLG---NRRIRVDVAD 96

>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 = 75.9 bits (186), Expect = 6e-16
 Identities = 19/120 (15%), Positives = 36/120 (30%), Gaps = 1/120 (0%)

Query: 210 SIFVGDLAPDVTDSILQETFSSK-YPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAM 268
           ++++G+L    TD  L E   S     +   K   +   G++KG+  V  G E    + M
Sbjct: 70  ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 129

Query: 269 TEMNGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNA 328
             +       +   +     +  S ++ Q                    GS         
Sbjct: 130 DLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSGQMSGEGKAGPPGGSSRAAFPQGG 189

>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 = 63.6 bits (154), Expect = 9e-12
 Identities = 27/165 (16%), Positives = 48/165 (29%), Gaps = 10/165 (6%)

Query: 284 DVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNN--ATIFVGALDSDVSD 341
           DV +P   +G   +       L    G +  +                +++G L    +D
Sbjct: 23  DVISPSANNGDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTD 82

Query: 342 EDLREPFSQFG--EILSVKIPV------GKGCGFVQFANRKDAEVALQKLQGTAIGKQTV 393
           EDL E     G  +IL +K          KG   V   +   ++  +  L    +  Q  
Sbjct: 83  EDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNP 142

Query: 394 RLSWGRNPGNKQWRGDHSNHWNGAHYGGQGYSGNGYAFPPNQDPN 438
            ++        Q+              G+G +G          P 
Sbjct: 143 VVTPVNKQFLSQFEMQSRKTTQSGQMSGEGKAGPPGGSSRAAFPQ 187

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Length = 229

 Score = 59.0 bits (142), Expect = 4e-10
 Identities = 23/135 (17%), Positives = 44/135 (32%), Gaps = 5/135 (3%)

Query: 63  QMMMYPHHYMPYGGGGHPYYQNGGGVKQQQQQQHGLSNGKQNGSNNNFTNDETKTIWIGD 122
           Q+ +Y     P    G                   +  G        +T      ++IG+
Sbjct: 17  QIDLYDDVISPSANNGDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIA-LYIGN 75

Query: 123 LFHWMDETFLHNCFSHTG--QVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGS 180
           L  W  +  L       G   ++ +K   N+  GQS+G+  V   S A+++K++      
Sbjct: 76  LTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKR 135

Query: 181 LMPNTDQPFRLNWAT 195
            +    Q   +    
Sbjct: 136 ELHG--QNPVVTPVN 148

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 72.0 bits (177), Expect = 9e-16
 Identities = 14/78 (17%), Positives = 34/78 (43%), Gaps = 6/78 (7%)

Query: 323 GESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDA 376
           G+     +    L+ +V +  L++   ++GE+  V+I +        G   V F + + A
Sbjct: 2   GQIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGA 61

Query: 377 EVALQKLQGTAIGKQTVR 394
           +  ++ L  T++    + 
Sbjct: 62  KETVKNLHLTSVMGNIIH 79

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 71.7 bits (176), Expect = 1e-15
 Identities = 10/81 (12%), Positives = 28/81 (34%), Gaps = 1/81 (1%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
            +    L  +V ++ L++    KY  V+  ++++   T +  G   V F         + 
Sbjct: 8   EVTFARLNDNVRETFLKDMCR-KYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVK 66

Query: 270 EMNGVYCSSRPMRIDVATPKK 290
            ++        +   +    +
Sbjct: 67  NLHLTSVMGNIIHAQLDIKGQ 87

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 64.0 bits (156), Expect = 7e-13
 Identities = 15/65 (23%), Positives = 31/65 (47%)

Query: 116 KTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQ 175
           K +    L   + ETFL +     G+V  V+++ + +T +  G   V F S   A++ ++
Sbjct: 7   KEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVK 66

Query: 176 SYSGS 180
           +   +
Sbjct: 67  NLHLT 71

>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 = 71.5 bits (176), Expect = 1e-15
 Identities = 22/80 (27%), Positives = 43/80 (53%), Gaps = 4/80 (5%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +FVG +   + ++ ++  F+ +Y SVK  K+I D  TG +KGYGFV F ++ +  + +  
Sbjct: 12  VFVGGIDVRMDETEIRSFFA-RYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVES 69

Query: 271 MNGVYCSSRPMRIDVATPKK 290
                   + +++  A  K+
Sbjct: 70  QINF--HGKKLKLGPAIRKQ 87

>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 = 66.5 bits (163), Expect = 8e-14
 Identities = 21/66 (31%), Positives = 36/66 (54%), Gaps = 5/66 (7%)

Query: 322 DGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV---G--KGCGFVQFANRKDA 376
           +G+    T+FVG +D  + + ++R  F+++G +  VKI     G  KG GFV F N  D 
Sbjct: 4   EGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDV 63

Query: 377 EVALQK 382
           +  ++ 
Sbjct: 64  QKIVES 69

>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 = 58.4 bits (142), Expect = 4e-11
 Identities = 24/63 (38%), Positives = 40/63 (63%), Gaps = 1/63 (1%)

Query: 115 TKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVL 174
             T+++G +   MDET + + F+  G V  VK+I ++ TG S+GYGFV FY+    +K++
Sbjct: 9   PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIV 67

Query: 175 QSY 177
           +S 
Sbjct: 68  ESQ 70

>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 = 71.6 bits (176), Expect = 1e-15
 Identities = 16/86 (18%), Positives = 39/86 (45%), Gaps = 4/86 (4%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +F+G +  ++ +  L+  F  ++  +    V+ D  TG  KG  F+ + +     +A + 
Sbjct: 16  LFIGQIPRNLDEKDLKPLFE-EFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSA 74

Query: 271 MNGVYC---SSRPMRIDVATPKKASG 293
           ++        +RP+++  A  +   G
Sbjct: 75  LHEQKTLPGMNRPIQVKPADSESRGG 100

>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 = 68.1 bits (167), Expect = 2e-14
 Identities = 18/78 (23%), Positives = 35/78 (44%), Gaps = 6/78 (7%)

Query: 317 QGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQF 370
            GS    + +   +F+G +  ++ ++DL+  F +FG+I  + +         KGC F+ +
Sbjct: 3   SGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTY 62

Query: 371 ANRKDAEVALQKLQGTAI 388
             R+ A  A   L     
Sbjct: 63  CERESALKAQSALHEQKT 80

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Length = 106

 Score = 60.8 bits (148), Expect = 8e-12
 Identities = 18/85 (21%), Positives = 41/85 (48%), Gaps = 1/85 (1%)

Query: 112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAE 171
           + +   ++IG +   +DE  L   F   G++  + V++++ TG  +G  F+ +  R +A 
Sbjct: 10  DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESAL 69

Query: 172 KVLQSYSGS-LMPNTDQPFRLNWAT 195
           K   +      +P  ++P ++  A 
Sbjct: 70  KAQSALHEQKTLPGMNRPIQVKPAD 94

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 71.9 bits (176), Expect = 2e-15
 Identities = 16/92 (17%), Positives = 37/92 (40%), Gaps = 7/92 (7%)

Query: 317 QGSQSDGESNNATIFVGALDSDVSDEDLREP----FSQFGEILSVKI---PVGKGCGFVQ 369
            GS       +  + +  ++ +V  E L+       S  G+IL + +       G  ++ 
Sbjct: 19  LGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIV 78

Query: 370 FANRKDAEVALQKLQGTAIGKQTVRLSWGRNP 401
           FA ++ A+  ++  QG       + +++   P
Sbjct: 79  FATQESAQAFVEAFQGYPFQGNPLVITFSETP 110

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 58.4 bits (141), Expect = 8e-11
 Identities = 11/84 (13%), Positives = 26/84 (30%), Gaps = 6/84 (7%)

Query: 210 SIFVGDLAPDVTDSILQETFS---SKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSR 266
            + + ++ P+V    LQ       S    +     I+   +    G  ++ F  +     
Sbjct: 31  VVLITNINPEVPKEKLQALLYALASSQGDILD---IVVDLSDDNSGKAYIVFATQESAQA 87

Query: 267 AMTEMNGVYCSSRPMRIDVATPKK 290
            +    G      P+ I  +   +
Sbjct: 88  FVEAFQGYPFQGNPLVITFSETPQ 111

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 43.7 bits (103), Expect = 1e-05
 Identities = 12/111 (10%), Positives = 42/111 (37%), Gaps = 16/111 (14%)

Query: 88  VKQQQQQQHGLSNGKQNGSNNNFTNDETKTIWIGDLFHWMDE----TFLHNCFSHTGQVV 143
            ++Q      L +   +   +         + I ++   + +      L+   S  G ++
Sbjct: 9   FERQHMDSPDLGSTPPHTEPSQ-------VVLITNINPEVPKEKLQALLYALASSQGDIL 61

Query: 144 NVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWA 194
           ++ V     +  + G  ++ F ++ +A+  ++++ G        P  + ++
Sbjct: 62  DIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPF--QGNPLVITFS 107

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 73.3 bits (180), Expect = 2e-15
 Identities = 24/79 (30%), Positives = 41/79 (51%), Gaps = 2/79 (2%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           + V +L   V+D+ +QE F+ ++ ++K A V  D  +GR+ G   V F    +  +AM +
Sbjct: 91  LLVSNLDFGVSDADIQELFA-EFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQ 148

Query: 271 MNGVYCSSRPMRIDVATPK 289
             GV    RPM I +   +
Sbjct: 149 YKGVPLDGRPMDIQLVASQ 167

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 71.4 bits (175), Expect = 7e-15
 Identities = 27/125 (21%), Positives = 45/125 (36%), Gaps = 6/125 (4%)

Query: 277 SSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALD 336
              P R   A  +        YS     L      +         +G    A + V  LD
Sbjct: 39  GGGPRRNRPAIARGGRNRPAPYSRPK-PLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLD 97

Query: 337 SDVSDEDLREPFSQFGEILSVKIPVG-----KGCGFVQFANRKDAEVALQKLQGTAIGKQ 391
             VSD D++E F++FG +    +         G   V F  R DA  A+++ +G  +  +
Sbjct: 98  FGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGR 157

Query: 392 TVRLS 396
            + + 
Sbjct: 158 PMDIQ 162

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 49.1 bits (117), Expect = 3e-07
 Identities = 22/107 (20%), Positives = 39/107 (36%), Gaps = 4/107 (3%)

Query: 73  PYGGGGHPYYQNGGGVKQQQQQQHGLSNGKQNGSNNNFTNDETKTIWIGDLFHWMDETFL 132
              GG +             + QH L +    G     T      + + +L   + +  +
Sbjct: 49  IARGGRNRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVETG---AKLLVSNLDFGVSDADI 105

Query: 133 HNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSG 179
              F+  G +    V  ++ +G+S G   V F  RA A K ++ Y G
Sbjct: 106 QELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKG 151

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 70.7 bits (174), Expect = 2e-15
 Identities = 24/91 (26%), Positives = 40/91 (43%), Gaps = 4/91 (4%)

Query: 325 SNNATIFVGALDS-DVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKL 383
              + +F+G L   +VS EDL   FS +G I+ + I      GF+QF N +    A++  
Sbjct: 8   PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--NAFGFIQFDNPQSVRDAIECE 65

Query: 384 QGTAIGKQTVRLSWGRNPGNKQW-RGDHSNH 413
                  + + L    +    Q+  GDH  +
Sbjct: 66  SQEMNFGKKLILEVSSSNARPQFDHGDHGTN 96

>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 = 16/103 (15%), Positives = 37/103 (35%), Gaps = 20/103 (19%)

Query: 211 IFVGDLAP-DVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           +F+G+L   +V+   L   FS  Y  +    +           +GF++F +      A+ 
Sbjct: 13  LFIGNLPLKNVSKEDLFRIFS-PYGHIMQINIK--------NAFGFIQFDNPQSVRDAIE 63

Query: 270 EMNGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSN 312
             +      + + ++V++      +            G  G+N
Sbjct: 64  CESQEMNFGKKLILEVSSSNARPQFDH----------GDHGTN 96

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 38.3 bits (90), Expect = 5e-04
 Identities = 11/70 (15%), Positives = 28/70 (40%), Gaps = 9/70 (12%)

Query: 114 ETKTIWIGDL-FHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEK 172
               ++IG+L    + +  L   FS  G ++ + +           +GF++F +  +   
Sbjct: 9   PKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN--------AFGFIQFDNPQSVRD 60

Query: 173 VLQSYSGSLM 182
            ++  S  + 
Sbjct: 61  AIECESQEMN 70

>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 = 70.4 bits (173), Expect = 2e-15
 Identities = 22/86 (25%), Positives = 35/86 (40%), Gaps = 9/86 (10%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGA--------KVIIDSNTGRTKGYGFVRFGDE 261
           +IFV  L  +VT   + + F  +   +K           +  D  TG+ KG   V F D 
Sbjct: 15  TIFVQGLGENVTIESVADYFK-QIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 73

Query: 262 NERSRAMTEMNGVYCSSRPMRIDVAT 287
                A+   +G   S  P+++  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 = 59.6 bits (145), Expect = 2e-11
 Identities = 21/91 (23%), Positives = 35/91 (38%), Gaps = 14/91 (15%)

Query: 320 QSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILS--------VKIPV------GKGC 365
                S+N TIFV  L  +V+ E + + F Q G I +        + +         KG 
Sbjct: 6   HHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGE 65

Query: 366 GFVQFANRKDAEVALQKLQGTAIGKQTVRLS 396
             V F +   A+ A+    G       +++S
Sbjct: 66  ATVSFDDPPSAKAAIDWFDGKEFSGNPIKVS 96

>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 = 50.0 bits (120), Expect = 4e-08
 Identities = 16/91 (17%), Positives = 38/91 (41%), Gaps = 12/91 (13%)

Query: 114 ETKTIWIGDLFHWMDETFLHNCFSHTGQV--------VNVKVIRNKQTGQSEGYGFVEFY 165
           +  TI++  L   +    + + F   G +          + +  +++TG+ +G   V F 
Sbjct: 12  DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD 71

Query: 166 SRAAAEKVLQSYSGS-LMPNTDQPFRLNWAT 195
              +A+  +  + G     N   P ++++AT
Sbjct: 72  DPPSAKAAIDWFDGKEFSGN---PIKVSFAT 99

>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 = 69.7 bits (171), Expect = 4e-15
 Identities = 13/78 (16%), Positives = 30/78 (38%), Gaps = 1/78 (1%)

Query: 323 GESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQK 382
           G S ++ I V  L  D + +++ +    +  +    +   K   FV   N + A+ A+Q 
Sbjct: 1   GSSGSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDRNKRTAFVTLLNGEQAQNAIQM 59

Query: 383 LQGTAIGKQTVRLSWGRN 400
               +   + + +     
Sbjct: 60  FHQYSFRGKDLIVQLQPT 77

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 51.6 bits (124), Expect = 9e-09
 Identities = 13/93 (13%), Positives = 25/93 (26%), Gaps = 14/93 (15%)

Query: 198 GSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVR 257
           GS   +       I V +L  D     + +     Y      K        R K   FV 
Sbjct: 1   GSSGSSG------ILVKNLPQDSNCQEVHDLLK-DY----DLKYC---YVDRNKRTAFVT 46

Query: 258 FGDENERSRAMTEMNGVYCSSRPMRIDVATPKK 290
             +  +   A+   +      + + + +     
Sbjct: 47  LLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDA 79

>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 = 69.7 bits (171), Expect = 4e-15
 Identities = 22/85 (25%), Positives = 36/85 (42%), Gaps = 3/85 (3%)

Query: 318 GSQSDGESNNATIFVGALDS-DVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDA 376
           G    G    + +F+G L   +VS EDL   FS +G I+ + I      GF+QF N +  
Sbjct: 13  GLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--NAFGFIQFDNPQSV 70

Query: 377 EVALQKLQGTAIGKQTVRLSWGRNP 401
             A++         + + L    + 
Sbjct: 71  RDAIEXESQEMNFGKKLILEVSSSN 95

>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 = 49.2 bits (118), Expect = 6e-08
 Identities = 13/81 (16%), Positives = 32/81 (39%), Gaps = 10/81 (12%)

Query: 211 IFVGDL-APDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           +F+G+L   +V+   L   FS  Y  +    +           +GF++F +      A+ 
Sbjct: 25  LFIGNLPLKNVSKEDLFRIFS-PYGHIMQINIK--------NAFGFIQFDNPQSVRDAIE 75

Query: 270 EMNGVYCSSRPMRIDVATPKK 290
             +      + + ++V++   
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 = 37.7 bits (88), Expect = 7e-04
 Identities = 13/92 (14%), Positives = 38/92 (41%), Gaps = 12/92 (13%)

Query: 105 GSNNNFTNDETKTIWIGDL-FHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVE 163
           G     ++ +++ ++IG+L    + +  L   FS  G ++ + +           +GF++
Sbjct: 13  GLVPRGSHMKSR-LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN--------AFGFIQ 63

Query: 164 FYSRAAAEKVLQSYSGSLMPNTDQPFRLNWAT 195
           F +  +    ++  S  +     +   L  ++
Sbjct: 64  FDNPQSVRDAIEXESQEMN--FGKKLILEVSS 93

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 69.7 bits (171), Expect = 4e-15
 Identities = 15/83 (18%), Positives = 36/83 (43%), Gaps = 7/83 (8%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKY--PSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRA 267
           +I + ++AP      +    S  Y   +V   ++I D  T + +G+ FV+     + S+ 
Sbjct: 11  TIILRNIAPHTVVDSIMTALS-PYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQL 69

Query: 268 MTEMNGVYCSS----RPMRIDVA 286
           +  +  ++       + + +D A
Sbjct: 70  LQILQSLHPPLKIDGKTIGVDFA 92

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 65.8 bits (161), Expect = 9e-14
 Identities = 16/94 (17%), Positives = 35/94 (37%), Gaps = 14/94 (14%)

Query: 318 GSQSDGESNNATIFVGALDSDVSDEDLREPFSQFG--EILSVKIP------VGKGCGFVQ 369
           G       +  TI +  +      + +    S +    + ++++         +G  FVQ
Sbjct: 2   GHHHHHHMD--TIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQ 59

Query: 370 FANRKDAEVALQKLQGT----AIGKQTVRLSWGR 399
            ++  DA   LQ LQ       I  +T+ + + +
Sbjct: 60  LSSAMDASQLLQILQSLHPPLKIDGKTIGVDFAK 93

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 65.8 bits (161), Expect = 1e-13
 Identities = 20/89 (22%), Positives = 42/89 (47%), Gaps = 6/89 (6%)

Query: 111 TNDETKTIWIGDL-FHWMDETFLHNCFSHTGQ--VVNVKVIRNKQTGQSEGYGFVEFYSR 167
            +    TI + ++  H + ++ +    S      V N+++I++KQT Q+ G+ FV+  S 
Sbjct: 5   HHHHMDTIILRNIAPHTVVDS-IMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSA 63

Query: 168 AAAEKVLQSYSGSLMPNT--DQPFRLNWA 194
             A ++LQ       P     +   +++A
Sbjct: 64  MDASQLLQILQSLHPPLKIDGKTIGVDFA 92

>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 = 70.6 bits (173), Expect = 6e-15
 Identities = 23/85 (27%), Positives = 40/85 (47%), Gaps = 6/85 (7%)

Query: 211 IFVGDLAPDVTDSILQETFSSKY--PSVKGAKVIID---SNTGRTKGYGFVRFGDENERS 265
           I+V +LA  V +  L+  F  +Y   S +  +++ D      GR KG  F+   +E   +
Sbjct: 48  IYVKNLAKHVQEKDLKYIFG-RYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAA 106

Query: 266 RAMTEMNGVYCSSRPMRIDVATPKK 290
           +A+ E NG     +PM +  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 = 64.8 bits (158), Expect = 7e-13
 Identities = 21/90 (23%), Positives = 38/90 (42%), Gaps = 11/90 (12%)

Query: 327 NATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-----------KGCGFVQFANRKD 375
           N  I+V  L   V ++DL+  F ++ +  S    +            KG  F+   N K 
Sbjct: 45  NCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKA 104

Query: 376 AEVALQKLQGTAIGKQTVRLSWGRNPGNKQ 405
           A  AL++  G  +  + + + + R+   KQ
Sbjct: 105 AAKALKEANGYVLFGKPMVVQFARSARPKQ 134

>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 = 44.0 bits (104), Expect = 1e-05
 Identities = 18/122 (14%), Positives = 44/122 (36%), Gaps = 12/122 (9%)

Query: 88  VKQQQQQQHGLSNGKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKV 147
             +  +++    +  ++             I++ +L   + E  L   F       +   
Sbjct: 22  KGRISREEMETLSVFRSYEPGE----PNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQ 77

Query: 148 -----IRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATFSGSDRR 202
                IR  + G+ +G  F+   +  AA K L+  +G ++    +P  + +A  S   ++
Sbjct: 78  RIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVL--FGKPMVVQFAR-SARPKQ 134

Query: 203 TE 204
             
Sbjct: 135 DP 136

>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 = 68.5 bits (168), Expect = 1e-14
 Identities = 28/101 (27%), Positives = 42/101 (41%), Gaps = 12/101 (11%)

Query: 307 GGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEI-LSVKIPVG--- 362
           G  GS+GA      S G+     I V  +   VS +++ + F  +  I  SV +      
Sbjct: 1   GSSGSSGA------SSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKG 54

Query: 363 --KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNP 401
              G   V F +R +A  A+  L    IG + V+L  G  P
Sbjct: 55  MPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLGSGP 95

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 63.1 bits (154), Expect = 1e-12
 Identities = 15/85 (17%), Positives = 35/85 (41%), Gaps = 1/85 (1%)

Query: 207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSR 266
               I V ++   V+   + + F   Y  + G+  +  +  G   G   V F   +E + 
Sbjct: 14  GPTIIKVQNMPFTVSIDEILDFFY-GYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATA 72

Query: 267 AMTEMNGVYCSSRPMRIDVATPKKA 291
           A+ ++N     SR +++ + +   +
Sbjct: 73  AVIDLNDRPIGSRKVKLVLGSGPSS 97

>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 = 40.7 bits (96), Expect = 6e-05
 Identities = 12/83 (14%), Positives = 26/83 (31%), Gaps = 2/83 (2%)

Query: 101 GKQNGSNNNFTNDETKTIWIGDL-FHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGY 159
           G    S  +        I + ++ F    +  + + F     +     ++  + G   G 
Sbjct: 1   GSSGSSGASSGKPGPTIIKVQNMPFTVSIDE-ILDFFYGYQVIPGSVCLKYNEKGMPTGE 59

Query: 160 GFVEFYSRAAAEKVLQSYSGSLM 182
             V F SR  A   +   +   +
Sbjct: 60  AMVAFESRDEATAAVIDLNDRPI 82

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 69.0 bits (169), Expect = 1e-14
 Identities = 22/89 (24%), Positives = 36/89 (40%), Gaps = 9/89 (10%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGA--------KVIIDSNTGRTKGYGFVRFGDE 261
           +IFV  L  +VT   + + F  +   +K           +  D  TG+ KG   V F D 
Sbjct: 9   TIFVQGLGENVTIESVADYFK-QIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 67

Query: 262 NERSRAMTEMNGVYCSSRPMRIDVATPKK 290
                A+   +G   S  P+++  AT + 
Sbjct: 68  PSAKAAIDWFDGKEFSGNPIKVSFATRRA 96

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 60.5 bits (147), Expect = 1e-11
 Identities = 24/122 (19%), Positives = 42/122 (34%), Gaps = 23/122 (18%)

Query: 322 DGESNNATIFVGALDSDVSDEDLREPFSQFGEILS--------VKIPV------GKGCGF 367
              S+N TIFV  L  +V+ E + + F Q G I +        + +         KG   
Sbjct: 2   QDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEAT 61

Query: 368 VQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQWRGDHSNHWNGAHYGGQGYSGN 427
           V F +   A+ A+    G       +++S+     +            G   G  G   +
Sbjct: 62  VSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFN---------RGGGNGRGGLEHH 112

Query: 428 GY 429
            +
Sbjct: 113 HH 114

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 48.5 bits (116), Expect = 2e-07
 Identities = 18/100 (18%), Positives = 40/100 (40%), Gaps = 12/100 (12%)

Query: 112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQV--------VNVKVIRNKQTGQSEGYGFVE 163
           N +  TI++  L   +    + + F   G +          + +  +++TG+ +G   V 
Sbjct: 4   NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVS 63

Query: 164 FYSRAAAEKVLQSYSGS-LMPNTDQPFRLNWATFSGSDRR 202
           F    +A+  +  + G     N   P ++++AT      R
Sbjct: 64  FDDPPSAKAAIDWFDGKEFSGN---PIKVSFATRRADFNR 100

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 68.9 bits (169), Expect = 1e-14
 Identities = 31/119 (26%), Positives = 53/119 (44%), Gaps = 6/119 (5%)

Query: 194 ATFSGSDRRTEACSDLS-IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKG 252
           ++ S     ++  +  + IFVG L    TD+ L++ F   +  ++ A VI D  TG+++G
Sbjct: 2   SSGSSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFE-GFGDIEEAVVITDRQTGKSRG 60

Query: 253 YGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGS 311
           YGFV   D     RA  + N +    R   +++A         Q   +  +    GP S
Sbjct: 61  YGFVTMADRAAAERACKDPNPII-DGRKANVNLAYLGAKPRSLQTGFAIGV---SGPSS 115

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 58.8 bits (143), Expect = 5e-11
 Identities = 23/76 (30%), Positives = 38/76 (50%)

Query: 100 NGKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGY 159
           +   +G + +  +     I++G L +   +  L   F   G +    VI ++QTG+S GY
Sbjct: 2   SSGSSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGY 61

Query: 160 GFVEFYSRAAAEKVLQ 175
           GFV    RAAAE+  +
Sbjct: 62  GFVTMADRAAAERACK 77

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 58.1 bits (141), Expect = 8e-11
 Identities = 27/88 (30%), Positives = 38/88 (43%), Gaps = 8/88 (9%)

Query: 310 GSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GK 363
            S  + + GSQ D       IFVG L    +D  LR+ F  FG+I    +         +
Sbjct: 2   SSGSSGMHGSQKDTTFTK--IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSR 59

Query: 364 GCGFVQFANRKDAEVALQKLQGTAIGKQ 391
           G GFV  A+R  AE A +       G++
Sbjct: 60  GYGFVTMADRAAAERACKDPNPIIDGRK 87

>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 = 68.0 bits (167), Expect = 2e-14
 Identities = 22/83 (26%), Positives = 41/83 (49%), Gaps = 2/83 (2%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           IFVG +  +  ++ L+E F  K+  V    +I D+   R +G+GF+ F DE    +A+  
Sbjct: 13  IFVGGIPHNCGETELREYFK-KFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV-N 70

Query: 271 MNGVYCSSRPMRIDVATPKKASG 293
           M+      + + +  A P+ +  
Sbjct: 71  MHFHDIMGKKVEVKRAEPRDSKS 93

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 58.0 bits (141), Expect = 6e-11
 Identities = 19/71 (26%), Positives = 33/71 (46%), Gaps = 6/71 (8%)

Query: 318 GSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFA 371
           GS     S +  IFVG +  +  + +LRE F +FG +  V +         +G GF+ F 
Sbjct: 1   GSSGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFE 60

Query: 372 NRKDAEVALQK 382
           + +  + A+  
Sbjct: 61  DEQSVDQAVNM 71

>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 = 55.7 bits (135), Expect = 4e-10
 Identities = 17/71 (23%), Positives = 35/71 (49%), Gaps = 1/71 (1%)

Query: 105 GSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEF 164
           GS+ + +  ++  I++G + H   ET L   F   G V  V +I + +  +  G+GF+ F
Sbjct: 1   GSSGS-SGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITF 59

Query: 165 YSRAAAEKVLQ 175
               + ++ + 
Sbjct: 60  EDEQSVDQAVN 70

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 67.5 bits (165), Expect = 3e-14
 Identities = 16/94 (17%), Positives = 29/94 (30%), Gaps = 2/94 (2%)

Query: 308 GPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGF 367
           G   +              +  + +  L   V + DL E   +FG I  V +   K    
Sbjct: 2   GHHHHHHMENYDDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQAL 61

Query: 368 VQFANRKDAEVALQKLQGTA--IGKQTVRLSWGR 399
           V+F +   A  A+         I      +++  
Sbjct: 62  VEFEDVLGACNAVNYAADNQIYIAGHPAFVNYST 95

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 49.8 bits (119), Expect = 5e-08
 Identities = 15/94 (15%), Positives = 29/94 (30%), Gaps = 6/94 (6%)

Query: 102 KQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGF 161
                ++      +  + I  L   + E  L       G +  V V+  K          
Sbjct: 8   HMENYDDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKK------RQAL 61

Query: 162 VEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWAT 195
           VEF     A   +   + + +     P  +N++T
Sbjct: 62  VEFEDVLGACNAVNYAADNQIYIAGHPAFVNYST 95

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 47.1 bits (112), Expect = 5e-07
 Identities = 16/84 (19%), Positives = 31/84 (36%), Gaps = 9/84 (10%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           + +  L   V ++ L E    ++  +    V+        K    V F D      A+  
Sbjct: 24  VHIRGLIDGVVEADLVEALQ-EFGPISYVVVM------PKKRQALVEFEDVLGACNAVNY 76

Query: 271 M--NGVYCSSRPMRIDVATPKKAS 292
              N +Y +  P  ++ +T +K S
Sbjct: 77  AADNQIYIAGHPAFVNYSTSQKIS 100

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 67.5 bits (165), Expect = 3e-14
 Identities = 13/78 (16%), Positives = 35/78 (44%), Gaps = 5/78 (6%)

Query: 324 ESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-----KGCGFVQFANRKDAEV 378
           +  N ++++    +D + +D++E     G++L++++        KG  FV F + + A+ 
Sbjct: 8   DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKK 67

Query: 379 ALQKLQGTAIGKQTVRLS 396
            ++           + L 
Sbjct: 68  FVETPGQKYKETDLLILF 85

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 52.0 bits (125), Expect = 9e-09
 Identities = 11/66 (16%), Positives = 20/66 (30%), Gaps = 2/66 (3%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           S+++     D T   ++E        V   ++         KG  FV F       + + 
Sbjct: 13  SVYIKGFPTDATLDDIKEWLE-DKGQVLNIQMRRT-LHKAFKGSIFVVFDSIESAKKFVE 70

Query: 270 EMNGVY 275
                Y
Sbjct: 71  TPGQKY 76

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 49.7 bits (119), Expect = 5e-08
 Identities = 13/62 (20%), Positives = 28/62 (45%), Gaps = 1/62 (1%)

Query: 114 ETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKV 173
           + ++++I           +       GQV+N+++ R       +G  FV F S  +A+K 
Sbjct: 10  KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKF 68

Query: 174 LQ 175
           ++
Sbjct: 69  VE 70

>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 = 66.9 bits (164), Expect = 4e-14
 Identities = 26/96 (27%), Positives = 41/96 (42%), Gaps = 12/96 (12%)

Query: 307 GGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEI-LSVKIPVG--- 362
           G  GS+G+      S G+     I V  +   VS +++ + F  +  I  SV +      
Sbjct: 1   GSSGSSGS------SSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKG 54

Query: 363 --KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLS 396
              G   V F +R +A  A+  L    IG + V+LS
Sbjct: 55  MPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLS 90

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 61.2 bits (149), Expect = 4e-12
 Identities = 15/77 (19%), Positives = 33/77 (42%), Gaps = 1/77 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           I V ++   V+   + + F   Y  + G+  +  +  G   G   V F   +E + A+ +
Sbjct: 18  IKVQNMPFTVSIDEILDFFY-GYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID 76

Query: 271 MNGVYCSSRPMRIDVAT 287
           +N     SR +++   +
Sbjct: 77  LNDRPIGSRKVKLSGPS 93

>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 = 42.3 bits (100), Expect = 2e-05
 Identities = 11/82 (13%), Positives = 26/82 (31%)

Query: 101 GKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYG 160
           G    S ++        I + ++   +    + + F     +     ++  + G   G  
Sbjct: 1   GSSGSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEA 60

Query: 161 FVEFYSRAAAEKVLQSYSGSLM 182
            V F SR  A   +   +   +
Sbjct: 61  MVAFESRDEATAAVIDLNDRPI 82

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 67.3 bits (165), Expect = 4e-14
 Identities = 22/82 (26%), Positives = 43/82 (52%), Gaps = 4/82 (4%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIID-SNTGRTKGYGFVRFGDENERSRAM 268
           + F+G+L  DVT+  ++E F     ++   ++  + SN  R KG+G+  F D +    A+
Sbjct: 17  TAFLGNLPYDVTEESIKEFFRGL--NISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL 74

Query: 269 TEMNGVYCSSRPMRIDVATPKK 290
             +N     ++ +R+DVA   +
Sbjct: 75  -SLNEESLGNKRIRVDVADQAQ 95

>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 = 62.7 bits (153), Expect = 2e-12
 Identities = 28/109 (25%), Positives = 48/109 (44%), Gaps = 15/109 (13%)

Query: 307 GGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV----- 361
           G  GS+G+R+  S         T F+G L  DV++E ++E F     I +V++P      
Sbjct: 1   GSSGSSGSRLPKSPPY------TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNP 53

Query: 362 --GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQWRG 408
              KG G+ +F +      AL  L   ++G + +R+       +K    
Sbjct: 54  ERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVADQAQDKDSGP 101

>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 = 47.3 bits (113), Expect = 4e-07
 Identities = 18/103 (17%), Positives = 38/103 (36%), Gaps = 5/103 (4%)

Query: 101 GKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQ-TGQSEGY 159
           G    S +        T ++G+L + + E  +   F     +  V++ R      + +G+
Sbjct: 1   GSSGSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRG-LNISAVRLPREPSNPERLKGF 59

Query: 160 GFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATFSGSDRR 202
           G+ EF    +    L     SL    ++  R++ A  +     
Sbjct: 60  GYAEFEDLDSLLSALSLNEESLG---NKRIRVDVADQAQDKDS 99

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 67.3 bits (165), Expect = 4e-14
 Identities = 27/97 (27%), Positives = 44/97 (45%), Gaps = 4/97 (4%)

Query: 197 SGSDRRTEACSDLS-IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGF 255
           SGS     A    S + V  L    T+  L+E FS  +  V   +V  D  TG +KG+GF
Sbjct: 3   SGSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFS-TFGEVLMVQVKKDLKTGHSKGFGF 61

Query: 256 VRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKAS 292
           VRF +   + + M++ + +    R     +   K++ 
Sbjct: 62  VRFTEYETQVKVMSQRHMI--DGRWCDCKLPNSKQSQ 96

>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 = 56.9 bits (138), Expect = 2e-10
 Identities = 21/79 (26%), Positives = 36/79 (45%), Gaps = 9/79 (11%)

Query: 310 GSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKI---PVG---K 363
           GS+G+             + + V  L    +++DL+E FS FGE+L V++         K
Sbjct: 1   GSSGS---SGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSK 57

Query: 364 GCGFVQFANRKDAEVALQK 382
           G GFV+F   +     + +
Sbjct: 58  GFGFVRFTEYETQVKVMSQ 76

>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 = 56.5 bits (137), Expect = 2e-10
 Identities = 22/75 (29%), Positives = 34/75 (45%)

Query: 101 GKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYG 160
           G    S       +T  + +  L     E  L   FS  G+V+ V+V ++ +TG S+G+G
Sbjct: 1   GSSGSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFG 60

Query: 161 FVEFYSRAAAEKVLQ 175
           FV F       KV+ 
Sbjct: 61  FVRFTEYETQVKVMS 75

>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 = 66.7 bits (163), Expect = 5e-14
 Identities = 23/95 (24%), Positives = 35/95 (36%), Gaps = 8/95 (8%)

Query: 307 GGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCG 366
           G  GS+G+  + S S        + V  L   V + DL E   +FG I  V +   K   
Sbjct: 1   GSSGSSGSHHKVSVS------PVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQA 54

Query: 367 FVQFANRKDAEVALQKLQGTA--IGKQTVRLSWGR 399
            V+F N   A+  +         I  Q    ++  
Sbjct: 55  LVEFENIDSAKECVTFAADVPVYIAGQQAFFNYST 89

>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 = 51.7 bits (124), Expect = 1e-08
 Identities = 15/95 (15%), Positives = 33/95 (34%), Gaps = 6/95 (6%)

Query: 101 GKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYG 160
           G    S ++     +  + +  L   + E  L       G +  V ++  K         
Sbjct: 1   GSSGSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFK------RQA 54

Query: 161 FVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWAT 195
            VEF +  +A++ +   +   +    Q    N++T
Sbjct: 55  LVEFENIDSAKECVTFAADVPVYIAGQQAFFNYST 89

>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 = 42.1 bits (99), Expect = 2e-05
 Identities = 14/82 (17%), Positives = 30/82 (36%), Gaps = 9/82 (10%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           + V  L   V ++ L E    K+ ++    ++        K    V F + +     +T 
Sbjct: 18  VHVRGLCESVVEADLVEALE-KFGTICYVMMM------PFKRQALVEFENIDSAKECVTF 70

Query: 271 M--NGVYCSSRPMRIDVATPKK 290
                VY + +    + +T K+
Sbjct: 71  AADVPVYIAGQQAFFNYSTSKR 92

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 66.0 bits (162), Expect = 6e-14
 Identities = 23/83 (27%), Positives = 38/83 (45%), Gaps = 11/83 (13%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +F+G L+   T   L+E F  ++  VK   V+ D  T R++G+GFV F D+    + +  
Sbjct: 3   MFIGGLSWQTTQEGLREYFG-QFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-- 59

Query: 271 MNGVYCSSRPMRID--VATPKKA 291
                 +     +D     PK A
Sbjct: 60  ------AQSRHELDSKTIDPKVA 76

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 56.0 bits (136), Expect = 2e-10
 Identities = 20/58 (34%), Positives = 29/58 (50%), Gaps = 6/58 (10%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKI---PVGK---GCGFVQFANRKDAEVALQ 381
           +F+G L    + E LRE F QFGE+    +   P+ K   G GFV F ++   +  L 
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 51.7 bits (125), Expect = 5e-09
 Identities = 20/58 (34%), Positives = 30/58 (51%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQ 175
           ++IG L     +  L   F   G+V    V+R+  T +S G+GFV F  +A  +KVL 
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 65.5 bits (160), Expect = 1e-13
 Identities = 17/99 (17%), Positives = 38/99 (38%), Gaps = 6/99 (6%)

Query: 310 GSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKI---PVGKGCG 366
           GS+G+     +         + +  +   +  E L     Q+G + S +           
Sbjct: 1   GSSGSSGSVPKRQRIRK---LQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVV 57

Query: 367 FVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQ 405
            V ++++  A  AL KL G  +   T+++++  +    Q
Sbjct: 58  NVTYSSKDQARQALDKLNGFQLENFTLKVAYIPDEMAAQ 96

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 56.3 bits (136), Expect = 2e-10
 Identities = 12/99 (12%), Positives = 38/99 (38%), Gaps = 4/99 (4%)

Query: 194 ATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGY 253
            +   S    +      + + ++ P +   +L      +Y  V+  + +   NT      
Sbjct: 1   GSSGSSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLV-QYGVVESCEQV---NTDSETAV 56

Query: 254 GFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKAS 292
             V +  +++  +A+ ++NG    +  +++     + A+
Sbjct: 57  VNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPDEMAA 95

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 42.4 bits (100), Expect = 2e-05
 Identities = 12/95 (12%), Positives = 30/95 (31%), Gaps = 5/95 (5%)

Query: 101 GKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYG 160
           G    S +       + + I ++   +    L +     G V + + +            
Sbjct: 1   GSSGSSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET---AVV 57

Query: 161 FVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWAT 195
            V + S+  A + L   +G  + N     ++ +  
Sbjct: 58  NVTYSSKDQARQALDKLNGFQLEN--FTLKVAYIP 90

>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 = 65.3 bits (160), Expect = 1e-13
 Identities = 25/83 (30%), Positives = 42/83 (50%), Gaps = 11/83 (13%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +FVG L+ D +   L++ F+ K+  V    + +D NTGR++G+GF+ F D     + + +
Sbjct: 14  MFVGGLSWDTSKKDLKDYFT-KFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQ 72

Query: 271 MNGVYCSSRPMRID--VATPKKA 291
                       +D  V  PKKA
Sbjct: 73  KEHR--------LDGRVIDPKKA 87

>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 = 57.2 bits (139), Expect = 7e-11
 Identities = 21/72 (29%), Positives = 38/72 (52%)

Query: 105 GSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEF 164
           G N +   ++   +++G L     +  L + F+  G+VV+  +  +  TG+S G+GF+ F
Sbjct: 1   GINASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILF 60

Query: 165 YSRAAAEKVLQS 176
              A+ EKVL  
Sbjct: 61  KDAASVEKVLDQ 72

>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 = 56.8 bits (138), Expect = 1e-10
 Identities = 22/69 (31%), Positives = 34/69 (49%), Gaps = 6/69 (8%)

Query: 319 SQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKI---PVGK---GCGFVQFAN 372
           + S  E +   +FVG L  D S +DL++ F++FGE++   I   P      G GF+ F +
Sbjct: 3   NASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKD 62

Query: 373 RKDAEVALQ 381
               E  L 
Sbjct: 63  AASVEKVLD 71

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 64.8 bits (159), Expect = 1e-13
 Identities = 22/83 (26%), Positives = 36/83 (43%), Gaps = 11/83 (13%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           IFVG L+ + T   ++  F  ++  V  A ++ D  T R +G+GFV F  E+   +    
Sbjct: 2   IFVGGLSVNTTVEDVKHYFE-QFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-- 58

Query: 271 MNGVYCSSRPMRID--VATPKKA 291
                       I+  +   KKA
Sbjct: 59  ------EIHFHEINNKMVECKKA 75

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 56.7 bits (138), Expect = 9e-11
 Identities = 17/59 (28%), Positives = 27/59 (45%), Gaps = 6/59 (10%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVALQK 382
           IFVG L  + + ED++  F QFG++    +         +G GFV F +    E   + 
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 52.9 bits (128), Expect = 2e-09
 Identities = 14/44 (31%), Positives = 24/44 (54%)

Query: 132 LHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQ 175
           + + F   G+V +  ++ +K T +  G+GFV F S    EKV +
Sbjct: 16  VKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE 59

>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 = 66.0 bits (161), Expect = 1e-13
 Identities = 19/82 (23%), Positives = 35/82 (42%), Gaps = 12/82 (14%)

Query: 329 TIFVGALDSDVSDEDL---REPFSQFGEILSVKIPVGK---------GCGFVQFANRKDA 376
            +FV  L   ++D ++    E F +FG+I  V I                +V +   +DA
Sbjct: 17  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 76

Query: 377 EVALQKLQGTAIGKQTVRLSWG 398
             A+Q +    +  +T++ S G
Sbjct: 77  LRAIQCVNNVVVDGRTLKASLG 98

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 51.8 bits (124), Expect = 1e-08
 Identities = 13/84 (15%), Positives = 33/84 (39%), Gaps = 5/84 (5%)

Query: 211 IFVGDLAPDVTDSILQETFS--SKYPSVKGAKVIIDSNTGRTK---GYGFVRFGDENERS 265
           +FV  L+  + D  + +      K+  +    +   ++   ++      +V +    +  
Sbjct: 18  VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77

Query: 266 RAMTEMNGVYCSSRPMRIDVATPK 289
           RA+  +N V    R ++  + T K
Sbjct: 78  RAIQCVNNVVVDGRTLKASLGTTK 101

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 46.8 bits (111), Expect = 7e-07
 Identities = 11/85 (12%), Positives = 29/85 (34%), Gaps = 8/85 (9%)

Query: 117 TIWIGDL-FHWMDETFL--HNCFSHTGQVVNVKVIRNKQTGQSE---GYGFVEFYSRAAA 170
            +++  L     D   L     F   G++  V +  +     S+      +V +     A
Sbjct: 17  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 76

Query: 171 EKVLQSYSGSLMPNTDQPFRLNWAT 195
            + +Q  +  ++    +  + +  T
Sbjct: 77  LRAIQCVNNVVVD--GRTLKASLGT 99

>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 = 65.6 bits (160), Expect = 2e-13
 Identities = 16/82 (19%), Positives = 35/82 (42%), Gaps = 10/82 (12%)

Query: 326 NNATIFVGALDSDVSDEDLREPFSQFGE-ILSVKIP-------VGKGCGFVQFANRKDAE 377
            N  +F+G +      E++ E  ++  E +L V +          +G  FV++ + + A 
Sbjct: 7   GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAA 66

Query: 378 VALQKLQ--GTAIGKQTVRLSW 397
           +A +KL      +    + + W
Sbjct: 67  MARRKLMPGRIQLWGHQIAVDW 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 = 56.3 bits (136), Expect = 3e-10
 Identities = 12/83 (14%), Positives = 30/83 (36%), Gaps = 3/83 (3%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDS-NTGRTKGYGFVRFGDENERSRAMT 269
           +F+G +        + E  +     V    V   + +  + +G+ FV +      + A  
Sbjct: 11  LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 70

Query: 270 EMN--GVYCSSRPMRIDVATPKK 290
           ++    +      + +D A P+ 
Sbjct: 71  KLMPGRIQLWGHQIAVDWAEPEI 93

>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 = 51.7 bits (124), Expect = 1e-08
 Identities = 17/81 (20%), Positives = 31/81 (38%), Gaps = 2/81 (2%)

Query: 117 TIWIGDL-FHWMDETFLHNCFSHTGQVVNVKVIRNKQ-TGQSEGYGFVEFYSRAAAEKVL 174
            ++IG +      E  L      T  V++V V  +     ++ G+ FVE+ S  AA    
Sbjct: 10  RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 69

Query: 175 QSYSGSLMPNTDQPFRLNWAT 195
           +      +        ++WA 
Sbjct: 70  RKLMPGRIQLWGHQIAVDWAE 90

>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 = 65.2 bits (159), Expect = 2e-13
 Identities = 20/90 (22%), Positives = 38/90 (42%), Gaps = 4/90 (4%)

Query: 310 GSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQ 369
           GS+G+         E+    + V  L    S +DL++   + G++    +    G G V+
Sbjct: 1   GSSGSSGGPPSRRSEN---RVVVSGLPPSGSWQDLKDHMREAGDVCYADV-YRDGTGVVE 56

Query: 370 FANRKDAEVALQKLQGTAIGKQTVRLSWGR 399
           F  ++D   A++KL  T         ++ R
Sbjct: 57  FVRKEDMTYAVRKLDNTKFRSHEGETAYIR 86

>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 = 47.5 bits (113), Expect = 3e-07
 Identities = 15/84 (17%), Positives = 28/84 (33%), Gaps = 8/84 (9%)

Query: 207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSR 266
           S+  + V  L P  +   L++    +   V  A V          G G V F  + + + 
Sbjct: 14  SENRVVVSGLPPSGSWQDLKDHMR-EAGDVCYADVY-------RDGTGVVEFVRKEDMTY 65

Query: 267 AMTEMNGVYCSSRPMRIDVATPKK 290
           A+ +++     S          K 
Sbjct: 66  AVRKLDNTKFRSHEGETAYIRVKV 89

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 65.1 bits (159), Expect = 3e-13
 Identities = 22/101 (21%), Positives = 37/101 (36%), Gaps = 9/101 (8%)

Query: 197 SGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVK--------GAKVIIDSNTG 248
             S    E   + +I+V  L   VT   L + F  +   VK           + +D  TG
Sbjct: 4   GSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFK-QCGVVKMNKRTGQPMIHIYLDKETG 62

Query: 249 RTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPK 289
           + KG   V + D      A+   +G       +++ +A  K
Sbjct: 63  KPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKK 103

>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 = 59.7 bits (145), Expect = 2e-11
 Identities = 22/107 (20%), Positives = 42/107 (39%), Gaps = 14/107 (13%)

Query: 313 GARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILS--------VKIPVG-- 362
           G+       D +S+N+ I+V  L+  V+ +DL + F Q G +          + I +   
Sbjct: 1   GSSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKE 60

Query: 363 ----KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQ 405
               KG   V + +   A+ A++   G       +++S  R      
Sbjct: 61  TGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMN 107

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 45.1 bits (107), Expect = 3e-06
 Identities = 16/104 (15%), Positives = 37/104 (35%), Gaps = 10/104 (9%)

Query: 101 GKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQV--------VNVKVIRNKQ 152
           G    S +   + +   I++  L   +    L + F   G V          + +  +K+
Sbjct: 1   GSSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKE 60

Query: 153 TGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATF 196
           TG+ +G   V +     A+  ++ + G          +++ A  
Sbjct: 61  TGKPKGDATVSYEDPPTAKAAVEWFDGKDFQ--GSKLKVSLARK 102

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 63.9 bits (156), Expect = 5e-13
 Identities = 20/72 (27%), Positives = 29/72 (40%), Gaps = 1/72 (1%)

Query: 321 SDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGC-GFVQFANRKDAEVA 379
           S G S   ++FV      V    L E F  FG + SV +   KG    V+  +    E  
Sbjct: 2   SSGSSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAV 61

Query: 380 LQKLQGTAIGKQ 391
           L + Q +  G +
Sbjct: 62  LSQSQHSLGGHR 73

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 49.6 bits (119), Expect = 4e-08
 Identities = 18/84 (21%), Positives = 30/84 (35%), Gaps = 7/84 (8%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           S+FV      V  + L E F   +  V  A V++D + G    +  V  GD   R   + 
Sbjct: 10  SVFVSGFPRGVDSAQLSEYF-LAFGPV--ASVVMDKDKGV---FAIVEMGDVGAREAVL- 62

Query: 270 EMNGVYCSSRPMRIDVATPKKASG 293
             +        +R+     K+   
Sbjct: 63  SQSQHSLGGHRLRVRPREQKEFQS 86

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 40.0 bits (94), Expect = 1e-04
 Identities = 13/63 (20%), Positives = 24/63 (38%), Gaps = 5/63 (7%)

Query: 113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEK 172
              +++++      +D   L   F   G V +V + ++K       +  VE     A E 
Sbjct: 6   SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGV-----FAIVEMGDVGAREA 60

Query: 173 VLQ 175
           VL 
Sbjct: 61  VLS 63

>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 = 64.2 bits (156), Expect = 8e-13
 Identities = 16/95 (16%), Positives = 39/95 (41%), Gaps = 3/95 (3%)

Query: 308 GPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGF 367
           G    G+ +  S+S G  +   I +  L  DV++ ++      FG++ ++ +  GK   F
Sbjct: 13  GLVPRGSHMGDSRSAGVPSR-VIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAF 71

Query: 368 VQFANRKDAEVALQKLQ--GTAIGKQTVRLSWGRN 400
           ++    + A   +         +  Q + + +  +
Sbjct: 72  IEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNH 106

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 46.8 bits (111), Expect = 7e-07
 Identities = 17/105 (16%), Positives = 38/105 (36%), Gaps = 6/105 (5%)

Query: 91  QQQQQHGLSNGKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRN 150
                 GL     +  ++      ++ I I  L   + E  + +     G+V N+ +++ 
Sbjct: 7   HHHHSSGLVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG 66

Query: 151 KQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWAT 195
           K         F+E  +  AA  ++  Y+        QP  + ++ 
Sbjct: 67  K------NQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSN 105

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 41.8 bits (98), Expect = 4e-05
 Identities = 12/82 (14%), Positives = 26/82 (31%), Gaps = 9/82 (10%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT- 269
           I +  L  DVT+  +       +  V    ++      + K   F+    E   +  +  
Sbjct: 34  IHIRKLPIDVTEGEVISLG-LPFGKVTNLLML------KGKNQAFIEMNTEEAANTMVNY 86

Query: 270 -EMNGVYCSSRPMRIDVATPKK 290
                     +P+ I  +  K+
Sbjct: 87  YTSVTPVLRGQPIYIQFSNHKE 108

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 63.7 bits (155), Expect = 8e-13
 Identities = 11/83 (13%), Positives = 30/83 (36%), Gaps = 2/83 (2%)

Query: 317 QGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDA 376
                     +  I +  L  DV++ ++      FG++ ++ +  GK   F++    + A
Sbjct: 6   HHHHHGSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAA 65

Query: 377 EVALQKLQ--GTAIGKQTVRLSW 397
              +         +  Q + + +
Sbjct: 66  NTMVNYYTSVTPVLRGQPIYIQF 88

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 45.2 bits (107), Expect = 2e-06
 Identities = 15/92 (16%), Positives = 38/92 (41%), Gaps = 6/92 (6%)

Query: 104 NGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVE 163
           +  +++ +   ++ I I  L   + E  + +     G+V N+ +++ K         F+E
Sbjct: 5   HHHHHHGSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK------NQAFIE 58

Query: 164 FYSRAAAEKVLQSYSGSLMPNTDQPFRLNWAT 195
             +  AA  ++  Y+        QP  + ++ 
Sbjct: 59  MNTEEAANTMVNYYTSVTPVLRGQPIYIQFSN 90

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 41.8 bits (98), Expect = 4e-05
 Identities = 12/82 (14%), Positives = 26/82 (31%), Gaps = 9/82 (10%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT- 269
           I +  L  DVT+  +       +  V    ++      + K   F+    E   +  +  
Sbjct: 19  IHIRKLPIDVTEGEVISLG-LPFGKVTNLLML------KGKNQAFIEMNTEEAANTMVNY 71

Query: 270 -EMNGVYCSSRPMRIDVATPKK 290
                     +P+ I  +  K+
Sbjct: 72  YTSVTPVLRGQPIYIQFSNHKE 93

>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 = 63.3 bits (154), Expect = 9e-13
 Identities = 16/93 (17%), Positives = 40/93 (43%), Gaps = 8/93 (8%)

Query: 307 GGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCG 366
           G  GS+G ++ G+ S        + +  L  +V++ ++      FG++ ++ +  GK   
Sbjct: 1   GSSGSSGDKMDGAPS------RVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQA 54

Query: 367 FVQFANRKDAEVALQ--KLQGTAIGKQTVRLSW 397
           F++ A  + A   +         +  Q + + +
Sbjct: 55  FLELATEEAAITMVNYYSAVTPHLRNQPIYIQY 87

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 101

 Score = 44.0 bits (104), Expect = 5e-06
 Identities = 18/95 (18%), Positives = 37/95 (38%), Gaps = 6/95 (6%)

Query: 101 GKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYG 160
           G    S +      ++ + I  L   + ET +       G+V N+ +++ K         
Sbjct: 1   GSSGSSGDKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGK------NQA 54

Query: 161 FVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWAT 195
           F+E  +  AA  ++  YS       +QP  + ++ 
Sbjct: 55  FLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSN 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 = 39.0 bits (91), Expect = 3e-04
 Identities = 10/82 (12%), Positives = 28/82 (34%), Gaps = 9/82 (10%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT- 269
           + +  L  +VT++ +       +  V    ++      + K   F+    E      +  
Sbjct: 18  LHIRKLPGEVTETEVIALG-LPFGKVTNILML------KGKNQAFLELATEEAAITMVNY 70

Query: 270 -EMNGVYCSSRPMRIDVATPKK 290
                 +  ++P+ I  +  K+
Sbjct: 71  YSAVTPHLRNQPIYIQYSNHKE 92

>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 = 62.6 bits (153), Expect = 1e-12
 Identities = 19/65 (29%), Positives = 34/65 (52%), Gaps = 1/65 (1%)

Query: 319 SQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV-GKGCGFVQFANRKDAE 377
                  + + +FVG    D++ E+L++ F Q+GE++ V IP   +   FV FA+ K A+
Sbjct: 3   GSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQ 62

Query: 378 VALQK 382
               +
Sbjct: 63  SLCGE 67

>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 = 47.2 bits (113), Expect = 3e-07
 Identities = 20/83 (24%), Positives = 29/83 (34%), Gaps = 14/83 (16%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +FVG    D+T   LQ+ F  +Y  V    +         + + FV F D+        E
Sbjct: 14  VFVGRCTEDMTAEELQQFF-CQYGEVVDVFIPKPF-----RAFAFVTFADDKVAQSLCGE 67

Query: 271 M---NGVYCSSRPMRIDVATPKK 290
                G       + I  A PK 
Sbjct: 68  DLIIKG-----ISVHISNAEPKH 85

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 39.5 bits (93), Expect = 1e-04
 Identities = 14/72 (19%), Positives = 28/72 (38%), Gaps = 7/72 (9%)

Query: 104 NGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVE 163
            GS+++  +     +++G     M    L   F   G+VV+V + +         + FV 
Sbjct: 2   RGSHHH--HHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPK-----PFRAFAFVT 54

Query: 164 FYSRAAAEKVLQ 175
           F     A+ +  
Sbjct: 55  FADDKVAQSLCG 66

>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 = 62.7 bits (153), Expect = 2e-12
 Identities = 24/82 (29%), Positives = 42/82 (51%), Gaps = 2/82 (2%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +F+G L+   T   L+E F  ++  VK   V+ D  T R++G+GFV F D+    + +  
Sbjct: 28  MFIGGLSWQTTQEGLREYFG-QFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-A 85

Query: 271 MNGVYCSSRPMRIDVATPKKAS 292
            +     S+ +   VA P++A 
Sbjct: 86  QSRHELDSKTIDPKVAFPRRAQ 107

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 58.8 bits (143), Expect = 4e-11
 Identities = 22/84 (26%), Positives = 36/84 (42%), Gaps = 1/84 (1%)

Query: 92  QQQQHGLSNGKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNK 151
               H   +       ++  +   K ++IG L     +  L   F   G+V    V+R+ 
Sbjct: 3   SSHHHHHHSSGLVPRGSHMGSSGCK-MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDP 61

Query: 152 QTGQSEGYGFVEFYSRAAAEKVLQ 175
            T +S G+GFV F  +A  +KVL 
Sbjct: 62  LTKRSRGFGFVTFMDQAGVDKVLA 85

>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 = 58.8 bits (143), Expect = 4e-11
 Identities = 20/77 (25%), Positives = 33/77 (42%), Gaps = 6/77 (7%)

Query: 311 SNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKG 364
            + + +    S   S+   +F+G L    + E LRE F QFGE+    +         +G
Sbjct: 9   HHSSGLVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRG 68

Query: 365 CGFVQFANRKDAEVALQ 381
            GFV F ++   +  L 
Sbjct: 69  FGFVTFMDQAGVDKVLA 85

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 68.0 bits (165), Expect = 2e-12
 Identities = 20/91 (21%), Positives = 37/91 (40%), Gaps = 6/91 (6%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVALQK 382
           T+FV  ++ D ++  LR  F  +G I  + +         +G  F+++ + +D   A + 
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163

Query: 383 LQGTAIGKQTVRLSWGRNPGNKQWRGDHSNH 413
             G  I  + V +   R    K WR      
Sbjct: 164 ADGKKIDGRRVLVDVERGRTVKGWRPRRLGG 194

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 61.8 bits (149), Expect = 2e-10
 Identities = 20/92 (21%), Positives = 41/92 (44%), Gaps = 1/92 (1%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           ++FV  +  D T+S L+  F   Y  +K   ++    +G+ +GY F+ +  E +   A  
Sbjct: 104 TLFVARVNYDTTESKLRREFE-VYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162

Query: 270 EMNGVYCSSRPMRIDVATPKKASGYQQQYSSQ 301
             +G     R + +DV   +   G++ +    
Sbjct: 163 HADGKKIDGRRVLVDVERGRTVKGWRPRRLGG 194

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 54.9 bits (131), Expect = 3e-08
 Identities = 16/99 (16%), Positives = 43/99 (43%), Gaps = 3/99 (3%)

Query: 89  KQQQQQQHGLSNGKQN---GSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNV 145
           ++ +++Q  +    +     ++ N   D  KT+++  + +   E+ L   F   G +  +
Sbjct: 73  EKIERRQQEVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRI 132

Query: 146 KVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPN 184
            ++ +K++G+  GY F+E+          +   G  +  
Sbjct: 133 HMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDG 171

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 62.7 bits (153), Expect = 2e-12
 Identities = 21/87 (24%), Positives = 41/87 (47%), Gaps = 10/87 (11%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT- 269
           +F+G L+ + T+  L+  +  ++  +    V+ D  + R++G+GFV F    E   AM  
Sbjct: 30  LFIGGLSFETTEESLRNYYE-QWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA 88

Query: 270 ---EMNGVYCSSRPMRIDVATPKKASG 293
               ++G     R +    A  ++ SG
Sbjct: 89  RPHSIDG-----RVVEPKRAVAREESG 110

>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 = 55.7 bits (135), Expect = 5e-10
 Identities = 22/87 (25%), Positives = 39/87 (44%), Gaps = 12/87 (13%)

Query: 307 GGPGSNG-----ARVQGSQSDGESNNAT-IFVGALDSDVSDEDLREPFSQFGEILSVKI- 359
           G  GS+G       V   +   E      +F+G L  + ++E LR  + Q+G++    + 
Sbjct: 1   GSSGSSGMEKTLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVM 60

Query: 360 --PVGK---GCGFVQFANRKDAEVALQ 381
             P  K   G GFV F++  + + A+ 
Sbjct: 61  RDPASKRSRGFGFVTFSSMAEVDAAMA 87

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 50.7 bits (122), Expect = 3e-08
 Identities = 17/65 (26%), Positives = 34/65 (52%)

Query: 112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAE 171
            ++ + ++IG L     E  L N +   G++ +  V+R+  + +S G+GFV F S A  +
Sbjct: 24  KEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVD 83

Query: 172 KVLQS 176
             + +
Sbjct: 84  AAMAA 88

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 62.5 bits (152), Expect = 2e-12
 Identities = 16/71 (22%), Positives = 31/71 (43%), Gaps = 1/71 (1%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAI 388
            + V  L    S +DL++   + G++    +    G G V+F  ++D   A++KL  T  
Sbjct: 18  RVVVSGLPPSGSWQDLKDHMREAGDVCYADV-YRDGTGVVEFVRKEDMTYAVRKLDNTKF 76

Query: 389 GKQTVRLSWGR 399
                  ++ R
Sbjct: 77  RSHEGETAYIR 87

>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 = 46.0 bits (109), Expect = 2e-06
 Identities = 15/84 (17%), Positives = 28/84 (33%), Gaps = 8/84 (9%)

Query: 207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSR 266
           S+  + V  L P  +   L++    +   V  A V          G G V F  + + + 
Sbjct: 15  SENRVVVSGLPPSGSWQDLKDHMR-EAGDVCYADVY-------RDGTGVVEFVRKEDMTY 66

Query: 267 AMTEMNGVYCSSRPMRIDVATPKK 290
           A+ +++     S          K 
Sbjct: 67  AVRKLDNTKFRSHEGETAYIRVKV 90

>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 = 61.1 bits (149), Expect = 4e-12
 Identities = 21/61 (34%), Positives = 38/61 (62%), Gaps = 1/61 (1%)

Query: 323 GESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV-GKGCGFVQFANRKDAEVALQ 381
           G S ++ +FVG    D+++++LRE FSQ+G+++ V IP   +   FV FA+ + A+    
Sbjct: 1   GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG 60

Query: 382 K 382
           +
Sbjct: 61  E 61

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 49.5 bits (119), Expect = 5e-08
 Identities = 22/86 (25%), Positives = 32/86 (37%), Gaps = 14/86 (16%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +FVG    D+T+  L+E F S+Y  V    +         + + FV F D+        E
Sbjct: 8   VFVGRCTGDMTEDELREFF-SQYGDVMDVFIPKPF-----RAFAFVTFADDQIAQSLCGE 61

Query: 271 M---NGVYCSSRPMRIDVATPKKASG 293
                G       + I  A PK  S 
Sbjct: 62  DLIIKG-----ISVHISNAEPKHNSN 82

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 13/64 (20%), Positives = 25/64 (39%), Gaps = 5/64 (7%)

Query: 112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAE 171
           +  +  +++G     M E  L   FS  G V++V + +         + FV F     A+
Sbjct: 2   SSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQ 56

Query: 172 KVLQ 175
            +  
Sbjct: 57  SLCG 60

>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 = 60.2 bits (147), Expect = 5e-12
 Identities = 17/58 (29%), Positives = 33/58 (56%), Gaps = 1/58 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAM 268
           IFVG L+PD  +  ++E F   +  V+  ++ +D+ T + +G+ F+ F +E    + M
Sbjct: 2   IFVGGLSPDTPEEKIREYFG-GFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 58

>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 = 59.1 bits (144), Expect = 1e-11
 Identities = 19/59 (32%), Positives = 32/59 (54%), Gaps = 6/59 (10%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVALQK 382
           IFVG L  D  +E +RE F  FGE+ S+++P+       +G  F+ F   +  +  ++K
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 50.6 bits (122), Expect = 1e-08
 Identities = 12/58 (20%), Positives = 29/58 (50%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQ 175
           I++G L     E  +   F   G+V ++++  + +T +  G+ F+ F      +K+++
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 59

>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 = 61.1 bits (149), Expect = 6e-12
 Identities = 25/84 (29%), Positives = 39/84 (46%), Gaps = 11/84 (13%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +FVG L    T   L+  FS +Y  V    ++ D  T +++G+GFV+F D N     +  
Sbjct: 19  LFVGGLDWSTTQETLRSYFS-QYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVL-- 75

Query: 271 MNGVYCSSRPMRID--VATPKKAS 292
                 +SRP  +D     PK  +
Sbjct: 76  ------ASRPHTLDGRNIDPKPCT 93

>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 = 56.5 bits (137), Expect = 2e-10
 Identities = 24/78 (30%), Positives = 34/78 (43%), Gaps = 8/78 (10%)

Query: 310 GSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKI---PVGK--- 363
           GS+G+    +    E     +FVG LD   + E LR  FSQ+GE++   I          
Sbjct: 1   GSSGSSGMNNSGADEIGK--LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSR 58

Query: 364 GCGFVQFANRKDAEVALQ 381
           G GFV+F +       L 
Sbjct: 59  GFGFVKFKDPNCVGTVLA 76

>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 = 53.4 bits (129), Expect = 3e-09
 Identities = 23/80 (28%), Positives = 40/80 (50%), Gaps = 3/80 (3%)

Query: 97  GLSNGKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQS 156
           G S      ++    ++  K +++G L     +  L + FS  G+VV+  ++++K T QS
Sbjct: 1   GSSGSSGMNNSGA--DEIGK-LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQS 57

Query: 157 EGYGFVEFYSRAAAEKVLQS 176
            G+GFV+F        VL S
Sbjct: 58  RGFGFVKFKDPNCVGTVLAS 77

>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 = 60.5 bits (147), Expect = 6e-12
 Identities = 12/78 (15%), Positives = 36/78 (46%), Gaps = 5/78 (6%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKG----AKVIIDSNTGRTKGYGFVRFGDENERS 265
            ++VG++   +T+  + + F+++             ++     + K + F+ F   +E +
Sbjct: 8   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67

Query: 266 RAMTEMNGVYCSSRPMRI 283
           +AM   +G+    + ++I
Sbjct: 68  QAM-AFDGIIFQGQSLKI 84

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 50.5 bits (121), Expect = 2e-08
 Identities = 13/76 (17%), Positives = 33/76 (43%), Gaps = 12/76 (15%)

Query: 330 IFVGALDSDVSDEDLREPFSQF-----------GEILSVKIPVGKGCGFVQFANRKDAEV 378
           ++VG +   +++E + + F+               +L+V+I   K   F++F +  +   
Sbjct: 9   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68

Query: 379 ALQKLQGTAIGKQTVR 394
           A+    G     Q+++
Sbjct: 69  AMA-FDGIIFQGQSLK 83

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 42.4 bits (100), Expect = 2e-05
 Identities = 9/65 (13%), Positives = 28/65 (43%), Gaps = 5/65 (7%)

Query: 116 KTIWIGDLFHWMDETFLHNCFSHTGQVVNVKV-----IRNKQTGQSEGYGFVEFYSRAAA 170
           + +++G++   + E  + + F+   ++  +       +   Q  Q + + F+EF S    
Sbjct: 7   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 66

Query: 171 EKVLQ 175
            + + 
Sbjct: 67  TQAMA 71

>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 = 60.5 bits (147), Expect = 1e-11
 Identities = 18/96 (18%), Positives = 33/96 (34%), Gaps = 13/96 (13%)

Query: 307 GGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEIL-SVKIPV---- 361
           G  GS+G      + D  S      +  +   ++  D+ +          +V + V    
Sbjct: 1   GSSGSSG------EGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNG 54

Query: 362 -GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLS 396
            G G   VQF N  DA  +  +L    +  +   + 
Sbjct: 55  QGLGQALVQFKNEDDARKSE-RLHRKKLNGREAFVH 89

>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 = 57.4 bits (139), Expect = 1e-10
 Identities = 16/102 (15%), Positives = 40/102 (39%), Gaps = 5/102 (4%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
              + ++   +T   + +      P  + A  ++  N G+  G   V+F +E++  ++  
Sbjct: 17  CAHITNIPFSITKMDVLQFLE-GIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSE- 74

Query: 270 EMNGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGS 311
            ++    + R   + V T +     ++   +Q      GP S
Sbjct: 75  RLHRKKLNGREAFVHVVTLEDMREIEKNPPAQG---KSGPSS 113

>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 = 41.3 bits (97), Expect = 6e-05
 Identities = 12/75 (16%), Positives = 21/75 (28%)

Query: 101 GKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYG 160
           G    S     N       I ++   + +  +           N   +     GQ  G  
Sbjct: 1   GSSGSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQA 60

Query: 161 FVEFYSRAAAEKVLQ 175
            V+F +   A K  +
Sbjct: 61  LVQFKNEDDARKSER 75

>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 = 59.5 bits (144), Expect = 5e-11
 Identities = 21/109 (19%), Positives = 39/109 (35%), Gaps = 8/109 (7%)

Query: 292 SGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQF 351
           SG   + S  A  + GG            +   +    + +  L    ++ D+   FS  
Sbjct: 12  SGLVPRGSHMA-SMTGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPL 70

Query: 352 GEILSVKIPVG-----KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRL 395
              + V I +G      G   V+FA  ++A  A+ K     +  + + L
Sbjct: 71  N-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAMSK-DRANMQHRYIEL 117

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 47.5 bits (113), Expect = 7e-07
 Identities = 17/96 (17%), Positives = 34/96 (35%), Gaps = 4/96 (4%)

Query: 197 SGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFV 256
             S+   ++ +   + +  L    T++ +   FS    +     + I  + GR  G   V
Sbjct: 35  GDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPL--NPVRVHIEIGPD-GRVTGEADV 91

Query: 257 RFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKAS 292
            F    E   AM   +      R + + + +   AS
Sbjct: 92  EFATHEEAVAAM-SKDRANMQHRYIELFLNSTTGAS 126

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 57.4 bits (139), Expect = 1e-10
 Identities = 18/63 (28%), Positives = 26/63 (41%), Gaps = 1/63 (1%)

Query: 212 FVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEM 271
            +      V    L   FS K   V   +  ID  TG+TKG+ FV  G  N+  + +   
Sbjct: 16  VIPSAKVPVLKKALTSLFS-KAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSF 74

Query: 272 NGV 274
           +G 
Sbjct: 75  HGK 77

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 56.3 bits (136), Expect = 2e-10
 Identities = 13/67 (19%), Positives = 31/67 (46%), Gaps = 6/67 (8%)

Query: 331 FVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKLQ 384
            + +    V  + L   FS+ G++++++ P+       KG  FV+  +  DA+  ++   
Sbjct: 16  VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75

Query: 385 GTAIGKQ 391
           G  +  +
Sbjct: 76  GKRLDLK 82

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 50.1 bits (120), Expect = 4e-08
 Identities = 18/51 (35%), Positives = 34/51 (66%)

Query: 129 ETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSG 179
           +  L + FS  G+VVN++   ++ TG+++G+ FVE  S   A+K+++S+ G
Sbjct: 26  KKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHG 76

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 56.9 bits (138), Expect = 1e-10
 Identities = 14/89 (15%), Positives = 39/89 (43%), Gaps = 7/89 (7%)

Query: 318 GSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-----KGCGFVQFAN 372
           GS     +   T+ +     +V+++++ E  +     ++++I         G  FV F+N
Sbjct: 1   GSSGSSGTTCHTVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAHGNKTGYIFVDFSN 59

Query: 373 RKDAEVALQKLQGTAIGKQTVRLSWGRNP 401
            ++ + AL+      +G + + +   ++ 
Sbjct: 60  EEEVKQALKC-NREYMGGRYIEVFREKSG 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 = 52.7 bits (127), Expect = 4e-09
 Identities = 17/92 (18%), Positives = 39/92 (42%), Gaps = 4/92 (4%)

Query: 202 RTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDE 261
            +   +  ++ +     +VT+  + E  +         +++ +++ G   GY FV F +E
Sbjct: 4   GSSGTTCHTVKLRGAPFNVTEKNVMEFLAP--LKPVAIRIVRNAH-GNKTGYIFVDFSNE 60

Query: 262 NERSRAMTEMNGVYCSSRPMRIDVATPKKASG 293
            E  +A+ + N  Y   R + +       +SG
Sbjct: 61  EEVKQAL-KCNREYMGGRYIEVFREKSGPSSG 91

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 57.1 bits (138), Expect = 2e-10
 Identities = 23/89 (25%), Positives = 41/89 (46%), Gaps = 7/89 (7%)

Query: 313 GARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEIL-SVKIPVG-----KGCG 366
           G+      S   +N+  + +  L    S E++ + FS    +   + +PV       G  
Sbjct: 1   GSSGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEA 60

Query: 367 FVQFANRKDAEVALQKLQGTAIGKQTVRL 395
           FVQFA+++ AE AL+K     IG + + +
Sbjct: 61  FVQFASQEIAEKALKK-HKERIGHRYIEI 88

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 54.8 bits (132), Expect = 9e-10
 Identities = 15/93 (16%), Positives = 33/93 (35%), Gaps = 2/93 (2%)

Query: 197 SGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFV 256
             S    +  +D  + +  L    +   + + FS     V     +     GR+ G  FV
Sbjct: 4   GSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFS-GLEIVPNGMTLPVDFQGRSTGEAFV 62

Query: 257 RFGDENERSRAMTEMNGVYCSSRPMRIDVATPK 289
           +F  +    +A+ + +      R + I  ++  
Sbjct: 63  QFASQEIAEKAL-KKHKERIGHRYIEIFKSSRA 94

>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 = 41.7 bits (98), Expect = 4e-05
 Identities = 21/76 (27%), Positives = 30/76 (39%), Gaps = 2/76 (2%)

Query: 101 GKQNGSNNNFTNDETKTIWIGDL-FHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGY 159
           G    S N+        + +  L F    E  +   FS    V N   +     G+S G 
Sbjct: 1   GSSGSSGNSPDTANDGFVRLRGLPFGCSKEE-IVQFFSGLEIVPNGMTLPVDFQGRSTGE 59

Query: 160 GFVEFYSRAAAEKVLQ 175
            FV+F S+  AEK L+
Sbjct: 60  AFVQFASQEIAEKALK 75

>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 = 56.3 bits (136), Expect = 3e-10
 Identities = 22/119 (18%), Positives = 47/119 (39%), Gaps = 15/119 (12%)

Query: 307 GGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG---- 362
           G  GS+G  +  +      ++  + V  +     + D+R+ F     + +V +       
Sbjct: 1   GSSGSSGKPLPIN-----PDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGR 54

Query: 363 -KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQWRGDHSNHWNGAHYG 420
             G G V+F + +D   AL++     + ++ V +S       +QW     +  +G   G
Sbjct: 55  NNGNGLVKFLSPQDTFEALKR-NRMLMIQRYVEVSPAT---ERQWVAAGGHITSGPSSG 109

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 54.4 bits (131), Expect = 1e-09
 Identities = 18/94 (19%), Positives = 36/94 (38%), Gaps = 4/94 (4%)

Query: 197 SGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFV 256
           S          DL + V  +     ++ +++ F      V    ++ D   GR  G G V
Sbjct: 5   SSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHG--LRVDAVHLLKDHV-GRNNGNGLV 61

Query: 257 RFGDENERSRAMTEMNGVYCSSRPMRIDVATPKK 290
           +F    +   A+ + N +    R + +  AT ++
Sbjct: 62  KFLSPQDTFEAL-KRNRMLMIQRYVEVSPATERQ 94

>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 = 56.4 bits (136), Expect = 4e-10
 Identities = 22/110 (20%), Positives = 43/110 (39%), Gaps = 5/110 (4%)

Query: 202 RTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDE 261
           R+   +   +++  L  +  +  + + F  K   V+ +  I     G+  G GFV F +E
Sbjct: 19  RSPHEAGFCVYLKGLPFEAENKHVIDFFK-KLDIVEDSIYIAYGPNGKATGEGFVEFRNE 77

Query: 262 NERSRAMTEMNGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGS 311
            +   A+   +  Y  +R +++   T K           +   L  GP S
Sbjct: 78  ADYKAAL-CRHKQYMGNRFIQVHPITKKGMLEKIDMIRKR---LQSGPSS 123

>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 = 55.6 bits (134), Expect = 7e-10
 Identities = 20/97 (20%), Positives = 44/97 (45%), Gaps = 8/97 (8%)

Query: 306 AGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEIL-SVKIPVG-- 362
           + G   +G +   S+S  E+    +++  L  +  ++ + + F +   +  S+ I  G  
Sbjct: 5   SSGKSPSGQKRSRSRSPHEAGF-CVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPN 63

Query: 363 ---KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLS 396
               G GFV+F N  D + AL +     +G + +++ 
Sbjct: 64  GKATGEGFVEFRNEADYKAALCR-HKQYMGNRFIQVH 99

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 55.1 bits (133), Expect = 5e-10
 Identities = 17/75 (22%), Positives = 33/75 (44%), Gaps = 10/75 (13%)

Query: 327 NATIFVGAL------DSDVSDEDLREPFSQFGEILSVKIPV----GKGCGFVQFANRKDA 376
           ++ I V  +        +     + + FS+FG+I +   P      KG  F+++A+   A
Sbjct: 1   DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHA 60

Query: 377 EVALQKLQGTAIGKQ 391
             A++   G  + KQ
Sbjct: 61  VDAVKNADGYKLDKQ 75

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 47.0 bits (112), Expect = 3e-07
 Identities = 15/71 (21%), Positives = 27/71 (38%), Gaps = 11/71 (15%)

Query: 211 IFVGDLAPDVTDS-------ILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENE 263
           I V ++ P V          ++ + FS K+  +           G+TKGY F+ +     
Sbjct: 4   IVVDNV-PQVGPDRLEKLKNVIHKIFS-KFGKIT--NDFYPEEDGKTKGYIFLEYASPAH 59

Query: 264 RSRAMTEMNGV 274
              A+   +G 
Sbjct: 60  AVDAVKNADGY 70

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 41.6 bits (98), Expect = 3e-05
 Identities = 14/51 (27%), Positives = 28/51 (54%), Gaps = 2/51 (3%)

Query: 129 ETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSG 179
           +  +H  FS  G++ N      ++ G+++GY F+E+ S A A   +++  G
Sbjct: 21  KNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADG 69

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 55.6 bits (134), Expect = 6e-10
 Identities = 15/98 (15%), Positives = 29/98 (29%), Gaps = 4/98 (4%)

Query: 307 GGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFG-EILSVKIPVG--K 363
                   R              I +  L    S +DL++   +   E     +      
Sbjct: 9   HHSSGLVPRGSHMSKLPAKRY-RITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFD 67

Query: 364 GCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNP 401
           G G ++F + +    AL++L         + +    NP
Sbjct: 68  GTGALEFPSEEILVEALERLNNIEFRGSVITVERDDNP 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 = 49.1 bits (117), Expect = 1e-07
 Identities = 14/87 (16%), Positives = 26/87 (29%), Gaps = 4/87 (4%)

Query: 197 SGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFV 256
            GS           I + +L    +   L++           + V    NT    G G +
Sbjct: 17  RGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSV----NTRDFDGTGAL 72

Query: 257 RFGDENERSRAMTEMNGVYCSSRPMRI 283
            F  E     A+  +N +      + +
Sbjct: 73  EFPSEEILVEALERLNNIEFRGSVITV 99

>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 = 55.7 bits (134), Expect = 7e-10
 Identities = 29/116 (25%), Positives = 50/116 (43%), Gaps = 11/116 (9%)

Query: 291 ASGYQQQYSSQALVLAGGPGSNGARVQ----GSQSDGESNNATIFVGALDSDVSDEDLRE 346
            S +   + S  LV  G   ++    Q    GS S   +N+  + +  L    + E++ +
Sbjct: 2   GSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQ 61

Query: 347 PFSQFGEI-LSVKIPVG-----KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLS 396
            FS    +   + +PV       G  FVQFA+++ AE AL K     IG + + + 
Sbjct: 62  FFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGK-HKERIGHRYIEVF 116

>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 = 54.9 bits (132), Expect = 2e-09
 Identities = 13/91 (14%), Positives = 32/91 (35%), Gaps = 2/91 (2%)

Query: 199 SDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRF 258
                ++ +D  + +  L    T   + + FS     V     +     G+  G  FV+F
Sbjct: 33  GSNSADSANDGFVRLRGLPFGCTKEEIVQFFS-GLEIVPNGITLPVDPEGKITGEAFVQF 91

Query: 259 GDENERSRAMTEMNGVYCSSRPMRIDVATPK 289
             +    +A+   +      R + +  ++ +
Sbjct: 92  ASQELAEKAL-GKHKERIGHRYIEVFKSSQE 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 = 40.2 bits (94), Expect = 2e-04
 Identities = 23/111 (20%), Positives = 37/111 (33%), Gaps = 9/111 (8%)

Query: 65  MMYPHHYMPYGGGGHPYYQNGGGVKQQQQQQHGLSNGKQNGSNNNFTNDETKTIWIGDLF 124
           M   HH+  +  G  P   +   +   QQ   G ++                 + +  L 
Sbjct: 1   MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSNSADS---------ANDGFVRLRGLP 51

Query: 125 HWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQ 175
               +  +   FS    V N   +     G+  G  FV+F S+  AEK L 
Sbjct: 52  FGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALG 102

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 54.7 bits (132), Expect = 9e-10
 Identities = 19/81 (23%), Positives = 35/81 (43%), Gaps = 12/81 (14%)

Query: 321 SDGESNNATIFVGAL------DSDVSDEDLREPFSQFGEILSVKIPV----GKGCGFVQF 370
           +DG  +   I V  +        +     + + FS+FG+I +   P      KG  F+++
Sbjct: 11  ADGIDS--VIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEY 68

Query: 371 ANRKDAEVALQKLQGTAIGKQ 391
           A+   A  A++   G  + KQ
Sbjct: 69  ASPAHAVDAVKNADGYKLDKQ 89

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 50.5 bits (121), Expect = 3e-08
 Identities = 16/73 (21%), Positives = 28/73 (38%), Gaps = 11/73 (15%)

Query: 208 DLSIFVGDLAPDVTDS-------ILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGD 260
           D  I V ++ P V          ++ + FS K+  +           G+TKGY F+ +  
Sbjct: 15  DSVIVVDNV-PQVGPDRLEKLKNVIHKIFS-KFGKIT--NDFYPEEDGKTKGYIFLEYAS 70

Query: 261 ENERSRAMTEMNG 273
                 A+   +G
Sbjct: 71  PAHAVDAVKNADG 83

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 41.6 bits (98), Expect = 4e-05
 Identities = 14/51 (27%), Positives = 26/51 (50%), Gaps = 2/51 (3%)

Query: 129 ETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSG 179
           +  +H  FS  G++ N         G+++GY F+E+ S A A   +++  G
Sbjct: 35  KNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHAVDAVKNADG 83

>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 = 54.3 bits (131), Expect = 1e-09
 Identities = 22/94 (23%), Positives = 36/94 (38%), Gaps = 13/94 (13%)

Query: 307 GGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG---- 362
           G  GS+G       S   +    + +  L    ++ D+   FS     + V I +G    
Sbjct: 1   GSSGSSG------SSFQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGR 53

Query: 363 -KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRL 395
             G   V+FA  +DA  A+ K     +  + V L
Sbjct: 54  VTGEADVEFATHEDAVAAMAK-DKANMQHRYVEL 86

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 48.9 bits (117), Expect = 1e-07
 Identities = 16/97 (16%), Positives = 33/97 (34%), Gaps = 4/97 (4%)

Query: 197 SGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFV 256
             S    ++ +   + +  L    T++ +   FS    +     + I  + GR  G   V
Sbjct: 4   GSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSP--LNPMRVHIEIGPD-GRVTGEADV 60

Query: 257 RFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKASG 293
            F    +   AM   +      R + + + +    SG
Sbjct: 61  EFATHEDAVAAM-AKDKANMQHRYVELFLNSTAGTSG 96

>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 = 38.5 bits (90), Expect = 5e-04
 Identities = 15/75 (20%), Positives = 28/75 (37%), Gaps = 2/75 (2%)

Query: 101 GKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYG 160
           G    S ++F +     + +  L +   E  ++N FS     + V +      G+  G  
Sbjct: 1   GSSGSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPD-GRVTGEA 58

Query: 161 FVEFYSRAAAEKVLQ 175
            VEF +   A   + 
Sbjct: 59  DVEFATHEDAVAAMA 73

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 53.0 bits (127), Expect = 6e-09
 Identities = 21/99 (21%), Positives = 37/99 (37%), Gaps = 10/99 (10%)

Query: 306 AGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEIL----SVKIPV 361
           + G    G   + +Q   + N   + +  L    + E++   F Q   I      +    
Sbjct: 2   SSGSSGGGTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVT 61

Query: 362 G-----KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRL 395
                  G  FV FA  + A+ AL+K     +GK+ + L
Sbjct: 62  YPDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIEL 99

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 45.3 bits (107), Expect = 3e-06
 Identities = 22/120 (18%), Positives = 40/120 (33%), Gaps = 8/120 (6%)

Query: 194 ATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVI--IDSNTGRTK 251
            T +   +     + + + +  L    T   +   F    P   G + I  +    GR  
Sbjct: 9   GTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPT 68

Query: 252 GYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGS 311
           G  FV F  E     A+   +      R + +  +T  +      ++SS +     GP S
Sbjct: 69  GDAFVLFACEEYAQNAL-RKHKDLLGKRYIELFRSTAAEVQQVLNRFSSAS-----GPSS 122

>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 = 52.5 bits (126), Expect = 6e-09
 Identities = 16/87 (18%), Positives = 35/87 (40%), Gaps = 10/87 (11%)

Query: 318 GSQSDGESNNA-TIFVGALDSDVSDEDLREPFSQF---GEILSVKIPVG-----KGCGFV 368
           GS+ + E ++   I    L    + ED+   FS          +   +      +G   +
Sbjct: 1   GSKLEEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALI 60

Query: 369 QFANRKDAEVALQKLQGTAIGKQTVRL 395
           +  + +D + AL+K     +G++ V +
Sbjct: 61  EMESEQDVQKALEK-HRMYMGQRYVEV 86

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 46.4 bits (110), Expect = 8e-07
 Identities = 15/106 (14%), Positives = 33/106 (31%), Gaps = 2/106 (1%)

Query: 198 GSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKV-IIDSNTGRTKGYGFV 256
           GS    E      I    L    T   +   FS          +  + +  G+ +G   +
Sbjct: 1   GSKLEEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALI 60

Query: 257 RFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKASGYQQQYSSQA 302
               E +  +A+ E + +Y   R + +     +      +    ++
Sbjct: 61  EMESEQDVQKAL-EKHRMYMGQRYVEVYEINNEDVDALMKSLQVKS 105

>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 = 51.5 bits (123), Expect = 2e-08
 Identities = 18/94 (19%), Positives = 36/94 (38%), Gaps = 10/94 (10%)

Query: 310 GSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQF---GEILSVKIPVG---- 362
           GS+G+       +G      + +  L    S ED++   S       +  V         
Sbjct: 1   GSSGSSGMMLGPEGG-EGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGR 59

Query: 363 -KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRL 395
             G  FV+  +  D ++AL+K    ++G + + +
Sbjct: 60  QSGEAFVELESEDDVKLALKK-DRESMGHRYIEV 92

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 44.5 bits (105), Expect = 6e-06
 Identities = 17/94 (18%), Positives = 30/94 (31%), Gaps = 2/94 (2%)

Query: 197 SGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKV-IIDSNTGRTKGYGF 255
           SG     E      + +  L    +   +Q   S        A V  I +  GR  G  F
Sbjct: 6   SGMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAF 65

Query: 256 VRFGDENERSRAMTEMNGVYCSSRPMRIDVATPK 289
           V    E++   A+ + +      R + +  +   
Sbjct: 66  VELESEDDVKLAL-KKDRESMGHRYIEVFKSHRT 98

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 121

 Score = 51.1 bits (122), Expect = 2e-08
 Identities = 21/64 (32%), Positives = 26/64 (40%), Gaps = 2/64 (3%)

Query: 331 FVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGK 390
           F G LD     EDL   FS  GEI  +    G   G + F     A+ AL K +    G 
Sbjct: 23  FSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKE--KAKEALGKAKDANNGN 80

Query: 391 QTVR 394
             +R
Sbjct: 81  LQLR 84

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 51.1 bits (122), Expect = 2e-08
 Identities = 15/70 (21%), Positives = 28/70 (40%), Gaps = 8/70 (11%)

Query: 321 SDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG--------KGCGFVQFAN 372
           S G S +  +FVG L  D+ ++++   F +FG ++               KG  F+ F  
Sbjct: 2   SSGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQE 61

Query: 373 RKDAEVALQK 382
               +  +  
Sbjct: 62  ESSVQALIDA 71

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 45.0 bits (106), Expect = 3e-06
 Identities = 15/87 (17%), Positives = 32/87 (36%), Gaps = 9/87 (10%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIID--SNTGRTKGYGFVRFGDENERSRAM 268
           +FVG L PD+ +  +  +F  ++  +           +    KGY F+ F +E+     +
Sbjct: 11  VFVGGLPPDIDEDEITASF-RRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALI 69

Query: 269 TEM------NGVYCSSRPMRIDVATPK 289
                      +  SS  ++      +
Sbjct: 70  DACLEEDGKLYLCVSSPTIKDKPVQIR 96

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 38.4 bits (89), Expect = 6e-04
 Identities = 11/66 (16%), Positives = 29/66 (43%), Gaps = 2/66 (3%)

Query: 113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNK--QTGQSEGYGFVEFYSRAAA 170
             ++ +++G L   +DE  +   F   G +V     + +       +GY F+ F   ++ 
Sbjct: 6   SGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSV 65

Query: 171 EKVLQS 176
           + ++ +
Sbjct: 66  QALIDA 71

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 50.8 bits (121), Expect = 5e-08
 Identities = 27/109 (24%), Positives = 44/109 (40%), Gaps = 9/109 (8%)

Query: 297 QYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILS 356
           Q  + AL       S  A   G    G+S    I V  L   V+ + L + FS+FG +L 
Sbjct: 3   QSGNLAL-----AASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLK 57

Query: 357 VKIPV--GKGCGFVQFANRKDAEVALQKLQGTAI--GKQTVRLSWGRNP 401
           +       +    +Q+A+   A+ A   L G  I     T+R+ + +  
Sbjct: 58  IITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLT 106

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 43.9 bits (103), Expect = 1e-05
 Identities = 14/92 (15%), Positives = 33/92 (35%), Gaps = 6/92 (6%)

Query: 105 GSNNNFTNDETKTIW--IGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFV 162
                    ++  +   + +LF+ +    LH  FS  G V+ +         Q      +
Sbjct: 16  VDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQ----ALL 71

Query: 163 EFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWA 194
           ++    +A+    S  G  + N     R++++
Sbjct: 72  QYADPVSAQHAKLSLDGQNIYNACCTLRIDFS 103

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 52.1 bits (124), Expect = 5e-08
 Identities = 12/71 (16%), Positives = 32/71 (45%), Gaps = 5/71 (7%)

Query: 326 NNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-----KGCGFVQFANRKDAEVAL 380
            N ++++    +D + +D++E     G++L++++        KG  FV F + + A+  +
Sbjct: 108 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFV 167

Query: 381 QKLQGTAIGKQ 391
           +          
Sbjct: 168 ETPGQKYKETD 178

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 44.8 bits (105), Expect = 1e-05
 Identities = 16/127 (12%), Positives = 44/127 (34%), Gaps = 2/127 (1%)

Query: 52  PAAAMAMMQQQQMMMYPHHYMPYGGGGHPYYQNGGGVKQQQQQQHGLSNGKQNGSNNNFT 111
           P   M    +   +    + +          +     + + + +   S      ++    
Sbjct: 47  PLEIMIKFNRLNRLTTDFNVIVEALS-KSKAELMEISEDKTKIRRSPSKPLPEVTDEYKN 105

Query: 112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAE 171
           + + ++++I           +       GQV+N+++ R       +G  FV F S  +A+
Sbjct: 106 DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAK 164

Query: 172 KVLQSYS 178
           K +++  
Sbjct: 165 KFVETPG 171

>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 = 50.8 bits (121), Expect = 5e-08
 Identities = 16/96 (16%), Positives = 30/96 (31%), Gaps = 9/96 (9%)

Query: 308 GPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQF---GEILSVKIPVG-- 362
             G    R              + +  L    S ED++   S          V       
Sbjct: 25  TGGQQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE 84

Query: 363 ---KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRL 395
               G  FV+  +  D ++AL+K    ++G + + +
Sbjct: 85  GRQSGEAFVELGSEDDVKMALKK-DRESMGHRYIEV 119

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 45.0 bits (106), Expect = 4e-06
 Identities = 14/94 (14%), Positives = 27/94 (28%), Gaps = 2/94 (2%)

Query: 197 SGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSS-KYPSVKGAKVIIDSNTGRTKGYGF 255
                  E      + +  L    +   +Q   S             I +  GR  G  F
Sbjct: 33  GSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAF 92

Query: 256 VRFGDENERSRAMTEMNGVYCSSRPMRIDVATPK 289
           V  G E++   A+ + +      R + +  +   
Sbjct: 93  VELGSEDDVKMAL-KKDRESMGHRYIEVFKSHRT 125

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 48.8 bits (116), Expect = 8e-08
 Identities = 21/91 (23%), Positives = 40/91 (43%), Gaps = 7/91 (7%)

Query: 321 SDGESNNATIFVGALDSDVSDEDLREP----FSQFGEILSVKIPV---GKGCGFVQFANR 373
           S    N A + V  +D  +S ++L++     F++ G++ SV++      +    VQ  N 
Sbjct: 3   SGSSGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENL 62

Query: 374 KDAEVALQKLQGTAIGKQTVRLSWGRNPGNK 404
           +DA  A+  L    IG + + +S        
Sbjct: 63  QDAIGAVNSLHRYKIGSKKILVSLATGASGP 93

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A Length = 164

 Score = 49.7 bits (118), Expect = 2e-07
 Identities = 29/132 (21%), Positives = 48/132 (36%), Gaps = 12/132 (9%)

Query: 274 VYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVG 333
           ++          A     S    Q  + AL       S  A   G    G+S    I V 
Sbjct: 1   MHHHHHHGSAQAALQAVNS---VQSGNLAL-----AASAAAVDAGMAMAGQSPVLRIIVE 52

Query: 334 ALDSDVSDEDLREPFSQFGEILSVKIPV--GKGCGFVQFANRKDAEVALQKLQGTAI--G 389
            L   V+ + L + FS+FG +L +       +    +Q+A+   A+ A   L G  I   
Sbjct: 53  NLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNA 112

Query: 390 KQTVRLSWGRNP 401
             T+R+ + +  
Sbjct: 113 CCTLRIDFSKLT 124

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A Length = 164

 Score = 42.8 bits (100), Expect = 5e-05
 Identities = 17/113 (15%), Positives = 36/113 (31%), Gaps = 10/113 (8%)

Query: 82  YQNGGGVKQQQQQQHGLSNGKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQ 141
               G +          +     G +          I + +LF+ +    LH  FS  G 
Sbjct: 19  SVQSGNLALAASAAAVDAGMAMAGQSP------VLRIIVENLFYPVTLDVLHQIFSKFGT 72

Query: 142 VVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWA 194
           V+ +         Q      +++    +A+    S  G  + N     R++++
Sbjct: 73  VLKIITFTKNNQFQ----ALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS 121

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A Length = 164

 Score = 41.6 bits (97), Expect = 1e-04
 Identities = 23/125 (18%), Positives = 45/125 (36%), Gaps = 9/125 (7%)

Query: 168 AAAEKVLQSYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQE 227
            +A+  LQ+ +     + +     + A              L I V +L   VT  +L +
Sbjct: 8   GSAQAALQAVNSV--QSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQ 65

Query: 228 TFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNG--VYCSSRPMRIDV 285
            F SK+ +V        +N         +++ D      A   ++G  +Y +   +RID 
Sbjct: 66  IF-SKFGTVLKIITFTKNNQ----FQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF 120

Query: 286 ATPKK 290
           +    
Sbjct: 121 SKLTS 125

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 48.4 bits (115), Expect = 2e-07
 Identities = 22/77 (28%), Positives = 28/77 (36%), Gaps = 11/77 (14%)

Query: 321 SDGESNNATIFVGALDSDVSDEDLREPF-----SQFGEILSVKIPVGKGCGFVQFANRKD 375
           S G S    + V  L   V DE L   F     S  G +LS +       G + F    D
Sbjct: 2   SSGSSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLGCG--GVLTFREPAD 59

Query: 376 AEVALQK----LQGTAI 388
           AE  L +    L G  +
Sbjct: 60  AERVLAQADHELHGAQL 76

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 39.9 bits (93), Expect = 1e-04
 Identities = 19/82 (23%), Positives = 35/82 (42%), Gaps = 8/82 (9%)

Query: 203 TEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDEN 262
           + +   +++ V  L P V D +L   F ++  S  G  V+   +  R    G + F +  
Sbjct: 3   SGSSGGVAVEVRGLPPAVPDELLTLYFENRRRS-GGGPVL---SWQRLGCGGVLTFREPA 58

Query: 263 ERSRAMT----EMNGVYCSSRP 280
           +  R +     E++G   S RP
Sbjct: 59  DAERVLAQADHELHGAQLSLRP 80

>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 = 45.4 bits (108), Expect = 2e-06
 Identities = 9/46 (19%), Positives = 21/46 (45%), Gaps = 2/46 (4%)

Query: 342 EDLREPFSQFGEILSVKIPVGKGCG--FVQFANRKDAEVALQKLQG 385
           +D+ E  ++ G ++ + +      G  +V+  +   A  A+  L G
Sbjct: 32  DDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHG 77

>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 = 44.2 bits (104), Expect = 6e-06
 Identities = 17/84 (20%), Positives = 30/84 (35%), Gaps = 2/84 (2%)

Query: 306 AGGPGSNGARVQGSQSDGESNNATIFVGAL-DSDVSDEDLREPFSQFGEILSVKIPVGKG 364
           + G    G   Q      E     I +  L  S  SD  + +    +G+I +  +   K 
Sbjct: 5   SSGKKPEGKPDQKFDQKQELGR-VIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKS 63

Query: 365 CGFVQFANRKDAEVALQKLQGTAI 388
             F++   R+DA   +      A+
Sbjct: 64  QAFIEMETREDAMAMVDHCLKKAL 87

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 43.2 bits (101), Expect = 9e-06
 Identities = 18/67 (26%), Positives = 31/67 (46%), Gaps = 3/67 (4%)

Query: 340 SDEDLREPFSQFGEILSVKIPVGK-GCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWG 398
           S + L     ++GE+L++ +   K G   V+FA  K AE+A+Q   G       +++SW 
Sbjct: 30  SKDVLLRLLQKYGEVLNLVLSSKKPGTAVVEFATVKAAELAVQNEVGLVDNP--LKISWL 87

Query: 399 RNPGNKQ 405
                  
Sbjct: 88  EGQPQDA 94

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 39.0 bits (90), Expect = 3e-04
 Identities = 18/79 (22%), Positives = 30/79 (37%), Gaps = 9/79 (11%)

Query: 127 MDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTD 186
             +  L       G+V+N+ +   K      G   VEF +  AAE  +Q+  G      D
Sbjct: 29  YSKDVLLRLLQKYGEVLNLVLSSKK-----PGTAVVEFATVKAAELAVQNEVG----LVD 79

Query: 187 QPFRLNWATFSGSDRRTEA 205
            P +++W      D    +
Sbjct: 80  NPLKISWLEGQPQDASGPS 98

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 43.1 bits (101), Expect = 2e-05
 Identities = 18/102 (17%), Positives = 38/102 (37%), Gaps = 7/102 (6%)

Query: 307 GGPGSNGARVQGSQSDGESNNAT----IFVGALDSDVSDEDLREPFSQFGEIL-SVKIPV 361
           G  GS+G R+    +  + +       + +      ++ + L    +  G++   V    
Sbjct: 1   GSSGSSGKRITRPGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR 60

Query: 362 GKGCGFVQFANRKDAEVALQKLQGTAI--GKQTVRLSWGRNP 401
                 V+F +   A+ A   L G  I  G  T+++ + R  
Sbjct: 61  NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPT 102

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 39.3 bits (91), Expect = 4e-04
 Identities = 16/100 (16%), Positives = 39/100 (39%), Gaps = 9/100 (9%)

Query: 99  SNGKQ--NGSNNNFTNDETKTIWIG--DLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTG 154
           S+GK+     N +  +   K + +   +  + +    L+   +  G+V  + + +     
Sbjct: 5   SSGKRITRPGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGI- 63

Query: 155 QSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWA 194
                  VEF S   A+K   + +G+ +       ++ +A
Sbjct: 64  ----QAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYA 99

>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 = 42.5 bits (100), Expect = 2e-05
 Identities = 17/52 (32%), Positives = 28/52 (53%), Gaps = 8/52 (15%)

Query: 342 EDLREPFSQFGEILSVKIPVGK--------GCGFVQFANRKDAEVALQKLQG 385
           ED+R+  S++G + S++IP           G  FV+F +  D + A+Q L G
Sbjct: 30  EDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG 81

>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* Length = 345

 Score = 44.8 bits (105), Expect = 4e-05
 Identities = 15/77 (19%), Positives = 31/77 (40%), Gaps = 4/77 (5%)

Query: 325 SNNAT--IFV--GALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVAL 380
            + AT  + V  G L + VS   L     + G + ++ +P  K   F ++   ++++ A 
Sbjct: 14  VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAY 73

Query: 381 QKLQGTAIGKQTVRLSW 397
             L G  +     +   
Sbjct: 74  VTLNGKEVVDDLGQKIT 90

>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 = 41.2 bits (97), Expect = 6e-05
 Identities = 15/46 (32%), Positives = 24/46 (52%), Gaps = 2/46 (4%)

Query: 342 EDLREPFSQFGEILSVKIPVG--KGCGFVQFANRKDAEVALQKLQG 385
           EDLR   S+FG+I  + +      G   V F + ++A+  +Q L G
Sbjct: 41  EDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDG 86

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 44.4 bits (104), Expect = 7e-05
 Identities = 13/83 (15%), Positives = 18/83 (21%)

Query: 13 AAAAAAVSGGAGGGSQPTPQQPYHWVPPHQQQWMAMMQYPAAAMAMMQQQQMMMYPHHYM 72
            A       A    QP    P          +  M   P  A+  M QQQ +      +
Sbjct: 10 PQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQL 69

Query: 73 PYGGGGHPYYQNGGGVKQQQQQQ 95
                     N   +       
Sbjct: 70 HQQIDQATTSMNDMHLHNVPLVD 92

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 42.9 bits (100), Expect = 2e-04
 Identities = 14/108 (12%), Positives = 20/108 (18%)

Query: 2   QQSNGGDANAAAAAAAAVSGGAGGGSQPTPQQPYHWVPPHQQQWMAMMQYPAAAMAMMQQ 61
           Q       NA      A        +          +PP         Q           
Sbjct: 11  QAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLH 70

Query: 62  QQMMMYPHHYMPYGGGGHPYYQNGGGVKQQQQQQHGLSNGKQNGSNNN 109
           QQ+               P       ++ Q   Q G    +Q      
Sbjct: 71  QQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAA 118

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 41.7 bits (97), Expect = 4e-04
 Identities = 17/120 (14%), Positives = 23/120 (19%), Gaps = 5/120 (4%)

Query: 1   MQQSNGGDANAAAAAAAAVSGGAGGGSQPTPQQPYHWVPPHQQQWMAMMQYPAAAMAMMQ 60
           M     G     A  +           +   QQ            M +   P        
Sbjct: 40  MSYGQMGMPPQGAVPSMGQQQFLTPAQEQLHQQIDQ--ATTSMNDMHLHNVPLVDPNAYM 97

Query: 61  QQQ---MMMYPHHYMPYGGGGHPYYQNGGGVKQQQQQQHGLSNGKQNGSNNNFTNDETKT 117
           Q Q    M  P            Y Q    + Q  +  + L              D T  
Sbjct: 98  QPQVPVQMGTPLQQQQQPMAAPAYGQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLP 157

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} PDB: 3us5_A 2dny_A Length = 118

 Score = 40.9 bits (96), Expect = 8e-05
 Identities = 14/61 (22%), Positives = 25/61 (40%), Gaps = 11/61 (18%)

Query: 335 LDSDVSDEDLREPFSQFGEILSVKIPV----------GKGCGFVQFANRKDAEVALQKLQ 384
           +D D+ + ++ E   +FG +  V I                 FV+F+   +   A+Q L 
Sbjct: 34  IDDDL-EGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALN 92

Query: 385 G 385
           G
Sbjct: 93  G 93

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster} Length = 89

 Score = 39.7 bits (92), Expect = 1e-04
 Identities = 12/71 (16%), Positives = 28/71 (39%)

Query: 323 GESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQK 382
               ++ + +  L + +    LR    Q G ++S    + +G    ++  R++A  A   
Sbjct: 3   MAWGSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLNQGIALCKYTTREEANKAQMA 62

Query: 383 LQGTAIGKQTV 393
           L    +   T+
Sbjct: 63  LNNCVLANTTI 73

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 102

 Score = 38.3 bits (89), Expect = 5e-04
 Identities = 17/94 (18%), Positives = 33/94 (35%), Gaps = 9/94 (9%)

Query: 307 GGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDE-DLREPFSQFGEILSVKIPVGKGC 365
           G  GS+G + +            + +       +    L +    FG I +  I      
Sbjct: 1   GSSGSSGQKGRVETR------RVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINE 54

Query: 366 GFVQFANRKDAEVALQKLQGTA--IGKQTVRLSW 397
            F++ A  +DA+ A+     T   +  + VR+  
Sbjct: 55  AFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHL 88

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	449
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	100.0
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	100.0
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	100.0
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	100.0
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	100.0
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	100.0
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	100.0
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	100.0
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	100.0
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.98
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.98
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.98
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.97
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.97
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.97
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.97
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.97
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.97
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.97
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.97
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.97
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.96
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.96
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.96
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.96
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.96
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.96
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.96
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.96
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.96
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.96
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.96
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.96
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.96
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.95
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.95
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.88
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.86
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.86
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.84
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.82
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.82
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.8
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.8
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.79
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.78
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.77
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.77
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.77
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.77
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.76
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.76
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.76
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.76
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.76
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.75
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.75
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.75
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.75
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.75
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.74
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.74
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.74
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.74
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.74
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.74
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.74
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.74
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.74
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.74
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.73
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.73
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.73
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.73
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.73
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.73
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.73
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.73
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.73
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.73
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.73
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.73
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.73
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.73
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.73
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.73
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.72
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.72
2div_A	99	TRNA selenocysteine associated protein; structural	99.72
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.72
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.72
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.72
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.72
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.72
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.72
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.72
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.72
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.72
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.72
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.72
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.72
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.72
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.72
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.72
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.72
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.72
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.72
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.72
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.72
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.72
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.72
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.72
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.72
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.72
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.71
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.71
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.71
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.71
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.71
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.71
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.71
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.71
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.71
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.71
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.71
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.71
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.71
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.71
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.71
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.71
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.71
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.71
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.71
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.71
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.7
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.7
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.7
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.7
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.7
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.7
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.7
1x5p_A	97	Negative elongation factor E; structure genomics,	99.7
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.7
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.7
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.7
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.7
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.7
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.7
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.7
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.7
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.7
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.7
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.7
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.69
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.69
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.69
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.69
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.69
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.69
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.69
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.69
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.69
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.69
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.69
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.69
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.69
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.69
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.69
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.69
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.69
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.69
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.69
2div_A	99	TRNA selenocysteine associated protein; structural	99.69
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.68
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.68
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.68
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.68
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.68
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.68
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.68
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.68
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.68
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.68
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.68
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.68
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.68
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.68
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.68
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.68
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.68
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.68
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.68
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.68
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.67
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.67
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.67
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.67
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.67
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.67
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.67
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.67
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.67
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.67
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.67
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.67
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.67
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.67
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.67
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.67
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.67
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.67
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.67
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.66
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.66
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.66
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.66
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.66
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.66
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.66
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.66
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.66
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.66
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.66
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.66
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.66
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.66
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.66
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.65
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.65
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.65
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.65
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.65
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.65
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.65
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.65
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.65
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.65
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.65
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.65
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.65
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.64
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.64
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.64
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.64
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.64
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.64
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.64
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.64
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.64
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.64
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.64
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.64
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.64
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.64
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.64
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.64
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.64
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.64
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.64
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.64
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.64
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.64
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.63
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.63
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.63
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.63
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.63
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.63
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.63
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.63
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.63
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.63
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.43
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.63
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.63
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.62
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.62
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.62
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.62
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.62
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.62
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.62
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.61
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.61
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.61
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.61
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.61
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.61
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.61
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.61
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.61
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.6
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.6
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.6
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.6
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.6
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.6
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.6
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.6
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.6
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.6
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.59
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.59
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.59
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.59
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.59
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.59
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.58
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.37
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.58
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.58
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.58
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.58
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.58
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.58
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.58
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.58
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.58
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.58
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.58
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.57
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.57
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.57
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.57
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.57
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.57
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.56
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.56
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.56
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.56
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.56
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.55
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.55
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.55
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.55
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.55
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.55
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.55
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.55
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.55
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.54
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.54
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.54
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.54
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.54
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.53
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.52
1x5p_A	97	Negative elongation factor E; structure genomics,	99.51
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.5
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.5
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.49
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.48
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.47
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.47
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.47
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.46
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.45
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.44
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.43
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.41
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.39
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.37
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.36
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.34
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.34
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.34
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.32
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.3
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.29
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.29
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.29
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.27
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.21
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.12
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	99.04
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.97
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.9
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.82
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.78
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.64
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.59
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.37
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	98.05
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.02
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.85
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.61
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.54
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.53
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.38
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.24
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.17
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	97.12
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	96.75
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.72
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.72
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.7
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	96.18
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.15
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	96.07
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	89.48
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	87.57
4eyt_A	129	Telomerase associated protein P65; RNA, LA protein	81.84
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	81.25

>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=1.3e-44  Score=339.46  Aligned_cols=241  Identities=19%  Similarity=0.312  Sum_probs=218.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      ..+++|||+|||+++|+++|+++|+.|| |.+|.+      ++++|||||+|.+.++|.+|++.|++..+.  ++.+++.
T Consensus        20 ~~~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~------~~~~g~afV~f~~~~~A~~A~~~l~~~~~~--g~~i~v~   90 (284)
T 3smz_A           20 RNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINAFHQSRLR--ERELSVQ   90 (284)
T ss_dssp             HCCCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTCEET--TEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEE------ecCCCEEEEEeCCHHHHHHHHHHcCCCeeC--CeEEEEE
Confidence            3678999999999999999999999999 999888      456789999999999999999999999985  4677777


Q ss_pred             ccccCCCCCccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC
Q 013141          193 WATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMN  272 (449)
Q Consensus       193 ~~~~~~~~~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~  272 (449)
                      ++.           ..++|||+|||+++|+++|+++|+ .||.|..+.++.+..++.++|+|||+|.+.++|.+|++.|+
T Consensus        91 ~~~-----------~~~~l~v~nlp~~~t~~~l~~~f~-~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~  158 (284)
T 3smz_A           91 LQP-----------TDALLCVANLPPSLTQQQFEELVR-PFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLL  158 (284)
T ss_dssp             ECC-----------CSCEEEEESCCTTCCHHHHHHHHG-GGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHT
T ss_pred             ecC-----------CCCEEEEcCCCCcCCHHHHHHHHH-hcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhC
Confidence            643           457999999999999999999995 99999999999999899999999999999999999999999


Q ss_pred             CceecCcceEEeecCCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCC-CHhHHHhhcccc
Q 013141          273 GVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDV-SDEDLREPFSQF  351 (449)
Q Consensus       273 g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~-t~~~L~~~f~~~  351 (449)
                      +..+.|+.|.|.++.++...                             ......++|||+|||.++ ++++|+++|+.|
T Consensus       159 ~~~~~g~~i~v~~a~~~~~~-----------------------------~~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~  209 (284)
T 3smz_A          159 GKPLGPRTLYVHWTDAGQLT-----------------------------PALLHSRCLCVDRLPPGFNDVDALCRALSAV  209 (284)
T ss_dssp             TCEETTEECEEEECCGGGCC-----------------------------TTTTSCSEEEEECCCTTCCCHHHHHHHTCSS
T ss_pred             CCEeCCcEEEEEECCCCCCC-----------------------------cccCCccEEEEecCCcccCCHHHHHHHhhCC
Confidence            99999999999999775432                             122457899999999995 999999999999


Q ss_pred             CceEEEEEeCC-----CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCCC
Q 013141          352 GEILSVKIPVG-----KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGN  403 (449)
Q Consensus       352 G~v~~v~i~~~-----~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~~  403 (449)
                      |.|.+|.|+++     +++|||+|.+.++|.+|++.|||..|+|+.|+|.|+++...
T Consensus       210 G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~  266 (284)
T 3smz_A          210 HSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPP  266 (284)
T ss_dssp             SCCSEEEEEECSSCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCSSSC
T ss_pred             CCeEEEEEEECCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEEecCCCc
Confidence            99999999875     78999999999999999999999999999999999987653

>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=1.6e-43  Score=333.59  Aligned_cols=247  Identities=17%  Similarity=0.352  Sum_probs=208.6

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcc
Q 013141          110 FTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPF  189 (449)
Q Consensus       110 ~~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~  189 (449)
                      ......++|||+|||+++|+++|+++|+.||.|.+|++++++.  .++|||||+|.+.++|.+|+ .+++..+.  ++.+
T Consensus        36 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~~~g~afV~f~~~~~A~~A~-~~~~~~~~--g~~i  110 (292)
T 2ghp_A           36 TRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK--KNFRFARIEFARYDGALAAI-TKTHKVVG--QNEI  110 (292)
T ss_dssp             ------CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT--SSSEEEEEEESSHHHHHHHH-TTTTCEET--TEEC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCC--CCcEEEEEEECCHHHHHHHH-HhCCcEeC--CcEE
Confidence            3456789999999999999999999999999999999999864  35799999999999999999 48998884  4667


Q ss_pred             cccccccCCCCCccccCCCceEEEcCCCCCCCHHHHHHHHhhhCC-CeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH
Q 013141          190 RLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYP-SVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAM  268 (449)
Q Consensus       190 ~~~~~~~~~~~~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g-~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~  268 (449)
                      .+.++            ..++|||+|||.++++++|+++|+ .|| .|..+.++.+.. +.++|||||+|.+.++|.+|+
T Consensus       111 ~v~~~------------~~~~l~v~nlp~~~t~~~l~~~f~-~~G~~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~  176 (292)
T 2ghp_A          111 IVSHL------------TECTLWMTNFPPSYTQRNIRDLLQ-DINVVALSIRLPSLRF-NTSRRFAYIDVTSKEDARYCV  176 (292)
T ss_dssp             EEEEC------------CSCEEEEECCCTTCCHHHHHHHHH-HTTCCCCEEECC--------CCEEEEECSSHHHHHHHH
T ss_pred             EEEEC------------CCCEEEEECCCCCCCHHHHHHHHH-HhCCCeEEEEEEeCCC-CCcceEEEEEECCHHHHHHHH
Confidence            76654            467999999999999999999995 999 999999998865 788999999999999999999


Q ss_pred             HHhCCceecCcceEEeecCCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCC-CCHhHHHhh
Q 013141          269 TEMNGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSD-VSDEDLREP  347 (449)
Q Consensus       269 ~~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~-~t~~~L~~~  347 (449)
                      +.|++..+.|+.|.|.++.+.......                         .......++|||+|||.. +++++|+++
T Consensus       177 ~~l~g~~~~g~~l~v~~a~~~~~~~~~-------------------------~~~~~~~~~l~v~nlp~~~~t~~~l~~~  231 (292)
T 2ghp_A          177 EKLNGLKIEGYTLVTKVSNPLEKSKRT-------------------------DSATLEGREIMIRNLSTELLDENLLRES  231 (292)
T ss_dssp             HHHTTCEETTEECEEEECCCC----------------------------------CCTTTEEEEEEECTTTCCHHHHHHH
T ss_pred             HHhCCCEeCCcEEEEEECCCCcccccc-------------------------cccCCCCceEEEECCCcccCCHHHHHHH
Confidence            999999999999999999876543110                         123456789999999999 999999999


Q ss_pred             ccccCceEEEEEeCC-------CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCC
Q 013141          348 FSQFGEILSVKIPVG-------KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNP  401 (449)
Q Consensus       348 f~~~G~v~~v~i~~~-------~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~  401 (449)
                      |+.||.|.+|.|+++       +|+|||+|.+.++|.+|+ .|||..|+|+.|+|.|++++
T Consensus       232 F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V~~a~~k  291 (292)
T 2ghp_A          232 FEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVSLADKK  291 (292)
T ss_dssp             HGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEEEECCCC
T ss_pred             HhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEEEEecCC
Confidence            999999999999763       589999999999999999 99999999999999999875

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=100.00  E-value=1.3e-33  Score=252.88  Aligned_cols=171  Identities=27%  Similarity=0.510  Sum_probs=151.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      .+.++|||+|||+++|+++|+++|++||.|++|+|++|+.+++++|||||+|.+.++|.+|++.+++..+.  ++.+++.
T Consensus        13 ~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~--g~~i~~~   90 (213)
T 4f02_A           13 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIK--GKPVRIM   90 (213)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEET--TEECEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcC--Ccccccc
Confidence            46789999999999999999999999999999999999999999999999999999999999999999884  4666766


Q ss_pred             ccccCCCCCccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC
Q 013141          193 WATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMN  272 (449)
Q Consensus       193 ~~~~~~~~~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~  272 (449)
                      ++....   ........+|||+|||+++|+++|+++|+ .||.|..+.++++.  +.++|||||+|.+.++|.+|++.||
T Consensus        91 ~~~~~~---~~~~~~~~~l~v~nl~~~~t~~~l~~~F~-~~G~i~~~~i~~d~--~~~~g~~fV~f~~~~~a~~Ai~~ln  164 (213)
T 4f02_A           91 WSQRDP---SLRKSGVGNIFIKNLDKSIDNKALYDTFS-AFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMN  164 (213)
T ss_dssp             ECCCCT---HHHHHCTTEEEEESCCTTCCHHHHHHHHG-GGSCEEEEEEEEET--TEEEEEEEEEESSHHHHHHHHHHHT
T ss_pred             cccccc---cccccccccceECCcccccHHHHHHHHHh-hcCCeEEEEeeccC--CCCceEEEEEeCCHHHHHHHHHHhC
Confidence            664322   22233456899999999999999999995 99999999999985  4579999999999999999999999


Q ss_pred             CceecCcceEEeecCCCCC
Q 013141          273 GVYCSSRPMRIDVATPKKA  291 (449)
Q Consensus       273 g~~~~g~~i~v~~~~~~~~  291 (449)
                      |..|+|+.|+|.++.++..
T Consensus       165 g~~~~g~~i~V~~a~~~~~  183 (213)
T 4f02_A          165 GMLLNDRKVFVGRFKSRKE  183 (213)
T ss_dssp             TCEETTEECEEEECCCHHH
T ss_pred             CCEECCEEEEEEEcCCCcc
Confidence            9999999999999987643

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=100.00  E-value=1.3e-32  Score=246.39  Aligned_cols=167  Identities=32%  Similarity=0.520  Sum_probs=150.7

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEe
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRID  284 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  284 (449)
                      ..+.++|||+|||+++|+++|+++|+ .||+|.+|++++|+.+++++|||||+|.+.++|.+|++.+++..+.|+.|++.
T Consensus        12 ~~p~~tlfVgnLp~~~te~~L~~~F~-~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~   90 (213)
T 4f02_A           12 SYPMASLYVGDLHPDVTEAMLYEKFS-PAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIM   90 (213)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHG-GGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHH-hhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccc
Confidence            34668999999999999999999995 99999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC--
Q 013141          285 VATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG--  362 (449)
Q Consensus       285 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~--  362 (449)
                      ++.......                              .....+|||+|||+++++++|+++|+.||.|.+|+|+++  
T Consensus        91 ~~~~~~~~~------------------------------~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~  140 (213)
T 4f02_A           91 WSQRDPSLR------------------------------KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN  140 (213)
T ss_dssp             ECCCCTHHH------------------------------HHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETT
T ss_pred             ccccccccc------------------------------ccccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCC
Confidence            987654321                              112468999999999999999999999999999999863  


Q ss_pred             --CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCC
Q 013141          363 --KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPG  402 (449)
Q Consensus       363 --~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~  402 (449)
                        +|+|||+|.+.++|.+|++.|||..|+|+.|+|.|++++.
T Consensus       141 ~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~~~  182 (213)
T 4f02_A          141 GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK  182 (213)
T ss_dssp             EEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCHH
T ss_pred             CCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCCCc
Confidence              6899999999999999999999999999999999998753

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=100.00  E-value=4e-32  Score=240.13  Aligned_cols=177  Identities=18%  Similarity=0.366  Sum_probs=149.3

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      .....++|||+|||+++|+++|+++|+.||.|.+|++++++.+++++|||||+|.+.++|.+||+. ++..+.  ++.+.
T Consensus         9 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~--g~~l~   85 (196)
T 1l3k_A            9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVD--GRVVE   85 (196)
T ss_dssp             CCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEET--TEECE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEEC--CEEee
Confidence            456789999999999999999999999999999999999999999999999999999999999965 777774  46677


Q ss_pred             ccccccCCCCC-ccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH
Q 013141          191 LNWATFSGSDR-RTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT  269 (449)
Q Consensus       191 ~~~~~~~~~~~-~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~  269 (449)
                      +.++....... .......++|||+|||.++|+++|+++|+ .||.|..+.++.+..++.++|||||+|.+.++|.+|++
T Consensus        86 v~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~-~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~  164 (196)
T 1l3k_A           86 PKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFE-QYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI  164 (196)
T ss_dssp             EEECCC-----------CCSEEEEECCTTTCCHHHHHHHHT-TTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH
T ss_pred             eecccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHh-cCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHH
Confidence            77765443222 22334568999999999999999999995 99999999999998899999999999999999999997


Q ss_pred             HhCCceecCcceEEeecCCCCCC
Q 013141          270 EMNGVYCSSRPMRIDVATPKKAS  292 (449)
Q Consensus       270 ~l~g~~~~g~~i~v~~~~~~~~~  292 (449)
                      . ++..|.|+.|.|.++.++...
T Consensus       165 ~-~~~~~~G~~i~v~~a~~k~~~  186 (196)
T 1l3k_A          165 Q-KYHTVNGHNCEVRKALSKQEM  186 (196)
T ss_dssp             C-SCCEETTEECEEEECC-----
T ss_pred             h-CCcEECCEEEEEEecCChhHh
Confidence            5 899999999999999988654

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=100.00  E-value=6.1e-32  Score=232.26  Aligned_cols=166  Identities=31%  Similarity=0.604  Sum_probs=151.1

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccccccc
Q 013141          116 KTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWAT  195 (449)
Q Consensus       116 ~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~~~  195 (449)
                      |+|||+|||+++|+++|+++|+.||.|.+|++++++ +++++|||||+|.+.++|.+|++.+++..+.  ++.+++.++.
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~--g~~i~v~~~~   77 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTLNGKQIE--NNIVKINWAF   77 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCC-C-CCEEEEEEEESSHHHHHHHHHHHTTCEET--TEECEEEECC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECC-CCCCCCEEEEEeCCHHHHHHHHHHcCCCccC--CCeeEEEEcC
Confidence            689999999999999999999999999999999997 4789999999999999999999999999984  5677777776


Q ss_pred             cCCCCCccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCce
Q 013141          196 FSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVY  275 (449)
Q Consensus       196 ~~~~~~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~  275 (449)
                      ....   ....+.++|||+|||.++++++|+++|+ .||.|..+.++++..++.++|+|||+|.+.++|.+|++.|++..
T Consensus        78 ~~~~---~~~~~~~~l~v~nl~~~~t~~~l~~~f~-~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~  153 (166)
T 3md3_A           78 QSQQ---SSSDDTFNLFVGDLNVNVDDETLRNAFK-DFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQD  153 (166)
T ss_dssp             CCCC---CCCTTCEEEEEESCCTTCCHHHHHHHHT-TSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCE
T ss_pred             CCCC---CCCCCCceEEECCCCCCCCHHHHHHHHh-ccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCc
Confidence            4432   3345678999999999999999999995 99999999999999999999999999999999999999999999


Q ss_pred             ecCcceEEeecCC
Q 013141          276 CSSRPMRIDVATP  288 (449)
Q Consensus       276 ~~g~~i~v~~~~~  288 (449)
                      +.|+.|+|.+++.
T Consensus       154 ~~g~~i~v~~a~~  166 (166)
T 3md3_A          154 LNGRPLRINWAAK  166 (166)
T ss_dssp             ETTEECEEEESCC
T ss_pred             cCCcEEEEEecCC
Confidence            9999999999863

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=100.00  E-value=6e-32  Score=242.85  Aligned_cols=176  Identities=20%  Similarity=0.392  Sum_probs=154.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      ...++|||+|||+++|+++|+++|+.||.|.+|++++++.+++++|||||+|.+.++|.+|++.|++..+.  ++.|++.
T Consensus        26 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~--g~~l~v~  103 (216)
T 2qfj_A           26 AIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLG--GRNIKVG  103 (216)
T ss_dssp             HHHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC---CCCEEE
T ss_pred             CcCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeC--CeeEEEe
Confidence            35789999999999999999999999999999999999889999999999999999999999999999885  4667776


Q ss_pred             ccccCCCCCc------cccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHH
Q 013141          193 WATFSGSDRR------TEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSR  266 (449)
Q Consensus       193 ~~~~~~~~~~------~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~  266 (449)
                      ++........      ......++|||+|||.++++++|+++|+ .||.|..+.++++..+++++|+|||+|.+.++|.+
T Consensus       104 ~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~-~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~  182 (216)
T 2qfj_A          104 RPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFE-AFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQD  182 (216)
T ss_dssp             CCSCCGGGHHHHHHHHHHHTTSCEEEEECCCTTCCHHHHHHHHT-TSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHH
T ss_pred             cCCCccccchhhhhhhcccCCCcEEEEeCCCCcCCHHHHHHHHh-ccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHH
Confidence            6543321111      1235668999999999999999999995 99999999999998899999999999999999999


Q ss_pred             HHHHhCCceecCcceEEeecCCCCC
Q 013141          267 AMTEMNGVYCSSRPMRIDVATPKKA  291 (449)
Q Consensus       267 A~~~l~g~~~~g~~i~v~~~~~~~~  291 (449)
                      |++.|++..|.|+.|+|.++.++..
T Consensus       183 A~~~l~g~~~~g~~i~V~~a~~~~~  207 (216)
T 2qfj_A          183 AVSSMNLFDLGGQYLRVGKAVTPPM  207 (216)
T ss_dssp             HHHHHTTCBCSSSBCEEEECSSCSS
T ss_pred             HHHHccCCEeCCcEEEEEEecCCCC
Confidence            9999999999999999999988754

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=100.00  E-value=7.1e-32  Score=232.42  Aligned_cols=165  Identities=26%  Similarity=0.502  Sum_probs=152.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccccc
Q 013141          114 ETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNW  193 (449)
Q Consensus       114 ~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~  193 (449)
                      +.++|||+|||+++++++|+++|+.||.|.+|++++++.+++++|||||+|.+.++|.+|++.|++..+.  ++.+++.|
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~--g~~l~v~~   79 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVR--NKRLKVSY   79 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEET--TEECEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeC--CcEEEEEe
Confidence            4689999999999999999999999999999999999989999999999999999999999999999884  56788888


Q ss_pred             cccCCCCCccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCC
Q 013141          194 ATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNG  273 (449)
Q Consensus       194 ~~~~~~~~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g  273 (449)
                      +....     .....++|||+|||.++++++|+++|+ .||.|..+.++++..++.++|+|||+|.+.++|.+|++.|++
T Consensus        80 ~~~~~-----~~~~~~~l~v~nl~~~~t~~~l~~~f~-~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g  153 (168)
T 1b7f_A           80 ARPGG-----ESIKDTNLYVTNLPRTITDDQLDTIFG-KYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNN  153 (168)
T ss_dssp             CCCCS-----STTTTCEEEEESCCTTCCHHHHHHHHT-SSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTT
T ss_pred             cCCCc-----ccCCCCCEEEeCCCCCCCHHHHHHhhh-cCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcC
Confidence            76443     234568999999999999999999995 999999999999988899999999999999999999999999


Q ss_pred             ceecC--cceEEeec
Q 013141          274 VYCSS--RPMRIDVA  286 (449)
Q Consensus       274 ~~~~g--~~i~v~~~  286 (449)
                      ..+.|  ++|+|+++
T Consensus       154 ~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          154 VIPEGGSQPLSVRLA  168 (168)
T ss_dssp             CCCTTCSSCCEEEEC
T ss_pred             CEecCCCeEEEEEeC
Confidence            99977  99999875

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=100.00  E-value=1.4e-31  Score=230.25  Aligned_cols=164  Identities=27%  Similarity=0.501  Sum_probs=149.9

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccccc
Q 013141          115 TKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWA  194 (449)
Q Consensus       115 ~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~~  194 (449)
                      +++|||+|||+++++++|+++|+.||.|.+|.+++++.+|+++|||||+|.+.++|.+|++.|++..+.  ++.+++.++
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~--g~~l~v~~~   79 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQ--TKTIKVSYA   79 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEET--TEECEEEEC
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccC--CceEEEEec
Confidence            689999999999999999999999999999999999989999999999999999999999999999884  567777777


Q ss_pred             ccCCCCCccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCc
Q 013141          195 TFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGV  274 (449)
Q Consensus       195 ~~~~~~~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~  274 (449)
                      ....     .....++|||+|||.++++++|+++|+ .||.|..+.++.+..++.++|+|||+|.+.++|.+|++.|+|.
T Consensus        80 ~~~~-----~~~~~~~l~v~nl~~~~t~~~l~~~f~-~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~  153 (167)
T 1fxl_A           80 RPSS-----ASIRDANLYVSGLPKTMTQKELEQLFS-QYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQ  153 (167)
T ss_dssp             CCCC-----GGGTTCEEEEESCCTTCCHHHHHHHHG-GGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCc-----ccCCCCcEEECCCCCcCCHHHHHHHHH-hcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCC
Confidence            6432     234567899999999999999999995 9999999999999888999999999999999999999999999


Q ss_pred             eecCcc--eEEeec
Q 013141          275 YCSSRP--MRIDVA  286 (449)
Q Consensus       275 ~~~g~~--i~v~~~  286 (449)
                      .+.|+.  |+|+|+
T Consensus       154 ~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          154 KPSGATEPITVKFA  167 (167)
T ss_dssp             CCTTCSSCCEEEEC
T ss_pred             ccCCCccceEEEeC
Confidence            999975  888775

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.98  E-value=3.8e-31  Score=229.37  Aligned_cols=168  Identities=23%  Similarity=0.436  Sum_probs=149.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCC--CcccEEEEEEccHHHHHHHHHHhcCCCC-CCCCCccc
Q 013141          114 ETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTG--QSEGYGFVEFYSRAAAEKVLQSYSGSLM-PNTDQPFR  190 (449)
Q Consensus       114 ~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g--~~~g~afV~f~~~~~A~~Al~~l~~~~~-~~~~~~~~  190 (449)
                      +.++|||+|||+++|+++|+++|+.||.|.+|++++++.++  +++|||||+|.+.++|.+|++.|++..+ .+..+.+.
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~   81 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQ   81 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceE
Confidence            57899999999999999999999999999999999998876  8999999999999999999999999765 44577777


Q ss_pred             ccccccCCCCCccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHH
Q 013141          191 LNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE  270 (449)
Q Consensus       191 ~~~~~~~~~~~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~  270 (449)
                      +.++.....    .....++|||+|||.++|+++|+++|+ .||.|.++.++++. ++.++|+|||+|.+.++|.+|++.
T Consensus        82 ~~~~~~~~~----~~~~~~~l~v~nl~~~~t~~~l~~~F~-~~G~i~~v~~~~~~-~g~~~g~afV~f~~~~~A~~A~~~  155 (175)
T 3nmr_A           82 MKPADSEKN----NAVEDRKLFIGMISKKCTENDIRVMFS-SFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKA  155 (175)
T ss_dssp             EEECGGGCC----SCGGGSEEEEESCCTTCCHHHHHHHHG-GGSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHH
T ss_pred             Ecccccccc----ccCCCCeEEEcCCCCcCCHHHHHHHHH-hCCCEEEEEEEECC-CCCEEEEEEEEECCHHHHHHHHHH
Confidence            777654432    233567999999999999999999995 99999999999995 589999999999999999999999


Q ss_pred             hCCceec---CcceEEeecC
Q 013141          271 MNGVYCS---SRPMRIDVAT  287 (449)
Q Consensus       271 l~g~~~~---g~~i~v~~~~  287 (449)
                      |||..+.   +++|+|+|++
T Consensus       156 l~g~~~~~g~~~~l~V~~ad  175 (175)
T 3nmr_A          156 MHQAQTMEGCSSPMVVKFAD  175 (175)
T ss_dssp             HTTSCCCTTCSSCCEEEECC
T ss_pred             hcCCcccCCCCCCeEEEecC
Confidence            9998875   4999999874

>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=99.98  E-value=2.4e-31  Score=235.16  Aligned_cols=173  Identities=23%  Similarity=0.406  Sum_probs=146.7

Q ss_pred             cccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceE
Q 013141          203 TEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMR  282 (449)
Q Consensus       203 ~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  282 (449)
                      ......++|||+|||+++|+++|+++|+ .||.|.+|.+++++.++.++|||||+|.+.++|.+|++. ++..+.|+.|.
T Consensus         8 ~~~~~~~~l~V~nLp~~~te~~l~~~F~-~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~   85 (196)
T 1l3k_A            8 KEPEQLRKLFIGGLSFETTDESLRSHFE-QWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVE   85 (196)
T ss_dssp             CCCGGGGEEEEESCCTTCCHHHHHHHHG-GGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHH-hCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEee
Confidence            3445678999999999999999999995 999999999999999999999999999999999999965 89999999999


Q ss_pred             EeecCCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC
Q 013141          283 IDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG  362 (449)
Q Consensus       283 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~  362 (449)
                      |.++.......                          ........++|||+|||.++++++|+++|+.||.|.+|.++.+
T Consensus        86 v~~~~~~~~~~--------------------------~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~  139 (196)
T 1l3k_A           86 PKRAVSREDSQ--------------------------RPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTD  139 (196)
T ss_dssp             EEECCC-------------------------------------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEEC
T ss_pred             eecccCccccc--------------------------ccccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeec
Confidence            99987754321                          0112345689999999999999999999999999999999864


Q ss_pred             ------CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCCCC
Q 013141          363 ------KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNK  404 (449)
Q Consensus       363 ------~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~~~  404 (449)
                            +|+|||+|.+.++|.+|++. ++..|+|+.|.|.|+.++...
T Consensus       140 ~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a~~k~~~  186 (196)
T 1l3k_A          140 RGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQEM  186 (196)
T ss_dssp             TTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEECC-----
T ss_pred             CCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEecCChhHh
Confidence                  58999999999999999986 899999999999999987654

>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=99.98  E-value=4.2e-31  Score=227.57  Aligned_cols=159  Identities=25%  Similarity=0.479  Sum_probs=147.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeec
Q 013141          207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVA  286 (449)
Q Consensus       207 ~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~  286 (449)
                      ++++|||+|||+++++++|+++|+ .||.|.++.+++++.++.++|+|||+|.+.++|.+|++.|++..+.|+.|+|.++
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~-~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~   80 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFR-AIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYA   80 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHH-TTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHH-hcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEec
Confidence            568999999999999999999995 9999999999999889999999999999999999999999999999999999999


Q ss_pred             CCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC----
Q 013141          287 TPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG----  362 (449)
Q Consensus       287 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~----  362 (449)
                      .+...                                ....++|+|+|||..+++++|+++|+.||.|.++.+.++    
T Consensus        81 ~~~~~--------------------------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~  128 (168)
T 1b7f_A           81 RPGGE--------------------------------SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTG  128 (168)
T ss_dssp             CCCSS--------------------------------TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTC
T ss_pred             CCCcc--------------------------------cCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCC
Confidence            76543                                234678999999999999999999999999999999875    


Q ss_pred             --CcEEEEEecCHHHHHHHHHHhcCCeeCC--eEEEEEec
Q 013141          363 --KGCGFVQFANRKDAEVALQKLQGTAIGK--QTVRLSWG  398 (449)
Q Consensus       363 --~g~afV~F~~~~~A~~A~~~l~g~~~~g--~~l~v~~~  398 (449)
                        +++|||+|.+.++|.+|++.|||..|.|  +.|+|+|+
T Consensus       129 ~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          129 RPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             CEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEEeC
Confidence              3899999999999999999999999987  99999986

>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=4.3e-31  Score=237.26  Aligned_cols=177  Identities=20%  Similarity=0.388  Sum_probs=152.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEee
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV  285 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  285 (449)
                      ...++|||+|||.++|+++|+++|+ .||.|.+|.++++..++.++|||||+|.+.++|.+|++.|++..|.|+.|+|.+
T Consensus        26 ~~~~~l~V~nLp~~~t~~~l~~~f~-~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~  104 (216)
T 2qfj_A           26 AIMSRVYVGSIYYELGEDTIRQAFA-PFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGR  104 (216)
T ss_dssp             HHHTEEEEECCCTTCCHHHHHHHHG-GGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEEC
T ss_pred             CcCCEEEEECCCCCCCHHHHHHHHH-hCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEec
Confidence            3467999999999999999999995 999999999999988899999999999999999999999999999999999998


Q ss_pred             cCCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC---
Q 013141          286 ATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG---  362 (449)
Q Consensus       286 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~---  362 (449)
                      +.............                     .......++|||+|||.++++++|+++|+.||.|.+|.|.++   
T Consensus       105 ~~~~~~~~~~~~~~---------------------~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~  163 (216)
T 2qfj_A          105 PSNIGQAQPIIDQL---------------------AEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTT  163 (216)
T ss_dssp             CSCCGGGHHHHHHH---------------------HHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTT
T ss_pred             CCCccccchhhhhh---------------------hcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCC
Confidence            87654321110000                     001234689999999999999999999999999999999875   


Q ss_pred             ---CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCCCC
Q 013141          363 ---KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNK  404 (449)
Q Consensus       363 ---~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~~~  404 (449)
                         +++|||+|.+.++|.+|++.||+..|+|+.|+|.|++++...
T Consensus       164 g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a~~~~~~  208 (216)
T 2qfj_A          164 GKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMP  208 (216)
T ss_dssp             CCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEECSSCSST
T ss_pred             CCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEecCCCCC
Confidence               689999999999999999999999999999999999987544

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.97  E-value=6.6e-31  Score=225.76  Aligned_cols=160  Identities=28%  Similarity=0.562  Sum_probs=146.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecCC
Q 013141          209 LSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATP  288 (449)
Q Consensus       209 ~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~~  288 (449)
                      ++|||+|||.++|+++|+++|+ .||.|.++.+++++. +.++|+|||+|.+.++|.+|++.|++..+.++.|.|.++..
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~-~~G~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~   78 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQ-VGGPIANIKIMIDKN-NKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQ   78 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHG-GGSCEEEEEEECCCC--CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHH-hcCCeEEEEEEECCC-CCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCC
Confidence            4899999999999999999995 999999999999864 77999999999999999999999999999999999999876


Q ss_pred             CCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC------
Q 013141          289 KKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------  362 (449)
Q Consensus       289 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~------  362 (449)
                      ....                              .....++|||+|||..+++++|+++|+.||.|.++.+..+      
T Consensus        79 ~~~~------------------------------~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~  128 (166)
T 3md3_A           79 SQQS------------------------------SSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSS  128 (166)
T ss_dssp             CCCC------------------------------CCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCE
T ss_pred             CCCC------------------------------CCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCc
Confidence            5431                              2345789999999999999999999999999999999854      


Q ss_pred             CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCC
Q 013141          363 KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRN  400 (449)
Q Consensus       363 ~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  400 (449)
                      +|+|||+|.+.++|.+|++.|||..|+|+.|+|.|++.
T Consensus       129 ~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  166 (166)
T 3md3_A          129 RGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK  166 (166)
T ss_dssp             EEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCC
T ss_pred             ceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEecCC
Confidence            58999999999999999999999999999999999873

>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=5.9e-32  Score=232.72  Aligned_cols=165  Identities=26%  Similarity=0.507  Sum_probs=146.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccccc
Q 013141          114 ETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNW  193 (449)
Q Consensus       114 ~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~  193 (449)
                      ++++|||+|||+++|+++|+++|+.||.|.+|++++++.+|+++|||||+|.+.++|.+|++.  +..+  .++.+.+.+
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~--~g~~i~v~~   77 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHIL--DGKVIDPKR   77 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEE--TTEECCCEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--cccc--CCeEccccc
Confidence            578999999999999999999999999999999999998999999999999999999999974  3444  345556655


Q ss_pred             cccCCCCCccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCC
Q 013141          194 ATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNG  273 (449)
Q Consensus       194 ~~~~~~~~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g  273 (449)
                      +...     ......++|||+|||.++++++|+++|+ .||.|..+.++.++.++.++|+|||+|.+.++|.+|++ +++
T Consensus        78 ~~~~-----~~~~~~~~l~V~nlp~~~t~~~l~~~F~-~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~  150 (167)
T 2cjk_A           78 AIPR-----DEQDKTGKIFVGGIGPDVRPKEFEEFFS-QWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKF  150 (167)
T ss_dssp             CCCH-----HHHHHCEEEEEEEECTTCCHHHHHHHHH-TTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSE
T ss_pred             ccch-----hhccCCCeEEECCCCCCCCHHHHHHHHH-hCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCC
Confidence            5422     2233567999999999999999999995 99999999999998899999999999999999999997 899


Q ss_pred             ceecCcceEEeecCCC
Q 013141          274 VYCSSRPMRIDVATPK  289 (449)
Q Consensus       274 ~~~~g~~i~v~~~~~~  289 (449)
                      ..+.|+.|+|.++.++
T Consensus       151 ~~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A          151 IDFKDRKIEIKRAEPR  166 (167)
T ss_dssp             ECSSSSCEEEEECCCC
T ss_pred             EEeCCeEEEEeecCCC
Confidence            9999999999999876

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.97  E-value=7.9e-31  Score=225.51  Aligned_cols=159  Identities=28%  Similarity=0.570  Sum_probs=146.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeec
Q 013141          207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVA  286 (449)
Q Consensus       207 ~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~  286 (449)
                      ++++|||+|||+++++++|+++|+ .||.|.++.+++++.++.++|+|||+|.+.++|.+|++.|++..+.|+.|+|.++
T Consensus         1 s~~~l~v~nlp~~~~~~~l~~~f~-~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~   79 (167)
T 1fxl_A            1 SKTNLIVNYLPQNMTQEEFRSLFG-SIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYA   79 (167)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHH-TTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CcceEEEcCCCCCCCHHHHHHHHH-hcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEec
Confidence            357999999999999999999995 9999999999999889999999999999999999999999999999999999999


Q ss_pred             CCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC----
Q 013141          287 TPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG----  362 (449)
Q Consensus       287 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~----  362 (449)
                      .+....                                ...++|+|+|||..+++++|+++|+.||.|.++.+..+    
T Consensus        80 ~~~~~~--------------------------------~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g  127 (167)
T 1fxl_A           80 RPSSAS--------------------------------IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTG  127 (167)
T ss_dssp             CCCCGG--------------------------------GTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTC
T ss_pred             CCCccc--------------------------------CCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCC
Confidence            765431                                23578999999999999999999999999999999864    


Q ss_pred             --CcEEEEEecCHHHHHHHHHHhcCCeeCCeE--EEEEec
Q 013141          363 --KGCGFVQFANRKDAEVALQKLQGTAIGKQT--VRLSWG  398 (449)
Q Consensus       363 --~g~afV~F~~~~~A~~A~~~l~g~~~~g~~--l~v~~~  398 (449)
                        +++|||+|.+.++|.+|++.|||..|.|+.  |+|+||
T Consensus       128 ~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          128 VSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             CEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEEeC
Confidence              589999999999999999999999999965  888886

>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=4.9e-30  Score=222.36  Aligned_cols=161  Identities=24%  Similarity=0.482  Sum_probs=143.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCC--CcceEEEEEeCCHHHHHHHHHHhCCceec---Ccce
Q 013141          207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTG--RTKGYGFVRFGDENERSRAMTEMNGVYCS---SRPM  281 (449)
Q Consensus       207 ~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~--~~~g~afV~f~~~~~A~~A~~~l~g~~~~---g~~i  281 (449)
                      ..++|||+|||+++|+++|+++|+ .||.|.++.++++..++  +++|||||+|.+.++|.+|++.|++..+.   ++.+
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~-~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~   80 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFE-QYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPI   80 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHH-TTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCC
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHH-hCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccce
Confidence            467999999999999999999995 99999999999998876  89999999999999999999999998875   6777


Q ss_pred             EEeecCCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeC
Q 013141          282 RIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV  361 (449)
Q Consensus       282 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~  361 (449)
                      .+.++......                               ....++|||+|||.++++++|+++|+.||.|.+|.+.+
T Consensus        81 ~~~~~~~~~~~-------------------------------~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~  129 (175)
T 3nmr_A           81 QMKPADSEKNN-------------------------------AVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILR  129 (175)
T ss_dssp             EEEECGGGCCS-------------------------------CGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEE
T ss_pred             EEccccccccc-------------------------------cCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEE
Confidence            77776554321                               23467899999999999999999999999999999987


Q ss_pred             C-----CcEEEEEecCHHHHHHHHHHhcCCeeC---CeEEEEEecC
Q 013141          362 G-----KGCGFVQFANRKDAEVALQKLQGTAIG---KQTVRLSWGR  399 (449)
Q Consensus       362 ~-----~g~afV~F~~~~~A~~A~~~l~g~~~~---g~~l~v~~~~  399 (449)
                      +     +|+|||+|.+.++|.+|++.|||..+.   ++.|+|.|+.
T Consensus       130 ~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~~ad  175 (175)
T 3nmr_A          130 GPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFAD  175 (175)
T ss_dssp             CTTSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEEECC
T ss_pred             CCCCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEEecC
Confidence            5     689999999999999999999998776   4999999984

>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=99.97  E-value=1e-29  Score=230.12  Aligned_cols=192  Identities=22%  Similarity=0.314  Sum_probs=150.5

Q ss_pred             ccCCCceEEEcCCCC-CCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceE
Q 013141          204 EACSDLSIFVGDLAP-DVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMR  282 (449)
Q Consensus       204 ~~~~~~~l~v~~lp~-~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  282 (449)
                      ...++++|||+|||+ ++++++|+++|+ .||.|.+|.++++.     +|||||+|.+.++|++|++.|++..+.|+.|.
T Consensus        30 ~~~~~~~l~V~nLp~~~~te~~L~~~F~-~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~  103 (229)
T 2adc_A           30 AGAGNSVLLVSNLNPERVTPQSLFILFG-VYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIR  103 (229)
T ss_dssp             GCCCCSEEEEESCCTTTCCHHHHHHHHH-HHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCE
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHH-hCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEE
Confidence            345678999999999 999999999995 99999999999874     78999999999999999999999999999999


Q ss_pred             EeecCCCCCCchhhcchhhhh---hhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccC-ceEEEE
Q 013141          283 IDVATPKKASGYQQQYSSQAL---VLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFG-EILSVK  358 (449)
Q Consensus       283 v~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G-~v~~v~  358 (449)
                      |.++.................   ........................++|||+|||..+++++|+++|+.|| .|.+|+
T Consensus       104 v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~  183 (229)
T 2adc_A          104 ITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFK  183 (229)
T ss_dssp             EECCSCCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEE
T ss_pred             EEEecCccccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEE
Confidence            999986532111100000000   0000000000000001112234579999999999999999999999999 999999


Q ss_pred             EeC-CCcEEEEEecCHHHHHHHHHHhcCCeeC-CeEEEEEecCCC
Q 013141          359 IPV-GKGCGFVQFANRKDAEVALQKLQGTAIG-KQTVRLSWGRNP  401 (449)
Q Consensus       359 i~~-~~g~afV~F~~~~~A~~A~~~l~g~~~~-g~~l~v~~~~~~  401 (449)
                      +.. ++++|||+|.+.++|.+|++.|||..|. |+.|+|+|++++
T Consensus       184 i~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          184 FFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             ECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             EEECCCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecCC
Confidence            954 7899999999999999999999999999 999999999864

>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=99.97  E-value=2.2e-29  Score=235.61  Aligned_cols=192  Identities=21%  Similarity=0.358  Sum_probs=149.9

Q ss_pred             cCCCceEEEcCCCCCCCHHHHH----HHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcc
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQ----ETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRP  280 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~----~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~  280 (449)
                      ..++++|||+|||.++|+++|+    ++|+ .||.|.+|++++   +++++|||||+|.+.++|.+|++.|++..|.|+.
T Consensus         6 ~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~-~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   81 (282)
T 3pgw_A            6 TRPNHTIYINNLNEKIKKDELKKSLYAIFS-QFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKP   81 (282)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHh-ccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcE
Confidence            4567899999999999999976    8995 999999999886   5788999999999999999999999999999999


Q ss_pred             eEEeecCCCCCCchhhcch------------------h-hhhhhc-CCCC-----CCCC---------------------
Q 013141          281 MRIDVATPKKASGYQQQYS------------------S-QALVLA-GGPG-----SNGA---------------------  314 (449)
Q Consensus       281 i~v~~~~~~~~~~~~~~~~------------------~-~~~~~~-~~~~-----~~~~---------------------  314 (449)
                      |+|.++.............                  . ...... ....     ....                     
T Consensus        82 l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~  161 (282)
T 3pgw_A           82 MRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQP  161 (282)
T ss_pred             EEEEEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccCCCCC
Confidence            9999997654210000000                  0 000000 0000     0000                     


Q ss_pred             ---------------------------------CcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeC
Q 013141          315 ---------------------------------RVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV  361 (449)
Q Consensus       315 ---------------------------------~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~  361 (449)
                                                       .............++|||+|||..+++++|+++|+.||.|.+|+|.+
T Consensus       162 ~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~  241 (282)
T 3pgw_A          162 PYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVP  241 (282)
T ss_pred             CCCCCCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEec
Confidence                                             00000112334578999999999999999999999999999999998


Q ss_pred             CC-cEEEEEecCHHHHHHHHHHhcCCeeC-CeEEEEEecCC
Q 013141          362 GK-GCGFVQFANRKDAEVALQKLQGTAIG-KQTVRLSWGRN  400 (449)
Q Consensus       362 ~~-g~afV~F~~~~~A~~A~~~l~g~~~~-g~~l~v~~~~~  400 (449)
                      ++ ++|||+|.+.++|.+|++.|||..|. |+.|+|+|+|.
T Consensus       242 ~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~akk  282 (282)
T 3pgw_A          242 GRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK  282 (282)
T ss_pred             CCCcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEecC
Confidence            76 99999999999999999999999999 99999999873

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=99.97  E-value=2e-29  Score=217.99  Aligned_cols=160  Identities=20%  Similarity=0.438  Sum_probs=141.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhcc----C-------CcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCC
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHT----G-------QVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSL  181 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~----G-------~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~  181 (449)
                      ++.++|||+|||+++|+++|+++|+.|    |       .|.++.+.+      ++|||||+|.+.++|.+|+ .+++..
T Consensus         2 r~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~------~~g~afV~f~~~~~A~~A~-~~~~~~   74 (172)
T 2g4b_A            2 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ------DKNFAFLEFRSVDETTQAM-AFDGII   74 (172)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEET------TTTEEEEEESSHHHHHHHG-GGTTCE
T ss_pred             CcccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecC------CCCEEEEEeCCHHHHHHHH-HhCCcE
Confidence            357899999999999999999999999    6       677777654      4689999999999999999 899998


Q ss_pred             CCCCCCcccccccccCCCCCccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCH
Q 013141          182 MPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDE  261 (449)
Q Consensus       182 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~  261 (449)
                      +.  ++.+++.++....     .....++|||+|||.++|+++|+++|+ .||.|..+.+++++.++.++|+|||+|.+.
T Consensus        75 ~~--g~~i~v~~~~~~~-----~~~~~~~l~v~nlp~~~t~~~l~~~f~-~~G~v~~v~i~~~~~~g~~~g~afV~f~~~  146 (172)
T 2g4b_A           75 FQ--GQSLKIRRPHDYQ-----PLPGAHKLFIGGLPNYLNDDQVKELLT-SFGPLKAFNLVKDSATGLSKGYAFCEYVDI  146 (172)
T ss_dssp             ET--TEECEEECCSSCC-----CCTTTTCEEEECCCTTCCHHHHHHHHH-TTSCEEEEEEEECTTTCSEEEEEEEEESST
T ss_pred             ec--CceeeecCCcccC-----CCCCCCEEEEEcCCCcCCHHHHHHHHH-hcCCceEEEEEecCCCCCcceEEEEEeCCH
Confidence            84  5677777665332     223478999999999999999999995 999999999999988999999999999999


Q ss_pred             HHHHHHHHHhCCceecCcceEEeecC
Q 013141          262 NERSRAMTEMNGVYCSSRPMRIDVAT  287 (449)
Q Consensus       262 ~~A~~A~~~l~g~~~~g~~i~v~~~~  287 (449)
                      ++|.+|++.|++..++|+.|+|+++.
T Consensus       147 ~~A~~A~~~l~g~~~~g~~l~V~~As  172 (172)
T 2g4b_A          147 NVTDQAIAGLNGMQLGDKKLLVQRAS  172 (172)
T ss_dssp             THHHHHHHHHTTCEETTEECEEEECC
T ss_pred             HHHHHHHHHcCCCEECCeEEEEEeCC
Confidence            99999999999999999999999873

>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=3e-30  Score=222.00  Aligned_cols=159  Identities=25%  Similarity=0.482  Sum_probs=144.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeec
Q 013141          207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVA  286 (449)
Q Consensus       207 ~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~  286 (449)
                      ++++|||+|||+++|+++|+++|+ .||.|.++.+++++.++.++|||||+|.+.++|.+|++.  +..+.|+.|.+.++
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~-~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~v~~~   78 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFG-KYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHILDGKVIDPKRA   78 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHT-TTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEETTEECCCEEC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHH-hCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--ccccCCeEcccccc
Confidence            467999999999999999999995 999999999999998999999999999999999999974  57899999999887


Q ss_pred             CCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC----
Q 013141          287 TPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG----  362 (449)
Q Consensus       287 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~----  362 (449)
                      .++...                                ....+|||+|||.++++++|+++|+.||.|.++.+..+    
T Consensus        79 ~~~~~~--------------------------------~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g  126 (167)
T 2cjk_A           79 IPRDEQ--------------------------------DKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTG  126 (167)
T ss_dssp             CCHHHH--------------------------------HHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSS
T ss_pred             cchhhc--------------------------------cCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCC
Confidence            654221                                12468999999999999999999999999999999864    


Q ss_pred             --CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCC
Q 013141          363 --KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNP  401 (449)
Q Consensus       363 --~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~  401 (449)
                        +|+|||+|.+.++|.+|++ +++..|+|+.|+|.|++++
T Consensus       127 ~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A          127 QSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAEPR  166 (167)
T ss_dssp             TTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECCCC
T ss_pred             ccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecCCC
Confidence              5899999999999999998 8999999999999999875

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.96  E-value=1.7e-29  Score=223.56  Aligned_cols=189  Identities=22%  Similarity=0.302  Sum_probs=148.4

Q ss_pred             CCceEEEcCCCC-CCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEee
Q 013141          207 SDLSIFVGDLAP-DVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV  285 (449)
Q Consensus       207 ~~~~l~v~~lp~-~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  285 (449)
                      .+++|||+|||+ ++++++|+++|+ .||.|.+|.++++.     +|||||+|.+.++|.+|++.|++..+.|+.|+|.+
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~-~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~   75 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFG-VYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITL   75 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHH-TTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEE
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHH-hcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEE
Confidence            357999999999 999999999995 99999999998764     78999999999999999999999999999999999


Q ss_pred             cCCCCCCchhhcchhh---hhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccC-ceEEEEEeC
Q 013141          286 ATPKKASGYQQQYSSQ---ALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFG-EILSVKIPV  361 (449)
Q Consensus       286 ~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G-~v~~v~i~~  361 (449)
                      +...............   ..+.....................+.++|||+|||..+++++|+++|+.|| .|.+|++.+
T Consensus        76 a~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~  155 (198)
T 1qm9_A           76 SKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ  155 (198)
T ss_dssp             CCCCSCCCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESS
T ss_pred             ecCCCcCCCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEe
Confidence            9865322111000000   000000000000000011112234589999999999999999999999999 999999955


Q ss_pred             -CCcEEEEEecCHHHHHHHHHHhcCCeeC-CeEEEEEecCCC
Q 013141          362 -GKGCGFVQFANRKDAEVALQKLQGTAIG-KQTVRLSWGRNP  401 (449)
Q Consensus       362 -~~g~afV~F~~~~~A~~A~~~l~g~~~~-g~~l~v~~~~~~  401 (449)
                       ++++|||+|.+.++|.+|++.|||..|+ |+.|+|.|++++
T Consensus       156 ~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          156 KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             TTSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECCC
T ss_pred             CCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeeccc
Confidence             7899999999999999999999999999 999999999864

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.96  E-value=7.5e-30  Score=221.30  Aligned_cols=164  Identities=22%  Similarity=0.442  Sum_probs=143.6

Q ss_pred             ccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEE
Q 013141          204 EACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRI  283 (449)
Q Consensus       204 ~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  283 (449)
                      .....++|||+|||.++|+++|+++|. .||.+.. .++.+..++.++|||||+|.+.++|.+|+ +|++..+.|+.|+|
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~-~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~v   85 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAIS-ELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKL   85 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHH-HHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHH-HGGGEEETTEEEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHH-HhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHH-hcCCCEeCCeEEEE
Confidence            345778999999999999999999995 8888766 34445566889999999999999999999 59999999999999


Q ss_pred             eecCCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEe--C
Q 013141          284 DVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIP--V  361 (449)
Q Consensus       284 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~--~  361 (449)
                      .++..+...                              .....++|||+|||.++++++|+++|+.||.|..+ ..  .
T Consensus        86 ~~~~~~~~~------------------------------~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-~~~~~  134 (175)
T 1fje_B           86 EKPKGRDSK------------------------------KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-SQDGK  134 (175)
T ss_dssp             ECCCCSSCS------------------------------TTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-CSSSS
T ss_pred             ecCCCcccc------------------------------ccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-cCCCC
Confidence            999876432                              12346899999999999999999999999999887 22  2


Q ss_pred             CCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCC
Q 013141          362 GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNP  401 (449)
Q Consensus       362 ~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~  401 (449)
                      ++++|||+|.+.++|.+|++.|||..|+|+.|+|+|++++
T Consensus       135 ~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          135 SKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             CCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECSSC
T ss_pred             CceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecCCC
Confidence            4799999999999999999999999999999999999875

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.96  E-value=4.7e-29  Score=220.76  Aligned_cols=169  Identities=20%  Similarity=0.405  Sum_probs=144.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhcc----C-------CcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCC
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHT----G-------QVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSL  181 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~----G-------~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~  181 (449)
                      ..+++|||+|||+++++++|+++|+.|    |       .|.++.+      ++++|||||+|.+.++|.+|+ .|++..
T Consensus         2 ~~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~------~~~~g~afV~F~~~~~A~~Al-~l~g~~   74 (198)
T 2yh0_A            2 AMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDKNFAFLEFRSVDETTQAM-AFDGII   74 (198)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE------ETTTTEEEEEESCSHHHHHHG-GGTTEE
T ss_pred             CceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe------cCCCCEEEEEeCCHHHHHHHH-HhcCCE
Confidence            357899999999999999999999999    5       5566655      345799999999999999999 899998


Q ss_pred             CCCCCCcccccccccCCCCC---------------ccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCC
Q 013141          182 MPNTDQPFRLNWATFSGSDR---------------RTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSN  246 (449)
Q Consensus       182 ~~~~~~~~~~~~~~~~~~~~---------------~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~  246 (449)
                      +.  ++.+++.++.......               .......++|||+|||.++++++|+++|+ .||.|..+.+++++.
T Consensus        75 ~~--g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~-~~G~v~~~~~~~~~~  151 (198)
T 2yh0_A           75 FQ--GQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLT-SFGPLKAFNLVKDSA  151 (198)
T ss_dssp             ET--TEEEEEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHH-TBSCEEEEEEEECTT
T ss_pred             Ec--CceEEEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHH-HcCCccEEEEeecCC
Confidence            84  5677777765432111               11225678999999999999999999995 999999999999988


Q ss_pred             CCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecCCCCC
Q 013141          247 TGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKA  291 (449)
Q Consensus       247 ~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~~~~~  291 (449)
                      ++.++|+|||+|.+.++|.+|++.|++..+.|+.|+|.++.++..
T Consensus       152 ~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  196 (198)
T 2yh0_A          152 TGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAK  196 (198)
T ss_dssp             TCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCCCC
T ss_pred             CCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            999999999999999999999999999999999999999988754

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.96  E-value=4.3e-30  Score=222.80  Aligned_cols=166  Identities=19%  Similarity=0.304  Sum_probs=143.9

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      .....++|||+|||+++++++|+++|..||.+.. .++.+..+++++|||||+|.+.++|.+|+ .|++..+.  ++.++
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~--g~~l~   84 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVF--GNEIK   84 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHH-HGGGEEET--TEEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHH-hcCCCEeC--CeEEE
Confidence            4467899999999999999999999999998766 34444467889999999999999999999 59999885  57788


Q ss_pred             ccccccCCCCCccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHH
Q 013141          191 LNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE  270 (449)
Q Consensus       191 ~~~~~~~~~~~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~  270 (449)
                      +.++.....   ......++|||+|||.++|+++|+++|+ .||.|..+     ..++.++|+|||+|.+.++|.+|++.
T Consensus        85 v~~~~~~~~---~~~~~~~~l~v~nlp~~~t~~~l~~~F~-~~g~v~~~-----~~~~~~~g~afV~f~~~~~A~~A~~~  155 (175)
T 1fje_B           85 LEKPKGRDS---KKVRAARTLLAKNLSFNITEDELKEVFE-DALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEE  155 (175)
T ss_dssp             EECCCCSSC---STTGGGGEEEEESCCSSCCHHHHHHHCT-TCSEEEEE-----CSSSSCCSEEEEECSSHHHHHHHHHH
T ss_pred             EecCCCccc---cccccCCEEEEeCCCCCCCHHHHHHHHH-hcCeEEEe-----cCCCCCceEEEEEECCHHHHHHHHHH
Confidence            888765432   2334678999999999999999999995 89987665     46788999999999999999999999


Q ss_pred             hCCceecCcceEEeecCCC
Q 013141          271 MNGVYCSSRPMRIDVATPK  289 (449)
Q Consensus       271 l~g~~~~g~~i~v~~~~~~  289 (449)
                      |+|..+.|+.|+|+++.++
T Consensus       156 l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          156 KQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             HTEEEETTEEEEEEECSSC
T ss_pred             hCCCEECCeEEEEEecCCC
Confidence            9999999999999999875

>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=99.96  E-value=1.1e-28  Score=231.10  Aligned_cols=173  Identities=16%  Similarity=0.302  Sum_probs=157.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccccc
Q 013141          114 ETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNW  193 (449)
Q Consensus       114 ~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~  193 (449)
                      ..++|||+|||+++++++|+++|+.||.|.++.++.++.+|+++|||||+|.+.++|.+|++.|++..+.  ++.+++.+
T Consensus        94 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~--g~~i~v~~  171 (284)
T 3smz_A           94 TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLG--PRTLYVHW  171 (284)
T ss_dssp             CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEET--TEECEEEE
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeC--CcEEEEEE
Confidence            4579999999999999999999999999999999999989999999999999999999999999999884  57888888


Q ss_pred             cccCCCCCccccCCCceEEEcCCCCCC-CHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC
Q 013141          194 ATFSGSDRRTEACSDLSIFVGDLAPDV-TDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMN  272 (449)
Q Consensus       194 ~~~~~~~~~~~~~~~~~l~v~~lp~~~-t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~  272 (449)
                      +......  ......++|||+|||.++ |+++|+++|+ .||.|..+.++++. ++.++|+|||+|.+.++|.+|++.|+
T Consensus       172 a~~~~~~--~~~~~~~~l~v~nlp~~~~~~~~l~~~f~-~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~  247 (284)
T 3smz_A          172 TDAGQLT--PALLHSRCLCVDRLPPGFNDVDALCRALS-AVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQAD  247 (284)
T ss_dssp             CCGGGCC--TTTTSCSEEEEECCCTTCCCHHHHHHHTC-SSSCCSEEEEEECS-SCCEEEEEEEECSSHHHHHHHHHHHT
T ss_pred             CCCCCCC--cccCCccEEEEecCCcccCCHHHHHHHhh-CCCCeEEEEEEECC-CCCcccEEEEEeCCHHHHHHHHHHhC
Confidence            8755432  233567899999999995 9999999995 99999999999986 68999999999999999999999999


Q ss_pred             CceecCcceEEeecCCCCCC
Q 013141          273 GVYCSSRPMRIDVATPKKAS  292 (449)
Q Consensus       273 g~~~~g~~i~v~~~~~~~~~  292 (449)
                      |..+.|+.|+|.++.++..+
T Consensus       248 g~~~~g~~l~v~~a~~~~~~  267 (284)
T 3smz_A          248 GLSLGGSHLRVSFCAPGPPG  267 (284)
T ss_dssp             TCEETTEECEEEECCSSSCH
T ss_pred             CCccCCeEEEEEEecCCCcc
Confidence            99999999999999887664

>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=4.8e-29  Score=220.70  Aligned_cols=163  Identities=14%  Similarity=0.181  Sum_probs=137.3

Q ss_pred             CCceEEEcCCC-CCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          114 ETKTIWIGDLF-HWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       114 ~~~~l~v~nLp-~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      +.++|||+||| +.+++++|+++|+.||.|.+|++++++     +|||||+|.+.++|++|++.||+..+.+  +.|+|.
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~~~g--~~l~v~   75 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDRAITHLNNNFMFG--QKMNVC   75 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTS-----TTCEEEEESSHHHHHHHHHHHTTCEETT--EECEEE
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCC-----CCEEEEEECCHHHHHHHHHHhCCCEECC--ceEEEE
Confidence            57899999999 899999999999999999999998763     5899999999999999999999999955  667777


Q ss_pred             ccccCCCCCc--------------------------------cccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCe--eE
Q 013141          193 WATFSGSDRR--------------------------------TEACSDLSIFVGDLAPDVTDSILQETFSSKYPSV--KG  238 (449)
Q Consensus       193 ~~~~~~~~~~--------------------------------~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v--~~  238 (449)
                      +++.......                                ....+.++|||+|||+++|+++|+++|+ .||.|  .+
T Consensus        76 ~s~~~~~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~-~~G~v~~~~  154 (205)
T 3tyt_A           76 VSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICD-ELGVKRPTS  154 (205)
T ss_dssp             ECSCSCCCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHH-HHTCCCCSE
T ss_pred             EccCCccCCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHH-hcCCcceEE
Confidence            7653221000                                0113456899999999999999999995 99999  89


Q ss_pred             EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCc----ceEEeec
Q 013141          239 AKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSR----PMRIDVA  286 (449)
Q Consensus       239 i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~----~i~v~~~  286 (449)
                      ++++.+.  +.++|+|||+|.+.++|.+||..||+..|.++    ++.|+++
T Consensus       155 v~~~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          155 VKVFSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             EEECSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEEE
T ss_pred             EEEEcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEEec
Confidence            9988774  45679999999999999999999999999776    5666654

>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=5.1e-29  Score=220.51  Aligned_cols=186  Identities=17%  Similarity=0.193  Sum_probs=140.4

Q ss_pred             CCceEEEcCCC-CCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEee
Q 013141          207 SDLSIFVGDLA-PDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV  285 (449)
Q Consensus       207 ~~~~l~v~~lp-~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  285 (449)
                      ++++|||+||+ .++|+++|+++|+ .||.|.+|+++++     .+|||||+|.+.++|++||+.|||..+.|+.|+|.+
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~-~~G~v~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   76 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFC-LYGNVEKVKFMKS-----KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCV   76 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHT-TTSCEEEEEECTT-----STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHH-hcCCeEEEEEecC-----CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEE
Confidence            46799999999 7999999999996 9999999999865     378999999999999999999999999999999999


Q ss_pred             cCCCCCCchhhc-chhhh---hhhcCCCCCCCCC-cCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCce--EEEE
Q 013141          286 ATPKKASGYQQQ-YSSQA---LVLAGGPGSNGAR-VQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEI--LSVK  358 (449)
Q Consensus       286 ~~~~~~~~~~~~-~~~~~---~~~~~~~~~~~~~-~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v--~~v~  358 (449)
                      ++.......... .....   ............. ..........+.++|||+|||+++++++|+++|++||.|  .+|+
T Consensus        77 s~~~~~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~  156 (205)
T 3tyt_A           77 SKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVK  156 (205)
T ss_dssp             CSCSCCCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEE
T ss_pred             ccCCccCCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEE
Confidence            975432110000 00000   0000000000000 000001123457899999999999999999999999999  8999


Q ss_pred             EeCC----CcEEEEEecCHHHHHHHHHHhcCCeeCCe----EEEEEec
Q 013141          359 IPVG----KGCGFVQFANRKDAEVALQKLQGTAIGKQ----TVRLSWG  398 (449)
Q Consensus       359 i~~~----~g~afV~F~~~~~A~~A~~~l~g~~~~g~----~l~v~~~  398 (449)
                      +..+    +++|||+|.+.++|.+|+..|||..|.|+    .+.|.|+
T Consensus       157 ~~~~~~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          157 VFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             ECSCCSSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEEE
T ss_pred             EEcCCCCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEEec
Confidence            8864    48999999999999999999999999886    4666553

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.96  E-value=1.6e-28  Score=229.76  Aligned_cols=166  Identities=23%  Similarity=0.403  Sum_probs=143.7

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHH----HHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCC
Q 013141          111 TNDETKTIWIGDLFHWMDETFLH----NCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTD  186 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~----~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~  186 (449)
                      ...++++|||+|||+++++++|+    ++|+.||.|.+|++++   +++++|||||+|.+.++|.+|++.|++..+.+  
T Consensus         5 ~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g--   79 (282)
T 3pgw_A            5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYD--   79 (282)
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCC--
Confidence            34678999999999999999977    8999999999999886   57899999999999999999999999998854  


Q ss_pred             CcccccccccCCCC------------------------------------------------------------------
Q 013141          187 QPFRLNWATFSGSD------------------------------------------------------------------  200 (449)
Q Consensus       187 ~~~~~~~~~~~~~~------------------------------------------------------------------  200 (449)
                      +.|+|.|+......                                                                  
T Consensus        80 ~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g  159 (282)
T 3pgw_A           80 KPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPG  159 (282)
T ss_pred             cEEEEEEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccCCC
Confidence            77777777543310                                                                  


Q ss_pred             ----------------------------------------CccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEE
Q 013141          201 ----------------------------------------RRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAK  240 (449)
Q Consensus       201 ----------------------------------------~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~  240 (449)
                                                              ......+.++|||+|||.++++++|+++|+ .||.|.+++
T Consensus       160 ~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~-~~G~i~~v~  238 (282)
T 3pgw_A          160 QPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFN-QFPGFKEVR  238 (282)
T ss_pred             CCCCCCCCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHHHHHHHH-hcCCeEEEE
Confidence                                                    001122467899999999999999999995 999999999


Q ss_pred             EeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceec-CcceEEeecC
Q 013141          241 VIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCS-SRPMRIDVAT  287 (449)
Q Consensus       241 ~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~-g~~i~v~~~~  287 (449)
                      ++.+.     +|+|||+|.+.++|.+|++.|||..|. |+.|+|+|++
T Consensus       239 ~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          239 LVPGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             EecCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            98653     589999999999999999999999999 9999999985

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.96  E-value=2.5e-28  Score=216.03  Aligned_cols=177  Identities=15%  Similarity=0.335  Sum_probs=143.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhhC----C-------CeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCce
Q 013141          207 SDLSIFVGDLAPDVTDSILQETFSSKY----P-------SVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVY  275 (449)
Q Consensus       207 ~~~~l~v~~lp~~~t~~~l~~~f~~~~----g-------~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~  275 (449)
                      ..++|||+|||+++|+++|+++|+ .|    |       .|.++.+      +.++|||||+|.+.++|.+|+ .|++..
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~-~~g~i~g~~~~~~~~v~~~~~------~~~~g~afV~F~~~~~A~~Al-~l~g~~   74 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFN-AQMRLGGLTQAPGNPVLAVQI------NQDKNFAFLEFRSVDETTQAM-AFDGII   74 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHH-HHHHHHTCCSSSSCSEEEEEE------ETTTTEEEEEESCSHHHHHHG-GGTTEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHH-HHHhhcccccCCCCceEEeEe------cCCCCEEEEEeCCHHHHHHHH-HhcCCE
Confidence            467999999999999999999995 88    4       5555554      355899999999999999999 899999


Q ss_pred             ecCcceEEeecCCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceE
Q 013141          276 CSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEIL  355 (449)
Q Consensus       276 ~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~  355 (449)
                      +.|+.|+|.++...........            ..................++|||+|||..+++++|+++|+.||.|.
T Consensus        75 ~~g~~i~v~~~~~~~~~~~~~~------------~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~  142 (198)
T 2yh0_A           75 FQGQSLKIRRPHDYQPLPGMSE------------NPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLK  142 (198)
T ss_dssp             ETTEEEEEECCCCCCCCCCSSS------------CSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEE
T ss_pred             EcCceEEEeCCCCCCCCCCCcC------------CCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcc
Confidence            9999999999877643211000            0000000111122335679999999999999999999999999999


Q ss_pred             EEEEeCC------CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCCC
Q 013141          356 SVKIPVG------KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGN  403 (449)
Q Consensus       356 ~v~i~~~------~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~~  403 (449)
                      +|.+.++      +++|||+|.+.++|.+|++.|||..|+|+.|+|.|++++..
T Consensus       143 ~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  196 (198)
T 2yh0_A          143 AFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAK  196 (198)
T ss_dssp             EEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCCCC
T ss_pred             EEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            9999865      68999999999999999999999999999999999998654

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=99.96  E-value=1.5e-28  Score=212.36  Aligned_cols=153  Identities=18%  Similarity=0.440  Sum_probs=137.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhhC----C-------CeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCce
Q 013141          207 SDLSIFVGDLAPDVTDSILQETFSSKY----P-------SVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVY  275 (449)
Q Consensus       207 ~~~~l~v~~lp~~~t~~~l~~~f~~~~----g-------~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~  275 (449)
                      +.++|||+|||+++|+++|+++|+ .|    |       .|.++.+.      +++|||||+|.+.++|.+|+ .+++..
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~-~~g~~~g~~~~~~~~v~~~~~~------~~~g~afV~f~~~~~A~~A~-~~~~~~   74 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFN-AQMRLGGLTQAPGNPVLAVQIN------QDKNFAFLEFRSVDETTQAM-AFDGII   74 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHH-HHHHHTTCCSSSSCSEEEEEEE------TTTTEEEEEESSHHHHHHHG-GGTTCE
T ss_pred             cccEEEEcCCCcccCHHHHHHHHH-HHhhhcccccCCCCceeeeEec------CCCCEEEEEeCCHHHHHHHH-HhCCcE
Confidence            467999999999999999999995 88    6       66666664      34789999999999999999 899999


Q ss_pred             ecCcceEEeecCCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceE
Q 013141          276 CSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEIL  355 (449)
Q Consensus       276 ~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~  355 (449)
                      +.|+.|+|.++.....                                ....++|||+|||..+++++|+++|++||.|.
T Consensus        75 ~~g~~i~v~~~~~~~~--------------------------------~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~  122 (172)
T 2g4b_A           75 FQGQSLKIRRPHDYQP--------------------------------LPGAHKLFIGGLPNYLNDDQVKELLTSFGPLK  122 (172)
T ss_dssp             ETTEECEEECCSSCCC--------------------------------CTTTTCEEEECCCTTCCHHHHHHHHHTTSCEE
T ss_pred             ecCceeeecCCcccCC--------------------------------CCCCCEEEEEcCCCcCCHHHHHHHHHhcCCce
Confidence            9999999998765432                                12368899999999999999999999999999


Q ss_pred             EEEEeCC------CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 013141          356 SVKIPVG------KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGR  399 (449)
Q Consensus       356 ~v~i~~~------~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  399 (449)
                      ++.+.++      +|+|||+|.+.++|.+|++.|||..|+|+.|+|+|+.
T Consensus       123 ~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~As  172 (172)
T 2g4b_A          123 AFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS  172 (172)
T ss_dssp             EEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             EEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeCC
Confidence            9999875      5899999999999999999999999999999999973

>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=3.5e-28  Score=219.95  Aligned_cols=165  Identities=16%  Similarity=0.289  Sum_probs=142.4

Q ss_pred             CCCCceEEEcCCCC-CCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          112 NDETKTIWIGDLFH-WMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       112 ~~~~~~l~v~nLp~-~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      ..++++|||+|||+ ++++++|+++|+.||.|.+|++++++     +|||||+|.+.++|.+|++.|++..+.  ++.|+
T Consensus        31 ~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~--g~~l~  103 (229)
T 2adc_A           31 GAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLH--GKPIR  103 (229)
T ss_dssp             CCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCS--SSBCE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeEC--CeEEE
Confidence            35789999999999 99999999999999999999999875     589999999999999999999999985  46777


Q ss_pred             ccccccCCCCCc------------------------------cccCCCceEEEcCCCCCCCHHHHHHHHhhhCC-CeeEE
Q 013141          191 LNWATFSGSDRR------------------------------TEACSDLSIFVGDLAPDVTDSILQETFSSKYP-SVKGA  239 (449)
Q Consensus       191 ~~~~~~~~~~~~------------------------------~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g-~v~~i  239 (449)
                      +.++........                              ....+.++|||+|||.++++++|+++|+ .|| .|..+
T Consensus       104 v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~-~~G~~i~~v  182 (229)
T 2adc_A          104 ITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFS-SNGGVVKGF  182 (229)
T ss_dssp             EECCSCCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHH-TTSCCEEEE
T ss_pred             EEEecCccccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHH-HcCCCeeEE
Confidence            777654311100                              1123468999999999999999999995 999 99999


Q ss_pred             EEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceec-CcceEEeecCCC
Q 013141          240 KVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCS-SRPMRIDVATPK  289 (449)
Q Consensus       240 ~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~-g~~i~v~~~~~~  289 (449)
                      .++.+     .+|+|||+|.+.++|.+|++.|++..+. |+.|+|.|++++
T Consensus       183 ~i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          183 KFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             EECSS-----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             EEEEC-----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecCC
Confidence            99753     3689999999999999999999999999 999999999764

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=99.96  E-value=1.3e-28  Score=231.44  Aligned_cols=171  Identities=13%  Similarity=0.297  Sum_probs=145.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccC-CcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          114 ETKTIWIGDLFHWMDETFLHNCFSHTG-QVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       114 ~~~~l~v~nLp~~~t~~~l~~~f~~~G-~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      ..++|||+|||+++++++|+++|+.|| .|.+|.+++++. ++++|||||+|.+.++|.+|++.|++..+.+  +.+++.
T Consensus       116 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g--~~l~v~  192 (292)
T 2ghp_A          116 TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRF-NTSRRFAYIDVTSKEDARYCVEKLNGLKIEG--YTLVTK  192 (292)
T ss_dssp             CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHHHHHHHHHHTTCEETT--EECEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCC-CCcceEEEEEECCHHHHHHHHHHhCCCEeCC--cEEEEE
Confidence            578999999999999999999999999 999999999875 8899999999999999999999999999954  778888


Q ss_pred             ccccCCCCCc--cccCCCceEEEcCCCCC-CCHHHHHHHHhhhCCCeeEEEEeecCC-CCCcceEEEEEeCCHHHHHHHH
Q 013141          193 WATFSGSDRR--TEACSDLSIFVGDLAPD-VTDSILQETFSSKYPSVKGAKVIIDSN-TGRTKGYGFVRFGDENERSRAM  268 (449)
Q Consensus       193 ~~~~~~~~~~--~~~~~~~~l~v~~lp~~-~t~~~l~~~f~~~~g~v~~i~~~~~~~-~~~~~g~afV~f~~~~~A~~A~  268 (449)
                      ++.+......  ......++|||+|||.+ +|+++|+++|+ .||.|..+.++++.. |+.++|+|||+|.+.++|.+|+
T Consensus       193 ~a~~~~~~~~~~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~-~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~  271 (292)
T 2ghp_A          193 VSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFE-GFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL  271 (292)
T ss_dssp             ECCCC---------CCTTTEEEEEEECTTTCCHHHHHHHHG-GGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG
T ss_pred             ECCCCcccccccccCCCCceEEEECCCcccCCHHHHHHHHh-ccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH
Confidence            8765543322  24456789999999999 99999999995 999999999999866 6899999999999999999999


Q ss_pred             HHhCCceecCcceEEeecCCC
Q 013141          269 TEMNGVYCSSRPMRIDVATPK  289 (449)
Q Consensus       269 ~~l~g~~~~g~~i~v~~~~~~  289 (449)
                       .|||..|.|+.|+|.++.++
T Consensus       272 -~l~g~~~~g~~i~V~~a~~k  291 (292)
T 2ghp_A          272 -QMNRSLLGNREISVSLADKK  291 (292)
T ss_dssp             -GGTTEEETTEEEEEEECCCC
T ss_pred             -HhcCCEECCcEEEEEEecCC
Confidence             99999999999999999876

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.96  E-value=4.3e-28  Score=214.57  Aligned_cols=163  Identities=17%  Similarity=0.292  Sum_probs=140.8

Q ss_pred             CCceEEEcCCCC-CCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          114 ETKTIWIGDLFH-WMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       114 ~~~~l~v~nLp~-~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      ..++|||+|||+ ++++++|+++|+.||.|.+|++++++     +|||||+|.+.++|.+|++.|++..+.  ++.+++.
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~--g~~l~v~   74 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLH--GKPIRIT   74 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCS--SCCCEEE
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeec--CeEEEEE
Confidence            368999999999 99999999999999999999998875     589999999999999999999999985  4677777


Q ss_pred             ccccCCCCCc------------------------------cccCCCceEEEcCCCCCCCHHHHHHHHhhhCC-CeeEEEE
Q 013141          193 WATFSGSDRR------------------------------TEACSDLSIFVGDLAPDVTDSILQETFSSKYP-SVKGAKV  241 (449)
Q Consensus       193 ~~~~~~~~~~------------------------------~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g-~v~~i~~  241 (449)
                      ++........                              ....+.++|||+|||.++++++|+++|+ .|| .|..+.+
T Consensus        75 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~-~~G~~v~~v~i  153 (198)
T 1qm9_A           75 LSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFS-SNGGVVKGFKF  153 (198)
T ss_dssp             ECCCCSCCCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHH-HTTSCCCEEEE
T ss_pred             EecCCCcCCCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHH-HcCCCceEEEE
Confidence            7654321100                              1123478999999999999999999995 999 9999999


Q ss_pred             eecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceec-CcceEEeecCCC
Q 013141          242 IIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCS-SRPMRIDVATPK  289 (449)
Q Consensus       242 ~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~-g~~i~v~~~~~~  289 (449)
                      +.+     .+|+|||+|.+.++|.+|++.|+|..+. |+.|+|.|+++.
T Consensus       154 ~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          154 FQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             SST-----TSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECCC
T ss_pred             EeC-----CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeeccc
Confidence            764     2789999999999999999999999999 999999998764

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.95  E-value=1.3e-27  Score=220.54  Aligned_cols=159  Identities=26%  Similarity=0.510  Sum_probs=142.4

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      .....++|||+|||+++|+++|+++|+.||.|.+|.+.++      +|||||+|.+.++|.+|++.+++..+.  ++.++
T Consensus        18 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~A~~A~~~l~g~~i~--g~~l~   89 (261)
T 3sde_A           18 TYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDGTILK--SRPLR   89 (261)
T ss_dssp             SSCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHTTCEET--TEECE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CcEEEEEECCHHHHHHHHHHcCCcEEC--CceeE
Confidence            3456789999999999999999999999999999999654      589999999999999999999999984  57788


Q ss_pred             ccccccCCCCCccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHH
Q 013141          191 LNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE  270 (449)
Q Consensus       191 ~~~~~~~~~~~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~  270 (449)
                      +.++.           +..+|||+|||.++|+++|+++|+ .||.|..+.++.+ .++.++|+|||+|.+.++|.+|++.
T Consensus        90 v~~a~-----------~~~~l~v~nl~~~~t~~~l~~~F~-~~G~i~~v~i~~~-~~g~~~g~afV~f~~~~~A~~A~~~  156 (261)
T 3sde_A           90 IRFAT-----------HGAALTVKNLSPVVSNELLEQAFS-QFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALER  156 (261)
T ss_dssp             EEECC-----------CSSEEEEESCCTTCCHHHHHHHHG-GGSCEEEEEEEEE-TTSCEEEEEEEEESSHHHHHHHHHH
T ss_pred             eeecc-----------cCCcccccCCCCCCCHHHHHHHHH-hcCCeEEEEeeeC-CCCCcCcEEEEEeCCHHHHHHHHHH
Confidence            87775           357999999999999999999995 9999999999999 5799999999999999999999999


Q ss_pred             hCC-ceec---CcceEEeecCCCC
Q 013141          271 MNG-VYCS---SRPMRIDVATPKK  290 (449)
Q Consensus       271 l~g-~~~~---g~~i~v~~~~~~~  290 (449)
                      |++ ..+.   +++|.|.++....
T Consensus       157 l~~~~~~~~~~~r~i~v~~~~~~~  180 (261)
T 3sde_A          157 CGDGAFLLTTTPRPVIVEPMEQFD  180 (261)
T ss_dssp             HHHSCEESSSSCCBCEEEECCCEE
T ss_pred             hcCCeEEecCCCceEEEeeccccC
Confidence            954 4444   9999999998754

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.95  E-value=1.3e-26  Score=213.97  Aligned_cols=155  Identities=30%  Similarity=0.464  Sum_probs=139.6

Q ss_pred             ccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEE
Q 013141          204 EACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRI  283 (449)
Q Consensus       204 ~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  283 (449)
                      .....++|||+|||+++|+++|+++|+ .||.|..|.+.++      +|||||+|.+.++|.+|++.|++..+.|+.|+|
T Consensus        18 ~~~~~~~l~V~nLp~~~te~~l~~~F~-~~G~i~~v~i~~~------kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v   90 (261)
T 3sde_A           18 TYTQRCRLFVGNLPTDITEEDFKRLFE-RYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDGTILKSRPLRI   90 (261)
T ss_dssp             SSCGGGEEEEESCCTTCCHHHHHHHTG-GGCCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHH-hcCCEEEEEEeCC------CcEEEEEECCHHHHHHHHHHcCCcEECCceeEe
Confidence            345668999999999999999999995 9999999998643      789999999999999999999999999999999


Q ss_pred             eecCCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC-
Q 013141          284 DVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-  362 (449)
Q Consensus       284 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~-  362 (449)
                      .++.+                                      ..+|||+|||..+|+++|+++|+.||.|.+|.|+.+ 
T Consensus        91 ~~a~~--------------------------------------~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~  132 (261)
T 3sde_A           91 RFATH--------------------------------------GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD  132 (261)
T ss_dssp             EECCC--------------------------------------SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET
T ss_pred             eeccc--------------------------------------CCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCC
Confidence            99854                                      357999999999999999999999999999999864 


Q ss_pred             ----CcEEEEEecCHHHHHHHHHHhc-CCeeC---CeEEEEEecCCCCC
Q 013141          363 ----KGCGFVQFANRKDAEVALQKLQ-GTAIG---KQTVRLSWGRNPGN  403 (449)
Q Consensus       363 ----~g~afV~F~~~~~A~~A~~~l~-g~~~~---g~~l~v~~~~~~~~  403 (449)
                          +|+|||+|.+.++|.+|++.|| +..+.   ++.|+|.+++....
T Consensus       133 ~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~~~~~~~~  181 (261)
T 3sde_A          133 RGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFDD  181 (261)
T ss_dssp             TSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEEECCCEES
T ss_pred             CCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEeeccccCc
Confidence                7899999999999999999994 55554   99999999987543

>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=99.88  E-value=5.7e-22  Score=168.39  Aligned_cols=146  Identities=23%  Similarity=0.324  Sum_probs=115.5

Q ss_pred             EEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCC-----Ccccccccc-cCCCCCccccCCCceEEEcCCC
Q 013141          144 NVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTD-----QPFRLNWAT-FSGSDRRTEACSDLSIFVGDLA  217 (449)
Q Consensus       144 ~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~-----~~~~~~~~~-~~~~~~~~~~~~~~~l~v~~lp  217 (449)
                      +++++.+..  +++||+||+|.+.++|++|++.+++.......     ......... .............++|||+|||
T Consensus         2 ~~kl~ln~~--~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~   79 (158)
T 2kn4_A            2 QYKLILNGK--TLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLT   79 (158)
T ss_dssp             EEEEEEECS--SCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEEECCCCCSSCCCCCCBCCEEEEESCC
T ss_pred             cEEEEecCc--cccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCccccccccccccccccccCCCCCCEEEEeCCC
Confidence            567888754  68999999999999999999887753321111     111111111 1111122334557899999999


Q ss_pred             CCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecCCCCCC
Q 013141          218 PDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKAS  292 (449)
Q Consensus       218 ~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~~~~~~  292 (449)
                      +++++++|+++|+ .||.|..+.+++++.++.++|||||+|.+.++|++|++.|++..|.|+.|+|.++.+....
T Consensus        80 ~~~~~~~l~~~F~-~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~  153 (158)
T 2kn4_A           80 YRTSPDTLRRVFE-KYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPP  153 (158)
T ss_dssp             TTCCHHHHHHHHH-HHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCSSCC
T ss_pred             CCCCHHHHHHHHH-hcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCCC
Confidence            9999999999995 9999999999999889999999999999999999999999999999999999999887543

>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=99.86  E-value=1.2e-21  Score=164.84  Aligned_cols=138  Identities=20%  Similarity=0.263  Sum_probs=115.2

Q ss_pred             CCcceEEEEEeCCHHHHHHHHHHh-CCceecCcceEEeecCCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCC
Q 013141          248 GRTKGYGFVRFGDENERSRAMTEM-NGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESN  326 (449)
Q Consensus       248 ~~~~g~afV~f~~~~~A~~A~~~l-~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  326 (449)
                      ...+|+++|+|.+.++|++|++.+ |+..++| .+.+.++..+.......                ..............
T Consensus        10 ~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~----------------~~~~~~~~~~~~~~   72 (150)
T 2i2y_A           10 KTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGS----------------HHHHHHMHRDSCPL   72 (150)
T ss_dssp             SSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSS----------------SSCCCCSCSSSSTT
T ss_pred             ccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCcccccccc----------------ccccccccccCCCC
Confidence            456899999999999999999999 9999999 99999876543211000                00011112334556


Q ss_pred             CcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC-CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCC
Q 013141          327 NATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPG  402 (449)
Q Consensus       327 ~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~-~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~  402 (449)
                      .++|||+|||+.+++++|+++|+.||.|.+|+++++ +|+|||+|.+.++|.+|++.|||..|.|+.|+|+|++++.
T Consensus        73 ~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  149 (150)
T 2i2y_A           73 DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGEK  149 (150)
T ss_dssp             SCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSSSCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCCC
Confidence            799999999999999999999999999999999987 8999999999999999999999999999999999998864

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=99.86  E-value=4.7e-21  Score=162.69  Aligned_cols=146  Identities=20%  Similarity=0.273  Sum_probs=109.1

Q ss_pred             EEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecCCCCCCchhhcchhhhhhhcCCCCCCCCCcC
Q 013141          238 GAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQ  317 (449)
Q Consensus       238 ~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  317 (449)
                      .+.++.+..  .++||+||+|.+.++|++|++.+++....+..+.+...........                   ....
T Consensus         2 ~~kl~ln~~--~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~~-------------------~~~~   60 (158)
T 2kn4_A            2 QYKLILNGK--TLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTE-------------------GSHH   60 (158)
T ss_dssp             EEEEEEECS--SCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEEEC-------------------CCCC
T ss_pred             cEEEEecCc--cccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCccccccccc-------------------cccc
Confidence            355666643  6899999999999999999988876433333333222211100000                   0000


Q ss_pred             CCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC------CcEEEEEecCHHHHHHHHHHhcCCeeCCe
Q 013141          318 GSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKLQGTAIGKQ  391 (449)
Q Consensus       318 ~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~------~g~afV~F~~~~~A~~A~~~l~g~~~~g~  391 (449)
                      ..........++|||+|||+++++++|+++|+.||.|.+|.|+++      +|+|||+|.+.++|.+|++.|||..|.|+
T Consensus        61 ~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~  140 (158)
T 2kn4_A           61 HHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGR  140 (158)
T ss_dssp             SSCCCCCCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSS
T ss_pred             cccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCe
Confidence            011223455789999999999999999999999999999999864      68999999999999999999999999999


Q ss_pred             EEEEEecCCCCCC
Q 013141          392 TVRLSWGRNPGNK  404 (449)
Q Consensus       392 ~l~v~~~~~~~~~  404 (449)
                      .|+|.|+++...+
T Consensus       141 ~l~v~~a~~~~~~  153 (158)
T 2kn4_A          141 ELRVQMARYGRPP  153 (158)
T ss_dssp             EEEEEEECCSSCC
T ss_pred             EEEEEECCCCCCC
Confidence            9999999986544

>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=99.84  E-value=3.7e-21  Score=153.79  Aligned_cols=107  Identities=24%  Similarity=0.422  Sum_probs=72.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccccc
Q 013141          114 ETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNW  193 (449)
Q Consensus       114 ~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~  193 (449)
                      .+.+|||+|||+++++++|+++|+.||.|.+|+|++++  +.++|||||+|.+.++|++||+.|++..+.  ++.|+|.+
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~--g~~i~V~~   79 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLN--DRKVFVGR   79 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEET--TEECEEEE
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEEC--CEEEEEEE
Confidence            46789999999999999999999999999999999986  468999999999999999999999999985  46788888


Q ss_pred             cccCCCCCc---cccCCCceEEEcCCCCCCCHHH
Q 013141          194 ATFSGSDRR---TEACSDLSIFVGDLAPDVTDSI  224 (449)
Q Consensus       194 ~~~~~~~~~---~~~~~~~~l~v~~lp~~~t~~~  224 (449)
                      +........   ......++|||+|||+++|++.
T Consensus        80 a~~~~~~~~~~~~~~~~~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           80 FKSRKEREAELGARAKEFTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             SSCCCC----------------------------
T ss_pred             CCCccccccccccccCCCCceEeCCCCCCccccc
Confidence            765433221   2233456799999999999864

>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=99.82  E-value=6.4e-20  Score=146.56  Aligned_cols=110  Identities=22%  Similarity=0.436  Sum_probs=75.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeec
Q 013141          207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVA  286 (449)
Q Consensus       207 ~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~  286 (449)
                      ...+|||+|||+++|+++|+++|+ .||.|.+++++++.  +.++|||||+|.+.++|++||+.|++..|.|+.|+|.++
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~-~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a   80 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFS-AFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRF   80 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHG-GGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHh-ccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            356899999999999999999995 99999999999985  457999999999999999999999999999999999999


Q ss_pred             CCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhH
Q 013141          287 TPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDED  343 (449)
Q Consensus       287 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~  343 (449)
                      .++..+....                        .......++|||+|||+++|++.
T Consensus        81 ~~~~~~~~~~------------------------~~~~~~~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           81 KSRKEREAEL------------------------GARAKEFTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             SCCCC----------------------------------------------------
T ss_pred             CCcccccccc------------------------ccccCCCCceEeCCCCCCccccc
Confidence            8765432110                        11122345799999999999864

>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=5.9e-20  Score=154.39  Aligned_cols=128  Identities=23%  Similarity=0.350  Sum_probs=110.5

Q ss_pred             CCcccEEEEEEccHHHHHHHHHHh-cCCCCCCCCCcccccccccCC-----------CCCccccCCCceEEEcCCCCCCC
Q 013141          154 GQSEGYGFVEFYSRAAAEKVLQSY-SGSLMPNTDQPFRLNWATFSG-----------SDRRTEACSDLSIFVGDLAPDVT  221 (449)
Q Consensus       154 g~~~g~afV~f~~~~~A~~Al~~l-~~~~~~~~~~~~~~~~~~~~~-----------~~~~~~~~~~~~l~v~~lp~~~t  221 (449)
                      .+.+|+++|+|.+.++|++|++.+ ++..+.+   .++++++....           ..........++|||+|||+++|
T Consensus        10 ~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G---~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~t   86 (150)
T 2i2y_A           10 KTLKGETTTEAVDAATAEKVFKQYANDNGVDG---EWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGN   86 (150)
T ss_dssp             SSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC---EEEEETTTTEEEEECSSSSCCCCSCSSSSTTSCEEEEESCCSCCS
T ss_pred             ccccccceeeecCHHHHHHHHHHHhcCCCCCC---ceecccccCccccccccccccccccccCCCCCCEEEEeCCCCCCC
Confidence            467899999999999999999999 9998866   67777665321           12233456678999999999999


Q ss_pred             HHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecCCCC
Q 013141          222 DSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKK  290 (449)
Q Consensus       222 ~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~~~~  290 (449)
                      +++|+++|+ .||.|.++.++++     ++|||||+|.+.++|.+|++.|++..|.|+.|+|+++.++.
T Consensus        87 ~~~l~~~F~-~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  149 (150)
T 2i2y_A           87 KTELERAFG-YYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGEK  149 (150)
T ss_dssp             CHHHHHHHH-HHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCCC
T ss_pred             HHHHHHHHH-hhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCCC
Confidence            999999996 9999999999876     58899999999999999999999999999999999998763

>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=99.80  E-value=1.7e-19  Score=139.74  Aligned_cols=82  Identities=27%  Similarity=0.464  Sum_probs=76.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      ...++|||+|||+++|+++|+++|+.||.|.+|++++++.+|+++|||||+|.+.++|.+|++.||+..+.  ++.|+|.
T Consensus        17 ~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~--gr~l~V~   94 (99)
T 4fxv_A           17 FQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQ--SKTIKVS   94 (99)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEET--TEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEEC--CEEEEEE
Confidence            35678999999999999999999999999999999999999999999999999999999999999999995  5788888


Q ss_pred             cccc
Q 013141          193 WATF  196 (449)
Q Consensus       193 ~~~~  196 (449)
                      |+++
T Consensus        95 ~AkP   98 (99)
T 4fxv_A           95 YARP   98 (99)
T ss_dssp             ECCB
T ss_pred             EeeC
Confidence            8864

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.80  E-value=5.3e-19  Score=146.54  Aligned_cols=87  Identities=24%  Similarity=0.424  Sum_probs=79.0

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      .....++|||+|||+++++++|+++|+.||.|.+|++++++.+++++|||||+|.+.++|++|++.|++..+.  ++.|+
T Consensus        38 ~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~l~  115 (139)
T 1u6f_A           38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNIL--NKRLK  115 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECS--SCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEEC--CeEEE
Confidence            3457899999999999999999999999999999999999999999999999999999999999999999985  57788


Q ss_pred             ccccccCCC
Q 013141          191 LNWATFSGS  199 (449)
Q Consensus       191 ~~~~~~~~~  199 (449)
                      |.++.....
T Consensus       116 v~~a~~~~~  124 (139)
T 1u6f_A          116 VALAASGHQ  124 (139)
T ss_dssp             EEESSCCCC
T ss_pred             EEECCCCCC
Confidence            888875543

>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=99.79  E-value=7.8e-19  Score=135.96  Aligned_cols=82  Identities=29%  Similarity=0.527  Sum_probs=78.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEee
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV  285 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  285 (449)
                      ...++|||+|||+++|+++|+++|+ .||.|.++.+++++.+++++|||||+|.+.++|++|++.|||..+.|+.|+|++
T Consensus        17 ~~gt~lfV~nLp~~~te~~L~~~F~-~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~   95 (99)
T 4fxv_A           17 FQGTNLIVNYLPQNMTQDELRSLFS-SIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSY   95 (99)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHH-TTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHH-hcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3457899999999999999999995 999999999999999999999999999999999999999999999999999999


Q ss_pred             cCC
Q 013141          286 ATP  288 (449)
Q Consensus       286 ~~~  288 (449)
                      ++|
T Consensus        96 AkP   98 (99)
T 4fxv_A           96 ARP   98 (99)
T ss_dssp             CCB
T ss_pred             eeC
Confidence            975

>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=99.78  E-value=6.7e-19  Score=148.91  Aligned_cols=82  Identities=27%  Similarity=0.491  Sum_probs=75.0

Q ss_pred             CCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC------CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 013141          324 ESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSW  397 (449)
Q Consensus       324 ~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~------~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  397 (449)
                      ....++|||+|||..+++++|+++|+.||.|.+|.|+.+      +++|||+|.+.++|.+||+.||+..|.|+.|+|+|
T Consensus        36 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  115 (156)
T 1h2v_Z           36 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDW  115 (156)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            346789999999999999999999999999999999764      47999999999999999999999999999999999


Q ss_pred             cCCCCCCC
Q 013141          398 GRNPGNKQ  405 (449)
Q Consensus       398 ~~~~~~~~  405 (449)
                      +++.....
T Consensus       116 a~~~~~~~  123 (156)
T 1h2v_Z          116 DAGFKEGR  123 (156)
T ss_dssp             ESCCCTTC
T ss_pred             CCCCCCcC
Confidence            99765443

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.77  E-value=1.9e-18  Score=132.00  Aligned_cols=79  Identities=19%  Similarity=0.253  Sum_probs=74.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCe--eCCeEEEEEecCC
Q 013141          323 GESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTA--IGKQTVRLSWGRN  400 (449)
Q Consensus       323 ~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~--~~g~~l~v~~~~~  400 (449)
                      ..+++++|||+|||+++|+++|+++|++||.|.+|.++++|++|||+|.+.++|.+|++.|++..  |.|+.|+|.|++.
T Consensus        17 ~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~S~~   96 (100)
T 3r27_A           17 KTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTS   96 (100)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEECSC
T ss_pred             cCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcCCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEeccc
Confidence            34568899999999999999999999999999999999999999999999999999999999875  7899999999987


Q ss_pred             C
Q 013141          401 P  401 (449)
Q Consensus       401 ~  401 (449)
                      .
T Consensus        97 k   97 (100)
T 3r27_A           97 Q   97 (100)
T ss_dssp             S
T ss_pred             c
Confidence            5

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=1.4e-18  Score=134.18  Aligned_cols=82  Identities=15%  Similarity=0.255  Sum_probs=75.4

Q ss_pred             CCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhc--CCeeCCeEEEEEecCC
Q 013141          323 GESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQ--GTAIGKQTVRLSWGRN  400 (449)
Q Consensus       323 ~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~--g~~~~g~~l~v~~~~~  400 (449)
                      .....++|||+|||+++++++|+++|++||.|.+|.|++++|+|||+|++.++|.+|++.|+  +..|.|+.|+|.|++.
T Consensus        12 ~~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~A~~   91 (105)
T 1sjq_A           12 SGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNH   91 (105)
T ss_dssp             CCCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETTTTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCCCSS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEcCC
Confidence            34567899999999999999999999999999999999999999999999999999999886  4789999999999987


Q ss_pred             CCCC
Q 013141          401 PGNK  404 (449)
Q Consensus       401 ~~~~  404 (449)
                      +...
T Consensus        92 ~~~~   95 (105)
T 1sjq_A           92 KELK   95 (105)
T ss_dssp             SSCC
T ss_pred             CCCC
Confidence            6544

>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=99.77  E-value=5.6e-18  Score=132.56  Aligned_cols=81  Identities=27%  Similarity=0.511  Sum_probs=74.7

Q ss_pred             CCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCCC
Q 013141          324 ESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGN  403 (449)
Q Consensus       324 ~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~~  403 (449)
                      ....++|||+|||.++++++|+++|+.||.|.+|.++  +++|||+|.+.++|.+|++.||+..|.|+.|+|.|+++...
T Consensus         8 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   85 (103)
T 2dgu_A            8 MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQ   85 (103)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcCCCcc
Confidence            4457899999999999999999999999999999998  56999999999999999999999999999999999998765


Q ss_pred             CCC
Q 013141          404 KQW  406 (449)
Q Consensus       404 ~~~  406 (449)
                      ...
T Consensus        86 ~~~   88 (103)
T 2dgu_A           86 KRK   88 (103)
T ss_dssp             CCC
T ss_pred             cch
Confidence            543

>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=99.77  E-value=5.5e-19  Score=173.35  Aligned_cols=82  Identities=23%  Similarity=0.493  Sum_probs=75.2

Q ss_pred             CCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC------CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 013141          325 SNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWG  398 (449)
Q Consensus       325 ~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~------~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~  398 (449)
                      ...++|||+|||+.+|+++|+++|+.||.|..|.|+.+      +|||||+|.+.++|.+||+.|||..|.|+.|.|.|+
T Consensus       100 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a  179 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  179 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            45689999999999999999999999999999999864      699999999999999999999999999999999999


Q ss_pred             CCCCCCCC
Q 013141          399 RNPGNKQW  406 (449)
Q Consensus       399 ~~~~~~~~  406 (449)
                      +.......
T Consensus       180 ~~~~~~~~  187 (437)
T 3pgw_S          180 RGRTVKGW  187 (437)
T ss_pred             CCCCCCCC
Confidence            97655443

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=1.1e-17  Score=129.46  Aligned_cols=83  Identities=13%  Similarity=0.243  Sum_probs=75.5

Q ss_pred             CCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHh--cCCeeCCeEEEEEecC
Q 013141          322 DGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKL--QGTAIGKQTVRLSWGR  399 (449)
Q Consensus       322 ~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l--~g~~~~g~~l~v~~~~  399 (449)
                      ....+.++|||+|||+++++++|+++|++||.|.+|.+++++++|||+|.+.++|.+|++.|  ++..|.|+.|+|.|++
T Consensus        10 ~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~   89 (101)
T 2cq1_A           10 MDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSN   89 (101)
T ss_dssp             CCSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECS
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECCCCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEEcC
Confidence            34456789999999999999999999999999999999999999999999999999999987  4678999999999999


Q ss_pred             CCCCC
Q 013141          400 NPGNK  404 (449)
Q Consensus       400 ~~~~~  404 (449)
                      ...-.
T Consensus        90 ~~~~~   94 (101)
T 2cq1_A           90 HKELK   94 (101)
T ss_dssp             CSSCC
T ss_pred             cccCc
Confidence            76544

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.76  E-value=3.6e-18  Score=131.92  Aligned_cols=79  Identities=16%  Similarity=0.166  Sum_probs=73.4

Q ss_pred             CCCCcEEEEcCCCC-CCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCC--eeCCeEEEEEecCC
Q 013141          324 ESNNATIFVGALDS-DVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGT--AIGKQTVRLSWGRN  400 (449)
Q Consensus       324 ~~~~~~l~V~nlp~-~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~--~~~g~~l~v~~~~~  400 (449)
                      ..++++|||+|||+ ++++++|+++|++||.|.+|.|++++++|||+|.+.++|.+|++.||+.  .|.|+.|+|.|++.
T Consensus        12 ~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~   91 (102)
T 1x4d_A           12 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQK   91 (102)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECC
T ss_pred             CCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcCCCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEECCC
Confidence            34688999999999 9999999999999999999999999999999999999999999999864  59999999999996


Q ss_pred             CC
Q 013141          401 PG  402 (449)
Q Consensus       401 ~~  402 (449)
                      ..
T Consensus        92 ~~   93 (102)
T 1x4d_A           92 YK   93 (102)
T ss_dssp             CT
T ss_pred             CC
Confidence            54

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.76  E-value=2.7e-18  Score=126.09  Aligned_cols=74  Identities=16%  Similarity=0.281  Sum_probs=71.4

Q ss_pred             CCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 013141          326 NNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGR  399 (449)
Q Consensus       326 ~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  399 (449)
                      .+..|+|+||++.+|+++|+++|.+||+|.++++..++|+|||+|.|.++|.+|++.||+..+.|+.|+|.++.
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLNQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcCCCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            36789999999999999999999999999999999999999999999999999999999999999999999985

>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=99.76  E-value=1.4e-17  Score=131.47  Aligned_cols=81  Identities=20%  Similarity=0.325  Sum_probs=75.7

Q ss_pred             CCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCC-----eEEEEEec
Q 013141          324 ESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGK-----QTVRLSWG  398 (449)
Q Consensus       324 ~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g-----~~l~v~~~  398 (449)
                      ....++|||+|||+++++++|+++|+.||.|.+|.|+.+ ++|||+|.+.++|.+||+.||+..|.|     +.|+|.++
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~V~~a   90 (108)
T 1x4c_A           12 RRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVD   90 (108)
T ss_dssp             CSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEEEEeC
Confidence            355789999999999999999999999999999999987 999999999999999999999999999     99999999


Q ss_pred             CCCCCCC
Q 013141          399 RNPGNKQ  405 (449)
Q Consensus       399 ~~~~~~~  405 (449)
                      +++....
T Consensus        91 ~~~~~~~   97 (108)
T 1x4c_A           91 GPRSPSY   97 (108)
T ss_dssp             SCCSCCC
T ss_pred             CCCCCCC
Confidence            9876553

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.76  E-value=2.9e-18  Score=135.34  Aligned_cols=81  Identities=19%  Similarity=0.197  Sum_probs=75.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      .+.++|||+|||+++++++|+++|++||.|.+|+|+.|+.+++++|||||+|.+.++|++|++.||+..+.  ++.|+|.
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~--gr~i~V~   81 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVM--GNIIHAQ   81 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEET--TEECEEE
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEEC--CeEEEEE
Confidence            46789999999999999999999999999999999999999999999999999999999999999999995  4667777


Q ss_pred             ccc
Q 013141          193 WAT  195 (449)
Q Consensus       193 ~~~  195 (449)
                      ++.
T Consensus        82 ~a~   84 (110)
T 3s8s_A           82 LDI   84 (110)
T ss_dssp             ECS
T ss_pred             ECC
Confidence            664

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.75  E-value=1e-17  Score=130.45  Aligned_cols=82  Identities=22%  Similarity=0.225  Sum_probs=74.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCC--eeCCeEEEEEecCC
Q 013141          323 GESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGT--AIGKQTVRLSWGRN  400 (449)
Q Consensus       323 ~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~--~~~g~~l~v~~~~~  400 (449)
                      ...+.++|||+|||+++++++|+++|++||.|.+|.+++++++|||+|.+.++|.+|++.|++.  .|.|+.|+|.|++.
T Consensus        11 ~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a~~   90 (104)
T 1wex_A           11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTS   90 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSS
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEccC
Confidence            3456789999999999999999999999999999999999999999999999999999998765  59999999999997


Q ss_pred             CCCC
Q 013141          401 PGNK  404 (449)
Q Consensus       401 ~~~~  404 (449)
                      ....
T Consensus        91 ~~~~   94 (104)
T 1wex_A           91 KRIT   94 (104)
T ss_dssp             SSCC
T ss_pred             cccc
Confidence            6543

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.75  E-value=8.8e-18  Score=132.54  Aligned_cols=84  Identities=12%  Similarity=0.214  Sum_probs=79.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEee
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV  285 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  285 (449)
                      .+.++|||+||++++++++|+++|+ .||.|.++.+++|+.+++++|||||+|.+.++|++|++.||+..+.|+.|+|++
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~-~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~   82 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCR-KYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQL   82 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHT-TTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHH-hcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            4568999999999999999999995 999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 013141          286 ATPKK  290 (449)
Q Consensus       286 ~~~~~  290 (449)
                      +....
T Consensus        83 a~~~~   87 (110)
T 3s8s_A           83 DIKGQ   87 (110)
T ss_dssp             CSTTH
T ss_pred             CCCCc
Confidence            97654

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.75  E-value=1.3e-18  Score=142.90  Aligned_cols=125  Identities=20%  Similarity=0.303  Sum_probs=83.7

Q ss_pred             EEEEEEccHHHHHHHHHHhcCCCCCCCCCcccccccccCCCCCccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeE
Q 013141          159 YGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKG  238 (449)
Q Consensus       159 ~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~  238 (449)
                      +.|++|.+...+..|++.+++....+...   ..+     ..........++|||+|||.++|+++|+++|+ .||.|..
T Consensus         6 ~~~~~~~~~~~~~~a~~~~~g~~~~g~~~---~~~-----~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~-~~G~i~~   76 (135)
T 2lea_A            6 HHHHHSSGLVPRGSHMASMTGGQQMGRGS---MSY-----GRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFE-KYGRVGD   76 (135)
T ss_dssp             --------------------------------CCS-----CCSCSSGGGCCCEEEECCCSSCHHHHHHHHHG-GGSCCSE
T ss_pred             cccccccCCCchhhhhhhccCCCCCCCCC---CCc-----CCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHH-hcCCEEE
Confidence            67888888889999998888765543321   111     12233445678999999999999999999995 9999999


Q ss_pred             EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecCCCCCC
Q 013141          239 AKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKAS  292 (449)
Q Consensus       239 i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~~~~~~  292 (449)
                      |.++.++.++.++|||||+|.+.++|++|++.|++..|.|+.|+|+++++....
T Consensus        77 v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~~~~  130 (135)
T 2lea_A           77 VYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPP  130 (135)
T ss_dssp             EECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCCCCC
T ss_pred             EEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCCC
Confidence            999999889999999999999999999999999999999999999999887553

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=2.4e-17  Score=130.38  Aligned_cols=84  Identities=24%  Similarity=0.450  Sum_probs=76.3

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC---CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 013141          321 SDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG---KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSW  397 (449)
Q Consensus       321 ~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~---~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  397 (449)
                      .......++|||+|||.++++++|+++|+.||.|.+|.|..+   +++|||+|.+.++|.+|++.||+..|.|+.|+|+|
T Consensus        16 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   95 (109)
T 1x4a_A           16 GPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF   95 (109)
T ss_dssp             CCCCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            344556789999999999999999999999999999999864   68999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 013141          398 GRNPGNK  404 (449)
Q Consensus       398 ~~~~~~~  404 (449)
                      +++....
T Consensus        96 a~~~~~~  102 (109)
T 1x4a_A           96 PRSGRGT  102 (109)
T ss_dssp             CCCCCCC
T ss_pred             cccCCCC
Confidence            9986543

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.75  E-value=1.1e-17  Score=138.60  Aligned_cols=83  Identities=25%  Similarity=0.436  Sum_probs=76.0

Q ss_pred             CCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC------CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEE
Q 013141          322 DGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRL  395 (449)
Q Consensus       322 ~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~------~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v  395 (449)
                      ......++|||+|||.++++++|+++|+.||.|.+|+|+++      +++|||+|.+.++|.+|++.||+..|.|+.|+|
T Consensus        37 ~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  116 (139)
T 1u6f_A           37 PEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKV  116 (139)
T ss_dssp             CCTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            34556789999999999999999999999999999999864      689999999999999999999999999999999


Q ss_pred             EecCCCCCC
Q 013141          396 SWGRNPGNK  404 (449)
Q Consensus       396 ~~~~~~~~~  404 (449)
                      .|+++...+
T Consensus       117 ~~a~~~~~~  125 (139)
T 1u6f_A          117 ALAASGHQR  125 (139)
T ss_dssp             EESSCCCCC
T ss_pred             EECCCCCCC
Confidence            999987544

>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=99.74  E-value=3.6e-17  Score=127.96  Aligned_cols=85  Identities=34%  Similarity=0.522  Sum_probs=77.9

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC----CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEE
Q 013141          321 SDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG----KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLS  396 (449)
Q Consensus       321 ~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~----~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~  396 (449)
                      .......++|||+|||..+++++|+++|+.||.|.+|.|+.+    +++|||+|.+.++|.+|++.||+..|+|+.|+|.
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   88 (103)
T 2cq3_A            9 SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN   88 (103)
T ss_dssp             SCCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            344566899999999999999999999999999999999875    7899999999999999999999999999999999


Q ss_pred             ecCCCCCCC
Q 013141          397 WGRNPGNKQ  405 (449)
Q Consensus       397 ~~~~~~~~~  405 (449)
                      |+++.....
T Consensus        89 ~a~~~~~~~   97 (103)
T 2cq3_A           89 NATARVMTN   97 (103)
T ss_dssp             ECCSSCCCC
T ss_pred             EcccCCCCC
Confidence            999876553

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.74  E-value=1.3e-18  Score=133.04  Aligned_cols=84  Identities=21%  Similarity=0.326  Sum_probs=75.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCC--cEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCC--CCCCCC
Q 013141          112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQ--VVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSL--MPNTDQ  187 (449)
Q Consensus       112 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~--v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~--~~~~~~  187 (449)
                      ...-.||||+|||+++|+++|+++|++||.  |.+|++++|+.+++++|||||+|.+.++|.+|++.|++..  +...++
T Consensus         6 ~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr   85 (95)
T 2lkz_A            6 HHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGK   85 (95)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTE
T ss_pred             CCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCE
Confidence            456789999999999999999999999994  7799999999999999999999999999999999999974  223567


Q ss_pred             cccccccc
Q 013141          188 PFRLNWAT  195 (449)
Q Consensus       188 ~~~~~~~~  195 (449)
                      .|+|+|++
T Consensus        86 ~i~V~~Ak   93 (95)
T 2lkz_A           86 TIGVDFAK   93 (95)
T ss_dssp             EEEEEECC
T ss_pred             EEEEEEcc
Confidence            88888876

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=1.2e-17  Score=132.37  Aligned_cols=83  Identities=14%  Similarity=0.254  Sum_probs=75.8

Q ss_pred             CCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhc--CCeeCCeEEEEEecC
Q 013141          322 DGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQ--GTAIGKQTVRLSWGR  399 (449)
Q Consensus       322 ~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~--g~~~~g~~l~v~~~~  399 (449)
                      ....++++|||+|||+++++++|+++|++||.|.+|.|++++++|||+|++.++|.+|++.|+  +..|.|+.|+|.|++
T Consensus        26 ~~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~~a~  105 (119)
T 2ad9_A           26 SAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSN  105 (119)
T ss_dssp             SCSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGGGTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEEECS
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCCCCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEEEcc
Confidence            344567899999999999999999999999999999999999999999999999999999987  468999999999998


Q ss_pred             CCCCC
Q 013141          400 NPGNK  404 (449)
Q Consensus       400 ~~~~~  404 (449)
                      ...-.
T Consensus       106 ~k~~~  110 (119)
T 2ad9_A          106 HKELK  110 (119)
T ss_dssp             SSSCC
T ss_pred             CCCCC
Confidence            76544

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.74  E-value=7.5e-19  Score=133.92  Aligned_cols=82  Identities=22%  Similarity=0.334  Sum_probs=73.1

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccC-CcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcC-CCCCCCCCccccc
Q 013141          115 TKTIWIGDLFHWMDETFLHNCFSHTG-QVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSG-SLMPNTDQPFRLN  192 (449)
Q Consensus       115 ~~~l~v~nLp~~~t~~~l~~~f~~~G-~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~-~~~~~~~~~~~~~  192 (449)
                      +++|||+|||+++|+++|+++|+.|| .|.+|++++++.+++++|||||+|.+.++|.+|++.+++ ..+  .++.|+|.
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~--~gr~i~V~   78 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNI--LGQKVSMH   78 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEE--TTEEEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEE--CCEEEEEE
Confidence            57999999999999999999999999 899999999999999999999999999999999987644 456  45788888


Q ss_pred             ccccCC
Q 013141          193 WATFSG  198 (449)
Q Consensus       193 ~~~~~~  198 (449)
                      ++.+..
T Consensus        79 ~a~~~~   84 (91)
T 2lxi_A           79 YSDPKP   84 (91)
T ss_dssp             CCCSCC
T ss_pred             EcCCCC
Confidence            887543

>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=99.74  E-value=1.4e-17  Score=128.75  Aligned_cols=81  Identities=21%  Similarity=0.467  Sum_probs=76.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeC--CeEEEEEecCC
Q 013141          323 GESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIG--KQTVRLSWGRN  400 (449)
Q Consensus       323 ~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~--g~~l~v~~~~~  400 (449)
                      .....++|||+|||..+++++|+++|++||.|.+|.+.+++++|||+|.+.++|.+|++.||+..|.  |+.|+|+|+++
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~a~~   92 (97)
T 1why_A           13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKS   92 (97)
T ss_dssp             CCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSSSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCCCCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEECCC
Confidence            3455789999999999999999999999999999999999999999999999999999999999999  99999999998


Q ss_pred             CCC
Q 013141          401 PGN  403 (449)
Q Consensus       401 ~~~  403 (449)
                      +..
T Consensus        93 ~~~   95 (97)
T 1why_A           93 GPS   95 (97)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.74  E-value=2.1e-17  Score=128.27  Aligned_cols=81  Identities=26%  Similarity=0.512  Sum_probs=76.4

Q ss_pred             CCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCC
Q 013141          323 GESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPG  402 (449)
Q Consensus       323 ~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~  402 (449)
                      .....++|||+|||..+++++|+++|+.||.|.+|.+.+++++|||+|.+.++|.+|++.||+..|.|+.|+|.|+++..
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~   90 (99)
T 2cpj_A           11 TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA   90 (99)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCS
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcCCCC
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999999864


Q ss_pred             C
Q 013141          403 N  403 (449)
Q Consensus       403 ~  403 (449)
                      .
T Consensus        91 ~   91 (99)
T 2cpj_A           91 S   91 (99)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.74  E-value=2.5e-18  Score=130.96  Aligned_cols=84  Identities=13%  Similarity=0.308  Sum_probs=77.1

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhhCC-CeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC-CceecCcceEEee
Q 013141          208 DLSIFVGDLAPDVTDSILQETFSSKYP-SVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMN-GVYCSSRPMRIDV  285 (449)
Q Consensus       208 ~~~l~v~~lp~~~t~~~l~~~f~~~~g-~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~-g~~~~g~~i~v~~  285 (449)
                      +++|||+|||+++|+++|+++|+ .|| .|.+|++++++.++.++|||||+|.+.++|.+|++.++ +..+.|+.|+|++
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~-~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~   79 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQ-SHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHY   79 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHH-HHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHH-HhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEE
Confidence            46899999999999999999995 999 89999999999999999999999999999999998874 5679999999999


Q ss_pred             cCCCCCC
Q 013141          286 ATPKKAS  292 (449)
Q Consensus       286 ~~~~~~~  292 (449)
                      +.++...
T Consensus        80 a~~~~~~   86 (91)
T 2lxi_A           80 SDPKPKI   86 (91)
T ss_dssp             CCSCCCC
T ss_pred             cCCCCCC
Confidence            9887543

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.74  E-value=2.3e-17  Score=131.85  Aligned_cols=89  Identities=27%  Similarity=0.542  Sum_probs=80.4

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcc
Q 013141          110 FTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPF  189 (449)
Q Consensus       110 ~~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~  189 (449)
                      ......++|||+|||+++++++|+++|..||.|.+|+|++++.+++++|||||+|.+.++|++|++.|++..+.  ++.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~l   87 (115)
T 2dgo_A           10 KDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLG--GRQI   87 (115)
T ss_dssp             CCSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEET--TEEC
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEEC--CEEE
Confidence            34567899999999999999999999999999999999999889999999999999999999999999999885  4788


Q ss_pred             cccccccCCCC
Q 013141          190 RLNWATFSGSD  200 (449)
Q Consensus       190 ~~~~~~~~~~~  200 (449)
                      +|.|+......
T Consensus        88 ~V~~a~~~~~~   98 (115)
T 2dgo_A           88 RTNWATRKPPA   98 (115)
T ss_dssp             EEEESSCCCCC
T ss_pred             EEEEccCCCCC
Confidence            88888765443

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=1.8e-17  Score=126.21  Aligned_cols=79  Identities=24%  Similarity=0.504  Sum_probs=74.3

Q ss_pred             CCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCCC
Q 013141          324 ESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGN  403 (449)
Q Consensus       324 ~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~~  403 (449)
                      ....++|||+|||.++++++|+++|+.||.|.+|.+.  +++|||+|.+.++|.+|++.||+..|.|+.|+|+|+++...
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   82 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSK   82 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSSCCCC
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECCCCCC
Confidence            4567899999999999999999999999999999998  78999999999999999999999999999999999998755


Q ss_pred             C
Q 013141          404 K  404 (449)
Q Consensus       404 ~  404 (449)
                      .
T Consensus        83 ~   83 (90)
T 2dnq_A           83 A   83 (90)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.74  E-value=1.8e-17  Score=130.13  Aligned_cols=87  Identities=30%  Similarity=0.515  Sum_probs=79.1

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      .....++|||+|||+++++++|+++|+.||.|.+|.++.++.+++++|||||+|.+.++|++|++.|++..+.  ++.|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~l~   88 (105)
T 1x5u_A           11 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLY--GKPIR   88 (105)
T ss_dssp             CCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCS--SCBCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeEC--CeEEE
Confidence            4467899999999999999999999999999999999999989999999999999999999999999999985  57788


Q ss_pred             ccccccCCC
Q 013141          191 LNWATFSGS  199 (449)
Q Consensus       191 ~~~~~~~~~  199 (449)
                      |.++.....
T Consensus        89 v~~a~~~~~   97 (105)
T 1x5u_A           89 VNKASAHNK   97 (105)
T ss_dssp             EEETTTTSC
T ss_pred             EEECCCCCc
Confidence            888875543

>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=1.8e-17  Score=132.40  Aligned_cols=88  Identities=24%  Similarity=0.322  Sum_probs=79.6

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      .....++|||+|||+++++++|+++|+.||.|.+|+|++++.+++++|||||+|.+.++|++|++.|++..+.  ++.|+
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~l~   98 (115)
T 2cpz_A           21 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIG--MKRLK   98 (115)
T ss_dssp             CCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEET--TEECE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEEC--CEEEE
Confidence            4457789999999999999999999999999999999999989999999999999999999999999999984  57888


Q ss_pred             ccccccCCCC
Q 013141          191 LNWATFSGSD  200 (449)
Q Consensus       191 ~~~~~~~~~~  200 (449)
                      |.|+......
T Consensus        99 V~~a~~~~~~  108 (115)
T 2cpz_A           99 VQLKRSKNDS  108 (115)
T ss_dssp             EECCCCSCCC
T ss_pred             EEEcCCCCcC
Confidence            8888765443

>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=99.73  E-value=2.4e-17  Score=127.98  Aligned_cols=82  Identities=24%  Similarity=0.393  Sum_probs=75.6

Q ss_pred             CCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC------CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 013141          324 ESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSW  397 (449)
Q Consensus       324 ~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~------~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  397 (449)
                      ....++|||+|||.++++++|+++|+.||.|.+|.|+.+      +++|||+|.+.++|.+|++.||+..|.|+.|+|.|
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   84 (99)
T 1whw_A            5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            345789999999999999999999999999999999864      48999999999999999999999999999999999


Q ss_pred             cCCCCCCC
Q 013141          398 GRNPGNKQ  405 (449)
Q Consensus       398 ~~~~~~~~  405 (449)
                      +++.....
T Consensus        85 a~~~~~~~   92 (99)
T 1whw_A           85 STIKKEAS   92 (99)
T ss_dssp             CCCCSTTC
T ss_pred             cCCCcccc
Confidence            99876553

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=1.9e-17  Score=129.37  Aligned_cols=88  Identities=25%  Similarity=0.455  Sum_probs=79.6

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      .....++|||+|||+++++++|+++|+.||.|.+|++++++.+++++|||||+|.+.++|.+|++.|++..+.  ++.|+
T Consensus         8 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~--g~~l~   85 (102)
T 1x5s_A            8 MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVD--GRQIR   85 (102)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTT--SCCCE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEEC--CeEEE
Confidence            3457899999999999999999999999999999999999989999999999999999999999999999984  57788


Q ss_pred             ccccccCCCC
Q 013141          191 LNWATFSGSD  200 (449)
Q Consensus       191 ~~~~~~~~~~  200 (449)
                      |.++......
T Consensus        86 v~~a~~~~~~   95 (102)
T 1x5s_A           86 VDQAGKSSDN   95 (102)
T ss_dssp             EEEEECCCCC
T ss_pred             EEECCCCCCC
Confidence            8888765443

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.73  E-value=2.8e-17  Score=126.55  Aligned_cols=80  Identities=26%  Similarity=0.500  Sum_probs=74.3

Q ss_pred             CCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC------CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 013141          325 SNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWG  398 (449)
Q Consensus       325 ~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~------~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~  398 (449)
                      ...++|||+|||.++++++|+++|+.||.|.+|.+.++      +++|||+|.+.++|.+|++.||+..|.|+.|+|+|+
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            45789999999999999999999999999999999874      579999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 013141          399 RNPGNK  404 (449)
Q Consensus       399 ~~~~~~  404 (449)
                      +++..+
T Consensus        83 ~~~~~~   88 (95)
T 2dnz_A           83 TERLDG   88 (95)
T ss_dssp             SCCCCC
T ss_pred             ccccCC
Confidence            986543

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=3.1e-17  Score=127.30  Aligned_cols=86  Identities=20%  Similarity=0.355  Sum_probs=77.5

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      .....++|||+|||+++++++|+++|+.||.|.+|.++.++.+++++|||||+|.+.++|++|++ +++..+.  ++.|+
T Consensus         6 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~--g~~l~   82 (99)
T 2dgs_A            6 SGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIM--GKKVE   82 (99)
T ss_dssp             CCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSS--SCBCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEEC--CeEEE
Confidence            34578999999999999999999999999999999999999899999999999999999999998 9999884  57788


Q ss_pred             ccccccCCC
Q 013141          191 LNWATFSGS  199 (449)
Q Consensus       191 ~~~~~~~~~  199 (449)
                      |.++.....
T Consensus        83 V~~a~~~~~   91 (99)
T 2dgs_A           83 VKRAEPRDS   91 (99)
T ss_dssp             EEECCCCCC
T ss_pred             EEECCCCcc
Confidence            888875543

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=4.8e-17  Score=127.23  Aligned_cols=83  Identities=29%  Similarity=0.529  Sum_probs=76.3

Q ss_pred             CCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeC----CCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 013141          322 DGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV----GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSW  397 (449)
Q Consensus       322 ~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~----~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  397 (449)
                      ......++|||+|||..+++++|+++|+.||.|.+|.|++    ++++|||+|.+.++|.+|++.||+..|.|+.|+|.|
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 2cqi_A           10 EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNW   89 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCCCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEE
Confidence            3455679999999999999999999999999999999987    368999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 013141          398 GRNPGNK  404 (449)
Q Consensus       398 ~~~~~~~  404 (449)
                      ++++..+
T Consensus        90 a~~~~~~   96 (103)
T 2cqi_A           90 ATTPSSQ   96 (103)
T ss_dssp             CCCTTCC
T ss_pred             CCCCccc
Confidence            9986544

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=3e-17  Score=128.44  Aligned_cols=84  Identities=29%  Similarity=0.522  Sum_probs=76.8

Q ss_pred             CCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC----CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 013141          322 DGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG----KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSW  397 (449)
Q Consensus       322 ~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~----~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  397 (449)
                      ......++|||+|||+.+++++|+++|+.||.|.+|.|..+    +++|||+|.+.++|.+|++.||+..|.|+.|+|.|
T Consensus        10 ~~~~~~~~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           10 ITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVAL   89 (103)
T ss_dssp             CCCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCCCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            34457889999999999999999999999999999999854    78999999999999999999999999999999999


Q ss_pred             cCCCCCCC
Q 013141          398 GRNPGNKQ  405 (449)
Q Consensus       398 ~~~~~~~~  405 (449)
                      +++...+.
T Consensus        90 a~~~~~~~   97 (103)
T 2d9p_A           90 AQRKEERQ   97 (103)
T ss_dssp             CSSCCCCC
T ss_pred             ecccccCC
Confidence            99876543

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=3.8e-17  Score=124.96  Aligned_cols=80  Identities=19%  Similarity=0.402  Sum_probs=74.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCC
Q 013141          323 GESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPG  402 (449)
Q Consensus       323 ~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~  402 (449)
                      .....++|||+|||..+++++|+++|+.||.|.+|.+.  +++|||+|.+.++|.+|++.||+..|.|+.|+|+|++++.
T Consensus         6 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~--~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   83 (92)
T 2dgt_A            6 SGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSRL   83 (92)
T ss_dssp             CCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC--SSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEESSCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE--CCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEccCCC
Confidence            45567999999999999999999999999999999998  4599999999999999999999999999999999999865


Q ss_pred             CC
Q 013141          403 NK  404 (449)
Q Consensus       403 ~~  404 (449)
                      ..
T Consensus        84 ~~   85 (92)
T 2dgt_A           84 RT   85 (92)
T ss_dssp             SC
T ss_pred             CC
Confidence            43

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.73  E-value=7.4e-17  Score=128.89  Aligned_cols=84  Identities=33%  Similarity=0.648  Sum_probs=76.7

Q ss_pred             CCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC------CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEE
Q 013141          322 DGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRL  395 (449)
Q Consensus       322 ~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~------~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v  395 (449)
                      ......++|||+|||..+++++|+++|+.||.|.+|.|+++      +++|||+|.+.++|.+|++.||+..|.|+.|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   89 (115)
T 2dgo_A           10 KDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRT   89 (115)
T ss_dssp             CCSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            34456889999999999999999999999999999999875      589999999999999999999999999999999


Q ss_pred             EecCCCCCCC
Q 013141          396 SWGRNPGNKQ  405 (449)
Q Consensus       396 ~~~~~~~~~~  405 (449)
                      .|+++.....
T Consensus        90 ~~a~~~~~~~   99 (115)
T 2dgo_A           90 NWATRKPPAP   99 (115)
T ss_dssp             EESSCCCCCS
T ss_pred             EEccCCCCCC
Confidence            9999876543

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=1.6e-17  Score=130.00  Aligned_cols=86  Identities=22%  Similarity=0.345  Sum_probs=78.7

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      ...+.++|||+|||+++++++|+++|+.||.|.+|.++.++.+++++|||||+|.+.++|++|++.|++..+.  ++.|+
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~--g~~l~   86 (103)
T 2dnm_A            9 DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELD--GRELR   86 (103)
T ss_dssp             CCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBT--TBCCE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEEC--CcEEE
Confidence            4567899999999999999999999999999999999999999999999999999999999999999999985  57788


Q ss_pred             ccccccCC
Q 013141          191 LNWATFSG  198 (449)
Q Consensus       191 ~~~~~~~~  198 (449)
                      |.++....
T Consensus        87 V~~a~~~~   94 (103)
T 2dnm_A           87 VQVARYGR   94 (103)
T ss_dssp             EEECSSCC
T ss_pred             EEECCcCC
Confidence            88887543

>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=99.73  E-value=4.8e-17  Score=127.75  Aligned_cols=88  Identities=20%  Similarity=0.343  Sum_probs=78.7

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCC-CCCcc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPN-TDQPF  189 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~-~~~~~  189 (449)
                      .....++|||+|||+++++++|+++|+.||.|.+|.|+.++ +++++|||||+|.+.++|++|++.|++..+.+ ..+.|
T Consensus        11 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l   89 (105)
T 2dnh_A           11 RGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSL   89 (105)
T ss_dssp             SCCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccE
Confidence            34578999999999999999999999999999999999997 79999999999999999999999999998753 33788


Q ss_pred             cccccccCCC
Q 013141          190 RLNWATFSGS  199 (449)
Q Consensus       190 ~~~~~~~~~~  199 (449)
                      +|.++.....
T Consensus        90 ~V~~a~~~~~   99 (105)
T 2dnh_A           90 VVKFADTDKE   99 (105)
T ss_dssp             EEEESCSSCC
T ss_pred             EEEECccCcc
Confidence            9988876543

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A

Probab=99.73  E-value=1.5e-17  Score=141.88  Aligned_cols=130  Identities=18%  Similarity=0.272  Sum_probs=80.6

Q ss_pred             EEEccHHHHHHHHHHhcCCCCCCCCCcccccccccC---------------CCCCccccCCCceEEEcCCCCCCCHHHHH
Q 013141          162 VEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATFS---------------GSDRRTEACSDLSIFVGDLAPDVTDSILQ  226 (449)
Q Consensus       162 V~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~~~~~---------------~~~~~~~~~~~~~l~v~~lp~~~t~~~l~  226 (449)
                      .+|.+.++|+.|+..+++......++..+..+....               ....+....+.++|||+|||+++++++|+
T Consensus        11 ee~e~~~d~e~~~~~~~~~~~~~kgr~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~   90 (165)
T 1rk8_A           11 EEFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQ   90 (165)
T ss_dssp             -------------------------------------------------------CCCCC-CEEEEEESCCTTCCHHHHH
T ss_pred             hhhhccccccccchhhccccccccCCCCCCCccccccccCccccccCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHH
Confidence            789999999999999888776545555554442211               11112334556789999999999999999


Q ss_pred             HHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecCCCCCC
Q 013141          227 ETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKAS  292 (449)
Q Consensus       227 ~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~~~~~~  292 (449)
                      ++|+ .||.|..|.++.++.++.++|||||+|.+.++|.+||+.|++..|.|+.|.|.++..+...
T Consensus        91 ~~F~-~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~  155 (165)
T 1rk8_A           91 EKFC-DYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPK  155 (165)
T ss_dssp             HHHG-GGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEECC--
T ss_pred             HHhh-cCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCCCC
Confidence            9995 9999999999999999999999999999999999999999999999999999999876543

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A

Probab=99.73  E-value=2.2e-17  Score=129.94  Aligned_cols=88  Identities=20%  Similarity=0.428  Sum_probs=80.1

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCC-CCCCCCcc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSL-MPNTDQPF  189 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~-~~~~~~~~  189 (449)
                      .....++|||+|||+++++++|+++|+.||.|.+|+++.++.+++++|||||+|.+.++|.+|++.|++.. +.+.++.|
T Consensus         9 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l   88 (106)
T 2dgp_A            9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPI   88 (106)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceE
Confidence            45678999999999999999999999999999999999999999999999999999999999999999976 45567889


Q ss_pred             cccccccCC
Q 013141          190 RLNWATFSG  198 (449)
Q Consensus       190 ~~~~~~~~~  198 (449)
                      +|.++....
T Consensus        89 ~v~~a~~~~   97 (106)
T 2dgp_A           89 QVKPADSES   97 (106)
T ss_dssp             EEEECCCCS
T ss_pred             EEEECCccc
Confidence            998887554

>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=99.73  E-value=2.2e-17  Score=129.28  Aligned_cols=81  Identities=15%  Similarity=0.172  Sum_probs=74.1

Q ss_pred             CCCCcEEEEcCCCCC-CCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcC--CeeCCeEEEEEecCC
Q 013141          324 ESNNATIFVGALDSD-VSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQG--TAIGKQTVRLSWGRN  400 (449)
Q Consensus       324 ~~~~~~l~V~nlp~~-~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g--~~~~g~~l~v~~~~~  400 (449)
                      ..++++|||+|||++ +++++|+++|++||.|.+|.|++++++|||+|.+.++|.+|++.|++  ..|.|+.|+|.|++.
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~  101 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEK  101 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECS
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEECcc
Confidence            456889999999998 99999999999999999999999999999999999999999998864  569999999999987


Q ss_pred             CCCC
Q 013141          401 PGNK  404 (449)
Q Consensus       401 ~~~~  404 (449)
                      ....
T Consensus       102 ~~~~  105 (112)
T 1x4f_A          102 YKKL  105 (112)
T ss_dssp             CSSS
T ss_pred             cccc
Confidence            6543

>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=99.73  E-value=1.3e-17  Score=126.17  Aligned_cols=82  Identities=29%  Similarity=0.606  Sum_probs=74.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      .+.++|||+|||+++++++|+++|+.||.|.+|.++.++.+++++|||||+|.+.++|++|++.|++..+.  ++.|+|.
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~--g~~l~v~   81 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLG--GRQIRTN   81 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEET--TEECEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEEC--CeEEEEE
Confidence            46789999999999999999999999999999999999889999999999999999999999999999884  4778888


Q ss_pred             cccc
Q 013141          193 WATF  196 (449)
Q Consensus       193 ~~~~  196 (449)
                      |+..
T Consensus        82 ~a~~   85 (87)
T 3bs9_A           82 WATR   85 (87)
T ss_dssp             EEC-
T ss_pred             ecCC
Confidence            7764

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.73  E-value=6.4e-18  Score=129.23  Aligned_cols=80  Identities=20%  Similarity=0.408  Sum_probs=74.4

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhhCCC--eeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCc----eecCcce
Q 013141          208 DLSIFVGDLAPDVTDSILQETFSSKYPS--VKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGV----YCSSRPM  281 (449)
Q Consensus       208 ~~~l~v~~lp~~~t~~~l~~~f~~~~g~--v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~----~~~g~~i  281 (449)
                      =++|||+|||+++|+++|+++|+ .||.  |.+|++++|+.+++++|||||+|.+.++|.+|++.||+.    .|+|+.|
T Consensus         9 m~tlfV~nL~~~~tee~L~~~F~-~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i   87 (95)
T 2lkz_A            9 MDTIILRNIAPHTVVDSIMTALS-PYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTI   87 (95)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHST-TTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEE
T ss_pred             cCEEEEeCCCCcCCHHHHHHHHH-hhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEE
Confidence            35899999999999999999995 9995  679999999999999999999999999999999999986    5899999


Q ss_pred             EEeecCC
Q 013141          282 RIDVATP  288 (449)
Q Consensus       282 ~v~~~~~  288 (449)
                      .|++++.
T Consensus        88 ~V~~Aks   94 (95)
T 2lkz_A           88 GVDFAKS   94 (95)
T ss_dssp             EEEECCC
T ss_pred             EEEEccC
Confidence            9999875

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=6.7e-17  Score=129.31  Aligned_cols=83  Identities=28%  Similarity=0.422  Sum_probs=74.7

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC------CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEE
Q 013141          321 SDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKLQGTAIGKQTVR  394 (449)
Q Consensus       321 ~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~------~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~  394 (449)
                      .......++|||+|||..+++++|+++|+.||.|.+|+|+++      +++|||+|.+.++|.+|++.|++ .|.|+.|+
T Consensus        11 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~   89 (116)
T 2cqd_A           11 SQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKAN   89 (116)
T ss_dssp             CCCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECE
T ss_pred             CcCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEE
Confidence            344567899999999999999999999999999999999874      58999999999999999999998 89999999


Q ss_pred             EEecCCCCCC
Q 013141          395 LSWGRNPGNK  404 (449)
Q Consensus       395 v~~~~~~~~~  404 (449)
                      |+|++.....
T Consensus        90 V~~a~~~~~~   99 (116)
T 2cqd_A           90 VNLAYLGAKP   99 (116)
T ss_dssp             EEESTTTCCC
T ss_pred             EEEcccCCCc
Confidence            9999875443

>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=99.72  E-value=3.3e-17  Score=129.55  Aligned_cols=81  Identities=30%  Similarity=0.642  Sum_probs=76.5

Q ss_pred             CCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCCC
Q 013141          324 ESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGN  403 (449)
Q Consensus       324 ~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~~  403 (449)
                      ....++|||+|||..+++++|+++|+.||.|.+|.|++++++|||+|.+.++|.+|++.||+..|.|+.|+|.|+++...
T Consensus        22 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  101 (109)
T 1x4g_A           22 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPD  101 (109)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCCS
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCCCCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecCCCCC
Confidence            44578999999999999999999999999999999999999999999999999999999999999999999999998754


Q ss_pred             C
Q 013141          404 K  404 (449)
Q Consensus       404 ~  404 (449)
                      .
T Consensus       102 ~  102 (109)
T 1x4g_A          102 M  102 (109)
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=99.72  E-value=2.4e-17  Score=127.93  Aligned_cols=86  Identities=43%  Similarity=0.797  Sum_probs=78.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCcE-EEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCc--
Q 013141          112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVV-NVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQP--  188 (449)
Q Consensus       112 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~-~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~--  188 (449)
                      ....++|||+|||+++++++|+++|+.||.|. +|++++++.+++++|||||+|.+.++|++|++.|++..+.++...  
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            45789999999999999999999999999999 999999999999999999999999999999999999998665422  


Q ss_pred             ccccccccC
Q 013141          189 FRLNWATFS  197 (449)
Q Consensus       189 ~~~~~~~~~  197 (449)
                      +++.|+...
T Consensus        86 l~v~~a~~~   94 (99)
T 2div_A           86 FKLNYATYS   94 (99)
T ss_dssp             CCEEETTCC
T ss_pred             EEEeecCCC
Confidence            888888654

>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=99.72  E-value=5.3e-17  Score=127.84  Aligned_cols=86  Identities=23%  Similarity=0.505  Sum_probs=78.2

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcc
Q 013141          110 FTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPF  189 (449)
Q Consensus       110 ~~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~  189 (449)
                      ......++|||+|||+++++++|+++|+.||.|.+|.+++++.+++++|||||+|.+.++|.+|++.|++..+.  ++.|
T Consensus        21 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~--g~~l   98 (108)
T 2jrs_A           21 KGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELA--GRPM   98 (108)
T ss_dssp             CSCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSS--SSCC
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEEC--CEEE
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999885  5778


Q ss_pred             cccccccC
Q 013141          190 RLNWATFS  197 (449)
Q Consensus       190 ~~~~~~~~  197 (449)
                      +|.++...
T Consensus        99 ~V~~a~~k  106 (108)
T 2jrs_A           99 KVGHVTER  106 (108)
T ss_dssp             EEECSCSS
T ss_pred             EEEEcccC
Confidence            88777643

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=1.9e-17  Score=127.46  Aligned_cols=84  Identities=20%  Similarity=0.312  Sum_probs=76.9

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcc
Q 013141          110 FTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPF  189 (449)
Q Consensus       110 ~~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~  189 (449)
                      ....+.++|||+|||+++++++|+++|+.||.|.+|.++.++.+++++|||||+|.+.++|.+|++.|++..+.  ++.|
T Consensus        10 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~--g~~l   87 (95)
T 2cqc_A           10 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELD--GRRI   87 (95)
T ss_dssp             CSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEET--TEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEEC--CEEE
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999884  5777


Q ss_pred             cccccc
Q 013141          190 RLNWAT  195 (449)
Q Consensus       190 ~~~~~~  195 (449)
                      +|.+++
T Consensus        88 ~v~~a~   93 (95)
T 2cqc_A           88 RVSGPS   93 (95)
T ss_dssp             EEECCS
T ss_pred             EEEecC
Confidence            877765

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.72  E-value=1.7e-17  Score=127.55  Aligned_cols=83  Identities=20%  Similarity=0.366  Sum_probs=75.7

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      .....++|||+|||+++++++|+++|+.||.|.+|.++.++.+++++|||||+|.+.++|++|++.|++..+.  ++.|+
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~--g~~l~   89 (94)
T 2e5h_A           12 LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLF--GRVIK   89 (94)
T ss_dssp             CCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEET--TEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeC--CcEEE
Confidence            3457889999999999999999999999999999999999989999999999999999999999999999884  57777


Q ss_pred             ccccc
Q 013141          191 LNWAT  195 (449)
Q Consensus       191 ~~~~~  195 (449)
                      |.|++
T Consensus        90 v~~ak   94 (94)
T 2e5h_A           90 ASIAI   94 (94)
T ss_dssp             EEECC
T ss_pred             EEecC
Confidence            77653

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A

Probab=99.72  E-value=2.8e-17  Score=133.73  Aligned_cols=86  Identities=20%  Similarity=0.326  Sum_probs=78.3

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcc
Q 013141          110 FTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPF  189 (449)
Q Consensus       110 ~~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~  189 (449)
                      ....+.++|||+|||+++++++|+++|+.||.|.+|++++++.+++++|||||+|.+.++|++||+.|++..+.  ++.|
T Consensus        41 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~--g~~l  118 (129)
T 2kxn_B           41 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELD--GRRI  118 (129)
T ss_dssp             SCCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSS--SSCC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEEC--CEEE
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999885  5778


Q ss_pred             cccccccC
Q 013141          190 RLNWATFS  197 (449)
Q Consensus       190 ~~~~~~~~  197 (449)
                      +|.|+...
T Consensus       119 ~V~~a~~~  126 (129)
T 2kxn_B          119 RVDFSITK  126 (129)
T ss_dssp             EESCCSSS
T ss_pred             EEEEecCC
Confidence            88887643

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.72  E-value=2.1e-17  Score=132.73  Aligned_cols=83  Identities=24%  Similarity=0.354  Sum_probs=75.7

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcc
Q 013141          110 FTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPF  189 (449)
Q Consensus       110 ~~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~  189 (449)
                      ......++|||+|||+++++++|+++|+.||.|.+|++++++.+++++|||||+|.+.++|++|++.|++..+.  ++.|
T Consensus        35 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~--g~~l  112 (118)
T 2khc_A           35 IEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVG--TKRL  112 (118)
T ss_dssp             CCCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEET--TEEC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEEC--CEEE
Confidence            34567899999999999999999999999999999999999989999999999999999999999999999885  4667


Q ss_pred             ccccc
Q 013141          190 RLNWA  194 (449)
Q Consensus       190 ~~~~~  194 (449)
                      +|.|+
T Consensus       113 ~V~~a  117 (118)
T 2khc_A          113 KVQLK  117 (118)
T ss_dssp             CEEEC
T ss_pred             EEEec
Confidence            77665

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=5.7e-17  Score=126.81  Aligned_cols=87  Identities=25%  Similarity=0.450  Sum_probs=78.1

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCc
Q 013141          109 NFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQP  188 (449)
Q Consensus       109 ~~~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~  188 (449)
                      .......++|||+|||+++++++|+++|+.||.|.+|.++.+  +++++|||||+|.+.++|.+|++.|++..+  .++.
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~   84 (103)
T 2d9p_A            9 RITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIV--ATKP   84 (103)
T ss_dssp             CCCCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBS--SSSB
T ss_pred             ccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEe--CCcE
Confidence            344568899999999999999999999999999999999998  799999999999999999999999999998  4578


Q ss_pred             ccccccccCCC
Q 013141          189 FRLNWATFSGS  199 (449)
Q Consensus       189 ~~~~~~~~~~~  199 (449)
                      |+|.++.....
T Consensus        85 l~V~~a~~~~~   95 (103)
T 2d9p_A           85 LYVALAQRKEE   95 (103)
T ss_dssp             CEEEECSSCCC
T ss_pred             EEEEEeccccc
Confidence            88888875543

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.72  E-value=4.2e-17  Score=126.53  Aligned_cols=82  Identities=17%  Similarity=0.392  Sum_probs=75.4

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEE--------EEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCC
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVN--------VKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLM  182 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~--------v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~  182 (449)
                      .....++|||+|||+++++++|+++|+.||.|.+        |+++.++.+++++|||||+|.+.++|.+|++.|++..+
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~   88 (99)
T 2la6_A            9 SHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEF   88 (99)
T ss_dssp             SCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEe
Confidence            4467899999999999999999999999999999        99999999999999999999999999999999999998


Q ss_pred             CCCCCccccccc
Q 013141          183 PNTDQPFRLNWA  194 (449)
Q Consensus       183 ~~~~~~~~~~~~  194 (449)
                      .  ++.|+|.++
T Consensus        89 ~--g~~l~V~~A   98 (99)
T 2la6_A           89 S--GNPIKVSFA   98 (99)
T ss_dssp             S--SSBCEEEEC
T ss_pred             C--CcEEEEEec
Confidence            5  467777765

>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=99.72  E-value=8.6e-18  Score=127.93  Aligned_cols=80  Identities=21%  Similarity=0.378  Sum_probs=69.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccC--CcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccccc
Q 013141          116 KTIWIGDLFHWMDETFLHNCFSHTG--QVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNW  193 (449)
Q Consensus       116 ~~l~v~nLp~~~t~~~l~~~f~~~G--~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~  193 (449)
                      .+|||+|||+++++++|+++|+.||  .|.+|+++.++.+|+++|||||+|.+.++|++|++.|++..+.  ++.|+|.+
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~--gr~i~V~~   79 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELH--GQNPVVTP   79 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSS--SCCCEECC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeC--CEEEEEEE
Confidence            4799999999999999999999999  9999999999999999999999999999999999999999995  46777777


Q ss_pred             cccC
Q 013141          194 ATFS  197 (449)
Q Consensus       194 ~~~~  197 (449)
                      +.+.
T Consensus        80 ~~~~   83 (90)
T 3p5t_L           80 SNKL   83 (90)
T ss_dssp             C---
T ss_pred             CCCC
Confidence            7644

>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=5.4e-17  Score=127.90  Aligned_cols=87  Identities=21%  Similarity=0.431  Sum_probs=78.7

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEec-CCCCCcccEEEEEEccHHHHHHHHHHh-cCCCCCCCCCc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRN-KQTGQSEGYGFVEFYSRAAAEKVLQSY-SGSLMPNTDQP  188 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~-~~~g~~~g~afV~f~~~~~A~~Al~~l-~~~~~~~~~~~  188 (449)
                      .....++|||+|||+++++++|+++|+.||.|.+|.++++ +.+++++|||||+|.+.++|.+|++.| ++..+.  ++.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~--g~~   88 (107)
T 2cph_A           11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLY--GRR   88 (107)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSS--SCB
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeEC--CCE
Confidence            4567899999999999999999999999999999999999 788999999999999999999999999 899885  578


Q ss_pred             ccccccccCCC
Q 013141          189 FRLNWATFSGS  199 (449)
Q Consensus       189 ~~~~~~~~~~~  199 (449)
                      |+|.|+.....
T Consensus        89 l~v~~a~~~~~   99 (107)
T 2cph_A           89 LVLEWADSEVT   99 (107)
T ss_dssp             CEEEECCCCCC
T ss_pred             EEEEeCCCCCC
Confidence            88888875543

>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=99.72  E-value=5.8e-17  Score=129.48  Aligned_cols=83  Identities=28%  Similarity=0.524  Sum_probs=75.7

Q ss_pred             CCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC------CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEE
Q 013141          322 DGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRL  395 (449)
Q Consensus       322 ~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~------~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v  395 (449)
                      ......++|||+|||.++++++|+++|+.||.|.+|+|+.+      +++|||+|.+.++|.+|++.||+..|.|+.|+|
T Consensus        20 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   99 (115)
T 2cpz_A           20 KEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKV   99 (115)
T ss_dssp             CCCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             cCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            34456789999999999999999999999999999999864      379999999999999999999999999999999


Q ss_pred             EecCCCCCC
Q 013141          396 SWGRNPGNK  404 (449)
Q Consensus       396 ~~~~~~~~~  404 (449)
                      +|+++...+
T Consensus       100 ~~a~~~~~~  108 (115)
T 2cpz_A          100 QLKRSKNDS  108 (115)
T ss_dssp             ECCCCSCCC
T ss_pred             EEcCCCCcC
Confidence            999987554

>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=4.7e-17  Score=128.25  Aligned_cols=83  Identities=28%  Similarity=0.544  Sum_probs=76.6

Q ss_pred             CCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC-------CcEEEEEecCHHHHHHHHHHh-cCCeeCCeEE
Q 013141          322 DGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-------KGCGFVQFANRKDAEVALQKL-QGTAIGKQTV  393 (449)
Q Consensus       322 ~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~-------~g~afV~F~~~~~A~~A~~~l-~g~~~~g~~l  393 (449)
                      ......++|||+|||..+++++|+++|+.||.|.+|.|+++       +++|||+|.+.++|.+|++.| |+..|.|+.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l   89 (107)
T 2cph_A           10 PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRL   89 (107)
T ss_dssp             CCSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBC
T ss_pred             ccCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEE
Confidence            34566899999999999999999999999999999999876       699999999999999999999 9999999999


Q ss_pred             EEEecCCCCCC
Q 013141          394 RLSWGRNPGNK  404 (449)
Q Consensus       394 ~v~~~~~~~~~  404 (449)
                      +|+|+++....
T Consensus        90 ~v~~a~~~~~~  100 (107)
T 2cph_A           90 VLEWADSEVTV  100 (107)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEeCCCCCCC
Confidence            99999987554

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=6.8e-17  Score=126.37  Aligned_cols=83  Identities=30%  Similarity=0.522  Sum_probs=76.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC------CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEE
Q 013141          323 GESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLS  396 (449)
Q Consensus       323 ~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~------~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~  396 (449)
                      .....++|||+|||..+++++|+++|+.||.|.+|.|+.+      +++|||+|.+.++|.+|++.||+..|.|+.|+|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   90 (103)
T 2cq0_A           11 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVE   90 (103)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            3556799999999999999999999999999999999864      4799999999999999999999999999999999


Q ss_pred             ecCCCCCCC
Q 013141          397 WGRNPGNKQ  405 (449)
Q Consensus       397 ~~~~~~~~~  405 (449)
                      |+++...+.
T Consensus        91 ~a~~~~~~~   99 (103)
T 2cq0_A           91 WAKPSTNSG   99 (103)
T ss_dssp             ESSCCCCSC
T ss_pred             ECCCCCCCC
Confidence            999876543

>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=99.72  E-value=3.8e-17  Score=130.49  Aligned_cols=81  Identities=21%  Similarity=0.498  Sum_probs=74.8

Q ss_pred             CCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC-----CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 013141          324 ESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-----KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWG  398 (449)
Q Consensus       324 ~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~-----~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~  398 (449)
                      ....++|||+|||.++++++|+++|+.||.|.+|.|..+     +++|||+|.+.++|.+|++.|||..|.|+.|+|+|+
T Consensus         4 ~~~~~~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            4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQA   83 (116)
T ss_dssp             TCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            345789999999999999999999999999999999875     499999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 013141          399 RNPGNK  404 (449)
Q Consensus       399 ~~~~~~  404 (449)
                      +.+...
T Consensus        84 ~~~~~~   89 (116)
T 2fy1_A           84 KKPSFQ   89 (116)
T ss_dssp             CCSSCS
T ss_pred             CCCCCC
Confidence            986543

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=8.7e-17  Score=124.75  Aligned_cols=81  Identities=25%  Similarity=0.419  Sum_probs=74.2

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHhHHHhhcccc--CceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 013141          321 SDGESNNATIFVGALDSDVSDEDLREPFSQF--GEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWG  398 (449)
Q Consensus       321 ~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~--G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~  398 (449)
                      .......++|||+|||..+++++|+++|+.|  |.|.+|.+.  +++|||+|.+.++|.+|++.||+..|.|+.|+|.|+
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   86 (99)
T 2cpd_A            9 EDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLA   86 (99)
T ss_dssp             CSCSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECC
T ss_pred             ccccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence            3445567899999999999999999999999  999999887  679999999999999999999999999999999999


Q ss_pred             CCCCC
Q 013141          399 RNPGN  403 (449)
Q Consensus       399 ~~~~~  403 (449)
                      ++...
T Consensus        87 ~~~~~   91 (99)
T 2cpd_A           87 KPVDK   91 (99)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            98654

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=2.1e-17  Score=127.55  Aligned_cols=81  Identities=30%  Similarity=0.565  Sum_probs=74.6

Q ss_pred             CCCcEEEEcCCCCCCCHhHHHhhccccCceEEE-EEeCC------CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 013141          325 SNNATIFVGALDSDVSDEDLREPFSQFGEILSV-KIPVG------KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSW  397 (449)
Q Consensus       325 ~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v-~i~~~------~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  397 (449)
                      ...++|||+|||..+++++|+++|+.||.|.+| .|+++      +++|||+|.+.++|.+|++.||+..|.|+.|+|+|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   82 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSY   82 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            357899999999999999999999999999999 88764      68999999999999999999999999999999999


Q ss_pred             cCCCCCCC
Q 013141          398 GRNPGNKQ  405 (449)
Q Consensus       398 ~~~~~~~~  405 (449)
                      +++...+.
T Consensus        83 a~~~~~~~   90 (96)
T 1x5t_A           83 AFKKDSKG   90 (96)
T ss_dssp             SCCCCCCC
T ss_pred             ecccCCCC
Confidence            99876543

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.72  E-value=1.4e-17  Score=136.32  Aligned_cols=86  Identities=19%  Similarity=0.287  Sum_probs=77.0

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEE--EEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCC----CCC
Q 013141          110 FTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVN--VKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGS----LMP  183 (449)
Q Consensus       110 ~~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~--v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~----~~~  183 (449)
                      ......++|||+|||+++|+++|+++|+.||.|..  |+|++|+.+|+++|||||+|.+. +|.+|++.|++.    .+ 
T Consensus        18 ~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~-   95 (131)
T 2m2b_A           18 SSENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTI-   95 (131)
T ss_dssp             CCSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCG-
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccC-
Confidence            34467889999999999999999999999999976  99999999999999999999999 999999999998    66 


Q ss_pred             CCCCcccccccccCC
Q 013141          184 NTDQPFRLNWATFSG  198 (449)
Q Consensus       184 ~~~~~~~~~~~~~~~  198 (449)
                       .++.|+|.++....
T Consensus        96 -~gr~l~V~~a~~~~  109 (131)
T 2m2b_A           96 -DGKTINVEFAKGSK  109 (131)
T ss_dssp             -GGCCCCCEECCCSC
T ss_pred             -CCEEEEEEECCCCC
Confidence             45778888887543

>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=99.72  E-value=1.6e-17  Score=125.08  Aligned_cols=82  Identities=22%  Similarity=0.434  Sum_probs=75.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccc
Q 013141          112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRL  191 (449)
Q Consensus       112 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~  191 (449)
                      ..+.++|||+|||+++++++|+++|+.||.|.+|.+++++.+++++|||||+|.+.++|.+|++.|++..+.  ++.|++
T Consensus         4 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~l~v   81 (85)
T 3mdf_A            4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELF--GRTIRV   81 (85)
T ss_dssp             CCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEET--TEECEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEEC--CcEEEE
Confidence            357899999999999999999999999999999999999889999999999999999999999999999984  567777


Q ss_pred             cccc
Q 013141          192 NWAT  195 (449)
Q Consensus       192 ~~~~  195 (449)
                      .|++
T Consensus        82 ~~ak   85 (85)
T 3mdf_A           82 NLAK   85 (85)
T ss_dssp             EECC
T ss_pred             EEcC
Confidence            7653

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.72  E-value=7e-17  Score=125.56  Aligned_cols=84  Identities=18%  Similarity=0.381  Sum_probs=76.3

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC-----CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEE
Q 013141          321 SDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-----KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRL  395 (449)
Q Consensus       321 ~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~-----~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v  395 (449)
                      .......++|||+|||..+++++|+++|+.||.|.+|.|..+     +++|||+|.+.++|.+|++.||+..|.|+.|+|
T Consensus        11 ~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   90 (100)
T 2do4_A           11 YSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKV   90 (100)
T ss_dssp             CSSCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEE
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            334566789999999999999999999999999999999874     489999999999999999999999999999999


Q ss_pred             EecCCCCCC
Q 013141          396 SWGRNPGNK  404 (449)
Q Consensus       396 ~~~~~~~~~  404 (449)
                      .|++++..+
T Consensus        91 ~~a~~~~~~   99 (100)
T 2do4_A           91 AISNSGPSS   99 (100)
T ss_dssp             EECCCCSCC
T ss_pred             EECCCCCCC
Confidence            999987543

>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=99.72  E-value=2.5e-17  Score=123.40  Aligned_cols=81  Identities=35%  Similarity=0.591  Sum_probs=75.0

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccccc
Q 013141          115 TKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWA  194 (449)
Q Consensus       115 ~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~~  194 (449)
                      +.+|||+|||+++++++|+++|+.||.|.+|.++.++.+++++|||||+|.+.++|++|++.|++..+.  ++.+++.++
T Consensus         1 t~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~--g~~l~v~~a   78 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLN--GRPLRINWA   78 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEET--TEECEEEEC
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeC--CcEEEEEec
Confidence            468999999999999999999999999999999999889999999999999999999999999999984  578888887


Q ss_pred             ccC
Q 013141          195 TFS  197 (449)
Q Consensus       195 ~~~  197 (449)
                      ...
T Consensus        79 ~~~   81 (83)
T 3md1_A           79 AKL   81 (83)
T ss_dssp             CCC
T ss_pred             CcC
Confidence            643

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} SCOP: d.58.7.0

Probab=99.72  E-value=6.3e-17  Score=121.19  Aligned_cols=81  Identities=37%  Similarity=0.705  Sum_probs=77.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecCC
Q 013141          209 LSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATP  288 (449)
Q Consensus       209 ~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~~  288 (449)
                      .+|||+|||.++++++|+++|+ .||.|.++.+++++.++.++|+|||+|.+.++|++|++.|++..+.|+.|+|+++.+
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~-~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~   80 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFK-DFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK   80 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHT-TSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHH-hcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCc
Confidence            5899999999999999999995 999999999999999999999999999999999999999999999999999999987


Q ss_pred             CC
Q 013141          289 KK  290 (449)
Q Consensus       289 ~~  290 (449)
                      +.
T Consensus        81 ~~   82 (83)
T 3md1_A           81 LE   82 (83)
T ss_dssp             CC
T ss_pred             CC
Confidence            63

>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=99.72  E-value=4.4e-17  Score=123.23  Aligned_cols=83  Identities=35%  Similarity=0.675  Sum_probs=76.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEee
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV  285 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  285 (449)
                      .+.++|||+|||.++++++|+++|+ .||.|.++.+++++.++.++|||||+|.+.++|++|++.|++..+.|+.|+|++
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~-~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   82 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFA-PFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNW   82 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHG-GGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHH-hcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEe
Confidence            3567999999999999999999995 999999999999988999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 013141          286 ATPK  289 (449)
Q Consensus       286 ~~~~  289 (449)
                      +.++
T Consensus        83 a~~k   86 (87)
T 3bs9_A           83 ATRK   86 (87)
T ss_dssp             EC--
T ss_pred             cCCC
Confidence            9765

>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=4.2e-17  Score=125.68  Aligned_cols=81  Identities=26%  Similarity=0.372  Sum_probs=75.1

Q ss_pred             CCCCcEEEEcCCCCCCCHhHHH----hhccccCceEEEEEeCC---CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEE
Q 013141          324 ESNNATIFVGALDSDVSDEDLR----EPFSQFGEILSVKIPVG---KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLS  396 (449)
Q Consensus       324 ~~~~~~l~V~nlp~~~t~~~L~----~~f~~~G~v~~v~i~~~---~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~  396 (449)
                      ....++|||+|||+.+++++|+    ++|++||.|.+|.|+.+   +++|||+|.+.++|.+|++.|||..|+|+.|+|+
T Consensus         6 ~~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~   85 (96)
T 2dgx_A            6 SGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVS   85 (96)
T ss_dssp             CSSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCCCeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            4456899999999999999999    99999999999999875   7899999999999999999999999999999999


Q ss_pred             ecCCCCCC
Q 013141          397 WGRNPGNK  404 (449)
Q Consensus       397 ~~~~~~~~  404 (449)
                      |+++...+
T Consensus        86 ~a~~~~~~   93 (96)
T 2dgx_A           86 LATGASGP   93 (96)
T ss_dssp             ECCCSSCC
T ss_pred             EcCCCCCC
Confidence            99886544

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=2.7e-17  Score=126.91  Aligned_cols=81  Identities=17%  Similarity=0.275  Sum_probs=70.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcC--CCCCCCCCcc
Q 013141          112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSG--SLMPNTDQPF  189 (449)
Q Consensus       112 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~--~~~~~~~~~~  189 (449)
                      ..+.++|||+|||+++|+++|+++|++||.|.+|+|+++      +|||||+|.+.++|++|++.|++  ..+  .+++|
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l--~Gr~l   84 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVL--RGQPI   84 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEE--TTEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceE--CCEEE
Confidence            357899999999999999999999999999999999876      48999999999999999998875  445  56889


Q ss_pred             cccccccCCCC
Q 013141          190 RLNWATFSGSD  200 (449)
Q Consensus       190 ~~~~~~~~~~~  200 (449)
                      +|.|++.....
T Consensus        85 ~V~~A~~~~~~   95 (105)
T 1sjq_A           85 YIQFSNHKELK   95 (105)
T ss_dssp             CBCCCSSSSCC
T ss_pred             EEEEcCCCCCC
Confidence            99998765433

>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=99.72  E-value=5.2e-17  Score=127.53  Aligned_cols=83  Identities=28%  Similarity=0.503  Sum_probs=76.2

Q ss_pred             CCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC------CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEE
Q 013141          322 DGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRL  395 (449)
Q Consensus       322 ~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~------~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v  395 (449)
                      ......++|||+|||..+++++|+++|+.||.|.+|.|+.+      +++|||+|.+.++|.+|++.||+..|.|+.|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   89 (105)
T 1x5u_A           10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRV   89 (105)
T ss_dssp             CCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            34556799999999999999999999999999999999864      579999999999999999999999999999999


Q ss_pred             EecCCCCCC
Q 013141          396 SWGRNPGNK  404 (449)
Q Consensus       396 ~~~~~~~~~  404 (449)
                      .|+++....
T Consensus        90 ~~a~~~~~~   98 (105)
T 1x5u_A           90 NKASAHNKN   98 (105)
T ss_dssp             EETTTTSCC
T ss_pred             EECCCCCcC
Confidence            999987654

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=4.1e-17  Score=127.41  Aligned_cols=82  Identities=27%  Similarity=0.557  Sum_probs=75.7

Q ss_pred             CCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC------CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 013141          324 ESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSW  397 (449)
Q Consensus       324 ~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~------~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  397 (449)
                      ....++|||+|||..+++++|+++|+.||.|.+|.|+.+      +++|||+|.+.++|.+|++.||+..|.|+.|+|.|
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            456789999999999999999999999999999999764      68999999999999999999999999999999999


Q ss_pred             cCCCCCCC
Q 013141          398 GRNPGNKQ  405 (449)
Q Consensus       398 ~~~~~~~~  405 (449)
                      +++...+.
T Consensus        89 a~~~~~~~   96 (102)
T 2cqb_A           89 AKPMRIKE   96 (102)
T ss_dssp             CCCCCCCC
T ss_pred             CCCCCCCC
Confidence            99876553

>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=6.1e-17  Score=127.14  Aligned_cols=82  Identities=27%  Similarity=0.539  Sum_probs=75.9

Q ss_pred             CCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC-----CcEEEEEecCHHHHHHHHHHhcCCeeCC---eEEEE
Q 013141          324 ESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-----KGCGFVQFANRKDAEVALQKLQGTAIGK---QTVRL  395 (449)
Q Consensus       324 ~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~-----~g~afV~F~~~~~A~~A~~~l~g~~~~g---~~l~v  395 (449)
                      ....++|||+|||..+++++|+++|+.||.|.+|.|+.+     +++|||+|.+.++|.+|++.||+..+.+   +.|+|
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V   91 (105)
T 2dnh_A           12 GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVV   91 (105)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEE
Confidence            456899999999999999999999999999999999875     6899999999999999999999999998   99999


Q ss_pred             EecCCCCCCC
Q 013141          396 SWGRNPGNKQ  405 (449)
Q Consensus       396 ~~~~~~~~~~  405 (449)
                      .|++....+.
T Consensus        92 ~~a~~~~~~~  101 (105)
T 2dnh_A           92 KFADTDKESG  101 (105)
T ss_dssp             EESCSSCCCS
T ss_pred             EECccCcccC
Confidence            9999876553

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.71  E-value=6.7e-17  Score=124.40  Aligned_cols=86  Identities=31%  Similarity=0.636  Sum_probs=81.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEee
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV  285 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  285 (449)
                      .+.++|||+|||.++++++|+++|+ .||.|..+.+++++.+++++|||||+|.+.++|++|++.|++..+.|+.|+|++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~-~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   81 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFE-PFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGH   81 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHT-TTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHH-hcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEE
Confidence            4678999999999999999999995 999999999999998999999999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 013141          286 ATPKKAS  292 (449)
Q Consensus       286 ~~~~~~~  292 (449)
                      +.++...
T Consensus        82 a~~~~~~   88 (95)
T 2dnz_A           82 VTERLDG   88 (95)
T ss_dssp             SSCCCCC
T ss_pred             cccccCC
Confidence            9887654

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=8e-17  Score=124.98  Aligned_cols=81  Identities=25%  Similarity=0.480  Sum_probs=74.4

Q ss_pred             CCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC------CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEE
Q 013141          323 GESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLS  396 (449)
Q Consensus       323 ~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~------~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~  396 (449)
                      .....++|||+|||..+++++|+++|+.||.|.+|.|+++      +++|||+|.+.++|.+|++ ||+..|.|+.|+|.
T Consensus         6 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~   84 (99)
T 2dgs_A            6 SGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVK   84 (99)
T ss_dssp             CCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEE
Confidence            3456789999999999999999999999999999999863      6899999999999999998 99999999999999


Q ss_pred             ecCCCCCC
Q 013141          397 WGRNPGNK  404 (449)
Q Consensus       397 ~~~~~~~~  404 (449)
                      |++++..+
T Consensus        85 ~a~~~~~~   92 (99)
T 2dgs_A           85 RAEPRDSK   92 (99)
T ss_dssp             ECCCCCCC
T ss_pred             ECCCCccc
Confidence            99987554

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.71  E-value=1e-16  Score=125.60  Aligned_cols=86  Identities=28%  Similarity=0.477  Sum_probs=77.2

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhc-cCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCC-CCCCCCc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSH-TGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSL-MPNTDQP  188 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~-~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~-~~~~~~~  188 (449)
                      .....++|||+|||+++++++|+++|+. ||.|.+|.|+.++ +++++|||||+|.+.++|.+|++.|++.. +.  ++.
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~--g~~   81 (104)
T 2dhg_A            5 SSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLG--SKP   81 (104)
T ss_dssp             CSSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSS--SSC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccC--CEe
Confidence            3457889999999999999999999999 9999999999998 89999999999999999999999999988 85  467


Q ss_pred             ccccccccCCC
Q 013141          189 FRLNWATFSGS  199 (449)
Q Consensus       189 ~~~~~~~~~~~  199 (449)
                      |+|.++.....
T Consensus        82 l~v~~a~~~~~   92 (104)
T 2dhg_A           82 VRLSVAIPKAS   92 (104)
T ss_dssp             CCCCBCCCCCS
T ss_pred             EEEEEccCCCc
Confidence            88888765443

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=5.2e-17  Score=127.75  Aligned_cols=84  Identities=20%  Similarity=0.426  Sum_probs=77.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccc
Q 013141          112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRL  191 (449)
Q Consensus       112 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~  191 (449)
                      ....++|||+|||+++++++|+++|+.||.|.+|.++.++.+++++|||||+|.+.++|.+|++.|++..+.  ++.|+|
T Consensus        20 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~l~V   97 (106)
T 1p27_B           20 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLM--GQPISV   97 (106)
T ss_dssp             BTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSS--SSBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEEC--CcEEEE
Confidence            356789999999999999999999999999999999999999999999999999999999999999999885  577888


Q ss_pred             cccccC
Q 013141          192 NWATFS  197 (449)
Q Consensus       192 ~~~~~~  197 (449)
                      .++...
T Consensus        98 ~~a~~~  103 (106)
T 1p27_B           98 DWCFVR  103 (106)
T ss_dssp             EESEES
T ss_pred             EeecCC
Confidence            887644

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=2.9e-17  Score=123.62  Aligned_cols=76  Identities=36%  Similarity=0.713  Sum_probs=72.7

Q ss_pred             CCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHh-cCCeeCCeEEEEEecC
Q 013141          324 ESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKL-QGTAIGKQTVRLSWGR  399 (449)
Q Consensus       324 ~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l-~g~~~~g~~l~v~~~~  399 (449)
                      ....++|||+|||..+++++|+++|++||.|.+|.+.+++++|||+|.+.++|.+|++.| ++..+.|+.|+|+|++
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~ak   85 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGR   85 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGGGTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEECC
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECCCCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEecC
Confidence            456789999999999999999999999999999999999999999999999999999999 9999999999999986

>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=99.71  E-value=6.6e-17  Score=128.31  Aligned_cols=86  Identities=26%  Similarity=0.388  Sum_probs=78.2

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhc------CCCCCC
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYS------GSLMPN  184 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~------~~~~~~  184 (449)
                      .....++|||+|||+++++++|+++|..||.|.+|.|++++.+++++|||||+|.+.++|.+|++.|+      +..+  
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~--   88 (111)
T 1x4h_A           11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKL--   88 (111)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEES--
T ss_pred             cCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEE--
Confidence            44678999999999999999999999999999999999999999999999999999999999999999      8888  


Q ss_pred             CCCcccccccccCC
Q 013141          185 TDQPFRLNWATFSG  198 (449)
Q Consensus       185 ~~~~~~~~~~~~~~  198 (449)
                      .++.|+|.++....
T Consensus        89 ~g~~l~v~~a~~~~  102 (111)
T 1x4h_A           89 DGRQLKVDLAVTRD  102 (111)
T ss_dssp             SSCEEEEECCCCCC
T ss_pred             cCEEEEEEECCCCc
Confidence            45788888887553

>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=99.71  E-value=1.2e-16  Score=125.89  Aligned_cols=88  Identities=28%  Similarity=0.662  Sum_probs=81.9

Q ss_pred             ccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcce
Q 013141          202 RTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPM  281 (449)
Q Consensus       202 ~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i  281 (449)
                      .......++|||+|||.++++++|+++|+ .||.|..+.+++++.++.++|||||+|.+.++|.+|++.|++..|.|+.|
T Consensus        20 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~-~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l   98 (108)
T 2jrs_A           20 QKGSAGPMRLYVGSLHFNITEDMLRGIFE-PFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPM   98 (108)
T ss_dssp             CCSCSSCEEEEEECCCSSCCHHHHHHHHT-TTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCC
T ss_pred             ccCCCCCCEEEEeCCCCCCCHHHHHHHHH-hcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            34456778999999999999999999995 99999999999999999999999999999999999999999999999999


Q ss_pred             EEeecCCCC
Q 013141          282 RIDVATPKK  290 (449)
Q Consensus       282 ~v~~~~~~~  290 (449)
                      +|+++.++.
T Consensus        99 ~V~~a~~k~  107 (108)
T 2jrs_A           99 KVGHVTERT  107 (108)
T ss_dssp             EEECSCSSC
T ss_pred             EEEEcccCC
Confidence            999998763

>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=6.7e-18  Score=138.61  Aligned_cols=120  Identities=22%  Similarity=0.332  Sum_probs=76.2

Q ss_pred             EEEEEeCCHHHHHHHHHHhCCceecCcceEEeecCCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEE
Q 013141          253 YGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFV  332 (449)
Q Consensus       253 ~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V  332 (449)
                      +.|++|.+...+..|++.+++....++.- +.+..                                ........++|||
T Consensus         6 ~~~~~~~~~~~~~~a~~~~~g~~~~g~~~-~~~~~--------------------------------~~~~~~~~~~l~V   52 (135)
T 2lea_A            6 HHHHHSSGLVPRGSHMASMTGGQQMGRGS-MSYGR--------------------------------PPPDVEGMTSLKV   52 (135)
T ss_dssp             ------------------------------CCSCC--------------------------------SCSSGGGCCCEEE
T ss_pred             cccccccCCCchhhhhhhccCCCCCCCCC-CCcCC--------------------------------CCCCCCCCCEEEE
Confidence            56888888888999998888765544321 11111                                1223345789999


Q ss_pred             cCCCCCCCHhHHHhhccccCceEEEEEeCC------CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCCCCC
Q 013141          333 GALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQ  405 (449)
Q Consensus       333 ~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~------~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~~~~  405 (449)
                      +|||..+++++|+++|+.||.|.+|.|+.+      +++|||+|.+.++|.+|++.||+..|.|+.|+|+|+++...+.
T Consensus        53 ~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~~~~~  131 (135)
T 2lea_A           53 DNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPD  131 (135)
T ss_dssp             ECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCCCCCT
T ss_pred             eCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCCCc
Confidence            999999999999999999999999999753      5899999999999999999999999999999999999865543

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.71  E-value=1.2e-16  Score=124.20  Aligned_cols=86  Identities=19%  Similarity=0.408  Sum_probs=80.2

Q ss_pred             ccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEE
Q 013141          204 EACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRI  283 (449)
Q Consensus       204 ~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  283 (449)
                      ...+.++|||+|||.++++++|+++|+ .||.|..+.++.+. +++++|||||+|.+.++|++|++.|++..+.|+.|+|
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 (100)
T 2do4_A           13 TSLEKHKLFISGLPFSCTKEELEEICK-AHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKV   90 (100)
T ss_dssp             SCCCCSCEEEESCCTTCCHHHHHHHHT-TTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHH-hCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            345678999999999999999999995 99999999999997 8999999999999999999999999999999999999


Q ss_pred             eecCCCCC
Q 013141          284 DVATPKKA  291 (449)
Q Consensus       284 ~~~~~~~~  291 (449)
                      .++.++..
T Consensus        91 ~~a~~~~~   98 (100)
T 2do4_A           91 AISNSGPS   98 (100)
T ss_dssp             EECCCCSC
T ss_pred             EECCCCCC
Confidence            99988754

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.71  E-value=2.1e-17  Score=128.74  Aligned_cols=95  Identities=24%  Similarity=0.332  Sum_probs=79.8

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccccccc
Q 013141          116 KTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWAT  195 (449)
Q Consensus       116 ~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~~~  195 (449)
                      ++|||+|||+++++++|+++|+.||.|.+|.++.+     ++|||||+|.+.++|++|++.|++..+.  ++.++|.++.
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~l~V~~a~   73 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDGKVIC--GSRVRVELST   73 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-----SSSEEEEECSSHHHHHHHHHHHHHSCSS--SCCCEEEESS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-----CCCEEEEEECCHHHHHHHHHHHCCCeEC--CcEEEEEEcc
Confidence            58999999999999999999999999999999887     5789999999999999999999999885  4668888887


Q ss_pred             cCCCCCc-----cccCCCceEEEcCCC
Q 013141          196 FSGSDRR-----TEACSDLSIFVGDLA  217 (449)
Q Consensus       196 ~~~~~~~-----~~~~~~~~l~v~~lp  217 (449)
                      .......     .......+|||+||+
T Consensus        74 ~~~~~~~~~~~~~~~~~~~~ifvg~L~  100 (101)
T 2hvz_A           74 GMPRRSRFDRPPARRKLLEVLFNGPLE  100 (101)
T ss_dssp             SCCCSSCCCSCCCSCCCCSCCCSCCCC
T ss_pred             CCCCcccCCCCCccccCCCceecCCCC
Confidence            6543322     122336689999986

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=7.8e-17  Score=126.03  Aligned_cols=89  Identities=26%  Similarity=0.439  Sum_probs=82.9

Q ss_pred             cccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceE
Q 013141          203 TEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMR  282 (449)
Q Consensus       203 ~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  282 (449)
                      ....+.++|||+|||.++++++|+++|+ .||.|..|.+++++.++.++|||||+|.+.++|.+|++.|++..|.|+.|+
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~-~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   88 (103)
T 2cq0_A           10 RRADDNATIRVTNLSEDTRETDLQELFR-PFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILN   88 (103)
T ss_dssp             CCCSSSEEEEEESCCTTCCHHHHHTTST-TTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHH-hCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEE
Confidence            3456778999999999999999999995 999999999999988999999999999999999999999999999999999


Q ss_pred             EeecCCCCCC
Q 013141          283 IDVATPKKAS  292 (449)
Q Consensus       283 v~~~~~~~~~  292 (449)
                      |.++.++...
T Consensus        89 v~~a~~~~~~   98 (103)
T 2cq0_A           89 VEWAKPSTNS   98 (103)
T ss_dssp             EEESSCCCCS
T ss_pred             EEECCCCCCC
Confidence            9999887654

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*

Probab=99.71  E-value=2.6e-17  Score=133.81  Aligned_cols=83  Identities=23%  Similarity=0.525  Sum_probs=75.9

Q ss_pred             CCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC------CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEE
Q 013141          322 DGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRL  395 (449)
Q Consensus       322 ~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~------~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v  395 (449)
                      ......++|||+|||..+++++|+++|+.||.|.+|.|+.+      +++|||+|.+.++|.+|++.||+..|.|+.|+|
T Consensus        17 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   96 (126)
T 3ex7_B           17 QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV   96 (126)
T ss_dssp             CCCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            34456789999999999999999999999999999999865      789999999999999999999999999999999


Q ss_pred             EecCCCCCC
Q 013141          396 SWGRNPGNK  404 (449)
Q Consensus       396 ~~~~~~~~~  404 (449)
                      .|+++....
T Consensus        97 ~~a~~~~~~  105 (126)
T 3ex7_B           97 DWCFVRGPP  105 (126)
T ss_dssp             EESEESSSC
T ss_pred             EEecCCCCC
Confidence            999876544

>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=99.71  E-value=6.9e-17  Score=124.55  Aligned_cols=85  Identities=26%  Similarity=0.457  Sum_probs=80.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeec
Q 013141          207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVA  286 (449)
Q Consensus       207 ~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~  286 (449)
                      ++++|||+|||.++++++|+++|+ .||.|.++.++.++.++.++|||||+|.+.++|.+|++.|++..+.|+.|+|+++
T Consensus         1 P~~~l~V~nLp~~~t~~~l~~~F~-~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   79 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQTEEQILDLCS-NVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYS   79 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHH-TTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHH-hcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEc
Confidence            467999999999999999999995 9999999999999989999999999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 013141          287 TPKKAS  292 (449)
Q Consensus       287 ~~~~~~  292 (449)
                      .++...
T Consensus        80 ~~~~~~   85 (96)
T 2x1f_A           80 SNSDIS   85 (96)
T ss_dssp             SCSSGG
T ss_pred             CCCCCC
Confidence            987653

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=1.2e-16  Score=123.05  Aligned_cols=85  Identities=24%  Similarity=0.407  Sum_probs=79.7

Q ss_pred             cccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceE
Q 013141          203 TEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMR  282 (449)
Q Consensus       203 ~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  282 (449)
                      ....+.++|||+|||.++++++|+++|+ .||.|..+.+++++.++.++|+|||+|.+.++|.+|++.|++..+.|+.|+
T Consensus        10 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~-~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   88 (95)
T 2cqc_A           10 ANPDPNCCLGVFGLSLYTTERDLREVFS-KYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR   88 (95)
T ss_dssp             CSCCGGGCEEEESCCSSCCHHHHHHHHH-TTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHH-hcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            3455678999999999999999999995 999999999999999999999999999999999999999999999999999


Q ss_pred             EeecCC
Q 013141          283 IDVATP  288 (449)
Q Consensus       283 v~~~~~  288 (449)
                      |++++.
T Consensus        89 v~~a~~   94 (95)
T 2cqc_A           89 VSGPSS   94 (95)
T ss_dssp             EECCSC
T ss_pred             EEecCC
Confidence            999864

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=5.3e-17  Score=126.97  Aligned_cols=82  Identities=27%  Similarity=0.443  Sum_probs=75.4

Q ss_pred             CCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC------CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEE
Q 013141          323 GESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLS  396 (449)
Q Consensus       323 ~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~------~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~  396 (449)
                      .....++|||+|||..+++++|+++|+.||.|.+|.|+.+      +++|||+|.+.++|.+|++.||+..|.|+.|+|.
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2dnm_A            9 DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQ   88 (103)
T ss_dssp             CCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            4456799999999999999999999999999999999863      6899999999999999999999999999999999


Q ss_pred             ecCCCCCC
Q 013141          397 WGRNPGNK  404 (449)
Q Consensus       397 ~~~~~~~~  404 (449)
                      |++.....
T Consensus        89 ~a~~~~~~   96 (103)
T 2dnm_A           89 VARYGRRD   96 (103)
T ss_dssp             ECSSCCSC
T ss_pred             ECCcCCCC
Confidence            99986544

>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=99.71  E-value=3.1e-17  Score=126.56  Aligned_cols=83  Identities=22%  Similarity=0.440  Sum_probs=76.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccccc
Q 013141          114 ETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNW  193 (449)
Q Consensus       114 ~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~  193 (449)
                      ++++|||+|||+++++++|+++|+.||.|.+|+++.++.+++++|||||+|.+.++|.+|++.|++..+.+  +.++|.+
T Consensus         1 P~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g--~~l~V~~   78 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGS--RFLKCGY   78 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETT--EECEEEE
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECC--eEEEEEE
Confidence            46899999999999999999999999999999999999899999999999999999999999999998854  7888888


Q ss_pred             cccCC
Q 013141          194 ATFSG  198 (449)
Q Consensus       194 ~~~~~  198 (449)
                      +....
T Consensus        79 a~~~~   83 (96)
T 2x1f_A           79 SSNSD   83 (96)
T ss_dssp             CSCSS
T ss_pred             cCCCC
Confidence            87543

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} SCOP: d.58.7.1 PDB: 2f9d_A 2f9j_A 2fho_B

Probab=99.71  E-value=2e-17  Score=132.26  Aligned_cols=105  Identities=12%  Similarity=0.182  Sum_probs=89.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccc
Q 013141          112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRL  191 (449)
Q Consensus       112 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~  191 (449)
                      ....++|||+|||+++++++|+++|+.||.|.+|.++.+   +.++|||||+|.+.++|.+|++.|++..+.  ++.++|
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~--g~~l~v   79 (115)
T 3lqv_A            5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVS--NRYLVV   79 (115)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSS--SCBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEEC--CeEEEE
Confidence            356789999999999999999999999999999999876   456899999999999999999999999995  577888


Q ss_pred             cccccCCCCCccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCC
Q 013141          192 NWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPS  235 (449)
Q Consensus       192 ~~~~~~~~~~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~  235 (449)
                      .++......             .+++...++++|.++|. .||.
T Consensus        80 ~~a~~~~~~-------------~~~~~~~~~~~l~~~~~-~~g~  109 (115)
T 3lqv_A           80 LYYNANRAF-------------QKMDTKKKEEQLKLLKE-KYGI  109 (115)
T ss_dssp             EECCHHHHT-------------TTSCHHHHHHHHHHHHH-HHCC
T ss_pred             EEecCChhh-------------hhhhHhHhHHHHHHHHH-HhCC
Confidence            887643211             56777888999999995 8874

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=7.5e-17  Score=122.73  Aligned_cols=80  Identities=21%  Similarity=0.447  Sum_probs=73.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCC
Q 013141          323 GESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPG  402 (449)
Q Consensus       323 ~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~  402 (449)
                      .....++|||+|||..+++++|+++|+.||.|.+|.+.+  ++|||+|.+.++|.+|++.||+..|.|+.|+|.|+++..
T Consensus         5 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~--~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   82 (90)
T 2dnp_A            5 SSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--DYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKGQ   82 (90)
T ss_dssp             SSCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS--SCEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC--CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEECCCCC
Confidence            345678999999999999999999999999999999984  599999999999999999999999999999999999865


Q ss_pred             CC
Q 013141          403 NK  404 (449)
Q Consensus       403 ~~  404 (449)
                      .+
T Consensus        83 ~~   84 (90)
T 2dnp_A           83 KK   84 (90)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.71  E-value=5.9e-17  Score=125.50  Aligned_cols=80  Identities=26%  Similarity=0.487  Sum_probs=73.6

Q ss_pred             CCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeC---------CCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEE
Q 013141          325 SNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV---------GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRL  395 (449)
Q Consensus       325 ~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~---------~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v  395 (449)
                      ...++|||+|||.++++++|+++|+.||.|.+|.|..         .+++|||+|.+.++|.+|++.||+..|.|+.|+|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   82 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEV   82 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            3568999999999999999999999999999999984         2579999999999999999999999999999999


Q ss_pred             EecCCCCCC
Q 013141          396 SWGRNPGNK  404 (449)
Q Consensus       396 ~~~~~~~~~  404 (449)
                      .|+++....
T Consensus        83 ~~a~~~~~~   91 (98)
T 2cpf_A           83 RISERATKP   91 (98)
T ss_dssp             ECSSCSSCC
T ss_pred             EEccCCCCC
Confidence            999986554

>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=99.70  E-value=8.1e-17  Score=124.96  Aligned_cols=87  Identities=26%  Similarity=0.367  Sum_probs=81.6

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEe
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRID  284 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  284 (449)
                      ..+.++|||+|||.++++++|+++|+ .||.|.++.+++++.++.++|||||+|.+.++|++|++.|++..|.|+.|+|+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~-~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   83 (99)
T 1whw_A            5 SSGSGRLFVRNLSYTSSEEDLEKLFS-AYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVL   83 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHH-TTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHH-hcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            34678999999999999999999995 99999999999998899999999999999999999999999999999999999


Q ss_pred             ecCCCCCC
Q 013141          285 VATPKKAS  292 (449)
Q Consensus       285 ~~~~~~~~  292 (449)
                      ++.++...
T Consensus        84 ~a~~~~~~   91 (99)
T 1whw_A           84 PSTIKKEA   91 (99)
T ss_dssp             ECCCCSTT
T ss_pred             EcCCCccc
Confidence            99987653

>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=99.70  E-value=3.5e-17  Score=139.55  Aligned_cols=138  Identities=19%  Similarity=0.375  Sum_probs=74.4

Q ss_pred             EEeCCHHHHHHHHHHhCCceec--CcceEEeecCCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEc
Q 013141          256 VRFGDENERSRAMTEMNGVYCS--SRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVG  333 (449)
Q Consensus       256 V~f~~~~~A~~A~~~l~g~~~~--g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~  333 (449)
                      .+|.+.++|+.++..+++....  |+.+...+............          .  ..........+......++|||+
T Consensus        11 ee~e~~~d~e~~~~~~~~~~~~~kgr~~~~~~~~~~~~~~~~~~----------~--~s~~~~~~~~~~~~~~~~~l~V~   78 (165)
T 1rk8_A           11 EEFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERV----------R--NEDDDELEPGPQRSVEGWILFVT   78 (165)
T ss_dssp             -------------------------------------------------------------------CCCCC-CEEEEEE
T ss_pred             hhhhccccccccchhhccccccccCCCCCCCccccccccCcccc----------c--cCCCCCCCCCCCCCCCCCEEEEe
Confidence            7899999999999988876553  44444444221110000000          0  00000011122334567899999


Q ss_pred             CCCCCCCHhHHHhhccccCceEEEEEeCC------CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCCCCC
Q 013141          334 ALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQ  405 (449)
Q Consensus       334 nlp~~~t~~~L~~~f~~~G~v~~v~i~~~------~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~~~~  405 (449)
                      |||..+++++|+++|+.||.|..|.|+.+      +++|||+|.+.++|.+||+.|||..|.|+.|+|.|++....+.
T Consensus        79 nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~~  156 (165)
T 1rk8_A           79 SIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKR  156 (165)
T ss_dssp             SCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEECC---
T ss_pred             CCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCCCCC
Confidence            99999999999999999999999999865      5899999999999999999999999999999999998765443

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=5.8e-17  Score=126.53  Aligned_cols=82  Identities=28%  Similarity=0.557  Sum_probs=75.4

Q ss_pred             CCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC------CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEE
Q 013141          323 GESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLS  396 (449)
Q Consensus       323 ~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~------~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~  396 (449)
                      .....++|||+|||.++++++|+++|+.||.|.+|.|+++      +++|||+|.+.++|.+|++.||+..|.|+.|+|.
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            3456789999999999999999999999999999999873      5899999999999999999999999999999999


Q ss_pred             ecCCCCCC
Q 013141          397 WGRNPGNK  404 (449)
Q Consensus       397 ~~~~~~~~  404 (449)
                      |+++....
T Consensus        88 ~a~~~~~~   95 (102)
T 1x5s_A           88 QAGKSSDN   95 (102)
T ss_dssp             EEECCCCC
T ss_pred             ECCCCCCC
Confidence            99986544

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.70  E-value=2.7e-17  Score=128.12  Aligned_cols=78  Identities=26%  Similarity=0.513  Sum_probs=74.0

Q ss_pred             CCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCC
Q 013141          324 ESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNP  401 (449)
Q Consensus       324 ~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~  401 (449)
                      ....++|||+|||.++++++|+++|+.||.|.+|++.+++++|||+|.+.++|.+|++.||+..|+|+.|+|.|++++
T Consensus        24 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  101 (101)
T 2la4_A           24 PPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKER  101 (101)
T ss_dssp             CSSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEETTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCCCC
T ss_pred             CCCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEecCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEeccCC
Confidence            345689999999999999999999999999999999999999999999999999999999999999999999999863

>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=99.70  E-value=1.3e-16  Score=125.05  Aligned_cols=80  Identities=29%  Similarity=0.518  Sum_probs=73.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC-------CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEE
Q 013141          323 GESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-------KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRL  395 (449)
Q Consensus       323 ~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~-------~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v  395 (449)
                      .....++|||+|||.++++++|+++|+.|| |.+|.|+.+       +++|||+|.+.++|.+|+ .||+..|.|+.|+|
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V   88 (104)
T 1wi8_A           11 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRV   88 (104)
T ss_dssp             CSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEE
T ss_pred             CCCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEE
Confidence            345679999999999999999999999999 999999754       679999999999999999 99999999999999


Q ss_pred             EecCCCCCC
Q 013141          396 SWGRNPGNK  404 (449)
Q Consensus       396 ~~~~~~~~~  404 (449)
                      .|++++..+
T Consensus        89 ~~a~~~~~~   97 (104)
T 1wi8_A           89 DVADQAQDK   97 (104)
T ss_dssp             EECCCCCCC
T ss_pred             EEccCCCCC
Confidence            999987654

>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=2.7e-16  Score=125.37  Aligned_cols=82  Identities=24%  Similarity=0.339  Sum_probs=74.9

Q ss_pred             CCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC-----CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 013141          323 GESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-----KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSW  397 (449)
Q Consensus       323 ~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~-----~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  397 (449)
                      .....++|||+|||..+++++|+++|+.||.|.+|.|+.+     +++|||+|.+.++|.+|++.||+..|.|+.|+|+|
T Consensus        11 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   90 (114)
T 2do0_A           11 AGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKM   90 (114)
T ss_dssp             CCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEE
Confidence            3455789999999999999999999999999999999875     68999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 013141          398 GRNPGNK  404 (449)
Q Consensus       398 ~~~~~~~  404 (449)
                      ++....+
T Consensus        91 a~~~~~~   97 (114)
T 2do0_A           91 DERALPK   97 (114)
T ss_dssp             CSCCCCC
T ss_pred             cccCCCC
Confidence            9865443

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=2.4e-17  Score=124.13  Aligned_cols=80  Identities=26%  Similarity=0.346  Sum_probs=73.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      .+.++|||+|||+++++++|+++|+.||.|.+|.++.++.+++++|||||+|.+.++|.+|++.||+..+.  ++.+++.
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~~~~~   80 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQ--AQMAKQS   80 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCC--EESCCSS
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEe--eEEEeec
Confidence            46889999999999999999999999999999999999989999999999999999999999999999884  4566665


Q ss_pred             cc
Q 013141          193 WA  194 (449)
Q Consensus       193 ~~  194 (449)
                      |+
T Consensus        81 ~~   82 (85)
T 1x4e_A           81 GP   82 (85)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=2.4e-16  Score=121.75  Aligned_cols=80  Identities=24%  Similarity=0.461  Sum_probs=74.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCC
Q 013141          323 GESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPG  402 (449)
Q Consensus       323 ~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~  402 (449)
                      .....++|||+||  ++++++|+++|+.||.|.+|.|.+++++|||+|.+.++|.+|++.||+..|.|+.|+|.|+++..
T Consensus        11 ~~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~~   88 (97)
T 1x5p_A           11 APRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQP   88 (97)
T ss_dssp             CCCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCSSCC
T ss_pred             CCCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEecCCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCCC
Confidence            3456789999996  89999999999999999999999999999999999999999999999999999999999999865


Q ss_pred             CC
Q 013141          403 NK  404 (449)
Q Consensus       403 ~~  404 (449)
                      ..
T Consensus        89 ~~   90 (97)
T 1x5p_A           89 ML   90 (97)
T ss_dssp             CC
T ss_pred             CC
Confidence            44

>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=99.70  E-value=7e-17  Score=121.51  Aligned_cols=82  Identities=26%  Similarity=0.515  Sum_probs=77.6

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEe
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRID  284 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  284 (449)
                      ..+.++|||+|||+++++++|+++|+ .||.|..+.+++++.++.++|+|||+|.+.++|.+|++.|++..+.|+.|+|+
T Consensus         4 ~~~~~~l~V~nl~~~~~~~~l~~~f~-~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   82 (85)
T 3mdf_A            4 ATTKRVLYVGGLAEEVDDKVLHAAFI-PFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN   82 (85)
T ss_dssp             CCCSSEEEEECCCTTCCHHHHHHHHG-GGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHh-ccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            34678999999999999999999995 99999999999998899999999999999999999999999999999999999


Q ss_pred             ecC
Q 013141          285 VAT  287 (449)
Q Consensus       285 ~~~  287 (449)
                      +++
T Consensus        83 ~ak   85 (85)
T 3mdf_A           83 LAK   85 (85)
T ss_dssp             ECC
T ss_pred             EcC
Confidence            874

>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=6.8e-17  Score=129.30  Aligned_cols=86  Identities=28%  Similarity=0.448  Sum_probs=77.5

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcc
Q 013141          110 FTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPF  189 (449)
Q Consensus       110 ~~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~  189 (449)
                      ......++|||+|||+++++++|+++|+.||.|.+|+|++++.+++++|||||+|.+.++|++||+.+++ .+  .++.|
T Consensus        12 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~--~g~~l   88 (116)
T 2cqd_A           12 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-II--DGRKA   88 (116)
T ss_dssp             CCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EE--TTEEC
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cC--CCEEE
Confidence            3456789999999999999999999999999999999999999999999999999999999999999887 66  45788


Q ss_pred             cccccccCC
Q 013141          190 RLNWATFSG  198 (449)
Q Consensus       190 ~~~~~~~~~  198 (449)
                      +|.++....
T Consensus        89 ~V~~a~~~~   97 (116)
T 2cqd_A           89 NVNLAYLGA   97 (116)
T ss_dssp             EEEESTTTC
T ss_pred             EEEEcccCC
Confidence            888886543

>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=99.70  E-value=2.2e-17  Score=125.65  Aligned_cols=82  Identities=17%  Similarity=0.272  Sum_probs=72.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhhCC--CeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeec
Q 013141          209 LSIFVGDLAPDVTDSILQETFSSKYP--SVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVA  286 (449)
Q Consensus       209 ~~l~v~~lp~~~t~~~l~~~f~~~~g--~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~  286 (449)
                      .+|||+|||+++|+++|+++|+ .||  .|.++.++.++.+++++|||||+|.+.++|++|++.||+..+.|+.|+|.++
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~-~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~   80 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVH-SLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPS   80 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHH-TTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHH-HhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEEC
Confidence            4799999999999999999995 999  9999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCC
Q 013141          287 TPKKA  291 (449)
Q Consensus       287 ~~~~~  291 (449)
                      .+...
T Consensus        81 ~~~~~   85 (90)
T 3p5t_L           81 NKLEH   85 (90)
T ss_dssp             -----
T ss_pred             CCCcc
Confidence            88654

>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=99.70  E-value=1.5e-16  Score=123.85  Aligned_cols=84  Identities=14%  Similarity=0.111  Sum_probs=72.7

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      ...++++|||+|||+++++++|+++|++||.|.+|.++++      +|||||+|.+.++|.+|++.|++..+...++.|+
T Consensus        11 ~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~   84 (104)
T 1wex_A           11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAF   84 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            4467899999999999999999999999999999998764      5899999999999999999998765444678899


Q ss_pred             ccccccCCCC
Q 013141          191 LNWATFSGSD  200 (449)
Q Consensus       191 ~~~~~~~~~~  200 (449)
                      |.|+......
T Consensus        85 V~~a~~~~~~   94 (104)
T 1wex_A           85 FNYSTSKRIT   94 (104)
T ss_dssp             EEECSSSSCC
T ss_pred             EEEccCcccc
Confidence            9998765443

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.70  E-value=1.5e-17  Score=129.11  Aligned_cols=82  Identities=24%  Similarity=0.308  Sum_probs=75.1

Q ss_pred             CCCceEEEcCCCC------CCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCC
Q 013141          113 DETKTIWIGDLFH------WMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTD  186 (449)
Q Consensus       113 ~~~~~l~v~nLp~------~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~  186 (449)
                      ...++|||+|||+      ++++++|+++|++||.|.+|+|++++.+++++|||||+|.+.++|.+|++.||+..+.+ .
T Consensus         4 ~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g-~   82 (100)
T 3ns6_A            4 GSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDL-K   82 (100)
T ss_dssp             CGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSS-S
T ss_pred             CcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCC-C
Confidence            3568999999999      99999999999999999999999999999999999999999999999999999999954 2


Q ss_pred             Ccccccccc
Q 013141          187 QPFRLNWAT  195 (449)
Q Consensus       187 ~~~~~~~~~  195 (449)
                      +.|+|.++.
T Consensus        83 r~l~V~~a~   91 (100)
T 3ns6_A           83 HRLFLYTMK   91 (100)
T ss_dssp             CBCEEEESH
T ss_pred             eEEEEEECc
Confidence            677777765

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=5.6e-17  Score=127.35  Aligned_cols=86  Identities=28%  Similarity=0.420  Sum_probs=77.6

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      .....++|||+|||+++++++|+++|+.||.|.+|.++.++.+++++|||||+|.+.++|.+||+. ++..+.  ++.|+
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~--g~~l~   88 (105)
T 2dh8_A           12 GADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLD--GRNID   88 (105)
T ss_dssp             CSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEET--TEEEB
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeEC--CEEEE
Confidence            456789999999999999999999999999999999999999999999999999999999999988 888884  56788


Q ss_pred             ccccccCCC
Q 013141          191 LNWATFSGS  199 (449)
Q Consensus       191 ~~~~~~~~~  199 (449)
                      |.++.....
T Consensus        89 V~~a~~~~~   97 (105)
T 2dh8_A           89 PKPCTPRGM   97 (105)
T ss_dssp             CCCSCCSSC
T ss_pred             EEEccCCCC
Confidence            888775543

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=1.1e-16  Score=125.82  Aligned_cols=87  Identities=23%  Similarity=0.431  Sum_probs=81.0

Q ss_pred             cccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceE
Q 013141          203 TEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMR  282 (449)
Q Consensus       203 ~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  282 (449)
                      ....+.++|||+|||.++++++|+++|+ .||.|..+.++.++.++.++|||||+|.+.++|.+|++.|++..|.|+.|+
T Consensus        18 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~-~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   96 (106)
T 1p27_B           18 QRSVEGWILFVTGVHEEATEEDIHDKFA-EYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPIS   96 (106)
T ss_dssp             CCBTTBEEEEEECCCTTCCHHHHHHHHG-GGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHh-ccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEE
Confidence            3345678999999999999999999995 999999999999999999999999999999999999999999999999999


Q ss_pred             EeecCCCC
Q 013141          283 IDVATPKK  290 (449)
Q Consensus       283 v~~~~~~~  290 (449)
                      |+++.++.
T Consensus        97 V~~a~~~~  104 (106)
T 1p27_B           97 VDWCFVRG  104 (106)
T ss_dssp             EEESEESS
T ss_pred             EEeecCCC
Confidence            99997764

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.70  E-value=1.5e-16  Score=123.35  Aligned_cols=84  Identities=26%  Similarity=0.387  Sum_probs=78.7

Q ss_pred             cccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeE--------EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCc
Q 013141          203 TEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKG--------AKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGV  274 (449)
Q Consensus       203 ~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~--------i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~  274 (449)
                      ....+.++|||+|||.++++++|+++|+ .||.|..        +.++.++.+++++|||||+|.+.++|.+|++.|++.
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~-~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~   86 (99)
T 2la6_A            8 HSHSDNNTIFVQGLGENVTIESVADYFK-QIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGK   86 (99)
T ss_dssp             CSCCCCSEEEEECCCSSCCHHHHHHHHT-TTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHH-HhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCC
Confidence            3455678999999999999999999995 9999999        999999999999999999999999999999999999


Q ss_pred             eecCcceEEeecC
Q 013141          275 YCSSRPMRIDVAT  287 (449)
Q Consensus       275 ~~~g~~i~v~~~~  287 (449)
                      .+.|+.|+|++++
T Consensus        87 ~~~g~~l~V~~A~   99 (99)
T 2la6_A           87 EFSGNPIKVSFAT   99 (99)
T ss_dssp             BSSSSBCEEEECC
T ss_pred             EeCCcEEEEEecC
Confidence            9999999999874

>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=99.70  E-value=1.7e-16  Score=125.59  Aligned_cols=80  Identities=28%  Similarity=0.539  Sum_probs=73.4

Q ss_pred             CCCCCcEEEEcCCCCC-CCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCC
Q 013141          323 GESNNATIFVGALDSD-VSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNP  401 (449)
Q Consensus       323 ~~~~~~~l~V~nlp~~-~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~  401 (449)
                      .....++|||+|||.. +++++|+++|+.||.|.+|.+  .+++|||+|.+.++|.+|++.||+..|+|+.|+|+|++.+
T Consensus        23 ~~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~  100 (110)
T 1wf1_A           23 PKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEP  100 (110)
T ss_dssp             CTTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEESCCC
T ss_pred             CCCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCC
Confidence            3445689999999999 999999999999999999999  5899999999999999999999999999999999999875


Q ss_pred             CCC
Q 013141          402 GNK  404 (449)
Q Consensus       402 ~~~  404 (449)
                      ...
T Consensus       101 ~~~  103 (110)
T 1wf1_A          101 KPD  103 (110)
T ss_dssp             CSC
T ss_pred             CCC
Confidence            443

>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=99.70  E-value=3.2e-17  Score=125.65  Aligned_cols=80  Identities=19%  Similarity=0.380  Sum_probs=71.5

Q ss_pred             CCCCcEEEEcCCCCCCCHhHHHhhccccCc-eEEEEEeCCCcEEEEEecCHHHHHHHHHHhcC-CeeCCeEEEEEecCCC
Q 013141          324 ESNNATIFVGALDSDVSDEDLREPFSQFGE-ILSVKIPVGKGCGFVQFANRKDAEVALQKLQG-TAIGKQTVRLSWGRNP  401 (449)
Q Consensus       324 ~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~-v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g-~~~~g~~l~v~~~~~~  401 (449)
                      ....++|||+|||.++++++|+++|++||. |..+.+ .++++|||+|.+.++|.+|++.||+ ..|+|+.|+|+|+++.
T Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~-~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~   83 (93)
T 2cqh_A            5 SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL-LKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSK   83 (93)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEE-EETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEE-cCCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEEccCc
Confidence            345789999999999999999999999999 555555 5689999999999999999999999 9999999999999986


Q ss_pred             CCC
Q 013141          402 GNK  404 (449)
Q Consensus       402 ~~~  404 (449)
                      ..+
T Consensus        84 ~~~   86 (93)
T 2cqh_A           84 KLR   86 (93)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            544

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.70  E-value=3e-17  Score=126.54  Aligned_cols=80  Identities=25%  Similarity=0.387  Sum_probs=72.4

Q ss_pred             CCCCCcEEEEcCCCC-CCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCC
Q 013141          323 GESNNATIFVGALDS-DVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNP  401 (449)
Q Consensus       323 ~~~~~~~l~V~nlp~-~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~  401 (449)
                      ...+.++|||+|||. .+++++|+++|+.||.|.+|.+.  +++|||+|.+.++|.+|++.||+..+.|+.|+|+|++..
T Consensus         6 ~~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~   83 (96)
T 2kvi_A            6 NIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSN   83 (96)
T ss_dssp             ---CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEEECC
T ss_pred             cCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEcCcC
Confidence            345688999999998 99999999999999999999996  799999999999999999999999999999999999886


Q ss_pred             CCC
Q 013141          402 GNK  404 (449)
Q Consensus       402 ~~~  404 (449)
                      ...
T Consensus        84 ~~~   86 (96)
T 2kvi_A           84 ARP   86 (96)
T ss_dssp             CC-
T ss_pred             CCC
Confidence            544

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=7.3e-17  Score=124.45  Aligned_cols=86  Identities=31%  Similarity=0.660  Sum_probs=80.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEE-EEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEe
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGA-KVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRID  284 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i-~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  284 (449)
                      .+.++|||+|||.++++++|+++|+ .||.|..+ .+++++.++.++|||||+|.+.++|++|++.|++..|.|+.|+|+
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~-~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   81 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFS-AFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVS   81 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHH-TTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHH-hcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            4678999999999999999999995 99999999 999998899999999999999999999999999999999999999


Q ss_pred             ecCCCCCC
Q 013141          285 VATPKKAS  292 (449)
Q Consensus       285 ~~~~~~~~  292 (449)
                      ++.++...
T Consensus        82 ~a~~~~~~   89 (96)
T 1x5t_A           82 YAFKKDSK   89 (96)
T ss_dssp             ESCCCCCC
T ss_pred             EecccCCC
Confidence            99887654

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.69  E-value=4.4e-17  Score=124.45  Aligned_cols=81  Identities=17%  Similarity=0.187  Sum_probs=71.7

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      ...++++|||+|||+++|+++|+++|++||.|.+|.++++      ||||||+|.+.++|.+|++.|++..+...+++|+
T Consensus        17 ~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~------kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~   90 (100)
T 3r27_A           17 KTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNYAADNQIYIAGHPAF   90 (100)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEE
T ss_pred             cCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEE
Confidence            4468899999999999999999999999999999999864      4899999999999999999999887544678899


Q ss_pred             ccccccC
Q 013141          191 LNWATFS  197 (449)
Q Consensus       191 ~~~~~~~  197 (449)
                      |.+++..
T Consensus        91 V~~S~~k   97 (100)
T 3r27_A           91 VNYSTSQ   97 (100)
T ss_dssp             EEECSCS
T ss_pred             EEecccc
Confidence            9888754

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.69  E-value=8e-17  Score=126.78  Aligned_cols=82  Identities=29%  Similarity=0.602  Sum_probs=73.9

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCC
Q 013141          321 SDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRN  400 (449)
Q Consensus       321 ~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  400 (449)
                      .......++|||+|||..+++++|+++|+.||.|.+|.+.  +|+|||+|.+.++|.+|++.|||..|+|+.|+|.|++.
T Consensus        25 ~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~  102 (108)
T 2jvo_A           25 QEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKL  102 (108)
T ss_dssp             ---CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESCSC
T ss_pred             cCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecC
Confidence            3445678999999999999999999999999999999998  89999999999999999999999999999999999998


Q ss_pred             CCCC
Q 013141          401 PGNK  404 (449)
Q Consensus       401 ~~~~  404 (449)
                      +..+
T Consensus       103 ~~~r  106 (108)
T 2jvo_A          103 PAKR  106 (108)
T ss_dssp             CC--
T ss_pred             CCCC
Confidence            7554

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=5.4e-17  Score=126.31  Aligned_cols=80  Identities=18%  Similarity=0.248  Sum_probs=71.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccc
Q 013141          112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRL  191 (449)
Q Consensus       112 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~  191 (449)
                      ....++|||+|||+++|+++|+++|+.||.|.+|.|++++. ++++|||||+|.+.++|.+|++ +++..+.+  +.|+|
T Consensus         8 ~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~g--r~l~V   83 (103)
T 1s79_A            8 DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKE--TDLLI   83 (103)
T ss_dssp             CSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTT--TTCEE
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCEECC--EEEEE
Confidence            34678999999999999999999999999999999999987 9999999999999999999997 88888854  66676


Q ss_pred             cccc
Q 013141          192 NWAT  195 (449)
Q Consensus       192 ~~~~  195 (449)
                      .|+.
T Consensus        84 ~~~~   87 (103)
T 1s79_A           84 LFKD   87 (103)
T ss_dssp             EEHH
T ss_pred             EEch
Confidence            6654

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=1e-16  Score=125.19  Aligned_cols=87  Identities=25%  Similarity=0.517  Sum_probs=81.7

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEe
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRID  284 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  284 (449)
                      ..+.++|||+|||.++++++|+++|+ .||.|..+.+++++.++.++|||||+|.+.++|++|++.|++..|.|+.|+|.
T Consensus         9 ~~~~~~l~V~nLp~~~t~~~l~~~f~-~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   87 (102)
T 2cqb_A            9 ATTKRVLYVGGLAEEVDDKVLHAAFI-PFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN   87 (102)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHT-TTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhh-ccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            45678999999999999999999995 99999999999998999999999999999999999999999999999999999


Q ss_pred             ecCCCCCC
Q 013141          285 VATPKKAS  292 (449)
Q Consensus       285 ~~~~~~~~  292 (449)
                      ++.++...
T Consensus        88 ~a~~~~~~   95 (102)
T 2cqb_A           88 LAKPMRIK   95 (102)
T ss_dssp             ECCCCCCC
T ss_pred             eCCCCCCC
Confidence            99887654

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=1.7e-16  Score=126.27  Aligned_cols=83  Identities=25%  Similarity=0.420  Sum_probs=75.3

Q ss_pred             CCCCCCcEEEEcCCCCCCCHhHHHhhccccCceE--------EEEEeCC------CcEEEEEecCHHHHHHHHHHhcCCe
Q 013141          322 DGESNNATIFVGALDSDVSDEDLREPFSQFGEIL--------SVKIPVG------KGCGFVQFANRKDAEVALQKLQGTA  387 (449)
Q Consensus       322 ~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~--------~v~i~~~------~g~afV~F~~~~~A~~A~~~l~g~~  387 (449)
                      ......++|||+|||..+++++|+++|+.||.|.        .|.|+.+      +++|||+|.+.++|.+|++.||+..
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~   89 (113)
T 2cpe_A           10 DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKD   89 (113)
T ss_dssp             CCCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCE
T ss_pred             ccCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCc
Confidence            3455689999999999999999999999999998        5888764      6899999999999999999999999


Q ss_pred             eCCeEEEEEecCCCCCC
Q 013141          388 IGKQTVRLSWGRNPGNK  404 (449)
Q Consensus       388 ~~g~~l~v~~~~~~~~~  404 (449)
                      |.|+.|+|+|++.....
T Consensus        90 ~~g~~l~V~~a~~~~~~  106 (113)
T 2cpe_A           90 FQGSKLKVSLARKKPPM  106 (113)
T ss_dssp             ETTEECEEECSSCCCCS
T ss_pred             cCCCEEEEEECCCCCCC
Confidence            99999999999987554

>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=5.1e-17  Score=136.52  Aligned_cols=81  Identities=25%  Similarity=0.457  Sum_probs=73.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccC--CcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTG--QVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G--~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      ...++|||+|||+++++++|+++|+.||  .|.+|+|+.|+.+|+++|||||+|.+.++|++||+.|++..+.  ++.|+
T Consensus        53 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~--Gr~l~  130 (156)
T 3n9u_C           53 NRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLN--GEKVD  130 (156)
T ss_dssp             ---CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEET--TEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEEC--CeEeE
Confidence            4578999999999999999999999999  9999999999999999999999999999999999999999985  46777


Q ss_pred             ccccc
Q 013141          191 LNWAT  195 (449)
Q Consensus       191 ~~~~~  195 (449)
                      |.++.
T Consensus       131 V~~a~  135 (156)
T 3n9u_C          131 VRPAT  135 (156)
T ss_dssp             EEECC
T ss_pred             EEEcC
Confidence            77765

>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=99.69  E-value=1.2e-16  Score=130.05  Aligned_cols=86  Identities=26%  Similarity=0.446  Sum_probs=81.0

Q ss_pred             ccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEE
Q 013141          204 EACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRI  283 (449)
Q Consensus       204 ~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  283 (449)
                      ...+.++|||+|||.++++++|+++|+ .||.|..|.+++++.+++++|||||+|.+.++|++|++.|++..|.|+.|+|
T Consensus        42 ~~~~~~~l~V~nLp~~~te~~L~~~F~-~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V  120 (129)
T 2kxn_B           42 NPDPNCCLGVFGLSLYTTERDLREVFS-KYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV  120 (129)
T ss_dssp             CCCCSSCBCEETCTTSCCHHHHHHHHT-TTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHH-hcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            445678999999999999999999995 9999999999999999999999999999999999999999999999999999


Q ss_pred             eecCCCC
Q 013141          284 DVATPKK  290 (449)
Q Consensus       284 ~~~~~~~  290 (449)
                      +++.++.
T Consensus       121 ~~a~~~~  127 (129)
T 2kxn_B          121 DFSITKR  127 (129)
T ss_dssp             SCCSSSS
T ss_pred             EEecCCC
Confidence            9998764

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.69  E-value=1.5e-16  Score=122.14  Aligned_cols=83  Identities=25%  Similarity=0.382  Sum_probs=78.0

Q ss_pred             ccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEE
Q 013141          204 EACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRI  283 (449)
Q Consensus       204 ~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  283 (449)
                      ...+.++|||+|||.++++++|+++|+ .||.|..+.+++++.++.++|||||+|.+.++|++|++.|++..|.|+.|+|
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~f~-~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   90 (94)
T 2e5h_A           12 LAPSKSTVYVSNLPFSLTNNDLYRIFS-KYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKA   90 (94)
T ss_dssp             CCCCTTSEEEESCCTTSCHHHHHHHTT-TTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHH-hcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEE
Confidence            345678999999999999999999995 9999999999999999999999999999999999999999999999999999


Q ss_pred             eecC
Q 013141          284 DVAT  287 (449)
Q Consensus       284 ~~~~  287 (449)
                      ++++
T Consensus        91 ~~ak   94 (94)
T 2e5h_A           91 SIAI   94 (94)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            9874

>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=99.69  E-value=6.8e-17  Score=128.01  Aligned_cols=85  Identities=19%  Similarity=0.384  Sum_probs=77.7

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      .....++|||+|||+++++++|+++|+.||.|.+|.++.++.+++++|||||+|.+.++|.+|++.|++..+.  ++.|+
T Consensus        22 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~--g~~l~   99 (110)
T 1oo0_B           22 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIM--GQTIQ   99 (110)
T ss_dssp             CBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEET--TEECE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEEC--CcEEE
Confidence            3456789999999999999999999999999999999999989999999999999999999999999999884  57888


Q ss_pred             ccccccC
Q 013141          191 LNWATFS  197 (449)
Q Consensus       191 ~~~~~~~  197 (449)
                      |.|+...
T Consensus       100 V~~a~~~  106 (110)
T 1oo0_B          100 VDWCFVK  106 (110)
T ss_dssp             EEESEES
T ss_pred             EEEcccC
Confidence            8887654

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.69  E-value=2.5e-16  Score=120.35  Aligned_cols=82  Identities=20%  Similarity=0.317  Sum_probs=74.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccc
Q 013141          112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRL  191 (449)
Q Consensus       112 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~  191 (449)
                      ....++|||+|||+++++++|+++|+.||.|.+|+++++  +++++|||||+|.+.++|++|++.|++..+.  ++.|+|
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~--g~~l~v   80 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLS--GREIDV   80 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBT--TBCCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEEC--CcEEEE
Confidence            357889999999999999999999999999999999985  6899999999999999999999999999985  467888


Q ss_pred             cccccC
Q 013141          192 NWATFS  197 (449)
Q Consensus       192 ~~~~~~  197 (449)
                      .++...
T Consensus        81 ~~a~~~   86 (92)
T 2dgv_A           81 RIDRNA   86 (92)
T ss_dssp             EECSCC
T ss_pred             EEcCCC
Confidence            777654

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.69  E-value=5.6e-17  Score=127.50  Aligned_cols=78  Identities=18%  Similarity=0.204  Sum_probs=71.6

Q ss_pred             CCCcEEEEcCCCCCCCHhHHHhhccccC-ceEEEEEe--CCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCC
Q 013141          325 SNNATIFVGALDSDVSDEDLREPFSQFG-EILSVKIP--VGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNP  401 (449)
Q Consensus       325 ~~~~~l~V~nlp~~~t~~~L~~~f~~~G-~v~~v~i~--~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~  401 (449)
                      ...++|||+|||+++++++|+++|+.|| .|..+.+.  +++|+|||+|.+.++|.+|++.|||..|+|+.|+|++++.+
T Consensus        26 ~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a~~~  105 (111)
T 2jvr_A           26 AKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDDNP  105 (111)
T ss_dssp             CCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSCSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEESCC-
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcCCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCC
Confidence            4568999999999999999999999999 99999986  36899999999999999999999999999999999999875


Q ss_pred             C
Q 013141          402 G  402 (449)
Q Consensus       402 ~  402 (449)
                      +
T Consensus       106 p  106 (111)
T 2jvr_A          106 P  106 (111)
T ss_dssp             -
T ss_pred             C
Confidence            4

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens}

Probab=99.69  E-value=1.2e-16  Score=121.02  Aligned_cols=78  Identities=29%  Similarity=0.541  Sum_probs=72.5

Q ss_pred             CCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeC-------CCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 013141          326 NNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV-------GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWG  398 (449)
Q Consensus       326 ~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~-------~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~  398 (449)
                      ..++|||+|||.++++++|+++|+.||.|.+|.++.       .+++|||+|.+.++|.+|++.|||..|+|+.|+|+++
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   82 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAV   82 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEEC
Confidence            468999999999999999999999999999999864       4789999999999999999999999999999999999


Q ss_pred             CCCCC
Q 013141          399 RNPGN  403 (449)
Q Consensus       399 ~~~~~  403 (449)
                      +++..
T Consensus        83 ~~~~~   87 (88)
T 4a8x_A           83 LAPWP   87 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87653

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.69  E-value=1.4e-16  Score=123.34  Aligned_cols=86  Identities=17%  Similarity=0.386  Sum_probs=79.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCC---CCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceE
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSN---TGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMR  282 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  282 (449)
                      .+.++|||+|||.++++++|+++|+ .||.|..+.++++..   ++.++|||||+|.+.++|++|++.|++..|.|+.|+
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~-~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   81 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFS-KVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLE   81 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHH-TTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHH-hcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEE
Confidence            4568999999999999999999995 999999999999876   668999999999999999999999999999999999


Q ss_pred             EeecCCCCCC
Q 013141          283 IDVATPKKAS  292 (449)
Q Consensus       283 v~~~~~~~~~  292 (449)
                      |+++.++...
T Consensus        82 V~~a~~~~~~   91 (98)
T 2cpf_A           82 VRISERATKP   91 (98)
T ss_dssp             EECSSCSSCC
T ss_pred             EEEccCCCCC
Confidence            9999887653

>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=99.69  E-value=2.8e-16  Score=122.80  Aligned_cols=86  Identities=22%  Similarity=0.412  Sum_probs=76.1

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcc
Q 013141          110 FTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPF  189 (449)
Q Consensus       110 ~~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~  189 (449)
                      ......++|||+|||+++++++|+++|+.||.|.+|+|+.++.  .++|||||+|.+.++|++|++.|++..+.  ++.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~l   85 (103)
T 2cq3_A           10 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVE--GRKI   85 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEET--TEEC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEEC--CEEE
Confidence            3456789999999999999999999999999999999999864  48999999999999999999999999984  5778


Q ss_pred             cccccccCCC
Q 013141          190 RLNWATFSGS  199 (449)
Q Consensus       190 ~~~~~~~~~~  199 (449)
                      +|.++.....
T Consensus        86 ~v~~a~~~~~   95 (103)
T 2cq3_A           86 EVNNATARVM   95 (103)
T ss_dssp             EEEECCSSCC
T ss_pred             EEEEcccCCC
Confidence            8888875543

>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=99.69  E-value=2.1e-16  Score=125.40  Aligned_cols=88  Identities=18%  Similarity=0.458  Sum_probs=82.1

Q ss_pred             ccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC------Cceec
Q 013141          204 EACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMN------GVYCS  277 (449)
Q Consensus       204 ~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~------g~~~~  277 (449)
                      ...+.++|||+|||+++++++|+++|+ .||.|..|.+++++.++.++|||||+|.+.++|.+|++.|+      +..|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~-~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~   89 (111)
T 1x4h_A           11 DVTEGKTVFIRNLSFDSEEEALGEVLQ-QFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLD   89 (111)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHH-TTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESS
T ss_pred             cCCCCCEEEEECCCCCCCHHHHHHHHH-hcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEc
Confidence            345678999999999999999999995 99999999999999999999999999999999999999999      99999


Q ss_pred             CcceEEeecCCCCCC
Q 013141          278 SRPMRIDVATPKKAS  292 (449)
Q Consensus       278 g~~i~v~~~~~~~~~  292 (449)
                      |+.|+|.++.++...
T Consensus        90 g~~l~v~~a~~~~~~  104 (111)
T 1x4h_A           90 GRQLKVDLAVTRDEA  104 (111)
T ss_dssp             SCEEEEECCCCCCCC
T ss_pred             CEEEEEEECCCCccC
Confidence            999999999887654

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.69  E-value=7.5e-17  Score=125.63  Aligned_cols=77  Identities=29%  Similarity=0.508  Sum_probs=73.1

Q ss_pred             cEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC-CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCCCC
Q 013141          328 ATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNK  404 (449)
Q Consensus       328 ~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~-~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~~~  404 (449)
                      ++|||+|||.++++++|+++|++||.|.+|.+..+ +++|||+|.+.++|.+|++.||+..|.|+.|+|+|+++...+
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~   78 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPRR   78 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESSSSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCCCS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCCCc
Confidence            47999999999999999999999999999999986 999999999999999999999999999999999999987644

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.69  E-value=2.4e-16  Score=124.91  Aligned_cols=79  Identities=24%  Similarity=0.380  Sum_probs=73.2

Q ss_pred             CCCCcEEEEcCCCCCCCHhHHH---hhccccCceEEEEEeCCC---------cEEEEEecCHHHHHHHHHHhcCCeeCCe
Q 013141          324 ESNNATIFVGALDSDVSDEDLR---EPFSQFGEILSVKIPVGK---------GCGFVQFANRKDAEVALQKLQGTAIGKQ  391 (449)
Q Consensus       324 ~~~~~~l~V~nlp~~~t~~~L~---~~f~~~G~v~~v~i~~~~---------g~afV~F~~~~~A~~A~~~l~g~~~~g~  391 (449)
                      ....++|||+|||+++++++|+   ++|++||.|.+|.|++++         |+|||+|.+.++|.+|++.||+..|+|+
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr   91 (111)
T 2cpi_A           12 VVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGR   91 (111)
T ss_dssp             CCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             ccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCE
Confidence            3457899999999999999999   999999999999998643         7999999999999999999999999999


Q ss_pred             EEEEEecCCCC
Q 013141          392 TVRLSWGRNPG  402 (449)
Q Consensus       392 ~l~v~~~~~~~  402 (449)
                      .|+|.|++++.
T Consensus        92 ~l~V~~a~~k~  102 (111)
T 2cpi_A           92 TLKASLGTTKY  102 (111)
T ss_dssp             EEEEESCCCCS
T ss_pred             EEEEEeccccc
Confidence            99999999865

>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=4e-17  Score=127.94  Aligned_cols=84  Identities=23%  Similarity=0.512  Sum_probs=76.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccc
Q 013141          112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRL  191 (449)
Q Consensus       112 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~  191 (449)
                      ....++|||+|||+++++++|+++|+.||.|.+|.++.++.+++++|||||+|.+.++|.+|++.|++..+.  ++.|+|
T Consensus         5 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~l~v   82 (104)
T 1p1t_A            5 DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFS--GRALRV   82 (104)
T ss_dssp             HHHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCS--SSCBEE
T ss_pred             CCCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeC--CcEEEE
Confidence            346789999999999999999999999999999999999989999999999999999999999999999984  577888


Q ss_pred             cccccC
Q 013141          192 NWATFS  197 (449)
Q Consensus       192 ~~~~~~  197 (449)
                      .++...
T Consensus        83 ~~a~~~   88 (104)
T 1p1t_A           83 DNAASE   88 (104)
T ss_dssp             EETTCT
T ss_pred             EeCCCc
Confidence            887644

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=2.1e-16  Score=122.57  Aligned_cols=86  Identities=23%  Similarity=0.429  Sum_probs=80.2

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhhCCCee-EEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcc---
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQETFSSKYPSVK-GAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRP---  280 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~-~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~---  280 (449)
                      ....++|||+|||+++++++|+++|+ .||.|. ++.+++++.++.++|||||+|.+.++|++|++.||+..+.|+.   
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~-~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~   84 (99)
T 2div_A            6 SGMAASLWMGDLEPYMDENFISRAFA-TMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAK   84 (99)
T ss_dssp             CSSSSEEEECSCCTTCCHHHHHHHHH-HTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCE
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHH-HhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcce
Confidence            34678999999999999999999995 999999 9999999999999999999999999999999999999999999   


Q ss_pred             -eEEeecCCCCC
Q 013141          281 -MRIDVATPKKA  291 (449)
Q Consensus       281 -i~v~~~~~~~~  291 (449)
                       |+|.++.+...
T Consensus        85 ~l~v~~a~~~~~   96 (99)
T 2div_A           85 RFKLNYATYSGP   96 (99)
T ss_dssp             ECCEEETTCCSS
T ss_pred             eEEEeecCCCCC
Confidence             99999987643

>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=99.68  E-value=5.7e-17  Score=125.58  Aligned_cols=83  Identities=12%  Similarity=0.147  Sum_probs=75.3

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      .....++|||+|||+++++++|+++|..||.|.++.++.++.+++++|||||+|.+.++|++|++.|++..+.  ++.|+
T Consensus        11 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~--g~~l~   88 (98)
T 2cqp_A           11 GKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIG--SRKVK   88 (98)
T ss_dssp             CCCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEET--TEECE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeC--CeEEE
Confidence            3456789999999999999999999999999999999999899999999999999999999999999999885  46777


Q ss_pred             ccccc
Q 013141          191 LNWAT  195 (449)
Q Consensus       191 ~~~~~  195 (449)
                      |.++.
T Consensus        89 V~~a~   93 (98)
T 2cqp_A           89 LVLGS   93 (98)
T ss_dssp             EEESS
T ss_pred             EEEcC
Confidence            77765

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.68  E-value=8.8e-17  Score=122.93  Aligned_cols=81  Identities=28%  Similarity=0.491  Sum_probs=74.7

Q ss_pred             CCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeC----CCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 013141          324 ESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV----GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGR  399 (449)
Q Consensus       324 ~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~----~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  399 (449)
                      ....++|||+|||..+++++|+++|+.||.|.+|.|.+    .+++|||+|.+.++|.+|++.||+..|.|+.|+|+|++
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~   84 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDR   84 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEESSSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEECS
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEccCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            44578999999999999999999999999999999986    36899999999999999999999999999999999999


Q ss_pred             CCCCC
Q 013141          400 NPGNK  404 (449)
Q Consensus       400 ~~~~~  404 (449)
                      +....
T Consensus        85 ~~~~~   89 (92)
T 2dgv_A           85 NASGP   89 (92)
T ss_dssp             CCSSC
T ss_pred             CCCCC
Confidence            86543

>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=3.2e-17  Score=130.98  Aligned_cols=105  Identities=18%  Similarity=0.310  Sum_probs=92.3

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEe
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRID  284 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  284 (449)
                      ..++++|||+|||.++++++|+++|+ .||.|.++.++++   +.++|||||+|.+.++|.+|++.|||..+.|+.|+|.
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~-~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   80 (115)
T 3lqv_A            5 PEVNRILYIRNLPYKITAEEMYDIFG-KYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVL   80 (115)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHH-TTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHH-hcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            34678999999999999999999996 9999999999876   4558999999999999999999999999999999999


Q ss_pred             ecCCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCc
Q 013141          285 VATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGE  353 (449)
Q Consensus       285 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~  353 (449)
                      ++.+....                                        .+++...++++|.++|++||.
T Consensus        81 ~a~~~~~~----------------------------------------~~~~~~~~~~~l~~~~~~~g~  109 (115)
T 3lqv_A           81 YYNANRAF----------------------------------------QKMDTKKKEEQLKLLKEKYGI  109 (115)
T ss_dssp             ECCHHHHT----------------------------------------TTSCHHHHHHHHHHHHHHHCC
T ss_pred             EecCChhh----------------------------------------hhhhHhHhHHHHHHHHHHhCC
Confidence            99765331                                        356677788999999999974

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=1.3e-16  Score=126.41  Aligned_cols=86  Identities=16%  Similarity=0.196  Sum_probs=72.6

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCc
Q 013141          109 NFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQP  188 (449)
Q Consensus       109 ~~~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~  188 (449)
                      .....++++|||+|||+++++++|+++|++||.|.+|+|+++      +|||||+|.+.++|.+|++.+++......++.
T Consensus        25 ~~~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~   98 (119)
T 2ad9_A           25 RSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQP   98 (119)
T ss_dssp             TSCSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBC
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeE
Confidence            344567899999999999999999999999999999999876      58999999999999999998885422235688


Q ss_pred             ccccccccCCCC
Q 013141          189 FRLNWATFSGSD  200 (449)
Q Consensus       189 ~~~~~~~~~~~~  200 (449)
                      |+|.+++.....
T Consensus        99 l~V~~a~~k~~~  110 (119)
T 2ad9_A           99 IYIQFSNHKELK  110 (119)
T ss_dssp             CEEEECSSSSCC
T ss_pred             EEEEEccCCCCC
Confidence            999988765443

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=1.2e-16  Score=123.48  Aligned_cols=84  Identities=18%  Similarity=0.234  Sum_probs=70.8

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcc
Q 013141          110 FTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPF  189 (449)
Q Consensus       110 ~~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~  189 (449)
                      ....++++|||+|||+++++++|+++|++||.|.+|.++++      +|||||+|.+.++|.+|++.|++......++.|
T Consensus        10 ~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l   83 (101)
T 2cq1_A           10 MDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPI   83 (101)
T ss_dssp             CCSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEEC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEE
Confidence            34467899999999999999999999999999999998875      589999999999999999987643322356889


Q ss_pred             cccccccCCC
Q 013141          190 RLNWATFSGS  199 (449)
Q Consensus       190 ~~~~~~~~~~  199 (449)
                      +|.|+.....
T Consensus        84 ~V~~a~~~~~   93 (101)
T 2cq1_A           84 YIQYSNHKEL   93 (101)
T ss_dssp             EEEECSCSSC
T ss_pred             EEEEcCcccC
Confidence            9998875543

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=3.9e-16  Score=124.46  Aligned_cols=85  Identities=25%  Similarity=0.494  Sum_probs=75.8

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCC------
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPN------  184 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~------  184 (449)
                      .....++|||+|||+++++++|+++|+.||.|.+|+++.++ +++++|||||+|.+.++|.+|++.||+..+.+      
T Consensus        21 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~   99 (114)
T 1x5o_A           21 QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSA   99 (114)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccC
Confidence            34567899999999999999999999999999999999998 89999999999999999999999999998854      


Q ss_pred             CCCccccccccc
Q 013141          185 TDQPFRLNWATF  196 (449)
Q Consensus       185 ~~~~~~~~~~~~  196 (449)
                      ..+++++.|+.+
T Consensus       100 ~~~~l~v~~a~p  111 (114)
T 1x5o_A          100 PTEPLLCKFSGP  111 (114)
T ss_dssp             CSSCBEEEECCC
T ss_pred             CCCceeEEccCC
Confidence            346677777653

>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=99.68  E-value=1.2e-16  Score=123.02  Aligned_cols=78  Identities=31%  Similarity=0.424  Sum_probs=73.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC-----CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 013141          323 GESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-----KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSW  397 (449)
Q Consensus       323 ~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~-----~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  397 (449)
                      .....++|||+|||..+++++|+++|+.||.|.+|.|+++     +++|||+|.+.++|.+|++.||+..|.|+.|+|+|
T Consensus        12 ~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   91 (95)
T 2ywk_A           12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSG   91 (95)
T ss_dssp             CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEE
Confidence            4456789999999999999999999999999999999875     68999999999999999999999999999999999


Q ss_pred             cCC
Q 013141          398 GRN  400 (449)
Q Consensus       398 ~~~  400 (449)
                      ++.
T Consensus        92 a~~   94 (95)
T 2ywk_A           92 PSS   94 (95)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            975

>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=99.68  E-value=9.8e-17  Score=125.65  Aligned_cols=81  Identities=20%  Similarity=0.316  Sum_probs=74.2

Q ss_pred             CCCcEEEE--cCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCee-----CCeEEEEEe
Q 013141          325 SNNATIFV--GALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAI-----GKQTVRLSW  397 (449)
Q Consensus       325 ~~~~~l~V--~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~-----~g~~l~v~~  397 (449)
                      .++++|||  +||++++++++|+++|++||.|.+|.++.+++||||+|.+.++|.+|++.|||+.|     .++.|.|.|
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~l~v~~  102 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNF  102 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTTCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEEE
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcEEEEEe
Confidence            45688999  77999999999999999999999999999999999999999999999999999998     689999999


Q ss_pred             cCCCCCCC
Q 013141          398 GRNPGNKQ  405 (449)
Q Consensus       398 ~~~~~~~~  405 (449)
                      +++..-..
T Consensus       103 a~~~p~~~  110 (114)
T 2cq2_A          103 VEKVQWSG  110 (114)
T ss_dssp             ESCCCCSS
T ss_pred             cccCcccC
Confidence            98765443

>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=99.68  E-value=8.3e-17  Score=121.68  Aligned_cols=80  Identities=24%  Similarity=0.427  Sum_probs=70.6

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      .....++|||+|||+++++++|+++|+.||.|.+|+++.++.+++++|||||+|.+.++|.+|++ +++..+  .++.|+
T Consensus         7 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~--~g~~i~   83 (87)
T 3s7r_A            7 NEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRL--DGRVID   83 (87)
T ss_dssp             CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEE--TTEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEE--CCEEEE
Confidence            45678999999999999999999999999999999999999999999999999999999999995 466666  345566


Q ss_pred             ccc
Q 013141          191 LNW  193 (449)
Q Consensus       191 ~~~  193 (449)
                      |.+
T Consensus        84 v~~   86 (87)
T 3s7r_A           84 PKK   86 (87)
T ss_dssp             EEE
T ss_pred             EEe
Confidence            554

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.68  E-value=4.9e-17  Score=128.72  Aligned_cols=76  Identities=22%  Similarity=0.382  Sum_probs=72.9

Q ss_pred             CCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCC
Q 013141          326 NNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNP  401 (449)
Q Consensus       326 ~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~  401 (449)
                      ..++|||+|||+.+++++|+++|++||.|.+|.|++++++|||+|.+.++|.+|++.|||..|.|+.|+|.|++..
T Consensus         9 ~~~~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            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCSSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCCCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCCC
Confidence            3679999999999999999999999999999999999999999999999999999999999999999999999864

>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=99.68  E-value=6.7e-17  Score=124.76  Aligned_cols=81  Identities=14%  Similarity=0.149  Sum_probs=71.0

Q ss_pred             CCCCCceEEEcCCCC-CCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcc
Q 013141          111 TNDETKTIWIGDLFH-WMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPF  189 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~-~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~  189 (449)
                      ...++++|||+|||+ ++++++|+++|++||.|.+|.|++++      |||||+|.+.++|.+|++.|++......++.|
T Consensus        11 ~~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~k------g~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l   84 (102)
T 1x4d_A           11 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI------NEAFIEMATTEDAQAAVDYYTTTPALVFGKPV   84 (102)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS------SCEEEEESSHHHHHHHHHHHHHSCCEETTEEC
T ss_pred             CCCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcCC------CEEEEEECCHHHHHHHHHHHcCCCceECCcEE
Confidence            445789999999999 99999999999999999999998763      79999999999999999999876533367889


Q ss_pred             cccccccC
Q 013141          190 RLNWATFS  197 (449)
Q Consensus       190 ~~~~~~~~  197 (449)
                      +|.++...
T Consensus        85 ~V~~a~~~   92 (102)
T 1x4d_A           85 RVHLSQKY   92 (102)
T ss_dssp             EEEEECCC
T ss_pred             EEEECCCC
Confidence            99988744

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.68  E-value=2.2e-16  Score=126.69  Aligned_cols=79  Identities=27%  Similarity=0.540  Sum_probs=72.4

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC------CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEE
Q 013141          321 SDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKLQGTAIGKQTVR  394 (449)
Q Consensus       321 ~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~------~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~  394 (449)
                      .......++|||+|||.++++++|+++|+.||.|.+|+|+++      +++|||+|.+.++|.+|++.||+..|+|+.|+
T Consensus        34 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~  113 (118)
T 2khc_A           34 QIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLK  113 (118)
T ss_dssp             SCCCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECC
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            344566799999999999999999999999999999999864      68999999999999999999999999999999


Q ss_pred             EEecC
Q 013141          395 LSWGR  399 (449)
Q Consensus       395 v~~~~  399 (449)
                      |+|+|
T Consensus       114 V~~ak  118 (118)
T 2khc_A          114 VQLKK  118 (118)
T ss_dssp             EEEC-
T ss_pred             EEecC
Confidence            99986

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.68  E-value=3.3e-16  Score=122.37  Aligned_cols=81  Identities=22%  Similarity=0.366  Sum_probs=73.2

Q ss_pred             CCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC------CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEE
Q 013141          322 DGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRL  395 (449)
Q Consensus       322 ~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~------~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v  395 (449)
                      ......++|||+|||.++++++|+++|+.|| |.+|.|+++      +++|||+|.+.++|.+|+ .||+..|.|+.|+|
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V   87 (103)
T 2dng_A           10 LPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRV   87 (103)
T ss_dssp             CCSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEE
T ss_pred             CCCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEE
Confidence            3445679999999999999999999999996 999999864      579999999999999999 89999999999999


Q ss_pred             EecCCCCCC
Q 013141          396 SWGRNPGNK  404 (449)
Q Consensus       396 ~~~~~~~~~  404 (449)
                      .|+++....
T Consensus        88 ~~a~~~~~~   96 (103)
T 2dng_A           88 DIAEGRKQD   96 (103)
T ss_dssp             EECCCCCCC
T ss_pred             EEecCCCCC
Confidence            999986544

>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=99.68  E-value=2.4e-16  Score=121.55  Aligned_cols=79  Identities=27%  Similarity=0.431  Sum_probs=72.6

Q ss_pred             CCCCCCcEEEEcCCCC-CCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCC
Q 013141          322 DGESNNATIFVGALDS-DVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRN  400 (449)
Q Consensus       322 ~~~~~~~~l~V~nlp~-~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  400 (449)
                      ......++|||+|||. .+++++|+++|+.||.|.+|.+.  +|+|||+|.+.++|.+|++.|||..|+|+.|+|+|++.
T Consensus        17 ~~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   94 (97)
T 2xnq_A           17 RGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSS   94 (97)
T ss_dssp             --CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEECCC
T ss_pred             CCCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCC
Confidence            3455689999999998 99999999999999999999995  89999999999999999999999999999999999987


Q ss_pred             CC
Q 013141          401 PG  402 (449)
Q Consensus       401 ~~  402 (449)
                      +.
T Consensus        95 ~~   96 (97)
T 2xnq_A           95 NA   96 (97)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.68  E-value=1.9e-16  Score=125.43  Aligned_cols=88  Identities=22%  Similarity=0.408  Sum_probs=81.5

Q ss_pred             cccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceE
Q 013141          203 TEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMR  282 (449)
Q Consensus       203 ~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  282 (449)
                      ....+.++|||+|||.++++++|+++|+ .||.|..+.++.+..++.++|||||+|.+.++|.+|++.|++..|.|+.|+
T Consensus        21 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~-~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~   99 (110)
T 1oo0_B           21 QRSVEGWILFVTSIHEEAQEDEIQEKFC-DYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQ   99 (110)
T ss_dssp             CCBTTBEEEEEESCCTTCCHHHHHHHHG-GGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHH-hcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEE
Confidence            3445678999999999999999999995 999999999999998999999999999999999999999999999999999


Q ss_pred             EeecCCCCC
Q 013141          283 IDVATPKKA  291 (449)
Q Consensus       283 v~~~~~~~~  291 (449)
                      |.++.++..
T Consensus       100 V~~a~~~~~  108 (110)
T 1oo0_B          100 VDWCFVKGP  108 (110)
T ss_dssp             EEESEESSC
T ss_pred             EEEcccCCC
Confidence            999987653

>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=1.4e-16  Score=125.70  Aligned_cols=81  Identities=35%  Similarity=0.565  Sum_probs=75.2

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC----CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEE
Q 013141          321 SDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG----KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLS  396 (449)
Q Consensus       321 ~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~----~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~  396 (449)
                      .......++|||+|||.++++++|+++|+.||.|.+|.+..+    +|+|||+|.+.++|.+|++.|||..|+|+.|+|+
T Consensus        23 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  102 (109)
T 2err_A           23 TENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN  102 (109)
T ss_dssp             CSCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTTBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEE
T ss_pred             ccCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            344567899999999999999999999999999999999875    7999999999999999999999999999999999


Q ss_pred             ecCCC
Q 013141          397 WGRNP  401 (449)
Q Consensus       397 ~~~~~  401 (449)
                      |++++
T Consensus       103 ~a~~~  107 (109)
T 2err_A          103 NATAR  107 (109)
T ss_dssp             ECCCS
T ss_pred             ECCCC
Confidence            99875

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.68  E-value=3.9e-16  Score=124.46  Aligned_cols=84  Identities=24%  Similarity=0.401  Sum_probs=75.6

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      .....++|||+|||+++++++|+++|..||.|.+|+|+.++ +++++|||||+|.+.++|++|++.|++..+.  ++.|+
T Consensus        11 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~l~   87 (114)
T 2do0_A           11 AGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLF--DRPMH   87 (114)
T ss_dssp             CCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEET--TEECE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeC--CCEEE
Confidence            34568899999999999999999999999999999999997 5999999999999999999999999999985  56777


Q ss_pred             ccccccC
Q 013141          191 LNWATFS  197 (449)
Q Consensus       191 ~~~~~~~  197 (449)
                      |.++...
T Consensus        88 v~~a~~~   94 (114)
T 2do0_A           88 VKMDERA   94 (114)
T ss_dssp             EEECSCC
T ss_pred             EEEcccC
Confidence            8777543

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.68  E-value=3.5e-16  Score=122.25  Aligned_cols=87  Identities=20%  Similarity=0.462  Sum_probs=80.1

Q ss_pred             cccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceE
Q 013141          203 TEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMR  282 (449)
Q Consensus       203 ~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  282 (449)
                      ....+.++|||+|||.++++++|+++|+ .|| |..|.+++++.+++++|||||+|.+.++|++|+ .|++..|.|+.|+
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~-~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~   86 (103)
T 2dng_A           10 LPTEPPYTAYVGNLPFNTVQGDIDAIFK-DLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLR   86 (103)
T ss_dssp             CCSSSCEEEEEESCCTTCCHHHHHHHTT-TSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECE
T ss_pred             CCCCCCeEEEEeCCCCCCCHHHHHHHHH-hCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEE
Confidence            3445678999999999999999999995 896 999999999999999999999999999999999 8999999999999


Q ss_pred             EeecCCCCCC
Q 013141          283 IDVATPKKAS  292 (449)
Q Consensus       283 v~~~~~~~~~  292 (449)
                      |.++.++...
T Consensus        87 V~~a~~~~~~   96 (103)
T 2dng_A           87 VDIAEGRKQD   96 (103)
T ss_dssp             EEECCCCCCC
T ss_pred             EEEecCCCCC
Confidence            9999887553

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.68  E-value=3.3e-17  Score=127.25  Aligned_cols=83  Identities=27%  Similarity=0.314  Sum_probs=78.5

Q ss_pred             CCCceEEEcCCCC------CCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecC-
Q 013141          206 CSDLSIFVGDLAP------DVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSS-  278 (449)
Q Consensus       206 ~~~~~l~v~~lp~------~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g-  278 (449)
                      ..+++|||+|||.      ++++++|+++|+ .||.|.++.+++++.+++++|||||+|.+.++|.+|++.|||..+.| 
T Consensus         4 ~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~-~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~   82 (100)
T 3ns6_A            4 GSDQYIVVNGAPVIPSAKVPVLKKALTSLFS-KAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLK   82 (100)
T ss_dssp             CGGGEEEEESCCCCBGGGHHHHHHHHHHHHH-TTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSS
T ss_pred             CcCcEEEEeCCCcCChHHHHHHHHHHHHHHH-hcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCC
Confidence            3467999999999      999999999996 99999999999999999999999999999999999999999999999 


Q ss_pred             cceEEeecCCC
Q 013141          279 RPMRIDVATPK  289 (449)
Q Consensus       279 ~~i~v~~~~~~  289 (449)
                      +.|+|.++.++
T Consensus        83 r~l~V~~a~~~   93 (100)
T 3ns6_A           83 HRLFLYTMKDV   93 (100)
T ss_dssp             CBCEEEESHHH
T ss_pred             eEEEEEECchh
Confidence            99999999764

>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=99.68  E-value=2.2e-16  Score=124.19  Aligned_cols=88  Identities=17%  Similarity=0.399  Sum_probs=81.5

Q ss_pred             ccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee---cCcc
Q 013141          204 EACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYC---SSRP  280 (449)
Q Consensus       204 ~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~---~g~~  280 (449)
                      ...+.++|||+|||.++++++|+++|+ .||.|.+|.++.++.++.++|||||+|.+.++|.+|++.|++..+   .++.
T Consensus         9 ~~~~~~~l~V~nlp~~~t~~~l~~~F~-~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~   87 (106)
T 2dgp_A            9 KDHDAIKLFIGQIPRNLDEKDLKPLFE-EFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRP   87 (106)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHH-HHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHH-hcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCce
Confidence            345678999999999999999999995 999999999999999999999999999999999999999999988   8999


Q ss_pred             eEEeecCCCCCC
Q 013141          281 MRIDVATPKKAS  292 (449)
Q Consensus       281 i~v~~~~~~~~~  292 (449)
                      |+|.++.++...
T Consensus        88 l~v~~a~~~~~~   99 (106)
T 2dgp_A           88 IQVKPADSESRG   99 (106)
T ss_dssp             CEEEECCCCSCC
T ss_pred             EEEEECCccccc
Confidence            999999887653

>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=99.67  E-value=2.8e-16  Score=125.42  Aligned_cols=86  Identities=21%  Similarity=0.444  Sum_probs=80.0

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEe
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRID  284 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  284 (449)
                      ....++|||+|||.++++++|+++|+ .||.|..|.++.+. ++.++|||||+|.+.++|++|++.|++..|.|+.|+|+
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~-~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~   81 (116)
T 2fy1_A            4 ADHPGKLFIGGLNRETNEKMLKAVFG-KHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVE   81 (116)
T ss_dssp             TCSCCEEEEECCTTTCCHHHHHHHHH-TSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHH-hcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34678999999999999999999995 99999999999997 89999999999999999999999999999999999999


Q ss_pred             ecCCCCCC
Q 013141          285 VATPKKAS  292 (449)
Q Consensus       285 ~~~~~~~~  292 (449)
                      ++.+....
T Consensus        82 ~a~~~~~~   89 (116)
T 2fy1_A           82 QAKKPSFQ   89 (116)
T ss_dssp             ECCCSSCS
T ss_pred             ECCCCCCC
Confidence            99876543

>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=99.67  E-value=1.9e-16  Score=128.65  Aligned_cols=86  Identities=21%  Similarity=0.441  Sum_probs=78.0

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      .....++|||+|||+++|+++|+++|+.||.|.+|.|+.++.+++++|||||+|.+.++|++|++.|++..+.  ++.|+
T Consensus        18 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~l~   95 (126)
T 3ex7_B           18 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLM--GQPIS   95 (126)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSS--SSBCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeC--CeEEE
Confidence            3456789999999999999999999999999999999999889999999999999999999999999999994  57788


Q ss_pred             ccccccCC
Q 013141          191 LNWATFSG  198 (449)
Q Consensus       191 ~~~~~~~~  198 (449)
                      |.|+....
T Consensus        96 v~~a~~~~  103 (126)
T 3ex7_B           96 VDWCFVRG  103 (126)
T ss_dssp             EEESEESS
T ss_pred             EEEecCCC
Confidence            88876543

>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=99.67  E-value=3.6e-17  Score=146.73  Aligned_cols=75  Identities=21%  Similarity=0.325  Sum_probs=69.3

Q ss_pred             CCcEEEEcCCCCCCCHhHHHhhccccC--ceEEEEEeCC------CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 013141          326 NNATIFVGALDSDVSDEDLREPFSQFG--EILSVKIPVG------KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSW  397 (449)
Q Consensus       326 ~~~~l~V~nlp~~~t~~~L~~~f~~~G--~v~~v~i~~~------~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  397 (449)
                      ..++|||+||++.+|+++|+++|+.||  .|++|+|+++      ++||||+|.+.++|.+||+.||+..|.|+.|+|.|
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            567999999999999999999999999  9999999864      58999999999999999999999999999999999


Q ss_pred             cCC
Q 013141          398 GRN  400 (449)
Q Consensus       398 ~~~  400 (449)
                      ++.
T Consensus       147 a~~  149 (229)
T 3q2s_C          147 VNK  149 (229)
T ss_dssp             CCH
T ss_pred             CCC
Confidence            863

>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=99.67  E-value=1.2e-16  Score=127.32  Aligned_cols=79  Identities=20%  Similarity=0.352  Sum_probs=68.5

Q ss_pred             CCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeE-----EEEEecC
Q 013141          325 SNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQT-----VRLSWGR  399 (449)
Q Consensus       325 ~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~-----l~v~~~~  399 (449)
                      ...++|||+|||+++++++|+++|+.||.|.+|.|+.+ ++|||+|.+.++|.+||+.||+..|+|+.     |+|..++
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~v~~~~   92 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDG   92 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEEeccCC
Confidence            34689999999999999999999999999999999987 99999999999999999999999999988     8888877


Q ss_pred             CCCCC
Q 013141          400 NPGNK  404 (449)
Q Consensus       400 ~~~~~  404 (449)
                      +....
T Consensus        93 ~~~~~   97 (115)
T 3beg_B           93 PRSPS   97 (115)
T ss_dssp             ----C
T ss_pred             CCCCC
Confidence            65443

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.67  E-value=2.4e-16  Score=123.42  Aligned_cols=86  Identities=52%  Similarity=0.913  Sum_probs=80.3

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhh-CCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCce-ecCcceE
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQETFSSK-YPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVY-CSSRPMR  282 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~~~f~~~-~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~-~~g~~i~  282 (449)
                      ..+.++|||+|||.++|+++|+++|+ . ||.|.++.++++. ++.++|||||+|.+.++|.+|++.|++.. +.|+.|+
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~-~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~   83 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFV-KVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVR   83 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHH-HHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHH-HhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEE
Confidence            45678999999999999999999996 8 9999999999998 89999999999999999999999999999 9999999


Q ss_pred             EeecCCCCCC
Q 013141          283 IDVATPKKAS  292 (449)
Q Consensus       283 v~~~~~~~~~  292 (449)
                      |.++.++...
T Consensus        84 v~~a~~~~~~   93 (104)
T 2dhg_A           84 LSVAIPKASR   93 (104)
T ss_dssp             CCBCCCCCSC
T ss_pred             EEEccCCCcC
Confidence            9999877654

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.67  E-value=4.4e-16  Score=126.08  Aligned_cols=85  Identities=19%  Similarity=0.290  Sum_probs=77.5

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      .....++|||+|||+++++++|+++|+.||.|.+|+++.++ +++++|||||+|.+.++|.+|++.|++..+.  ++.|+
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~--g~~l~  107 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLD--GRPMD  107 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESS--SCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEEC--CcEEE
Confidence            44678899999999999999999999999999999999998 8999999999999999999999999999884  57888


Q ss_pred             ccccccCC
Q 013141          191 LNWATFSG  198 (449)
Q Consensus       191 ~~~~~~~~  198 (449)
                      |.++....
T Consensus       108 V~~a~~~~  115 (124)
T 2kt5_A          108 IQLVASQI  115 (124)
T ss_dssp             EEEECCTT
T ss_pred             EEEeCCCC
Confidence            88887543

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=6.1e-16  Score=120.41  Aligned_cols=79  Identities=28%  Similarity=0.431  Sum_probs=70.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 013141          323 GESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV-----GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSW  397 (449)
Q Consensus       323 ~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~-----~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  397 (449)
                      .....++|||+|||..+++++|+++|+.||.|   +++.     .+++|||+|.+.++|.+|++.||+..|.|+.|+|.|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   87 (101)
T 2fc9_A           11 WSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLEL   87 (101)
T ss_dssp             CSCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEE
Confidence            34568999999999999999999999999987   3333     379999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 013141          398 GRNPGNK  404 (449)
Q Consensus       398 ~~~~~~~  404 (449)
                      ++++...
T Consensus        88 a~~~~~~   94 (101)
T 2fc9_A           88 QGPRGSP   94 (101)
T ss_dssp             CSSCCCC
T ss_pred             cCCCCCC
Confidence            9987543

>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=99.67  E-value=1.3e-16  Score=121.13  Aligned_cols=80  Identities=19%  Similarity=0.384  Sum_probs=73.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccccc
Q 013141          114 ETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNW  193 (449)
Q Consensus       114 ~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~  193 (449)
                      ..++|||+|||+++++++|+++|+.||.|.+|.++.++.+++++|||||+|.+.++|++|+ .+++..+.  ++.|+|.+
T Consensus         5 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~--g~~l~V~~   81 (89)
T 3ucg_A            5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFR--GRQIKVIP   81 (89)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEET--TEECEEEE
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEEC--CcEEEEEE
Confidence            4689999999999999999999999999999999999889999999999999999999999 99999984  57778877


Q ss_pred             ccc
Q 013141          194 ATF  196 (449)
Q Consensus       194 ~~~  196 (449)
                      ++.
T Consensus        82 a~~   84 (89)
T 3ucg_A           82 KRT   84 (89)
T ss_dssp             TTT
T ss_pred             ccC
Confidence            764

>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=99.67  E-value=1.9e-16  Score=124.78  Aligned_cols=82  Identities=20%  Similarity=0.338  Sum_probs=74.6

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      .....++|||+|||+++++++|+++|+.||.|.+|+++.++ +++++|||||+|.+.++|.+|++.|++..+.  ++.|+
T Consensus        25 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~l~  101 (107)
T 3ulh_A           25 GVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLD--GRPMN  101 (107)
T ss_dssp             CCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEET--TEECE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeC--CcEEE
Confidence            34678999999999999999999999999999999999998 8999999999999999999999999999984  46777


Q ss_pred             ccccc
Q 013141          191 LNWAT  195 (449)
Q Consensus       191 ~~~~~  195 (449)
                      |.++.
T Consensus       102 V~~a~  106 (107)
T 3ulh_A          102 IQLVT  106 (107)
T ss_dssp             EEEEC
T ss_pred             EEEeC
Confidence            76653

>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=99.67  E-value=2.1e-16  Score=122.98  Aligned_cols=81  Identities=17%  Similarity=0.158  Sum_probs=70.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccc
Q 013141          112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRL  191 (449)
Q Consensus       112 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~  191 (449)
                      ....++|||+|||+++|+++|+++|+.||.+ +|+|+.++ +++++|||||+|.+.++|++|| .+++..+.+  +.|+|
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~g--r~i~V   86 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGP-DGRVTGEADVEFATHEDAVAAM-AKDKANMQH--RYVEL   86 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESS-SSCEEEEEEEECSSSHHHHHHH-TTSSCCSSS--SCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECC-CCCEeeEEEEEECCHHHHHHHH-HhCCCeECC--cEEEE
Confidence            3567899999999999999999999999955 99999997 8999999999999999999999 578888854  56777


Q ss_pred             cccccC
Q 013141          192 NWATFS  197 (449)
Q Consensus       192 ~~~~~~  197 (449)
                      .++...
T Consensus        87 ~~~~~~   92 (102)
T 1wez_A           87 FLNSTA   92 (102)
T ss_dssp             EEECCC
T ss_pred             EECCCC
Confidence            666543

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.67  E-value=7.7e-17  Score=118.16  Aligned_cols=75  Identities=25%  Similarity=0.334  Sum_probs=68.2

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccccc
Q 013141          117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWA  194 (449)
Q Consensus       117 ~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~~  194 (449)
                      +|||+|||+++++++|+++|+.||.|.+|.++.++.+++++|||||+|.+.++|++|++ +++..+.+  +.+++.++
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-IHFHEINN--KMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSS--CCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECC--EEEEEEeC
Confidence            59999999999999999999999999999999998899999999999999999999997 89988854  56666553

>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=99.67  E-value=2.5e-16  Score=119.30  Aligned_cols=83  Identities=22%  Similarity=0.406  Sum_probs=77.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCC-cceEEEEEeCCHHHHHHHHHHhCCceecCcceEEee
Q 013141          207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGR-TKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV  285 (449)
Q Consensus       207 ~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~-~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  285 (449)
                      ..++|||+|||.++++++|+++|+ .||.|.++.++.+..++. ++|+|||+|.+.++|.+|++.|++..+.|+.|+|++
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~-~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   81 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFS-TYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATA   81 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHH-TTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHH-hCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEE
Confidence            457999999999999999999995 999999999999987665 899999999999999999999999999999999999


Q ss_pred             cCCCC
Q 013141          286 ATPKK  290 (449)
Q Consensus       286 ~~~~~  290 (449)
                      +.+..
T Consensus        82 a~~~~   86 (88)
T 4a8x_A           82 VLAPW   86 (88)
T ss_dssp             ECCCC
T ss_pred             CCCCC
Confidence            97754

>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=99.67  E-value=4.7e-16  Score=121.53  Aligned_cols=84  Identities=24%  Similarity=0.322  Sum_probs=74.2

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      .....++|||+|||+++++++|+++|..||.|.+|.++.++.+++++|||||+|.+.++|.+||+  ++..+  .++.|+
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~--~g~~l~   86 (103)
T 2cqg_A           11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMI--DGRWCD   86 (103)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEE--TTEEEE
T ss_pred             ccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCee--CCeEEE
Confidence            45678899999999999999999999999999999999999899999999999999999999997  34555  457788


Q ss_pred             ccccccCC
Q 013141          191 LNWATFSG  198 (449)
Q Consensus       191 ~~~~~~~~  198 (449)
                      |.++....
T Consensus        87 v~~a~~~~   94 (103)
T 2cqg_A           87 CKLPNSKQ   94 (103)
T ss_dssp             EECCCTTC
T ss_pred             EEecCCCC
Confidence            88876543

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=3.5e-16  Score=124.51  Aligned_cols=88  Identities=24%  Similarity=0.334  Sum_probs=81.7

Q ss_pred             ccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCee--------EEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCce
Q 013141          204 EACSDLSIFVGDLAPDVTDSILQETFSSKYPSVK--------GAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVY  275 (449)
Q Consensus       204 ~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~--------~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~  275 (449)
                      .....++|||+|||.++|+++|+++|+ .||.|.        .+.++.++.+++++|||||+|.+.++|.+|++.|++..
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~-~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~   89 (113)
T 2cpe_A           11 EDSDNSAIYVQGLNDSVTLDDLADFFK-QCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKD   89 (113)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHT-TTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCE
T ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHHH-hcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCc
Confidence            345678999999999999999999995 999999        69999998899999999999999999999999999999


Q ss_pred             ecCcceEEeecCCCCCC
Q 013141          276 CSSRPMRIDVATPKKAS  292 (449)
Q Consensus       276 ~~g~~i~v~~~~~~~~~  292 (449)
                      |.|+.|+|+++.++...
T Consensus        90 ~~g~~l~V~~a~~~~~~  106 (113)
T 2cpe_A           90 FQGSKLKVSLARKKPPM  106 (113)
T ss_dssp             ETTEECEEECSSCCCCS
T ss_pred             cCCCEEEEEECCCCCCC
Confidence            99999999999887654

>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=99.67  E-value=4e-16  Score=120.01  Aligned_cols=83  Identities=28%  Similarity=0.499  Sum_probs=77.2

Q ss_pred             ccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEE
Q 013141          204 EACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRI  283 (449)
Q Consensus       204 ~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  283 (449)
                      .....++|||+|||+++++++|+++|+ .||.|.++.+++++. +.++|||||+|.+.++|.+|++.|++..+.|+.|+|
T Consensus        12 ~~~~~~~l~v~nlp~~~~~~~l~~~F~-~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   89 (95)
T 2ywk_A           12 QEEADRTVFVGNLEARVREEILYELFL-QAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINV   89 (95)
T ss_dssp             CTTGGGEEEEECCCTTCCHHHHHHHHG-GGSCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHH-hcCCEEEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEE
Confidence            345678999999999999999999995 999999999999976 899999999999999999999999999999999999


Q ss_pred             eecCC
Q 013141          284 DVATP  288 (449)
Q Consensus       284 ~~~~~  288 (449)
                      ++++.
T Consensus        90 ~~a~~   94 (95)
T 2ywk_A           90 SGPSS   94 (95)
T ss_dssp             ECCCC
T ss_pred             EEcCC
Confidence            99864

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*

Probab=99.67  E-value=2.6e-17  Score=161.48  Aligned_cols=157  Identities=18%  Similarity=0.335  Sum_probs=109.7

Q ss_pred             HHHHhhccCCcEEEEEEec----C-CCCCcccEE--EEEEccHHHHHHHHHHhcCCCCCCC-------------CCcccc
Q 013141          132 LHNCFSHTGQVVNVKVIRN----K-QTGQSEGYG--FVEFYSRAAAEKVLQSYSGSLMPNT-------------DQPFRL  191 (449)
Q Consensus       132 l~~~f~~~G~v~~v~~~~~----~-~~g~~~g~a--fV~f~~~~~A~~Al~~l~~~~~~~~-------------~~~~~~  191 (449)
                      |.++|.++++|..|..+..    + .+....|++  |++|.+...+..++..++.......             ...+.+
T Consensus         9 L~~lF~p~pPl~~~~P~~~~p~~~~~~~~~~gia~~~~~f~~~~~~~~~~~~e~~~~~~~~~~~~k~~~~~~~~~~~~~~   88 (437)
T 3pgw_S            9 LLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRDAPPPTRAETREERMERKRREKIERRQQEVETELKM   88 (437)
T ss_pred             HHHhcCCCCCCcCCCCcccccccccCCCCcccHHHHHHhhcCcccccccccccCHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence            7899999999988743322    1 112223333  7788776554433321111100000             000000


Q ss_pred             cccccCCCCCccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh
Q 013141          192 NWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEM  271 (449)
Q Consensus       192 ~~~~~~~~~~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l  271 (449)
                       |.  ..........+.++|||+|||+++|+++|.++|+ .||.|..|.|+.+..++.++|||||+|.+.++|.+||+.|
T Consensus        89 -~~--p~~~~~~~~~~~~~lfV~nL~~~~te~~L~~~F~-~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~l  164 (437)
T 3pgw_S           89 -WD--PHNDPNAQGDAFKTLFVARVNYDTTESKLRREFE-VYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA  164 (437)
T ss_pred             -cC--CcccccccCCCCCEEEEeCCCCCCCHHHHHHHHH-HcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHc
Confidence             00  0011112234567999999999999999999995 9999999999999989999999999999999999999999


Q ss_pred             CCceecCcceEEeecCCCCCC
Q 013141          272 NGVYCSSRPMRIDVATPKKAS  292 (449)
Q Consensus       272 ~g~~~~g~~i~v~~~~~~~~~  292 (449)
                      |+..|.|+.|.|.++......
T Consensus       165 ng~~i~gr~i~V~~a~~~~~~  185 (437)
T 3pgw_S          165 DGKKIDGRRVLVDVERGRTVK  185 (437)
T ss_pred             CCCEECCEEEEEEEeCCCCCC
Confidence            999999999999999876543

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens}

Probab=99.67  E-value=9.2e-17  Score=124.77  Aligned_cols=83  Identities=18%  Similarity=0.302  Sum_probs=71.8

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecC-CCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNK-QTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPF  189 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~-~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~  189 (449)
                      .....++|||+|||+++++++|+++|+.|| |.+|.+++++ .+|+++|||||+|.+.++|.+|+ .|++..+.  ++.|
T Consensus        15 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~--g~~l   90 (100)
T 2j76_E           15 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLG--NRRI   90 (100)
T ss_dssp             -----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBT--TBCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEEC--CeEE
Confidence            345789999999999999999999999999 9999999998 68999999999999999999999 89999984  5677


Q ss_pred             cccccccC
Q 013141          190 RLNWATFS  197 (449)
Q Consensus       190 ~~~~~~~~  197 (449)
                      +|.++...
T Consensus        91 ~V~~a~~~   98 (100)
T 2j76_E           91 RVDVADQA   98 (100)
T ss_dssp             CCEECCCS
T ss_pred             EEEeccCC
Confidence            88777643

>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=99.67  E-value=3.6e-16  Score=122.42  Aligned_cols=86  Identities=23%  Similarity=0.445  Sum_probs=79.7

Q ss_pred             ccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCC-CCcceEEEEEeCCHHHHHHHHHHhCCceecCcceE
Q 013141          204 EACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNT-GRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMR  282 (449)
Q Consensus       204 ~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~-~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  282 (449)
                      ...+.++|||+|||+++++++|+++|+ .|| |..|.+++++.+ ++++|||||+|.+.++|++|+ .|++..|.|+.|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~-~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~   87 (104)
T 1wi8_A           11 PKSPPYTAFLGNLPYDVTEESIKEFFR-GLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIR   87 (104)
T ss_dssp             CSSSCEEEEEESCCSSCCHHHHHHHTT-TSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECE
T ss_pred             CCCCCCEEEEeCCCCcCCHHHHHHHHH-HCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEE
Confidence            345678999999999999999999995 999 999999999887 999999999999999999999 9999999999999


Q ss_pred             EeecCCCCCC
Q 013141          283 IDVATPKKAS  292 (449)
Q Consensus       283 v~~~~~~~~~  292 (449)
                      |+++.++...
T Consensus        88 V~~a~~~~~~   97 (104)
T 1wi8_A           88 VDVADQAQDK   97 (104)
T ss_dssp             EEECCCCCCC
T ss_pred             EEEccCCCCC
Confidence            9999887654

>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=99.67  E-value=6.3e-16  Score=122.13  Aligned_cols=83  Identities=16%  Similarity=0.272  Sum_probs=73.4

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      .....++|||+|||+++++++|+++|+.||.|.+|.+..+   ++++|||||+|.+.++|++|++.|++..+.  ++.|+
T Consensus        18 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~--g~~l~   92 (109)
T 1x4a_A           18 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYD--GYRLR   92 (109)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEET--TEECE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCCEEC--CeEEE
Confidence            4457899999999999999999999999999999999654   568999999999999999999999999884  57888


Q ss_pred             ccccccCC
Q 013141          191 LNWATFSG  198 (449)
Q Consensus       191 ~~~~~~~~  198 (449)
                      |.|++...
T Consensus        93 V~~a~~~~  100 (109)
T 1x4a_A           93 VEFPRSGR  100 (109)
T ss_dssp             EECCCCCC
T ss_pred             EEEcccCC
Confidence            88887543

>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=99.66  E-value=4.9e-16  Score=117.97  Aligned_cols=81  Identities=20%  Similarity=0.411  Sum_probs=77.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeec
Q 013141          207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVA  286 (449)
Q Consensus       207 ~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~  286 (449)
                      ..++|||+|||.++++++|+++|+ .||.|.++.++.++.++.++|+|||+|.+.++|++|+ .|++..+.|+.|+|.++
T Consensus         5 ~~~~l~V~nlp~~~t~~~l~~~F~-~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a   82 (89)
T 3ucg_A            5 DARSIYVGNVDYGATAEELEAHFH-GCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPK   82 (89)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHG-GGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEET
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHH-hCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEc
Confidence            357999999999999999999995 9999999999999889999999999999999999999 99999999999999999


Q ss_pred             CCC
Q 013141          287 TPK  289 (449)
Q Consensus       287 ~~~  289 (449)
                      ++.
T Consensus        83 ~~~   85 (89)
T 3ucg_A           83 RTN   85 (89)
T ss_dssp             TTT
T ss_pred             cCC
Confidence            774

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.66  E-value=3.9e-16  Score=131.13  Aligned_cols=84  Identities=20%  Similarity=0.267  Sum_probs=78.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhhCC--CeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEe
Q 013141          207 SDLSIFVGDLAPDVTDSILQETFSSKYP--SVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRID  284 (449)
Q Consensus       207 ~~~~l~v~~lp~~~t~~~l~~~f~~~~g--~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  284 (449)
                      ..++|||+|||+++|+++|+++|+ .||  .|.+|.+++|+.+++++|||||+|.+.++|++||+.|++..|.|+.|+|.
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~-~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~  132 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIR-SIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVR  132 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHH-HTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHH-HHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEE
Confidence            457999999999999999999995 999  99999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 013141          285 VATPKKA  291 (449)
Q Consensus       285 ~~~~~~~  291 (449)
                      ++.++..
T Consensus       133 ~a~~~~~  139 (156)
T 3n9u_C          133 PATRQNL  139 (156)
T ss_dssp             ECCHHHH
T ss_pred             EcCCCcc
Confidence            9987543

>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=99.66  E-value=6.3e-17  Score=124.55  Aligned_cols=81  Identities=12%  Similarity=0.153  Sum_probs=72.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      ...++|||+|||+++++++|+++|+.||.|.++.++.++.+++++|||||+|.+.++|++|++.|++..+.  ++.|+|.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~--gr~l~v~   90 (95)
T 2ek1_A           13 PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIG--SRKVKLS   90 (95)
T ss_dssp             --CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEET--TEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeEC--CcEEEEE
Confidence            45689999999999999999999999999999999999999999999999999999999999999999985  4667766


Q ss_pred             ccc
Q 013141          193 WAT  195 (449)
Q Consensus       193 ~~~  195 (449)
                      ++.
T Consensus        91 ~a~   93 (95)
T 2ek1_A           91 GPS   93 (95)
T ss_dssp             CCC
T ss_pred             ecc
Confidence            553

>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=99.66  E-value=6.4e-16  Score=116.75  Aligned_cols=80  Identities=26%  Similarity=0.455  Sum_probs=74.6

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEe
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRID  284 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  284 (449)
                      ..+.++|||+|||+++++++|+++|+ .||.|..+.+++++.+++++|||||+|.+.++|.+|++ +++..+.|+.|+|+
T Consensus         8 ~~~~~~l~V~nlp~~~t~~~l~~~F~-~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~   85 (87)
T 3s7r_A            8 EEDAGKMFVGGLSWDTSKKDLKDYFT-KFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPK   85 (87)
T ss_dssp             CSCTTEEEEECCCTTCCHHHHHHHHT-TTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHH-hCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEE
Confidence            45678999999999999999999995 99999999999999999999999999999999999995 68889999999998


Q ss_pred             ec
Q 013141          285 VA  286 (449)
Q Consensus       285 ~~  286 (449)
                      ++
T Consensus        86 ~A   87 (87)
T 3s7r_A           86 KA   87 (87)
T ss_dssp             EC
T ss_pred             eC
Confidence            75

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.66  E-value=1.2e-16  Score=126.07  Aligned_cols=84  Identities=25%  Similarity=0.354  Sum_probs=71.4

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      .....++|||+|||+++++++|+++|+.||.|.+|.+++++.+|+++|||||+|.+.++|++|++.+ +..+  .++.++
T Consensus        21 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l--~g~~l~   97 (109)
T 2rs2_A           21 MGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHEL--DSKTID   97 (109)
T ss_dssp             -----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEE--TTEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcC--CCEEEE
Confidence            4467899999999999999999999999999999999999999999999999999999999999875 4666  457778


Q ss_pred             ccccccC
Q 013141          191 LNWATFS  197 (449)
Q Consensus       191 ~~~~~~~  197 (449)
                      +.++...
T Consensus        98 V~~a~~~  104 (109)
T 2rs2_A           98 PKVAFPR  104 (109)
T ss_dssp             EEECCCC
T ss_pred             EEEccCC
Confidence            8777644

>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=99.66  E-value=1.9e-16  Score=124.00  Aligned_cols=86  Identities=34%  Similarity=0.573  Sum_probs=80.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEee
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV  285 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  285 (449)
                      ...++|||+|||.++++++|+++|+ .||.|..+.+++++.++.++|||||+|.+.++|.+|++.|++..+.|+.|+|++
T Consensus         6 ~~~~~l~V~nlp~~~~~~~l~~~f~-~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   84 (104)
T 1p1t_A            6 RSLRSVFVGNIPYEATEEQLKDIFS-EVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDN   84 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHH-TTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEE
T ss_pred             CCccEEEEeCCCCcCCHHHHHHHHH-hcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Confidence            3467999999999999999999995 999999999999988999999999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 013141          286 ATPKKAS  292 (449)
Q Consensus       286 ~~~~~~~  292 (449)
                      +.++...
T Consensus        85 a~~~~~~   91 (104)
T 1p1t_A           85 AASEKNK   91 (104)
T ss_dssp             TTCTTHH
T ss_pred             CCCccch
Confidence            9887553

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.66  E-value=4e-16  Score=122.42  Aligned_cols=87  Identities=26%  Similarity=0.399  Sum_probs=81.1

Q ss_pred             ccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEE
Q 013141          204 EACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRI  283 (449)
Q Consensus       204 ~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  283 (449)
                      .....++|||+|||+++++++|+++|+ .||.|..|.+++++.++.++|||||+|.+.++|.+|++. ++..|.|+.|+|
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~F~-~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V   89 (105)
T 2dh8_A           12 GADEIGKLFVGGLDWSTTQETLRSYFS-QYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDP   89 (105)
T ss_dssp             CSSSSSEECCBSCCTTCCHHHHHHHHH-TTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHH-hcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEE
Confidence            455678999999999999999999995 999999999999999999999999999999999999988 999999999999


Q ss_pred             eecCCCCCC
Q 013141          284 DVATPKKAS  292 (449)
Q Consensus       284 ~~~~~~~~~  292 (449)
                      +++.++...
T Consensus        90 ~~a~~~~~~   98 (105)
T 2dh8_A           90 KPCTPRGMQ   98 (105)
T ss_dssp             CCSCCSSCC
T ss_pred             EEccCCCCC
Confidence            999887654

>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=99.66  E-value=2.8e-16  Score=121.64  Aligned_cols=84  Identities=18%  Similarity=0.253  Sum_probs=78.5

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEe
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRID  284 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  284 (449)
                      ....++|||+|||+++++++|+++|+ .||.|..+.++.++.+++++|||||+|.+.++|++|++.|++..|.|+.|+|+
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~-~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~   90 (98)
T 2cqp_A           12 KPGPTIIKVQNMPFTVSIDEILDFFY-GYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLV   90 (98)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTT-TSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHH-HcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            34568999999999999999999995 99999999899998999999999999999999999999999999999999999


Q ss_pred             ecCCC
Q 013141          285 VATPK  289 (449)
Q Consensus       285 ~~~~~  289 (449)
                      ++...
T Consensus        91 ~a~~~   95 (98)
T 2cqp_A           91 LGSGP   95 (98)
T ss_dssp             ESSCS
T ss_pred             EcCCC
Confidence            98764

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.66  E-value=5.6e-16  Score=119.61  Aligned_cols=80  Identities=24%  Similarity=0.490  Sum_probs=71.8

Q ss_pred             CCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEe--CCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCC
Q 013141          323 GESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIP--VGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRN  400 (449)
Q Consensus       323 ~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~--~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  400 (449)
                      .....++|||+|||+.+++++|+++|+.||.|. +.++  ..+++|||+|.+.++|.+|++.||+..|.|+.|+|+|+++
T Consensus        15 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~   93 (97)
T 2e5j_A           15 GAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQ   93 (97)
T ss_dssp             SSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEECCC
T ss_pred             CCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcCCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCC
Confidence            445678999999999999999999999999986 4554  4589999999999999999999999999999999999998


Q ss_pred             CCC
Q 013141          401 PGN  403 (449)
Q Consensus       401 ~~~  403 (449)
                      +..
T Consensus        94 ~~~   96 (97)
T 2e5j_A           94 QRD   96 (97)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            643

>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=99.66  E-value=3.9e-16  Score=122.08  Aligned_cols=81  Identities=20%  Similarity=0.191  Sum_probs=71.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCcEE-EEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVN-VKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       112 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~-v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      ....++|||+|||+++++++|+++|..||.|.+ |.|+.+ .+++++|||||+|.+.++|++||+. ++..+.+  +.|+
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~g--r~i~   87 (104)
T 1wg5_A           12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-HKERIGH--RYIE   87 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSS--SCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-CcchhCC--cEEE
Confidence            356789999999999999999999999999987 888888 6899999999999999999999986 8888854  5677


Q ss_pred             cccccc
Q 013141          191 LNWATF  196 (449)
Q Consensus       191 ~~~~~~  196 (449)
                      |.++..
T Consensus        88 v~~~~~   93 (104)
T 1wg5_A           88 IFKSSR   93 (104)
T ss_dssp             EEEECT
T ss_pred             EEECCH
Confidence            766653

>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=99.66  E-value=7.1e-16  Score=121.42  Aligned_cols=82  Identities=32%  Similarity=0.470  Sum_probs=77.2

Q ss_pred             ccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEE
Q 013141          204 EACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRI  283 (449)
Q Consensus       204 ~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  283 (449)
                      ...+.++|||+|||+++++++|+++|+ .||.|..+.++.+. ++.++|+|||+|.+.++|++|++.|++..|.|+.|+|
T Consensus        25 ~~~~~~~l~V~nlp~~~t~~~l~~~F~-~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V  102 (107)
T 3ulh_A           25 GVETGGKLLVSNLDFGVSDADIQELFA-EFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNI  102 (107)
T ss_dssp             CCCCSEEEEEESCCTTCCHHHHHHHHH-TTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHH-hcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            345678999999999999999999995 99999999999998 8999999999999999999999999999999999999


Q ss_pred             eecC
Q 013141          284 DVAT  287 (449)
Q Consensus       284 ~~~~  287 (449)
                      +++.
T Consensus       103 ~~a~  106 (107)
T 3ulh_A          103 QLVT  106 (107)
T ss_dssp             EEEC
T ss_pred             EEeC
Confidence            9975

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.66  E-value=8e-17  Score=118.75  Aligned_cols=76  Identities=28%  Similarity=0.421  Sum_probs=69.0

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccccc
Q 013141          116 KTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWA  194 (449)
Q Consensus       116 ~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~~  194 (449)
                      ++|||+|||+++++++|+++|+.||.|.+|.+++++.+++++|||||+|.+.++|++|++.++ ..+.  ++.+++.++
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-HELD--SKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCS--SCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccC--CEEEEEEec
Confidence            589999999999999999999999999999999999899999999999999999999999888 6664  466666654

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.66  E-value=1.1e-15  Score=122.10  Aligned_cols=77  Identities=17%  Similarity=0.164  Sum_probs=70.2

Q ss_pred             CcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcE-EEEEecCHHHHHHHHHHhcCCeeCC--eEEEEEecCCCCC
Q 013141          327 NATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGC-GFVQFANRKDAEVALQKLQGTAIGK--QTVRLSWGRNPGN  403 (449)
Q Consensus       327 ~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~-afV~F~~~~~A~~A~~~l~g~~~~g--~~l~v~~~~~~~~  403 (449)
                      ...|||+||++.+++++|+++|++||.|.+|+|....|+ |||+|.+.++|.+|++.|||..|.|  +.|+|.|++++..
T Consensus        25 vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak~~~l  104 (124)
T 2e5i_A           25 VLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPTRL  104 (124)
T ss_dssp             EEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEESSSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCSCSCC
T ss_pred             EEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEecCCcc
Confidence            345789999999999999999999999999998766686 9999999999999999999999987  6999999998653

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=3.6e-16  Score=121.65  Aligned_cols=81  Identities=15%  Similarity=0.133  Sum_probs=75.5

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEe
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRID  284 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  284 (449)
                      ....++|||+|||+++|+++|+++|+ .||.|.+|.+++++. +.++|||||+|.+.++|.+|++ +++..+.|+.|.|.
T Consensus         8 ~~~~~~lfV~~Lp~~~te~~L~~~F~-~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~   84 (103)
T 1s79_A            8 DVKNRSVYIKGFPTDATLDDIKEWLE-DKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLIL   84 (103)
T ss_dssp             CSGGGCEEEECCCTTCCHHHHHHHHH-TSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEE
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHh-hcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEE
Confidence            34568999999999999999999995 999999999999977 9999999999999999999997 99999999999999


Q ss_pred             ecCC
Q 013141          285 VATP  288 (449)
Q Consensus       285 ~~~~  288 (449)
                      ++..
T Consensus        85 ~~~~   88 (103)
T 1s79_A           85 FKDD   88 (103)
T ss_dssp             EHHH
T ss_pred             EchH
Confidence            8765

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.66  E-value=9.6e-16  Score=119.54  Aligned_cols=83  Identities=29%  Similarity=0.476  Sum_probs=69.0

Q ss_pred             CCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeC---CCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 013141          322 DGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV---GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWG  398 (449)
Q Consensus       322 ~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~---~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~  398 (449)
                      ......++|||+|||.++++++|+++|+.|+.|.-+....   .+++|||+|.+.++|.+|++.||+..|.|+.|+|.|+
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   89 (102)
T 2fc8_A           10 ARSQPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWA   89 (102)
T ss_dssp             SSSCCCSSEEEECCCTTCCHHHHHHTSTTCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCCCEEEEeCCCCccCHHHHHHHhcCCeEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEe
Confidence            3455678999999999999999999999885433222211   2589999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 013141          399 RNPGNK  404 (449)
Q Consensus       399 ~~~~~~  404 (449)
                      +++..+
T Consensus        90 ~~~~~~   95 (102)
T 2fc8_A           90 KPKGEG   95 (102)
T ss_dssp             CCCCSS
T ss_pred             cCCCCC
Confidence            986543

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.65  E-value=1.1e-15  Score=116.55  Aligned_cols=83  Identities=18%  Similarity=0.281  Sum_probs=77.0

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEe
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRID  284 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  284 (449)
                      ....++|||+|||+++++++|+++|+ .| .|..+.++++ .+++++|+|||+|.+.++|.+|++ |++..|.|+.|+|.
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~-~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~   82 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLA-PL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVF   82 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHT-TS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEE
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHh-hC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEE
Confidence            34568999999999999999999995 89 9999999999 789999999999999999999999 99999999999999


Q ss_pred             ecCCCCC
Q 013141          285 VATPKKA  291 (449)
Q Consensus       285 ~~~~~~~  291 (449)
                      ++.++..
T Consensus        83 ~a~~~~~   89 (91)
T 2dgw_A           83 REKSGPS   89 (91)
T ss_dssp             EESSCCC
T ss_pred             ECCcCCC
Confidence            9987743

>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=99.65  E-value=1.2e-15  Score=119.27  Aligned_cols=86  Identities=24%  Similarity=0.464  Sum_probs=78.2

Q ss_pred             ccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEE
Q 013141          204 EACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRI  283 (449)
Q Consensus       204 ~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  283 (449)
                      .....++|||+|||.++++++|+++|+ .||.|..|.++++..+  ++|||||+|.+.++|.+|++.|++..|.|+.|+|
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~-~~G~i~~v~i~~~~~~--~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   87 (103)
T 2cqi_A           11 DDGQPRTLYVGNLSRDVTEVLILQLFS-QIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKV   87 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHH-HHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCEEEEeCCCccCCHHHHHHHHH-hcCCEeEEEEEecCCC--CCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEE
Confidence            345678999999999999999999995 9999999999998543  6899999999999999999999999999999999


Q ss_pred             eecCCCCCC
Q 013141          284 DVATPKKAS  292 (449)
Q Consensus       284 ~~~~~~~~~  292 (449)
                      .++.++...
T Consensus        88 ~~a~~~~~~   96 (103)
T 2cqi_A           88 NWATTPSSQ   96 (103)
T ss_dssp             EECCCTTCC
T ss_pred             EECCCCccc
Confidence            999887543

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.65  E-value=3.6e-16  Score=114.79  Aligned_cols=74  Identities=8%  Similarity=0.205  Sum_probs=69.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeec
Q 013141          207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVA  286 (449)
Q Consensus       207 ~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~  286 (449)
                      .+.-|||+||++.+|+++|+++|. .||+|.++++..      ++|||||+|.++++|++|++.||+..+.|++|+|+++
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~-q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A   78 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCM-QHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESP   78 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHH-HHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECC
T ss_pred             ccceEEEeCCCccCCHHHHHHHHH-hhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEEC
Confidence            356899999999999999999995 999999999864      5899999999999999999999999999999999999


Q ss_pred             C
Q 013141          287 T  287 (449)
Q Consensus       287 ~  287 (449)
                      .
T Consensus        79 ~   79 (89)
T 2wbr_A           79 S   79 (89)
T ss_dssp             C
T ss_pred             C
Confidence            4

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.65  E-value=9.5e-16  Score=118.34  Aligned_cols=81  Identities=17%  Similarity=0.374  Sum_probs=72.2

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      ...+.++|||+|||+++++++|+++|+.||.|.+|.+.++      +|||||+|.+.++|++|++.|++..+.+.++.|+
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~   86 (97)
T 1why_A           13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLR   86 (97)
T ss_dssp             CCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEE
Confidence            3456789999999999999999999999999999998764      5799999999999999999999999964478899


Q ss_pred             ccccccC
Q 013141          191 LNWATFS  197 (449)
Q Consensus       191 ~~~~~~~  197 (449)
                      |.|+...
T Consensus        87 V~~a~~~   93 (97)
T 1why_A           87 VDFAKSG   93 (97)
T ss_dssp             EEECCCC
T ss_pred             EEECCCC
Confidence            9888754

>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=99.65  E-value=8.5e-16  Score=129.74  Aligned_cols=87  Identities=24%  Similarity=0.303  Sum_probs=81.3

Q ss_pred             ccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEE
Q 013141          204 EACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRI  283 (449)
Q Consensus       204 ~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  283 (449)
                      ...+.++|||+|||.++|+++|+++|+ .||.|..|.++.++.++.++|||||+|.+.++|++||+.|++..|.++.|+|
T Consensus        35 ~~~~~~~l~V~nlp~~~t~~~l~~~F~-~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  113 (156)
T 1h2v_Z           35 LLKKSCTLYVGNLSFYTTEEQIYELFS-KSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRT  113 (156)
T ss_dssp             TTTTCCEEEEESCCTTCCHHHHHHHHG-GGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHH-hcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            345678999999999999999999995 9999999999999999999999999999999999999999999999999999


Q ss_pred             eecCCCCC
Q 013141          284 DVATPKKA  291 (449)
Q Consensus       284 ~~~~~~~~  291 (449)
                      +++.+...
T Consensus       114 ~~a~~~~~  121 (156)
T 1h2v_Z          114 DWDAGFKE  121 (156)
T ss_dssp             EEESCCCT
T ss_pred             EECCCCCC
Confidence            99987644

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.65  E-value=4.9e-16  Score=122.58  Aligned_cols=87  Identities=29%  Similarity=0.454  Sum_probs=76.5

Q ss_pred             cccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceE
Q 013141          203 TEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMR  282 (449)
Q Consensus       203 ~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  282 (449)
                      ......++|||+|||.++++++|+++|+ .||.|.++.+++++.++.++|||||+|.+.++|++|++.+ +..+.|+.|+
T Consensus        20 ~~~~~~~~lfV~nLp~~~te~~L~~~F~-~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~   97 (109)
T 2rs2_A           20 HMGSSGCKMFIGGLSWQTTQEGLREYFG-QFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTID   97 (109)
T ss_dssp             ------CCEEEESCCTTCCHHHHHHHHT-TTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHH-ccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEE
Confidence            3445678999999999999999999995 9999999999999999999999999999999999999876 5999999999


Q ss_pred             EeecCCCCC
Q 013141          283 IDVATPKKA  291 (449)
Q Consensus       283 v~~~~~~~~  291 (449)
                      |.++.++..
T Consensus        98 V~~a~~~~~  106 (109)
T 2rs2_A           98 PKVAFPRRA  106 (109)
T ss_dssp             EEECCCCCC
T ss_pred             EEEccCCCC
Confidence            999988754

>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=99.65  E-value=5.8e-16  Score=128.90  Aligned_cols=80  Identities=25%  Similarity=0.289  Sum_probs=72.0

Q ss_pred             CCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeC--CCcEEEEEecCHHHHHHHHHHhcCCeeCC--eEEEEEecC
Q 013141          324 ESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV--GKGCGFVQFANRKDAEVALQKLQGTAIGK--QTVRLSWGR  399 (449)
Q Consensus       324 ~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~--~~g~afV~F~~~~~A~~A~~~l~g~~~~g--~~l~v~~~~  399 (449)
                      .....+|||+||++.+++++|+++|++||.|++|.|..  .+++|||+|.+.++|.+|++.|||..|.|  +.|+|+|++
T Consensus        43 ps~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak  122 (164)
T 1sjr_A           43 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK  122 (164)
T ss_dssp             CCCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESSSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECS
T ss_pred             CCceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEec
Confidence            34457799999999999999999999999999999874  36799999999999999999999999965  999999999


Q ss_pred             CCCC
Q 013141          400 NPGN  403 (449)
Q Consensus       400 ~~~~  403 (449)
                      ++..
T Consensus       123 ~~~l  126 (164)
T 1sjr_A          123 LTSL  126 (164)
T ss_dssp             SSSC
T ss_pred             CCcc
Confidence            8653

>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=99.65  E-value=3.5e-16  Score=123.69  Aligned_cols=85  Identities=16%  Similarity=0.243  Sum_probs=75.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCC-cEEEEEE-ecCCCCCcccEEEEEEccHHHHHHHHHHhc--CCCCCCCCCc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQ-VVNVKVI-RNKQTGQSEGYGFVEFYSRAAAEKVLQSYS--GSLMPNTDQP  188 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~-v~~v~~~-~~~~~g~~~g~afV~f~~~~~A~~Al~~l~--~~~~~~~~~~  188 (449)
                      .+.++|||+|||+++++++|+++|..||. |.+|.++ .++.+++++|||||+|.+.++|.+|++.|+  +..+.  ++.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~--g~~   83 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLW--GHQ   83 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBT--TBC
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceec--CCe
Confidence            46789999999999999999999999998 9999998 788889999999999999999999999996  46774  578


Q ss_pred             ccccccccCCC
Q 013141          189 FRLNWATFSGS  199 (449)
Q Consensus       189 ~~~~~~~~~~~  199 (449)
                      |+|.|+.....
T Consensus        84 l~V~~a~~~~~   94 (109)
T 2dis_A           84 IAVDWAEPEID   94 (109)
T ss_dssp             CEEEESCSSCS
T ss_pred             EEEEEcCCCCC
Confidence            88888876543

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.65  E-value=2.1e-15  Score=122.08  Aligned_cols=86  Identities=28%  Similarity=0.428  Sum_probs=80.4

Q ss_pred             ccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEE
Q 013141          204 EACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRI  283 (449)
Q Consensus       204 ~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  283 (449)
                      .....++|||+|||.++++++|+++|+ .||.|..+.++.+. +++++|||||+|.+.++|++|++.|++..+.|+.|+|
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~-~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  108 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFA-EFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDI  108 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHH-TTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHH-hcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEE
Confidence            446678999999999999999999995 99999999999997 8999999999999999999999999999999999999


Q ss_pred             eecCCCCC
Q 013141          284 DVATPKKA  291 (449)
Q Consensus       284 ~~~~~~~~  291 (449)
                      +++.+...
T Consensus       109 ~~a~~~~~  116 (124)
T 2kt5_A          109 QLVASQID  116 (124)
T ss_dssp             EEECCTTC
T ss_pred             EEeCCCCC
Confidence            99988654

>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=99.65  E-value=2.6e-16  Score=121.09  Aligned_cols=82  Identities=18%  Similarity=0.267  Sum_probs=75.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEee
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV  285 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  285 (449)
                      ...++|||+|||+++++++|+++|. .||.|..+.++.++.+++++|||||+|.+.++|++|++.|++..|.|+.|+|++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~-~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~   91 (95)
T 2ek1_A           13 PGPTVIKVQNMPFTVSIDEILDFFY-GYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSG   91 (95)
T ss_dssp             --CEEEEEECCCTTCCHHHHHHHTT-TSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHH-hcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEe
Confidence            3458999999999999999999995 999999999999989999999999999999999999999999999999999998


Q ss_pred             cCC
Q 013141          286 ATP  288 (449)
Q Consensus       286 ~~~  288 (449)
                      +..
T Consensus        92 a~s   94 (95)
T 2ek1_A           92 PSS   94 (95)
T ss_dssp             CC-
T ss_pred             ccC
Confidence            753

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.65  E-value=4.1e-16  Score=129.27  Aligned_cols=82  Identities=22%  Similarity=0.439  Sum_probs=73.9

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      .....++|||+|||+++++++|+++|+.||.|.+|++++++.+++++|||||+|.+.++|++|++.|++..+.  ++.|+
T Consensus        59 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~l~  136 (140)
T 2ku7_A           59 SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELF--GRTIR  136 (140)
T ss_dssp             SCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEET--TEEEE
T ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEEC--CEEEE
Confidence            3457899999999999999999999999999999999999989999999999999999999999999998885  46666


Q ss_pred             cccc
Q 013141          191 LNWA  194 (449)
Q Consensus       191 ~~~~  194 (449)
                      |.++
T Consensus       137 v~~A  140 (140)
T 2ku7_A          137 VNLA  140 (140)
T ss_dssp             EEC-
T ss_pred             EEeC
Confidence            6553

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ...

Probab=99.65  E-value=5.3e-16  Score=119.84  Aligned_cols=79  Identities=27%  Similarity=0.534  Sum_probs=73.3

Q ss_pred             CCCCcEEEEcCCCCCCCHhHHH----hhccccCceEEEEEeC---CCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEE
Q 013141          324 ESNNATIFVGALDSDVSDEDLR----EPFSQFGEILSVKIPV---GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLS  396 (449)
Q Consensus       324 ~~~~~~l~V~nlp~~~t~~~L~----~~f~~~G~v~~v~i~~---~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~  396 (449)
                      ..+.++|||+|||.++++++|+    ++|+.||.|.+|.+.+   ++++|||+|.+.++|.+|++.|||..|.|+.|+|.
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   84 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ   84 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEcCCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            3467899999999999999999    9999999999999984   57999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 013141          397 WGRNPG  402 (449)
Q Consensus       397 ~~~~~~  402 (449)
                      |+++..
T Consensus        85 ~a~~~~   90 (97)
T 1nu4_A           85 YAKTDS   90 (97)
T ss_dssp             ECSSCC
T ss_pred             EccCCC
Confidence            999864

>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=99.65  E-value=7.7e-16  Score=118.53  Aligned_cols=82  Identities=15%  Similarity=0.198  Sum_probs=75.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHH----HHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcce
Q 013141          206 CSDLSIFVGDLAPDVTDSILQ----ETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPM  281 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~----~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i  281 (449)
                      ...++|||+|||.++++++|+    ++|+ .||.|.++.++.++.+   +|||||+|.+.++|.+|++.||+..+.|+.|
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~-~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l   82 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFA-RHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKI   82 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHH-HHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhcc-ccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEE
Confidence            356799999999999999999    9995 9999999999988765   8899999999999999999999999999999


Q ss_pred             EEeecCCCCC
Q 013141          282 RIDVATPKKA  291 (449)
Q Consensus       282 ~v~~~~~~~~  291 (449)
                      +|+++.+...
T Consensus        83 ~V~~a~~~~~   92 (96)
T 2dgx_A           83 LVSLATGASG   92 (96)
T ss_dssp             EEEECCCSSC
T ss_pred             EEEEcCCCCC
Confidence            9999987654

>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=99.64  E-value=2.1e-16  Score=127.96  Aligned_cols=82  Identities=18%  Similarity=0.235  Sum_probs=72.5

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      .....++|||+|||+++|+++|+++|..||.|.++.++.+..+|+++|||||+|.+.++|++||+ +++..|.  ++.|+
T Consensus        21 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~--gr~i~   97 (124)
T 1wel_A           21 PHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMG--NRFIQ   97 (124)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCST--TSCBE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeEC--CcEEE
Confidence            34567899999999999999999999999999987777777899999999999999999999998 9999985  46677


Q ss_pred             ccccc
Q 013141          191 LNWAT  195 (449)
Q Consensus       191 ~~~~~  195 (449)
                      |.++.
T Consensus        98 V~~a~  102 (124)
T 1wel_A           98 VHPIT  102 (124)
T ss_dssp             EEEEC
T ss_pred             EEECC
Confidence            76664

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=4.9e-16  Score=124.27  Aligned_cols=79  Identities=20%  Similarity=0.424  Sum_probs=72.7

Q ss_pred             CCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC------CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 013141          325 SNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWG  398 (449)
Q Consensus       325 ~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~------~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~  398 (449)
                      ...++|||+|||..+++++|+++|+.||.|.+|.|+.+      +++|||+|.+.++|.+|++. ++..|+|+.|+|.|+
T Consensus        25 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a  103 (116)
T 1x4b_A           25 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRA  103 (116)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEEC
Confidence            34689999999999999999999999999999999874      58999999999999999987 999999999999999


Q ss_pred             CCCCCC
Q 013141          399 RNPGNK  404 (449)
Q Consensus       399 ~~~~~~  404 (449)
                      +++...
T Consensus       104 ~~~~~~  109 (116)
T 1x4b_A          104 VAREES  109 (116)
T ss_dssp             SSCCCC
T ss_pred             CCCccC
Confidence            987544

>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=99.64  E-value=9.6e-17  Score=122.18  Aligned_cols=79  Identities=24%  Similarity=0.449  Sum_probs=71.7

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccccccc
Q 013141          116 KTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWAT  195 (449)
Q Consensus       116 ~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~~~  195 (449)
                      ++|||+|||+++++++|+++|+.||.|.+|.+++++.+++++|||||+|.+.+ |.+|+..|++..+.  ++.+++.++.
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~--g~~l~V~~a~   78 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFM--GRTIRVTEAN   78 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCS--SSSCSEEEC-
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEEC--CeEEEEEEcC
Confidence            68999999999999999999999999999999999989999999999999999 99999999999985  5778888876


Q ss_pred             cC
Q 013141          196 FS  197 (449)
Q Consensus       196 ~~  197 (449)
                      ..
T Consensus        79 ~~   80 (90)
T 2ki2_A           79 PK   80 (90)
T ss_dssp             --
T ss_pred             CC
Confidence            44

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=9.2e-16  Score=116.93  Aligned_cols=78  Identities=15%  Similarity=0.280  Sum_probs=72.1

Q ss_pred             CCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC-----CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 013141          324 ESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-----KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWG  398 (449)
Q Consensus       324 ~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~-----~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~  398 (449)
                      ....++|||+|||+++++++|+++|+.| .|.+|.|+++     +|+|||+|.+.++|.+|++ ||+..|+|+.|+|.++
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~a   84 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFRE   84 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEEE
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEEC
Confidence            4567899999999999999999999999 9999999864     6899999999999999999 9999999999999999


Q ss_pred             CCCCC
Q 013141          399 RNPGN  403 (449)
Q Consensus       399 ~~~~~  403 (449)
                      ++...
T Consensus        85 ~~~~~   89 (91)
T 2dgw_A           85 KSGPS   89 (91)
T ss_dssp             SSCCC
T ss_pred             CcCCC
Confidence            88643

>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=99.64  E-value=1.2e-16  Score=127.45  Aligned_cols=81  Identities=20%  Similarity=0.376  Sum_probs=74.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      ...++|||+|||+++++++|+++|+.||.|.+|.|+.++.+++++|||||+|.+.++|++|| .|++..+.  ++.|+|.
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~--g~~l~V~   99 (114)
T 2cq4_A           23 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLL--GVPIIVQ   99 (114)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEET--TEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeC--CeEEEEE
Confidence            45689999999999999999999999999999999999999999999999999999999999 99999984  4677777


Q ss_pred             cccc
Q 013141          193 WATF  196 (449)
Q Consensus       193 ~~~~  196 (449)
                      ++..
T Consensus       100 ~a~~  103 (114)
T 2cq4_A          100 ASQA  103 (114)
T ss_dssp             EHHH
T ss_pred             ecCC
Confidence            7653

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.64  E-value=9.6e-16  Score=122.87  Aligned_cols=79  Identities=25%  Similarity=0.307  Sum_probs=71.6

Q ss_pred             CCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeC-CCcE-EEEEecCHHHHHHHHHHhcCCeeCC--eEEEEEecCC
Q 013141          325 SNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV-GKGC-GFVQFANRKDAEVALQKLQGTAIGK--QTVRLSWGRN  400 (449)
Q Consensus       325 ~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~-~~g~-afV~F~~~~~A~~A~~~l~g~~~~g--~~l~v~~~~~  400 (449)
                      .....|||+||++.+|+++|+++|++||.|.+|.+.. .+++ |||+|.+.++|.+|++.|||..|.|  +.|+|+|++.
T Consensus        26 s~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak~  105 (130)
T 3zzy_A           26 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKL  105 (130)
T ss_dssp             CSEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECSC
T ss_pred             CceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCCCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecCC
Confidence            4456788999999999999999999999999998875 4677 9999999999999999999999988  9999999998


Q ss_pred             CCC
Q 013141          401 PGN  403 (449)
Q Consensus       401 ~~~  403 (449)
                      ..-
T Consensus       106 ~~l  108 (130)
T 3zzy_A          106 TSL  108 (130)
T ss_dssp             SSC
T ss_pred             Cce
Confidence            643

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=1.5e-16  Score=119.61  Aligned_cols=81  Identities=23%  Similarity=0.432  Sum_probs=76.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEee
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV  285 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  285 (449)
                      .+.++|||+|||+++++++|+++|+ .||.|..+.++.++.++.++|||||+|.+.++|.+|++.||+..+.|+.+++.+
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~-~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~   81 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQ-PYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSG   81 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTST-TTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHH-hcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecC
Confidence            4678999999999999999999995 999999999999998999999999999999999999999999999999998876


Q ss_pred             cC
Q 013141          286 AT  287 (449)
Q Consensus       286 ~~  287 (449)
                      ..
T Consensus        82 ~~   83 (85)
T 1x4e_A           82 PS   83 (85)
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=99.64  E-value=5.2e-16  Score=125.21  Aligned_cols=79  Identities=18%  Similarity=0.431  Sum_probs=72.0

Q ss_pred             CCCCcEEEEcCCCCCCCHhHHH----hhccccCceEEEEEeC---CCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEE
Q 013141          324 ESNNATIFVGALDSDVSDEDLR----EPFSQFGEILSVKIPV---GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLS  396 (449)
Q Consensus       324 ~~~~~~l~V~nlp~~~t~~~L~----~~f~~~G~v~~v~i~~---~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~  396 (449)
                      ..+.++|||+|||+.+++++|+    ++|++||.|.+|.+.+   ++|+|||+|.+.++|.+|++.|||..|.|+.|+|.
T Consensus        26 ~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V~  105 (127)
T 2a3j_A           26 TEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVIT  105 (127)
T ss_dssp             CSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECCCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEeccCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEEE
Confidence            3457899999999999999876    6999999999999864   57999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 013141          397 WGRNPG  402 (449)
Q Consensus       397 ~~~~~~  402 (449)
                      |++.+.
T Consensus       106 ~a~~~~  111 (127)
T 2a3j_A          106 FSETPQ  111 (127)
T ss_dssp             ECCCCC
T ss_pred             EccCcc
Confidence            999754

>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=99.64  E-value=5.6e-16  Score=117.26  Aligned_cols=76  Identities=14%  Similarity=0.253  Sum_probs=71.9

Q ss_pred             CCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCC
Q 013141          326 NNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPG  402 (449)
Q Consensus       326 ~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~  402 (449)
                      ..++|||+|||+++++++|+++|++| .|.++.+.+++|+|||+|.+.++|.+|++.||+..++|+.|+|+|++...
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~~   79 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDA   79 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEEGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEeCCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCCCc
Confidence            46789999999999999999999999 99999998889999999999999999999999999999999999997653

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.64  E-value=3e-16  Score=114.95  Aligned_cols=75  Identities=25%  Similarity=0.435  Sum_probs=71.5

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeec
Q 013141          210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVA  286 (449)
Q Consensus       210 ~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~  286 (449)
                      +|||+|||+++++++|+++|+ .||.|.++.++.++.++.++|||||+|.+.++|++|++ +++..+.|+.|+|+++
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 KIFVGGLSVNTTVEDVKHYFE-QFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHH-TTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHH-hcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            589999999999999999995 99999999999998899999999999999999999996 9999999999999875

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens}

Probab=99.64  E-value=2.7e-16  Score=123.72  Aligned_cols=81  Identities=17%  Similarity=0.141  Sum_probs=72.1

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCC---cEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCC
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQ---VVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQ  187 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~---v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~  187 (449)
                      .....++|||+|||+++|+++|+++|+.||.   |.+|.|+.++. |+++|||||+|.+.++|++||+ +++..+.  ++
T Consensus         7 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~--gr   82 (107)
T 2lmi_A            7 EVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRMYMG--QR   82 (107)
T ss_dssp             CCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTCCSS--SS
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcceeC--Ce
Confidence            4467889999999999999999999999998   89999999987 9999999999999999999998 8998884  45


Q ss_pred             cccccccc
Q 013141          188 PFRLNWAT  195 (449)
Q Consensus       188 ~~~~~~~~  195 (449)
                      .|+|.++.
T Consensus        83 ~i~V~~a~   90 (107)
T 2lmi_A           83 YVEVYEIN   90 (107)
T ss_dssp             CCCCEECC
T ss_pred             EEEEEECC
Confidence            66766654

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.64  E-value=8.7e-16  Score=123.92  Aligned_cols=81  Identities=12%  Similarity=0.325  Sum_probs=71.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHH----HHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCC
Q 013141          112 NDETKTIWIGDLFHWMDETFLH----NCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQ  187 (449)
Q Consensus       112 ~~~~~~l~v~nLp~~~t~~~l~----~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~  187 (449)
                      ..+.++|||+|||+.+++++|+    ++|++||.|.+|.+.+   +++++|||||+|.+.++|.+|++.||+..+.  ++
T Consensus        26 ~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~--gr  100 (127)
T 2a3j_A           26 TEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQ--GN  100 (127)
T ss_dssp             CSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTTCCCT--TS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCCCEeC--CC
Confidence            3567899999999999999876    6999999999988754   5789999999999999999999999999985  56


Q ss_pred             cccccccccC
Q 013141          188 PFRLNWATFS  197 (449)
Q Consensus       188 ~~~~~~~~~~  197 (449)
                      .|+|.|+...
T Consensus       101 ~l~V~~a~~~  110 (127)
T 2a3j_A          101 PLVITFSETP  110 (127)
T ss_dssp             CCEEEECCCC
T ss_pred             EEEEEEccCc
Confidence            8888888744

>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=99.64  E-value=6e-16  Score=121.13  Aligned_cols=80  Identities=13%  Similarity=0.169  Sum_probs=69.6

Q ss_pred             CCCCceEEEcCCCCC-CCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          112 NDETKTIWIGDLFHW-MDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       112 ~~~~~~l~v~nLp~~-~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      ..++++|||+|||++ +++++|+++|++||.|.+|+|++.      +|||||+|.+.++|.+|++.|++......++.|+
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~   95 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   95 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            457899999999998 999999999999999999999753      5899999999999999999987655333678899


Q ss_pred             ccccccC
Q 013141          191 LNWATFS  197 (449)
Q Consensus       191 ~~~~~~~  197 (449)
                      |.++...
T Consensus        96 V~~a~~~  102 (112)
T 1x4f_A           96 VDLSEKY  102 (112)
T ss_dssp             EEEECSC
T ss_pred             EEECccc
Confidence            9888644

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.64  E-value=2e-16  Score=129.41  Aligned_cols=87  Identities=16%  Similarity=0.355  Sum_probs=80.3

Q ss_pred             ccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeE--EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCc----eec
Q 013141          204 EACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKG--AKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGV----YCS  277 (449)
Q Consensus       204 ~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~--i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~----~~~  277 (449)
                      .....++|||+|||+++|+++|+++|+ .||.|..  |++++|+.+++++|||||+|.+. +|.+|++.|++.    .+.
T Consensus        19 ~~~~~~~lfV~nL~~~~te~~L~~~F~-~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~   96 (131)
T 2m2b_A           19 SENANDTIILRNLNPHSTMDSILGALA-PYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTID   96 (131)
T ss_dssp             CSCCCCEEEECSCCTTCCSHHHHHHHG-GGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGG
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHH-HhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCC
Confidence            345678999999999999999999995 9999977  99999998999999999999999 999999999999    999


Q ss_pred             CcceEEeecCCCCCC
Q 013141          278 SRPMRIDVATPKKAS  292 (449)
Q Consensus       278 g~~i~v~~~~~~~~~  292 (449)
                      |+.|+|+++.++...
T Consensus        97 gr~l~V~~a~~~~~~  111 (131)
T 2m2b_A           97 GKTINVEFAKGSKRD  111 (131)
T ss_dssp             GCCCCCEECCCSCCC
T ss_pred             CEEEEEEECCCCCCC
Confidence            999999999886543

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=7.5e-16  Score=123.17  Aligned_cols=87  Identities=23%  Similarity=0.386  Sum_probs=80.3

Q ss_pred             ccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEE
Q 013141          204 EACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRI  283 (449)
Q Consensus       204 ~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  283 (449)
                      .....++|||+|||.++++++|+++|. .||.|..|.++.++.++.++|||||+|.+.++|.+||+. ++..|.|+.|+|
T Consensus        23 ~~~~~~~l~V~nLp~~~te~~l~~~F~-~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V  100 (116)
T 1x4b_A           23 EKEQFRKLFIGGLSFETTEESLRNYYE-QWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEP  100 (116)
T ss_dssp             HHHHHTEEEEECCTTCCCHHHHHHHHT-SSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEE
T ss_pred             ccCCCCEEEEeCCCCCCCHHHHHHHHH-hcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEE
Confidence            344568999999999999999999995 999999999999999999999999999999999999977 999999999999


Q ss_pred             eecCCCCCC
Q 013141          284 DVATPKKAS  292 (449)
Q Consensus       284 ~~~~~~~~~  292 (449)
                      .++.++...
T Consensus       101 ~~a~~~~~~  109 (116)
T 1x4b_A          101 KRAVAREES  109 (116)
T ss_dssp             ECCSSCCCC
T ss_pred             EECCCCccC
Confidence            999887653

>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=99.64  E-value=1.8e-16  Score=126.24  Aligned_cols=82  Identities=15%  Similarity=0.120  Sum_probs=72.8

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCc-EEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQV-VNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPF  189 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v-~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~  189 (449)
                      .....++|||+|||+++|+++|+++|+.||.| .+|+|+.++ +++++|||||+|.+.++|++||+. ++..|.  ++.|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~--gr~i   86 (114)
T 2cpy_A           11 VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRKKLN--GREA   86 (114)
T ss_dssp             CCSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSEEET--TEEE
T ss_pred             CCCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCCccC--CeEE
Confidence            34577899999999999999999999999999 899999998 899999999999999999999976 888884  4677


Q ss_pred             ccccccc
Q 013141          190 RLNWATF  196 (449)
Q Consensus       190 ~~~~~~~  196 (449)
                      +|.++..
T Consensus        87 ~v~~a~~   93 (114)
T 2cpy_A           87 FVHVVTL   93 (114)
T ss_dssp             EEEEECH
T ss_pred             EEEECCH
Confidence            7777653

>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=99.64  E-value=2.5e-15  Score=117.36  Aligned_cols=87  Identities=25%  Similarity=0.347  Sum_probs=79.3

Q ss_pred             cccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceE
Q 013141          203 TEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMR  282 (449)
Q Consensus       203 ~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  282 (449)
                      ....+.++|||+|||.++++++|+++|+ .||.|..+.++.++.++.++|||||+|.+.++|.+|++  ++..|.|+.|+
T Consensus        10 ~~~~~~~~l~v~nlp~~~t~~~l~~~F~-~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~   86 (103)
T 2cqg_A           10 RAVQKTSDLIVLGLPWKTTEQDLKEYFS-TFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCD   86 (103)
T ss_dssp             CCCCCCCCEEEESCCSSCCHHHHHHHHG-GGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEE
T ss_pred             CccCCCCEEEEEcCCCcCCHHHHHHHHH-hcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEE
Confidence            3445678999999999999999999995 99999999999999999999999999999999999997  47789999999


Q ss_pred             EeecCCCCCC
Q 013141          283 IDVATPKKAS  292 (449)
Q Consensus       283 v~~~~~~~~~  292 (449)
                      |.++.++...
T Consensus        87 v~~a~~~~~~   96 (103)
T 2cqg_A           87 CKLPNSKQSQ   96 (103)
T ss_dssp             EECCCTTCCC
T ss_pred             EEecCCCCcC
Confidence            9999887653

>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=2.6e-16  Score=128.46  Aligned_cols=80  Identities=18%  Similarity=0.152  Sum_probs=71.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCC---cEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCc
Q 013141          112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQ---VVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQP  188 (449)
Q Consensus       112 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~---v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~  188 (449)
                      ....++|||+|||+++|+++|+++|+.||.   |.+|+|+.++. |+++|||||+|.+.++|++||+ +++..+.  ++.
T Consensus        41 ~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~~l~--gr~  116 (136)
T 2hgl_A           41 GGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMG--HRY  116 (136)
T ss_dssp             CCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESS--SSE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEEC--CEE
Confidence            356789999999999999999999999999   89999999987 9999999999999999999998 9998884  456


Q ss_pred             ccccccc
Q 013141          189 FRLNWAT  195 (449)
Q Consensus       189 ~~~~~~~  195 (449)
                      |+|.++.
T Consensus       117 i~V~~a~  123 (136)
T 2hgl_A          117 IEVFKSH  123 (136)
T ss_dssp             EEEEECC
T ss_pred             EEEEECC
Confidence            6665543

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.64  E-value=2.6e-16  Score=126.02  Aligned_cols=80  Identities=19%  Similarity=0.170  Sum_probs=71.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCC---cEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCc
Q 013141          112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQ---VVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQP  188 (449)
Q Consensus       112 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~---v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~  188 (449)
                      ....++|||+|||+++|+++|+++|+.||.   |.+|+|+.++. |+++|||||+|.+.++|++||+ +++..+.  ++.
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g~~~~--gr~   89 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDRESMG--HRY   89 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTTEEET--TEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCeEC--CeE
Confidence            356789999999999999999999999998   89999999976 9999999999999999999998 8998884  456


Q ss_pred             ccccccc
Q 013141          189 FRLNWAT  195 (449)
Q Consensus       189 ~~~~~~~  195 (449)
                      |+|.++.
T Consensus        90 i~V~~a~   96 (118)
T 2db1_A           90 IEVFKSH   96 (118)
T ss_dssp             EEEEEEC
T ss_pred             EEEEECC
Confidence            6666553

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A

Probab=99.64  E-value=9.3e-16  Score=127.68  Aligned_cols=84  Identities=17%  Similarity=0.288  Sum_probs=74.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      ....+|||+||++.+|+++|+++|++||.|.+|+|+.++    ++|||||+|.+.++|++|++.|++..|.+.++.|+|.
T Consensus        44 s~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~----~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~  119 (164)
T 1sjr_A           44 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID  119 (164)
T ss_dssp             CCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESS----SCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEE
T ss_pred             CceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCC----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEE
Confidence            455679999999999999999999999999999987542    5689999999999999999999999998777899999


Q ss_pred             ccccCCCC
Q 013141          193 WATFSGSD  200 (449)
Q Consensus       193 ~~~~~~~~  200 (449)
                      |++.....
T Consensus       120 ~Ak~~~l~  127 (164)
T 1sjr_A          120 FSKLTSLN  127 (164)
T ss_dssp             ECSSSSCC
T ss_pred             EecCCccc
Confidence            99876443

>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=99.64  E-value=1.1e-15  Score=118.90  Aligned_cols=78  Identities=22%  Similarity=0.353  Sum_probs=69.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC-----CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 013141          323 GESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-----KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSW  397 (449)
Q Consensus       323 ~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~-----~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  397 (449)
                      .....++|||+|||+++++++|+++|+.||.| +|+|+.+     +|+|||+|.+.++|.+||+ +|+..|+++.|+|.+
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~   88 (102)
T 1wez_A           11 QSTTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFL   88 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEE
Confidence            34567899999999999999999999999955 8888754     6899999999999999995 799999999999999


Q ss_pred             cCCCC
Q 013141          398 GRNPG  402 (449)
Q Consensus       398 ~~~~~  402 (449)
                      +....
T Consensus        89 ~~~~~   93 (102)
T 1wez_A           89 NSTAG   93 (102)
T ss_dssp             ECCCC
T ss_pred             CCCCC
Confidence            88754

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=1.5e-15  Score=121.31  Aligned_cols=83  Identities=22%  Similarity=0.414  Sum_probs=73.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHhHHHhhccccCce----EEEEEeC--CCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEE
Q 013141          323 GESNNATIFVGALDSDVSDEDLREPFSQFGEI----LSVKIPV--GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLS  396 (449)
Q Consensus       323 ~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v----~~v~i~~--~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~  396 (449)
                      .....++|||+|||..+++++|+++|+.||.|    ..+++..  .+++|||+|.+.++|.+|++.||+..|.|+.|+|.
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~  100 (115)
T 2cpx_A           21 PGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIE  100 (115)
T ss_dssp             CCSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            34567899999999999999999999999998    5666654  47999999999999999999999999999999999


Q ss_pred             ecCCCCCCC
Q 013141          397 WGRNPGNKQ  405 (449)
Q Consensus       397 ~~~~~~~~~  405 (449)
                      |+++...+.
T Consensus       101 ~a~~~~~~~  109 (115)
T 2cpx_A          101 FGKNKKQRS  109 (115)
T ss_dssp             ECCCCSCCC
T ss_pred             EccCCCCCC
Confidence            999876543

>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=99.63  E-value=9e-16  Score=121.57  Aligned_cols=86  Identities=17%  Similarity=0.279  Sum_probs=78.0

Q ss_pred             cCCCceEEEcCCCCCCCHHHHH---HHHhhhCCCeeEEEEeecCCCC---CcceEEEEEeCCHHHHHHHHHHhCCceecC
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQ---ETFSSKYPSVKGAKVIIDSNTG---RTKGYGFVRFGDENERSRAMTEMNGVYCSS  278 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~---~~f~~~~g~v~~i~~~~~~~~~---~~~g~afV~f~~~~~A~~A~~~l~g~~~~g  278 (449)
                      ....++|||+|||+++++++|+   ++|+ .||.|.++.++++..++   .++|||||+|.+.++|++|++.||+..|.|
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~~~~F~-~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~g   90 (111)
T 2cpi_A           12 VVQKNLVFVVGLSQRLADPEVLKRPEYFG-KFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDG   90 (111)
T ss_dssp             CCCSSCEEEEEECTTTCCHHHHHSTTTTT-TTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             ccCCCEEEEECCCCCCCHHHHHHHHHHhh-ccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECC
Confidence            3456799999999999999999   9995 99999999999887644   566999999999999999999999999999


Q ss_pred             cceEEeecCCCCC
Q 013141          279 RPMRIDVATPKKA  291 (449)
Q Consensus       279 ~~i~v~~~~~~~~  291 (449)
                      +.|+|+++.++..
T Consensus        91 r~l~V~~a~~k~~  103 (111)
T 2cpi_A           91 RTLKASLGTTKYC  103 (111)
T ss_dssp             EEEEEESCCCCSC
T ss_pred             EEEEEEecccccc
Confidence            9999999988764

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.63  E-value=5.1e-16  Score=115.52  Aligned_cols=69  Identities=22%  Similarity=0.335  Sum_probs=63.4

Q ss_pred             CceEEEcCCCCCC------CHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCC
Q 013141          115 TKTIWIGDLFHWM------DETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNT  185 (449)
Q Consensus       115 ~~~l~v~nLp~~~------t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~  185 (449)
                      +++|||+|||+.+      ++++|+++|++||.|.+|.+.+  .+|+++|||||+|.+.++|.+|++.||+..+.++
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~--~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~   75 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE--EDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ   75 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCC--BTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSS
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecC--CCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCc
Confidence            4799999999999      7799999999999999999873  5789999999999999999999999999998654

>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=99.63  E-value=3.1e-16  Score=121.74  Aligned_cols=85  Identities=26%  Similarity=0.464  Sum_probs=75.1

Q ss_pred             cccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecC-CCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcce
Q 013141          203 TEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDS-NTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPM  281 (449)
Q Consensus       203 ~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~-~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i  281 (449)
                      ......++|||+|||.++++++|+++|+ .|| |.++.++++. .+++++|||||+|.+.++|.+|+ .|++..|.|+.|
T Consensus        14 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~-~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l   90 (100)
T 2j76_E           14 LPKSPPYTAFLGNLPYDVTEESIKEFFR-GLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRI   90 (100)
T ss_dssp             ------CEEEESCCSSCCSSSHHHHHSC-SSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCC
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHH-hcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEE
Confidence            3445678999999999999999999995 999 9999999998 58999999999999999999999 899999999999


Q ss_pred             EEeecCCCC
Q 013141          282 RIDVATPKK  290 (449)
Q Consensus       282 ~v~~~~~~~  290 (449)
                      +|+++.++.
T Consensus        91 ~V~~a~~~~   99 (100)
T 2j76_E           91 RVDVADQAQ   99 (100)
T ss_dssp             CCEECCCSC
T ss_pred             EEEeccCCC
Confidence            999998763

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=1e-15  Score=120.72  Aligned_cols=84  Identities=20%  Similarity=0.459  Sum_probs=77.1

Q ss_pred             cccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceE
Q 013141          203 TEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMR  282 (449)
Q Consensus       203 ~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  282 (449)
                      ......++|||+|||.++++++|+++|+ .||.|..+.++++.  +.++|||||+|.+.++|++|++.|++..+.|+.|+
T Consensus        24 ~~~~~~~~l~V~nLp~~~te~~l~~~F~-~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~  100 (109)
T 2err_A           24 ENKSQPKRLHVSNIPFRFRDPDLRQMFG-QFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIE  100 (109)
T ss_dssp             SCTTCCCEEEEESCCTTCCHHHHHHHGG-GTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECE
T ss_pred             cCCCCCCEEEEECCCCcCCHHHHHHHHH-hcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            4455678999999999999999999995 99999999999885  34899999999999999999999999999999999


Q ss_pred             EeecCCC
Q 013141          283 IDVATPK  289 (449)
Q Consensus       283 v~~~~~~  289 (449)
                      |+++.++
T Consensus       101 V~~a~~~  107 (109)
T 2err_A          101 VNNATAR  107 (109)
T ss_dssp             EEECCCS
T ss_pred             EEECCCC
Confidence            9999875

>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=99.63  E-value=2.6e-15  Score=119.64  Aligned_cols=83  Identities=17%  Similarity=0.451  Sum_probs=76.9

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee--------
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYC--------  276 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~--------  276 (449)
                      ....++|||+|||+++++++|+++|+ .||.|..+.++++. ++.++|||||+|.+.++|++|++.||+..|        
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~-~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~   99 (114)
T 1x5o_A           22 EQDPTNLYISNLPLSMDEQELENMLK-PFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSA   99 (114)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTT-TTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHH-hcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccC
Confidence            45678999999999999999999995 99999999999997 899999999999999999999999999999        


Q ss_pred             cCcceEEeecCCC
Q 013141          277 SSRPMRIDVATPK  289 (449)
Q Consensus       277 ~g~~i~v~~~~~~  289 (449)
                      .+++|.|.++.++
T Consensus       100 ~~~~l~v~~a~p~  112 (114)
T 1x5o_A          100 PTEPLLCKFSGPS  112 (114)
T ss_dssp             CSSCBEEEECCCS
T ss_pred             CCCceeEEccCCC
Confidence            5788999999864

>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=99.63  E-value=9.3e-16  Score=121.19  Aligned_cols=85  Identities=15%  Similarity=0.286  Sum_probs=78.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCC-eeEEEEe-ecCCCCCcceEEEEEeCCHHHHHHHHHHhC--CceecCcce
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPS-VKGAKVI-IDSNTGRTKGYGFVRFGDENERSRAMTEMN--GVYCSSRPM  281 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~-v~~i~~~-~~~~~~~~~g~afV~f~~~~~A~~A~~~l~--g~~~~g~~i  281 (449)
                      .+.++|||+|||.++|+++|+++|. .||. |.++.++ .+..++.++|||||+|.+.++|.+|++.|+  +..+.|+.|
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~-~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l   84 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIA-KVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQI   84 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHH-HHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCC
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHH-HhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeE
Confidence            4578999999999999999999995 9998 9999998 788888999999999999999999999996  589999999


Q ss_pred             EEeecCCCCC
Q 013141          282 RIDVATPKKA  291 (449)
Q Consensus       282 ~v~~~~~~~~  291 (449)
                      +|+++.++..
T Consensus        85 ~V~~a~~~~~   94 (109)
T 2dis_A           85 AVDWAEPEID   94 (109)
T ss_dssp             EEEESCSSCS
T ss_pred             EEEEcCCCCC
Confidence            9999988755

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.63  E-value=1.1e-15  Score=119.72  Aligned_cols=80  Identities=24%  Similarity=0.309  Sum_probs=72.6

Q ss_pred             CCCCCcEEEEcCCCCCC------CHhHHHhhccccCceEEEEEeC----CCcEEEEEecCHHHHHHHHHHhcCCeeCCe-
Q 013141          323 GESNNATIFVGALDSDV------SDEDLREPFSQFGEILSVKIPV----GKGCGFVQFANRKDAEVALQKLQGTAIGKQ-  391 (449)
Q Consensus       323 ~~~~~~~l~V~nlp~~~------t~~~L~~~f~~~G~v~~v~i~~----~~g~afV~F~~~~~A~~A~~~l~g~~~~g~-  391 (449)
                      .....++|||+|||+.+      ++++|+++|+.||.|.+|.|++    ++|+|||+|.+.++|.+|++.|||..|.|+ 
T Consensus        11 ~~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~   90 (105)
T 2nlw_A           11 ADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQH   90 (105)
T ss_dssp             CCSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCCBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTC
T ss_pred             CCCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeCCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCc
Confidence            34457899999999999      7899999999999999999984    479999999999999999999999999998 


Q ss_pred             EEEEEecCCCC
Q 013141          392 TVRLSWGRNPG  402 (449)
Q Consensus       392 ~l~v~~~~~~~  402 (449)
                      .|+|.|+++..
T Consensus        91 ~l~V~~a~~~~  101 (105)
T 2nlw_A           91 TFRVNLFTDFD  101 (105)
T ss_dssp             EEEEECSCCCC
T ss_pred             eEEEEEcchHh
Confidence            99999998653

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.63  E-value=3.5e-15  Score=123.60  Aligned_cols=83  Identities=25%  Similarity=0.505  Sum_probs=77.6

Q ss_pred             cccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceE
Q 013141          203 TEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMR  282 (449)
Q Consensus       203 ~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  282 (449)
                      ....+.++|||+|||.++++++|+++|+ .||.|..+.+++++.+++++|||||+|.+.++|++|++.|++..|.|+.|+
T Consensus        58 ~~~~~~~~l~v~nlp~~~~~~~l~~~f~-~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  136 (140)
T 2ku7_A           58 GSATTKRVLYVGGLAEEVDDKVLHAAFI-PFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIR  136 (140)
T ss_dssp             SSCSSCCEEEEECCCTTCCHHHHHHHHG-GGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEE
T ss_pred             CCCCCCcEEEEEeCCCCCCHHHHHHHHH-hcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            4456778999999999999999999995 999999999999999999999999999999999999999999999999999


Q ss_pred             Eeec
Q 013141          283 IDVA  286 (449)
Q Consensus       283 v~~~  286 (449)
                      |+++
T Consensus       137 v~~A  140 (140)
T 2ku7_A          137 VNLA  140 (140)
T ss_dssp             EEC-
T ss_pred             EEeC
Confidence            9875

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.63  E-value=7.5e-16  Score=124.78  Aligned_cols=78  Identities=24%  Similarity=0.458  Sum_probs=71.8

Q ss_pred             CCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC------CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 013141          326 NNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGR  399 (449)
Q Consensus       326 ~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~------~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  399 (449)
                      ..++|||+|||.++++++|+++|+.||.|.+|.++.+      +++|||+|.+.++|.+|+ .||+..|+|+.|+|.|++
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~  113 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKR  113 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            3589999999999999999999999999999999764      689999999999999999 799999999999999999


Q ss_pred             CCCCC
Q 013141          400 NPGNK  404 (449)
Q Consensus       400 ~~~~~  404 (449)
                      .....
T Consensus       114 ~~~~~  118 (124)
T 2jwn_A          114 TNMPG  118 (124)
T ss_dssp             CCCSS
T ss_pred             CCCCC
Confidence            75443

>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=99.63  E-value=7.3e-16  Score=122.83  Aligned_cols=83  Identities=23%  Similarity=0.382  Sum_probs=78.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEee
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV  285 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  285 (449)
                      ...++|||+|||.++++++|+++|+ .||.|..|.++.++.++.++|||||+|.+.++|++|+ .|++..|.|+.|+|.+
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~-~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~  100 (114)
T 2cq4_A           23 RDARTVFCMQLAARIRPRDLEDFFS-AVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQA  100 (114)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHT-TTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHH-hCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEe
Confidence            4567999999999999999999995 9999999999999999999999999999999999999 9999999999999999


Q ss_pred             cCCCC
Q 013141          286 ATPKK  290 (449)
Q Consensus       286 ~~~~~  290 (449)
                      +.++.
T Consensus       101 a~~~~  105 (114)
T 2cq4_A          101 SQAEK  105 (114)
T ss_dssp             HHHHH
T ss_pred             cCCCc
Confidence            87653

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.43  E-value=2.4e-17  Score=131.91  Aligned_cols=81  Identities=26%  Similarity=0.436  Sum_probs=73.3

Q ss_pred             CCCCcEEEEcCCCCCCCHhHHHhhccccCceEE--------EEEeCC------CcEEEEEecCHHHHHHHHHHhcCCeeC
Q 013141          324 ESNNATIFVGALDSDVSDEDLREPFSQFGEILS--------VKIPVG------KGCGFVQFANRKDAEVALQKLQGTAIG  389 (449)
Q Consensus       324 ~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~--------v~i~~~------~g~afV~F~~~~~A~~A~~~l~g~~~~  389 (449)
                      ....++|||+|||..+++++|+++|+.||.|.+        |.|+.+      +++|||+|.+.++|.+|++.||+..|.
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   83 (116)
T 2lcw_A            4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   83 (116)
Confidence            345789999999999999999999999999998        777754      689999999999999999999999999


Q ss_pred             CeEEEEEecCCCCCC
Q 013141          390 KQTVRLSWGRNPGNK  404 (449)
Q Consensus       390 g~~l~v~~~~~~~~~  404 (449)
                      |+.|+|.|++++...
T Consensus        84 g~~l~V~~a~~~~~~   98 (116)
T 2lcw_A           84 GNPIKVSFATRRADF   98 (116)
Confidence            999999999986543

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=3.7e-16  Score=122.56  Aligned_cols=77  Identities=18%  Similarity=0.234  Sum_probs=68.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      ...++|||+|||+++++++|+++|+.| .|.+|.|+.++. |+++|||||+|.+.++|++|| .+++..|.+  +.|+|.
T Consensus        14 ~~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~-g~~~G~afV~F~~~~~a~~Al-~~~~~~~~g--r~i~V~   88 (109)
T 2dnn_A           14 PDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQ--RYVEVS   88 (109)
T ss_dssp             HHHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHH-HTTTEEETT--EEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHH-hcCCCeECC--eEEEEE
Confidence            356799999999999999999999999 899999999975 999999999999999999999 789988854  456654


Q ss_pred             cc
Q 013141          193 WA  194 (449)
Q Consensus       193 ~~  194 (449)
                      .+
T Consensus        89 ~a   90 (109)
T 2dnn_A           89 PA   90 (109)
T ss_dssp             EC
T ss_pred             EC
Confidence            44

>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=1.9e-16  Score=123.26  Aligned_cols=82  Identities=20%  Similarity=0.237  Sum_probs=73.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccc
Q 013141          112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRL  191 (449)
Q Consensus       112 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~  191 (449)
                      ....++|||+|||+++++++|+++|+.||.|.+ .++.++.+++++|||||+|.+.++|.+|++ |++..+.  ++.|+|
T Consensus        14 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~--g~~l~V   89 (101)
T 1fj7_A           14 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVF--GNEIKL   89 (101)
T ss_dssp             CSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBT--TBCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEEC--CcEEEE
Confidence            446789999999999999999999999999888 677777789999999999999999999998 9999985  578888


Q ss_pred             cccccC
Q 013141          192 NWATFS  197 (449)
Q Consensus       192 ~~~~~~  197 (449)
                      .++...
T Consensus        90 ~~a~~~   95 (101)
T 1fj7_A           90 EKPKGR   95 (101)
T ss_dssp             ECCSCC
T ss_pred             EEcCCC
Confidence            887654

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.62  E-value=4.5e-16  Score=114.64  Aligned_cols=76  Identities=29%  Similarity=0.465  Sum_probs=72.6

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeec
Q 013141          209 LSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVA  286 (449)
Q Consensus       209 ~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~  286 (449)
                      ++|||+|||.++++++|+++|+ .||.|..+.+++++.+++++|+|||+|.+.++|++|++.++ ..+.|+.|+|+++
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 CKMFIGGLSWQTTQEGLREYFG-QFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHT-TTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHH-hcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            4799999999999999999995 99999999999998899999999999999999999999999 9999999999986

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.62  E-value=2.3e-15  Score=115.43  Aligned_cols=79  Identities=23%  Similarity=0.344  Sum_probs=69.1

Q ss_pred             CCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCc-EEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCCC
Q 013141          325 SNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKG-CGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGN  403 (449)
Q Consensus       325 ~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g-~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~~  403 (449)
                      ...++|||+|||.++++++|+++|+.||.|.+|.+.+..+ +|||+|.+.++|.+|++ ||+..|+|+.|+|.++.+...
T Consensus         6 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v~~~~~~g~~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a~~~~~   84 (94)
T 2e5g_A            6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPREQKEF   84 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEEEECSSSCCEEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSCCSCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEcCCCCcEEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECCcCCC
Confidence            3467999999999999999999999999999984433322 99999999999999999 999999999999999886554


Q ss_pred             C
Q 013141          404 K  404 (449)
Q Consensus       404 ~  404 (449)
                      .
T Consensus        85 ~   85 (94)
T 2e5g_A           85 Q   85 (94)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.62  E-value=1.2e-16  Score=130.80  Aligned_cols=79  Identities=19%  Similarity=0.330  Sum_probs=69.5

Q ss_pred             CCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC-----CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 013141          323 GESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-----KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSW  397 (449)
Q Consensus       323 ~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~-----~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  397 (449)
                      .....++|||+|||+++|+++|+++|++|| |.+|.|+.+     +|+|||+|.+.++|++|| .+|+..|+++.|+|.+
T Consensus        42 ~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~  119 (139)
T 2hgn_A           42 QSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFL  119 (139)
T ss_dssp             ---CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEE
Confidence            345578999999999999999999999999 669998853     789999999999999999 7899999999999999


Q ss_pred             cCCCCC
Q 013141          398 GRNPGN  403 (449)
Q Consensus       398 ~~~~~~  403 (449)
                      +.....
T Consensus       120 a~~~~~  125 (139)
T 2hgn_A          120 NSTTGA  125 (139)
T ss_dssp             CCCSCC
T ss_pred             CCCCCC
Confidence            887643

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.62  E-value=3.3e-15  Score=115.29  Aligned_cols=80  Identities=15%  Similarity=0.240  Sum_probs=69.4

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      .....++|||+|||+++++++|+++|+.||.|. +.++.+    +++|||||+|.+.++|.+|++.|++..+.  ++.|+
T Consensus        15 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~----~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~l~   87 (97)
T 2e5j_A           15 GAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ----GPRRRAFLHYPDSAAAQQAVSCLQGLRLG--TDTLR   87 (97)
T ss_dssp             SSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE----TTTTEEEEECSSHHHHHHHHHHHTTCCSS--SSCCE
T ss_pred             CCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC----CCCcEEEEEECCHHHHHHHHHHhCCCEEC--CcEEE
Confidence            345688999999999999999999999999996 666654    57899999999999999999999999985  46788


Q ss_pred             ccccccC
Q 013141          191 LNWATFS  197 (449)
Q Consensus       191 ~~~~~~~  197 (449)
                      |.++...
T Consensus        88 V~~a~~~   94 (97)
T 2e5j_A           88 VALARQQ   94 (97)
T ss_dssp             EEECCCC
T ss_pred             EEEcCCC
Confidence            8887643

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.62  E-value=1.6e-15  Score=116.80  Aligned_cols=79  Identities=16%  Similarity=0.245  Sum_probs=71.7

Q ss_pred             CCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEE-EeCC--CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCC
Q 013141          324 ESNNATIFVGALDSDVSDEDLREPFSQFGEILSVK-IPVG--KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRN  400 (449)
Q Consensus       324 ~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~-i~~~--~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  400 (449)
                      ....++|||+|||+.+++++|+++|+.||.|.+|+ ++.+  .+.|||+|.+.++|.+|++.|||..|.|+.|+|.|+++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~   91 (96)
T 2e44_A           12 RQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPD   91 (96)
T ss_dssp             CCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEECCC
T ss_pred             CCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCc
Confidence            34568999999999999999999999999999994 7765  35599999999999999999999999999999999998


Q ss_pred             CC
Q 013141          401 PG  402 (449)
Q Consensus       401 ~~  402 (449)
                      ..
T Consensus        92 ~~   93 (96)
T 2e44_A           92 EM   93 (96)
T ss_dssp             CC
T ss_pred             cc
Confidence            64

>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=99.62  E-value=2.7e-16  Score=119.70  Aligned_cols=81  Identities=33%  Similarity=0.580  Sum_probs=73.6

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecCC
Q 013141          209 LSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATP  288 (449)
Q Consensus       209 ~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~~  288 (449)
                      ++|||+|||.++++++|+++|+ .||.|.++.+++++.++.++|||||+|.+.+ |.+|++.|++..+.|+.|+|+++.+
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~-~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~   79 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFS-QFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANP   79 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHH-HHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC--
T ss_pred             cEEEECCCCCCCCHHHHHHHHH-hcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCC
Confidence            4899999999999999999995 9999999999999999999999999999999 9999999999999999999999988


Q ss_pred             CCC
Q 013141          289 KKA  291 (449)
Q Consensus       289 ~~~  291 (449)
                      ...
T Consensus        80 ~~~   82 (90)
T 2ki2_A           80 KKS   82 (90)
T ss_dssp             ---
T ss_pred             CCC
Confidence            654

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.62  E-value=2.3e-15  Score=121.87  Aligned_cols=84  Identities=21%  Similarity=0.408  Sum_probs=78.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEee
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV  285 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  285 (449)
                      ...++|||+|||.++|+++|+++|+ .||.|.++.+++++.++.++|||||+|.+.++|++|+ .|++..|.|+.|+|++
T Consensus        34 ~~~~~l~V~nlp~~~t~~~l~~~F~-~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~  111 (124)
T 2jwn_A           34 IDKRSVYVGNVDYGSTAQDLEAHFS-SCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLP  111 (124)
T ss_dssp             HHHTEEEEEEECTTCCHHHHHHHHH-TTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHH-hcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEE
Confidence            4568999999999999999999995 9999999999999889999999999999999999999 8999999999999999


Q ss_pred             cCCCCC
Q 013141          286 ATPKKA  291 (449)
Q Consensus       286 ~~~~~~  291 (449)
                      +.....
T Consensus       112 a~~~~~  117 (124)
T 2jwn_A          112 KRTNMP  117 (124)
T ss_dssp             SSCCCS
T ss_pred             CCCCCC
Confidence            987543

>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=99.61  E-value=2.2e-16  Score=129.33  Aligned_cols=124  Identities=14%  Similarity=0.115  Sum_probs=75.0

Q ss_pred             cEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccccccccCCCCCccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCee
Q 013141          158 GYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVK  237 (449)
Q Consensus       158 g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~  237 (449)
                      |+||.+|..++.+..++..+....- +...  -   ...............++|||+|||+++|+++|+++|+ .|| |.
T Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~~g-g~~~--g---~~~g~~~~~~~~~~~~~lfV~nLp~~~te~dL~~~F~-~~G-i~   73 (139)
T 2hgn_A            2 GSSHHHHHHSSGLVPRGSHMASMTG-GQQM--G---RGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFS-PLN-PV   73 (139)
T ss_dssp             -------------------------------------------------CCCCEECCSCCTTCCHHHHHHHHC-SCC-CS
T ss_pred             CcccccccCccccchhcccchhccC-CCCC--C---CCCCCcccCCCCCCCCEEEEeCCCCCCCHHHHHHHHH-hcC-Ce
Confidence            5788888888887777755333211 1100  0   0000111122345567999999999999999999995 999 67


Q ss_pred             EEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecCCCCC
Q 013141          238 GAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKA  291 (449)
Q Consensus       238 ~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~~~~~  291 (449)
                      +|.|++++. ++++|||||+|.+.++|++|| .+++..|.++.|+|.++.....
T Consensus        74 ~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a~~~~~  125 (139)
T 2hgn_A           74 RVHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNSTTGA  125 (139)
T ss_dssp             EEECCCSSS-SCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEECCCSCC
T ss_pred             EEEEEECCC-CCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEECCCCCC
Confidence            999999976 999999999999999999999 8999999999999999887654

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.61  E-value=1.7e-15  Score=112.28  Aligned_cols=74  Identities=18%  Similarity=0.310  Sum_probs=66.2

Q ss_pred             CcEEEEcCCCCCCCHhH----HHhhcccc-CceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCC
Q 013141          327 NATIFVGALDSDVSDED----LREPFSQF-GEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNP  401 (449)
Q Consensus       327 ~~~l~V~nlp~~~t~~~----L~~~f~~~-G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~  401 (449)
                      .+.|||+|||+++++++    |+++|++| |.|.+|.    .|+|||+|.+.++|.+|++.|+|..|.|+.|+|.|++.+
T Consensus         9 ~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~Vt----gG~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~~A~~~   84 (96)
T 2diu_A            9 HTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSIT----GCSAILRFINQDSAERAQKRMENEDVFGNRIIVSFTPKN   84 (96)
T ss_dssp             SEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEECC----TTCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEESSCCS
T ss_pred             ceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEEe----cCEEEEEECCHHHHHHHHHHhcCCccCCceEEEEecCCC
Confidence            34499999999999988    55899999 5999992    399999999999999999999999999999999999986


Q ss_pred             CCC
Q 013141          402 GNK  404 (449)
Q Consensus       402 ~~~  404 (449)
                      ..-
T Consensus        85 sd~   87 (96)
T 2diu_A           85 REL   87 (96)
T ss_dssp             CCC
T ss_pred             cce
Confidence            544

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.61  E-value=1.8e-15  Score=118.52  Aligned_cols=83  Identities=19%  Similarity=0.334  Sum_probs=75.6

Q ss_pred             cCCCceEEEcCCCCCC------CHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecC
Q 013141          205 ACSDLSIFVGDLAPDV------TDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSS  278 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~------t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g  278 (449)
                      ....++|||+|||+.+      |+++|+++|+ .||.|.++.++  ..+++++|||||+|.+.++|.+|++.|||..|.|
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~-~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g   88 (105)
T 2nlw_A           12 DGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFS-KFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDK   88 (105)
T ss_dssp             CSCCSEEEEESCCCCCTTTTTHHHHHHHHHHG-GGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECST
T ss_pred             CCCCCEEEEeCCCcchhhhhHHHHHHHHHHHh-cCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCC
Confidence            3456899999999999      7899999995 99999999988  3678999999999999999999999999999999


Q ss_pred             c-ceEEeecCCCC
Q 013141          279 R-PMRIDVATPKK  290 (449)
Q Consensus       279 ~-~i~v~~~~~~~  290 (449)
                      + .|+|.++....
T Consensus        89 ~~~l~V~~a~~~~  101 (105)
T 2nlw_A           89 QHTFRVNLFTDFD  101 (105)
T ss_dssp             TCEEEEECSCCCC
T ss_pred             CceEEEEEcchHh
Confidence            9 99999997654

>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=99.61  E-value=2.8e-15  Score=116.13  Aligned_cols=79  Identities=20%  Similarity=0.372  Sum_probs=70.9

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      .....++|||+|||+++++++|+++|+.||.|.+|++.++      +|||||+|.+.++|++|++.|++..+.  ++.|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~--g~~l~   82 (99)
T 2cpj_A           11 TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLR--GKQLR   82 (99)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBT--TBCCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeC--CceEE
Confidence            4467889999999999999999999999999999999865      589999999999999999999999985  47788


Q ss_pred             ccccccC
Q 013141          191 LNWATFS  197 (449)
Q Consensus       191 ~~~~~~~  197 (449)
                      |.++...
T Consensus        83 v~~a~~~   89 (99)
T 2cpj_A           83 VRFACHS   89 (99)
T ss_dssp             EEESSCC
T ss_pred             EEEcCCC
Confidence            8888754

>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=99.61  E-value=3.8e-16  Score=114.41  Aligned_cols=74  Identities=16%  Similarity=0.309  Sum_probs=66.0

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccccc
Q 013141          117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNW  193 (449)
Q Consensus       117 ~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~  193 (449)
                      +|||+|||+++++++|+++|+.||.|.+|.++.++.+++++|||||+|.+.++|++|++. ++..+.+  +.+++.+
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g--~~l~v~~   74 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGL--SKCEIKV   74 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-SSCCBTT--BCCCEEE
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-CCCeECC--EEEEEEE
Confidence            699999999999999999999999999999999999999999999999999999999974 7777744  4555443

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.61  E-value=4.1e-15  Score=115.91  Aligned_cols=86  Identities=29%  Similarity=0.502  Sum_probs=77.5

Q ss_pred             cccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceE
Q 013141          203 TEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMR  282 (449)
Q Consensus       203 ~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  282 (449)
                      ....+.++|||+|||.++++++|+++|+ .|   ..+.++.+..++.++|||||+|.+.++|++|++.|++..|.|+.|+
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~-~~---~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   85 (102)
T 2fc8_A           10 ARSQPSKTLFVKGLSEDTTEETLKESFD-GS---VRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVT   85 (102)
T ss_dssp             SSSCCCSSEEEECCCTTCCHHHHHHTST-TC---SEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCEEEEeCCCCccCHHHHHHHhc-CC---eEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEE
Confidence            3455678999999999999999999995 66   4788888888899999999999999999999999999999999999


Q ss_pred             EeecCCCCCC
Q 013141          283 IDVATPKKAS  292 (449)
Q Consensus       283 v~~~~~~~~~  292 (449)
                      |+++.++...
T Consensus        86 V~~a~~~~~~   95 (102)
T 2fc8_A           86 LDWAKPKGEG   95 (102)
T ss_dssp             EEECCCCCSS
T ss_pred             EEEecCCCCC
Confidence            9999987654

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.61  E-value=2.9e-15  Score=115.41  Aligned_cols=82  Identities=26%  Similarity=0.414  Sum_probs=72.3

Q ss_pred             CCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeC--CCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 013141          322 DGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV--GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGR  399 (449)
Q Consensus       322 ~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~--~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  399 (449)
                      ......++|||+|||..+++++|+++|+.||.|..+ ...  .+|+|||+|.+.++|.+|++.||+..|.|+.|+|.|++
T Consensus        11 ~~~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   89 (96)
T 1fjc_A           11 KKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTG   89 (96)
T ss_dssp             STTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECS
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcC
Confidence            344567899999999999999999999999998877 222  37899999999999999999999999999999999998


Q ss_pred             CCCCC
Q 013141          400 NPGNK  404 (449)
Q Consensus       400 ~~~~~  404 (449)
                      ++...
T Consensus        90 ~~~~~   94 (96)
T 1fjc_A           90 EKGGT   94 (96)
T ss_dssp             SSCCC
T ss_pred             CCCCC
Confidence            86543

>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=99.61  E-value=2.5e-15  Score=117.49  Aligned_cols=84  Identities=18%  Similarity=0.239  Sum_probs=76.3

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeE-EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEE
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKG-AKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRI  283 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~-i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  283 (449)
                      ....++|||+|||+++|+++|+++|+ .||.|.. |.++.+ .+++++|||||+|.+.++|++||+. ++..+.++.|+|
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~-~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v   88 (104)
T 1wg5_A           12 TANDGFVRLRGLPFGCSKEEIVQFFS-GLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEI   88 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTT-TCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHH-hcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEE
Confidence            34568999999999999999999995 9999987 888888 7899999999999999999999986 999999999999


Q ss_pred             eecCCCCC
Q 013141          284 DVATPKKA  291 (449)
Q Consensus       284 ~~~~~~~~  291 (449)
                      .++..+..
T Consensus        89 ~~~~~~~~   96 (104)
T 1wg5_A           89 FKSSRAEV   96 (104)
T ss_dssp             EEECTTTS
T ss_pred             EECCHHHH
Confidence            99877644

>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=99.61  E-value=1.3e-15  Score=124.36  Aligned_cols=82  Identities=17%  Similarity=0.224  Sum_probs=76.2

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhhCCC---eeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcce
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQETFSSKYPS---VKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPM  281 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~---v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i  281 (449)
                      ....++|||+|||+++|+++|+++|+ .||.   |.+|++++++. ++++|||||+|.+.++|++||+ +++..|.++.|
T Consensus        41 ~~~~~~lfVgnLp~~~te~dL~~~F~-~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i  117 (136)
T 2hgl_A           41 GGEGFVVKLRGLPWSCSVEDVQNFLS-DCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRYI  117 (136)
T ss_dssp             CCTTCEEEEESCCTTCCHHHHHHHTT-TCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHH-HhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEE
Confidence            44678999999999999999999995 9999   89999999977 9999999999999999999998 99999999999


Q ss_pred             EEeecCCC
Q 013141          282 RIDVATPK  289 (449)
Q Consensus       282 ~v~~~~~~  289 (449)
                      +|.++..+
T Consensus       118 ~V~~a~~~  125 (136)
T 2hgl_A          118 EVFKSHRT  125 (136)
T ss_dssp             EEEECCHH
T ss_pred             EEEECChH
Confidence            99998654

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.60  E-value=2.5e-15  Score=117.85  Aligned_cols=79  Identities=22%  Similarity=0.352  Sum_probs=72.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeec
Q 013141          207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVA  286 (449)
Q Consensus       207 ~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~  286 (449)
                      ...+|||+|||+++|+++|+++|+ .| .|.+|.|++++. ++++|||||+|.+.++|++|| .+++..|.++.|+|..+
T Consensus        15 ~~~~v~V~nLp~~~te~dl~~~F~-~~-~v~~v~i~~d~~-g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a   90 (109)
T 2dnn_A           15 DDLYVSVHGMPFSAMENDVRDFFH-GL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPA   90 (109)
T ss_dssp             HHHEEEEECCCSSCCHHHHHHHTT-TS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhc-cC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEEC
Confidence            457999999999999999999995 89 899999999976 999999999999999999999 79999999999999888


Q ss_pred             CCC
Q 013141          287 TPK  289 (449)
Q Consensus       287 ~~~  289 (449)
                      ..+
T Consensus        91 ~~~   93 (109)
T 2dnn_A           91 TER   93 (109)
T ss_dssp             CHH
T ss_pred             Ccc
Confidence            653

>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=99.60  E-value=1.8e-15  Score=120.47  Aligned_cols=83  Identities=14%  Similarity=0.266  Sum_probs=76.9

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhhCCCe-eEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEE
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQETFSSKYPSV-KGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRI  283 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v-~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  283 (449)
                      ....++|||+|||+++|+++|+++|+ .||.| ..|.+++++ +++++|||||+|.+.++|++||+. ++..|.|+.|+|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~-~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v   88 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLE-GIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFV   88 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTT-TSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHH-hCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEE
Confidence            45678999999999999999999995 99999 899999997 899999999999999999999976 999999999999


Q ss_pred             eecCCCC
Q 013141          284 DVATPKK  290 (449)
Q Consensus       284 ~~~~~~~  290 (449)
                      .++.++.
T Consensus        89 ~~a~~~~   95 (114)
T 2cpy_A           89 HVVTLED   95 (114)
T ss_dssp             EEECHHH
T ss_pred             EECCHHH
Confidence            9997754

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.60  E-value=1.9e-15  Score=120.97  Aligned_cols=82  Identities=17%  Similarity=0.194  Sum_probs=75.9

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhhCCC---eeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcce
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQETFSSKYPS---VKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPM  281 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~---v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i  281 (449)
                      ....++|||+|||+++|+++|+++|+ .||.   |..|+++++.. ++++|||||+|.+.++|++||+ +++..|.++.|
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~-~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i   90 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLS-DCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDRESMGHRYI   90 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTT-TSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHH-HcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEE
Confidence            44568999999999999999999995 9999   89999999977 9999999999999999999998 99999999999


Q ss_pred             EEeecCCC
Q 013141          282 RIDVATPK  289 (449)
Q Consensus       282 ~v~~~~~~  289 (449)
                      +|.++..+
T Consensus        91 ~V~~a~~~   98 (118)
T 2db1_A           91 EVFKSHRT   98 (118)
T ss_dssp             EEEEECHH
T ss_pred             EEEECCHH
Confidence            99998654

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.60  E-value=6.6e-15  Score=111.87  Aligned_cols=79  Identities=20%  Similarity=0.451  Sum_probs=73.0

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEe
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRID  284 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  284 (449)
                      ..+.++|||+|||.++++++|+++|+ .||.|.++.++        ++||||+|.+.++|++|++.|++..+.|+.|+|+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~-~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   75 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFE-QYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVE   75 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHH-TSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHH-hCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEE
Confidence            35678999999999999999999995 99999999987        5799999999999999999999999999999999


Q ss_pred             ecCCCCCC
Q 013141          285 VATPKKAS  292 (449)
Q Consensus       285 ~~~~~~~~  292 (449)
                      ++.++...
T Consensus        76 ~a~~~~~~   83 (90)
T 2dnq_A           76 ASKNKSKA   83 (90)
T ss_dssp             CSSCCCCC
T ss_pred             ECCCCCCC
Confidence            99887653

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.60  E-value=4.2e-15  Score=115.64  Aligned_cols=83  Identities=24%  Similarity=0.451  Sum_probs=74.6

Q ss_pred             ccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEE
Q 013141          204 EACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRI  283 (449)
Q Consensus       204 ~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  283 (449)
                      ...+.++|||+|||.++++++|+++|+ .||.|   .++.+ .+++++|||||+|.+.++|++|++.|++..|.++.|+|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~-~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   85 (101)
T 2fc9_A           11 WSGESKTLVLSNLSYSATEETLQEVFE-KATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRL   85 (101)
T ss_dssp             CSCCCSEEEEESCCTTCCHHHHHHHCS-SCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHH-hCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEE
Confidence            345678999999999999999999995 89976   56666 67899999999999999999999999999999999999


Q ss_pred             eecCCCCC
Q 013141          284 DVATPKKA  291 (449)
Q Consensus       284 ~~~~~~~~  291 (449)
                      +++.++..
T Consensus        86 ~~a~~~~~   93 (101)
T 2fc9_A           86 ELQGPRGS   93 (101)
T ss_dssp             EECSSCCC
T ss_pred             EEcCCCCC
Confidence            99988754

>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=99.60  E-value=3.9e-15  Score=116.23  Aligned_cols=80  Identities=21%  Similarity=0.411  Sum_probs=70.2

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      .....++|||+|||+++++++|+++|+.||.|.+|.+++        +||||+|.+.++|++|++.|++..+.  ++.|+
T Consensus         7 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~--g~~l~   76 (103)
T 2dgu_A            7 GMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK--------DYAFIHFDERDGAVKAMEEMNGKDLE--GENIE   76 (103)
T ss_dssp             CCCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESSHHHHHHHHHHHTTEEET--TEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEC--------CEEEEEeCCHHHHHHHHHHHCCCccC--CCEEE
Confidence            345689999999999999999999999999999999863        59999999999999999999999885  57888


Q ss_pred             ccccccCCCC
Q 013141          191 LNWATFSGSD  200 (449)
Q Consensus       191 ~~~~~~~~~~  200 (449)
                      |.++......
T Consensus        77 v~~a~~~~~~   86 (103)
T 2dgu_A           77 IVFAKPPDQK   86 (103)
T ss_dssp             EEECCCCCCC
T ss_pred             EEEcCCCccc
Confidence            8888765443

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A

Probab=99.60  E-value=1.6e-15  Score=121.78  Aligned_cols=79  Identities=18%  Similarity=0.219  Sum_probs=67.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCcE--EEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcc
Q 013141          112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVV--NVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPF  189 (449)
Q Consensus       112 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~--~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~  189 (449)
                      ....++|||+|||+++|+++|+++|+.| .|+  +|+|+.++. |+++|||||+|.+.++|++||+. ++..|.  ++.|
T Consensus        39 ~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~~-~~~~l~--gR~I  113 (126)
T 2hgm_A           39 SANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALGK-HKERIG--HRYI  113 (126)
T ss_dssp             SSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHTT-TTCCBT--TBCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHHH-CCCEEC--CEEE
Confidence            3567899999999999999999999999 677  999999986 99999999999999999999974 667774  4566


Q ss_pred             cccccc
Q 013141          190 RLNWAT  195 (449)
Q Consensus       190 ~~~~~~  195 (449)
                      +|..+.
T Consensus       114 ~V~~a~  119 (126)
T 2hgm_A          114 EVFKSS  119 (126)
T ss_dssp             CCEEEC
T ss_pred             EEEECC
Confidence            665553

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.60  E-value=7.7e-15  Score=117.18  Aligned_cols=79  Identities=16%  Similarity=0.200  Sum_probs=70.0

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccE-EEEEEccHHHHHHHHHHhcCCCCCCCCCcccccc
Q 013141          115 TKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGY-GFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNW  193 (449)
Q Consensus       115 ~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~-afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~  193 (449)
                      ...|||+||++.+++++|+++|++||.|.+|+|+..      .|| |||+|.+.++|.+|++.|++..|.+..+.|+|.+
T Consensus        25 vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~------~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~   98 (124)
T 2e5i_A           25 VLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR------NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEY   98 (124)
T ss_dssp             EEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES------SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEEC
T ss_pred             EEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEE
Confidence            344689999999999999999999999999999752      276 9999999999999999999999988778999999


Q ss_pred             cccCCC
Q 013141          194 ATFSGS  199 (449)
Q Consensus       194 ~~~~~~  199 (449)
                      ++....
T Consensus        99 Ak~~~l  104 (124)
T 2e5i_A           99 ARPTRL  104 (124)
T ss_dssp             CSCSCC
T ss_pred             ecCCcc
Confidence            986643

>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=99.60  E-value=2.2e-15  Score=135.01  Aligned_cols=82  Identities=17%  Similarity=0.280  Sum_probs=77.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhhCC--CeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEe
Q 013141          207 SDLSIFVGDLAPDVTDSILQETFSSKYP--SVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRID  284 (449)
Q Consensus       207 ~~~~l~v~~lp~~~t~~~l~~~f~~~~g--~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  284 (449)
                      ..++|||+||++++|+++|+++|+ .||  .|.+|+|++++.+++++|||||+|.+.++|++||+.||+..|.|+.|+|.
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~-~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~  145 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVH-SLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVT  145 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHH-TTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHH-HHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEE
Confidence            567899999999999999999995 999  99999999999999999999999999999999999999999999999999


Q ss_pred             ecCCC
Q 013141          285 VATPK  289 (449)
Q Consensus       285 ~~~~~  289 (449)
                      ++...
T Consensus       146 ~a~~~  150 (229)
T 3q2s_C          146 PVNKQ  150 (229)
T ss_dssp             ECCHH
T ss_pred             ECCCC
Confidence            99764

>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=7.2e-15  Score=115.74  Aligned_cols=79  Identities=24%  Similarity=0.310  Sum_probs=73.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecC-----cc
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSS-----RP  280 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g-----~~  280 (449)
                      ...++|||+|||+++|+++|+++|+ .||.|..+.++.+       |||||+|.+.++|++||+.||+..|.+     +.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~-~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~   84 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMR-EAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAY   84 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHG-GGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHH-hcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceE
Confidence            4578999999999999999999995 9999999999876       799999999999999999999999999     99


Q ss_pred             eEEeecCCCCCC
Q 013141          281 MRIDVATPKKAS  292 (449)
Q Consensus       281 i~v~~~~~~~~~  292 (449)
                      |+|+++.++...
T Consensus        85 i~V~~a~~~~~~   96 (108)
T 1x4c_A           85 IRVKVDGPRSPS   96 (108)
T ss_dssp             EEEEESSCCSCC
T ss_pred             EEEEeCCCCCCC
Confidence            999999886543

>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=1.1e-15  Score=122.46  Aligned_cols=78  Identities=14%  Similarity=0.190  Sum_probs=67.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCc----EEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQV----VNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQP  188 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v----~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~  188 (449)
                      ...++|||+|||+++|+++|+++|+.||.|    .+|.|+.++ +|+++|||||+|.+.++|++||+. ++..|.+  +.
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~-~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~g--R~   96 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP-DGRPTGDAFVLFACEEYAQNALRK-HKDLLGK--RY   96 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECT-TSCEEEEEEECCSSHHHHHHHHTT-TTEESSS--CE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECC-CCCEeeEEEEEECCHHHHHHHHHh-CCCeeCC--eE
Confidence            457899999999999999999999999975    689999984 899999999999999999999975 8877754  45


Q ss_pred             cccccc
Q 013141          189 FRLNWA  194 (449)
Q Consensus       189 ~~~~~~  194 (449)
                      |+|..+
T Consensus        97 i~V~~a  102 (123)
T 2dha_A           97 IELFRS  102 (123)
T ss_dssp             ECCEEE
T ss_pred             EEEEEC
Confidence            555433

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.59  E-value=1.4e-15  Score=113.07  Aligned_cols=74  Identities=20%  Similarity=0.399  Sum_probs=67.6

Q ss_pred             CceEEEcCCCCCC------CHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCc-c
Q 013141          208 DLSIFVGDLAPDV------TDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSR-P  280 (449)
Q Consensus       208 ~~~l~v~~lp~~~------t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~-~  280 (449)
                      +++|||+|||.++      ++++|+++|+ .||.|.++.+.  +.+++++|||||+|.+.++|.+|++.|||..+.|+ .
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~-~~G~i~~v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~   77 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFS-KFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHT   77 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHH-TTCCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHh-hcCCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCcee
Confidence            3689999999999      7799999995 99999999987  36789999999999999999999999999999999 8


Q ss_pred             eEEe
Q 013141          281 MRID  284 (449)
Q Consensus       281 i~v~  284 (449)
                      |+|+
T Consensus        78 l~V~   81 (81)
T 2krb_A           78 FRVN   81 (81)
T ss_dssp             CCCC
T ss_pred             EEeC
Confidence            8763

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.59  E-value=5.6e-16  Score=120.65  Aligned_cols=85  Identities=16%  Similarity=0.452  Sum_probs=76.8

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEe
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRID  284 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  284 (449)
                      ....++|||+|||.++|+++|+++|+ .||.|.. .++.+..++.++|||||+|.+.++|.+|++ |++..|.|+.|+|.
T Consensus        14 ~~~~~~l~V~nLp~~~t~~~l~~~F~-~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~   90 (101)
T 1fj7_A           14 STTPFNLFIGNLNPNKSVAELKVAIS-ELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLE   90 (101)
T ss_dssp             CSCSEEEEEECCCTTSCHHHHHHHHH-HHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHH-HhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEE
Confidence            34678999999999999999999995 9999988 667777788999999999999999999998 99999999999999


Q ss_pred             ecCCCCCC
Q 013141          285 VATPKKAS  292 (449)
Q Consensus       285 ~~~~~~~~  292 (449)
                      ++.++..+
T Consensus        91 ~a~~~~~~   98 (101)
T 1fj7_A           91 KPKGRDGT   98 (101)
T ss_dssp             CCSCCCCS
T ss_pred             EcCCCCCC
Confidence            99887543

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.59  E-value=2.6e-15  Score=120.31  Aligned_cols=83  Identities=17%  Similarity=0.318  Sum_probs=73.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccE-EEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          114 ETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGY-GFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       114 ~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~-afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      ....|||+||++.+|+++|+++|++||.|.+|+++.+.     +|| |||+|.+.++|++|++.|||..+.+..+.|+|.
T Consensus        27 ~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~-----~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~  101 (130)
T 3zzy_A           27 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN-----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID  101 (130)
T ss_dssp             SEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEET-----TEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEE
T ss_pred             ceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCC-----CCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEE
Confidence            44568899999999999999999999999999988753     477 999999999999999999999998777899999


Q ss_pred             ccccCCCCC
Q 013141          193 WATFSGSDR  201 (449)
Q Consensus       193 ~~~~~~~~~  201 (449)
                      |++.....-
T Consensus       102 ~ak~~~l~v  110 (130)
T 3zzy_A          102 FSKLTSLNV  110 (130)
T ss_dssp             ECSCSSCCC
T ss_pred             ecCCCceeE
Confidence            998765433

>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=99.59  E-value=1.7e-15  Score=122.62  Aligned_cols=84  Identities=20%  Similarity=0.342  Sum_probs=76.7

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEe
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRID  284 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  284 (449)
                      ....++|||+|||+++|+++|+++|+ .||.|..+.++.+..+++++|||||+|.+.++|++||+ |++..|.|+.|+|.
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~-~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~   99 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFK-KLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVH   99 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSC-SSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHH-hcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEE
Confidence            34568999999999999999999995 99999987777777889999999999999999999998 99999999999999


Q ss_pred             ecCCCC
Q 013141          285 VATPKK  290 (449)
Q Consensus       285 ~~~~~~  290 (449)
                      ++..+.
T Consensus       100 ~a~~~~  105 (124)
T 1wel_A          100 PITKKG  105 (124)
T ss_dssp             EECHHH
T ss_pred             ECCHHH
Confidence            997654

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.58  E-value=3.6e-15  Score=117.17  Aligned_cols=79  Identities=13%  Similarity=0.131  Sum_probs=71.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCC-CeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEe
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYP-SVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRID  284 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g-~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  284 (449)
                      ...++|||+|||+++++++|+++|+ .|| +|..+.+..+    .++|||||+|.+.++|++||+.||+..|.|+.|+|+
T Consensus        26 ~~~~~l~VgnLp~~~te~dL~~~F~-~~G~~v~~v~i~~~----~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~  100 (111)
T 2jvr_A           26 AKRYRITMKNLPEGCSWQDLKDLAR-ENSLETTFSSVNTR----DFDGTGALEFPSEEILVEALERLNNIEFRGSVITVE  100 (111)
T ss_dssp             CCCEEEEEECSSCCCCHHHHHHHHH-HHTCCCSEEECSSC----SSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHH-HhCCeeEEEEEEcC----CCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            3567999999999999999999995 999 8999988533    478999999999999999999999999999999999


Q ss_pred             ecCCC
Q 013141          285 VATPK  289 (449)
Q Consensus       285 ~~~~~  289 (449)
                      ++...
T Consensus       101 ~a~~~  105 (111)
T 2jvr_A          101 RDDNP  105 (111)
T ss_dssp             ESCC-
T ss_pred             ECCCC
Confidence            98765

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.37  E-value=1.1e-16  Score=127.95  Aligned_cols=85  Identities=19%  Similarity=0.381  Sum_probs=77.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCcEE--------EEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCC
Q 013141          112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVN--------VKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMP  183 (449)
Q Consensus       112 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~--------v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~  183 (449)
                      ..+.++|||+|||+++++++|+++|+.||.|.+        |.++.++.+++++|||||+|.+.++|.+|++.|++..+.
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   83 (116)
T 2lcw_A            4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   83 (116)
Confidence            457889999999999999999999999999999        999999888999999999999999999999999999885


Q ss_pred             CCCCcccccccccCC
Q 013141          184 NTDQPFRLNWATFSG  198 (449)
Q Consensus       184 ~~~~~~~~~~~~~~~  198 (449)
                        ++.|+|.++....
T Consensus        84 --g~~l~V~~a~~~~   96 (116)
T 2lcw_A           84 --GNPIKVSFATRRA   96 (116)
Confidence              5678888876543

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.58  E-value=5.1e-15  Score=115.13  Aligned_cols=77  Identities=13%  Similarity=0.253  Sum_probs=71.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEee
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV  285 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  285 (449)
                      ...++|||+|||.++++++|+++|+ .||.|.++.+.      +++|||||+|.+.++|++|++.|++..+.|+.|+|++
T Consensus        25 ~~~~~l~V~nlp~~~~~~~l~~~f~-~~G~i~~~~~~------~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   97 (101)
T 2la4_A           25 PRVTTAYIGNIPHFATEADLIPLFQ-NFGFILDFKHY------PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGW   97 (101)
T ss_dssp             SSCCEEEEESCCTTCCHHHHHHHHH-TTSCCSEEEEE------TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCB
T ss_pred             CCCCEEEEcCCCcccCHHHHHHHHH-hCCCEEEEEEe------cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEe
Confidence            4468999999999999999999995 99999999987      3478999999999999999999999999999999999


Q ss_pred             cCCC
Q 013141          286 ATPK  289 (449)
Q Consensus       286 ~~~~  289 (449)
                      ++++
T Consensus        98 a~~~  101 (101)
T 2la4_A           98 GKER  101 (101)
T ss_dssp             CCCC
T ss_pred             ccCC
Confidence            8763

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.58  E-value=4.5e-15  Score=116.42  Aligned_cols=82  Identities=15%  Similarity=0.213  Sum_probs=73.5

Q ss_pred             ceEEEcCC----CCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCC----HHH----HHHHHH--HhCCc
Q 013141          209 LSIFVGDL----APDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGD----ENE----RSRAMT--EMNGV  274 (449)
Q Consensus       209 ~~l~v~~l----p~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~----~~~----A~~A~~--~l~g~  274 (449)
                      +.|||+||    |+++++++|+++|+ .||+|.++.++.|+.||+++|||||+|.+    +++    |.+|++  .+++.
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs-~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~   81 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFK-KYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGC   81 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHH-TTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHH-hcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCC
Confidence            58999999    99999999999996 99999999999999999999999999996    323    788888  78999


Q ss_pred             eecCcceEEeecCCCCC
Q 013141          275 YCSSRPMRIDVATPKKA  291 (449)
Q Consensus       275 ~~~g~~i~v~~~~~~~~  291 (449)
                      .|+|+.|+|.+.+....
T Consensus        82 ~I~Gr~irV~ln~~g~~   98 (136)
T 2j8a_A           82 FIMGFKFEVILNKHSIL   98 (136)
T ss_dssp             EETTEEEEEEECCTTHH
T ss_pred             eecCcEEEEEECcccHH
Confidence            99999999998877543

>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=99.58  E-value=1.3e-15  Score=111.48  Aligned_cols=75  Identities=27%  Similarity=0.502  Sum_probs=70.8

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeec
Q 013141          210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVA  286 (449)
Q Consensus       210 ~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~  286 (449)
                      +|||+|||.++++++|+++|+ .||.|.++.+++++.++.++|||||+|.+.++|++|++ +++..+.|+.|+|+++
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 KIFVGGLSPDTPEEKIREYFG-GFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHH-HHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHT-TSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHH-hcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHH-hCCCeECCEEEEEEEC
Confidence            589999999999999999995 99999999999999999999999999999999999996 5889999999999875

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.58  E-value=1.7e-14  Score=110.05  Aligned_cols=80  Identities=18%  Similarity=0.417  Sum_probs=72.9

Q ss_pred             ccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEE
Q 013141          204 EACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRI  283 (449)
Q Consensus       204 ~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  283 (449)
                      .....++|||+|||.++++++|+++|+ .||.|..+.+++        +||||+|.+.++|.+|++.|++..+.|+.|+|
T Consensus         6 ~~~~~~~l~V~nLp~~~t~~~l~~~F~-~~G~v~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   76 (92)
T 2dgt_A            6 SGKASTKLHVGNISPTCTNQELRAKFE-EYGPVIECDIVK--------DYAFVHMERAEDAVEAIRGLDNTEFQGKRMHV   76 (92)
T ss_dssp             CCCSSEEEEEESCCSSCCHHHHHHHHH-TTSCCCEEEECS--------SEEEEEESCHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHH-hcCCeEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCeeCCcEEEE
Confidence            345678999999999999999999995 999999999873        39999999999999999999999999999999


Q ss_pred             eecCCCCCC
Q 013141          284 DVATPKKAS  292 (449)
Q Consensus       284 ~~~~~~~~~  292 (449)
                      +++.++...
T Consensus        77 ~~a~~~~~~   85 (92)
T 2dgt_A           77 QLSTSRLRT   85 (92)
T ss_dssp             EESSCCCSC
T ss_pred             EEccCCCCC
Confidence            999887553

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.58  E-value=5.1e-15  Score=127.13  Aligned_cols=83  Identities=19%  Similarity=0.314  Sum_probs=75.6

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      .....++|||+|||+++++++|+++|+.||.|++|.|+.++ +++++|||||+|.+.++|.+|++.|++..+.  ++.|+
T Consensus        84 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~--Gr~l~  160 (177)
T 2f3j_A           84 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLD--GRPMD  160 (177)
T ss_dssp             SCTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCS--SSBCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEEC--CEEEE
Confidence            34567899999999999999999999999999999999998 8999999999999999999999999999885  47788


Q ss_pred             cccccc
Q 013141          191 LNWATF  196 (449)
Q Consensus       191 ~~~~~~  196 (449)
                      |.|+..
T Consensus       161 V~~a~~  166 (177)
T 2f3j_A          161 IQLVAS  166 (177)
T ss_dssp             EEEESS
T ss_pred             EEEecC
Confidence            887753

>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=99.58  E-value=1.1e-14  Score=109.45  Aligned_cols=77  Identities=17%  Similarity=0.365  Sum_probs=70.6

Q ss_pred             ccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh-CCceecCcceE
Q 013141          204 EACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEM-NGVYCSSRPMR  282 (449)
Q Consensus       204 ~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l-~g~~~~g~~i~  282 (449)
                      .....++|||+|||.++++++|+++|+ .||.|..+.++++      +|+|||+|.+.++|.+|++.| ++..+.|+.|+
T Consensus         8 ~~~~~~~l~V~~l~~~~t~~~l~~~f~-~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~   80 (85)
T 2ytc_A            8 EDKTITTLYVGGLGDTITETDLRNHFY-QFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLN   80 (85)
T ss_dssp             SCSSCCCEEEECCTTTSCHHHHHHHHH-TTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTEECC
T ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHH-hCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEE
Confidence            345678999999999999999999995 9999999999864      789999999999999999989 99999999999


Q ss_pred             EeecC
Q 013141          283 IDVAT  287 (449)
Q Consensus       283 v~~~~  287 (449)
                      |++++
T Consensus        81 v~~ak   85 (85)
T 2ytc_A           81 VKWGR   85 (85)
T ss_dssp             EEECC
T ss_pred             EEecC
Confidence            99874

>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=99.58  E-value=9.2e-15  Score=115.36  Aligned_cols=81  Identities=22%  Similarity=0.467  Sum_probs=74.7

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEe
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRID  284 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  284 (449)
                      ....++|||+|||.++++++|+++|+ .||.|..|.++++      +|||||+|.+.++|.+|++.|++..|.|+.|+|.
T Consensus        22 ~~~~~~l~V~nl~~~~t~~~l~~~F~-~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   94 (109)
T 1x4g_A           22 SPKNCTVYCGGIASGLTDQLMRQTFS-PFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCY   94 (109)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHH-HHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHH-hcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            45678999999999999999999995 9999999999876      7899999999999999999999999999999999


Q ss_pred             ecCCCCCC
Q 013141          285 VATPKKAS  292 (449)
Q Consensus       285 ~~~~~~~~  292 (449)
                      ++.++...
T Consensus        95 ~a~~~~~~  102 (109)
T 1x4g_A           95 WGKESPDM  102 (109)
T ss_dssp             CCCCCCSS
T ss_pred             ecCCCCCC
Confidence            99887653

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.58  E-value=9.3e-16  Score=119.60  Aligned_cols=81  Identities=32%  Similarity=0.532  Sum_probs=70.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccc
Q 013141          112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRL  191 (449)
Q Consensus       112 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~  191 (449)
                      ....++|||+|||+++++++|+++|+.||.|.+|.++.++ +++++|||||+|.+.++|++|++  ++..+.  ++.+.+
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~--g~~l~v   80 (102)
T 2xs2_A            6 KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQINFH--GKKLKL   80 (102)
T ss_dssp             EEEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT--CCCEET--TEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh--CCCeEC--CEEEEE
Confidence            3467899999999999999999999999999999999998 89999999999999999999997  666664  456666


Q ss_pred             cccccC
Q 013141          192 NWATFS  197 (449)
Q Consensus       192 ~~~~~~  197 (449)
                      .++...
T Consensus        81 ~~a~~~   86 (102)
T 2xs2_A           81 GPAIRK   86 (102)
T ss_dssp             EEEEEC
T ss_pred             EECCcC
Confidence            666533

>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=99.58  E-value=2.5e-15  Score=119.91  Aligned_cols=87  Identities=23%  Similarity=0.405  Sum_probs=75.0

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEe
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRID  284 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  284 (449)
                      ..+.++|||+|||.++|+++|+++|+ .||.|..+.+..+..++.++|||||+|.+.++|.+|++.|++..|.|+.|+|.
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~-~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~  100 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFA-RFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIE  100 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTH-HHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHH-HhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            45678999999999999999999995 99999544333332378899999999999999999999999999999999999


Q ss_pred             ecCCCCCC
Q 013141          285 VATPKKAS  292 (449)
Q Consensus       285 ~~~~~~~~  292 (449)
                      ++.++...
T Consensus       101 ~a~~~~~~  108 (115)
T 2cpx_A          101 FGKNKKQR  108 (115)
T ss_dssp             ECCCCSCC
T ss_pred             EccCCCCC
Confidence            99887654

>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=99.58  E-value=3.9e-15  Score=112.42  Aligned_cols=71  Identities=20%  Similarity=0.453  Sum_probs=68.0

Q ss_pred             CCcEEEEcCCCCCCCHhHHHhhcccc----C-------ceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEE
Q 013141          326 NNATIFVGALDSDVSDEDLREPFSQF----G-------EILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVR  394 (449)
Q Consensus       326 ~~~~l~V~nlp~~~t~~~L~~~f~~~----G-------~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~  394 (449)
                      ..++|||+|||+++++++|+++|+.|    |       .|.++.+.+++++|||+|.+.++|.+|+ .||+..|.|+.|+
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~kg~afV~f~~~~~a~~A~-~l~g~~~~g~~l~   83 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLK   83 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSSSSEEEEEESSHHHHHHHG-GGTTCEETTEECE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCCCcEEEEEcCCHHHHHHHH-hcCCCEECCeEEE
Confidence            46899999999999999999999999    8       9999999999999999999999999999 9999999999999


Q ss_pred             EEe
Q 013141          395 LSW  397 (449)
Q Consensus       395 v~~  397 (449)
                      |+.
T Consensus        84 V~r   86 (87)
T 2hzc_A           84 IRR   86 (87)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            973

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.58  E-value=8e-15  Score=112.84  Aligned_cols=77  Identities=16%  Similarity=0.310  Sum_probs=67.6

Q ss_pred             CCCCceEEEcCCCC-CCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          112 NDETKTIWIGDLFH-WMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       112 ~~~~~~l~v~nLp~-~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      ..+.++|||+|||+ ++++++|+++|+.||.|.+|.+.        +|||||+|.+.++|.+|++.|++..+.  ++.++
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~--g~~l~   76 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNF--GKKLI   76 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCB--TTTBC
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeC--CcEEE
Confidence            45789999999998 99999999999999999999984        579999999999999999999999985  57778


Q ss_pred             ccccccCC
Q 013141          191 LNWATFSG  198 (449)
Q Consensus       191 ~~~~~~~~  198 (449)
                      |.++....
T Consensus        77 V~~a~~~~   84 (96)
T 2kvi_A           77 LEVSSSNA   84 (96)
T ss_dssp             EEEEECCC
T ss_pred             EEEcCcCC
Confidence            88876543

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.57  E-value=1.1e-14  Score=114.52  Aligned_cols=80  Identities=24%  Similarity=0.481  Sum_probs=72.3

Q ss_pred             cccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceE
Q 013141          203 TEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMR  282 (449)
Q Consensus       203 ~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  282 (449)
                      ......++|||+|||.++++++|+++|+ .||.|..+.++        +|||||+|.+.++|++|++.|++..+.|+.|+
T Consensus        26 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~-~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~   96 (108)
T 2jvo_A           26 EGELSNTRLFVRPFPLDVQESELNEIFG-PFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLE   96 (108)
T ss_dssp             --CCSCSEEEECSSCTTCCHHHHHHHHT-TTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHH-hcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEE
Confidence            3456678999999999999999999995 99999999987        68999999999999999999999999999999


Q ss_pred             EeecCCCCC
Q 013141          283 IDVATPKKA  291 (449)
Q Consensus       283 v~~~~~~~~  291 (449)
                      |.++.+...
T Consensus        97 V~~a~~~~~  105 (108)
T 2jvo_A           97 VVYSKLPAK  105 (108)
T ss_dssp             EESCSCCC-
T ss_pred             EEEecCCCC
Confidence            999988654

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.57  E-value=1.4e-14  Score=110.92  Aligned_cols=78  Identities=21%  Similarity=0.296  Sum_probs=66.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccc
Q 013141          112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRL  191 (449)
Q Consensus       112 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~  191 (449)
                      ....++|||+|||+++++++|+++|+.||.|.+|  +.++.+++   ||||+|.+.++|.+|++ |++..+.+  +.|+|
T Consensus         5 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g--~~l~V   76 (94)
T 2e5g_A            5 SSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGG--HRLRV   76 (94)
T ss_dssp             CTTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETT--EECCC
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECC--EEEEE
Confidence            3467899999999999999999999999999987  56655555   99999999999999998 99999854  66777


Q ss_pred             cccccC
Q 013141          192 NWATFS  197 (449)
Q Consensus       192 ~~~~~~  197 (449)
                      .++...
T Consensus        77 ~~a~~~   82 (94)
T 2e5g_A           77 RPREQK   82 (94)
T ss_dssp             BCSCCS
T ss_pred             EECCcC
Confidence            776544

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.57  E-value=2.5e-14  Score=110.71  Aligned_cols=80  Identities=23%  Similarity=0.471  Sum_probs=72.2

Q ss_pred             cccCCCceEEEcCCCCCCCHHHHHHHHhhhC--CCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcc
Q 013141          203 TEACSDLSIFVGDLAPDVTDSILQETFSSKY--PSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRP  280 (449)
Q Consensus       203 ~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~--g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~  280 (449)
                      ....+.++|||+|||+++|+++|+++|+ .|  |.|..+.+.        +|||||+|.+.++|.+|++.|++..|.|+.
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~-~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   80 (99)
T 2cpd_A           10 DTMSSVKILYVRNLMLSTSEEMIEKEFN-NIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSP   80 (99)
T ss_dssp             SCSSCCCEEEEESCCTTCCHHHHHHHHH-TTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEE
T ss_pred             cccCCcCEEEEeCCCCCCCHHHHHHHHH-hcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcE
Confidence            3445678999999999999999999995 99  999988764        569999999999999999999999999999


Q ss_pred             eEEeecCCCCC
Q 013141          281 MRIDVATPKKA  291 (449)
Q Consensus       281 i~v~~~~~~~~  291 (449)
                      |+|.++.++..
T Consensus        81 l~v~~a~~~~~   91 (99)
T 2cpd_A           81 IEVTLAKPVDK   91 (99)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEEECCCCCC
Confidence            99999988754

>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=99.57  E-value=4.2e-15  Score=112.42  Aligned_cols=77  Identities=30%  Similarity=0.500  Sum_probs=65.9

Q ss_pred             CCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC-CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCCCC
Q 013141          326 NNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNK  404 (449)
Q Consensus       326 ~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~-~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~~~  404 (449)
                      ..++|||+|||.++++++|+++|+.||.|.+|.|+++ +++|||+|.+.++|++|+.  ....+.++.|+|.|++++...
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~~~~--~~~~~~g~~l~v~~a~~~~~~   81 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEPKHNS   81 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCCCCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecCCCCEEEEEECCHHHHHHHhc--CCceeCCEEEEEEecCCCCCC
Confidence            4689999999999999999999999999999999865 8999999999999975432  123458999999999886543

>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=99.57  E-value=1.8e-14  Score=110.91  Aligned_cols=78  Identities=17%  Similarity=0.363  Sum_probs=70.7

Q ss_pred             cccCCCceEEEcCCCC-CCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcce
Q 013141          203 TEACSDLSIFVGDLAP-DVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPM  281 (449)
Q Consensus       203 ~~~~~~~~l~v~~lp~-~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i  281 (449)
                      ....+.++|||+|||. ++++++|+++|+ .||.|..+.+.        +|||||+|.+.++|.+|++.|++..+.|+.|
T Consensus        17 ~~~~~~~~l~V~nLp~~~~t~~~L~~~F~-~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l   87 (97)
T 2xnq_A           17 RGSHMKSRLFIGNLPLKNVSKEDLFRIFS-PYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKL   87 (97)
T ss_dssp             --CCTTCEEEEESCCSSCCCHHHHHHHHG-GGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEEC
T ss_pred             CCCCCCCEEEEeCCCcccCCHHHHHHHHH-hcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            3455778999999998 999999999995 99999999883        7899999999999999999999999999999


Q ss_pred             EEeecCCC
Q 013141          282 RIDVATPK  289 (449)
Q Consensus       282 ~v~~~~~~  289 (449)
                      +|+++..+
T Consensus        88 ~V~~a~~~   95 (97)
T 2xnq_A           88 ILEVSSSN   95 (97)
T ss_dssp             EEEECCCC
T ss_pred             EEEecCCC
Confidence            99998765

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.57  E-value=2.5e-14  Score=105.99  Aligned_cols=77  Identities=14%  Similarity=0.193  Sum_probs=65.9

Q ss_pred             CCCce-EEEcCCCCCCCHHH----HHHHhhcc-CCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCC
Q 013141          113 DETKT-IWIGDLFHWMDETF----LHNCFSHT-GQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTD  186 (449)
Q Consensus       113 ~~~~~-l~v~nLp~~~t~~~----l~~~f~~~-G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~  186 (449)
                      .++.| |||+|||+++++++    |+++|++| |.|.+|       ++   |+|||+|.+.++|.+|++.|++..+  .+
T Consensus         6 ~p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l--~g   73 (96)
T 2diu_A            6 SGCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDV--FG   73 (96)
T ss_dssp             CCSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCS--SS
T ss_pred             CCcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCcc--CC
Confidence            34556 99999999999988    55899999 599988       23   8999999999999999999999999  56


Q ss_pred             CcccccccccCCCCC
Q 013141          187 QPFRLNWATFSGSDR  201 (449)
Q Consensus       187 ~~~~~~~~~~~~~~~  201 (449)
                      ++|++.+++...+..
T Consensus        74 r~i~v~~A~~~sd~~   88 (96)
T 2diu_A           74 NRIIVSFTPKNRELC   88 (96)
T ss_dssp             SCCEEESSCCSCCCC
T ss_pred             ceEEEEecCCCccee
Confidence            889999988665443

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus}

Probab=99.56  E-value=1.2e-14  Score=109.88  Aligned_cols=77  Identities=31%  Similarity=0.501  Sum_probs=62.8

Q ss_pred             CCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeC-CCcEEEEEecCHHHHHHHHHHhcCCee--CCeEEEEEecC
Q 013141          323 GESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV-GKGCGFVQFANRKDAEVALQKLQGTAI--GKQTVRLSWGR  399 (449)
Q Consensus       323 ~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~-~~g~afV~F~~~~~A~~A~~~l~g~~~--~g~~l~v~~~~  399 (449)
                      .....++|||+|||+++|+++|+++|++||.|.+|.|++ ++|+|||+|.+.++|.+    |++..+  .|+.|.|.+++
T Consensus         7 ~~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~~a~   82 (89)
T 3d2w_A            7 HHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQS----LCGEDLIIKGISVHISNAE   82 (89)
T ss_dssp             ----CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSSCCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEEECC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeCCCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEEEcC
Confidence            345678999999999999999999999999999999987 48999999999999883    566654  59999999998


Q ss_pred             CCCC
Q 013141          400 NPGN  403 (449)
Q Consensus       400 ~~~~  403 (449)
                      ++..
T Consensus        83 ~k~~   86 (89)
T 3d2w_A           83 PKHN   86 (89)
T ss_dssp             ----
T ss_pred             CCCc
Confidence            7643

>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=99.56  E-value=2.5e-15  Score=118.15  Aligned_cols=84  Identities=15%  Similarity=0.242  Sum_probs=76.7

Q ss_pred             ccCCCceEEEcCCCCCCCHHHHHHHHhhhCCC---eeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcc
Q 013141          204 EACSDLSIFVGDLAPDVTDSILQETFSSKYPS---VKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRP  280 (449)
Q Consensus       204 ~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~---v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~  280 (449)
                      .....++|||+|||+++|+++|+++|+ .||.   |..|.+++++. ++++|||||+|.+.++|++||+ +++..++|+.
T Consensus         7 ~~~~~~~l~V~nLp~~~te~~l~~~F~-~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~   83 (107)
T 2lmi_A            7 EVDDVFLIRAQGLPWSCTMEDVLNFFS-DCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRMYMGQRY   83 (107)
T ss_dssp             CCSSCCEEEEECCCSSCCSHHHHHHTT-TSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSC
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHH-hcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcceeCCeE
Confidence            345678999999999999999999995 9888   89999999977 9999999999999999999998 9999999999


Q ss_pred             eEEeecCCCC
Q 013141          281 MRIDVATPKK  290 (449)
Q Consensus       281 i~v~~~~~~~  290 (449)
                      |+|.++.++.
T Consensus        84 i~V~~a~~~~   93 (107)
T 2lmi_A           84 VEVYEINNED   93 (107)
T ss_dssp             CCCEECCHHH
T ss_pred             EEEEECCHHH
Confidence            9999987643

>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=99.56  E-value=5.8e-15  Score=115.55  Aligned_cols=77  Identities=16%  Similarity=0.258  Sum_probs=66.2

Q ss_pred             CCCceEEE--cCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCC---CCCCC
Q 013141          113 DETKTIWI--GDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLM---PNTDQ  187 (449)
Q Consensus       113 ~~~~~l~v--~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~---~~~~~  187 (449)
                      .++++|||  +||++++++++|+++|++||.|.+|.++.+      +|||||+|.+.++|++|++.||+..+   .+.++
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~------rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~   96 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKI   96 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEE
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHhCCCEEccccCCCc
Confidence            46789999  779999999999999999999999987643      58999999999999999999999865   33466


Q ss_pred             cccccccc
Q 013141          188 PFRLNWAT  195 (449)
Q Consensus       188 ~~~~~~~~  195 (449)
                      ++.+.++.
T Consensus        97 ~l~v~~a~  104 (114)
T 2cq2_A           97 TLYLNFVE  104 (114)
T ss_dssp             ECEEEEES
T ss_pred             EEEEEecc
Confidence            77776665

>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=99.56  E-value=2.3e-14  Score=113.22  Aligned_cols=78  Identities=31%  Similarity=0.529  Sum_probs=71.2

Q ss_pred             cCCCceEEEcCCCCC-CCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEE
Q 013141          205 ACSDLSIFVGDLAPD-VTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRI  283 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~-~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  283 (449)
                      ....++|||+|||++ +++++|+++|+ .||.|..+.+        ++|||||+|.+.++|++|++.|++..|.|+.|+|
T Consensus        24 ~~~~~~l~V~nl~~~~~t~~~l~~~F~-~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   94 (110)
T 1wf1_A           24 KSINSRVFIGNLNTALVKKSDVETIFS-KYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDI   94 (110)
T ss_dssp             TTCSSEEEECSCCCSSCCHHHHHHHHG-GGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCE
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHH-hCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEE
Confidence            345689999999999 99999999995 9999999988        4789999999999999999999999999999999


Q ss_pred             eecCCCCC
Q 013141          284 DVATPKKA  291 (449)
Q Consensus       284 ~~~~~~~~  291 (449)
                      +++.....
T Consensus        95 ~~a~~~~~  102 (110)
T 1wf1_A           95 NMAGEPKP  102 (110)
T ss_dssp             EESCCCCS
T ss_pred             EECCCCCC
Confidence            99986543

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.56  E-value=5.9e-15  Score=118.20  Aligned_cols=81  Identities=17%  Similarity=0.189  Sum_probs=73.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCe----eEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcce
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSV----KGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPM  281 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v----~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i  281 (449)
                      ....+|||+|||+++|+++|+++|+ .||.|    ..|.|+++ .+++++|||||+|.+.++|++||+. ++..|.++.|
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~-~~g~v~g~v~~v~i~~d-~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i   97 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFG-QHCPITGGKEGILFVTY-PDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYI   97 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHH-TTSCCTTGGGGEEEEEC-TTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHH-hhCCccCCcceEEEEEC-CCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEE
Confidence            4567999999999999999999995 99875    68999998 5799999999999999999999975 9999999999


Q ss_pred             EEeecCCC
Q 013141          282 RIDVATPK  289 (449)
Q Consensus       282 ~v~~~~~~  289 (449)
                      +|..+..+
T Consensus        98 ~V~~a~~~  105 (123)
T 2dha_A           98 ELFRSTAA  105 (123)
T ss_dssp             CCEEECHH
T ss_pred             EEEECCHH
Confidence            99988654

>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=99.55  E-value=7.2e-15  Score=113.39  Aligned_cols=83  Identities=22%  Similarity=0.404  Sum_probs=75.2

Q ss_pred             cCCCceEEEcCCCCCCCHHHHH----HHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcc
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQ----ETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRP  280 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~----~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~  280 (449)
                      ..+.++|||+|||.++++++|+    ++|+ .||.|..+.+.+   ++.++|||||+|.+.++|.+|++.|++..+.|+.
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~-~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   80 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFS-RFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKP   80 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHG-GGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHH-hCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcE
Confidence            3567899999999999999999    9995 999999998874   4678899999999999999999999999999999


Q ss_pred             eEEeecCCCCC
Q 013141          281 MRIDVATPKKA  291 (449)
Q Consensus       281 i~v~~~~~~~~  291 (449)
                      |+|+++.++..
T Consensus        81 l~v~~a~~~~~   91 (97)
T 1nu4_A           81 MRIQYAKTDSD   91 (97)
T ss_dssp             CEEEECSSCCT
T ss_pred             EEEEEccCCCc
Confidence            99999988654

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.55  E-value=1.4e-14  Score=111.50  Aligned_cols=79  Identities=14%  Similarity=0.209  Sum_probs=69.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCcEEE-EEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNV-KVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRL  191 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v-~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~  191 (449)
                      ...++|||+|||+++++++|+++|+.||.|.+| .++.++.++    .|||+|.+.++|.+|++.|++..+.  ++.|+|
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~----~afV~f~~~~~a~~Ai~~l~g~~~~--g~~l~V   86 (96)
T 2e44_A           13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETA----VVNVTYSSKDQARQALDKLNGFQLE--NFTLKV   86 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSE----EEEEEESSHHHHHHHHHHHTTCBCS--SCBCEE
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCC----EEEEEECCHHHHHHHHHHhCCCEEC--CcEEEE
Confidence            457899999999999999999999999999999 488776543    4999999999999999999999995  577888


Q ss_pred             cccccC
Q 013141          192 NWATFS  197 (449)
Q Consensus       192 ~~~~~~  197 (449)
                      .++.+.
T Consensus        87 ~~a~~~   92 (96)
T 2e44_A           87 AYIPDE   92 (96)
T ss_dssp             EECCCC
T ss_pred             EEcCcc
Confidence            887654

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.55  E-value=8e-15  Score=112.90  Aligned_cols=81  Identities=19%  Similarity=0.373  Sum_probs=72.6

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEe
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRID  284 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  284 (449)
                      ..+.++|||+|||.++++++|+++|+ .||.|..+     ..++.++|||||+|.+.++|.+|++.|++..+.|+.|+|.
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~-~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   86 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFE-DALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLY   86 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHC-SEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHh-hCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            34678999999999999999999995 89887766     2568899999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 013141          285 VATPKKA  291 (449)
Q Consensus       285 ~~~~~~~  291 (449)
                      ++.++..
T Consensus        87 ~a~~~~~   93 (96)
T 1fjc_A           87 YTGEKGG   93 (96)
T ss_dssp             ECSSSCC
T ss_pred             EcCCCCC
Confidence            9987654

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.55  E-value=7.4e-15  Score=116.85  Aligned_cols=64  Identities=19%  Similarity=0.397  Sum_probs=60.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCC---CCcccEEEEEEccHHHHHHHHHHh
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQT---GQSEGYGFVEFYSRAAAEKVLQSY  177 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~---g~~~g~afV~f~~~~~A~~Al~~l  177 (449)
                      ...++|||+|||+++++++|+++|++||.|. +.++.++.+   |+++|||||+|.+.++|++||+.|
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~   72 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDAC   72 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHS
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhh
Confidence            5679999999999999999999999999999 888888777   799999999999999999999988

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.55  E-value=1.3e-14  Score=124.58  Aligned_cols=85  Identities=28%  Similarity=0.436  Sum_probs=79.2

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEe
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRID  284 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  284 (449)
                      ....++|||+|||+++++++|+++|+ .||.|..|.++.+. ++.++|||||+|.+.++|.+|++.|++..|.|+.|+|+
T Consensus        85 ~~~~~~l~V~nLp~~~te~~L~~~F~-~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~  162 (177)
T 2f3j_A           85 VETGAKLLVSNLDFGVSDADIQELFA-EFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ  162 (177)
T ss_dssp             CTTCEEEEEECCCSCCCHHHHHHHHH-HTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHH-hcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            45678999999999999999999995 99999999999997 89999999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 013141          285 VATPKKA  291 (449)
Q Consensus       285 ~~~~~~~  291 (449)
                      ++.....
T Consensus       163 ~a~~~~~  169 (177)
T 2f3j_A          163 LVASQID  169 (177)
T ss_dssp             EESSGGG
T ss_pred             EecCCCC
Confidence            9977543

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.55  E-value=2.2e-14  Score=108.94  Aligned_cols=78  Identities=22%  Similarity=0.428  Sum_probs=71.8

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEe
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRID  284 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  284 (449)
                      ....++|||+|||.++|+++|+++|+ .||.|..+.+++        +||||+|.+.++|++|++.|++..+.|+.|+|+
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~-~~G~v~~~~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   76 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFE-RRGRVIECDVVK--------DYAFVHMEKEADAKAAIAQLNGKEVKGKRINVE   76 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHH-HHSCEEEEEECS--------SCEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHH-cCCCEEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            45678999999999999999999995 999999999973        399999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 013141          285 VATPKKA  291 (449)
Q Consensus       285 ~~~~~~~  291 (449)
                      ++.+...
T Consensus        77 ~a~~~~~   83 (90)
T 2dnp_A           77 LSTKGQK   83 (90)
T ss_dssp             ESCCCCC
T ss_pred             ECCCCCC
Confidence            9988754

>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=99.55  E-value=4.7e-15  Score=112.20  Aligned_cols=77  Identities=18%  Similarity=0.268  Sum_probs=63.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccc
Q 013141          112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRL  191 (449)
Q Consensus       112 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~  191 (449)
                      .....+|||+|||+++|+++|+++|++||.|.+|+++++     ++|||||+|.+.++|++    +++..+.+.++.+.+
T Consensus         8 ~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v   78 (89)
T 3d2w_A            8 HHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS----LCGEDLIIKGISVHI   78 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHH----HTTCEEEETTEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHH----HcCCCcccCCEEEEE
Confidence            457889999999999999999999999999999999874     67999999999999983    466666667788888


Q ss_pred             cccccC
Q 013141          192 NWATFS  197 (449)
Q Consensus       192 ~~~~~~  197 (449)
                      .++.+.
T Consensus        79 ~~a~~k   84 (89)
T 3d2w_A           79 SNAEPK   84 (89)
T ss_dssp             EECC--
T ss_pred             EEcCCC
Confidence            887643

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.55  E-value=2.6e-15  Score=117.79  Aligned_cols=75  Identities=12%  Similarity=0.163  Sum_probs=64.6

Q ss_pred             ceEEEcCC----CCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEcc----HHH----HHHHHH--HhcCCC
Q 013141          116 KTIWIGDL----FHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYS----RAA----AEKVLQ--SYSGSL  181 (449)
Q Consensus       116 ~~l~v~nL----p~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~----~~~----A~~Al~--~l~~~~  181 (449)
                      ..|||+||    |+.+++.+|+++|+.||+|.+|.++.|+.||+++|||||+|.+    +++    |.+|+.  .+++..
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            68999999    9999999999999999999999999999999999999999996    333    888887  678888


Q ss_pred             CCCCCCccccc
Q 013141          182 MPNTDQPFRLN  192 (449)
Q Consensus       182 ~~~~~~~~~~~  192 (449)
                      +.+  +.++|.
T Consensus        83 I~G--r~irV~   91 (136)
T 2j8a_A           83 IMG--FKFEVI   91 (136)
T ss_dssp             ETT--EEEEEE
T ss_pred             ecC--cEEEEE
Confidence            855  444443

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.55  E-value=5.5e-15  Score=131.57  Aligned_cols=82  Identities=24%  Similarity=0.534  Sum_probs=72.6

Q ss_pred             CCCCcEEEEcCCCCCC---------CHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCee------
Q 013141          324 ESNNATIFVGALDSDV---------SDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAI------  388 (449)
Q Consensus       324 ~~~~~~l~V~nlp~~~---------t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~------  388 (449)
                      ....++|||+||+..+         ++++|+++|++||.|.+|+|+.++|+|||+|.+.++|..|++.|+|..|      
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~kG~AFV~F~~~~~Ae~A~~am~g~~l~~~~~~  210 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSDK  210 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGGGTEEEEEESSHHHHHHHHHHHTTCCCCCTTST
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECCCCEEEEEeCCHHHHHHHHHHhCCCEEeccccc
Confidence            3467899999999998         7999999999999999999999999999999999999999999999999      


Q ss_pred             ------CCeEEEEEecCCCCCCC
Q 013141          389 ------GKQTVRLSWGRNPGNKQ  405 (449)
Q Consensus       389 ------~g~~l~v~~~~~~~~~~  405 (449)
                            .|+.|.|.|++...+..
T Consensus       211 e~~~~~~gr~L~V~wA~~~pnp~  233 (240)
T 3u1l_A          211 EWDDRREGTGLLVKWANEDPDPA  233 (240)
T ss_dssp             TGGGGGGSCCCEEEECC------
T ss_pred             cccccCCCCEEEEEEccCCCCHH
Confidence                  89999999999866543

>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=99.54  E-value=7.4e-15  Score=117.85  Aligned_cols=81  Identities=17%  Similarity=0.269  Sum_probs=72.5

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhhCCCee--EEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceE
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQETFSSKYPSVK--GAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMR  282 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~--~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  282 (449)
                      ....++|||+|||+++|+++|+++|+ .| .|.  +|+|++++. ++++|||||+|.+.++|++||+ +++..|.|+.|+
T Consensus        39 ~~~~~~lfVgnLp~~~te~dL~~~F~-~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~-~~~~~l~gR~I~  114 (126)
T 2hgm_A           39 SANDGFVRLRGLPFGCTKEEIVQFFS-GL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALG-KHKERIGHRYIE  114 (126)
T ss_dssp             SSSCCEEEEECCCTTCCHHHHHHHTT-TS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHT-TTTCCBTTBCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHh-cC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHH-HCCCEECCEEEE
Confidence            34567999999999999999999995 89 677  899999977 9999999999999999999997 577999999999


Q ss_pred             EeecCCC
Q 013141          283 IDVATPK  289 (449)
Q Consensus       283 v~~~~~~  289 (449)
                      |..+..+
T Consensus       115 V~~a~~~  121 (126)
T 2hgm_A          115 VFKSSQE  121 (126)
T ss_dssp             CEEECHH
T ss_pred             EEECCHH
Confidence            9888654

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.54  E-value=6.6e-15  Score=114.72  Aligned_cols=82  Identities=27%  Similarity=0.524  Sum_probs=75.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEee
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV  285 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  285 (449)
                      ...++|||+|||.++++++|+++|+ .||.|..+.++.+. ++.++|||||+|.+.++|++|++  ++..+.|+.|.|.+
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~-~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~   82 (102)
T 2xs2_A            7 IMPNTVFVGGIDVRMDETEIRSFFA-RYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGP   82 (102)
T ss_dssp             EEEEEEEEECCCTTCCHHHHHHHHG-GGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHH-hCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEE
Confidence            3567999999999999999999995 99999999999997 89999999999999999999997  99999999999999


Q ss_pred             cCCCCC
Q 013141          286 ATPKKA  291 (449)
Q Consensus       286 ~~~~~~  291 (449)
                      +..+..
T Consensus        83 a~~~~~   88 (102)
T 2xs2_A           83 AIRKQN   88 (102)
T ss_dssp             EEECC-
T ss_pred             CCcCcc
Confidence            876643

>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=1.6e-14  Score=110.48  Aligned_cols=79  Identities=28%  Similarity=0.500  Sum_probs=70.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCC-eeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCC-ceecCcceEE
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPS-VKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNG-VYCSSRPMRI  283 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~-v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g-~~~~g~~i~v  283 (449)
                      ...++|||+|||.++|+++|+++|+ .||. |..+.+.       ++|||||+|.+.++|++|++.||+ ..+.|+.|+|
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~-~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v   77 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFG-DRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEV   77 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHH-HTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHH-HcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEE
Confidence            4567999999999999999999995 9999 6666553       478999999999999999999999 9999999999


Q ss_pred             eecCCCCCC
Q 013141          284 DVATPKKAS  292 (449)
Q Consensus       284 ~~~~~~~~~  292 (449)
                      +++.++..+
T Consensus        78 ~~a~~~~~~   86 (93)
T 2cqh_A           78 DYSVSKKLR   86 (93)
T ss_dssp             EECCCCCCC
T ss_pred             EEccCcccc
Confidence            999887554

>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=99.54  E-value=1.5e-14  Score=114.37  Aligned_cols=77  Identities=19%  Similarity=0.182  Sum_probs=70.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeec
Q 013141          207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVA  286 (449)
Q Consensus       207 ~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~  286 (449)
                      ..++|||+|||+++++++|+++|+ .||.|..|.+++      +++||||+|.+.++|++|++.||+..+.|+.|.|+|+
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~-~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   81 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFS-RFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWA   81 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHH-TTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHH-hcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            467999999999999999999995 999999998864      4789999999999999999999999999999999999


Q ss_pred             CCCC
Q 013141          287 TPKK  290 (449)
Q Consensus       287 ~~~~  290 (449)
                      ....
T Consensus        82 ~~~~   85 (111)
T 1whx_A           82 PIGV   85 (111)
T ss_dssp             ETTT
T ss_pred             CCCc
Confidence            7654

>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=99.54  E-value=1.5e-14  Score=120.20  Aligned_cols=81  Identities=25%  Similarity=0.405  Sum_probs=70.9

Q ss_pred             CCCCcEEEEcCCCCCCCHhHHHhhccccCceEE--------EEEe---CCCcEEEEEecCHHHHHHHHHHhcCCeeCCeE
Q 013141          324 ESNNATIFVGALDSDVSDEDLREPFSQFGEILS--------VKIP---VGKGCGFVQFANRKDAEVALQKLQGTAIGKQT  392 (449)
Q Consensus       324 ~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~--------v~i~---~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~  392 (449)
                      ....++|||+|||+.+++++|+++|+.||.|..        +.+.   ..+|+|||+|.+.++|.+|++.|||..|.|+.
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~  121 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKP  121 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcE
Confidence            445789999999999999999999999998876        3333   35799999999999999999999999999999


Q ss_pred             EEEEecCCCCCC
Q 013141          393 VRLSWGRNPGNK  404 (449)
Q Consensus       393 l~v~~~~~~~~~  404 (449)
                      |+|.|++....+
T Consensus       122 l~V~~a~~~~~~  133 (143)
T 3egn_A          122 MVVQFARSARPK  133 (143)
T ss_dssp             CEEEECCCSCC-
T ss_pred             EEEEECCCCCCc
Confidence            999999875443

>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=2.5e-14  Score=108.08  Aligned_cols=76  Identities=16%  Similarity=0.237  Sum_probs=69.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeec
Q 013141          207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVA  286 (449)
Q Consensus       207 ~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~  286 (449)
                      ..++|||+|||+++++++|+++|+ .| .|.++.+.      +++|||||+|.+.++|++|++.|++..+.|+.|+|+++
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~-~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a   75 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLK-DY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQ   75 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTC-SS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHh-hC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEc
Confidence            567999999999999999999995 89 99999884      56899999999999999999999999999999999998


Q ss_pred             CCCC
Q 013141          287 TPKK  290 (449)
Q Consensus       287 ~~~~  290 (449)
                      ....
T Consensus        76 ~~~~   79 (88)
T 1wg1_A           76 PTDA   79 (88)
T ss_dssp             CCCC
T ss_pred             CCCc
Confidence            6653

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.52  E-value=5.8e-14  Score=109.28  Aligned_cols=76  Identities=14%  Similarity=0.189  Sum_probs=67.6

Q ss_pred             CCCcEEEEcCCCC-----CCCHhHHHhhccccCceEEEEEeCC-------CcEEEEEecCHHHHHHHHHHhcCCeeCCeE
Q 013141          325 SNNATIFVGALDS-----DVSDEDLREPFSQFGEILSVKIPVG-------KGCGFVQFANRKDAEVALQKLQGTAIGKQT  392 (449)
Q Consensus       325 ~~~~~l~V~nlp~-----~~t~~~L~~~f~~~G~v~~v~i~~~-------~g~afV~F~~~~~A~~A~~~l~g~~~~g~~  392 (449)
                      ..+++|+|.||..     +.++++|+++|++||.|.+|.|+++       +|+|||+|.+.++|.+|++.|||+.|.|+.
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~   85 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRV   85 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcE
Confidence            4578999999963     2378999999999999999999752       689999999999999999999999999999


Q ss_pred             EEEEecCC
Q 013141          393 VRLSWGRN  400 (449)
Q Consensus       393 l~v~~~~~  400 (449)
                      |+|.|++.
T Consensus        86 i~v~~a~~   93 (105)
T 2pe8_A           86 VKACFYNL   93 (105)
T ss_dssp             CEEEECCH
T ss_pred             EEEEEcCH
Confidence            99999874

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.51  E-value=1.8e-13  Score=105.47  Aligned_cols=79  Identities=18%  Similarity=0.344  Sum_probs=71.2

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEe
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRID  284 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  284 (449)
                      ..+.++|||+||  ++|+++|+++|+ .||.|..|.+.      .++|||||+|.+.++|.+|++.|++..|.|+.|+|.
T Consensus        12 ~~~~~~l~V~n~--~~t~~~l~~~F~-~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~   82 (97)
T 1x5p_A           12 PRKGNTLYVYGE--DMTPTLLRGAFS-PFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVN   82 (97)
T ss_dssp             CCCCSEEEEECS--SCCHHHHHHHHT-TTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEE
T ss_pred             CCCCCEEEEcCC--CCCHHHHHHHHh-hCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            446789999996  899999999995 99999999884      458899999999999999999999999999999999


Q ss_pred             ecCCCCCC
Q 013141          285 VATPKKAS  292 (449)
Q Consensus       285 ~~~~~~~~  292 (449)
                      ++.++...
T Consensus        83 ~a~~~~~~   90 (97)
T 1x5p_A           83 IARKQPML   90 (97)
T ss_dssp             CCSSCCCC
T ss_pred             ECCCCCCC
Confidence            99887543

>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=99.50  E-value=2.2e-13  Score=107.79  Aligned_cols=81  Identities=20%  Similarity=0.304  Sum_probs=70.2

Q ss_pred             CCCCCcEEEEcCCCCCCC-----------HhHHHhhccccCceEEEEEeC--CCcEEEEEecCHHHHHHHHHHhcCCeeC
Q 013141          323 GESNNATIFVGALDSDVS-----------DEDLREPFSQFGEILSVKIPV--GKGCGFVQFANRKDAEVALQKLQGTAIG  389 (449)
Q Consensus       323 ~~~~~~~l~V~nlp~~~t-----------~~~L~~~f~~~G~v~~v~i~~--~~g~afV~F~~~~~A~~A~~~l~g~~~~  389 (449)
                      ....+++|+|.||....+           +++|+++|++||.|.+|.|..  .+|+|||+|.+.++|.+|++.|||..|.
T Consensus        11 ~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~   90 (112)
T 2dit_A           11 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFG   90 (112)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEET
T ss_pred             CCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEEecCCCCEEEEEEECCHHHHHHHHHHcCCCEEC
Confidence            445689999999954432           589999999999999997753  4799999999999999999999999999


Q ss_pred             CeEEEEEecCCCCC
Q 013141          390 KQTVRLSWGRNPGN  403 (449)
Q Consensus       390 g~~l~v~~~~~~~~  403 (449)
                      |+.|+|.|+++...
T Consensus        91 gr~l~v~~a~~~~~  104 (112)
T 2dit_A           91 GRQITAQAWDGTTD  104 (112)
T ss_dssp             TEECEEEECCSCCC
T ss_pred             CcEEEEEEeCCCCC
Confidence            99999999987543

>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=99.50  E-value=1.5e-14  Score=120.21  Aligned_cols=84  Identities=25%  Similarity=0.480  Sum_probs=73.6

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEE--------EEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGA--------KVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYC  276 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i--------~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~  276 (449)
                      ..++++|||+|||+++|+++|+++|+ .||.|..+        .+.   .++.++|||||+|.+.++|.+|++.||+..|
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~-~~G~i~~~~~~~~~di~~~---~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~  117 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFG-RYVDFSSETQRIMFDIRLM---KEGRMKGQAFIGLPNEKAAAKALKEANGYVL  117 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHG-GGCCTTCHHHHHHCEEEEE---EETTTEEEEEEECSSHHHHHHHHHHHTTBEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHH-HhCCcccccccceeeEEec---cCCCcccEEEEEeCCHHHHHHHHHHhCCCEe
Confidence            45678999999999999999999995 99998764        333   4588999999999999999999999999999


Q ss_pred             cCcceEEeecCCCCCC
Q 013141          277 SSRPMRIDVATPKKAS  292 (449)
Q Consensus       277 ~g~~i~v~~~~~~~~~  292 (449)
                      .|+.|.|.++.....+
T Consensus       118 ~g~~l~V~~a~~~~~~  133 (143)
T 3egn_A          118 FGKPMVVQFARSARPK  133 (143)
T ss_dssp             TTEECEEEECCCSCC-
T ss_pred             CCcEEEEEECCCCCCc
Confidence            9999999999876543

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.49  E-value=2.2e-13  Score=106.00  Aligned_cols=84  Identities=14%  Similarity=0.227  Sum_probs=73.5

Q ss_pred             cCCCceEEEcCCCC-----CCCHHHHHHHHhhhCCCeeEEEEeecCCC-CCcceEEEEEeCCHHHHHHHHHHhCCceecC
Q 013141          205 ACSDLSIFVGDLAP-----DVTDSILQETFSSKYPSVKGAKVIIDSNT-GRTKGYGFVRFGDENERSRAMTEMNGVYCSS  278 (449)
Q Consensus       205 ~~~~~~l~v~~lp~-----~~t~~~l~~~f~~~~g~v~~i~~~~~~~~-~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g  278 (449)
                      ..++++|+|.|+..     +-++++|+++|+ +||.|.++.+++++.+ ++++|++||+|.+.++|.+|++.|||+.+.|
T Consensus         5 ~~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~-~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~G   83 (105)
T 2pe8_A            5 KCPTKVVLLRNMVGAGEVDEDLEVETKEECE-KYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGG   83 (105)
T ss_dssp             GSCCSEEEEESSSCSCCC---CHHHHHHHGG-GGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCCEEEEEcCCChHHhhHHHHHHHHHHHH-hcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            35678999999962     237899999995 9999999999998654 6889999999999999999999999999999


Q ss_pred             cceEEeecCCC
Q 013141          279 RPMRIDVATPK  289 (449)
Q Consensus       279 ~~i~v~~~~~~  289 (449)
                      +.|.|.++...
T Consensus        84 r~i~v~~a~~~   94 (105)
T 2pe8_A           84 RVVKACFYNLD   94 (105)
T ss_dssp             EECEEEECCHH
T ss_pred             cEEEEEEcCHH
Confidence            99999998653

>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=99.48  E-value=6.3e-14  Score=111.54  Aligned_cols=77  Identities=23%  Similarity=0.323  Sum_probs=66.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcc-----
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRP-----  280 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~-----  280 (449)
                      ...++|||+|||+++++++|+++|. .||+|..+.++.+       |||||+|.+.++|++||+.||+..|.|+.     
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~-~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~   85 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMR-EAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAY   85 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHG-GGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCB
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHH-hcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEE
Confidence            3467999999999999999999995 9999999999765       79999999999999999999999999998     


Q ss_pred             eEEeecCCCC
Q 013141          281 MRIDVATPKK  290 (449)
Q Consensus       281 i~v~~~~~~~  290 (449)
                      |+|..+.+..
T Consensus        86 i~v~~~~~~~   95 (115)
T 3beg_B           86 IRVKVDGPRS   95 (115)
T ss_dssp             CEEEECC---
T ss_pred             EEeccCCCCC
Confidence            7777666543

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.47  E-value=9.3e-14  Score=110.43  Aligned_cols=78  Identities=17%  Similarity=0.304  Sum_probs=66.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCC---CCcceEEEEEeCCHHHHHHHHHHhCCceecCcceE
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNT---GRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMR  282 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  282 (449)
                      ...++|||+|||+++|+++|+++|+ .||.|. +.++.+..+   ++++|||||+|.+.++|++||+.|+  .++|+.+.
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~-~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~   81 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFR-RFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYL   81 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTT-TTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHH-hcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEE
Confidence            4568999999999999999999995 999999 888888776   7999999999999999999999883  35666666


Q ss_pred             EeecC
Q 013141          283 IDVAT  287 (449)
Q Consensus       283 v~~~~  287 (449)
                      +..+.
T Consensus        82 ~~~~~   86 (114)
T 2dnl_A           82 CVSSP   86 (114)
T ss_dssp             EECCS
T ss_pred             eccCC
Confidence            55443

>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=99.47  E-value=4.2e-14  Score=106.90  Aligned_cols=78  Identities=19%  Similarity=0.267  Sum_probs=65.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      ..+++|||+|||+++++++|+++|+.||.|.+|+++.+     ++|||||+|.+.++|++|    ++..+...++.+++.
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~----~~~~~~~~g~~l~v~   73 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSL----CGEDLIIKGISVHIS   73 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHT----TTCEEEETTEEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHH----hcCCceeCCEEEEEE
Confidence            46799999999999999999999999999999999865     579999999999999754    444555567888888


Q ss_pred             ccccCCC
Q 013141          193 WATFSGS  199 (449)
Q Consensus       193 ~~~~~~~  199 (449)
                      ++.....
T Consensus        74 ~a~~~~~   80 (88)
T 1wf0_A           74 NAEPKHN   80 (88)
T ss_dssp             CCCCCCC
T ss_pred             ecCCCCC
Confidence            8875543

>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=2e-13  Score=118.92  Aligned_cols=122  Identities=11%  Similarity=0.004  Sum_probs=88.2

Q ss_pred             cHHHHHHHHHHh--cCCCCCCCCCcccccccccCCCCC--ccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEE
Q 013141          166 SRAAAEKVLQSY--SGSLMPNTDQPFRLNWATFSGSDR--RTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKV  241 (449)
Q Consensus       166 ~~~~A~~Al~~l--~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~  241 (449)
                      +.+.+..|++..  ....+......++.....+.+...  .......++|||+|||+++|+++|+++|+ .||.|..|++
T Consensus        63 d~~~I~~Al~~S~~~~lev~ed~~~vrR~~~~p~p~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~-~~G~v~~v~i  141 (193)
T 2voo_A           63 DFNVIVEALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLE-DKGQVLNIQM  141 (193)
T ss_dssp             CHHHHHHHHHTCSSCCEEECTTSSEEEECTTSCCCCCCHHHHHHHHHTEEEEECCCTTCCHHHHHHHHT-TSCCEEEEEE
T ss_pred             CHHHHHHHHhhcccceEEEecccceEEecccCCCcccchhhhhccccCEEEecCCCCcCCHHHHHHHHh-cCCCEEEEEE
Confidence            667788888655  222333333333322111110000  01223468999999999999999999995 9999999999


Q ss_pred             eecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecCCCC
Q 013141          242 IIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKK  290 (449)
Q Consensus       242 ~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~~~~  290 (449)
                      +++. ++.++|||||+|.+.++|.+|++.++ ..+.|+.|+|.+.....
T Consensus       142 ~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~~-~~~~Gr~l~V~~~~~y~  188 (193)
T 2voo_A          142 RRTL-HKAFKGSIFVVFDSIESAKKFVETPG-QKYKETDLLILFKDDYF  188 (193)
T ss_dssp             EECT-TCCEEEEEEEEESSHHHHHHHHHCTT-CEETTEECEEEETTTC-
T ss_pred             EECC-CCCcccEEEEEECCHHHHHHHHHhCC-CeECCEEEEEEEhHHHH
Confidence            9985 48999999999999999999997654 58999999999987653

>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=99.46  E-value=1.7e-13  Score=103.27  Aligned_cols=72  Identities=21%  Similarity=0.455  Sum_probs=66.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhC----C-------CeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCc
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKY----P-------SVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGV  274 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~----g-------~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~  274 (449)
                      .+.++|||+|||+++++++|+++|+ .|    |       .|.++.+.++      +|||||+|.+.++|.+|+ .|++.
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~-~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~l~g~   75 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFN-AQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDGI   75 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHH-HHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-GGTTC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHH-HHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-hcCCC
Confidence            3568999999999999999999995 88    8       8999988754      789999999999999999 99999


Q ss_pred             eecCcceEEee
Q 013141          275 YCSSRPMRIDV  285 (449)
Q Consensus       275 ~~~g~~i~v~~  285 (449)
                      .+.|+.|+|++
T Consensus        76 ~~~g~~l~V~r   86 (87)
T 2hzc_A           76 IFQGQSLKIRR   86 (87)
T ss_dssp             EETTEECEEEC
T ss_pred             EECCeEEEEeC
Confidence            99999999975

>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=99.45  E-value=6.4e-13  Score=115.74  Aligned_cols=117  Identities=16%  Similarity=0.267  Sum_probs=87.1

Q ss_pred             CHHHHHHHHHHh--CCceecCcceEEeecCCCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCC
Q 013141          260 DENERSRAMTEM--NGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDS  337 (449)
Q Consensus       260 ~~~~A~~A~~~l--~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~  337 (449)
                      +.+....|++..  ....+.+....|...............                       ......++|||+|||.
T Consensus        63 d~~~I~~Al~~S~~~~lev~ed~~~vrR~~~~p~p~~~~~~-----------------------~~~~~~~~l~V~nLp~  119 (193)
T 2voo_A           63 DFNVIVEALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEY-----------------------KNDVKNRSVYIKGFPT  119 (193)
T ss_dssp             CHHHHHHHHHTCSSCCEEECTTSSEEEECTTSCCCCCCHHH-----------------------HHHHHHTEEEEECCCT
T ss_pred             CHHHHHHHHhhcccceEEEecccceEEecccCCCcccchhh-----------------------hhccccCEEEecCCCC
Confidence            567777888766  555666666666555221111000000                       0012357899999999


Q ss_pred             CCCHhHHHhhccccCceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCC
Q 013141          338 DVSDEDLREPFSQFGEILSVKIPV-----GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRN  400 (449)
Q Consensus       338 ~~t~~~L~~~f~~~G~v~~v~i~~-----~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  400 (449)
                      ++++++|+++|+.||.|.+|+|++     .+|+|||+|.+.++|.+|++.++ ..|+|+.|+|.|++.
T Consensus       120 ~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~~-~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          120 DATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPG-QKYKETDLLILFKDD  186 (193)
T ss_dssp             TCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCTT-CEETTEECEEEETTT
T ss_pred             cCCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhCC-CeECCEEEEEEEhHH
Confidence            999999999999999999999986     36999999999999999997654 599999999999876

>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=99.44  E-value=2.7e-13  Score=105.56  Aligned_cols=76  Identities=24%  Similarity=0.371  Sum_probs=66.5

Q ss_pred             CCCcEEEEcCC--CCCCC--------HhHHHhhccccCceEEEEEeCC--------CcEEEEEecCHHHHHHHHHHhcCC
Q 013141          325 SNNATIFVGAL--DSDVS--------DEDLREPFSQFGEILSVKIPVG--------KGCGFVQFANRKDAEVALQKLQGT  386 (449)
Q Consensus       325 ~~~~~l~V~nl--p~~~t--------~~~L~~~f~~~G~v~~v~i~~~--------~g~afV~F~~~~~A~~A~~~l~g~  386 (449)
                      .++++|.|.|+  +..+.        +++|+++|++||.|.+|.|+++        +|++||+|.+.++|.+|++.|||+
T Consensus         3 ~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~   82 (105)
T 3v4m_A            3 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   82 (105)
T ss_dssp             SCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCC
Confidence            35789999998  33333        3789999999999999999853        699999999999999999999999


Q ss_pred             eeCCeEEEEEecCC
Q 013141          387 AIGKQTVRLSWGRN  400 (449)
Q Consensus       387 ~~~g~~l~v~~~~~  400 (449)
                      .|+|+.|+|.|...
T Consensus        83 ~f~GR~i~v~~~~~   96 (105)
T 3v4m_A           83 KFANRVVVTKYCDP   96 (105)
T ss_dssp             EETTEECEEEEECH
T ss_pred             EeCCCEEEEEEeCH
Confidence            99999999999764

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.41  E-value=1.6e-12  Score=99.80  Aligned_cols=76  Identities=22%  Similarity=0.359  Sum_probs=64.2

Q ss_pred             CcEEEEcCCC-------CCCCHhHHHhhccccCceEEEEEe-CCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 013141          327 NATIFVGALD-------SDVSDEDLREPFSQFGEILSVKIP-VGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWG  398 (449)
Q Consensus       327 ~~~l~V~nlp-------~~~t~~~L~~~f~~~G~v~~v~i~-~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~  398 (449)
                      ..+|.|.-..       ..+++++|+++|++||.|.+|.|+ +.+|+|||+|.+.++|.+|++.+++  +.++.|+|.|+
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a   87 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLSSKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWL   87 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEESSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECS
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEccCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEc
Confidence            4566666554       458999999999999999999998 4689999999999999999997544  68999999999


Q ss_pred             CCCCCC
Q 013141          399 RNPGNK  404 (449)
Q Consensus       399 ~~~~~~  404 (449)
                      +++...
T Consensus        88 ~~~~~~   93 (100)
T 2d9o_A           88 EGQPQD   93 (100)
T ss_dssp             SCCCCC
T ss_pred             cCCCCC
Confidence            987543

>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=99.39  E-value=8.5e-13  Score=104.70  Aligned_cols=75  Identities=19%  Similarity=0.210  Sum_probs=66.1

Q ss_pred             CCcEEEEcCCCC--C---CCHhHHHhhccccCceEEEEEeCC----------CcEEEEEecCHHHHHHHHHHhcCCeeCC
Q 013141          326 NNATIFVGALDS--D---VSDEDLREPFSQFGEILSVKIPVG----------KGCGFVQFANRKDAEVALQKLQGTAIGK  390 (449)
Q Consensus       326 ~~~~l~V~nlp~--~---~t~~~L~~~f~~~G~v~~v~i~~~----------~g~afV~F~~~~~A~~A~~~l~g~~~~g  390 (449)
                      ++++|+|.|+-.  +   -.++||+++|++||.|.+|.|+++          +|++||+|.+.++|.+|++.|||+.|.|
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~G   98 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG   98 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            578999999942  2   246899999999999999999863          3799999999999999999999999999


Q ss_pred             eEEEEEecCC
Q 013141          391 QTVRLSWGRN  400 (449)
Q Consensus       391 ~~l~v~~~~~  400 (449)
                      +.|+|.|+..
T Consensus        99 R~i~v~~~~~  108 (118)
T 3ue2_A           99 RKVVAEVYDQ  108 (118)
T ss_dssp             EECEEEEECH
T ss_pred             cEEEEEEcCh
Confidence            9999999764

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.37  E-value=1.2e-12  Score=116.56  Aligned_cols=80  Identities=16%  Similarity=0.271  Sum_probs=70.7

Q ss_pred             cCCCceEEEcCCCCCC---------CHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCce
Q 013141          205 ACSDLSIFVGDLAPDV---------TDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVY  275 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~---------t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~  275 (449)
                      ....++|||+||+.++         ++++|+++|+ .||+|.+|+++.+      +|||||+|.+.++|+.|++.|++..
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~-~fG~I~~v~v~~~------kG~AFV~F~~~~~Ae~A~~am~g~~  203 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFS-RLGDIDRIRYVES------KNCGFVKFKYQANAEFAKEAMSNQT  203 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHH-TTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHHHTTCC
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHH-ccCCEEEEEEECC------CCEEEEEeCCHHHHHHHHHHhCCCE
Confidence            4567899999999998         7999999995 9999999999853      7899999999999999999999999


Q ss_pred             e------------cCcceEEeecCCCCC
Q 013141          276 C------------SSRPMRIDVATPKKA  291 (449)
Q Consensus       276 ~------------~g~~i~v~~~~~~~~  291 (449)
                      |            .|+.|.|.|+.....
T Consensus       204 l~~~~~~e~~~~~~gr~L~V~wA~~~pn  231 (240)
T 3u1l_A          204 LLLPSDKEWDDRREGTGLLVKWANEDPD  231 (240)
T ss_dssp             CCCTTSTTGGGGGGSCCCEEEECC----
T ss_pred             EeccccccccccCCCCEEEEEEccCCCC
Confidence            9            899999999987654

>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=99.36  E-value=2.6e-12  Score=101.13  Aligned_cols=75  Identities=12%  Similarity=0.202  Sum_probs=66.1

Q ss_pred             CCCcEEEEcCCCCCC----------CHhHHHhhccccCceEEEEEeCC--CcEEEEEecCHHHHHHHHHHhcCCeeCCeE
Q 013141          325 SNNATIFVGALDSDV----------SDEDLREPFSQFGEILSVKIPVG--KGCGFVQFANRKDAEVALQKLQGTAIGKQT  392 (449)
Q Consensus       325 ~~~~~l~V~nlp~~~----------t~~~L~~~f~~~G~v~~v~i~~~--~g~afV~F~~~~~A~~A~~~l~g~~~~g~~  392 (449)
                      .++++|.|.|+=...          .++||+++|++||.|.+|.|.++  +|++||+|.+.++|.+|++.|||+.|+|+.
T Consensus         5 ~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~~~G~~fV~f~~~e~A~~Ai~~lnG~~f~GR~   84 (114)
T 3s6e_A            5 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKM   84 (114)
T ss_dssp             CCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTCTTCCEEEECSSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEE
Confidence            457889999984322          23688999999999999999875  699999999999999999999999999999


Q ss_pred             EEEEecC
Q 013141          393 VRLSWGR  399 (449)
Q Consensus       393 l~v~~~~  399 (449)
                      |+|.|+.
T Consensus        85 i~v~~~~   91 (114)
T 3s6e_A           85 ITAAYVP   91 (114)
T ss_dssp             CEEEEEC
T ss_pred             EEEEEEc
Confidence            9999986

>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=99.34  E-value=6.8e-12  Score=99.19  Aligned_cols=83  Identities=13%  Similarity=0.246  Sum_probs=70.5

Q ss_pred             ccCCCceEEEcCCCCCCC-----------HHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC
Q 013141          204 EACSDLSIFVGDLAPDVT-----------DSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMN  272 (449)
Q Consensus       204 ~~~~~~~l~v~~lp~~~t-----------~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~  272 (449)
                      ...++++|+|.||....+           +++|+++|+ .||.|.++.+ .+.   .++|||||+|.+.++|.+|++.||
T Consensus        11 ~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~-~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~ln   85 (112)
T 2dit_A           11 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECS-KFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLD   85 (112)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGG-GTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHST
T ss_pred             CCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHH-ccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcC
Confidence            445788999999944332           579999995 9999999965 553   379999999999999999999999


Q ss_pred             CceecCcceEEeecCCCCC
Q 013141          273 GVYCSSRPMRIDVATPKKA  291 (449)
Q Consensus       273 g~~~~g~~i~v~~~~~~~~  291 (449)
                      |..|.|+.|+|.++.++..
T Consensus        86 g~~~~gr~l~v~~a~~~~~  104 (112)
T 2dit_A           86 GRWFGGRQITAQAWDGTTD  104 (112)
T ss_dssp             TCEETTEECEEEECCSCCC
T ss_pred             CCEECCcEEEEEEeCCCCC
Confidence            9999999999999987644

>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=99.34  E-value=1.9e-12  Score=121.56  Aligned_cols=77  Identities=19%  Similarity=0.309  Sum_probs=69.2

Q ss_pred             CCCCCcEEEEcC--CCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeC---Ce--EEEE
Q 013141          323 GESNNATIFVGA--LDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIG---KQ--TVRL  395 (449)
Q Consensus       323 ~~~~~~~l~V~n--lp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~---g~--~l~v  395 (449)
                      ...++.+|||+|  |+..+|+++|+++|++||.|.+|.+.++|+||||+|.+.++|++|++.|||+.+-   |+  .|.|
T Consensus        14 ~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~ly~   93 (345)
T 3tht_A           14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYL   93 (345)
T ss_dssp             CSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCTTCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEE
T ss_pred             cCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCccccccCCceEEEE
Confidence            356678999999  5789999999999999999999999999999999999999999999999999883   44  6888


Q ss_pred             EecC
Q 013141          396 SWGR  399 (449)
Q Consensus       396 ~~~~  399 (449)
                      .|..
T Consensus        94 ~~~~   97 (345)
T 3tht_A           94 NFVE   97 (345)
T ss_dssp             EECS
T ss_pred             EEee
Confidence            8885

>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=99.34  E-value=3.1e-12  Score=99.53  Aligned_cols=83  Identities=17%  Similarity=0.190  Sum_probs=70.9

Q ss_pred             CCCceEEEcCC--CCCCC--------HHHHHHHHhhhCCCeeEEEEeecCCC--CCcceEEEEEeCCHHHHHHHHHHhCC
Q 013141          206 CSDLSIFVGDL--APDVT--------DSILQETFSSKYPSVKGAKVIIDSNT--GRTKGYGFVRFGDENERSRAMTEMNG  273 (449)
Q Consensus       206 ~~~~~l~v~~l--p~~~t--------~~~l~~~f~~~~g~v~~i~~~~~~~~--~~~~g~afV~f~~~~~A~~A~~~l~g  273 (449)
                      .+++.|.|.|+  +.++.        +++|++.|+ +||.|.+|.++++..+  ++++|++||+|.+.++|.+|++.|||
T Consensus         3 ~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~-k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG   81 (105)
T 3v4m_A            3 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECS-KYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG   81 (105)
T ss_dssp             SCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHH-TTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHH-ccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCC
Confidence            35678899987  33333        368999996 9999999999988654  46899999999999999999999999


Q ss_pred             ceecCcceEEeecCCC
Q 013141          274 VYCSSRPMRIDVATPK  289 (449)
Q Consensus       274 ~~~~g~~i~v~~~~~~  289 (449)
                      +.+.||.|+|.++...
T Consensus        82 ~~f~GR~i~v~~~~~~   97 (105)
T 3v4m_A           82 RKFANRVVVTKYCDPD   97 (105)
T ss_dssp             CEETTEECEEEEECHH
T ss_pred             CEeCCCEEEEEEeCHH
Confidence            9999999999998654

>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=99.32  E-value=5.9e-12  Score=99.84  Aligned_cols=81  Identities=16%  Similarity=0.281  Sum_probs=70.5

Q ss_pred             CCceEEEcCCCC--CC---CHHHHHHHHhhhCCCeeEEEEeecCC----CCCcceEEEEEeCCHHHHHHHHHHhCCceec
Q 013141          207 SDLSIFVGDLAP--DV---TDSILQETFSSKYPSVKGAKVIIDSN----TGRTKGYGFVRFGDENERSRAMTEMNGVYCS  277 (449)
Q Consensus       207 ~~~~l~v~~lp~--~~---t~~~l~~~f~~~~g~v~~i~~~~~~~----~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~  277 (449)
                      ++++|+|.|+-.  ++   .+++|++.|+ +||.|.+|.|+++..    +++++|++||+|.+.++|.+|++.|||+.+.
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~-k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~   97 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECG-KFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFA   97 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHT-TTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEET
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHh-ccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEEC
Confidence            577899999832  22   3689999995 999999999998864    4577899999999999999999999999999


Q ss_pred             CcceEEeecCC
Q 013141          278 SRPMRIDVATP  288 (449)
Q Consensus       278 g~~i~v~~~~~  288 (449)
                      ||.|+|.++..
T Consensus        98 GR~i~v~~~~~  108 (118)
T 3ue2_A           98 GRKVVAEVYDQ  108 (118)
T ss_dssp             TEECEEEEECH
T ss_pred             CcEEEEEEcCh
Confidence            99999999865

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.30  E-value=2.2e-11  Score=93.36  Aligned_cols=77  Identities=22%  Similarity=0.319  Sum_probs=63.7

Q ss_pred             CCCceEEEcCCC-------CCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCC
Q 013141          113 DETKTIWIGDLF-------HWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNT  185 (449)
Q Consensus       113 ~~~~~l~v~nLp-------~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~  185 (449)
                      ...++|.|.-..       .++++++|+++|++||.|.+|.|+     ++++|||||+|.+.++|++|++.+++  +  .
T Consensus         8 ~~~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~~--~--~   78 (100)
T 2d9o_A            8 QGTPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEVG--L--V   78 (100)
T ss_dssp             CSSCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCCB--C--S
T ss_pred             CccceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcCC--C--C
Confidence            346788888765       458999999999999999999987     36789999999999999999987544  2  4


Q ss_pred             CCcccccccccCC
Q 013141          186 DQPFRLNWATFSG  198 (449)
Q Consensus       186 ~~~~~~~~~~~~~  198 (449)
                      .++|+|.|+....
T Consensus        79 g~~l~V~~a~~~~   91 (100)
T 2d9o_A           79 DNPLKISWLEGQP   91 (100)
T ss_dssp             SSBCEEECSSCCC
T ss_pred             CCeEEEEEccCCC
Confidence            6788999987554

>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=99.29  E-value=7.3e-13  Score=102.96  Aligned_cols=67  Identities=25%  Similarity=0.416  Sum_probs=57.4

Q ss_pred             EcCCCCCCCHhHHHhhc------------cccCceEEEEEeCC-----CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEE
Q 013141          332 VGALDSDVSDEDLREPF------------SQFGEILSVKIPVG-----KGCGFVQFANRKDAEVALQKLQGTAIGKQTVR  394 (449)
Q Consensus       332 V~nlp~~~t~~~L~~~f------------~~~G~v~~v~i~~~-----~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~  394 (449)
                      +.+|+..+++++|+++|            ++||.|.+|.|+++     +|+|||+|.+.++|.+|++.|||+.|.|+.|+
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i~   99 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH   99 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEEE
Confidence            45566666666665555            99999999999864     69999999999999999999999999999999


Q ss_pred             EEec
Q 013141          395 LSWG  398 (449)
Q Consensus       395 v~~~  398 (449)
                      |.|+
T Consensus       100 v~~s  103 (104)
T 1jmt_A          100 AELS  103 (104)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            9986

>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=99.29  E-value=1.6e-12  Score=101.00  Aligned_cols=72  Identities=22%  Similarity=0.441  Sum_probs=62.1

Q ss_pred             EcCCCCCCCHHHHHHHH------------hhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcc
Q 013141          213 VGDLAPDVTDSILQETF------------SSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRP  280 (449)
Q Consensus       213 v~~lp~~~t~~~l~~~f------------~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~  280 (449)
                      +.+|+..+++++|++.|            + +||.|.++.++++.. ++++|||||+|.+.++|.+|++.|||+.+.|+.
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~-~~G~V~~v~i~~~~~-~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~   97 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEE-KYGEVEEMNVCDNLG-DHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQP   97 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HTCCEEEEEECCSSS-SSSEEEEEEEESCHHHHHHHHHHHTTCEETTEE
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhc-cCCceEEEEEEeCCC-CCccEEEEEEECCHHHHHHHHHHHCCCEECCEE
Confidence            45666667776666555            7 999999999998854 789999999999999999999999999999999


Q ss_pred             eEEeec
Q 013141          281 MRIDVA  286 (449)
Q Consensus       281 i~v~~~  286 (449)
                      |+|.++
T Consensus        98 i~v~~s  103 (104)
T 1jmt_A           98 IHAELS  103 (104)
T ss_dssp             CCEEEC
T ss_pred             EEEEEc
Confidence            999886

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.29  E-value=1.5e-11  Score=96.67  Aligned_cols=78  Identities=21%  Similarity=0.164  Sum_probs=71.3

Q ss_pred             CCCCCCcEEEEcCCCCC-CCHhHHHhhccccCceEEEEEeCCCcEEEEEecC-HHHHHHHHHHh--cCCeeCCeEEEEEe
Q 013141          322 DGESNNATIFVGALDSD-VSDEDLREPFSQFGEILSVKIPVGKGCGFVQFAN-RKDAEVALQKL--QGTAIGKQTVRLSW  397 (449)
Q Consensus       322 ~~~~~~~~l~V~nlp~~-~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~-~~~A~~A~~~l--~g~~~~g~~l~v~~  397 (449)
                      .....+++|+|+||+.. +++++|+++|+.||.|.+|.+.++..+|||+|.+ .++|..|++.|  ++..|.|..++++.
T Consensus        13 ~~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~ev   92 (121)
T 1owx_A           13 LEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEV   92 (121)
T ss_dssp             CSCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEE
T ss_pred             ccccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCEEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEEEE
Confidence            44667899999999999 9999999999999999999999999999999999 89999999999  47789999999886


Q ss_pred             cC
Q 013141          398 GR  399 (449)
Q Consensus       398 ~~  399 (449)
                      ..
T Consensus        93 L~   94 (121)
T 1owx_A           93 LE   94 (121)
T ss_dssp             CC
T ss_pred             CC
Confidence            55

>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=99.27  E-value=5.6e-12  Score=118.34  Aligned_cols=79  Identities=13%  Similarity=0.228  Sum_probs=65.7

Q ss_pred             CCCCCceEEEcC--CCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCC---CC
Q 013141          111 TNDETKTIWIGD--LFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMP---NT  185 (449)
Q Consensus       111 ~~~~~~~l~v~n--Lp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~---~~  185 (449)
                      ...++++|||+|  |++.+||++|+++|++||.|.+|.+.+      +||||||+|.+.++|++|++.||+..+.   ++
T Consensus        14 ~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~   87 (345)
T 3tht_A           14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQ   87 (345)
T ss_dssp             CSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSC
T ss_pred             cCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCccccccCC
Confidence            356889999999  579999999999999999999987743      4689999999999999999999998773   22


Q ss_pred             CCcccccccc
Q 013141          186 DQPFRLNWAT  195 (449)
Q Consensus       186 ~~~~~~~~~~  195 (449)
                      ..++.+.+..
T Consensus        88 ~~~ly~~~~~   97 (345)
T 3tht_A           88 KITLYLNFVE   97 (345)
T ss_dssp             EEECEEEECS
T ss_pred             ceEEEEEEee
Confidence            2356666653

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.21  E-value=5.6e-11  Score=87.22  Aligned_cols=74  Identities=24%  Similarity=0.425  Sum_probs=62.3

Q ss_pred             CCCcEEEEcCCCC----CCCH----hHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEE
Q 013141          325 SNNATIFVGALDS----DVSD----EDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLS  396 (449)
Q Consensus       325 ~~~~~l~V~nlp~----~~t~----~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~  396 (449)
                      ++..+|+|.-.+.    ...+    .+|.+.|.+||.|..++|..++  +||+|.+.++|.+|++ |||..++|+.|+|+
T Consensus         5 Ppd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--~fVtF~d~~sAlaAi~-mnG~~v~Gr~LkV~   81 (91)
T 2dnr_A            5 SSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--MWVTFLEGSSALNVLS-LNGKELLNRTITIA   81 (91)
T ss_dssp             CSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--EEEEESSHHHHHHGGG-GTTCEETTEEEEEE
T ss_pred             CCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--EEEEECChHHHHHHHh-cCCeEeCCeEEEEE
Confidence            3455677766652    3333    6788999999999999999876  8999999999999998 99999999999999


Q ss_pred             ecCCC
Q 013141          397 WGRNP  401 (449)
Q Consensus       397 ~~~~~  401 (449)
                      ++++.
T Consensus        82 lkt~d   86 (91)
T 2dnr_A           82 LKSPS   86 (91)
T ss_dssp             ECCCS
T ss_pred             eCCCC
Confidence            99874

>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=99.12  E-value=2.5e-10  Score=89.72  Aligned_cols=79  Identities=11%  Similarity=0.087  Sum_probs=65.5

Q ss_pred             CCCceEEEcCCCCCC----------CHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCce
Q 013141          206 CSDLSIFVGDLAPDV----------TDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVY  275 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~----------t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~  275 (449)
                      .+++.|.|.|+=...          .+++|++.|+ +||.|.+|.+.++.    ++|++||+|.+.++|.+|++.|||+.
T Consensus         5 ~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~-kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~   79 (114)
T 3s6e_A            5 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECN-KHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRW   79 (114)
T ss_dssp             CCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHT-TTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCE
T ss_pred             CCCcEEEEECCCChHHccChhHHHHHHHHHHHHHh-ccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCE
Confidence            456678888763211          1358899995 99999999987653    48999999999999999999999999


Q ss_pred             ecCcceEEeecCCC
Q 013141          276 CSSRPMRIDVATPK  289 (449)
Q Consensus       276 ~~g~~i~v~~~~~~  289 (449)
                      ++|+.|+|.++...
T Consensus        80 f~GR~i~v~~~~~~   93 (114)
T 3s6e_A           80 FAGKMITAAYVPLP   93 (114)
T ss_dssp             ETTEECEEEEECHH
T ss_pred             ECCEEEEEEEEcHH
Confidence            99999999998654

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.04  E-value=4.7e-10  Score=82.69  Aligned_cols=75  Identities=23%  Similarity=0.349  Sum_probs=63.3

Q ss_pred             CCCCCcEEEEcCCCCC-----CCH----hHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEE
Q 013141          323 GESNNATIFVGALDSD-----VSD----EDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTV  393 (449)
Q Consensus       323 ~~~~~~~l~V~nlp~~-----~t~----~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l  393 (449)
                      ..++..+|+|.-++.+     +.+    .+|.+.|.+||.|..++|..++  +||+|.+.++|.+|++ |||..++||.|
T Consensus        11 ~GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--~fVtF~d~~sAl~AI~-ldG~~v~Gr~L   87 (95)
T 1ufw_A           11 QGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--MLVTFADSHSALSVLD-VDGMKVKGRAV   87 (95)
T ss_dssp             CCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--EEEECSCSHHHHHHHH-GGGSEETTEEE
T ss_pred             cCCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--EEEEEcChHHHHHHHh-cCCeeeCCeEE
Confidence            3455678888877643     222    5688999999999999999776  9999999999999998 99999999999


Q ss_pred             EEEecCC
Q 013141          394 RLSWGRN  400 (449)
Q Consensus       394 ~v~~~~~  400 (449)
                      +|++..+
T Consensus        88 ~V~~k~~   94 (95)
T 1ufw_A           88 KISGPSS   94 (95)
T ss_dssp             EEECCCC
T ss_pred             EEeccCC
Confidence            9998654

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.97  E-value=1.9e-09  Score=84.73  Aligned_cols=66  Identities=14%  Similarity=0.106  Sum_probs=58.3

Q ss_pred             CCCCCceEEEcCCCCC-CCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEcc-HHHHHHHHHHhcCCCC
Q 013141          111 TNDETKTIWIGDLFHW-MDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYS-RAAAEKVLQSYSGSLM  182 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~-~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~-~~~A~~Al~~l~~~~~  182 (449)
                      .-...+.|+|+||+++ +++++|+++|+.||.|..|.+.++..      .|||+|.+ .++|..|++.++...+
T Consensus        14 ~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~   81 (121)
T 1owx_A           14 EEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNL   81 (121)
T ss_dssp             SCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCB
T ss_pred             cccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCc
Confidence            3456789999999999 99999999999999999999998864      69999999 8999999999864433

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.90  E-value=7.5e-09  Score=77.58  Aligned_cols=73  Identities=16%  Similarity=0.154  Sum_probs=69.3

Q ss_pred             CCCCcEEEEcCCCCCCCHhHHHhhcccc-----CceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEE
Q 013141          324 ESNNATIFVGALDSDVSDEDLREPFSQF-----GEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLS  396 (449)
Q Consensus       324 ~~~~~~l~V~nlp~~~t~~~L~~~f~~~-----G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~  396 (449)
                      .+..++|-|-+||..+++..|+.+++++     |.|..|.+..+.+-|+|+|.|...|.+|...|+|.+|.|++|+|.
T Consensus        18 ~~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~g   95 (117)
T 2l9w_A           18 KELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDFNGAIIIFRDSKFAAKMLMILNGSQFQGKVIRSG   95 (117)
T ss_dssp             TTTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTTTEEEEECSCHHHHHHHHHHHSSEEETTEEEEEE
T ss_pred             ccCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCCCceEEEEccchhhHHHHhhcCCeeecCeEEEec
Confidence            3457889999999999999999999999     999999999999999999999999999999999999999999996

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.82  E-value=1.3e-08  Score=74.69  Aligned_cols=73  Identities=18%  Similarity=0.270  Sum_probs=60.4

Q ss_pred             CCceEEEcCCCC----CC-C---HHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecC
Q 013141          207 SDLSIFVGDLAP----DV-T---DSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSS  278 (449)
Q Consensus       207 ~~~~l~v~~lp~----~~-t---~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g  278 (449)
                      +..+|+|.-.+.    ++ +   ..+|.+.|+ .||+|..++++.+.        +||+|.+.++|.+||+ |+|..++|
T Consensus         6 pd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~-~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~-mnG~~v~G   75 (91)
T 2dnr_A            6 SGGTVLVSIKSSLPENNFFDDALIDELLQQFA-SFGEVILIRFVEDK--------MWVTFLEGSSALNVLS-LNGKELLN   75 (91)
T ss_dssp             SSCEEEEEEECSSTTTCSCCHHHHHHHHHHHH-TTCCEEEEEECSSS--------EEEEESSHHHHHHGGG-GTTCEETT
T ss_pred             CCCeEEEEeccCccccccCCHHHHHHHHHHHH-hCCCeEEEEEecCC--------EEEEECChHHHHHHHh-cCCeEeCC
Confidence            455777765551    22 3   257899996 99999999999763        8999999999999997 99999999


Q ss_pred             cceEEeecCCC
Q 013141          279 RPMRIDVATPK  289 (449)
Q Consensus       279 ~~i~v~~~~~~  289 (449)
                      |.|+|+.+++.
T Consensus        76 r~LkV~lkt~d   86 (91)
T 2dnr_A           76 RTITIALKSPS   86 (91)
T ss_dssp             EEEEEEECCCS
T ss_pred             eEEEEEeCCCC
Confidence            99999998864

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=98.78  E-value=1.5e-08  Score=90.38  Aligned_cols=73  Identities=19%  Similarity=0.190  Sum_probs=61.3

Q ss_pred             cEEEEcCCC-----CCCCHhHHHhhccccCceEEEEEeC----------CCcEEEEEecCHHHHHHHHHHhcCCeeCCeE
Q 013141          328 ATIFVGALD-----SDVSDEDLREPFSQFGEILSVKIPV----------GKGCGFVQFANRKDAEVALQKLQGTAIGKQT  392 (449)
Q Consensus       328 ~~l~V~nlp-----~~~t~~~L~~~f~~~G~v~~v~i~~----------~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~  392 (449)
                      ..+.+.|+-     ..-.+++|++.|++||.|.+|.|.+          ++|++||+|.+.++|.+|++.|||+.|.||.
T Consensus       125 ~v~~l~n~v~~~e~~~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~  204 (222)
T 3dxb_A          125 TVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRK  204 (222)
T ss_dssp             SEEEEESSCCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSB
T ss_pred             ccchhhcCCCHHHHHHHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeE
Confidence            445555542     2235688999999999999999973          4689999999999999999999999999999


Q ss_pred             EEEEecCC
Q 013141          393 VRLSWGRN  400 (449)
Q Consensus       393 l~v~~~~~  400 (449)
                      |+|.|...
T Consensus       205 i~~~~~~~  212 (222)
T 3dxb_A          205 VVAEVYDQ  212 (222)
T ss_dssp             CEEEECCH
T ss_pred             EEEEEcCH
Confidence            99999763

>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=98.64  E-value=6.8e-08  Score=86.05  Aligned_cols=68  Identities=18%  Similarity=0.252  Sum_probs=60.9

Q ss_pred             CCHHHHHHHHhhhCCCeeEEEEeecCC----CCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecCC
Q 013141          220 VTDSILQETFSSKYPSVKGAKVIIDSN----TGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATP  288 (449)
Q Consensus       220 ~t~~~l~~~f~~~~g~v~~i~~~~~~~----~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~~  288 (449)
                      -.+++|++.|+ +||.|.++.+.++..    +++++|++||+|.+.++|.+|++.|+|+.+.||.|.+.+...
T Consensus       141 e~~~dl~~e~~-~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~  212 (222)
T 3dxb_A          141 DLEGEVTEECG-KFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQ  212 (222)
T ss_dssp             THHHHHHHHHT-TTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECCH
T ss_pred             HHHHHHHHHHH-ccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcCH
Confidence            35679999996 999999999986644    458999999999999999999999999999999999999864

>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=98.59  E-value=1e-07  Score=70.27  Aligned_cols=73  Identities=16%  Similarity=0.290  Sum_probs=60.5

Q ss_pred             CCCceEEEcCCCCC------CC---HHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee
Q 013141          206 CSDLSIFVGDLAPD------VT---DSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYC  276 (449)
Q Consensus       206 ~~~~~l~v~~lp~~------~t---~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~  276 (449)
                      .+..+|+|.-++.+      .+   ..+|.+.|. .||+|..+++..++        +||+|.+.++|.+||+ |+|..+
T Consensus        13 PpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~-~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~-ldG~~v   82 (95)
T 1ufw_A           13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLG-SYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDGMKV   82 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHH-HHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGGSEE
T ss_pred             CCCCeEEEEecCCcccccccCCHHHHHHHHHHHH-HCCCEEEEEEecCc--------EEEEEcChHHHHHHHh-cCCeee
Confidence            45678888777643      23   257889996 89999999999773        8999999999999997 999999


Q ss_pred             cCcceEEeecCC
Q 013141          277 SSRPMRIDVATP  288 (449)
Q Consensus       277 ~g~~i~v~~~~~  288 (449)
                      +||.|+|++-.+
T Consensus        83 ~Gr~L~V~~k~~   94 (95)
T 1ufw_A           83 KGRAVKISGPSS   94 (95)
T ss_dssp             TTEEEEEECCCC
T ss_pred             CCeEEEEeccCC
Confidence            999999987543

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.37  E-value=2.5e-06  Score=64.08  Aligned_cols=74  Identities=15%  Similarity=0.193  Sum_probs=66.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhC-----CCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcc
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKY-----PSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRP  280 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~-----g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~  280 (449)
                      ...++|-+-+||..++...|+.++ +.+     |.+..|.+..|..      -|+|+|.|...|.+|.-.|+|.+|.|+.
T Consensus        19 ~~~rtiaL~~ipDtvndarIr~lv-e~~~~i~~g~i~KI~L~pDH~------GAivef~d~~~AgKasLaL~G~ef~gr~   91 (117)
T 2l9w_A           19 ELETLICLFPLSDKVSPSLICQFL-QEEIHINEKDIRKILLVSDFN------GAIIIFRDSKFAAKMLMILNGSQFQGKV   91 (117)
T ss_dssp             TTTSCEEEECCCTTCCHHHHHHHH-HHHTCCCTTTCSEEEEETTTT------EEEEECSCHHHHHHHHHHHSSEEETTEE
T ss_pred             cCCcEEEEecCCCCCCHHHHHHHH-hhhhccCccceeEEEEecCCC------ceEEEEccchhhHHHHhhcCCeeecCeE
Confidence            346789999999999999999999 599     9999999998843      6999999999999999999999999999


Q ss_pred             eEEeec
Q 013141          281 MRIDVA  286 (449)
Q Consensus       281 i~v~~~  286 (449)
                      |++...
T Consensus        92 Lr~gTv   97 (117)
T 2l9w_A           92 IRSGTI   97 (117)
T ss_dssp             EEEECH
T ss_pred             EEecCH
Confidence            998654

>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=98.05  E-value=8.7e-06  Score=61.07  Aligned_cols=76  Identities=14%  Similarity=0.171  Sum_probs=67.0

Q ss_pred             CCcEEEEcCCCCCC-CH----hHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCC
Q 013141          326 NNATIFVGALDSDV-SD----EDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRN  400 (449)
Q Consensus       326 ~~~~l~V~nlp~~~-t~----~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  400 (449)
                      ..++|+|.||+.++ ..    +.++++|..|+.+......++-.-..|.|.+.++|.+|...||+..|.|+.|+|=|+.+
T Consensus         4 ~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSFRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YFgq~   83 (104)
T 1wey_A            4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQT   83 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCC
T ss_pred             CCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcceEEEEEeCChHHHHHHHHHhccceecCceeEEEecCC
Confidence            35789999998765 32    56788999999999999999877889999999999999999999999999999999985


Q ss_pred             C
Q 013141          401 P  401 (449)
Q Consensus       401 ~  401 (449)
                      .
T Consensus        84 ~   84 (104)
T 1wey_A           84 L   84 (104)
T ss_dssp             S
T ss_pred             C
Confidence            4

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.02  E-value=5.4e-05  Score=56.48  Aligned_cols=89  Identities=18%  Similarity=0.239  Sum_probs=66.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhcc-----CCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCC
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHT-----GQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQ  187 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~-----G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~  187 (449)
                      ...++|.|.|||+++.++.|.-+|+.-     |+|.++....        +-|+|+|.+.+.|++.|+. ..+.|.+  .
T Consensus         6 ~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k-~~H~L~~--~   74 (104)
T 2dhx_A            6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQ-ADHELHG--A   74 (104)
T ss_dssp             CCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTC-SCCBSSS--S
T ss_pred             cCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcC-CcceecC--e
Confidence            457899999999999999999999872     4888888765        2599999999999999954 2444433  3


Q ss_pred             cccccccccCCCCCccccCCCceEEEcCCCCCCC
Q 013141          188 PFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVT  221 (449)
Q Consensus       188 ~~~~~~~~~~~~~~~~~~~~~~~l~v~~lp~~~t  221 (449)
                      .+.|...         ......+|++.+|++.++
T Consensus        75 ~LsV~P~---------~~~~~~r~ll~gl~~~t~   99 (104)
T 2dhx_A           75 QLSLRPA---------PPRAPARLLLQGLPPGTS   99 (104)
T ss_dssp             BCEEEEC---------CCCCCCCCCCCSCCCCCC
T ss_pred             EEEEEcC---------CCCCcceEeeecCCCCCC
Confidence            4444221         123556889999998775

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.85  E-value=0.00013  Score=54.36  Aligned_cols=75  Identities=24%  Similarity=0.220  Sum_probs=63.0

Q ss_pred             CCCcEEEEcCCCCCCCHhHHHhhcccc-----CceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 013141          325 SNNATIFVGALDSDVSDEDLREPFSQF-----GEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGR  399 (449)
Q Consensus       325 ~~~~~l~V~nlp~~~t~~~L~~~f~~~-----G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  399 (449)
                      ....+|.|.|||..++++.|.-+|++-     |.|.+|....  ..|+|+|.+.+.|++.++. ....|.+..|.|....
T Consensus         6 ~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--~~AvItF~d~~va~rVL~k-~~H~L~~~~LsV~P~~   82 (104)
T 2dhx_A            6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--CGGVLTFREPADAERVLAQ-ADHELHGAQLSLRPAP   82 (104)
T ss_dssp             CCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--TEEEEEESSHHHHHHHHTC-SCCBSSSSBCEEEECC
T ss_pred             cCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--CcEEEEEcChHHHHHHhcC-CcceecCeEEEEEcCC
Confidence            346899999999999999999999872     6899999876  8999999999999998863 3668889999998755


Q ss_pred             CCC
Q 013141          400 NPG  402 (449)
Q Consensus       400 ~~~  402 (449)
                      +..
T Consensus        83 ~~~   85 (104)
T 2dhx_A           83 PRA   85 (104)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=97.61  E-value=0.0002  Score=52.83  Aligned_cols=67  Identities=9%  Similarity=0.098  Sum_probs=56.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCC--cccEEEEEEccHHHHHHHHHHhcCCCC
Q 013141          116 KTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQ--SEGYGFVEFYSRAAAEKVLQSYSGSLM  182 (449)
Q Consensus       116 ~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~--~~g~afV~f~~~~~A~~Al~~l~~~~~  182 (449)
                      ++|.||+||+.+||+++.+.+..+..+.....+..+.+.+  ...-|||.|.+.+++....+.++|..+
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F   70 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVF   70 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEE
Confidence            5799999999999999999999998877777766654333  234599999999999999999999876

>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=97.54  E-value=0.00027  Score=52.14  Aligned_cols=72  Identities=13%  Similarity=0.236  Sum_probs=59.4

Q ss_pred             cEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC--------CcEEEEEecCHHHHHHHHHHhcCCeeCCe-----EEE
Q 013141          328 ATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG--------KGCGFVQFANRKDAEVALQKLQGTAIGKQ-----TVR  394 (449)
Q Consensus       328 ~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~--------~g~afV~F~~~~~A~~A~~~l~g~~~~g~-----~l~  394 (449)
                      ++|.|++||+.+|++++.+.+.....+....+..+        ..-|||.|.+.+++....+.++|..|.+.     ...
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D~kg~~~~a~   81 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAI   81 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEcCCCCEeeeE
Confidence            57999999999999999999999888877777643        26799999999999999999999988542     334


Q ss_pred             EEecC
Q 013141          395 LSWGR  399 (449)
Q Consensus       395 v~~~~  399 (449)
                      |+||-
T Consensus        82 VE~AP   86 (91)
T 1uw4_A           82 VEFAP   86 (91)
T ss_dssp             EEECS
T ss_pred             EEEcC
Confidence            56553

>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=97.53  E-value=0.00025  Score=54.82  Aligned_cols=74  Identities=15%  Similarity=0.188  Sum_probs=62.7

Q ss_pred             CCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCC-eEEEEEecC
Q 013141          324 ESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGK-QTVRLSWGR  399 (449)
Q Consensus       324 ~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g-~~l~v~~~~  399 (449)
                      ....+-|.|.+.|... .+.|..+|++||+|.+...........|+|.++.+|++||. .||..|.+ ..|-|.+..
T Consensus        21 ~~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~~~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p~~   95 (119)
T 1wwh_A           21 HLDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMSNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCI   95 (119)
T ss_dssp             CGGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECC
T ss_pred             CCCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCCCCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEECC
Confidence            3456789999999885 67888999999999999987678899999999999999997 59999985 667777754

>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=97.38  E-value=0.0012  Score=48.65  Aligned_cols=57  Identities=12%  Similarity=0.194  Sum_probs=47.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYS  178 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~  178 (449)
                      .....++| ++|++....||.++|+.||. ..|+-+.|.       .|||.|.+++.|..|+..+.
T Consensus        14 ~r~HVf~l-~FP~ewKt~DI~~lFs~fgg-v~I~WidDT-------sAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           14 KRDHVLHV-TFPKEWKTSDLYQLFSAFGN-IQISWIDDT-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCSEEEE-ECCTTCCHHHHHHHHTTTCS-CCCEEEETT-------EEEEECSCHHHHHHHHHHHH
T ss_pred             CCCeEEEE-eCChhhhhHHHHHHhhccCC-EEEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            34455667 99999999999999999984 466666663       69999999999999998664

>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=97.24  E-value=0.0011  Score=49.72  Aligned_cols=76  Identities=11%  Similarity=0.088  Sum_probs=63.1

Q ss_pred             CCceEEEcCCCCCC-C----HHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcce
Q 013141          207 SDLSIFVGDLAPDV-T----DSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPM  281 (449)
Q Consensus       207 ~~~~l~v~~lp~~~-t----~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i  281 (449)
                      -.++|+|.||+.++ .    .+.++++|. .|+++.....++.-      .-..|.|.+.++|.+|...|++..+.|+.+
T Consensus         4 ~pntLiitnl~~~vF~~~~lk~~~e~Lf~-~~~~~~tF~~lkSF------RRirv~F~~~~~A~~AR~~Lh~~~f~g~~~   76 (104)
T 1wey_A            4 GSSGLIACVANDDVFSESETRAKFESLFR-TYDKDTTFQYFKSF------KRVRINFSNPLSAADARLRLHKTEFLGKEM   76 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHH-TTCSSCEEEEETTT------TEEEEECSSTTHHHHHHHTSTTSEETTEEC
T ss_pred             CCceEEEecCCHHHcCCHHHHHHHHHHHH-hhCcCcceeecCcc------eEEEEEeCChHHHHHHHHHhccceecCcee
Confidence            45689999998765 2    257789995 99999888777542      246899999999999999999999999999


Q ss_pred             EEeecCCC
Q 013141          282 RIDVATPK  289 (449)
Q Consensus       282 ~v~~~~~~  289 (449)
                      +|.++.+.
T Consensus        77 r~YFgq~~   84 (104)
T 1wey_A           77 KLYFAQTL   84 (104)
T ss_dssp             EEECCCCS
T ss_pred             EEEecCCC
Confidence            99999854

>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=97.17  E-value=0.0027  Score=46.70  Aligned_cols=56  Identities=20%  Similarity=0.388  Sum_probs=45.6

Q ss_pred             CCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhc
Q 013141          326 NNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQ  384 (449)
Q Consensus       326 ~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~  384 (449)
                      ...+++| +.|.++...||.++|+.||.| .|..+. ...|||.|.+++.|..|+..+.
T Consensus        15 r~HVf~l-~FP~ewKt~DI~~lFs~fggv-~I~Wid-DTsAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           15 RDHVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWID-DTSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCSEEEE-ECCTTCCHHHHHHHHTTTCSC-CCEEEE-TTEEEEECSCHHHHHHHHHHHH
T ss_pred             CCeEEEE-eCChhhhhHHHHHHhhccCCE-EEEEEc-CCeEEEEecCHHHHHHHHHhcc
Confidence            3456666 999999999999999999843 333333 5799999999999999998774

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=97.12  E-value=0.0013  Score=48.73  Aligned_cols=74  Identities=11%  Similarity=0.187  Sum_probs=57.7

Q ss_pred             CCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC--------CcEEEEEecCHHHHHHHHHHhcCCeeCC-----eE
Q 013141          326 NNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG--------KGCGFVQFANRKDAEVALQKLQGTAIGK-----QT  392 (449)
Q Consensus       326 ~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~--------~g~afV~F~~~~~A~~A~~~l~g~~~~g-----~~  392 (449)
                      .+.+|.|+.||+.+|++++.+.+...-.+....+..+        -.-|||.|.+.++.....+.++|..|.+     ..
T Consensus         8 ~~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~~~   87 (97)
T 2l08_A            8 HSHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLEYP   87 (97)
T ss_dssp             CCCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCEEE
T ss_pred             cceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCEee
Confidence            4678999999999999999999988655544444332        2568999999999999999999998854     24


Q ss_pred             EEEEecC
Q 013141          393 VRLSWGR  399 (449)
Q Consensus       393 l~v~~~~  399 (449)
                      ..|+||-
T Consensus        88 a~VE~AP   94 (97)
T 2l08_A           88 AVVEFAP   94 (97)
T ss_dssp             EEEEECC
T ss_pred             eEEEecC
Confidence            5566653

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=96.75  E-value=0.001  Score=49.27  Aligned_cols=69  Identities=7%  Similarity=0.037  Sum_probs=51.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCC--cccEEEEEEccHHHHHHHHHHhcCCCC
Q 013141          114 ETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQ--SEGYGFVEFYSRAAAEKVLQSYSGSLM  182 (449)
Q Consensus       114 ~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~--~~g~afV~f~~~~~A~~Al~~l~~~~~  182 (449)
                      -+-+|.||.||+.+||+++.+.+..+=.+.....+..+.+-+  ...-|||.|.+.+++....+.+++..+
T Consensus         8 ~~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F   78 (97)
T 2l08_A            8 HSHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIF   78 (97)
T ss_dssp             CCCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEE
T ss_pred             cceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEE
Confidence            456899999999999999998888764443333333222221  123489999999999999999999776

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=96.72  E-value=0.0025  Score=47.03  Aligned_cols=53  Identities=13%  Similarity=0.177  Sum_probs=45.5

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhc
Q 013141          117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYS  178 (449)
Q Consensus       117 ~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~  178 (449)
                      .++| ++|++....||.++|+.|| -..|+-+.|.       .|||.|.+++.|..|+..+.
T Consensus         8 V~~l-~FP~ewKt~Di~~lFs~fg-gv~I~WidDT-------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            8 VLHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDDT-------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEE-ECCTTCCHHHHHHHTTTSE-EEEEEEEETT-------EEEEEEEEECHHHHHHHHHT
T ss_pred             EEEE-eCChhhhhHHHHHHHhccC-CEEEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            4566 9999999999999999998 4567777763       69999999999999998764

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=96.72  E-value=0.0027  Score=46.88  Aligned_cols=54  Identities=19%  Similarity=0.377  Sum_probs=44.8

Q ss_pred             cEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhc
Q 013141          328 ATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQ  384 (449)
Q Consensus       328 ~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~  384 (449)
                      .+++| +.|.++...||.++|+.||. ..|..+. ...|||.|.+++.|..|+..+.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fgg-v~I~Wid-DTsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFGN-IQISWID-DTSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSEE-EEEEEEE-TTEEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccCC-EEEEEEc-CCeEEEEecCHHHHHHHHHhcc
Confidence            45666 99999999999999999983 3444443 5799999999999999999874

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.70  E-value=0.001  Score=52.04  Aligned_cols=71  Identities=18%  Similarity=0.218  Sum_probs=55.2

Q ss_pred             CcEEEEcCCCCCCCHhHHHhhccccCceEE-EEEeC-------------------CCcEEEEEecCHHHHHHHHHHhcCC
Q 013141          327 NATIFVGALDSDVSDEDLREPFSQFGEILS-VKIPV-------------------GKGCGFVQFANRKDAEVALQKLQGT  386 (449)
Q Consensus       327 ~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~-v~i~~-------------------~~g~afV~F~~~~~A~~A~~~l~g~  386 (449)
                      ..-|.|-+.|.+.+ ..|.+.|++||.|.+ +.+.+                   ......|+|++..+|.+||. -||.
T Consensus         7 e~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~   84 (132)
T 3p3d_A            7 ELAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGA   84 (132)
T ss_dssp             -CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTC
T ss_pred             ceEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCe
Confidence            45677778866654 667788999999877 22211                   35678999999999999996 5999


Q ss_pred             eeCCeEEEEEecC
Q 013141          387 AIGKQTVRLSWGR  399 (449)
Q Consensus       387 ~~~g~~l~v~~~~  399 (449)
                      .|.|..|-|.+.+
T Consensus        85 ii~G~mIGV~Py~   97 (132)
T 3p3d_A           85 VFNGVLLGVIPYT   97 (132)
T ss_dssp             EETTEECEEEECC
T ss_pred             EeCcEEEEEEECC
Confidence            9999988888776

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=96.18  E-value=0.0022  Score=62.25  Aligned_cols=56  Identities=18%  Similarity=0.194  Sum_probs=43.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHH
Q 013141          114 ETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQ  175 (449)
Q Consensus       114 ~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~  175 (449)
                      ..|+|+|. .|..+++.+|.++|++||+|.++.+.+++.     -||.|||.+.+++..+++
T Consensus        52 a~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~g-----~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           52 AQRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESFG-----LYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             HHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSSS-----EEEEEECC---CCHHHHS
T ss_pred             hcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccCC-----eEEEEEeCCHHHHHHHHh
Confidence            34789997 799999999999999999999999887642     499999999999998874

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=96.15  E-value=0.024  Score=43.70  Aligned_cols=74  Identities=12%  Similarity=0.155  Sum_probs=57.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecC-cceEEe
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSS-RPMRID  284 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g-~~i~v~  284 (449)
                      ...+-|.|.++|+.. .+.|.+.|. .||+|.+.....      ...+-.|.|.+..+|++|+ ..||..|.+ ..|-|.
T Consensus        22 ~~~~wVtVFGFp~~~-~~~VL~~F~-~~G~Iv~~~~~~------~~NWihI~Y~s~~~A~rAL-~kNG~ii~g~~mIGV~   92 (119)
T 1wwh_A           22 LDDTWVTVFGFPQAS-ASYILLQFA-QYGNILKHVMSN------TGNWMHIRYQSKLQARKAL-SKDGRIFGESIMIGVK   92 (119)
T ss_dssp             GGGGEEEEECCCGGG-HHHHHHHHH-TTSCEEEEEECS------SSSEEEEEESSHHHHHHHH-TTTTCEETTTEECEEE
T ss_pred             CCCCEEEEECCCHHH-HHHHHHHHH-hhCcEEEeccCC------CCCeEEEEeCCHHHHHHHH-HhCCeEecCCEEEEEE
Confidence            346789999999985 667778884 999999887621      2358999999999999999 579999874 556666


Q ss_pred             ecCC
Q 013141          285 VATP  288 (449)
Q Consensus       285 ~~~~  288 (449)
                      ...+
T Consensus        93 p~~d   96 (119)
T 1wwh_A           93 PCID   96 (119)
T ss_dssp             ECCC
T ss_pred             ECCC
Confidence            6543

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=96.07  E-value=0.0033  Score=60.98  Aligned_cols=54  Identities=19%  Similarity=0.277  Sum_probs=42.2

Q ss_pred             CcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCc-EEEEEecCHHHHHHHHH
Q 013141          327 NATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKG-CGFVQFANRKDAEVALQ  381 (449)
Q Consensus       327 ~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g-~afV~F~~~~~A~~A~~  381 (449)
                      .++|+|. .+..+++.+|.++|++||.|.++.+.+++| +|.|+|.+.+++..++.
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~g~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESFGLYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSSSEEEEEECC---CCHHHHS
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccCCeEEEEEeCCHHHHHHHHh
Confidence            4789997 799999999999999999999999988765 99999999999886653

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=89.48  E-value=0.3  Score=38.19  Aligned_cols=78  Identities=12%  Similarity=0.123  Sum_probs=54.4

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEE-Eeec------------CCCC-CcceEEEEEeCCHHHHHHHHHHhCC
Q 013141          208 DLSIFVGDLAPDVTDSILQETFSSKYPSVKGAK-VIID------------SNTG-RTKGYGFVRFGDENERSRAMTEMNG  273 (449)
Q Consensus       208 ~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~-~~~~------------~~~~-~~~g~afV~f~~~~~A~~A~~~l~g  273 (449)
                      ..-|.|.+.|++.+ ..+.+.|+ +||.|.+-. ..++            +... ....+..|+|.+..+|.+|| ..||
T Consensus         7 e~~VtVFGFp~~~~-~~VI~~Fs-~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL-~~NG   83 (132)
T 3p3d_A            7 ELAILVFGYPETMA-NQVIAYFQ-EFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDAL-LENG   83 (132)
T ss_dssp             -CEEEEECCCGGGH-HHHHHHHG-GGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHH-TTTT
T ss_pred             ceEEEEEecCHHHH-HHHHHHHH-hhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHH-HhCC
Confidence            45688889987654 46677784 899987621 1110            0000 12457899999999999999 6999


Q ss_pred             ceecCcceEEeecCC
Q 013141          274 VYCSSRPMRIDVATP  288 (449)
Q Consensus       274 ~~~~g~~i~v~~~~~  288 (449)
                      ..|.|.-|=|...++
T Consensus        84 ~ii~G~mIGV~Py~~   98 (132)
T 3p3d_A           84 AVFNGVLLGVIPYTK   98 (132)
T ss_dssp             CEETTEECEEEECCH
T ss_pred             eEeCcEEEEEEECCH
Confidence            999998777777654

>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=87.57  E-value=1.6  Score=43.12  Aligned_cols=56  Identities=13%  Similarity=0.162  Sum_probs=45.6

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcC
Q 013141          115 TKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSG  179 (449)
Q Consensus       115 ~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~  179 (449)
                      ...++|+ +|..+...+|.++|+.||. .+|+.+.+.       .|||.|.+.+.|..+++.+..
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~-v~V~widdt-------~a~V~~~~~~~a~~~l~~~~~  495 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGN-IQISWIDDT-------SAFVSLSQPEQVQIAVNTSKY  495 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCC-CEEEECSSS-------EEEEECSCHHHHHHHHHHHTT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCC-EEEEEEcCC-------eEEEEECCHHHHHHHHHHHHh
Confidence            4466676 9999999999999999995 456555442       799999999999999988754

>4eyt_A Telomerase associated protein P65; RNA, LA protein, LARP7, RRM, XRRM, RNA binding protein; 2.50A {Tetrahymena thermophila} PDB: 4erd_A

Probab=81.84  E-value=8.2  Score=27.42  Aligned_cols=56  Identities=18%  Similarity=0.283  Sum_probs=46.3

Q ss_pred             CCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHh
Q 013141          326 NNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKL  383 (449)
Q Consensus       326 ~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l  383 (449)
                      ..+.|.|-|+|..+-..++.-.....|---++..+  .|.|.|+|.+.++-+.|+..|
T Consensus        11 qnclikiinipqgtlkaevvlavrhlgyefycdyi--dgqamirfqnsdeqrlaiqkl   66 (129)
T 4eyt_A           11 QNCLIKIINIPQGTLKAEVVLAVRHLGYEFYCDYI--DGQAMIRFQNSDEQRLAIQKL   66 (129)
T ss_dssp             CSCEEEEECCCTTCCHHHHHHHHHTTCCCEEEEEC--SSCEEEEESSHHHHHHHHHHH
T ss_pred             hCcEEEEEecCCCceeeeeEEeehhcCeeEeeeee--cCeeEEEecCChHHHHHHHHH
Confidence            35778999999998888877666666766667666  578999999999999999988

>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=81.25  E-value=3.6  Score=40.60  Aligned_cols=55  Identities=20%  Similarity=0.401  Sum_probs=44.9

Q ss_pred             CcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhc
Q 013141          327 NATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQ  384 (449)
Q Consensus       327 ~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~  384 (449)
                      ...++|+ +|..+...+|.++|+.||.| +|..+ +...|||.|.+.+.|..+++.++
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~wi-ddt~a~V~~~~~~~a~~~l~~~~  494 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWI-DDTSAFVSLSQPEQVQIAVNTSK  494 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEEC-SSSEEEEECSCHHHHHHHHHHHT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEE-cCCeEEEEECCHHHHHHHHHHHH
Confidence            4566665 88899999999999999954 44443 45789999999999999999885

---

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	449
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	8e-21
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	2e-14
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	2e-07
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	2e-07
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	2e-19
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	7e-11
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	2e-08
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-17
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-12
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	6e-07
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	3e-17
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	3e-15
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	3e-13
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	8e-16
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	9e-10
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	5e-07
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	3e-15
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	2e-13
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	4e-08
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	1e-14
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	4e-11
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	2e-08
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	2e-14
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	1e-08
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	3e-05
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	3e-14
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	4e-14
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	6e-12
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	4e-14
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	1e-12
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	3e-07
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	4e-14
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	4e-13
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	6e-11
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	8e-14
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	1e-12
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	2e-12
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	2e-13
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	5e-11
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	2e-09
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	6e-13
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	7e-12
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	3e-07
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	7e-13
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-12
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-08
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	8e-13
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	8e-11
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	1e-06
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	9e-13
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	1e-12
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	9e-09
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	1e-12
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	6e-11
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	2e-06
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	1e-12
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	2e-11
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	7e-07
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	1e-12
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	1e-11
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	8e-06
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	2e-12
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	2e-12
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	1e-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	6e-11
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	0.002
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	2e-12
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	6e-10
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	3e-09
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	2e-12
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	3e-11
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	1e-10
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	2e-12
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	1e-09
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	3e-12
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	1e-10
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	3e-09
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	6e-12
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	1e-10
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	3e-08
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	7e-12
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	7e-10
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	7e-12
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	4e-09
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	3e-05
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	8e-12
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	2e-07
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	8e-12
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	3e-11
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	5e-07
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	8e-12
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	6e-11
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	1e-09
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	1e-11
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	1e-09
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	1e-05
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	1e-11
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	8e-09
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	2e-07
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	2e-11
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	3e-06
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	5e-04
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	4e-11
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	8e-11
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	4e-04
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	4e-11
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	1e-09
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	5e-07
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	7e-11
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	1e-06
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	8e-04
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	7e-11
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	7e-08
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	9e-06
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	8e-11
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	0.002
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	1e-10
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	3e-10
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	3e-08
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	1e-10
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	2e-09
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	2e-08
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	1e-10
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	4e-10
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	1e-10
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	7e-09
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	2e-10
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	3e-10
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	5e-06
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	2e-10
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	3e-09
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	8e-06
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	5e-10
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	6e-06
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	6e-10
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	2e-09
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	1e-05
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	7e-10
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	2e-07
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	3e-05
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	1e-09
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	2e-08
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-09
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	6e-09
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-07
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-09
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-08
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-06
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	1e-09
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	4e-06
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	2e-09
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	3e-08
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	3e-04
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	2e-09
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	5e-05
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	6e-09
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-04
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-04
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	6e-09
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	8e-07
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	2e-04
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	6e-09
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	3e-05
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	1e-04
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	8e-09
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	1e-08
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	3e-05
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	1e-08
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	4e-08
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	1e-06
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	5e-08
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	5e-05
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	7e-08
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	7e-08
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	3e-06
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	9e-08
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	2e-06
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	1e-07
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	2e-06
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	2e-06
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	1e-07
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	0.001
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	4e-07
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	5e-05
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	6e-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:) 5e-07
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 8e-06
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 2e-05
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	5e-07
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	0.002
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	6e-07
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	8e-07
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	3e-06
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	0.002
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	2e-06
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	2e-06
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	7e-06
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	2e-06
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	2e-05
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-06
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-06
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	6e-06
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	7e-06
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	1e-05
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	2e-05
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	2e-05
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	4e-05
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	0.002
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	2e-04
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	2e-04
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	2e-04
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	4e-04
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	6e-04

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 87.4 bits (215), Expect = 8e-21
 Identities = 33/178 (18%), Positives = 72/178 (40%), Gaps = 4/178 (2%)

Query: 113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEK 172
           ++ + ++IG L     +  L + F   G + +  V+R+  T +S G+GFV + +    + 
Sbjct: 4   EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 63

Query: 173 VLQSYSGSLMPNTDQPFRLNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSK 232
            + +    +     +P R      S             IFVG +  D  +  L   +  +
Sbjct: 64  AMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVK--KIFVGGIKEDTEEHHL-RDYFEQ 120

Query: 233 YPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKK 290
           Y  ++  +++ D  +G+ +G+ FV F D +   + +        +     +  A  K+
Sbjct: 121 YGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNCEVRKALSKQ 177

>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 = 69.6 bits (169), Expect = 2e-14
 Identities = 39/193 (20%), Positives = 69/193 (35%), Gaps = 35/193 (18%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +F+G L+ + TD  L+  F  ++ ++    V+ D NT R++G+GFV +    E   AM  
Sbjct: 9   LFIGGLSFETTDESLRSHFE-QWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67

Query: 271 MNGVYCSSRPMRIDVATPKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATI 330
                            PK+A   +      A                           I
Sbjct: 68  RPHKVDGRVVE------PKRAVSREDSQRPGA---------------------HLTVKKI 100

Query: 331 FVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVALQKLQ 384
           FVG +  D  +  LR+ F Q+G+I  ++I         +G  FV F +    +  +   +
Sbjct: 101 FVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQK 159

Query: 385 GTAIGKQTVRLSW 397
              +      +  
Sbjct: 160 YHTVNGHNCEVRK 172

>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 = 48.8 bits (115), Expect = 2e-07
 Identities = 19/142 (13%), Positives = 48/142 (33%), Gaps = 4/142 (2%)

Query: 55  AMAMMQQQQMMMYPHHYMPYGGGGHPYY-QNGGGVKQQQQQQHGLSNGKQNGSNNNFTND 113
            + M            ++ Y          N    K   +         +  S     + 
Sbjct: 36  CVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHL 95

Query: 114 ETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKV 173
             K I++G +    +E  L + F   G++  ++++ ++ +G+  G+ FV F    + +K+
Sbjct: 96  TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 155

Query: 174 LQSYSGSLMPNTDQPFRLNWAT 195
           +     ++         +  A 
Sbjct: 156 VIQKYHTVN---GHNCEVRKAL 174

>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 = 48.8 bits (115), Expect = 2e-07
 Identities = 17/92 (18%), Positives = 35/92 (38%), Gaps = 6/92 (6%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIP------VGKGCGFVQFANRKDAEVALQK 382
            +F+G L  + +DE LR  F Q+G +    +         +G GFV +A  ++ + A+  
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67

Query: 383 LQGTAIGKQTVRLSWGRNPGNKQWRGDHSNHW 414
                 G+            +++     +   
Sbjct: 68  RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKK 99

>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 = 81.2 bits (200), Expect = 2e-19
 Identities = 25/89 (28%), Positives = 48/89 (53%)

Query: 315 RVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRK 374
           R +   +     N T++ G + S ++D+ +R+ FS FG+I+ +++   KG  FV+F+  +
Sbjct: 6   RFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHE 65

Query: 375 DAEVALQKLQGTAIGKQTVRLSWGRNPGN 403
            A  A+  + GT I    V+  WG+   +
Sbjct: 66  SAAHAIVSVNGTTIEGHVVKCYWGKESPD 94

>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 = 56.5 bits (136), Expect = 7e-11
 Identities = 18/80 (22%), Positives = 35/80 (43%), Gaps = 7/80 (8%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           +++ G +A  +TD ++++TFS  +  +   +V         KGY FVRF      + A+ 
Sbjct: 20  TVYCGGIASGLTDQLMRQTFS-PFGQIMEIRVF------PEKGYSFVRFSTHESAAHAIV 72

Query: 270 EMNGVYCSSRPMRIDVATPK 289
            +NG       ++       
Sbjct: 73  SVNGTTIEGHVVKCYWGKES 92

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.6 bits (118), Expect = 2e-08
 Identities = 19/97 (19%), Positives = 40/97 (41%), Gaps = 10/97 (10%)

Query: 100 NGKQNGSNNNF--TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSE 157
           N KQ    +    ++ +  T++ G +   + +  +   FS  GQ++ ++V   K      
Sbjct: 1   NTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG----- 55

Query: 158 GYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWA 194
            Y FV F +  +A   + S +G+ +       +  W 
Sbjct: 56  -YSFVRFSTHESAAHAIVSVNGTTIEG--HVVKCYWG 89

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 75.7 bits (186), Expect = 1e-17
 Identities = 27/97 (27%), Positives = 50/97 (51%), Gaps = 6/97 (6%)

Query: 310 GSNGARVQGSQSDGESNNATIFVGALDSD-VSDEDLREPFSQFGEILSVKIPVGKGCGFV 368
           GS+G+     ++D  S N+ +F+G L++  V   D+   FS++G+I+   +   KG  FV
Sbjct: 1   GSSGSS---GKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH--KGFAFV 55

Query: 369 QFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQ 405
           Q+ N ++A  A+    G  I  Q + ++    P   +
Sbjct: 56  QYVNERNARAAVAGEDGRMIAGQVLDINLAAEPKVNR 92

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.9 bits (145), Expect = 5e-12
 Identities = 25/95 (26%), Positives = 42/95 (44%), Gaps = 9/95 (9%)

Query: 197 SGSDRRTEACSDLS-IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGF 255
           SGS  +T+  S  S +F+G+L   V      E   SKY  + G  V          G+ F
Sbjct: 3   SGSSGKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHK--------GFAF 54

Query: 256 VRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKK 290
           V++ +E     A+   +G   + + + I++A   K
Sbjct: 55  VQYVNERNARAAVAGEDGRMIAGQVLDINLAAEPK 89

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.2 bits (107), Expect = 6e-07
 Identities = 19/103 (18%), Positives = 38/103 (36%), Gaps = 11/103 (10%)

Query: 101 GKQNGSNNNFTNDETKTIWIGDL-FHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGY 159
           G    S           ++IG+L    + ++ +   FS  G++V   V +        G+
Sbjct: 1   GSSGSSGKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHK--------GF 52

Query: 160 GFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATFSGSDRR 202
            FV++ +   A   +    G ++    Q   +N A     +R 
Sbjct: 53  AFVQYVNERNARAAVAGEDGRMIAG--QVLDINLAAEPKVNRS 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 = 74.2 bits (182), Expect = 3e-17
 Identities = 26/76 (34%), Positives = 38/76 (50%), Gaps = 6/76 (7%)

Query: 328 ATIFVGALDSDVSDEDLREPFSQFGEILSVKIP------VGKGCGFVQFANRKDAEVALQ 381
           A+++VG L  DV++  L E FS  G ILS+++          G  +V F    DAE AL 
Sbjct: 1   ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 60

Query: 382 KLQGTAIGKQTVRLSW 397
            +    I  + VR+ W
Sbjct: 61  TMNFDVIKGKPVRIMW 76

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 68.4 bits (167), Expect = 3e-15
 Identities = 28/78 (35%), Positives = 42/78 (53%), Gaps = 1/78 (1%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           S++VGDL PDVT+++L E FS     +   +V  D  T R+ GY +V F    +  RA+ 
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFS-PAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 60

Query: 270 EMNGVYCSSRPMRIDVAT 287
            MN      +P+RI  + 
Sbjct: 61  TMNFDVIKGKPVRIMWSQ 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 = 62.6 bits (152), Expect = 3e-13
 Identities = 23/79 (29%), Positives = 45/79 (56%), Gaps = 2/79 (2%)

Query: 117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQS 176
           ++++GDL   + E  L+  FS  G +++++V R+  T +S GY +V F   A AE+ L +
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 177 YSGSLMPNTDQPFRLNWAT 195
            +  ++    +P R+ W+ 
Sbjct: 62  MNFDVIKG--KPVRIMWSQ 78

>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 = 70.5 bits (172), Expect = 8e-16
 Identities = 24/86 (27%), Positives = 42/86 (48%), Gaps = 4/86 (4%)

Query: 324 ESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKG----CGFVQFANRKDAEVA 379
           +    T++VG L  DV++  + + FSQ G   S K+           FV+F   +DA  A
Sbjct: 5   DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAA 64

Query: 380 LQKLQGTAIGKQTVRLSWGRNPGNKQ 405
           L  + G  I  + V+++W   P +++
Sbjct: 65  LAAMNGRKILGKEVKVNWATTPSSQK 90

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.1 bits (127), Expect = 9e-10
 Identities = 19/81 (23%), Positives = 39/81 (48%), Gaps = 3/81 (3%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           +++VG+L+ DVT+ ++ + FS   P        + +       Y FV F +  + + A+ 
Sbjct: 10  TLYVGNLSRDVTEVLILQLFSQIGPCKS---CKMITEHTSNDPYCFVEFYEHRDAAAALA 66

Query: 270 EMNGVYCSSRPMRIDVATPKK 290
            MNG     + ++++ AT   
Sbjct: 67  AMNGRKILGKEVKVNWATTPS 87

>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 = 45.4 bits (107), Expect = 5e-07
 Identities = 23/91 (25%), Positives = 45/91 (49%), Gaps = 5/91 (5%)

Query: 112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAE 171
           + + +T+++G+L   + E  +   FS  G   + K+I       ++ Y FVEFY    A 
Sbjct: 5   DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH--TSNDPYCFVEFYEHRDAA 62

Query: 172 KVLQSYSGSLMPNTDQPFRLNWATFSGSDRR 202
             L + +G  +    +  ++NWAT + S ++
Sbjct: 63  AALAAMNGRKILG--KEVKVNWAT-TPSSQK 90

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 69.3 bits (169), Expect = 3e-15
 Identities = 15/85 (17%), Positives = 35/85 (41%), Gaps = 3/85 (3%)

Query: 326 NNATIFVGALDSDVSDEDLREPFSQFGEILS---VKIPVGKGCGFVQFANRKDAEVALQK 382
            N  +++  L   ++ E++ + F ++G I        P  +G  +V + +  DA+ A   
Sbjct: 6   VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDH 65

Query: 383 LQGTAIGKQTVRLSWGRNPGNKQWR 407
           L G  +  + + + +       Q  
Sbjct: 66  LSGFNVCNRYLVVLYYNANRAFQKM 90

>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 = 64.3 bits (156), Expect = 2e-13
 Identities = 15/81 (18%), Positives = 34/81 (41%), Gaps = 4/81 (4%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +++ +L   +T   + +    KY  ++    I   NT  T+G  +V + D  +   A   
Sbjct: 10  LYIRNLPYKITAEEMYD-IFGKYGPIR---QIRVGNTPETRGTAYVVYEDIFDAKNACDH 65

Query: 271 MNGVYCSSRPMRIDVATPKKA 291
           ++G    +R + +      +A
Sbjct: 66  LSGFNVCNRYLVVLYYNANRA 86

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.2 bits (117), Expect = 4e-08
 Identities = 12/93 (12%), Positives = 39/93 (41%), Gaps = 5/93 (5%)

Query: 113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEK 172
           +  + ++I +L + +    +++ F   G    ++ IR   T ++ G  +V +     A+ 
Sbjct: 5   EVNRILYIRNLPYKITAEEMYDIFGKYG---PIRQIRVGNTPETRGTAYVVYEDIFDAKN 61

Query: 173 VLQSYSGSLMPNTDQPFRLNWATFSGSDRRTEA 205
                SG  +   ++   + +   + + ++ + 
Sbjct: 62  ACDHLSGFNV--CNRYLVVLYYNANRAFQKMDT 92

>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 = 66.7 bits (162), Expect = 1e-14
 Identities = 28/83 (33%), Positives = 49/83 (59%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           IF+G+L P++ + +L +TFS+    ++  K++ D +TG +KGY F+ F   +    A+  
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 271 MNGVYCSSRPMRIDVATPKKASG 293
           MNG Y  +RP+ +  A  K + G
Sbjct: 61  MNGQYLCNRPITVSYAFKKDSKG 83

>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 = 56.7 bits (136), Expect = 4e-11
 Identities = 21/82 (25%), Positives = 40/82 (48%), Gaps = 7/82 (8%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKI-------PVGKGCGFVQFANRKDAEVALQK 382
           IF+G LD ++ ++ L + FS FG IL              KG  F+ FA+   ++ A++ 
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 383 LQGTAIGKQTVRLSWGRNPGNK 404
           + G  +  + + +S+     +K
Sbjct: 61  MNGQYLCNRPITVSYAFKKDSK 82

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.0 bits (116), Expect = 2e-08
 Identities = 25/79 (31%), Positives = 47/79 (59%), Gaps = 3/79 (3%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQV-VNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQS 176
           I+IG+L   +DE  L++ FS  G +    K++R+  TG S+GY F+ F S  A++  +++
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 177 YSGSLMPNTDQPFRLNWAT 195
            +G  + N  +P  +++A 
Sbjct: 61  MNGQYLCN--RPITVSYAF 77

>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 = 66.5 bits (162), Expect = 2e-14
 Identities = 21/79 (26%), Positives = 44/79 (55%)

Query: 325 SNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQ 384
           +  + +FVG L  D+++E++R+ F ++G+   V I   KG GF++   R  AE+A  +L 
Sbjct: 6   TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELD 65

Query: 385 GTAIGKQTVRLSWGRNPGN 403
              +  + +R+ +  +  +
Sbjct: 66  NMPLRGKQLRVRFACHSAS 84

>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 = 50.0 bits (119), Expect = 1e-08
 Identities = 18/81 (22%), Positives = 35/81 (43%), Gaps = 7/81 (8%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +FVG+L PD+T+  +++ F  KY       +  D        +GF+R         A  E
Sbjct: 11  LFVGNLPPDITEEEMRKLFE-KYGKAGEVFIHKDKG------FGFIRLETRTLAEIAKVE 63

Query: 271 MNGVYCSSRPMRIDVATPKKA 291
           ++ +    + +R+  A    +
Sbjct: 64  LDNMPLRGKQLRVRFACHSAS 84

>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 = 39.9 bits (93), Expect = 3e-05
 Identities = 16/83 (19%), Positives = 33/83 (39%), Gaps = 8/83 (9%)

Query: 117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQS 176
            +++G+L   + E  +   F   G+   V + ++K       +GF+   +R  AE     
Sbjct: 10  RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG------FGFIRLETRTLAEIAKVE 63

Query: 177 YSGSLMPNTDQPFRLNWATFSGS 199
                +    +  R+ +A  S S
Sbjct: 64  LDNMPLRG--KQLRVRFACHSAS 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 = 66.1 bits (161), Expect = 3e-14
 Identities = 25/94 (26%), Positives = 42/94 (44%), Gaps = 8/94 (8%)

Query: 320 QSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK-------GCGFVQFAN 372
           Q   +   + I V  +    +  ++RE FS FGE+ +V++P          G GFV F  
Sbjct: 1   QVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFIT 60

Query: 373 RKDAEVALQKL-QGTAIGKQTVRLSWGRNPGNKQ 405
           ++DA+ A   L   T +  + + L W  +    Q
Sbjct: 61  KQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQ 94

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 65.7 bits (160), Expect = 4e-14
 Identities = 16/82 (19%), Positives = 36/82 (43%), Gaps = 3/82 (3%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSN-TGRTKGYGFVRFGDENERSRAMT 269
           I V ++        ++E F S +  +K  ++      TG  +G+GFV F  + +  +A  
Sbjct: 11  ILVRNIPFQANQREIRELF-STFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFN 69

Query: 270 EM-NGVYCSSRPMRIDVATPKK 290
            + +  +   R + ++ A  + 
Sbjct: 70  ALCHSTHLYGRRLVLEWADSEV 91

>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 = 59.6 bits (144), Expect = 6e-12
 Identities = 20/93 (21%), Positives = 40/93 (43%), Gaps = 5/93 (5%)

Query: 113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRN-KQTGQSEGYGFVEFYSRAAAE 171
             T  I + ++    ++  +   FS  G++  V++ +    TG   G+GFV+F ++  A+
Sbjct: 6   QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAK 65

Query: 172 KVLQSYSGSLMPNTDQPFRLNWATFSGSDRRTE 204
           K   +   S      +   L WA    S+   +
Sbjct: 66  KAFNALCHSTHLY-GRRLVLEWAD---SEVTVQ 94

>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 = 65.4 bits (159), Expect = 4e-14
 Identities = 22/83 (26%), Positives = 40/83 (48%), Gaps = 7/83 (8%)

Query: 326 NNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCG------FVQFANRKDAEVA 379
           +N  + V  L  D++D +L   F   G I + +I      G      FV F +  D++ A
Sbjct: 1   SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 60

Query: 380 LQKLQGTAIGKQTVRLSWGRNPG 402
           ++ L G  +  + +++S+ R PG
Sbjct: 61  IKVLNGITVRNKRLKVSYAR-PG 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 = 61.2 bits (148), Expect = 1e-12
 Identities = 23/82 (28%), Positives = 41/82 (50%), Gaps = 1/82 (1%)

Query: 207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSR 266
           S+ ++ V  L  D+TD  L   F      +   +++ D  TG + GY FV F  E +  R
Sbjct: 1   SNTNLIVNYLPQDMTDRELYALFR-AIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 59

Query: 267 AMTEMNGVYCSSRPMRIDVATP 288
           A+  +NG+   ++ +++  A P
Sbjct: 60  AIKVLNGITVRNKRLKVSYARP 81

>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 = 45.8 bits (108), Expect = 3e-07
 Identities = 18/79 (22%), Positives = 41/79 (51%), Gaps = 2/79 (2%)

Query: 117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQS 176
            + +  L   M +  L+  F   G +   +++R+ +TG S GY FV+F S   +++ ++ 
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 177 YSGSLMPNTDQPFRLNWAT 195
            +G  + N  +  ++++A 
Sbjct: 64  LNGITVRN--KRLKVSYAR 80

>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 = 65.4 bits (159), Expect = 4e-14
 Identities = 23/88 (26%), Positives = 45/88 (51%), Gaps = 7/88 (7%)

Query: 326 NNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGC------GFVQFANRKDAEVA 379
            + T++VG L    ++E + E FS+ G+I  + + + K         FV++ +R DAE A
Sbjct: 6   KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENA 65

Query: 380 LQKLQGTAIGKQTVRLSWGRNP-GNKQW 406
           ++ + GT +  + +R  W       +Q+
Sbjct: 66  MRYINGTRLDDRIIRTDWDAGFKEGRQY 93

>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 = 62.7 bits (152), Expect = 4e-13
 Identities = 21/81 (25%), Positives = 36/81 (44%), Gaps = 1/81 (1%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           +++VG+L+   T+  + E FS K   +K   + +D       G+ FV +    +   AM 
Sbjct: 9   TLYVGNLSFYTTEEQIYELFS-KSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 67

Query: 270 EMNGVYCSSRPMRIDVATPKK 290
            +NG     R +R D     K
Sbjct: 68  YINGTRLDDRIIRTDWDAGFK 88

>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 = 56.5 bits (136), Expect = 6e-11
 Identities = 22/90 (24%), Positives = 48/90 (53%), Gaps = 2/90 (2%)

Query: 113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEK 172
            ++ T+++G+L  +  E  ++  FS +G +  + +  +K    + G+ FVE+YSRA AE 
Sbjct: 5   KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAEN 64

Query: 173 VLQSYSGSLMPNTDQPFRLNWATFSGSDRR 202
            ++  +G+ + +  +  R +W       R+
Sbjct: 65  AMRYINGTRLDD--RIIRTDWDAGFKEGRQ 92

>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 = 8e-14
 Identities = 20/84 (23%), Positives = 38/84 (45%), Gaps = 9/84 (10%)

Query: 323 GES-NNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKD 375
           GES  +  ++V  L   ++D+ L   F ++G I+   I         +G  FV++  R++
Sbjct: 1   GESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREE 60

Query: 376 AEVALQKLQGTAI--GKQTVRLSW 397
           A+ A+  L       G Q + +  
Sbjct: 61  AQEAISALNNVIPEGGSQPLSVRL 84

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 61.1 bits (148), Expect = 1e-12
 Identities = 25/85 (29%), Positives = 43/85 (50%), Gaps = 3/85 (3%)

Query: 204 EACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENE 263
           E+  D +++V +L   +TD  L   F  KY S+    ++ D  TGR +G  FVR+    E
Sbjct: 2   ESIKDTNLYVTNLPRTITDDQLDTIFG-KYGSIVQKNILRDKLTGRPRGVAFVRYNKREE 60

Query: 264 RSRAMTEMNG--VYCSSRPMRIDVA 286
              A++ +N       S+P+ + +A
Sbjct: 61  AQEAISALNNVIPEGGSQPLSVRLA 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 = 60.4 bits (146), Expect = 2e-12
 Identities = 17/78 (21%), Positives = 36/78 (46%)

Query: 117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQS 176
            +++ +L   + +  L   F   G +V   ++R+K TG+  G  FV +  R  A++ + +
Sbjct: 8   NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 67

Query: 177 YSGSLMPNTDQPFRLNWA 194
            +  +     QP  +  A
Sbjct: 68  LNNVIPEGGSQPLSVRLA 85

>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 = 63.9 bits (155), Expect = 2e-13
 Identities = 18/81 (22%), Positives = 35/81 (43%), Gaps = 2/81 (2%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           ++F   LA  +    L++ F S    V+  ++I D N+ R+KG  +V F +         
Sbjct: 20  TVFCMQLAARIRPRDLEDFF-SAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQS-VPLAI 77

Query: 270 EMNGVYCSSRPMRIDVATPKK 290
            + G      P+ +  +  +K
Sbjct: 78  GLTGQRLLGVPIIVQASQAEK 98

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.0 bits (137), Expect = 5e-11
 Identities = 19/90 (21%), Positives = 35/90 (38%), Gaps = 7/90 (7%)

Query: 321 SDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRK 374
           S  E +  T+F   L + +   DL + FS  G++  V+I         KG  +V+F   +
Sbjct: 12  SPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQ 71

Query: 375 DAEVALQKLQGTAIGKQTVRLSWGRNPGNK 404
                   L G  +    + +   +   N+
Sbjct: 72  SVP-LAIGLTGQRLLGVPIIVQASQAEKNR 100

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.7 bits (126), Expect = 2e-09
 Identities = 14/62 (22%), Positives = 32/62 (51%)

Query: 114 ETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKV 173
           + +T++   L   +    L + FS  G+V +V++I ++ + +S+G  +VEF    +    
Sbjct: 17  DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLA 76

Query: 174 LQ 175
           + 
Sbjct: 77  IG 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 = 61.9 bits (150), Expect = 6e-13
 Identities = 18/73 (24%), Positives = 33/73 (45%), Gaps = 5/73 (6%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPV-----GKGCGFVQFANRKDAEVALQKLQ 384
           + V  LD  VSD D++E F++FG +    +         G   V F  + DA  A+++  
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 62

Query: 385 GTAIGKQTVRLSW 397
           G  +  + + +  
Sbjct: 63  GVPLDGRPMNIQL 75

>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 = 58.8 bits (142), Expect = 7e-12
 Identities = 23/77 (29%), Positives = 37/77 (48%), Gaps = 2/77 (2%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           + V +L   V+D+ +QE F+      K    +    +GR+ G   V F  + +  +AM +
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKA--AVHYDRSGRSLGTADVHFERKADALKAMKQ 60

Query: 271 MNGVYCSSRPMRIDVAT 287
            NGV    RPM I + T
Sbjct: 61  YNGVPLDGRPMNIQLVT 77

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 45.7 bits (108), Expect = 3e-07
 Identities = 16/78 (20%), Positives = 35/78 (44%), Gaps = 3/78 (3%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY 177
           + + +L   + +  +   F+  G +    V  + ++G+S G   V F  +A A K ++ Y
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAMKQY 61

Query: 178 SGSLMPNTDQPFRLNWAT 195
           +G  +    +P  +   T
Sbjct: 62  NGVPLDG--RPMNIQLVT 77

>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 = 62.0 bits (150), Expect = 7e-13
 Identities = 20/80 (25%), Positives = 40/80 (50%), Gaps = 1/80 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +F+G L   + D  ++E   + +  +K   ++ DS TG +KGY F  + D N   +A+  
Sbjct: 4   LFIGGLPNYLNDDQVKE-LLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62

Query: 271 MNGVYCSSRPMRIDVATPKK 290
           +NG+    + + +  A+   
Sbjct: 63  LNGMQLGDKKLLVQRASVGA 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 = 59.6 bits (144), Expect = 4e-12
 Identities = 16/82 (19%), Positives = 38/82 (46%), Gaps = 7/82 (8%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVALQKL 383
           +F+G L + ++D+ ++E  + FG + +  +         KG  F ++ +    + A+  L
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 384 QGTAIGKQTVRLSWGRNPGNKQ 405
            G  +G + + +    + G K 
Sbjct: 64  NGMQLGDKKLLVQRA-SVGAKN 84

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.9 bits (116), Expect = 3e-08
 Identities = 13/83 (15%), Positives = 39/83 (46%), Gaps = 2/83 (2%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY 177
           ++IG L +++++  +    +  G +    ++++  TG S+GY F E+      ++ +   
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 178 SGSLMPNTDQPFRLNWATFSGSD 200
           +G  + +  +   +  A+    +
Sbjct: 64  NGMQLGD--KKLLVQRASVGAKN 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 = 62.0 bits (150), Expect = 8e-13
 Identities = 26/79 (32%), Positives = 41/79 (51%), Gaps = 4/79 (5%)

Query: 325 SNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV----GKGCGFVQFANRKDAEVAL 380
           S    IF+  LD  + ++ L + FS FG ILS K+       KG GFV F  ++ AE A+
Sbjct: 6   SGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAI 65

Query: 381 QKLQGTAIGKQTVRLSWGR 399
           +K+ G  +  + V +   +
Sbjct: 66  EKMNGMLLNDRKVFVGRFK 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 = 56.2 bits (135), Expect = 8e-11
 Identities = 23/92 (25%), Positives = 44/92 (47%), Gaps = 6/92 (6%)

Query: 199 SDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRF 258
           S R++   +   IF+ +L   + +  L +TFS+    +      +  +   +KGYGFV F
Sbjct: 2   SLRKSGVGN---IFIKNLDKSIDNKALYDTFSAFGNILS---CKVVCDENGSKGYGFVHF 55

Query: 259 GDENERSRAMTEMNGVYCSSRPMRIDVATPKK 290
             +    RA+ +MNG+  + R + +     +K
Sbjct: 56  ETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK 87

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.3 bits (104), Expect = 1e-06
 Identities = 22/81 (27%), Positives = 44/81 (54%), Gaps = 4/81 (4%)

Query: 115 TKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVL 174
              I+I +L   +D   L++ FS  G +++ KV+ ++    S+GYGFV F ++ AAE+ +
Sbjct: 8   VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAI 65

Query: 175 QSYSGSLMPNTDQPFRLNWAT 195
           +  +G L+ +  +   +    
Sbjct: 66  EKMNGMLLND--RKVFVGRFK 84

>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 = 61.6 bits (149), Expect = 9e-13
 Identities = 24/86 (27%), Positives = 47/86 (54%), Gaps = 7/86 (8%)

Query: 318 GSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKG------CGFVQFA 371
           G  S+  + +AT++VG LD  VS+  L E F Q G +++  +P  +        GFV+F 
Sbjct: 1   GPISE-RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFL 59

Query: 372 NRKDAEVALQKLQGTAIGKQTVRLSW 397
           + +DA+ A++ +    +  + +R++ 
Sbjct: 60  SEEDADYAIKIMDMIKLYGKPIRVNK 85

>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 = 61.2 bits (148), Expect = 1e-12
 Identities = 25/91 (27%), Positives = 46/91 (50%), Gaps = 1/91 (1%)

Query: 202 RTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDE 261
            +E   D +++VG L   V++ +L E F  +   V    +  D  TG+ +GYGFV F  E
Sbjct: 3   ISERNQDATVYVGGLDEKVSEPLLWELFL-QAGPVVNTHMPKDRVTGQHQGYGFVEFLSE 61

Query: 262 NERSRAMTEMNGVYCSSRPMRIDVATPKKAS 292
            +   A+  M+ +    +P+R++ A+    +
Sbjct: 62  EDADYAIKIMDMIKLYGKPIRVNKASAHNKN 92

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.4 bits (120), Expect = 9e-09
 Identities = 26/84 (30%), Positives = 44/84 (52%), Gaps = 2/84 (2%)

Query: 112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAE 171
            ++  T+++G L   + E  L   F   G VVN  + +++ TGQ +GYGFVEF S   A+
Sbjct: 6   RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDAD 65

Query: 172 KVLQSYSGSLMPNTDQPFRLNWAT 195
             ++      +    +P R+N A+
Sbjct: 66  YAIKIMDMIKLYG--KPIRVNKAS 87

>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 = 61.6 bits (149), Expect = 1e-12
 Identities = 21/84 (25%), Positives = 42/84 (50%), Gaps = 7/84 (8%)

Query: 327 NATIFVGALDSDVSDEDLREP----FSQFGEILSVKIPV---GKGCGFVQFANRKDAEVA 379
           N TI++  L+  +  ++L++     FS+FG+IL + +      +G  FV F     A  A
Sbjct: 3   NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 62

Query: 380 LQKLQGTAIGKQTVRLSWGRNPGN 403
           L+ +QG     + +R+ + +   +
Sbjct: 63  LRSMQGFPFYDKPMRIQYAKTDSD 86

>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 = 56.6 bits (136), Expect = 6e-11
 Identities = 17/80 (21%), Positives = 36/80 (45%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           +I++ +L   +    L+++  + +        I+ S + + +G  FV F + +  + A+ 
Sbjct: 5   TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALR 64

Query: 270 EMNGVYCSSRPMRIDVATPK 289
            M G     +PMRI  A   
Sbjct: 65  SMQGFPFYDKPMRIQYAKTD 84

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.5 bits (102), Expect = 2e-06
 Identities = 19/88 (21%), Positives = 38/88 (43%), Gaps = 4/88 (4%)

Query: 115 TKTIWIGDLFHWMDETFL-HNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKV 173
             TI+I +L   + +  L  +  +   +   +  I   ++ +  G  FV F   ++A   
Sbjct: 3   NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 62

Query: 174 LQSYSGSLMPNTDQPFRLNWATFSGSDR 201
           L+S  G    +  +P R+ +A  + SD 
Sbjct: 63  LRSMQGFPFYD--KPMRIQYAK-TDSDI 87

>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 = 61.2 bits (148), Expect = 1e-12
 Identities = 19/85 (22%), Positives = 39/85 (45%), Gaps = 1/85 (1%)

Query: 321 SDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVAL 380
            D  S+   ++V  L    S+E + + F+        ++   +   FV F+NR+DA  A+
Sbjct: 2   EDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAM 61

Query: 381 QKLQGTAIGKQTVRLSWGRNPGNKQ 405
           + L G  +    + ++  + P +K 
Sbjct: 62  KALNGKVLDGSPIEVTLAK-PVDKD 85

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.1 bits (140), Expect = 2e-11
 Identities = 15/80 (18%), Positives = 34/80 (42%), Gaps = 7/80 (8%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           ++V +L    ++ ++++ F++  P              + + Y FV F +  +   AM  
Sbjct: 11  LYVRNLMLSTSEEMIEKEFNNIKP-------GAVERVKKIRDYAFVHFSNREDAVEAMKA 63

Query: 271 MNGVYCSSRPMRIDVATPKK 290
           +NG      P+ + +A P  
Sbjct: 64  LNGKVLDGSPIEVTLAKPVD 83

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.0 bits (106), Expect = 7e-07
 Identities = 14/82 (17%), Positives = 33/82 (40%), Gaps = 8/82 (9%)

Query: 113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEK 172
              K +++ +L     E  +   F++       +V + +       Y FV F +R  A +
Sbjct: 6   SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRD------YAFVHFSNREDAVE 59

Query: 173 VLQSYSGSLMPNTDQPFRLNWA 194
            +++ +G ++     P  +  A
Sbjct: 60  AMKALNGKVLDG--SPIEVTLA 79

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 61.2 bits (148), Expect = 1e-12
 Identities = 20/81 (24%), Positives = 36/81 (44%), Gaps = 9/81 (11%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGC---------GFVQFANRKDAEVAL 380
           +F+  L+   ++E L+  FS+ G I S  I   K           GFV++   + A+ AL
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 381 QKLQGTAIGKQTVRLSWGRNP 401
           ++LQG  +    + +      
Sbjct: 61  KQLQGHTVDGHKLEVRISERA 81

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 58.5 bits (141), Expect = 1e-11
 Identities = 15/83 (18%), Positives = 35/83 (42%), Gaps = 4/83 (4%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSN---TGRTKGYGFVRFGDENERSRA 267
           +F+ +L    T+  L+  FS K  ++K   +    N      + G+GFV +    +  +A
Sbjct: 1   LFIKNLNFSTTEETLKGVFS-KVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKA 59

Query: 268 MTEMNGVYCSSRPMRIDVATPKK 290
           + ++ G       + + ++    
Sbjct: 60  LKQLQGHTVDGHKLEVRISERAT 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 = 41.9 bits (98), Expect = 8e-06
 Identities = 18/80 (22%), Positives = 32/80 (40%), Gaps = 5/80 (6%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNK---QTGQSEGYGFVEFYSRAAAEKVL 174
           ++I +L     E  L   FS  G + +  + + K       S G+GFVE+     A+K L
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 175 QSYSGSLMPNTDQPFRLNWA 194
           +   G  +        +  +
Sbjct: 61  KQLQGHTVD--GHKLEVRIS 78

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.8 bits (147), Expect = 2e-12
 Identities = 22/87 (25%), Positives = 44/87 (50%), Gaps = 6/87 (6%)

Query: 325 SNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEV 378
           +    ++VG L  +V D+ L   F  FG+I  ++IP+       +G  FV+F   +DA  
Sbjct: 3   TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 62

Query: 379 ALQKLQGTAIGKQTVRLSWGRNPGNKQ 405
           A+  +  + +  +T+R++  +    K+
Sbjct: 63  AIDNMNESELFGRTIRVNLAKPMRIKE 89

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.4 bits (146), Expect = 2e-12
 Identities = 20/81 (24%), Positives = 40/81 (49%), Gaps = 1/81 (1%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
            ++VG LA +V D +L       +  +   ++ +D  T + +G+ FV F    + + A+ 
Sbjct: 7   VLYVGGLAEEVDDKVLHA-AFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65

Query: 270 EMNGVYCSSRPMRIDVATPKK 290
            MN      R +R+++A P +
Sbjct: 66  NMNESELFGRTIRVNLAKPMR 86

>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 = 49.7 bits (118), Expect = 1e-08
 Identities = 18/79 (22%), Positives = 39/79 (49%), Gaps = 2/79 (2%)

Query: 116 KTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQ 175
           + +++G L   +D+  LH  F   G + ++++  + +T +  G+ FVEF     A   + 
Sbjct: 6   RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65

Query: 176 SYSGSLMPNTDQPFRLNWA 194
           + + S +    +  R+N A
Sbjct: 66  NMNESELFG--RTIRVNLA 82

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.8 bits (147), Expect = 2e-12
 Identities = 24/96 (25%), Positives = 45/96 (46%), Gaps = 6/96 (6%)

Query: 311 SNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIP---VGKGCGF 367
           S G  ++G   +   N+  I+VG L  D+  +D+ + F ++G I  + +     G    F
Sbjct: 1   SGGGVIRGPAGN---NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAF 57

Query: 368 VQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGN 403
           V+F + +DAE A+    G       +R+ + R+   
Sbjct: 58  VEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRG 93

>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 = 56.6 bits (136), Expect = 6e-11
 Identities = 20/96 (20%), Positives = 37/96 (38%), Gaps = 4/96 (4%)

Query: 198 GSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVR 257
           G  R     +D  I+VG+L PD+    +++ F          + I   N      + FV 
Sbjct: 4   GVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGA----IRDIDLKNRRGGPPFAFVE 59

Query: 258 FGDENERSRAMTEMNGVYCSSRPMRIDVATPKKASG 293
           F D  +   A+   +G       +R++     + +G
Sbjct: 60  FEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGTG 95

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.0 bits (80), Expect = 0.002
 Identities = 13/82 (15%), Positives = 29/82 (35%), Gaps = 5/82 (6%)

Query: 113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEK 172
           +    I++G+L   +    + + F   G + ++ +   +       + FVEF     AE 
Sbjct: 12  NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGP---PFAFVEFEDPRDAED 68

Query: 173 VLQSYSGSLMPNTDQPFRLNWA 194
            +    G          R+ + 
Sbjct: 69  AVYGRDGYDYDG--YRLRVEFP 88

>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 = 61.2 bits (148), Expect = 2e-12
 Identities = 20/83 (24%), Positives = 38/83 (45%), Gaps = 2/83 (2%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +F+G L+ + T+  L+  +  ++  +    V+ D  + R++G+GFV F    E   AM  
Sbjct: 23  LFIGGLSFETTEESLRNYY-EQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM-A 80

Query: 271 MNGVYCSSRPMRIDVATPKKASG 293
                   R +    A  ++ SG
Sbjct: 81  ARPHSIDGRVVEPKRAVAREESG 103

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.9 bits (129), Expect = 6e-10
 Identities = 19/84 (22%), Positives = 38/84 (45%), Gaps = 3/84 (3%)

Query: 112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAE 171
            ++ + ++IG L     E  L N +   G++ +  V+R+  + +S G+GFV F S A  +
Sbjct: 17  KEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVD 76

Query: 172 KVLQSYSGSLMPNTDQPFRLNWAT 195
             + +   S+     +      A 
Sbjct: 77  AAMAARPHSID---GRVVEPKRAV 97

>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 = 52.4 bits (125), Expect = 3e-09
 Identities = 16/75 (21%), Positives = 35/75 (46%), Gaps = 7/75 (9%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVALQK 382
            +F+G L  + ++E LR  + Q+G++    +         +G GFV F++  + + A+  
Sbjct: 22  KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM-A 80

Query: 383 LQGTAIGKQTVRLSW 397
            +  +I  + V    
Sbjct: 81  ARPHSIDGRVVEPKR 95

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.4 bits (146), Expect = 2e-12
 Identities = 22/75 (29%), Positives = 41/75 (54%), Gaps = 6/75 (8%)

Query: 327 NATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK------GCGFVQFANRKDAEVAL 380
           +A ++V  L   ++ ++L + FSQ+G I++ +I V +      G GF++F  R +AE A+
Sbjct: 6   DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 65

Query: 381 QKLQGTAIGKQTVRL 395
           + L G      T  +
Sbjct: 66  KGLNGQKPSGATEPI 80

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.4 bits (138), Expect = 3e-11
 Identities = 19/78 (24%), Positives = 39/78 (50%)

Query: 117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQS 176
            +++  L   M +  L   FS  G+++  +++ ++ TG S G GF+ F  R  AE+ ++ 
Sbjct: 8   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 67

Query: 177 YSGSLMPNTDQPFRLNWA 194
            +G       +P  + +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 = 55.8 bits (134), Expect = 1e-10
 Identities = 22/81 (27%), Positives = 44/81 (54%), Gaps = 3/81 (3%)

Query: 208 DLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRA 267
           D +++V  L   +T   L++ FS +Y  +  +++++D  TG ++G GF+RF    E   A
Sbjct: 6   DANLYVSGLPKTMTQKELEQLFS-QYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 64

Query: 268 MTEMNG--VYCSSRPMRIDVA 286
           +  +NG     ++ P+ +  A
Sbjct: 65  IKGLNGQKPSGATEPITVKFA 85

>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 = 61.2 bits (148), Expect = 2e-12
 Identities = 21/94 (22%), Positives = 39/94 (41%), Gaps = 4/94 (4%)

Query: 323 GESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV--GKGCGFVQFANRKDAEVAL 380
           G+S    I V  L   V+ + L + FS+FG +L +       +    +Q+A+   A+ A 
Sbjct: 3   GQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAK 62

Query: 381 QKLQGTAI--GKQTVRLSWGRNPGNKQWRGDHSN 412
             L G  I     T+R+ + +         +  +
Sbjct: 63  LSLDGQNIYNACCTLRIDFSKLTSLNVKYNNDKS 96

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.5 bits (128), Expect = 1e-09
 Identities = 18/94 (19%), Positives = 34/94 (36%), Gaps = 7/94 (7%)

Query: 209 LSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAM 268
           L I V +L   VT  +L +   SK+ +V              +    +++ D      A 
Sbjct: 8   LRIIVENLFYPVTLDVLHQ-IFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAK 62

Query: 269 TEMNG--VYCSSRPMRIDVATPKKASGYQQQYSS 300
             ++G  +Y +   +RID +     +       S
Sbjct: 63  LSLDGQNIYNACCTLRIDFSKLTSLNVKYNNDKS 96

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.4 bits (146), Expect = 3e-12
 Identities = 22/81 (27%), Positives = 38/81 (46%), Gaps = 3/81 (3%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
            + V  L    T+  L+E FS  +  V   +V  D  TG +KG+GFVRF +   + + M+
Sbjct: 10  DLIVLGLPWKTTEQDLKEYFS-TFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS 68

Query: 270 EMNGVYCSSRPMRIDVATPKK 290
           + + +    R     +   K+
Sbjct: 69  QRHMI--DGRWCDCKLPNSKQ 87

>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 = 55.7 bits (134), Expect = 1e-10
 Identities = 18/88 (20%), Positives = 35/88 (39%), Gaps = 8/88 (9%)

Query: 323 GESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK------GCGFVQFANRKDA 376
                + + V  L    +++DL+E FS FGE+L V++          G GFV+F   +  
Sbjct: 4   AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQ 63

Query: 377 EVALQKLQGTAIGKQTVRLSWGRNPGNK 404
              + +     I  +        +  ++
Sbjct: 64  VKVMSQRHM--IDGRWCDCKLPNSKQSQ 89

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.9 bits (124), Expect = 3e-09
 Identities = 20/63 (31%), Positives = 32/63 (50%)

Query: 113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEK 172
            +T  + +  L     E  L   FS  G+V+ V+V ++ +TG S+G+GFV F       K
Sbjct: 6   QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVK 65

Query: 173 VLQ 175
           V+ 
Sbjct: 66  VMS 68

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.3 bits (143), Expect = 6e-12
 Identities = 23/82 (28%), Positives = 35/82 (42%), Gaps = 6/82 (7%)

Query: 324 ESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKG------CGFVQFANRKDAE 377
             +NATI V  L  D  + DL+E F  FG I  + +   K         F+ F  R+DA 
Sbjct: 5   ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAA 64

Query: 378 VALQKLQGTAIGKQTVRLSWGR 399
            A+  + G       + + W +
Sbjct: 65  RAIAGVSGFGYDHLILNVEWAK 86

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.4 bits (133), Expect = 1e-10
 Identities = 22/91 (24%), Positives = 44/91 (48%), Gaps = 4/91 (4%)

Query: 199 SDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRF 258
           + R  +  +   I V +L+ D  ++ LQE F   + S+    +  D  TG++KG+ F+ F
Sbjct: 2   NRRADDNAT---IRVTNLSEDTRETDLQELFR-PFGSISRIYLAKDKTTGQSKGFAFISF 57

Query: 259 GDENERSRAMTEMNGVYCSSRPMRIDVATPK 289
               + +RA+  ++G       + ++ A P 
Sbjct: 58  HRREDAARAIAGVSGFGYDHLILNVEWAKPS 88

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.9 bits (116), Expect = 3e-08
 Identities = 23/82 (28%), Positives = 39/82 (47%), Gaps = 2/82 (2%)

Query: 113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEK 172
           D+  TI + +L     ET L   F   G +  + + ++K TGQS+G+ F+ F+ R  A +
Sbjct: 6   DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAAR 65

Query: 173 VLQSYSGSLMPNTDQPFRLNWA 194
            +   SG    +      + WA
Sbjct: 66  AIAGVSGFGYDH--LILNVEWA 85

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.9 bits (142), Expect = 7e-12
 Identities = 19/73 (26%), Positives = 37/73 (50%), Gaps = 2/73 (2%)

Query: 327 NATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGT 386
             T++V   D  ++   LR  FS FG I+ + +   + C FV +   + A+ A+ +L GT
Sbjct: 5   GNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGT 62

Query: 387 AIGKQTVRLSWGR 399
            +    ++++  R
Sbjct: 63  QVESVQLKVNIAR 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 = 53.1 bits (127), Expect = 7e-10
 Identities = 17/80 (21%), Positives = 36/80 (45%), Gaps = 9/80 (11%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           +++V     D+T ++L+  FS           IID +    +   FV +       +A+ 
Sbjct: 7   TLYVYGE--DMTPTLLRGAFSPFGN-------IIDLSMDPPRNCAFVTYEKMESADQAVA 57

Query: 270 EMNGVYCSSRPMRIDVATPK 289
           E+NG    S  +++++A  +
Sbjct: 58  ELNGTQVESVQLKVNIARKQ 77

>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 = 59.4 bits (143), Expect = 7e-12
 Identities = 19/92 (20%), Positives = 36/92 (39%), Gaps = 14/92 (15%)

Query: 322 DGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGC--------------GF 367
           D +S+N+ I+V  L+  V+ +DL + F Q G +   K                       
Sbjct: 3   DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDAT 62

Query: 368 VQFANRKDAEVALQKLQGTAIGKQTVRLSWGR 399
           V + +   A+ A++   G       +++S  R
Sbjct: 63  VSYEDPPTAKAAVEWFDGKDFQGSKLKVSLAR 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 = 51.7 bits (123), Expect = 4e-09
 Identities = 19/87 (21%), Positives = 32/87 (36%), Gaps = 7/87 (8%)

Query: 210 SIFVGDLAPDVTDSILQETFSS-------KYPSVKGAKVIIDSNTGRTKGYGFVRFGDEN 262
           +I+V  L   VT   L + F         K        + +D  TG+ KG   V + D  
Sbjct: 10  AIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPP 69

Query: 263 ERSRAMTEMNGVYCSSRPMRIDVATPK 289
               A+   +G       +++ +A  K
Sbjct: 70  TAKAAVEWFDGKDFQGSKLKVSLARKK 96

>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 = 40.9 bits (95), Expect = 3e-05
 Identities = 15/92 (16%), Positives = 33/92 (35%), Gaps = 10/92 (10%)

Query: 112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVI--------RNKQTGQSEGYGFVE 163
           + +   I++  L   +    L + F   G V   K           +K+TG+ +G   V 
Sbjct: 5   DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVS 64

Query: 164 FYSRAAAEKVLQSYSGSLMPNTDQPFRLNWAT 195
           +     A+  ++ + G          +++ A 
Sbjct: 65  YEDPPTAKAAVEWFDGKDFQG--SKLKVSLAR 94

>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 = 59.4 bits (143), Expect = 8e-12
 Identities = 12/84 (14%), Positives = 29/84 (34%), Gaps = 5/84 (5%)

Query: 323 GESNNATIFVGALDSDV-----SDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAE 377
           G S ++ +     + DV     +       F  + +  + +         + F+N   A 
Sbjct: 1   GSSGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAA 60

Query: 378 VALQKLQGTAIGKQTVRLSWGRNP 401
            A  +L  T    + ++L + +  
Sbjct: 61  DARLRLHKTEFLGKEMKLYFAQTL 84

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.7 bits (110), Expect = 2e-07
 Identities = 8/88 (9%), Positives = 21/88 (23%), Gaps = 2/88 (2%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
            +       DV      ET +      +           ++     + F +    + A  
Sbjct: 7   GLIACVANDDVFSE--SETRAKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAADARL 64

Query: 270 EMNGVYCSSRPMRIDVATPKKASGYQQQ 297
            ++      + M++  A           
Sbjct: 65  RLHKTEFLGKEMKLYFAQTLHIGSSHLA 92

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 59.3 bits (143), Expect = 8e-12
 Identities = 24/91 (26%), Positives = 41/91 (45%), Gaps = 3/91 (3%)

Query: 319 SQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIP-VGKGCGFVQFANRKDAE 377
             S       T+    L  ++++++L+E F    EI  V      KG  +++F +  DAE
Sbjct: 8   CTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAE 67

Query: 378 VALQKLQGTAIGKQTVRLSWGRNPGNKQWRG 408
             L++ QG  I  ++V L +    G    RG
Sbjct: 68  KNLEEKQGAEIDGRSVSLYYTGEKGGT--RG 96

>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 = 57.7 bits (139), Expect = 3e-11
 Identities = 15/83 (18%), Positives = 35/83 (42%), Gaps = 6/83 (7%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           ++   +L+ ++T+  L+E F           + + S  G++KG  ++ F  E +  + + 
Sbjct: 18  TLLAKNLSFNITEDELKEVFEDALE------IRLVSQDGKSKGIAYIEFKSEADAEKNLE 71

Query: 270 EMNGVYCSSRPMRIDVATPKKAS 292
           E  G     R + +     K  +
Sbjct: 72  EKQGAEIDGRSVSLYYTGEKGGT 94

>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 = 45.4 bits (107), Expect = 5e-07
 Identities = 21/88 (23%), Positives = 36/88 (40%), Gaps = 7/88 (7%)

Query: 114 ETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKV 173
             +T+   +L   + E  L   F    ++  V        G+S+G  ++EF S A AEK 
Sbjct: 15  AARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAYIEFKSEADAEKN 69

Query: 174 LQSYSGSLMPNTDQPFRLNWATFSGSDR 201
           L+   G+ +    +   L +    G  R
Sbjct: 70  LEEKQGAEIDG--RSVSLYYTGEKGGTR 95

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 58.5 bits (141), Expect = 8e-12
 Identities = 22/76 (28%), Positives = 38/76 (50%), Gaps = 2/76 (2%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +F+G L+   T   L+E F  ++  VK   V+ D  T R++G+GFV F D+    + +  
Sbjct: 3   MFIGGLSWQTTQEGLREYF-GQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-A 60

Query: 271 MNGVYCSSRPMRIDVA 286
            +     S+ +   VA
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 = 56.1 bits (135), Expect = 6e-11
 Identities = 19/74 (25%), Positives = 30/74 (40%), Gaps = 7/74 (9%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK------GCGFVQFANRKDAEVALQKL 383
           +F+G L    + E LRE F QFGE+    +          G GFV F ++   +  L   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQ 61

Query: 384 QGTAIGKQTVRLSW 397
               +  +T+    
Sbjct: 62  SRHELDSKTIDPKV 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 = 52.3 bits (125), Expect = 1e-09
 Identities = 20/58 (34%), Positives = 30/58 (51%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQ 175
           ++IG L     +  L   F   G+V    V+R+  T +S G+GFV F  +A  +KVL 
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.5 bits (141), Expect = 1e-11
 Identities = 29/86 (33%), Positives = 43/86 (50%), Gaps = 4/86 (4%)

Query: 318 GSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKI----PVGKGCGFVQFANR 373
              S+ +S    + V  +     D DLR+ F QFG+IL V+I       KG GFV F N 
Sbjct: 2   SGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENS 61

Query: 374 KDAEVALQKLQGTAIGKQTVRLSWGR 399
            DA+ A +KL GT +  + + ++   
Sbjct: 62  ADADRAREKLHGTVVEGRKIEVNNAT 87

>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 = 52.8 bits (126), Expect = 1e-09
 Identities = 15/79 (18%), Positives = 37/79 (46%), Gaps = 3/79 (3%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           + V ++     D  L++ F  ++  +   ++I +    +   +GFV F +  +  RA  +
Sbjct: 14  LHVSNIPFRFRDPDLRQMFG-QFGKILDVEIIFNERGSKG--FGFVTFENSADADRAREK 70

Query: 271 MNGVYCSSRPMRIDVATPK 289
           ++G     R + ++ AT +
Sbjct: 71  LHGTVVEGRKIEVNNATAR 89

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.6 bits (97), Expect = 1e-05
 Identities = 21/90 (23%), Positives = 47/90 (52%), Gaps = 4/90 (4%)

Query: 106 SNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFY 165
           S N+ +    K + + ++     +  L   F   G++++V++I N++   S+G+GFV F 
Sbjct: 2   SGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFE 59

Query: 166 SRAAAEKVLQSYSGSLMPNTDQPFRLNWAT 195
           + A A++  +   G+++    +   +N AT
Sbjct: 60  NSADADRAREKLHGTVVEG--RKIEVNNAT 87

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.2 bits (140), Expect = 1e-11
 Identities = 22/83 (26%), Positives = 40/83 (48%), Gaps = 7/83 (8%)

Query: 318 GSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILS------VKIPVGKGCGFVQFA 371
           G++++ + N   + V  L    ++ DLRE FS++G I         +    +G  FV F 
Sbjct: 1   GNRANPDPNC-CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFE 59

Query: 372 NRKDAEVALQKLQGTAIGKQTVR 394
           N  DA+ A ++  G  +  + +R
Sbjct: 60  NVDDAKEAKERANGMELDGRRIR 82

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.1 bits (119), Expect = 8e-09
 Identities = 20/74 (27%), Positives = 37/74 (50%), Gaps = 1/74 (1%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
            + V  L+   T+  L+E FS KY  +    ++ D  + R++G+ FV F + ++   A  
Sbjct: 11  CLGVFGLSLYTTERDLREVFS-KYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 69

Query: 270 EMNGVYCSSRPMRI 283
             NG+    R +R+
Sbjct: 70  RANGMELDGRRIRV 83

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.2 bits (109), Expect = 2e-07
 Identities = 16/70 (22%), Positives = 34/70 (48%)

Query: 113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEK 172
           D    + +  L  +  E  L   FS  G + +V ++ ++Q+ +S G+ FV F +   A++
Sbjct: 7   DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 66

Query: 173 VLQSYSGSLM 182
             +  +G  +
Sbjct: 67  AKERANGMEL 76

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.7 bits (139), Expect = 2e-11
 Identities = 23/84 (27%), Positives = 42/84 (50%), Gaps = 3/84 (3%)

Query: 323 GESNNATIFVGALDSDVSDEDLREPFSQFGEILSVK-IPVGKGCGFVQFANRKDAEVALQ 381
           G S ++ +FVG    D+++++LRE FSQ+G+++ V      +   FV FA+ + A+    
Sbjct: 1   GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG 60

Query: 382 KLQGTAIGKQTVRLSWGRNPGNKQ 405
             +   I   +V +S      N  
Sbjct: 61  --EDLIIKGISVHISNAEPKHNSN 82

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.1 bits (101), Expect = 3e-06
 Identities = 18/84 (21%), Positives = 28/84 (33%), Gaps = 8/84 (9%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
            +FVG    D+T+  L+E FS     +              + + FV F D+        
Sbjct: 7   GVFVGRCTGDMTEDELREFFSQYGDVMD------VFIPKPFRAFAFVTFADDQIAQSLC- 59

Query: 270 EMNGVYCSSRPMRIDVATPKKASG 293
               +      + I  A PK  S 
Sbjct: 60  -GEDLIIKGISVHISNAEPKHNSN 82

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.9 bits (85), Expect = 5e-04
 Identities = 13/64 (20%), Positives = 26/64 (40%), Gaps = 5/64 (7%)

Query: 112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAE 171
           +  +  +++G     M E  L   FS  G V++V + +  +      + FV F     A+
Sbjct: 2   SSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFR-----AFAFVTFADDQIAQ 56

Query: 172 KVLQ 175
            +  
Sbjct: 57  SLCG 60

>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 = 56.6 bits (136), Expect = 4e-11
 Identities = 15/77 (19%), Positives = 37/77 (48%), Gaps = 1/77 (1%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTA- 387
            +++G L   V+ +DLR+ F      L+ ++ +  G  FV + ++  A  A++ L G   
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVE 62

Query: 388 IGKQTVRLSWGRNPGNK 404
           +  + + + +  +   +
Sbjct: 63  LHGKIMEVDYSVSKKLR 79

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.8 bits (134), Expect = 8e-11
 Identities = 21/81 (25%), Positives = 38/81 (46%), Gaps = 8/81 (9%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +++G+L+P VT   L++ F          K+ +        GY FV + D+N   RA+  
Sbjct: 4   LYIGNLSPAVTADDLRQLFGD-------RKLPLAGQVLLKSGYAFVDYPDQNWAIRAIET 56

Query: 271 MNGVY-CSSRPMRIDVATPKK 290
           ++G      + M +D +  KK
Sbjct: 57  LSGKVELHGKIMEVDYSVSKK 77

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.6 bits (84), Expect = 4e-04
 Identities = 13/79 (16%), Positives = 34/79 (43%), Gaps = 7/79 (8%)

Query: 117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQS 176
            ++IG+L   +    L   F      +  +V+         GY FV++  +  A + +++
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKS------GYAFVDYPDQNWAIRAIET 56

Query: 177 YSGSLMPNTDQPFRLNWAT 195
            SG +  +  +   ++++ 
Sbjct: 57  LSGKVELH-GKIMEVDYSV 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 = 57.0 bits (137), Expect = 4e-11
 Identities = 15/81 (18%), Positives = 33/81 (40%), Gaps = 10/81 (12%)

Query: 327 NATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV--------GKGCGFVQFANRKDAEV 378
           N  +F+G +      E++ E  ++  E +   I           +G  FV++ + + A +
Sbjct: 1   NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAM 60

Query: 379 ALQKLQG--TAIGKQTVRLSW 397
           A +KL      +    + + W
Sbjct: 61  ARRKLMPGRIQLWGHQIAVDW 81

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.8 bits (126), Expect = 1e-09
 Identities = 12/83 (14%), Positives = 30/83 (36%), Gaps = 3/83 (3%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVI-IDSNTGRTKGYGFVRFGDENERSRAMT 269
           +F+G +        + E  +     V    V    ++  + +G+ FV +      + A  
Sbjct: 4   LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 63

Query: 270 EMNG--VYCSSRPMRIDVATPKK 290
           ++    +      + +D A P+ 
Sbjct: 64  KLMPGRIQLWGHQIAVDWAEPEI 86

>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 = 45.5 bits (107), Expect = 5e-07
 Identities = 12/80 (15%), Positives = 27/80 (33%), Gaps = 2/80 (2%)

Query: 117 TIWIGDLFHWMDETFLHNCFSHTGQVVN--VKVIRNKQTGQSEGYGFVEFYSRAAAEKVL 174
            ++IG +        +    +   + V   +         ++ G+ FVE+ S  AA    
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 175 QSYSGSLMPNTDQPFRLNWA 194
           +      +        ++WA
Sbjct: 63  RKLMPGRIQLWGHQIAVDWA 82

>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 = 56.7 bits (136), Expect = 7e-11
 Identities = 15/78 (19%), Positives = 34/78 (43%), Gaps = 5/78 (6%)

Query: 325 SNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQ 384
           + +  +  G L + VS   L     + G + ++ +P  K   F ++   ++++ A   L 
Sbjct: 18  TQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLN 77

Query: 385 GTAIG-----KQTVRLSW 397
           G  +      K T+ L++
Sbjct: 78  GKEVVDDLGQKITLYLNF 95

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.3 bits (104), Expect = 1e-06
 Identities = 17/91 (18%), Positives = 27/91 (29%), Gaps = 8/91 (8%)

Query: 196 FSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGF 255
             G +  + A   L +  G L   V+ + L                +        K Y F
Sbjct: 8   HEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGL-------VDALLMPPNKPYSF 60

Query: 256 VRFGDENERSRAMTEMNGVY-CSSRPMRIDV 285
            R+    E  RA   +NG         +I +
Sbjct: 61  ARYRTTEESKRAYVTLNGKEVVDDLGQKITL 91

>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 = 36.6 bits (84), Expect = 8e-04
 Identities = 14/96 (14%), Positives = 33/96 (34%), Gaps = 9/96 (9%)

Query: 102 KQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGF 161
           +  G        ++  +  G L + +    L       G V  + +  NK       Y F
Sbjct: 7   RHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP------YSF 60

Query: 162 VEFYSRAAAEKVLQSYSGS-LMPNTDQP--FRLNWA 194
             + +   +++   + +G  ++ +  Q     LN+ 
Sbjct: 61  ARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFV 96

>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 = 56.6 bits (136), Expect = 7e-11
 Identities = 22/94 (23%), Positives = 36/94 (38%), Gaps = 6/94 (6%)

Query: 321 SDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK------GCGFVQFANRK 374
           S G S +  +FV  L    S+EDL + FS +G +  +  P+        G  FV F   +
Sbjct: 2   SSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPE 61

Query: 375 DAEVALQKLQGTAIGKQTVRLSWGRNPGNKQWRG 408
            A  A  ++ G     + + +            G
Sbjct: 62  HAVKAYAEVDGQVFQGRMLHVLPSTIKKEASQSG 95

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.2 bits (114), Expect = 7e-08
 Identities = 23/82 (28%), Positives = 40/82 (48%), Gaps = 1/82 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +FV +L+   ++  L++ FS  Y  +      IDS T + KG+ FV F       +A  E
Sbjct: 11  LFVRNLSYTSSEEDLEKLFS-AYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69

Query: 271 MNGVYCSSRPMRIDVATPKKAS 292
           ++G     R + +  +T KK +
Sbjct: 70  VDGQVFQGRMLHVLPSTIKKEA 91

>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 = 42.0 bits (98), Expect = 9e-06
 Identities = 15/83 (18%), Positives = 31/83 (37%), Gaps = 2/83 (2%)

Query: 113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEK 172
             +  +++ +L +   E  L   FS  G +  +    +  T + +G+ FV F     A K
Sbjct: 6   SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVK 65

Query: 173 VLQSYSGSLMPNTDQPFRLNWAT 195
                 G +     +   +  +T
Sbjct: 66  AYAEVDGQVFQG--RMLHVLPST 86

>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 = 56.7 bits (136), Expect = 8e-11
 Identities = 19/90 (21%), Positives = 31/90 (34%), Gaps = 1/90 (1%)

Query: 317 QGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANR-KD 375
                + +      F G LD     EDL   FS  GEI  +    G   G + F  + K+
Sbjct: 1   HHGSLEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAKE 60

Query: 376 AEVALQKLQGTAIGKQTVRLSWGRNPGNKQ 405
           A    +      +  +   ++W    G  +
Sbjct: 61  ALGKAKDANNGNLQLRNKEVTWEVLEGEVE 90

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.9 bits (82), Expect = 0.002
 Identities = 17/93 (18%), Positives = 27/93 (29%), Gaps = 10/93 (10%)

Query: 198 GSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVR 257
           GS      C  L  F GDL        L   FS+          I   +  R    G + 
Sbjct: 3   GSLEEKIGC--LLKFSGDLDDQTCREDLHILFSNHGE-------IKWIDFVRGAKEGIIL 53

Query: 258 FGDENERS-RAMTEMNGVYCSSRPMRIDVATPK 289
           F ++ + +     + N      R   +     +
Sbjct: 54  FKEKAKEALGKAKDANNGNLQLRNKEVTWEVLE 86

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.4 bits (133), Expect = 1e-10
 Identities = 19/68 (27%), Positives = 32/68 (47%), Gaps = 6/68 (8%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK------GCGFVQFANRKDAEVALQKL 383
           IFVG L  D  +E +RE F  FGE+ S+++P+        G  F+ F   +  +  ++K 
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61

Query: 384 QGTAIGKQ 391
                  +
Sbjct: 62  YHNVGLSK 69

>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 = 21/76 (27%), Positives = 37/76 (48%), Gaps = 2/76 (2%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           IFVG L+PD  +  ++E F   +  V+  ++ +D+ T + +G+ F+ F +E    + M E
Sbjct: 2   IFVGGLSPDTPEEKIREYF-GGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM-E 59

Query: 271 MNGVYCSSRPMRIDVA 286
                       I VA
Sbjct: 60  KKYHNVGLSKCEIKVA 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 = 48.4 bits (115), Expect = 3e-08
 Identities = 12/58 (20%), Positives = 29/58 (50%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQ 175
           I++G L     E  +   F   G+V ++++  + +T +  G+ F+ F      +K+++
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 59

>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 = 55.4 bits (133), Expect = 1e-10
 Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 2/76 (2%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +F+G L+ + TD  L+  F  ++ ++    V+ D NT R++G+GFV +    E   AM  
Sbjct: 9   LFIGGLSFETTDESLRSHF-EQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-N 66

Query: 271 MNGVYCSSRPMRIDVA 286
                   R +    A
Sbjct: 67  ARPHKVDGRVVEPKRA 82

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.0 bits (124), Expect = 2e-09
 Identities = 14/70 (20%), Positives = 33/70 (47%)

Query: 113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEK 172
           ++ + ++IG L     +  L + F   G + +  V+R+  T +S G+GFV + +    + 
Sbjct: 4   EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 63

Query: 173 VLQSYSGSLM 182
            + +    + 
Sbjct: 64  AMNARPHKVD 73

>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 = 49.3 bits (117), Expect = 2e-08
 Identities = 17/69 (24%), Positives = 31/69 (44%), Gaps = 6/69 (8%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVALQK 382
            +F+G L  + +DE LR  F Q+G +    +         +G GFV +A  ++ + A+  
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67

Query: 383 LQGTAIGKQ 391
                 G+ 
Sbjct: 68  RPHKVDGRV 76

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.1 bits (132), Expect = 1e-10
 Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 6/77 (7%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVALQK 382
            + V  L  +++ E+ R  F   GEI S K+          G GFV + + KDAE A+  
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 383 LQGTAIGKQTVRLSWGR 399
           L G  +  +T+++S+ R
Sbjct: 64  LNGLRLQTKTIKVSYAR 80

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.0 bits (129), Expect = 4e-10
 Identities = 20/82 (24%), Positives = 42/82 (51%), Gaps = 1/82 (1%)

Query: 207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSR 266
           S  ++ V  L  ++T    +  F      ++  K++ D  TG++ GYGFV + D  +  +
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFG-SIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEK 59

Query: 267 AMTEMNGVYCSSRPMRIDVATP 288
           A+  +NG+   ++ +++  A P
Sbjct: 60  AINTLNGLRLQTKTIKVSYARP 81

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 55.4 bits (133), Expect = 1e-10
 Identities = 15/76 (19%), Positives = 32/76 (42%), Gaps = 1/76 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           I V ++   V+   +   F   Y  + G+  +  +  G   G   V F   +E + A+ +
Sbjct: 12  IKVQNMPFTVSIDEIL-DFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID 70

Query: 271 MNGVYCSSRPMRIDVA 286
           +N     SR +++ + 
Sbjct: 71  LNDRPIGSRKVKLVLG 86

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 50.4 bits (120), Expect = 7e-09
 Identities = 20/84 (23%), Positives = 32/84 (38%), Gaps = 6/84 (7%)

Query: 321 SDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRK 374
           S G+     I V  +   VS +++ + F  +  I               G   V F +R 
Sbjct: 3   SSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRD 62

Query: 375 DAEVALQKLQGTAIGKQTVRLSWG 398
           +A  A+  L    IG + V+L  G
Sbjct: 63  EATAAVIDLNDRPIGSRKVKLVLG 86

>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 = 55.5 bits (133), Expect = 2e-10
 Identities = 23/102 (22%), Positives = 41/102 (40%), Gaps = 1/102 (0%)

Query: 191 LNWATFSGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRT 250
           L   +   +  + E     ++F+  L  +  D  L + F      V   KV ID  T  +
Sbjct: 1   LTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSA-KVFIDKQTNLS 59

Query: 251 KGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKAS 292
           K +GFV + +      A+  MNG     + +++ +   K  S
Sbjct: 60  KCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDS 101

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.1 bits (132), Expect = 3e-10
 Identities = 25/88 (28%), Positives = 43/88 (48%), Gaps = 7/88 (7%)

Query: 318 GSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCG------FVQFA 371
           GSQ +G      +F+  L  +  D+DL + F  FG ++S K+ + K         FV + 
Sbjct: 10  GSQKEGPEGA-NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYD 68

Query: 372 NRKDAEVALQKLQGTAIGKQTVRLSWGR 399
           N   A+ A+Q + G  IG + +++   R
Sbjct: 69  NPVSAQAAIQSMNGFQIGMKRLKVQLKR 96

>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 = 42.8 bits (100), Expect = 5e-06
 Identities = 27/110 (24%), Positives = 49/110 (44%), Gaps = 10/110 (9%)

Query: 93  QQQHGLSNGKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQ 152
           QQ  G +  ++ G        E   ++I  L     +  L   F   G VV+ KV  +KQ
Sbjct: 3   QQSIGAAGSQKEG-------PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQ 55

Query: 153 TGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATFSGSDRR 202
           T  S+ +GFV + +  +A+  +QS +G  +    +  ++     S +D +
Sbjct: 56  TNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGM--KRLKVQLKR-SKNDSK 102

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.8 bits (131), Expect = 2e-10
 Identities = 26/80 (32%), Positives = 41/80 (51%), Gaps = 1/80 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +FVG L+ D  +  L++ FS      +   V+ D  T R++G+GFV F + ++   AM  
Sbjct: 8   LFVGGLSFDTNEQSLEQVFSKYGQISEV-VVVKDRETQRSRGFGFVTFENIDDAKDAMMA 66

Query: 271 MNGVYCSSRPMRIDVATPKK 290
           MNG     R +R+D A    
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 = 51.7 bits (123), Expect = 3e-09
 Identities = 23/88 (26%), Positives = 44/88 (50%), Gaps = 6/88 (6%)

Query: 324 ESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAE 377
            S+   +FVG L  D +++ L + FS++G+I  V +         +G GFV F N  DA+
Sbjct: 2   ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAK 61

Query: 378 VALQKLQGTAIGKQTVRLSWGRNPGNKQ 405
            A+  + G ++  + +R+       + +
Sbjct: 62  DAMMAMNGKSVDGRQIRVDQAGKSSDNR 89

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.0 bits (98), Expect = 8e-06
 Identities = 24/90 (26%), Positives = 47/90 (52%), Gaps = 3/90 (3%)

Query: 114 ETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKV 173
           +   +++G L    +E  L   FS  GQ+  V V+++++T +S G+GFV F +   A+  
Sbjct: 4   DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 63

Query: 174 LQSYSGSLMPNTDQPFRLNWATFSGSDRRT 203
           + + +G  +    +  R++ A    SD R+
Sbjct: 64  MMAMNGKSVDG--RQIRVDQAG-KSSDNRS 90

>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 = 53.8 bits (129), Expect = 5e-10
 Identities = 11/75 (14%), Positives = 27/75 (36%), Gaps = 1/75 (1%)

Query: 326 NNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQG 385
           ++  + V       +   L + F+Q+G IL   +        +++ ++  A  AL K   
Sbjct: 3   DDTWVTVFGFPQASASYILLQ-FAQYGNILKHVMSNTGNWMHIRYQSKLQARKALSKDGR 61

Query: 386 TAIGKQTVRLSWGRN 400
                  + +    +
Sbjct: 62  IFGESIMIGVKPCID 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 = 42.2 bits (99), Expect = 6e-06
 Identities = 10/83 (12%), Positives = 22/83 (26%), Gaps = 10/83 (12%)

Query: 208 DLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRA 267
           D  + V          IL +               +      T  +  +R+  + +  +A
Sbjct: 4   DTWVTVFGFPQASASYILLQFAQYGNI--------LKHVMSNTGNWMHIRYQSKLQARKA 55

Query: 268 MTEMNGVYCSSRPM-RIDVATPK 289
           +   +G       M  +     K
Sbjct: 56  L-SKDGRIFGESIMIGVKPCIDK 77

>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 = 54.0 bits (129), Expect = 6e-10
 Identities = 31/96 (32%), Positives = 51/96 (53%), Gaps = 1/96 (1%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           S+FVG++  + T+  L++ FS   P V   +++ D  TG+ KGYGF  + D+     AM 
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSF-RLVYDRETGKPKGYGFCEYQDQETALSAMR 68

Query: 270 EMNGVYCSSRPMRIDVATPKKASGYQQQYSSQALVL 305
            +NG   S R +R+D A  +K     +   + A V+
Sbjct: 69  NLNGREFSGRALRVDNAASEKNKEELKSLGTGAPVI 104

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.5 bits (125), Expect = 2e-09
 Identities = 20/88 (22%), Positives = 47/88 (53%), Gaps = 6/88 (6%)

Query: 324 ESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAE 377
           + +  ++FVG +  + ++E L++ FS+ G ++S ++         KG GF ++ +++ A 
Sbjct: 5   DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETAL 64

Query: 378 VALQKLQGTAIGKQTVRLSWGRNPGNKQ 405
            A++ L G     + +R+    +  NK+
Sbjct: 65  SAMRNLNGREFSGRALRVDNAASEKNKE 92

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.1 bits (98), Expect = 1e-05
 Identities = 19/84 (22%), Positives = 47/84 (55%), Gaps = 2/84 (2%)

Query: 112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAE 171
           +   +++++G++ +   E  L + FS  G VV+ +++ +++TG+ +GYGF E+  +  A 
Sbjct: 5   DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETAL 64

Query: 172 KVLQSYSGSLMPNTDQPFRLNWAT 195
             +++ +G       +  R++ A 
Sbjct: 65  SAMRNLNGREFSG--RALRVDNAA 86

>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 = 54.0 bits (129), Expect = 7e-10
 Identities = 19/80 (23%), Positives = 39/80 (48%), Gaps = 1/80 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +++ +L+P VT+  L     +++   KG  +     TGR +G  F+ F ++    +A+  
Sbjct: 21  LYLKNLSPRVTERDLVS-LFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 79

Query: 271 MNGVYCSSRPMRIDVATPKK 290
           +NG     + + I+    KK
Sbjct: 80  VNGYKLYGKILVIEFGKNKK 99

>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 = 46.7 bits (110), Expect = 2e-07
 Identities = 22/92 (23%), Positives = 41/92 (44%), Gaps = 7/92 (7%)

Query: 319 SQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK------GCGFVQFAN 372
           S + GE N   +++  L   V++ DL   F++F E     I          G  F+ F N
Sbjct: 11  SYNPGEPNK-VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPN 69

Query: 373 RKDAEVALQKLQGTAIGKQTVRLSWGRNPGNK 404
           ++ A  AL  + G  +  + + + +G+N   +
Sbjct: 70  KEIAWQALHLVNGYKLYGKILVIEFGKNKKQR 101

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.5 bits (94), Expect = 3e-05
 Identities = 13/88 (14%), Positives = 34/88 (38%), Gaps = 2/88 (2%)

Query: 108 NNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSR 167
           +    +  K +++ +L   + E  L + F+   +     +     TG+  G  F+ F ++
Sbjct: 11  SYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNK 70

Query: 168 AAAEKVLQSYSGSLMPNTDQPFRLNWAT 195
             A + L   +G  +    +   + +  
Sbjct: 71  EIAWQALHLVNGYKLYG--KILVIEFGK 96

>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 = 53.2 bits (127), Expect = 1e-09
 Identities = 18/82 (21%), Positives = 39/82 (47%), Gaps = 6/82 (7%)

Query: 327 NATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGC------GFVQFANRKDAEVAL 380
              +FV ++  +  +++++E F  +GEI ++ + + +          V++   K A  A 
Sbjct: 7   GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAK 66

Query: 381 QKLQGTAIGKQTVRLSWGRNPG 402
           + L G  I  QT+++ W    G
Sbjct: 67  EALNGAEIMGQTIQVDWCFVKG 88

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 49.3 bits (117), Expect = 2e-08
 Identities = 19/80 (23%), Positives = 35/80 (43%), Gaps = 1/80 (1%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
            +FV  +  +  +  +QE F   Y  +K   + +D  TG +KGY  V +    +   A  
Sbjct: 9   ILFVTSIHEEAQEDEIQEKFC-DYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 67

Query: 270 EMNGVYCSSRPMRIDVATPK 289
            +NG     + +++D    K
Sbjct: 68  ALNGAEIMGQTIQVDWCFVK 87

>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 = 52.3 bits (125), Expect = 1e-09
 Identities = 21/76 (27%), Positives = 38/76 (50%), Gaps = 2/76 (2%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +F+G L+ D T   L++ F SK+  V    + +D  TGR++G+GFV F +     + M +
Sbjct: 2   MFIGGLSWDTTKKDLKDYF-SKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVM-D 59

Query: 271 MNGVYCSSRPMRIDVA 286
                 + + +    A
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 = 50.4 bits (120), Expect = 6e-09
 Identities = 15/71 (21%), Positives = 33/71 (46%), Gaps = 7/71 (9%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKG------CGFVQFANRKDAEVALQKL 383
           +F+G L  D + +DL++ FS+FGE++   + +          GFV F   +  +  +   
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVM-DQ 60

Query: 384 QGTAIGKQTVR 394
           +   +  + + 
Sbjct: 61  KEHKLNGKVID 71

>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 = 46.5 bits (110), Expect = 1e-07
 Identities = 20/65 (30%), Positives = 33/65 (50%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY 177
           ++IG L     +  L + FS  G+VV+  +  +  TG+S G+GFV F    + +KV+   
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61

Query: 178 SGSLM 182
              L 
Sbjct: 62  EHKLN 66

>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 = 52.4 bits (125), Expect = 1e-09
 Identities = 15/90 (16%), Positives = 40/90 (44%), Gaps = 12/90 (13%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKV-----IIDSNTGRTKGYGFVRFGDENERS 265
           ++VG++   +T+  + + F+     + G        ++     + K + F+ F   +E +
Sbjct: 4   LYVGNIPFGITEEAMMDFFN-AQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 266 RAMTEMNGVYCSSRPMRIDVATPKKASGYQ 295
           +AM   +G+    + ++I     ++   YQ
Sbjct: 63  QAMA-FDGIIFQGQSLKI-----RRPHDYQ 86

>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 = 50.1 bits (119), Expect = 1e-08
 Identities = 13/89 (14%), Positives = 34/89 (38%), Gaps = 16/89 (17%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-----------KGCGFVQFANRKDAE 377
            ++VG +   +++E + + F+    +  +    G           K   F++F +  +  
Sbjct: 3   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 378 VALQKLQGTAIGKQTVRLSWGRN----PG 402
            A+    G     Q++++    +    PG
Sbjct: 63  QAMA-FDGIIFQGQSLKIRRPHDYQPLPG 90

>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 = 44.0 bits (103), Expect = 2e-06
 Identities = 9/65 (13%), Positives = 28/65 (43%), Gaps = 5/65 (7%)

Query: 116 KTIWIGDLFHWMDETFLHNCFSHTGQVVNVKV-----IRNKQTGQSEGYGFVEFYSRAAA 170
           + +++G++   + E  + + F+   ++  +       +   Q  Q + + F+EF S    
Sbjct: 2   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 61

Query: 171 EKVLQ 175
            + + 
Sbjct: 62  TQAMA 66

>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 = 53.4 bits (127), Expect = 1e-09
 Identities = 19/83 (22%), Positives = 32/83 (38%)

Query: 318 GSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAE 377
           GS      +   I    L +     +++E FS+FG +  V +P G     V+F    +A 
Sbjct: 1   GSSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEAR 60

Query: 378 VALQKLQGTAIGKQTVRLSWGRN 400
            A + L  +      + L W   
Sbjct: 61  KAFRHLAYSKFHHVPLYLEWAPI 83

>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 = 43.4 bits (101), Expect = 4e-06
 Identities = 21/105 (20%), Positives = 31/105 (29%), Gaps = 11/105 (10%)

Query: 197 SGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFV 256
           SGS  R    S   I   +L      + +QETFS                         V
Sbjct: 3   SGSSGR----SKTVILAKNLPAGTLAAEIQETFSRFGSLG-------RVLLPEGGITAIV 51

Query: 257 RFGDENERSRAMTEMNGVYCSSRPMRIDVATPKKASGYQQQYSSQ 301
            F +  E  +A   +        P+ ++ A         Q+  SQ
Sbjct: 52  EFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQ 96

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.2 bits (125), Expect = 2e-09
 Identities = 16/58 (27%), Positives = 27/58 (46%), Gaps = 2/58 (3%)

Query: 342 EDLREPFSQFGEILSVKIPVG--KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSW 397
           EDLR   S+FG+I  + +      G   V F + ++A+  +Q L G   G + +    
Sbjct: 34  EDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQA 91

>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 = 49.1 bits (117), Expect = 3e-08
 Identities = 10/78 (12%), Positives = 22/78 (28%), Gaps = 10/78 (12%)

Query: 212 FVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEM 271
            + ++  D+          SK+  +      +        G   V F D  E    +  +
Sbjct: 28  VLNEIREDL------RVECSKFGQI----RKLLLFDRHPDGVASVSFRDPEEADYCIQTL 77

Query: 272 NGVYCSSRPMRIDVATPK 289
           +G +   R +        
Sbjct: 78  DGRWFGGRQITAQAWDGT 95

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.6 bits (87), Expect = 3e-04
 Identities = 11/75 (14%), Positives = 25/75 (33%), Gaps = 11/75 (14%)

Query: 108 NNFTNDETKT--IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFY 165
           N F   + +   + + ++   +         S  GQ+  + +         +G   V F 
Sbjct: 15  NMFHPMDFEDDPLVLNEIREDLRV-----ECSKFGQIRKLLLFDRHP----DGVASVSFR 65

Query: 166 SRAAAEKVLQSYSGS 180
               A+  +Q+  G 
Sbjct: 66  DPEEADYCIQTLDGR 80

>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 = 51.7 bits (123), Expect = 2e-09
 Identities = 16/81 (19%), Positives = 35/81 (43%), Gaps = 2/81 (2%)

Query: 210 SIFVGDLAPDVTD-SILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAM 268
            I + +L+ ++ D ++L+E+F       K                 F+ F +++   RA+
Sbjct: 6   EIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL 65

Query: 269 TEMNGVYCSSRPMRIDVATPK 289
            +MN     +R + + +A  K
Sbjct: 66  -QMNRSLLGNREISVSLADKK 85

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 39.3 bits (91), Expect = 5e-05
 Identities = 23/79 (29%), Positives = 38/79 (48%), Gaps = 9/79 (11%)

Query: 329 TIFVGALDSDVSDED-LREPFSQFGEILSVKIPV-------GKGCGFVQFANRKDAEVAL 380
            I +  L +++ DE+ LRE F  FG I  + IP           C F+ F N+  AE AL
Sbjct: 6   EIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL 65

Query: 381 QKLQGTAIGKQTVRLSWGR 399
            ++  + +G + + +S   
Sbjct: 66  -QMNRSLLGNREISVSLAD 83

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 51.3 bits (122), Expect = 6e-09
 Identities = 23/96 (23%), Positives = 36/96 (37%), Gaps = 8/96 (8%)

Query: 307 GGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCG 366
           G  GS+G+  + S S        + V  L   V + DL E   +FG I  V +   K   
Sbjct: 1   GSSGSSGSHHKVSVS------PVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQA 54

Query: 367 FVQFANRKDAEVALQKLQGTA--IGKQTVRLSWGRN 400
            V+F N   A+  +         I  Q    ++  +
Sbjct: 55  LVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTS 90

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 38.2 bits (88), Expect = 3e-04
 Identities = 16/104 (15%), Positives = 35/104 (33%), Gaps = 6/104 (5%)

Query: 101 GKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYG 160
           G    S ++     +  + +  L   + E  L       G +  V ++  K+        
Sbjct: 1   GSSGSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR------QA 54

Query: 161 FVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATFSGSDRRTE 204
            VEF +  +A++ +   +   +    Q    N++T     R   
Sbjct: 55  LVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRITRPGN 98

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.9 bits (87), Expect = 3e-04
 Identities = 16/98 (16%), Positives = 29/98 (29%), Gaps = 11/98 (11%)

Query: 197 SGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFV 256
           SGS  +        + V  L   V ++ L E                       K    V
Sbjct: 6   SGSHHKVSVSP--VVHVRGLCESVVEADLVEALEKFGTIC-------YVMMMPFKRQALV 56

Query: 257 RFGDENERSRAMTEM--NGVYCSSRPMRIDVATPKKAS 292
            F + +     +T      VY + +    + +T K+ +
Sbjct: 57  EFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRIT 94

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 50.8 bits (121), Expect = 6e-09
 Identities = 23/94 (24%), Positives = 46/94 (48%), Gaps = 5/94 (5%)

Query: 310 GSNGARVQGSQSDGESN-NATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFV 368
           GS+G+   G    G++N    ++VG L  + S   L   F +FG I ++    G    ++
Sbjct: 1   GSSGS--SGKIGYGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYI 58

Query: 369 QFANRKDAEVALQKLQGTAIGKQT--VRLSWGRN 400
           Q+ +   A+ A  K++G  +G     +R+ + ++
Sbjct: 59  QYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKS 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 = 45.1 bits (106), Expect = 8e-07
 Identities = 16/85 (18%), Positives = 34/85 (40%), Gaps = 9/85 (10%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           ++VG L P+ + + L   F            I   +  +   + ++++   +    A  +
Sbjct: 20  LWVGGLGPNTSLAALAREFDRFGS-------IRTIDHVKGDSFAYIQYESLDAAQAACAK 72

Query: 271 MNG--VYCSSRPMRIDVATPKKASG 293
           M G  +    R +R+D A    +SG
Sbjct: 73  MRGFPLGGPDRRLRVDFAKSGPSSG 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 = 38.1 bits (88), Expect = 2e-04
 Identities = 14/80 (17%), Positives = 31/80 (38%), Gaps = 6/80 (7%)

Query: 115 TKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVL 174
           T  +W+G L        L   F   G +  +  ++         + ++++ S  AA+   
Sbjct: 17  TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDS------FAYIQYESLDAAQAAC 70

Query: 175 QSYSGSLMPNTDQPFRLNWA 194
               G  +   D+  R+++A
Sbjct: 71  AKMRGFPLGGPDRRLRVDFA 90

>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 = 50.5 bits (120), Expect = 6e-09
 Identities = 15/76 (19%), Positives = 35/76 (46%), Gaps = 2/76 (2%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           IFVG +  D  +  L++ +  +Y  ++  +++ D  +G+ +G+ FV F D +   + +  
Sbjct: 5   IFVGGIKEDTEEHHLRD-YFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-I 62

Query: 271 MNGVYCSSRPMRIDVA 286
                 +     +  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 = 40.1 bits (93), Expect = 3e-05
 Identities = 17/72 (23%), Positives = 30/72 (41%), Gaps = 7/72 (9%)

Query: 329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK------GCGFVQFANRKDAEVALQK 382
            IFVG +  D  +  LR+ F Q+G+I  ++I   +      G  FV F +  D+   +  
Sbjct: 4   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH-DSVDKIVI 62

Query: 383 LQGTAIGKQTVR 394
            +   +      
Sbjct: 63  QKYHTVNGHNCE 74

>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 = 38.5 bits (89), Expect = 1e-04
 Identities = 13/60 (21%), Positives = 33/60 (55%)

Query: 116 KTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQ 175
           K I++G +    +E  L + F   G++  ++++ ++ +G+  G+ FV F    + +K++ 
Sbjct: 3   KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 62

>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 = 50.2 bits (119), Expect = 8e-09
 Identities = 9/79 (11%), Positives = 26/79 (32%), Gaps = 6/79 (7%)

Query: 327 NATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANRKDAEVAL 380
             T+++       +  ++R+       +              +   ++   +++DA   +
Sbjct: 1   ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCV 60

Query: 381 QKLQGTAIGKQTVRLSWGR 399
           +KL G  I   T+      
Sbjct: 61  EKLNGLKIEGYTLVTKVSN 79

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 49.8 bits (118), Expect = 1e-08
 Identities = 7/81 (8%), Positives = 31/81 (38%), Gaps = 1/81 (1%)

Query: 208 DLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRA 267
           + ++++ +  P  T   +++        V  +  +       ++ + ++    + +    
Sbjct: 1   ECTLWMTNFPPSYTQRNIRDLLQ-DINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYC 59

Query: 268 MTEMNGVYCSSRPMRIDVATP 288
           + ++NG+      +   V+ P
Sbjct: 60  VEKLNGLKIEGYTLVTKVSNP 80

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 40.2 bits (93), Expect = 3e-05
 Identities = 7/78 (8%), Positives = 26/78 (33%), Gaps = 2/78 (2%)

Query: 117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQS 176
           T+W+ +      +  + +       V     + + +   S  + +++  S+  A   ++ 
Sbjct: 3   TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEK 62

Query: 177 YSGSLMPNTDQPFRLNWA 194
            +G  +           +
Sbjct: 63  LNGLKIEG--YTLVTKVS 78

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 49.3 bits (117), Expect = 1e-08
 Identities = 20/76 (26%), Positives = 38/76 (50%), Gaps = 2/76 (2%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           IFVG L+ + T   ++  F  ++  V  A ++ D  T R +G+GFV F  E+   +   E
Sbjct: 2   IFVGGLSVNTTVEDVKHYF-EQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-E 59

Query: 271 MNGVYCSSRPMRIDVA 286
           ++    +++ +    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 = 48.2 bits (114), Expect = 4e-08
 Identities = 19/74 (25%), Positives = 30/74 (40%), Gaps = 7/74 (9%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKG------CGFVQFANRKDAEVALQKL 383
           IFVG L  + + ED++  F QFG++    +   K        GFV F +    E    ++
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-EI 60

Query: 384 QGTAIGKQTVRLSW 397
               I  + V    
Sbjct: 61  HFHEINNKMVECKK 74

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.9 bits (103), Expect = 1e-06
 Identities = 17/58 (29%), Positives = 29/58 (50%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQ 175
           I++G L        + + F   G+V +  ++ +K T +  G+GFV F S    EKV +
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE 59

>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 = 5e-08
 Identities = 22/97 (22%), Positives = 43/97 (44%), Gaps = 2/97 (2%)

Query: 327 NATIFVGALD-SDVSDEDLREPFSQFGEILSVKIPVGKG-CGFVQFANRKDAEVALQKLQ 384
           N+ + V  L+   V+ + L   F  +G++  VKI   K     VQ A+   A++A+  L 
Sbjct: 2   NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLN 61

Query: 385 GTAIGKQTVRLSWGRNPGNKQWRGDHSNHWNGAHYGG 421
           G  +  + +R++  ++   +  R    +      YG 
Sbjct: 62  GHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGN 98

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.1 bits (93), Expect = 5e-05
 Identities = 22/110 (20%), Positives = 41/110 (37%), Gaps = 14/110 (12%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           + V +L P+             Y  V+  K++ +           V+  D N+   AM+ 
Sbjct: 5   LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKE-----NALVQMADGNQAQLAMSH 59

Query: 271 MNGVYCSSRPMRIDVATPK---------KASGYQQQYSSQALVLAGGPGS 311
           +NG     +P+RI ++  +         +  G  + Y +  L     PGS
Sbjct: 60  LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGS 109

>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 = 48.2 bits (114), Expect = 7e-08
 Identities = 25/80 (31%), Positives = 40/80 (50%), Gaps = 2/80 (2%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           IFVG L    TD+ L++ +   +  ++ A VI D  TG+++GYGFV   D     RA  +
Sbjct: 13  IFVGGLPYHTTDASLRK-YFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 71

Query: 271 MNGVYCSSRPMRIDVATPKK 290
            N +    R   +++A    
Sbjct: 72  PNPIID-GRKANVNLAYLGA 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 = 48.2 bits (114), Expect = 7e-08
 Identities = 29/100 (29%), Positives = 42/100 (42%), Gaps = 9/100 (9%)

Query: 316 VQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK------GCGFVQ 369
           + GSQ D  +    IFVG L    +D  LR+ F  FG+I    +   +      G GFV 
Sbjct: 1   MHGSQKD--TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVT 58

Query: 370 FANRKDAEVALQKLQGTAIGKQ-TVRLSWGRNPGNKQWRG 408
            A+R  AE A +       G++  V L++          G
Sbjct: 59  MADRAAAERACKDPNPIIDGRKANVNLAYLGAKPRSLQTG 98

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.6 bits (102), Expect = 3e-06
 Identities = 24/81 (29%), Positives = 38/81 (46%), Gaps = 3/81 (3%)

Query: 115 TKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVL 174
              I++G L +   +  L   F   G +    VI ++QTG+S GYGFV    RAAAE+  
Sbjct: 10  FTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERAC 69

Query: 175 QSYSGSLMPNTDQPFRLNWAT 195
           +  +  +     +   +N A 
Sbjct: 70  KDPNPIID---GRKANVNLAY 87

>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 = 47.5 bits (112), Expect = 9e-08
 Identities = 11/78 (14%), Positives = 30/78 (38%), Gaps = 5/78 (6%)

Query: 211 IFVGDLAPDVTDSIL--QETFSSKYPSVKGAKVIIDSNTGRT---KGYGFVRFGDENERS 265
           +FV  L+  + D  +  +  +  K+  +    +   ++   +       +V +    +  
Sbjct: 11  VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 70

Query: 266 RAMTEMNGVYCSSRPMRI 283
           RA+  +N V    R ++ 
Sbjct: 71  RAIQCVNNVVVDGRTLKA 88

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.7 bits (102), Expect = 2e-06
 Identities = 18/80 (22%), Positives = 34/80 (42%), Gaps = 12/80 (15%)

Query: 329 TIFVGALDSDVSDEDLR---EPFSQFGEILSVKIPVGK---------GCGFVQFANRKDA 376
            +FV  L   ++D ++    E F +FG+I  V I                +V +   +DA
Sbjct: 10  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 69

Query: 377 EVALQKLQGTAIGKQTVRLS 396
             A+Q +    +  +T++ S
Sbjct: 70  LRAIQCVNNVVVDGRTLKAS 89

>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 = 47.5 bits (112), Expect = 1e-07
 Identities = 16/87 (18%), Positives = 41/87 (47%), Gaps = 7/87 (8%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           ++F+ +L+ D  +  L E    ++  +K  +V++  +T  +KG  F +F  +    + + 
Sbjct: 10  TVFIRNLSFDSEEEALGE-VLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 68

Query: 270 EMN------GVYCSSRPMRIDVATPKK 290
             +      G+    R +++D+A  + 
Sbjct: 69  AASLEAEGGGLKLDGRQLKVDLAVTRD 95

>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 = 44.4 bits (104), Expect = 2e-06
 Identities = 19/87 (21%), Positives = 36/87 (41%), Gaps = 12/87 (13%)

Query: 325 SNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGK------GCGFVQFANRKDAEV 378
           +   T+F+  L  D  +E L E   QFG++  V++ +        GC F QF  ++ A+ 
Sbjct: 6   TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQK 65

Query: 379 ALQKLQ------GTAIGKQTVRLSWGR 399
            L          G  +  + +++    
Sbjct: 66  CLAAASLEAEGGGLKLDGRQLKVDLAV 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 = 44.0 bits (103), Expect = 2e-06
 Identities = 21/87 (24%), Positives = 39/87 (44%), Gaps = 4/87 (4%)

Query: 113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEK 172
            E KT++I +L    +E  L       G +  V+V+ +  T  S+G  F +F ++ AA+K
Sbjct: 6   TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQK 65

Query: 173 VLQSYSGSLMPNT----DQPFRLNWAT 195
            L + S            +  +++ A 
Sbjct: 66  CLAAASLEAEGGGLKLDGRQLKVDLAV 92

>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 = 47.0 bits (111), Expect = 1e-07
 Identities = 13/78 (16%), Positives = 29/78 (37%), Gaps = 1/78 (1%)

Query: 323 GESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQK 382
           G S ++ I V  L  D + +++ +    +       +   K   FV   N + A+ A+Q 
Sbjct: 1   GSSGSSGILVKNLPQDSNCQEVHDLLKDYDLK-YCYVDRNKRTAFVTLLNGEQAQNAIQM 59

Query: 383 LQGTAIGKQTVRLSWGRN 400
               +   + + +     
Sbjct: 60  FHQYSFRGKDLIVQLQPT 77

>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 = 9/80 (11%), Positives = 20/80 (25%), Gaps = 8/80 (10%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
            I V +L  D     + +                     R K   FV   +  +   A+ 
Sbjct: 7   GILVKNLPQDSNCQEVHDLLKDYDLKYC--------YVDRNKRTAFVTLLNGEQAQNAIQ 58

Query: 270 EMNGVYCSSRPMRIDVATPK 289
             +      + + + +    
Sbjct: 59  MFHQYSFRGKDLIVQLQPTD 78

>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 = 45.1 bits (106), Expect = 4e-07
 Identities = 17/71 (23%), Positives = 34/71 (47%), Gaps = 6/71 (8%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKG------CGFVQFANRKDAEVALQKL 383
           +++  L    +D+DL +    +G+I+S K  + K        GFV F +   A+ A+  L
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 384 QGTAIGKQTVR 394
           + + +  Q  +
Sbjct: 61  KASGVQAQMAK 71

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.4 bits (91), Expect = 5e-05
 Identities = 19/72 (26%), Positives = 33/72 (45%), Gaps = 1/72 (1%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +++  L P  TD  L +     Y  +   K I+D  T + KGYGFV F   +   +A+T 
Sbjct: 1   LYIRGLQPGTTDQDLVK-LCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTA 59

Query: 271 MNGVYCSSRPMR 282
           +      ++  +
Sbjct: 60  LKASGVQAQMAK 71

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.3 bits (83), Expect = 6e-04
 Identities = 20/63 (31%), Positives = 34/63 (53%)

Query: 118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY 177
           ++I  L     +  L       G++V+ K I +K T + +GYGFV+F S +AA+K + + 
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 178 SGS 180
             S
Sbjct: 61  KAS 63

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.8 bits (108), Expect = 5e-07
 Identities = 15/85 (17%), Positives = 32/85 (37%), Gaps = 6/85 (7%)

Query: 319 SQSDGESNNAT-IFVGALDSDVSDEDLREPFSQFGEILSVKIP-----VGKGCGFVQFAN 372
             +DG  +  + + +     +  +E   E   ++GE+  + +         G  +V+F  
Sbjct: 18  QSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRR 77

Query: 373 RKDAEVALQKLQGTAIGKQTVRLSW 397
            +DAE A+  L       Q +    
Sbjct: 78  EEDAEKAVIDLNNRWFNGQPIHAEL 102

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.3 bits (99), Expect = 8e-06
 Identities = 16/88 (18%), Positives = 38/88 (43%), Gaps = 4/88 (4%)

Query: 197 SGSDRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFV 256
             +D    A SD+   + +   +  + +  E    KY  V+    + D+      G  +V
Sbjct: 18  QSADGLRSAVSDV--EMQEHYDEFFEEVFTEMEE-KYGEVEEMN-VCDNLGDHLVGNVYV 73

Query: 257 RFGDENERSRAMTEMNGVYCSSRPMRID 284
           +F  E +  +A+ ++N  + + +P+  +
Sbjct: 74  KFRREEDAEKAVIDLNNRWFNGQPIHAE 101

>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 = 41.2 bits (96), Expect = 2e-05
 Identities = 13/79 (16%), Positives = 26/79 (32%), Gaps = 6/79 (7%)

Query: 104 NGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVE 163
           +G  +  ++ E +     + +    E          G+V  + V  N       G  +V+
Sbjct: 21  DGLRSAVSDVEMQ-----EHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVK 74

Query: 164 FYSRAAAEKVLQSYSGSLM 182
           F     AEK +   +    
Sbjct: 75  FRREEDAEKAVIDLNNRWF 93

>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 = 45.1 bits (106), Expect = 5e-07
 Identities = 13/79 (16%), Positives = 38/79 (48%), Gaps = 6/79 (7%)

Query: 324 ESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV-----GKGCGFVQFANRKDAEV 378
           +  N ++++    +D + +D++E     G++L++++        KG  FV F + + A+ 
Sbjct: 3   DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKK 62

Query: 379 ALQKLQGTAIGKQTVRLSW 397
            + +  G    +  + + +
Sbjct: 63  FV-ETPGQKYKETDLLILF 80

>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 = 35.1 bits (80), Expect = 0.002
 Identities = 13/77 (16%), Positives = 24/77 (31%), Gaps = 3/77 (3%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           S+++     D T   ++E    K   +     +  +     KG  FV F       + + 
Sbjct: 8   SVYIKGFPTDATLDDIKEWLEDKGQVLN--IQMRRTLHKAFKGSIFVVFDSIESAKKFV- 64

Query: 270 EMNGVYCSSRPMRIDVA 286
           E  G       + I   
Sbjct: 65  ETPGQKYKETDLLILFK 81

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 45.1 bits (106), Expect = 6e-07
 Identities = 12/80 (15%), Positives = 26/80 (32%), Gaps = 3/80 (3%)

Query: 329 TIFVGALDSD-VSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQ--KLQG 385
            + +            L +    FG I +  I       F++ A  +DA+ A+       
Sbjct: 10  VVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTP 69

Query: 386 TAIGKQTVRLSWGRNPGNKQ 405
             +  + VR+   +     +
Sbjct: 70  ALVFGKPVRVHLSQKYKRIK 89

>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 = 45.1 bits (106), Expect = 8e-07
 Identities = 22/80 (27%), Positives = 37/80 (46%), Gaps = 2/80 (2%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
            F+G+L  DVT+  ++E F               SN  R KG+G+  F D +    A+  
Sbjct: 18  AFLGNLPYDVTEESIKEFFR-GLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-S 75

Query: 271 MNGVYCSSRPMRIDVATPKK 290
           +N     ++ +R+DVA   +
Sbjct: 76  LNEESLGNKRIRVDVADQAQ 95

>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 = 43.6 bits (102), Expect = 3e-06
 Identities = 24/102 (23%), Positives = 41/102 (40%), Gaps = 10/102 (9%)

Query: 310 GSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GK 363
           GS+G+   GS+        T F+G L  DV++E ++E F                    K
Sbjct: 1   GSSGSS--GSRLPKSPPY-TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLK 57

Query: 364 GCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQ 405
           G G+ +F +      AL  L   ++G + +R+       +K 
Sbjct: 58  GFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVADQAQDKD 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 = 35.9 bits (82), Expect = 0.002
 Identities = 16/95 (16%), Positives = 32/95 (33%), Gaps = 3/95 (3%)

Query: 101 GKQNGSNNNFTNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYG 160
           G    S +        T ++G+L + + E  +   F                  + +G+G
Sbjct: 1   GSSGSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFG 60

Query: 161 FVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWAT 195
           + EF    +    L     SL    ++  R++ A 
Sbjct: 61  YAEFEDLDSLLSALSLNEESLG---NKRIRVDVAD 92

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 43.7 bits (102), Expect = 2e-06
 Identities = 17/83 (20%), Positives = 38/83 (45%), Gaps = 3/83 (3%)

Query: 319 SQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKG-CGFVQFANRKDAE 377
           +Q++   N   +F+  L  + ++  L   F+QF     V++   +    FV+F     + 
Sbjct: 1   AQTEQPPNQ-ILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSN 59

Query: 378 VALQKLQGTAIGK-QTVRLSWGR 399
            A + LQG  I     +++++ +
Sbjct: 60  AAKEALQGFKITPTHAMKITFAK 82

>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 = 44.9 bits (105), Expect = 2e-06
 Identities = 25/107 (23%), Positives = 44/107 (41%), Gaps = 13/107 (12%)

Query: 324 ESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGC------GFVQFANRKDAE 377
                 + V  + + V +  LR+ F ++G I SVKI   +        GFV+F +   A+
Sbjct: 39  PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQ 98

Query: 378 VALQKLQGTAIGKQTVRLSWGRNPGNKQWRGDHSNHWNGAHYGGQGY 424
            A+  L G  I  + ++++   +   +           GA   G GY
Sbjct: 99  QAIAGLNGFNILNKRLKVALAASGHQRPGIA-------GAVGDGNGY 138

>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 = 43.4 bits (101), Expect = 7e-06
 Identities = 17/81 (20%), Positives = 42/81 (51%), Gaps = 1/81 (1%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           ++ V  +   V +  L++    +Y  ++  K++ D  T +++GYGFV+F   +   +A+ 
Sbjct: 44  NLMVNYIPTTVDEVQLRQ-LFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIA 102

Query: 270 EMNGVYCSSRPMRIDVATPKK 290
            +NG    ++ +++ +A    
Sbjct: 103 GLNGFNILNKRLKVALAASGH 123

>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 = 21/96 (21%), Positives = 39/96 (40%), Gaps = 4/96 (4%)

Query: 310 GSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQ 369
           GS+G+           ++  + V  L    S +DL++   + G++         G G V+
Sbjct: 1   GSSGSS---GGPPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDV-CYADVQKDGMGMVE 56

Query: 370 FANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQ 405
           +  ++D E AL+KL  T         S+ R    + 
Sbjct: 57  YLRKEDMEYALRKLDDTKFRSHEGETSYIRVYPERS 92

>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 = 41.3 bits (96), Expect = 2e-05
 Identities = 11/84 (13%), Positives = 24/84 (28%), Gaps = 8/84 (9%)

Query: 207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSR 266
           SD  + V  L P  +   L++               +     +  G G V +  + +   
Sbjct: 14  SDFRVLVSGLPPSGSWQDLKDHMREAGD--------VCYADVQKDGMGMVEYLRKEDMEY 65

Query: 267 AMTEMNGVYCSSRPMRIDVATPKK 290
           A+ +++     S            
Sbjct: 66  ALRKLDDTKFRSHEGETSYIRVYP 89

>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 = 43.4 bits (102), Expect = 3e-06
 Identities = 19/71 (26%), Positives = 34/71 (47%), Gaps = 8/71 (11%)

Query: 335 LDSDVSDEDLREPFSQFGEILSVKIP--------VGKGCGFVQFANRKDAEVALQKLQGT 386
            + +   ED+R+  S++G + S++IP         G G  FV+F +  D + A+Q L G 
Sbjct: 22  EEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR 81

Query: 387 AIGKQTVRLSW 397
               + V   +
Sbjct: 82  KFANRVVVTKY 92

>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 = 43.0 bits (101), Expect = 4e-06
 Identities = 17/83 (20%), Positives = 28/83 (33%), Gaps = 5/83 (6%)

Query: 213 VGDLAPDVTDSILQE---TFSSKYPSVKGAKVIIDSNTGRTKGYGF--VRFGDENERSRA 267
             +L  D     + E      SKY  VK  ++    +     G G   V F    +  +A
Sbjct: 15  PEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKA 74

Query: 268 MTEMNGVYCSSRPMRIDVATPKK 290
           M  + G   ++R +      P  
Sbjct: 75  MQGLTGRKFANRVVVTKYCDPDS 97

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.5 bits (99), Expect = 6e-06
 Identities = 12/79 (15%), Positives = 30/79 (37%), Gaps = 2/79 (2%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           ++++ +L   + +  L+         +     I+  ++G ++G GF R     +    + 
Sbjct: 20  NLYISNLPLSMDEQELENMLKPFGQVIS--TRILRDSSGTSRGVGFARMESTEKCEAVIG 77

Query: 270 EMNGVYCSSRPMRIDVATP 288
             NG +  + P       P
Sbjct: 78  HFNGKFIKTPPGVSAPTEP 96

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.5 bits (99), Expect = 7e-06
 Identities = 15/94 (15%), Positives = 38/94 (40%), Gaps = 6/94 (6%)

Query: 311 SNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV-----GKGC 365
           ++G + Q ++   E +   +++  L   + +++L      FG+++S +I        +G 
Sbjct: 3   ASGVQAQMAKQQ-EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGV 61

Query: 366 GFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGR 399
           GF +  + +  E  +    G  I       +   
Sbjct: 62  GFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE 95

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.1 bits (95), Expect = 1e-05
 Identities = 12/77 (15%), Positives = 24/77 (31%), Gaps = 8/77 (10%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           I +  L  DVT+  + +  S                  + KG  FV   +  +   A+  
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDYELKYC--------FVDKYKGTAFVTLLNGEQAEAAINT 52

Query: 271 MNGVYCSSRPMRIDVAT 287
            +      R + + +  
Sbjct: 53  FHQSRLRERELSVQLQP 69

>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 = 40.6 bits (94), Expect = 2e-05
 Identities = 8/78 (10%), Positives = 26/78 (33%), Gaps = 4/78 (5%)

Query: 210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMT 269
           ++ V +L      + + + +      +    V    +  +   +  + F   +    A+T
Sbjct: 2   TVLVKNLPKSYNQNKVYK-YFKHCGPIIHVDVA--DSLKKNFRFARIEFARYDGALAAIT 58

Query: 270 EMNGVYCSSRPMRIDVAT 287
           + + V      + +   T
Sbjct: 59  KTHKVVG-QNEIIVSHLT 75

>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 = 41.4 bits (96), Expect = 2e-05
 Identities = 12/92 (13%), Positives = 28/92 (30%), Gaps = 7/92 (7%)

Query: 320 QSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV------GKGCGFVQFANR 373
           + D  S      +  +   ++  D+ +         +    +      G G   VQF N 
Sbjct: 1   EGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNE 60

Query: 374 KDAEVALQKLQGTAIGKQTVRLSWGRNPGNKQ 405
            DA  +  +L    +  +   +        ++
Sbjct: 61  DDARKSE-RLHRKKLNGREAFVHVVTLEDMRE 91

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 39.9 bits (92), Expect = 4e-05
 Identities = 15/87 (17%), Positives = 42/87 (48%), Gaps = 3/87 (3%)

Query: 203 TEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDEN 262
           +E+ +  ++F+G+L P+ + + L+    S+  +     V+    TG  + +G+V F    
Sbjct: 8   SESTTPFNLFIGNLNPNKSVAELKV-AISELFAKNDLAVVDV-RTGTNRKFGYVDFESAE 65

Query: 263 ERSRAMTEMNGVYCSSRPMRIDVATPK 289
           +  +A+  + G+      ++++    +
Sbjct: 66  DLEKALE-LTGLKVFGNEIKLEKPKGR 91

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 35.7 bits (81), Expect = 0.002
 Identities = 22/95 (23%), Positives = 44/95 (46%), Gaps = 11/95 (11%)

Query: 310 GSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSV-----KIPVGKG 364
           GS+   V+GS+S   +    +F+G L+ + S  +L+   S+      +     +    + 
Sbjct: 1   GSH--MVEGSES---TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRK 55

Query: 365 CGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGR 399
            G+V F + +D E AL+ L G  +    ++L   +
Sbjct: 56  FGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPK 89

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.2 bits (88), Expect = 2e-04
 Identities = 16/88 (18%), Positives = 30/88 (34%), Gaps = 7/88 (7%)

Query: 109 NFTN--DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYS 166
           NF N    + T+ + ++   + E  L   FS  G VV       K          ++  S
Sbjct: 2   NFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDR----KMALIQMGS 57

Query: 167 RAAAEKVLQSYSGSLMPNTDQPFRLNWA 194
              A + L       +       R++++
Sbjct: 58  VEEAVQALIDLHNHDLGEN-HHLRVSFS 84

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.8 bits (87), Expect = 2e-04
 Identities = 14/80 (17%), Positives = 32/80 (40%), Gaps = 6/80 (7%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           + + ++ P V++  L+  FSS    VKG K               ++ G   E  +A+ +
Sbjct: 13  LHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRK-----MALIQMGSVEEAVQALID 67

Query: 271 MNGVY-CSSRPMRIDVATPK 289
           ++      +  +R+  +   
Sbjct: 68  LHNHDLGENHHLRVSFSKST 87

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.3 bits (88), Expect = 2e-04
 Identities = 17/80 (21%), Positives = 34/80 (42%), Gaps = 2/80 (2%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           +++  L  +  +  +   F  K   V+ +  I     G+  G GFV F +E +   A+  
Sbjct: 21  VYLKGLPFEAENKHVI-DFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAAL-C 78

Query: 271 MNGVYCSSRPMRIDVATPKK 290
            +  Y  +R +++   T K 
Sbjct: 79  RHKQYMGNRFIQVHPITKKG 98

>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 = 15/70 (21%), Positives = 28/70 (40%), Gaps = 1/70 (1%)

Query: 330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIG 389
           + V  L    S +DL++   +    +        G G V+F  ++D   A++KL  T   
Sbjct: 3   VVVSGLPPSGSWQDLKD-HMREAGDVCYADVYRDGTGVVEFVRKEDMTYAVRKLDNTKFR 61

Query: 390 KQTVRLSWGR 399
                 ++ R
Sbjct: 62  SHEGETAYIR 71

>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 = 6e-04
 Identities = 12/89 (13%), Positives = 24/89 (26%), Gaps = 8/89 (8%)

Query: 211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTE 270
           + V  L P  +   L++               +        G G V F  + + + A+ +
Sbjct: 3   VVVSGLPPSGSWQDLKDHMREAGD--------VCYADVYRDGTGVVEFVRKEDMTYAVRK 54

Query: 271 MNGVYCSSRPMRIDVATPKKASGYQQQYS 299
           ++     S          K        Y 
Sbjct: 55  LDNTKFRSHEGETAYIRVKVDGPRSPSYG 83

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	449
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.97
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.96
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.82
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.81
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.79
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.79
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.79
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.79
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.78
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.78
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.78
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.78
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.78
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.78
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.78
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.78
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.78
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.78
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.77
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.77
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.77
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.77
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.77
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.77
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.77
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.77
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.76
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.76
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.76
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.76
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.76
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.76
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.76
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.76
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.76
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.76
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.75
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.75
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.75
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.75
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.75
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.75
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.75
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.74
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.74
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.74
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.74
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.74
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.74
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.74
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.74
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.74
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.74
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.74
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.74
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.73
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.73
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.73
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.73
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.73
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.73
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.73
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.73
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.73
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.73
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.72
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.72
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.72
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.72
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.72
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.72
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.72
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.72
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.72
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.71
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.71
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.71
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.71
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.71
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.71
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.71
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.71
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.71
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.71
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.71
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.7
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.7
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.7
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.7
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.7
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.7
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.7
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.7
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.7
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.69
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.69
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.69
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.69
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.69
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.69
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.68
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.68
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.68
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.68
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.68
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.68
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.68
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.68
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.68
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.68
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.67
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.67
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.67
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.67
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.67
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.67
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.67
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.66
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.66
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.66
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.66
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.65
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.65
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.64
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.64
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.64
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.64
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.64
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.64
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.64
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.64
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.64
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.64
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.64
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.64
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.63
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.63
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.63
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.63
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.63
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.62
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.62
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.62
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.61
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.61
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.61
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.6
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.6
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.59
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.59
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.58
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.58
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.57
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.56
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.55
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.55
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.53
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.52
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.51
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.49
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.46
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.42
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.42
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.42
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.4
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	99.4
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.39
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	99.39
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.33
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.25
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.17
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.16
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.83
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.73
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.64
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.54
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	96.99
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	96.75
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	95.97
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	94.73

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=1.5e-30  Score=225.25  Aligned_cols=172  Identities=19%  Similarity=0.376  Sum_probs=145.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccccc
Q 013141          114 ETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNW  193 (449)
Q Consensus       114 ~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~  193 (449)
                      ..|+|||+|||+++|+++|+++|++||.|.++.++++..++.++|||||+|.+.++|.+|+..++. .+..  ..+.+.+
T Consensus         5 ~~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~~-~~~~--~~~~~~~   81 (183)
T d1u1qa_           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPH-KVDG--RVVEPKR   81 (183)
T ss_dssp             HHHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSC-EETT--EECEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHhcCC-cccc--cchhhhh
Confidence            458999999999999999999999999999999999999999999999999999999999965443 3322  2233222


Q ss_pred             cccCCC-CCccccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC
Q 013141          194 ATFSGS-DRRTEACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMN  272 (449)
Q Consensus       194 ~~~~~~-~~~~~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~  272 (449)
                      ...... .........++|||+|||+++|+++|+++|+ .||.|..+.++.+..++.++|+|||+|.+.++|.+|++ ++
T Consensus        82 ~~~~~~~~~~~~~~~~~~i~V~~lp~~~te~~L~~~f~-~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~  159 (183)
T d1u1qa_          82 AVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFE-QYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QK  159 (183)
T ss_dssp             CCCTTGGGSTTTTCCCSEEEEECCCTTCCHHHHHHHHG-GGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SS
T ss_pred             hhhcccccccccccccceeEEccCCCcCCHHHHhhhhc-cCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hC
Confidence            221111 1123345667999999999999999999995 99999999999999999999999999999999999995 78


Q ss_pred             CceecCcceEEeecCCCC
Q 013141          273 GVYCSSRPMRIDVATPKK  290 (449)
Q Consensus       273 g~~~~g~~i~v~~~~~~~  290 (449)
                      +..+.|+.|+|.++.++.
T Consensus       160 ~~~~~G~~i~V~~A~~k~  177 (183)
T d1u1qa_         160 YHTVNGHNCEVRKALSKQ  177 (183)
T ss_dssp             CEEETTEEEEEEECCCHH
T ss_pred             CCeECCEEEEEEecCCcc
Confidence            999999999999987753

>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=7.8e-28  Score=207.99  Aligned_cols=165  Identities=23%  Similarity=0.419  Sum_probs=144.3

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecC
Q 013141          208 DLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVAT  287 (449)
Q Consensus       208 ~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~  287 (449)
                      .++|||+|||+++|+++|+++|+ .||.|.++.++++..++.++|+|||+|.+.++|.+|+. +++..+..+.+.+.+..
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~-~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~-~~~~~~~~~~~~~~~~~   83 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFE-QWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHG-GGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHH-HcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHH-hcCCcccccchhhhhhh
Confidence            36999999999999999999995 99999999999999999999999999999999999995 66677888888888776


Q ss_pred             CCCCCchhhcchhhhhhhcCCCCCCCCCcCCCCCCCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC-----
Q 013141          288 PKKASGYQQQYSSQALVLAGGPGSNGARVQGSQSDGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-----  362 (449)
Q Consensus       288 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~-----  362 (449)
                      ......                          ........++|||+|||..+|+++|+++|+.||.|..+.|..+     
T Consensus        84 ~~~~~~--------------------------~~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~  137 (183)
T d1u1qa_          84 SREDSQ--------------------------RPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGK  137 (183)
T ss_dssp             CTTGGG--------------------------STTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCC
T ss_pred             hccccc--------------------------ccccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCc
Confidence            554321                          1122345678999999999999999999999999999998753     


Q ss_pred             -CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCC
Q 013141          363 -KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNP  401 (449)
Q Consensus       363 -~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~  401 (449)
                       +|+|||+|.+.++|.+|++ +++..|.|+.|+|.|+.++
T Consensus       138 ~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~A~~k  176 (183)
T d1u1qa_         138 KRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKALSK  176 (183)
T ss_dssp             EEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEECCCH
T ss_pred             cceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEecCCc
Confidence             5799999999999999997 7889999999999998764

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=4.8e-20  Score=136.53  Aligned_cols=81  Identities=23%  Similarity=0.501  Sum_probs=77.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccccc
Q 013141          114 ETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNW  193 (449)
Q Consensus       114 ~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~  193 (449)
                      ..++|||+|||+++|+++|+++|++||+|.+|++++++.+|+++|||||+|.+.++|++|++.||+..+.++.++|+|.|
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~   84 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKF   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEe
Confidence            34689999999999999999999999999999999999999999999999999999999999999999998889999987


Q ss_pred             c
Q 013141          194 A  194 (449)
Q Consensus       194 ~  194 (449)
                      +
T Consensus        85 A   85 (85)
T d1fxla2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.81  E-value=1e-19  Score=134.83  Aligned_cols=81  Identities=21%  Similarity=0.463  Sum_probs=76.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccccc
Q 013141          114 ETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNW  193 (449)
Q Consensus       114 ~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~  193 (449)
                      ..++|||+|||+++++++|+++|++||.|.+|++++++.+++++|||||+|.+.++|.+|++.||+..+.+..++++|.|
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            45679999999999999999999999999999999999999999999999999999999999999999988788899887


Q ss_pred             c
Q 013141          194 A  194 (449)
Q Consensus       194 ~  194 (449)
                      |
T Consensus        85 A   85 (85)
T d1b7fa2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.79  E-value=2.1e-19  Score=135.43  Aligned_cols=84  Identities=31%  Similarity=0.532  Sum_probs=77.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      ...++|||+|||+++|+++|+++|++||.|.+|++++++.+|+++|||||+|.+.++|++|++.|++..+.  ++.|+|.
T Consensus         7 ~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~--g~~l~V~   84 (93)
T d1x5ua1           7 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLY--GKPIRVN   84 (93)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCS--SCBCEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEEC--CEEEEEE
Confidence            34679999999999999999999999999999999999999999999999999999999999999999984  5788898


Q ss_pred             ccccCC
Q 013141          193 WATFSG  198 (449)
Q Consensus       193 ~~~~~~  198 (449)
                      |+....
T Consensus        85 ~A~~~~   90 (93)
T d1x5ua1          85 KASAHN   90 (93)
T ss_dssp             ETTTTS
T ss_pred             EcCCCC
Confidence            887543

>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=99.79  E-value=2.2e-19  Score=133.87  Aligned_cols=83  Identities=19%  Similarity=0.390  Sum_probs=76.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      .+.++|||+|||+++++++|+++|+.||.|.+|++++|+.+|+++|||||+|.+.++|++|++.||+..+.  ++.|+|+
T Consensus         5 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~--g~~l~V~   82 (88)
T d1rk8a_           5 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIM--GQTIQVD   82 (88)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEET--TEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEEC--CEEEEEE
Confidence            45789999999999999999999999999999999999999999999999999999999999999999884  5789999


Q ss_pred             ccccC
Q 013141          193 WATFS  197 (449)
Q Consensus       193 ~~~~~  197 (449)
                      |+..+
T Consensus        83 ~a~~k   87 (88)
T d1rk8a_          83 WCFVK   87 (88)
T ss_dssp             ESEEC
T ss_pred             EecCC
Confidence            88643

>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=99.79  E-value=2.7e-19  Score=131.82  Aligned_cols=80  Identities=28%  Similarity=0.519  Sum_probs=77.0

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecC
Q 013141          208 DLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVAT  287 (449)
Q Consensus       208 ~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~  287 (449)
                      +++|||+|||+++|+++|+++|+ .||.|.++.+++++.++.++|||||+|.+.++|++|++.||+..+.|+.|+|++++
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~-~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~   80 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFR-AIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR   80 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHH-TTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHH-HhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            56899999999999999999995 99999999999999999999999999999999999999999999999999999997


Q ss_pred             C
Q 013141          288 P  288 (449)
Q Consensus       288 ~  288 (449)
                      +
T Consensus        81 p   81 (82)
T d1b7fa1          81 P   81 (82)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.79  E-value=3.6e-19  Score=145.16  Aligned_cols=86  Identities=24%  Similarity=0.429  Sum_probs=78.3

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      .....++|||+|||+++|+++|+++|+.||.|.+|+|++++.+++++|||||+|.+.++|.+||+.||+..|.  ++.|+
T Consensus        38 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~--gr~l~  115 (139)
T d1u6fa1          38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNIL--NKRLK  115 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECS--SCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEEC--CEEEE
Confidence            3445679999999999999999999999999999999999999999999999999999999999999999995  57888


Q ss_pred             ccccccCC
Q 013141          191 LNWATFSG  198 (449)
Q Consensus       191 ~~~~~~~~  198 (449)
                      |.++....
T Consensus       116 V~~a~~~~  123 (139)
T d1u6fa1         116 VALAASGH  123 (139)
T ss_dssp             EEESSCCC
T ss_pred             EEEcCCCC
Confidence            88886543

>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=99.78  E-value=3.1e-19  Score=134.41  Aligned_cols=82  Identities=27%  Similarity=0.522  Sum_probs=76.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      ..+++|||+|||+++|+++|+++|+.||.|.+|.+++++.+++++|||||+|.+.++|..|++.||+..+.  ++.|+|+
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~--gr~i~V~   82 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLD--DRIIRTD   82 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEET--TEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEEC--CEEEEEE
Confidence            56889999999999999999999999999999999999999999999999999999999999999999994  5788898


Q ss_pred             cccc
Q 013141          193 WATF  196 (449)
Q Consensus       193 ~~~~  196 (449)
                      |+..
T Consensus        83 ~a~~   86 (93)
T d1h2vz_          83 WDAG   86 (93)
T ss_dssp             EESC
T ss_pred             EcCC
Confidence            8753

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=3e-19  Score=135.23  Aligned_cols=78  Identities=31%  Similarity=0.663  Sum_probs=74.2

Q ss_pred             CCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCC
Q 013141          325 SNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPG  402 (449)
Q Consensus       325 ~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~  402 (449)
                      +..++|||+|||..+++++|+++|++||.|.+|+|.+++++|||+|.+.++|.+|++.|||..|.|+.|+|+|+++.+
T Consensus        16 ~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~~p   93 (96)
T d1x4ga1          16 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESP   93 (96)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCC
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEecceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            345789999999999999999999999999999999999999999999999999999999999999999999998754

>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=99.78  E-value=1.4e-19  Score=133.33  Aligned_cols=80  Identities=21%  Similarity=0.412  Sum_probs=74.8

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccccc
Q 013141          115 TKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWA  194 (449)
Q Consensus       115 ~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~~  194 (449)
                      .++|||+|||+++|+++|+++|++||.|.+|++++++.+|+++|||||+|.+.++|++|++.||+..+  .++.|+|.|+
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~--~g~~l~v~~a   79 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITV--RNKRLKVSYA   79 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEE--TTEECEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEE--CCEEEEEEEc
Confidence            46899999999999999999999999999999999999999999999999999999999999999988  4578888888


Q ss_pred             cc
Q 013141          195 TF  196 (449)
Q Consensus       195 ~~  196 (449)
                      ++
T Consensus        80 ~p   81 (82)
T d1b7fa1          80 RP   81 (82)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=99.78  E-value=3.9e-19  Score=136.37  Aligned_cols=84  Identities=25%  Similarity=0.332  Sum_probs=77.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      .+.++|||+|||+++++++|+++|+.||.|.+++++.++.+|+++|||||+|.+.++|.+||+.||+..+.  ++.|+|.
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~--g~~i~V~   93 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIG--MKRLKVQ   93 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEET--TEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEEC--CEEEEEE
Confidence            35678999999999999999999999999999999999999999999999999999999999999999984  5788998


Q ss_pred             ccccCC
Q 013141          193 WATFSG  198 (449)
Q Consensus       193 ~~~~~~  198 (449)
                      |+.++.
T Consensus        94 ~a~~k~   99 (102)
T d2cpza1          94 LKRSKN   99 (102)
T ss_dssp             CCCCSC
T ss_pred             EeCCCC
Confidence            887654

>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=99.78  E-value=1.9e-19  Score=134.91  Aligned_cols=84  Identities=29%  Similarity=0.447  Sum_probs=77.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccc
Q 013141          112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRL  191 (449)
Q Consensus       112 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~  191 (449)
                      ..+.++|||+|||.++++++|+++|+.||.|.+|++++++.+++++|||||+|.+.++|.+|++.|++..+  .++.|+|
T Consensus         5 ~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~--~g~~i~v   82 (90)
T d2cq0a1           5 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGY--DHLILNV   82 (90)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEE--TTEECEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEE--CCEEEEE
Confidence            34678999999999999999999999999999999999999999999999999999999999999999988  4578899


Q ss_pred             cccccC
Q 013141          192 NWATFS  197 (449)
Q Consensus       192 ~~~~~~  197 (449)
                      .|+++.
T Consensus        83 ~~akp~   88 (90)
T d2cq0a1          83 EWAKPS   88 (90)
T ss_dssp             EESSCC
T ss_pred             EeeeCC
Confidence            998754

>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=99.78  E-value=4.7e-19  Score=132.06  Aligned_cols=83  Identities=23%  Similarity=0.429  Sum_probs=78.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEee
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV  285 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  285 (449)
                      ...++|||+|||.++|+++|+++|+ .||.|.++++++|+.+++++|||||+|.+.++|++|++.|||..+.|+.|+|+|
T Consensus         5 ~~~~~l~V~nL~~~~t~~~l~~~F~-~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~   83 (88)
T d1rk8a_           5 VEGWILFVTSIHEEAQEDEIQEKFC-DYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW   83 (88)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHG-GGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHH-HcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            4567999999999999999999995 999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 013141          286 ATPK  289 (449)
Q Consensus       286 ~~~~  289 (449)
                      +.++
T Consensus        84 a~~k   87 (88)
T d1rk8a_          84 CFVK   87 (88)
T ss_dssp             SEEC
T ss_pred             ecCC
Confidence            9765

>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=99.78  E-value=3.1e-19  Score=131.50  Aligned_cols=80  Identities=26%  Similarity=0.480  Sum_probs=74.6

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccccc
Q 013141          115 TKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWA  194 (449)
Q Consensus       115 ~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~~  194 (449)
                      .++|||+|||+++++++|+++|++||.|.+|+++++..+++++|||||+|.+.++|++|++.|++..+.  ++.|++.|+
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~--g~~l~v~~A   79 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQ--TKTIKVSYA   79 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEET--TEECEEEEC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEEC--CEEEEEEEe
Confidence            357999999999999999999999999999999999999999999999999999999999999999984  578888888


Q ss_pred             cc
Q 013141          195 TF  196 (449)
Q Consensus       195 ~~  196 (449)
                      ++
T Consensus        80 kP   81 (82)
T d1fxla1          80 RP   81 (82)
T ss_dssp             CC
T ss_pred             eC
Confidence            64

>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=99.78  E-value=9.1e-19  Score=128.95  Aligned_cols=80  Identities=24%  Similarity=0.524  Sum_probs=76.7

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecC
Q 013141          208 DLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVAT  287 (449)
Q Consensus       208 ~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~  287 (449)
                      .++|||+|||+++++++|+++|+ .||.|.+++++++..++.++|||||+|.+.++|++|++.|++..+.|+.|+|++++
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~-~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~Ak   80 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFG-SIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYAR   80 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHH-TTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHH-HhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            45799999999999999999995 99999999999999999999999999999999999999999999999999999997


Q ss_pred             C
Q 013141          288 P  288 (449)
Q Consensus       288 ~  288 (449)
                      |
T Consensus        81 P   81 (82)
T d1fxla1          81 P   81 (82)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.78  E-value=2.5e-19  Score=131.07  Aligned_cols=77  Identities=30%  Similarity=0.600  Sum_probs=73.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccccccc
Q 013141          117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWAT  195 (449)
Q Consensus       117 ~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~~~  195 (449)
                      +|||+|||+++|+++|+++|++||+|.+|+|++++.+|+++|||||+|.+.++|.+|++.|++..+.  ++.|+|.|++
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 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIK--GKPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEET--TEECEEEECC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEEC--CEEEEEEEeC
Confidence            6999999999999999999999999999999999999999999999999999999999999999995  4788888875

>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=99.78  E-value=6.5e-19  Score=132.66  Aligned_cols=85  Identities=28%  Similarity=0.498  Sum_probs=80.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEee
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV  285 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  285 (449)
                      ...++|||+|||.++|+++|+++|+ .||.|.++.+++++.++.++|||||+|.+.++|++|++.|++..|.|+.|+|++
T Consensus         7 ~~~~tlfV~nLp~~~t~~~l~~~F~-~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   85 (93)
T d1x5ua1           7 NQDATVYVGGLDEKVSEPLLWELFL-QAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNK   85 (93)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHH-TTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHH-HhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            3457999999999999999999995 999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 013141          286 ATPKKA  291 (449)
Q Consensus       286 ~~~~~~  291 (449)
                      +.++..
T Consensus        86 A~~~~~   91 (93)
T d1x5ua1          86 ASAHNK   91 (93)
T ss_dssp             TTTTSC
T ss_pred             cCCCCC
Confidence            988754

>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=99.77  E-value=8.4e-19  Score=131.31  Aligned_cols=84  Identities=25%  Similarity=0.447  Sum_probs=79.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEee
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV  285 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  285 (449)
                      .+.++|||+|||.++++++|+++|+ .||.|.++.+++++.++.++|||||+|.+.++|.+|++.|++..++|+.|+|+|
T Consensus         6 ~~~~~i~V~nLp~~~t~~~l~~~f~-~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~   84 (90)
T d2cq0a1           6 DDNATIRVTNLSEDTRETDLQELFR-PFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   84 (90)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTST-TTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHH-HhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            4567899999999999999999995 999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 013141          286 ATPKK  290 (449)
Q Consensus       286 ~~~~~  290 (449)
                      ++++.
T Consensus        85 akp~~   89 (90)
T d2cq0a1          85 AKPST   89 (90)
T ss_dssp             SSCCC
T ss_pred             eeCCC
Confidence            98763

>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=99.77  E-value=4.4e-19  Score=132.59  Aligned_cols=85  Identities=25%  Similarity=0.520  Sum_probs=79.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEee
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV  285 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  285 (449)
                      ...++|||+|||+++|+++|+++|+ .||.|.++.+++|+.++.++|||||+|.+.++|++|++.|++..++|+.|+|++
T Consensus         3 ~~~~tlfV~nLp~~~te~~l~~~F~-~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~   81 (89)
T d2cqba1           3 TTKRVLYVGGLAEEVDDKVLHAAFI-PFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   81 (89)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHT-TTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHh-hCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            3567999999999999999999995 999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 013141          286 ATPKKA  291 (449)
Q Consensus       286 ~~~~~~  291 (449)
                      +.++..
T Consensus        82 a~p~~~   87 (89)
T d2cqba1          82 AKPMRI   87 (89)
T ss_dssp             CCCCCC
T ss_pred             eCCCCC
Confidence            987643

>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=99.77  E-value=1.3e-18  Score=133.30  Aligned_cols=85  Identities=25%  Similarity=0.430  Sum_probs=80.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEee
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV  285 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  285 (449)
                      .+.++|||+|||+++++++|+++|+ .||.|.++.++.+..++.++|||||+|.+.++|++||+.||+..|.|+.|+|++
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~-~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~   94 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFM-PFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQL   94 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHG-GGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHH-hhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4567899999999999999999995 999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 013141          286 ATPKKA  291 (449)
Q Consensus       286 ~~~~~~  291 (449)
                      +.++..
T Consensus        95 a~~k~~  100 (102)
T d2cpza1          95 KRSKND  100 (102)
T ss_dssp             CCCSCC
T ss_pred             eCCCCC
Confidence            988765

>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=99.77  E-value=4.2e-19  Score=131.27  Aligned_cols=80  Identities=18%  Similarity=0.462  Sum_probs=74.7

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccccccc
Q 013141          116 KTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWAT  195 (449)
Q Consensus       116 ~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~~~  195 (449)
                      .+|||+|||+++|+++|+++|+.||+|.+|++++|+.+|+++|||||+|.+.++|.+|++.|++..+.  ++.|+|.|+.
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~   79 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLG--DKKLLVQRAS   79 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCS--SSCCEEEECC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEEC--CEEEEEEECC
Confidence            47999999999999999999999999999999999999999999999999999999999999999985  5778888886


Q ss_pred             cC
Q 013141          196 FS  197 (449)
Q Consensus       196 ~~  197 (449)
                      ..
T Consensus        80 ~~   81 (85)
T d2u2fa_          80 VG   81 (85)
T ss_dssp             CC
T ss_pred             CC
Confidence            44

>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=99.77  E-value=1.8e-19  Score=134.73  Aligned_cols=83  Identities=22%  Similarity=0.409  Sum_probs=76.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      ...++|||+|||+++++++|+++|+.||+|.+|.++.|+.+++++|||||+|.+.++|++|++.|++..+.  ++.|+|.
T Consensus         3 ~~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~--g~~l~v~   80 (89)
T d2cqba1           3 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELF--GRTIRVN   80 (89)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEET--TEEEEEE
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEEC--CEEEEEE
Confidence            35689999999999999999999999999999999999999999999999999999999999999999885  5788888


Q ss_pred             ccccC
Q 013141          193 WATFS  197 (449)
Q Consensus       193 ~~~~~  197 (449)
                      |+.+.
T Consensus        81 ~a~p~   85 (89)
T d2cqba1          81 LAKPM   85 (89)
T ss_dssp             ECCCC
T ss_pred             EeCCC
Confidence            88643

>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=99.77  E-value=1.6e-18  Score=132.40  Aligned_cols=80  Identities=25%  Similarity=0.401  Sum_probs=73.8

Q ss_pred             CCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC------CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 013141          325 SNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWG  398 (449)
Q Consensus       325 ~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~------~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~  398 (449)
                      ...++|||+|||+.+++++|+++|+.||.|.+|+|+.+      +++|||+|.+.++|.+|++.||+..|+|+.|+|.++
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a   85 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            44678999999999999999999999999999999763      689999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 013141          399 RNPGNK  404 (449)
Q Consensus       399 ~~~~~~  404 (449)
                      +.+...
T Consensus        86 ~~~~~~   91 (99)
T d1whwa_          86 TIKKEA   91 (99)
T ss_dssp             CCCSTT
T ss_pred             CCCCcc
Confidence            986544

>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=99.77  E-value=5e-19  Score=130.54  Aligned_cols=73  Identities=22%  Similarity=0.337  Sum_probs=69.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCC
Q 013141          112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPN  184 (449)
Q Consensus       112 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~  184 (449)
                      +.++++|||+|||+++|+++|+++|++||.|.+|+++.++.+++++|||||+|.+.++|.+|++.|++..+.+
T Consensus         6 p~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   78 (83)
T d2cqca1           6 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDG   78 (83)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECC
Confidence            3467899999999999999999999999999999999999999999999999999999999999999998854

>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=99.77  E-value=2e-18  Score=129.94  Aligned_cols=84  Identities=25%  Similarity=0.330  Sum_probs=79.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEee
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV  285 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  285 (449)
                      ..+++|||+|||+++|+++|+++|+ .||.|.+|.+++++.++.++|||||+|.+.++|..|++.||+..++|+.|+|+|
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~-~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~   83 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFS-KSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDW   83 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHG-GGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHH-HHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4567999999999999999999995 999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 013141          286 ATPKK  290 (449)
Q Consensus       286 ~~~~~  290 (449)
                      +....
T Consensus        84 a~~~~   88 (93)
T d1h2vz_          84 DAGFK   88 (93)
T ss_dssp             ESCCC
T ss_pred             cCCCC
Confidence            86543

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.76  E-value=1e-18  Score=129.44  Aligned_cols=77  Identities=27%  Similarity=0.549  Sum_probs=73.6

Q ss_pred             CCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCC
Q 013141          326 NNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPG  402 (449)
Q Consensus       326 ~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~  402 (449)
                      ..++|||+|||.++++++|+++|+.||.|.+|++.+++++|||+|.+.++|.+|++.|||..|.|+.|+|+|+.+..
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~~~   83 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA   83 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCcC
Confidence            35679999999999999999999999999999999999999999999999999999999999999999999998764

>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=99.76  E-value=9.8e-19  Score=131.14  Aligned_cols=84  Identities=26%  Similarity=0.470  Sum_probs=77.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      .+.++|||+|||+++++++|+++|+.||.|.++.++.++.++.++|||||+|.+.++|++|++.|++..+.  ++.|+|.
T Consensus         3 ~~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~--g~~l~V~   80 (90)
T d1x5sa1           3 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVD--GRQIRVD   80 (90)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTT--SCCCEEE
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEEC--CEEEEEE
Confidence            46788999999999999999999999999999999999899999999999999999999999999999984  5788888


Q ss_pred             ccccCC
Q 013141          193 WATFSG  198 (449)
Q Consensus       193 ~~~~~~  198 (449)
                      |+....
T Consensus        81 ~a~~~~   86 (90)
T d1x5sa1          81 QAGKSS   86 (90)
T ss_dssp             EEECCC
T ss_pred             EcCCCC
Confidence            886554

>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=99.76  E-value=1.2e-18  Score=127.33  Aligned_cols=77  Identities=36%  Similarity=0.560  Sum_probs=74.6

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecC
Q 013141          210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVAT  287 (449)
Q Consensus       210 ~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~  287 (449)
                      +|||+|||+++|+++|+++|+ .||+|.++++++++.+++++|||||+|.+.++|.+|++.|+|..+.|+.|+|.|+.
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 SLYVGDLHPDVTEAMLYEKFS-PAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHG-GGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             EEEEeCCCCcCCHHHHHHHHH-HhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            699999999999999999995 99999999999999999999999999999999999999999999999999999985

>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=99.76  E-value=2.1e-18  Score=129.13  Aligned_cols=81  Identities=30%  Similarity=0.525  Sum_probs=74.2

Q ss_pred             CCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC----CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 013141          324 ESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG----KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGR  399 (449)
Q Consensus       324 ~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~----~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  399 (449)
                      ....++|||+|||.++++++|+++|+.||.|.+|.+.++    +++|||+|.+.++|.+|++.|||..|.|+.|+|.|++
T Consensus         5 ~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~   84 (90)
T d2cqia1           5 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWAT   84 (90)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCccceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            344679999999999999999999999999999999763    6899999999999999999999999999999999999


Q ss_pred             CCCCC
Q 013141          400 NPGNK  404 (449)
Q Consensus       400 ~~~~~  404 (449)
                      ++..+
T Consensus        85 ~~~~~   89 (90)
T d2cqia1          85 TPSSQ   89 (90)
T ss_dssp             CTTCC
T ss_pred             CCCCC
Confidence            86543

>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=99.76  E-value=1.6e-18  Score=130.77  Aligned_cols=83  Identities=22%  Similarity=0.449  Sum_probs=75.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecC-CCCCcccEEEEEEccHHHHHHHHHHh-cCCCCCCCCCccc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNK-QTGQSEGYGFVEFYSRAAAEKVLQSY-SGSLMPNTDQPFR  190 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~-~~g~~~g~afV~f~~~~~A~~Al~~l-~~~~~~~~~~~~~  190 (449)
                      ..+++|||+|||+++++++|+++|+.||.|.+|+++++. .+|+++|||||+|.+.++|.+|++.| ++..+.  ++.|+
T Consensus         6 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~--Gr~l~   83 (94)
T d2cpha1           6 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLY--GRRLV   83 (94)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSS--SCBCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEEC--CEEEE
Confidence            467889999999999999999999999999999999875 47899999999999999999999998 788884  57899


Q ss_pred             ccccccC
Q 013141          191 LNWATFS  197 (449)
Q Consensus       191 ~~~~~~~  197 (449)
                      |+|++..
T Consensus        84 V~~A~~~   90 (94)
T d2cpha1          84 LEWADSE   90 (94)
T ss_dssp             EEECCCC
T ss_pred             EEEcCCC
Confidence            9998754

>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=99.76  E-value=4e-18  Score=128.35  Aligned_cols=81  Identities=35%  Similarity=0.524  Sum_probs=74.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC----CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 013141          323 GESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG----KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWG  398 (449)
Q Consensus       323 ~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~----~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~  398 (449)
                      .....++|||+|||+++++++|+++|+.||.|.+|.++.+    +++|||+|.+.++|.+|++.||+..|+|+.|+|+|+
T Consensus         7 ~~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A   86 (93)
T d2cq3a1           7 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA   86 (93)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            4455778999999999999999999999999999999864    689999999999999999999999999999999999


Q ss_pred             CCCCC
Q 013141          399 RNPGN  403 (449)
Q Consensus       399 ~~~~~  403 (449)
                      +++..
T Consensus        87 ~~r~~   91 (93)
T d2cq3a1          87 TARVM   91 (93)
T ss_dssp             CSSCC
T ss_pred             CcCCC
Confidence            98654

>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=99.76  E-value=9.8e-19  Score=130.41  Aligned_cols=82  Identities=24%  Similarity=0.328  Sum_probs=72.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccc
Q 013141          112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRL  191 (449)
Q Consensus       112 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~  191 (449)
                      ....++|||+|||+++|+++|+++|+.||.|.+|+|++|+.+|+++|||||+|.+.++|++||+.+  ..+  .++.|.+
T Consensus         5 ~~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~~--~~l--~Gr~i~v   80 (90)
T d2cqga1           5 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR--HMI--DGRWCDC   80 (90)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSC--EEE--TTEEEEE
T ss_pred             CcCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcC--Ccc--CCEEeEE
Confidence            356789999999999999999999999999999999999999999999999999999999999743  355  3567888


Q ss_pred             cccccC
Q 013141          192 NWATFS  197 (449)
Q Consensus       192 ~~~~~~  197 (449)
                      .++...
T Consensus        81 ~~a~~k   86 (90)
T d2cqga1          81 KLPNSK   86 (90)
T ss_dssp             ECCCTT
T ss_pred             EeCCCC
Confidence            777654

>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=99.76  E-value=4e-19  Score=137.12  Aligned_cols=82  Identities=23%  Similarity=0.515  Sum_probs=75.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      ...++|||+|||+++++++|+++|+.||.|.+|++++++.+|+++|||||+|.+.++|++|++.|++..+.  ++.|+|+
T Consensus         6 ~~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~--g~~i~V~   83 (104)
T d1p1ta_           6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFS--GRALRVD   83 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCS--SSCBEEE
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEEC--CEEEEEE
Confidence            45679999999999999999999999999999999999999999999999999999999999999999985  5778888


Q ss_pred             cccc
Q 013141          193 WATF  196 (449)
Q Consensus       193 ~~~~  196 (449)
                      |+..
T Consensus        84 ~a~~   87 (104)
T d1p1ta_          84 NAAS   87 (104)
T ss_dssp             ETTC
T ss_pred             ECCC
Confidence            8753

>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=99.76  E-value=2.2e-18  Score=131.52  Aligned_cols=85  Identities=27%  Similarity=0.367  Sum_probs=80.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEee
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV  285 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  285 (449)
                      ...++|||+|||+++++++|+++|. .||.|.++++++++.+++++|||||+|.+.++|.+||+.||+..|.|+.|+|.+
T Consensus         6 ~~~~~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_           6 SGSGRLFVRNLSYTSSEEDLEKLFS-AYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHH-TTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHH-hcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            4567899999999999999999995 999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 013141          286 ATPKKA  291 (449)
Q Consensus       286 ~~~~~~  291 (449)
                      +..+..
T Consensus        85 a~~~~~   90 (99)
T d1whwa_          85 STIKKE   90 (99)
T ss_dssp             CCCCST
T ss_pred             CCCCCc
Confidence            988754

>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=99.76  E-value=1.3e-18  Score=128.54  Aligned_cols=81  Identities=25%  Similarity=0.472  Sum_probs=77.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecCC
Q 013141          209 LSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATP  288 (449)
Q Consensus       209 ~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~~  288 (449)
                      .+|||+|||+++|+++|+++|+ .||+|.++++++|+.++.++|||||+|.+.++|..|++.|++..+.|+.|+|+++.+
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~~   80 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLT-SFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASV   80 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHT-SSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHH-hcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            4799999999999999999995 999999999999999999999999999999999999999999999999999999987


Q ss_pred             CC
Q 013141          289 KK  290 (449)
Q Consensus       289 ~~  290 (449)
                      ..
T Consensus        81 ~~   82 (85)
T d2u2fa_          81 GA   82 (85)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.75  E-value=3.3e-18  Score=126.01  Aligned_cols=77  Identities=26%  Similarity=0.443  Sum_probs=73.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEE
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRI  283 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  283 (449)
                      .++++|||+|||+++|+++|+++|+ .||.|.++.+++++.+++++|||||+|.+.++|.+|++.|++..|.|+.|+|
T Consensus         7 ~~~~~l~V~nL~~~~te~~l~~~F~-~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           7 DPNCCLGVFGLSLYTTERDLREVFS-KYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHH-TTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHH-HhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            4567999999999999999999995 9999999999999999999999999999999999999999999999999987

>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=99.75  E-value=5e-19  Score=127.95  Aligned_cols=76  Identities=29%  Similarity=0.429  Sum_probs=68.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccccc
Q 013141          116 KTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWA  194 (449)
Q Consensus       116 ~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~~  194 (449)
                      |+|||+|||+++|+++|+++|++||.|.++++++|+.+|+++|||||+|.+.++|++||+ +++..+.+  +.|+|..+
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~G--r~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDS--KTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSS--CCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECC--eEEEEEEC
Confidence            689999999999999999999999999999999999999999999999999999999996 68888855  55555443

>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=99.75  E-value=3.2e-18  Score=127.00  Aligned_cols=79  Identities=20%  Similarity=0.339  Sum_probs=74.1

Q ss_pred             CCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCCC
Q 013141          325 SNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGN  403 (449)
Q Consensus       325 ~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~~  403 (449)
                      ...++|||+|||..+++++|+++|+.||.|..+.+.+++++|||+|.+.++|.+|+..||+..|.|+.|+|.|++++.+
T Consensus         6 ~~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP~~~   84 (86)
T d2cpda1           6 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDK   84 (86)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCCCC
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEccccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccCCCC
Confidence            3457899999999999999999999999999999988999999999999999999999999999999999999997654

>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=99.75  E-value=4.2e-18  Score=126.01  Aligned_cols=80  Identities=30%  Similarity=0.576  Sum_probs=74.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecC--cceEE
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSS--RPMRI  283 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g--~~i~v  283 (449)
                      ..+++|||+|||.++++++|+++|+ .||.|.++++++++.++.++|||||+|.+.++|.+|++.||+..+.+  ++|+|
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~-~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V   82 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFG-KYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSV   82 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHT-SSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHH-hhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEE
Confidence            3567899999999999999999995 99999999999999999999999999999999999999999999876  88999


Q ss_pred             eec
Q 013141          284 DVA  286 (449)
Q Consensus       284 ~~~  286 (449)
                      +||
T Consensus        83 ~~A   85 (85)
T d1b7fa2          83 RLA   85 (85)
T ss_dssp             EEC
T ss_pred             EEC
Confidence            986

>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=1.7e-18  Score=132.92  Aligned_cols=82  Identities=29%  Similarity=0.469  Sum_probs=73.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      ...++|||+|||+++++++|+++|+.||.|.+|++++++.+|+++|||||+|.+.++|++||+.+++ .+  .++.|+|.
T Consensus         8 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l--~Gr~l~V~   84 (103)
T d2cqda1           8 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-II--DGRKANVN   84 (103)
T ss_dssp             CSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EE--TTEECEEE
T ss_pred             CCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cC--CCEEEEEE
Confidence            4567899999999999999999999999999999999999999999999999999999999988776 46  45778888


Q ss_pred             ccccC
Q 013141          193 WATFS  197 (449)
Q Consensus       193 ~~~~~  197 (449)
                      ++...
T Consensus        85 ~a~~~   89 (103)
T d2cqda1          85 LAYLG   89 (103)
T ss_dssp             ESTTT
T ss_pred             EcCCC
Confidence            77644

>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=99.75  E-value=5.1e-18  Score=128.34  Aligned_cols=78  Identities=27%  Similarity=0.518  Sum_probs=72.4

Q ss_pred             CCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeC---CCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCC
Q 013141          324 ESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV---GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRN  400 (449)
Q Consensus       324 ~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~---~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  400 (449)
                      ....++|||+|||+.+++++|+++|+.||.|..+.+..   .+++|||+|.+.++|.+|++.||+..|.|+.|+|+|+++
T Consensus        11 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~~   90 (95)
T d1x4aa1          11 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRS   90 (95)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeccC
Confidence            34567899999999999999999999999999999875   478999999999999999999999999999999999987


Q ss_pred             C
Q 013141          401 P  401 (449)
Q Consensus       401 ~  401 (449)
                      .
T Consensus        91 ~   91 (95)
T d1x4aa1          91 G   91 (95)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.75  E-value=4.6e-18  Score=125.68  Aligned_cols=79  Identities=29%  Similarity=0.579  Sum_probs=73.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecC--cceEEe
Q 013141          207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSS--RPMRID  284 (449)
Q Consensus       207 ~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g--~~i~v~  284 (449)
                      .+++|||+|||+++|+++|+++|+ .||+|.++++++++.++.++|||||+|.+.++|++|++.|||..+.|  ++|+|+
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~-~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~   83 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFS-QYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVK   83 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHG-GGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHH-HhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEE
Confidence            456899999999999999999995 99999999999999999999999999999999999999999999987  558888


Q ss_pred             ec
Q 013141          285 VA  286 (449)
Q Consensus       285 ~~  286 (449)
                      |+
T Consensus        84 ~A   85 (85)
T d1fxla2          84 FA   85 (85)
T ss_dssp             EC
T ss_pred             eC
Confidence            75

>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=99.74  E-value=2.2e-18  Score=126.99  Aligned_cols=79  Identities=19%  Similarity=0.367  Sum_probs=70.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      +..++|||+|||+++|+++|+++|+.||.|.+|.|++|+.+|+++|||||+|.+.++|++|++ +++..+.  ++.|+|.
T Consensus         4 e~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~--Gr~i~V~   80 (84)
T d1l3ka1           4 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVD--GRVVEPK   80 (84)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEET--TEECEEE
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEEC--CEEEEEE
Confidence            456899999999999999999999999999999999999999999999999999999999996 5887774  4566665


Q ss_pred             cc
Q 013141          193 WA  194 (449)
Q Consensus       193 ~~  194 (449)
                      .+
T Consensus        81 ~A   82 (84)
T d1l3ka1          81 RA   82 (84)
T ss_dssp             EC
T ss_pred             ee
Confidence            54

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=5.9e-18  Score=128.38  Aligned_cols=78  Identities=29%  Similarity=0.552  Sum_probs=70.5

Q ss_pred             CCCCCcEEEEcCCC-CCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCC
Q 013141          323 GESNNATIFVGALD-SDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNP  401 (449)
Q Consensus       323 ~~~~~~~l~V~nlp-~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~  401 (449)
                      .....++|||+||+ ..+++++|+++|++||.|.+|.|.  +++|||+|.+.++|.+|++.|||+.|.|+.|+|+|++++
T Consensus        11 ~~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~--rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~   88 (98)
T d1wf2a_          11 PRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH--KGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEP   88 (98)
T ss_dssp             CSSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE--TEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETTSC
T ss_pred             CCCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe--CCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            34456789999997 568889999999999999999995  799999999999999999999999999999999999865


Q ss_pred             C
Q 013141          402 G  402 (449)
Q Consensus       402 ~  402 (449)
                      .
T Consensus        89 ~   89 (98)
T d1wf2a_          89 K   89 (98)
T ss_dssp             C
T ss_pred             C
Confidence            3

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=5.3e-18  Score=126.35  Aligned_cols=83  Identities=27%  Similarity=0.368  Sum_probs=76.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEee
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV  285 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  285 (449)
                      ...++|||+|||+++|+++|+++|+ .||.|.++.+++|+.+++++|||||+|.+.++|++||+.  ...|+|+.|.|++
T Consensus         6 ~~~~~lfV~nLp~~~te~~l~~~F~-~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~i~v~~   82 (90)
T d2cqga1           6 QKTSDLIVLGLPWKTTEQDLKEYFS-TFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCKL   82 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHG-GGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEEC
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHH-hhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccCCEEeEEEe
Confidence            3567899999999999999999995 999999999999999999999999999999999999974  4579999999999


Q ss_pred             cCCCCC
Q 013141          286 ATPKKA  291 (449)
Q Consensus       286 ~~~~~~  291 (449)
                      +.++..
T Consensus        83 a~~k~~   88 (90)
T d2cqga1          83 PNSKQS   88 (90)
T ss_dssp             CCTTCC
T ss_pred             CCCCCC
Confidence            988654

>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=99.74  E-value=2.6e-18  Score=123.66  Aligned_cols=73  Identities=26%  Similarity=0.419  Sum_probs=66.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       117 ~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      +|||+|||+++|+++|+++|++||.|.+|.+++++.+++++|||||+|.+.++|++||+ +++..+.+  +.|+|.
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~G--r~i~V~   73 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNG--KVIDPK   73 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTT--BCCEEC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECC--CEEEee
Confidence            59999999999999999999999999999999999999999999999999999999996 68887754  556554

>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=99.74  E-value=3.1e-18  Score=125.63  Aligned_cols=80  Identities=9%  Similarity=0.274  Sum_probs=69.7

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecC
Q 013141          208 DLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVAT  287 (449)
Q Consensus       208 ~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~  287 (449)
                      +++|||+|||+++|+++|+++|+ .||.|..+.++.+..++.++|||||+|.+.++|.+|++.||+..+.|++|+|++++
T Consensus         1 d~tl~v~nLp~~~t~~~l~~~f~-~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~   79 (81)
T d2ghpa1           1 ECTLWMTNFPPSYTQRNIRDLLQ-DINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSN   79 (81)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHH-HTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CcEEEEECCCCcCCHHHHHHHHH-HhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcc
Confidence            36899999999999999999995 99999999888888889999999999999999999999999999999999999997


Q ss_pred             C
Q 013141          288 P  288 (449)
Q Consensus       288 ~  288 (449)
                      |
T Consensus        80 P   80 (81)
T d2ghpa1          80 P   80 (81)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.74  E-value=2.6e-18  Score=125.08  Aligned_cols=74  Identities=26%  Similarity=0.526  Sum_probs=70.5

Q ss_pred             CCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCC
Q 013141          326 NNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNP  401 (449)
Q Consensus       326 ~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~  401 (449)
                      .+++|||+|++  +|+++|+++|++||.|.+|.+.+++++|||+|.+.++|.+|++.|||..|+|+.|+|+|+++.
T Consensus         4 ~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~   77 (79)
T d2bz2a1           4 KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQ   77 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETTTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCSS
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCccceeeeccCCCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecCC
Confidence            46789999996  899999999999999999999999999999999999999999999999999999999999865

>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=99.74  E-value=1.2e-18  Score=127.93  Aligned_cols=79  Identities=9%  Similarity=0.159  Sum_probs=66.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccccccc
Q 013141          116 KTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWAT  195 (449)
Q Consensus       116 ~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~~~  195 (449)
                      ++|||+|||+++|+++|+++|+.||.|..+.++.+..+|+++|||||+|.+.++|.+|++.||+..+  .++.|++.+++
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~--~g~~i~V~~a~   79 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKI--EGYTLVTKVSN   79 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEE--TTEECEEEECC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEE--CCEEEEEEEcc
Confidence            6999999999999999999999999999999988888899999999999999999999999999999  45777777765


Q ss_pred             c
Q 013141          196 F  196 (449)
Q Consensus       196 ~  196 (449)
                      +
T Consensus        80 P   80 (81)
T d2ghpa1          80 P   80 (81)
T ss_dssp             C
T ss_pred             C
Confidence            3

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=4.1e-18  Score=130.35  Aligned_cols=84  Identities=23%  Similarity=0.394  Sum_probs=78.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeec
Q 013141          207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVA  286 (449)
Q Consensus       207 ~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~  286 (449)
                      ..++|||+|||+++++++|+++|+ .||.|..+.|++|+.++.++|||||+|.+.++|.+|+ .+++..|.|+.|.|+++
T Consensus        19 ~~~~lfVgnLp~~~te~~L~~~F~-~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al-~~~~~~l~G~~i~V~~a   96 (103)
T d1x4ba1          19 QFRKLFIGGLSFETTEESLRNYYE-QWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM-AARPHSIDGRVVEPKRA   96 (103)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHT-SSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHH-TSCSEEETTEEEEEECC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHH-hhCcccceeecccccCCCccCeEEEEECCHHHHHHHH-HhCCCeECCEEEEEEEC
Confidence            347899999999999999999995 9999999999999999999999999999999999999 58999999999999999


Q ss_pred             CCCCCC
Q 013141          287 TPKKAS  292 (449)
Q Consensus       287 ~~~~~~  292 (449)
                      .++..+
T Consensus        97 ~~ke~~  102 (103)
T d1x4ba1          97 VAREES  102 (103)
T ss_dssp             SSCCCC
T ss_pred             cccCCC
Confidence            887653

>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=99.74  E-value=6.7e-18  Score=127.28  Aligned_cols=85  Identities=19%  Similarity=0.363  Sum_probs=77.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecC-CCCCcceEEEEEeCCHHHHHHHHHHh-CCceecCcceEE
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDS-NTGRTKGYGFVRFGDENERSRAMTEM-NGVYCSSRPMRI  283 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~-~~~~~~g~afV~f~~~~~A~~A~~~l-~g~~~~g~~i~v  283 (449)
                      ..+++|||+|||+++++++|+++|+ .||.|.+++++++. .+|.++|||||+|.+.++|.+|++.| ++..+.|+.|.|
T Consensus         6 ~~~~~l~V~nLp~~~~e~~l~~~F~-~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V   84 (94)
T d2cpha1           6 QTTSKILVRNIPFQANQREIRELFS-TFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL   84 (94)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHH-TTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHH-HhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEE
Confidence            4567899999999999999999995 99999999998875 47899999999999999999999998 899999999999


Q ss_pred             eecCCCCC
Q 013141          284 DVATPKKA  291 (449)
Q Consensus       284 ~~~~~~~~  291 (449)
                      +|+.....
T Consensus        85 ~~A~~~~~   92 (94)
T d2cpha1          85 EWADSEVT   92 (94)
T ss_dssp             EECCCCCC
T ss_pred             EEcCCCCC
Confidence            99987643

>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=99.74  E-value=5.7e-18  Score=125.88  Aligned_cols=76  Identities=14%  Similarity=0.242  Sum_probs=69.6

Q ss_pred             CCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCC
Q 013141          326 NNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPG  402 (449)
Q Consensus       326 ~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~  402 (449)
                      .+++|||+|||++++++||+++|++|| +..+.+.+.+++|||+|.+.++|.+|++.||+..|+|+.|+|+|+++..
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~~~   79 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDA   79 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEEEGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeeeeccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            357899999999999999999999999 4556677789999999999999999999999999999999999998754

>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=99.74  E-value=7.8e-18  Score=137.12  Aligned_cols=87  Identities=21%  Similarity=0.466  Sum_probs=80.7

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEe
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRID  284 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  284 (449)
                      ....++|||+|||+++|+++|+++|+ .||.|.+|.+++++.+++++|||||+|.+.++|.+||+.||+..|+|+.|+|+
T Consensus        39 ~~~~~~l~V~nLp~~~te~~l~~~F~-~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~  117 (139)
T d1u6fa1          39 PDVLRNLMVNYIPTTVDEVQLRQLFE-RYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA  117 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHH-HHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHH-hhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34457899999999999999999995 99999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCCC
Q 013141          285 VATPKKAS  292 (449)
Q Consensus       285 ~~~~~~~~  292 (449)
                      ++..+..+
T Consensus       118 ~a~~~~~~  125 (139)
T d1u6fa1         118 LAASGHQR  125 (139)
T ss_dssp             ESSCCCCC
T ss_pred             EcCCCCCC
Confidence            99876543

>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=99.74  E-value=8.7e-18  Score=127.51  Aligned_cols=80  Identities=21%  Similarity=0.471  Sum_probs=74.2

Q ss_pred             CCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCC--eEEEEEecCCC
Q 013141          324 ESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGK--QTVRLSWGRNP  401 (449)
Q Consensus       324 ~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g--~~l~v~~~~~~  401 (449)
                      ..++++|||+|||+++++++|+++|++||.|..|++.+++++|||+|.+.++|.+|++.||+..|.|  +.|+|+|+++.
T Consensus        14 ~~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~ak~~   93 (97)
T d1whya_          14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSG   93 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSSSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCC
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeeccccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeCCCC
Confidence            3457899999999999999999999999999999999999999999999999999999999999986  58999999975


Q ss_pred             CC
Q 013141          402 GN  403 (449)
Q Consensus       402 ~~  403 (449)
                      +.
T Consensus        94 ~~   95 (97)
T d1whya_          94 PS   95 (97)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.73  E-value=4.4e-18  Score=127.50  Aligned_cols=85  Identities=33%  Similarity=0.584  Sum_probs=79.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEee
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV  285 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  285 (449)
                      ...++|||+|||+++++++|+++|+ .||.|..+.++++..++.++|||||+|.+.++|++|++.|++..|.|+.|+|++
T Consensus         3 ~~~~kifV~nLp~~~t~~~l~~~F~-~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~   81 (90)
T d1x5sa1           3 SDEGKLFVGGLSFDTNEQSLEQVFS-KYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQ   81 (90)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHH-HHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEE
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhh-ccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            3567899999999999999999995 999999999999989999999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 013141          286 ATPKKA  291 (449)
Q Consensus       286 ~~~~~~  291 (449)
                      +.++..
T Consensus        82 a~~~~~   87 (90)
T d1x5sa1          82 AGKSSD   87 (90)
T ss_dssp             EECCCC
T ss_pred             cCCCCC
Confidence            977654

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.73  E-value=6.3e-18  Score=124.37  Aligned_cols=77  Identities=21%  Similarity=0.406  Sum_probs=70.8

Q ss_pred             CCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC-CcEEEEEecCHHHHHHHHHHhcCCeeC-CeEEEEEecCC
Q 013141          324 ESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-KGCGFVQFANRKDAEVALQKLQGTAIG-KQTVRLSWGRN  400 (449)
Q Consensus       324 ~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~-~g~afV~F~~~~~A~~A~~~l~g~~~~-g~~l~v~~~~~  400 (449)
                      .+++++|||+|||..+++++|+++|+.||.|.+|++.++ +++|||+|.+.++|..|++.|||..|. |+.|+|+|+|.
T Consensus         5 ~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~akk   83 (83)
T d2b0ga1           5 QPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAKK   83 (83)
T ss_dssp             CSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTTCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEECCC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecccceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEecC
Confidence            445789999999999999999999999999999999875 589999999999999999999999985 68999999973

>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=99.73  E-value=4.4e-18  Score=125.42  Aligned_cols=81  Identities=33%  Similarity=0.703  Sum_probs=75.2

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhhCCCeeE-EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecCCC
Q 013141          211 IFVGDLAPDVTDSILQETFSSKYPSVKG-AKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPK  289 (449)
Q Consensus       211 l~v~~lp~~~t~~~l~~~f~~~~g~v~~-i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~~~  289 (449)
                      |||+|||+++|+++|+++|+ .||.|.+ +.++++..+++++|||||+|.+.++|++|++.|++..+.|++|+|+++.++
T Consensus         1 lfV~nLp~~~te~~l~~~F~-~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k   79 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFS-AFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKK   79 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHH-TTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHH-HhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCC
Confidence            79999999999999999996 9999866 478889899999999999999999999999999999999999999999887


Q ss_pred             CCC
Q 013141          290 KAS  292 (449)
Q Consensus       290 ~~~  292 (449)
                      ..+
T Consensus        80 ~~k   82 (83)
T d1x5ta1          80 DSK   82 (83)
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=99.73  E-value=1.4e-18  Score=126.78  Aligned_cols=76  Identities=20%  Similarity=0.386  Sum_probs=71.4

Q ss_pred             cEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCC-eeCCeEEEEEecCCCCC
Q 013141          328 ATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGT-AIGKQTVRLSWGRNPGN  403 (449)
Q Consensus       328 ~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~-~~~g~~l~v~~~~~~~~  403 (449)
                      .+|||+|||.++|+++|+++|++||.|.++.+..++++|||+|.+.++|.+|++.|||. .|+|+.|+|+|++++..
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k~~   78 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKL   78 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCcCc
Confidence            46999999999999999999999999999888889999999999999999999999996 69999999999998654

>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=99.73  E-value=1e-18  Score=133.37  Aligned_cols=79  Identities=20%  Similarity=0.397  Sum_probs=72.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccccc
Q 013141          114 ETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNW  193 (449)
Q Consensus       114 ~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~  193 (449)
                      ..++|||+|||+++++++|+++|+.||.|.+|++++++.+|+++|||||+|.+.++|.+|+ .|++..+.+  +.|+|.+
T Consensus        17 ~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~-~l~g~~~~G--~~l~V~~   93 (101)
T d2cq4a1          17 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLG--VPIIVQA   93 (101)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETT--EEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHH-HHCCCEECC--EEEEEEE
Confidence            4679999999999999999999999999999999999999999999999999999999999 599999854  6777766


Q ss_pred             cc
Q 013141          194 AT  195 (449)
Q Consensus       194 ~~  195 (449)
                      +.
T Consensus        94 a~   95 (101)
T d2cq4a1          94 SQ   95 (101)
T ss_dssp             HH
T ss_pred             CC
Confidence            54

>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=99.73  E-value=3.8e-18  Score=127.37  Aligned_cols=77  Identities=32%  Similarity=0.581  Sum_probs=71.9

Q ss_pred             CcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC----CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCC
Q 013141          327 NATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG----KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPG  402 (449)
Q Consensus       327 ~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~----~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~  402 (449)
                      ..+|||+|||+++++++|+++|+.||.|.++.|+.+    +|+|||+|.+.++|.+|++.|||..|+|+.|+|.|+++..
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~~   87 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK   87 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTTBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecCCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            457999999999999999999999999999999874    6899999999999999999999999999999999999765


Q ss_pred             C
Q 013141          403 N  403 (449)
Q Consensus       403 ~  403 (449)
                      .
T Consensus        88 ~   88 (89)
T d1cvja2          88 E   88 (89)
T ss_dssp             T
T ss_pred             C
Confidence            3

>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=99.73  E-value=1.4e-17  Score=122.54  Aligned_cols=79  Identities=27%  Similarity=0.443  Sum_probs=74.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeec
Q 013141          207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVA  286 (449)
Q Consensus       207 ~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~  286 (449)
                      ..++|||+|||+++|+++|+++|+ .||.|.++.+++|+.++.++|||||+|.+.++|++|++ +++..|.|+.|+|+.|
T Consensus         5 ~~~~lfV~nlp~~~te~~l~~~F~-~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A   82 (84)
T d1l3ka1           5 QLRKLFIGGLSFETTDESLRSHFE-QWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRA   82 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHG-GGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEEC
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHH-hhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEee
Confidence            456899999999999999999995 99999999999999999999999999999999999995 7999999999999887


Q ss_pred             C
Q 013141          287 T  287 (449)
Q Consensus       287 ~  287 (449)
                      .
T Consensus        83 ~   83 (84)
T d1l3ka1          83 V   83 (84)
T ss_dssp             C
T ss_pred             e
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=99.73  E-value=4.2e-18  Score=131.27  Aligned_cols=82  Identities=34%  Similarity=0.602  Sum_probs=77.9

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecC
Q 013141          208 DLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVAT  287 (449)
Q Consensus       208 ~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~  287 (449)
                      .++|||+|||+++++++|+++|+ .||+|.++.+++++.+++++|||||+|.+.++|++|++.|++..|.|+.|+|+++.
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~-~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~   86 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFS-EVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHH-TTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CCEEEEECCCCcCCHHHHHHhhh-ccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            46899999999999999999996 99999999999999999999999999999999999999999999999999999987


Q ss_pred             CCC
Q 013141          288 PKK  290 (449)
Q Consensus       288 ~~~  290 (449)
                      +..
T Consensus        87 ~~~   89 (104)
T d1p1ta_          87 SEK   89 (104)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            754

>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=99.73  E-value=2.6e-18  Score=124.10  Aligned_cols=76  Identities=29%  Similarity=0.457  Sum_probs=72.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeec
Q 013141          209 LSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVA  286 (449)
Q Consensus       209 ~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~  286 (449)
                      ++|||+|||+++|+++|+++|+ .||.|.++++++|+.+++++|||||+|.+.++|.+|++ +++..++|+.|+|+++
T Consensus         1 cklfV~nLp~~~te~~l~~~F~-~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFG-QFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHT-TTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHH-HhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            4799999999999999999995 99999999999999999999999999999999999996 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=99.73  E-value=5.3e-18  Score=125.58  Aligned_cols=77  Identities=23%  Similarity=0.417  Sum_probs=69.9

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCC---CcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccccc
Q 013141          118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTG---QSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWA  194 (449)
Q Consensus       118 l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g---~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~~  194 (449)
                      |||+|||+++|+++|+++|+.||.|.+|+|++++.++   +++|||||+|.+.++|.+|++.||+..+.  ++.|+|.|+
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~--g~~i~V~~a   78 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVD--GHKLEVRIS   78 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEET--TEECEEECS
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEEC--CEEEEEEEC
Confidence            7999999999999999999999999999999987665   46899999999999999999999999885  568888887


Q ss_pred             cc
Q 013141          195 TF  196 (449)
Q Consensus       195 ~~  196 (449)
                      ..
T Consensus        79 ~~   80 (85)
T d2cpfa1          79 ER   80 (85)
T ss_dssp             SC
T ss_pred             CC
Confidence            53

>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=99.72  E-value=1e-17  Score=121.63  Aligned_cols=76  Identities=34%  Similarity=0.535  Sum_probs=72.6

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecC
Q 013141          210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVAT  287 (449)
Q Consensus       210 ~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~  287 (449)
                      +|||+|||+++++++|+++|+ .||.|.++++..++ +++++|||||+|.+.++|.+|++.||+..+.|+.|+|++++
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 KLLVSNLDFGVSDADIQELFA-EFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHH-HHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHH-HhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            699999999999999999995 99999999999885 68999999999999999999999999999999999999875

>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=99.72  E-value=8.2e-18  Score=122.09  Aligned_cols=71  Identities=25%  Similarity=0.454  Sum_probs=67.7

Q ss_pred             EEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC-----CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 013141          329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-----KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGR  399 (449)
Q Consensus       329 ~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~-----~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  399 (449)
                      +|||+|||+++++++|+++|++||.|.+++|..+     +|+|||+|.+.++|.+|++.|||..++|+.|+|++++
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            5999999999999999999999999999999863     6899999999999999999999999999999999986

>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=99.72  E-value=1.3e-17  Score=127.98  Aligned_cols=83  Identities=31%  Similarity=0.502  Sum_probs=76.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeec
Q 013141          207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVA  286 (449)
Q Consensus       207 ~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~  286 (449)
                      ..++|||+|||+++++++|+++|+ .||.|.++++++++.+++++|||||+|.+.++|++||+.+++ .|.|+.|+|+++
T Consensus         9 ~~~~lfV~nLp~~~te~~l~~~F~-~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a   86 (103)
T d2cqda1           9 TFTKIFVGGLPYHTTDASLRKYFE-GFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLA   86 (103)
T ss_dssp             SSSEEEEECCCSSCCHHHHHHHHH-TTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEES
T ss_pred             CCcEEEEeCCCCcCcHHHHHHHHh-hcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEc
Confidence            456899999999999999999995 999999999999999999999999999999999999988876 799999999998


Q ss_pred             CCCCC
Q 013141          287 TPKKA  291 (449)
Q Consensus       287 ~~~~~  291 (449)
                      ..+..
T Consensus        87 ~~~~~   91 (103)
T d2cqda1          87 YLGAK   91 (103)
T ss_dssp             TTTCC
T ss_pred             CCCCC
Confidence            76543

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.72  E-value=4.9e-18  Score=132.85  Aligned_cols=77  Identities=22%  Similarity=0.362  Sum_probs=73.2

Q ss_pred             CCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCC
Q 013141          326 NNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPG  402 (449)
Q Consensus       326 ~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~  402 (449)
                      ..++|||+|||+++++++|+++|+.||.|.+|.|.+.+++|||+|.+.++|.+|++.|||..|.|+.|+|+|++...
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~~~   85 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGV   85 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCSSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETTT
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeeccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCCCc
Confidence            35789999999999999999999999999999999999999999999999999999999999999999999997643

>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=99.72  E-value=2.3e-17  Score=123.34  Aligned_cols=83  Identities=25%  Similarity=0.470  Sum_probs=75.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEee
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV  285 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  285 (449)
                      ...++|||+|||.++|+++|+++|+ .||.|.++.++++..++  ++||||+|.+.++|.+|++.|++..+.|+.|+|.|
T Consensus         6 ~~~~tl~V~nLp~~~te~~l~~~F~-~~G~i~~v~i~~d~~~~--~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~   82 (90)
T d2cqia1           6 GQPRTLYVGNLSRDVTEVLILQLFS-QIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNW   82 (90)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHH-HHSCEEEEEEECCCCSS--CCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHH-hcCCceeeeeecccCcc--ceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            4567999999999999999999995 99999999999886654  78999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 013141          286 ATPKKA  291 (449)
Q Consensus       286 ~~~~~~  291 (449)
                      +.+...
T Consensus        83 a~~~~~   88 (90)
T d2cqia1          83 ATTPSS   88 (90)
T ss_dssp             CCCTTC
T ss_pred             cCCCCC
Confidence            987543

>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=99.72  E-value=3.1e-18  Score=126.27  Aligned_cols=78  Identities=31%  Similarity=0.603  Sum_probs=71.2

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCCcEEE-EEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccccccc
Q 013141          118 IWIGDLFHWMDETFLHNCFSHTGQVVNV-KVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWATF  196 (449)
Q Consensus       118 l~v~nLp~~~t~~~l~~~f~~~G~v~~v-~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~~~~  196 (449)
                      |||+|||+++|+++|+++|++||.|.++ ++++++.+|+++|||||+|.+.++|++|++.|++..+.  ++.|++.|+.+
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~--gr~l~v~~a~~   78 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLC--NRPITVSYAFK   78 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEET--TEECEEEESCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEEC--CEEEEEEEecC
Confidence            8999999999999999999999998764 78889899999999999999999999999999999984  57888888864


Q ss_pred             C
Q 013141          197 S  197 (449)
Q Consensus       197 ~  197 (449)
                      .
T Consensus        79 k   79 (83)
T d1x5ta1          79 K   79 (83)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.72  E-value=2.9e-17  Score=122.30  Aligned_cols=80  Identities=13%  Similarity=0.263  Sum_probs=74.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHh--cCCeeCCeEEEEEecCC
Q 013141          323 GESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKL--QGTAIGKQTVRLSWGRN  400 (449)
Q Consensus       323 ~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l--~g~~~~g~~l~v~~~~~  400 (449)
                      ...++++|||+|||.++++++|+++|++||.|.++.+.+++++|||+|.+.++|.+|++.+  ++..+.|+.|+|.|++.
T Consensus         4 ~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~~sk~   83 (88)
T d2cq1a1           4 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNH   83 (88)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcccccccccccccceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEEECCC
Confidence            3557899999999999999999999999999999999999999999999999999999876  57789999999999987


Q ss_pred             CC
Q 013141          401 PG  402 (449)
Q Consensus       401 ~~  402 (449)
                      ..
T Consensus        84 ~~   85 (88)
T d2cq1a1          84 KE   85 (88)
T ss_dssp             SS
T ss_pred             CC
Confidence            54

>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=99.72  E-value=1.1e-17  Score=120.43  Aligned_cols=75  Identities=28%  Similarity=0.486  Sum_probs=71.0

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeec
Q 013141          210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVA  286 (449)
Q Consensus       210 ~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~  286 (449)
                      +|||+|||+++|+++|+++|+ .||.|.++.+++++.+++++|||||+|.+.++|++|++ +++..|.|+.|+|+.+
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 KMFIGGLSWDTTKKDLKDYFS-KFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHH-TTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHH-hhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeEC
Confidence            589999999999999999995 99999999999999999999999999999999999996 7999999999999764

>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=99.72  E-value=1.8e-17  Score=122.60  Aligned_cols=79  Identities=19%  Similarity=0.444  Sum_probs=72.8

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCC---CcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecC
Q 013141          211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTG---RTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVAT  287 (449)
Q Consensus       211 l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~---~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~  287 (449)
                      |||+|||+++|+++|+++|+ .||.|.++.+++++.++   .++|||||+|.+.++|.+|++.||+..+.|+.|+|+++.
T Consensus         1 LfV~nLp~~~t~~~l~~~F~-~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~   79 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFS-KVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISE   79 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHH-TTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSS
T ss_pred             CEEcCCCCCCCHHHHHHHHH-HhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            79999999999999999995 99999999999887655   468999999999999999999999999999999999986


Q ss_pred             CCC
Q 013141          288 PKK  290 (449)
Q Consensus       288 ~~~  290 (449)
                      ...
T Consensus        80 ~~~   82 (85)
T d2cpfa1          80 RAT   82 (85)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            543

>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=99.71  E-value=4.9e-17  Score=122.23  Aligned_cols=84  Identities=20%  Similarity=0.456  Sum_probs=76.5

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEe
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRID  284 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  284 (449)
                      ....++|||+|||+++++++|+++|+ .||.|.++.++.+..  .++|||||+|.+.++|.+|++.|++..|.|+.|+|+
T Consensus         8 ~~~~~~l~v~nLp~~~t~~~L~~~F~-~~G~v~~v~~~~~~~--~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~   84 (93)
T d2cq3a1           8 KSTPKRLHVSNIPFRFRDPDLRQMFG-QFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN   84 (93)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGG-GTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHh-hcceeeecccccccc--CCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34567899999999999999999995 999999999998864  368999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 013141          285 VATPKKA  291 (449)
Q Consensus       285 ~~~~~~~  291 (449)
                      ++.++..
T Consensus        85 ~A~~r~~   91 (93)
T d2cq3a1          85 NATARVM   91 (93)
T ss_dssp             ECCSSCC
T ss_pred             ecCcCCC
Confidence            9988643

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.71  E-value=2.2e-17  Score=118.57  Aligned_cols=72  Identities=18%  Similarity=0.370  Sum_probs=68.3

Q ss_pred             EEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCC
Q 013141          330 IFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPG  402 (449)
Q Consensus       330 l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~  402 (449)
                      |||+|||+++++++|+++|++|| +..+.+.+++++|||+|.+.++|.+|++.|||..++|+.|+|+|++...
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d~   72 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTDA   72 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCSTT
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceeecccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCCC
Confidence            79999999999999999999998 7788888899999999999999999999999999999999999998653

>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=99.71  E-value=6.3e-17  Score=124.36  Aligned_cols=81  Identities=22%  Similarity=0.215  Sum_probs=73.9

Q ss_pred             CCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHh--cCCeeCCeEEEEEecCC
Q 013141          323 GESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKL--QGTAIGKQTVRLSWGRN  400 (449)
Q Consensus       323 ~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l--~g~~~~g~~l~v~~~~~  400 (449)
                      ...++++|||+|||..+++++|+++|+.||.|.++.+.+++++|||+|.+.++|..|++.|  ++..+.|+.|+|.|++.
T Consensus        11 ~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~s~~   90 (104)
T d1wexa_          11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTS   90 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSS
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEecceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEEcCC
Confidence            4456889999999999999999999999999999999999999999999999999999988  45678899999999987


Q ss_pred             CCC
Q 013141          401 PGN  403 (449)
Q Consensus       401 ~~~  403 (449)
                      ...
T Consensus        91 ~~~   93 (104)
T d1wexa_          91 KRI   93 (104)
T ss_dssp             SSC
T ss_pred             Ccc
Confidence            543

>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=99.71  E-value=1.3e-17  Score=124.23  Aligned_cols=77  Identities=22%  Similarity=0.355  Sum_probs=70.4

Q ss_pred             CCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeC--CCcEEEEEecCHHHHHHHHHHhcCCee-CCeEEEEEecCCC
Q 013141          325 SNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV--GKGCGFVQFANRKDAEVALQKLQGTAI-GKQTVRLSWGRNP  401 (449)
Q Consensus       325 ~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~--~~g~afV~F~~~~~A~~A~~~l~g~~~-~g~~l~v~~~~~~  401 (449)
                      +++++|||+|||.++++++|+++|+.||.|.++.+..  ++++|||+|.+.++|.+|+..|||..+ +|+.|+|+|+|++
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk~~   87 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST   87 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeeecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCCCC
Confidence            4578999999999999999999999999998887764  578999999999999999999999988 5899999999874

>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=99.71  E-value=3.5e-18  Score=122.54  Aligned_cols=68  Identities=18%  Similarity=0.343  Sum_probs=62.3

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCC
Q 013141          117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNT  185 (449)
Q Consensus       117 ~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~  185 (449)
                      +|||+|||+++|+++|+++|++||.|.+|++++++.+++++|||||+|.+.++|++||+. ++..+.++
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 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLS   68 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTC-SSCCBTTB
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhh-CCCEECCE
Confidence            599999999999999999999999999999999999999999999999999999999964 55566443

>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=99.71  E-value=2e-17  Score=129.80  Aligned_cols=76  Identities=17%  Similarity=0.378  Sum_probs=71.5

Q ss_pred             CCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC---CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCC
Q 013141          325 SNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG---KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRN  400 (449)
Q Consensus       325 ~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~---~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  400 (449)
                      +.+++|||+|||..+++++|+++|+.||.|.+|++..+   +|+|||+|.+.++|..|++.|||..|.|+.|+|.|+..
T Consensus         5 ~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~   83 (114)
T d2f9da1           5 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNA   83 (114)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccccCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            45689999999999999999999999999999999864   78999999999999999999999999999999999874

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=3.5e-17  Score=125.10  Aligned_cols=80  Identities=26%  Similarity=0.456  Sum_probs=71.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      ...++|||+|||+++++++|+++|+.||.|.++.+..+. +++++|||||+|.+.++|.+|++.|||..+.  ++++.+.
T Consensus        16 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~--gr~~~v~   92 (101)
T d1x5oa1          16 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIK--TPPGVSA   92 (101)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCC--CCTTSCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccc-ccccccceeEEeCCHHHHHHHHHHhCCCEEC--CcCCccC
Confidence            456899999999999999999999999999999999885 7899999999999999999999999999995  4666666


Q ss_pred             ccc
Q 013141          193 WAT  195 (449)
Q Consensus       193 ~~~  195 (449)
                      +++
T Consensus        93 ~~~   95 (101)
T d1x5oa1          93 PTE   95 (101)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            554

>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=99.71  E-value=1.2e-17  Score=121.85  Aligned_cols=77  Identities=18%  Similarity=0.421  Sum_probs=69.9

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccccc
Q 013141          115 TKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWA  194 (449)
Q Consensus       115 ~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~~  194 (449)
                      .++|||+|||+++|+++|+++|+.||.|..+.++.++.+++++|||||+|.+.++|.+|+ .+++..|.+  +.|+|..+
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al-~~~~~~l~G--r~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNG--HNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHH-HCSCCEETT--EECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHH-HhCCCEECC--EEEEEEEC
Confidence            579999999999999999999999999999999999999999999999999999999999 589998855  56666543

>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=99.71  E-value=7.1e-18  Score=128.99  Aligned_cols=81  Identities=22%  Similarity=0.368  Sum_probs=73.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccccc
Q 013141          114 ETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNW  193 (449)
Q Consensus       114 ~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~  193 (449)
                      ..++|||+|||+++++++|+++|++||.|.++.|.+|+.++.++|||||+|.+.++|.+||+ +++..|  .++.|.|.+
T Consensus        19 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l--~G~~i~V~~   95 (103)
T d1x4ba1          19 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSI--DGRVVEPKR   95 (103)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEE--TTEEEEEEC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeE--CCEEEEEEE
Confidence            45799999999999999999999999999999999999999999999999999999999995 688877  457788877


Q ss_pred             cccC
Q 013141          194 ATFS  197 (449)
Q Consensus       194 ~~~~  197 (449)
                      +.+.
T Consensus        96 a~~k   99 (103)
T d1x4ba1          96 AVAR   99 (103)
T ss_dssp             CSSC
T ss_pred             Cccc
Confidence            7644

>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=99.71  E-value=1.7e-17  Score=125.86  Aligned_cols=78  Identities=23%  Similarity=0.359  Sum_probs=72.3

Q ss_pred             CCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCCC
Q 013141          325 SNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGN  403 (449)
Q Consensus       325 ~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~~  403 (449)
                      ....+|||+|||+.+++++|+++|+.||.|.++.+.+ +++|||+|.+.++|.+||+.||+..|.|+.|+|.|.+....
T Consensus        13 ~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~~~~~   90 (98)
T d1wg4a_          13 RSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYPE   90 (98)
T ss_dssp             SCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEecCCC
Confidence            3567899999999999999999999999999999875 68999999999999999999999999999999999987543

>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=99.71  E-value=1.9e-17  Score=126.32  Aligned_cols=86  Identities=24%  Similarity=0.322  Sum_probs=75.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCC----CCCC
Q 013141          112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMP----NTDQ  187 (449)
Q Consensus       112 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~----~~~~  187 (449)
                      ..+.++|||+|||+++|+++|+++|++||.|.++.++.++.+++++|||||+|.+.++|.+||+.+++....    ..++
T Consensus         5 ~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr   84 (98)
T d1x4ha1           5 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR   84 (98)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSC
T ss_pred             CCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCE
Confidence            346789999999999999999999999999999999999999999999999999999999999998854321    2457


Q ss_pred             cccccccccC
Q 013141          188 PFRLNWATFS  197 (449)
Q Consensus       188 ~~~~~~~~~~  197 (449)
                      .|+|.|+...
T Consensus        85 ~l~v~~a~~k   94 (98)
T d1x4ha1          85 QLKVDLAVTR   94 (98)
T ss_dssp             EEEEECCCCC
T ss_pred             EEEEEECCCC
Confidence            7888887643

>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=99.70  E-value=4.9e-18  Score=126.11  Aligned_cols=72  Identities=22%  Similarity=0.356  Sum_probs=67.8

Q ss_pred             EEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCC
Q 013141          329 TIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNP  401 (449)
Q Consensus       329 ~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~  401 (449)
                      +|||+|||+.+++++|+++|++||.|.++.+.+ +|+|||+|.+.++|.+||+.|||..|.|+.|+|.+++..
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 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR-DGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   73 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEECT-TSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhcccccccccc-cceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecC
Confidence            699999999999999999999999999999876 489999999999999999999999999999999987654

>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=99.70  E-value=2.7e-17  Score=128.03  Aligned_cols=77  Identities=25%  Similarity=0.461  Sum_probs=70.9

Q ss_pred             CcEEEEcCCCC-CCCHhHHHhhccccCceEEEEEeCC-CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCCC
Q 013141          327 NATIFVGALDS-DVSDEDLREPFSQFGEILSVKIPVG-KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGN  403 (449)
Q Consensus       327 ~~~l~V~nlp~-~~t~~~L~~~f~~~G~v~~v~i~~~-~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~~  403 (449)
                      +++|||+||++ .+++++|+++|+.||.|.+|.|+++ +|+|||+|.+.++|.+|++.|||..|.|+.|+|+|++....
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~~~~~   80 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNV   80 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCCCC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCCC
Confidence            57899999965 5999999999999999999999876 68999999999999999999999999999999999986543

>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=99.70  E-value=2.2e-17  Score=123.20  Aligned_cols=81  Identities=31%  Similarity=0.559  Sum_probs=74.6

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecC
Q 013141          208 DLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVAT  287 (449)
Q Consensus       208 ~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~  287 (449)
                      ..+|||+|||+++|+++|+++|+ .||.|.++.++.+..  .++|||||+|.+.++|.+|++.|||..|.|+.|+|+++.
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~-~~G~v~~~~i~~~~~--~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~   84 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFS-AFGNILSCKVVCDEN--GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK   84 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHH-TTSCEEEEEECCBTT--BCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHH-hcCCceEEEEEeecC--CCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            45799999999999999999996 999999999998854  468999999999999999999999999999999999998


Q ss_pred             CCCC
Q 013141          288 PKKA  291 (449)
Q Consensus       288 ~~~~  291 (449)
                      ++..
T Consensus        85 ~~~~   88 (89)
T d1cvja2          85 SRKE   88 (89)
T ss_dssp             CTTT
T ss_pred             CCCC
Confidence            7653

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=1.8e-17  Score=125.58  Aligned_cols=84  Identities=17%  Similarity=0.244  Sum_probs=74.8

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCC-cEEEEEEecC-CCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccccc
Q 013141          116 KTIWIGDLFHWMDETFLHNCFSHTGQ-VVNVKVIRNK-QTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNW  193 (449)
Q Consensus       116 ~~l~v~nLp~~~t~~~l~~~f~~~G~-v~~v~~~~~~-~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~  193 (449)
                      ++|||+|||.++++++|+++|+.||+ |.++.++++. .+++++|||||+|.+.++|.+|++.|++..+...++.|+|.|
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            68999999999999999999999996 8999999875 468899999999999999999999998776655678999999


Q ss_pred             cccCCC
Q 013141          194 ATFSGS  199 (449)
Q Consensus       194 ~~~~~~  199 (449)
                      +++...
T Consensus        82 A~p~~~   87 (96)
T d2disa1          82 AEPEID   87 (96)
T ss_dssp             SCSSCS
T ss_pred             cCCCCC
Confidence            976543

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.70  E-value=2.7e-17  Score=124.54  Aligned_cols=80  Identities=26%  Similarity=0.429  Sum_probs=72.3

Q ss_pred             CCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEe-CCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCC
Q 013141          324 ESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIP-VGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPG  402 (449)
Q Consensus       324 ~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~-~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~  402 (449)
                      ....++|||+|||.++++++|+++|+.||.|..+... +++++|||+|.+.++|.+|++.||+..|.|+.|+|.|++++.
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~~k~   92 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKG   92 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSSC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeeecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeCCCC
Confidence            4457899999999999999999999999998877654 357999999999999999999999999999999999999865


Q ss_pred             C
Q 013141          403 N  403 (449)
Q Consensus       403 ~  403 (449)
                      .
T Consensus        93 ~   93 (96)
T d1fjca_          93 G   93 (96)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.70  E-value=7.1e-17  Score=122.38  Aligned_cols=79  Identities=18%  Similarity=0.384  Sum_probs=73.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      .++++|||+|||+++++++|+++|++||.|.+|++.++      ++||||+|.+.++|.+|++.|++..+.+..+.|+|+
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~   88 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVD   88 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEE
Confidence            46799999999999999999999999999999999765      369999999999999999999999998888999999


Q ss_pred             ccccC
Q 013141          193 WATFS  197 (449)
Q Consensus       193 ~~~~~  197 (449)
                      |++..
T Consensus        89 ~ak~~   93 (97)
T d1whya_          89 FAKSG   93 (97)
T ss_dssp             ECCCC
T ss_pred             eCCCC
Confidence            98754

>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=99.70  E-value=5.6e-17  Score=123.64  Aligned_cols=85  Identities=19%  Similarity=0.459  Sum_probs=78.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC------CceecCc
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMN------GVYCSSR  279 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~------g~~~~g~  279 (449)
                      ...++|||+|||+++|+++|+++|+ .||.|.++.++.+..++.++|||||+|.+.++|.+|++.|+      +..+.|+
T Consensus         6 ~~~~tlfV~nLp~~~te~~l~~~f~-~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr   84 (98)
T d1x4ha1           6 TEGKTVFIRNLSFDSEEEALGEVLQ-QFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR   84 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHH-TTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSC
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHh-ccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCE
Confidence            4567899999999999999999995 99999999999999999999999999999999999999886      6778999


Q ss_pred             ceEEeecCCCCC
Q 013141          280 PMRIDVATPKKA  291 (449)
Q Consensus       280 ~i~v~~~~~~~~  291 (449)
                      .|+|+++.++..
T Consensus        85 ~l~v~~a~~k~~   96 (98)
T d1x4ha1          85 QLKVDLAVTRDE   96 (98)
T ss_dssp             EEEEECCCCCCC
T ss_pred             EEEEEECCCCCc
Confidence            999999988653

>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=99.70  E-value=2.5e-17  Score=125.52  Aligned_cols=81  Identities=22%  Similarity=0.387  Sum_probs=75.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeec
Q 013141          207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVA  286 (449)
Q Consensus       207 ~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~  286 (449)
                      ..++|||+|||+++++++|+++|+ .||.|.++.++++..+++++|||||+|.+.++|.+|+ .|++..|.|+.|+|.++
T Consensus        17 ~~~tifV~nL~~~~te~~l~~~F~-~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~-~l~g~~~~G~~l~V~~a   94 (101)
T d2cq4a1          17 DARTVFCMQLAARIRPRDLEDFFS-AVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQAS   94 (101)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHT-TTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHc-CCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHH-HHCCCEECCEEEEEEEC
Confidence            346899999999999999999995 9999999999999999999999999999999999999 59999999999999987


Q ss_pred             CCC
Q 013141          287 TPK  289 (449)
Q Consensus       287 ~~~  289 (449)
                      .++
T Consensus        95 ~~~   97 (101)
T d2cq4a1          95 QAE   97 (101)
T ss_dssp             HHH
T ss_pred             CCC
Confidence            543

>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=99.70  E-value=1.4e-17  Score=120.22  Aligned_cols=75  Identities=24%  Similarity=0.327  Sum_probs=68.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccccc
Q 013141          117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWA  194 (449)
Q Consensus       117 ~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~~  194 (449)
                      +|||+|||+++|+++|+++|+.||.|.++.++.++.++.++|||||+|.+.++|++|++ +++..+.  ++.|+|.+|
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-IHFHEIN--NKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBT--TBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEEC--CeEEEEEEC
Confidence            59999999999999999999999999999999999999999999999999999999995 9999995  466666543

>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=99.69  E-value=2.8e-17  Score=126.07  Aligned_cols=85  Identities=16%  Similarity=0.302  Sum_probs=76.0

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCc--------EEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCC
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQV--------VNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLM  182 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v--------~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~  182 (449)
                      .+...++|||+|||+++|+++|+++|+.||.|        ..+.+..++.+++++|||||+|.+.++|.+|++.|++..+
T Consensus         4 ~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~   83 (101)
T d2cpea1           4 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   83 (101)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEE
Confidence            44567899999999999999999999999987        4677888888899999999999999999999999999998


Q ss_pred             CCCCCcccccccccC
Q 013141          183 PNTDQPFRLNWATFS  197 (449)
Q Consensus       183 ~~~~~~~~~~~~~~~  197 (449)
                        .++.|+|.+++..
T Consensus        84 --~gr~i~V~~a~~~   96 (101)
T d2cpea1          84 --QGSKLKVSLARKK   96 (101)
T ss_dssp             --TTEECEEECSSCC
T ss_pred             --CCEEEEEEEcCCC
Confidence              5688888888754

>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=99.69  E-value=2.7e-17  Score=121.77  Aligned_cols=75  Identities=29%  Similarity=0.589  Sum_probs=67.6

Q ss_pred             CCcEEEEcCCCCCCC-HhHHHhhccccCceEEEEEeC-------CCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 013141          326 NNATIFVGALDSDVS-DEDLREPFSQFGEILSVKIPV-------GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSW  397 (449)
Q Consensus       326 ~~~~l~V~nlp~~~t-~~~L~~~f~~~G~v~~v~i~~-------~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  397 (449)
                      ..++|||+|||.+++ +++|+++|++||.|.+|+|..       ++|+|||+|.+.++|.+|++ ||+..|+|+.|+|+|
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~   81 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSL   81 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEE
Confidence            468999999999976 456999999999999999864       26899999999999999996 999999999999999


Q ss_pred             cCCC
Q 013141          398 GRNP  401 (449)
Q Consensus       398 ~~~~  401 (449)
                      +++.
T Consensus        82 a~~k   85 (86)
T d2ghpa3          82 ADKK   85 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9875

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.69  E-value=5.4e-17  Score=119.26  Aligned_cols=79  Identities=15%  Similarity=0.318  Sum_probs=70.1

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      ...++++|||+|||+++++++|+++|+.||.|.+|++++++     +|||||+|.+.++|.+|++.|++..+.+ ++.|+
T Consensus         4 ~~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~-~~~i~   77 (83)
T d2b0ga1           4 EQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFTTELQSNAAKEALQGFKITP-THAMK   77 (83)
T ss_dssp             CCSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT-----CSCEEEEESSHHHHHHHHHHHTTCBSST-TCBCE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc-----ceeEEEecCCHHHHHHHHHHhCCcEeCC-CcEEE
Confidence            34567899999999999999999999999999999997653     5899999999999999999999988743 46789


Q ss_pred             ccccc
Q 013141          191 LNWAT  195 (449)
Q Consensus       191 ~~~~~  195 (449)
                      ++|++
T Consensus        78 v~~ak   82 (83)
T d2b0ga1          78 ITFAK   82 (83)
T ss_dssp             EEECC
T ss_pred             EEEec
Confidence            99886

>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=99.69  E-value=2.4e-17  Score=122.62  Aligned_cols=77  Identities=30%  Similarity=0.484  Sum_probs=70.0

Q ss_pred             CCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeC-CCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCCCCCC
Q 013141          326 NNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV-GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRNPGNK  404 (449)
Q Consensus       326 ~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~-~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~~~  404 (449)
                      .+++|||+|||+++|+++|+++|++||.|.+|++.. .+++|||+|.+.++|++|+.  ++..|+|+.|+|.|++++...
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~~k~~~   81 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEPKHNS   81 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCCCCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeeccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCCCCCCC
Confidence            468999999999999999999999999999998876 47999999999999999985  788999999999999876543

>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=99.69  E-value=1.5e-17  Score=119.29  Aligned_cols=75  Identities=27%  Similarity=0.502  Sum_probs=70.3

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeec
Q 013141          210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVA  286 (449)
Q Consensus       210 ~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~  286 (449)
                      +|||+|||+++|+++|+++|+ .||.|.++.+++++.+++++|||||+|.+.++|++||+ +++..++|+.|+|+.|
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 KIFVGGLSPDTPEEKIREYFG-GFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHH-HHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHH-HhCCcccccccccccccccccEEEEEECCHHHHHHHHh-hCCCEECCEEeEEEEC
Confidence            599999999999999999996 99999999999999999999999999999999999995 5778899999999864

>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=99.69  E-value=8.2e-17  Score=117.28  Aligned_cols=77  Identities=21%  Similarity=0.440  Sum_probs=72.7

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeec
Q 013141          208 DLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVA  286 (449)
Q Consensus       208 ~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~  286 (449)
                      -++|||+|||+++|+++|+++|+ .||.|..+.+..++.++.++|+|||+|.+.+++.+|+ .+++..|.|+.|+|+.|
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~-~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al-~~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFE-QYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHT-TTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHH-HCSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHH-HhccccccccccCCCCcccccEEEEEEcCHHHHHHHH-HhCCCEECCEEEEEEEC
Confidence            36899999999999999999995 9999999999999999999999999999999999998 58999999999999876

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=4.5e-17  Score=126.18  Aligned_cols=84  Identities=17%  Similarity=0.288  Sum_probs=76.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      .+..+|||+|||+++|+++|+++|++||.|.+|.++.++    .+|||||+|.+.++|++|++.|++..+....+.+++.
T Consensus         5 s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~   80 (108)
T d2adba1           5 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID   80 (108)
T ss_dssp             CCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEE
T ss_pred             CCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEE
Confidence            567889999999999999999999999999999999874    4799999999999999999999999998888999999


Q ss_pred             ccccCCCC
Q 013141          193 WATFSGSD  200 (449)
Q Consensus       193 ~~~~~~~~  200 (449)
                      +++.....
T Consensus        81 ~s~~~~~~   88 (108)
T d2adba1          81 FSKLTSLN   88 (108)
T ss_dssp             ECSSCSCC
T ss_pred             ecCCcccc
Confidence            98765433

>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=99.68  E-value=8.2e-17  Score=122.30  Aligned_cols=79  Identities=15%  Similarity=0.188  Sum_probs=72.2

Q ss_pred             CCCCcEEEEcCCCCC-CCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHH--HhcCCeeCCeEEEEEecCC
Q 013141          324 ESNNATIFVGALDSD-VSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQ--KLQGTAIGKQTVRLSWGRN  400 (449)
Q Consensus       324 ~~~~~~l~V~nlp~~-~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~--~l~g~~~~g~~l~v~~~~~  400 (449)
                      ...+++|||+|||.+ +|+++|+++|+.||.|.+|.+.+++++|||+|.+.++|.+|++  .+++..|+|+.|+|.|++.
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~~s~~   94 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEK   94 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECS
T ss_pred             CCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeecCCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEEEcCC
Confidence            345789999999985 8999999999999999999999999999999999999999998  4688899999999999976


Q ss_pred             CC
Q 013141          401 PG  402 (449)
Q Consensus       401 ~~  402 (449)
                      ..
T Consensus        95 ~~   96 (99)
T d1x4fa1          95 YK   96 (99)
T ss_dssp             CS
T ss_pred             cc
Confidence            53

>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=99.68  E-value=8.9e-17  Score=123.18  Aligned_cols=86  Identities=23%  Similarity=0.333  Sum_probs=77.8

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhhCCCee--------EEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQETFSSKYPSVK--------GAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYC  276 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~--------~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~  276 (449)
                      ....++|||+|||.++|+++|+++|+ .||.|.        .+.+.++..+++++|||||+|.+.++|.+|++.|++..|
T Consensus         5 ~~~~~~i~V~nLp~~~te~~l~~~F~-~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~   83 (101)
T d2cpea1           5 DSDNSAIYVQGLNDSVTLDDLADFFK-QCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   83 (101)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHT-TTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHH-HCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEE
Confidence            34577999999999999999999995 999874        466778888899999999999999999999999999999


Q ss_pred             cCcceEEeecCCCCC
Q 013141          277 SSRPMRIDVATPKKA  291 (449)
Q Consensus       277 ~g~~i~v~~~~~~~~  291 (449)
                      .|+.|+|+++.++..
T Consensus        84 ~gr~i~V~~a~~~~p   98 (101)
T d2cpea1          84 QGSKLKVSLARKKPP   98 (101)
T ss_dssp             TTEECEEECSSCCCC
T ss_pred             CCEEEEEEEcCCCCC
Confidence            999999999988654

>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=99.68  E-value=1.9e-17  Score=127.27  Aligned_cols=84  Identities=15%  Similarity=0.228  Sum_probs=77.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccc
Q 013141          112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRL  191 (449)
Q Consensus       112 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~  191 (449)
                      ..++++|||+|||.++++++|+++|..||.|.++.++.+..+|+++|||||+|.+.++|.+|++.|++..+  .++.|+|
T Consensus        15 ~~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~--~g~~l~V   92 (102)
T d2cpxa1          15 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKL--YGKILVI   92 (102)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBC--SSCBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEE--CCEEEEE
Confidence            35678999999999999999999999999999999999888899999999999999999999999999988  4688999


Q ss_pred             cccccC
Q 013141          192 NWATFS  197 (449)
Q Consensus       192 ~~~~~~  197 (449)
                      .|++..
T Consensus        93 ~~ak~k   98 (102)
T d2cpxa1          93 EFGKNK   98 (102)
T ss_dssp             EECCCC
T ss_pred             EeCCCc
Confidence            998754

>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=1.7e-16  Score=122.08  Aligned_cols=78  Identities=29%  Similarity=0.517  Sum_probs=67.8

Q ss_pred             CCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeC-------CCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 013141          325 SNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV-------GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSW  397 (449)
Q Consensus       325 ~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~-------~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  397 (449)
                      .+.++|||+|||+++++++|+++|+.|| |.++.++.       .+++|||+|.+.++|++|+ .||+..|.|+.|+|.|
T Consensus        13 ~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~gr~l~V~~   90 (104)
T d1wi8a_          13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEECCEEEEEEE
Confidence            3568999999999999999999999998 66776654       2579999999999998776 5999999999999999


Q ss_pred             cCCCCCC
Q 013141          398 GRNPGNK  404 (449)
Q Consensus       398 ~~~~~~~  404 (449)
                      +++....
T Consensus        91 a~~~~~~   97 (104)
T d1wi8a_          91 ADQAQDK   97 (104)
T ss_dssp             CCCCCCC
T ss_pred             CCCCCCC
Confidence            9876543

>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=99.68  E-value=1.1e-16  Score=118.93  Aligned_cols=79  Identities=15%  Similarity=0.154  Sum_probs=72.7

Q ss_pred             CCCCcEEEEcCCCCC-CCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHh--cCCeeCCeEEEEEecCC
Q 013141          324 ESNNATIFVGALDSD-VSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKL--QGTAIGKQTVRLSWGRN  400 (449)
Q Consensus       324 ~~~~~~l~V~nlp~~-~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l--~g~~~~g~~l~v~~~~~  400 (449)
                      ...+++|||+|||.. +|++||+++|++||.|.+|.+.+++++|||+|++.++|..|++.|  ++..+.|+.|+|.|++.
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V~~s~~   84 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQK   84 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECC
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEEECCC
Confidence            456889999999986 789999999999999999999999999999999999999999976  67789999999999986


Q ss_pred             CC
Q 013141          401 PG  402 (449)
Q Consensus       401 ~~  402 (449)
                      ..
T Consensus        85 ~~   86 (89)
T d1x4da1          85 YK   86 (89)
T ss_dssp             CT
T ss_pred             cc
Confidence            43

>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=99.68  E-value=4.5e-17  Score=117.50  Aligned_cols=75  Identities=25%  Similarity=0.435  Sum_probs=71.5

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeec
Q 013141          210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVA  286 (449)
Q Consensus       210 ~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~  286 (449)
                      +|||+|||+++|+++|+++|+ .||.|..+.++.++.++.++++|||+|.+.++|++|++ +++..|+|+.|+|++|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~-~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFE-QFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHH-TTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHH-HhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            589999999999999999995 99999999999999999999999999999999999995 9999999999999875

>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=99.68  E-value=1.7e-16  Score=122.00  Aligned_cols=84  Identities=19%  Similarity=0.154  Sum_probs=72.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccc
Q 013141          112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRL  191 (449)
Q Consensus       112 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~  191 (449)
                      .....+|||+|||+++|++||+++|..+|.|..+.++.+..+++++|||||+|.+.++|++|++ +++..|  .++.|+|
T Consensus        12 ~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i--~gR~i~V   88 (104)
T d1wg5a_          12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERI--GHRYIEI   88 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCS--SSSCCEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEE--cceEEEE
Confidence            3456689999999999999999999999999887777877889999999999999999999995 899888  4567777


Q ss_pred             cccccCC
Q 013141          192 NWATFSG  198 (449)
Q Consensus       192 ~~~~~~~  198 (449)
                      .++...+
T Consensus        89 ~~~~~~~   95 (104)
T d1wg5a_          89 FKSSRAE   95 (104)
T ss_dssp             EEECTTT
T ss_pred             EECCHHH
Confidence            7776543

>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=99.68  E-value=2.1e-17  Score=118.07  Aligned_cols=67  Identities=30%  Similarity=0.430  Sum_probs=64.8

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCC
Q 013141          118 IWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPN  184 (449)
Q Consensus       118 l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~  184 (449)
                      |||+|||+++|+++|+++|+.||.|.++++++++.+++++|||||+|.+.++|++|++.||+..+.+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~G   67 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQA   67 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCE
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECC
Confidence            7999999999999999999999999999999999999999999999999999999999999998855

>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=99.68  E-value=5.2e-17  Score=119.74  Aligned_cols=78  Identities=18%  Similarity=0.259  Sum_probs=68.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccccc
Q 013141          114 ETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNW  193 (449)
Q Consensus       114 ~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~  193 (449)
                      ..++|||+|||+++|+++|+++|+.||.|.+|++..+. +++++|||||+|.+.++|.+||+ +++..+.  ++.+++.|
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~-~~~~~~~--g~~l~v~~   80 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE-TPGQKYK--ETDLLILF   80 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHT-CCCCEET--TEECEEEE
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHH-HCCCEEC--CEEEEEEE
Confidence            46799999999999999999999999999999998875 79999999999999999999995 6888874  46666666


Q ss_pred             cc
Q 013141          194 AT  195 (449)
Q Consensus       194 ~~  195 (449)
                      ..
T Consensus        81 ~~   82 (85)
T d1zh5a2          81 KD   82 (85)
T ss_dssp             GG
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=99.67  E-value=5e-17  Score=120.28  Aligned_cols=81  Identities=19%  Similarity=0.405  Sum_probs=70.6

Q ss_pred             CCceEEEcCCCCCCC-HHHHHHHHhhhCCCeeEEEEeec-CCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEe
Q 013141          207 SDLSIFVGDLAPDVT-DSILQETFSSKYPSVKGAKVIID-SNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRID  284 (449)
Q Consensus       207 ~~~~l~v~~lp~~~t-~~~l~~~f~~~~g~v~~i~~~~~-~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  284 (449)
                      ..++|||+|||++++ +++|+++|+ .||.|.++.+..+ ..+++++|||||+|.+.++|.+|+ +||+..+.|+.|+|+
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~-~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al-~~n~~~~~gr~l~V~   80 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFE-GFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVS   80 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHG-GGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHH-hhhhccceeeecccCCccccceeeeEEECCHHHHHHHH-hcCCCEECCEEEEEE
Confidence            467999999999986 566999995 9999999998765 568899999999999999999999 599999999999999


Q ss_pred             ecCCC
Q 013141          285 VATPK  289 (449)
Q Consensus       285 ~~~~~  289 (449)
                      ++.++
T Consensus        81 ~a~~k   85 (86)
T d2ghpa3          81 LADKK   85 (86)
T ss_dssp             ECCCC
T ss_pred             EcCCC
Confidence            99875

>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=99.67  E-value=1.8e-16  Score=119.74  Aligned_cols=82  Identities=21%  Similarity=0.433  Sum_probs=73.8

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEe
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRID  284 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  284 (449)
                      ..++++|||+|||+++|+++|+++|+ .||.|..+.+..+   ..+++||||+|.+.++|++||+.||+..|.|+.|+|+
T Consensus        11 ~~~~~~l~V~nLp~~~t~~~l~~~F~-~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~   86 (95)
T d1x4aa1          11 GNNDCRIYVGNLPPDIRTKDIEDVFY-KYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVE   86 (95)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHG-GGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHh-cCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            45667899999999999999999995 9999999887654   4568999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 013141          285 VATPKK  290 (449)
Q Consensus       285 ~~~~~~  290 (449)
                      +++...
T Consensus        87 ~a~~~r   92 (95)
T d1x4aa1          87 FPRSGR   92 (95)
T ss_dssp             CCCCCC
T ss_pred             eccCCC
Confidence            987653

>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=99.67  E-value=1.1e-16  Score=123.19  Aligned_cols=83  Identities=18%  Similarity=0.297  Sum_probs=71.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecC-CCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNK-QTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       112 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~-~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      ..+.++|||+|||+++++++|+++|+.|| ++++.++.++ .+++++|||||+|.+.++|++|+ .|++..+.  ++.|+
T Consensus        12 ~~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~--gr~l~   87 (104)
T d1wi8a_          12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLG--NKRIR   87 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEET--TEECE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEEC--CEEEE
Confidence            45678999999999999999999999998 7788777765 47889999999999999999887 59999884  57888


Q ss_pred             ccccccCC
Q 013141          191 LNWATFSG  198 (449)
Q Consensus       191 ~~~~~~~~  198 (449)
                      |.++....
T Consensus        88 V~~a~~~~   95 (104)
T d1wi8a_          88 VDVADQAQ   95 (104)
T ss_dssp             EEECCCCC
T ss_pred             EEECCCCC
Confidence            88876543

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=9.3e-17  Score=120.22  Aligned_cols=76  Identities=28%  Similarity=0.566  Sum_probs=70.1

Q ss_pred             CcEEEEcCCCCCCCHhHHHh----hccccCceEEEEEeC---CCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 013141          327 NATIFVGALDSDVSDEDLRE----PFSQFGEILSVKIPV---GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGR  399 (449)
Q Consensus       327 ~~~l~V~nlp~~~t~~~L~~----~f~~~G~v~~v~i~~---~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  399 (449)
                      +++|||+|||..++++||++    +|+.||.|.+|.+.+   .+++|||+|.+.++|.+|++.||+..|+|+.|+|.|++
T Consensus         3 ~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~ak   82 (91)
T d1nu4a_           3 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAK   82 (91)
T ss_dssp             CSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEeeeccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeC
Confidence            57999999999999999864    689999999999876   47999999999999999999999999999999999999


Q ss_pred             CCC
Q 013141          400 NPG  402 (449)
Q Consensus       400 ~~~  402 (449)
                      ...
T Consensus        83 ~~~   85 (91)
T d1nu4a_          83 TDS   85 (91)
T ss_dssp             SCC
T ss_pred             CCc
Confidence            764

>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=99.67  E-value=2e-16  Score=124.04  Aligned_cols=80  Identities=16%  Similarity=0.282  Sum_probs=73.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEee
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV  285 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  285 (449)
                      ..+++|||+|||.++|+++|+++|+ .||.|.+|++..+   +.++|||||+|.+.++|..|++.|||..|.|+.|+|.+
T Consensus         5 ~~~r~l~V~nLp~~~te~~l~~~F~-~~G~v~~i~~~~~---~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~   80 (114)
T d2f9da1           5 EVNRILYIRNLPYKITAEEMYDIFG-KYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLY   80 (114)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHH-TTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHh-hcCCeEeeccccc---CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4567999999999999999999995 9999999999865   56789999999999999999999999999999999999


Q ss_pred             cCCC
Q 013141          286 ATPK  289 (449)
Q Consensus       286 ~~~~  289 (449)
                      +...
T Consensus        81 a~~~   84 (114)
T d2f9da1          81 YNAN   84 (114)
T ss_dssp             CCHH
T ss_pred             cCCC
Confidence            8653

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.67  E-value=2.4e-17  Score=123.23  Aligned_cols=77  Identities=21%  Similarity=0.358  Sum_probs=69.6

Q ss_pred             CCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 013141          324 ESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV-----GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWG  398 (449)
Q Consensus       324 ~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~-----~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~  398 (449)
                      .....+|||+|||+++++++|+++|+.||.|.++.|+.     ++|+|||+|.+.++|.+||+ ||+..|+|+.|+|.++
T Consensus        10 ~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~a   88 (91)
T d1fjeb1          10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   88 (91)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECC
T ss_pred             CCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEec
Confidence            44567999999999999999999999999988877753     57999999999999999996 9999999999999999


Q ss_pred             CCC
Q 013141          399 RNP  401 (449)
Q Consensus       399 ~~~  401 (449)
                      +.+
T Consensus        89 k~k   91 (91)
T d1fjeb1          89 KGR   91 (91)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            863

>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=99.67  E-value=3.2e-17  Score=125.92  Aligned_cols=86  Identities=23%  Similarity=0.407  Sum_probs=80.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEee
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV  285 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  285 (449)
                      .++++|||+|||.++++++|+++|+ .||.|..+.+..+..++.++|||||+|.+.++|.+|++.|++..|.|+.|+|+|
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~-~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   94 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFA-RFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF   94 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTH-HHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHh-hccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            4578999999999999999999996 999999999998888899999999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 013141          286 ATPKKAS  292 (449)
Q Consensus       286 ~~~~~~~  292 (449)
                      ++++..+
T Consensus        95 ak~k~~r  101 (102)
T d2cpxa1          95 GKNKKQR  101 (102)
T ss_dssp             CCCCSCC
T ss_pred             CCCcccC
Confidence            9887653

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.66  E-value=3.7e-16  Score=120.00  Aligned_cols=86  Identities=15%  Similarity=0.123  Sum_probs=74.0

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      ...++++|||+|||+++++++|+++|+.||.|.+|++.++      +++|||+|.+.++|++|++.++...+...++.|+
T Consensus        11 ~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~   84 (104)
T d1wexa_          11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAF   84 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEE
Confidence            3467899999999999999999999999999999999765      4799999999999999999987666555778999


Q ss_pred             ccccccCCCCCc
Q 013141          191 LNWATFSGSDRR  202 (449)
Q Consensus       191 ~~~~~~~~~~~~  202 (449)
                      |.|++......+
T Consensus        85 v~~s~~~~~~~~   96 (104)
T d1wexa_          85 FNYSTSKRITRP   96 (104)
T ss_dssp             EEECSSSSCCCS
T ss_pred             EEEcCCCccCCC
Confidence            999876554443

>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=99.66  E-value=1.6e-16  Score=121.34  Aligned_cols=81  Identities=16%  Similarity=0.413  Sum_probs=74.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEee
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV  285 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  285 (449)
                      ...++|||+|||+++++++|+++|+ .||.|..+.+..+ .++.++|||||+|.+.++|.+|++.|||..|.|+++.|.+
T Consensus        16 ~~~~~lfV~nLp~~~te~~L~~~F~-~~G~i~~~~~~~~-~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~   93 (101)
T d1x5oa1          16 QDPTNLYISNLPLSMDEQELENMLK-PFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAP   93 (101)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTT-TTSCEEEEEEEEC-SSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHh-hcccccceeeecc-cccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCC
Confidence            3457899999999999999999995 9999999999888 4689999999999999999999999999999999999887


Q ss_pred             cCC
Q 013141          286 ATP  288 (449)
Q Consensus       286 ~~~  288 (449)
                      +.+
T Consensus        94 ~~P   96 (101)
T d1x5oa1          94 TEP   96 (101)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            765

>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=99.66  E-value=2.2e-16  Score=117.48  Aligned_cols=79  Identities=15%  Similarity=0.175  Sum_probs=69.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      .++++|||+|||+++++++|+++|+.||.|.++.++..    +.+|||||+|.+.++|.+|+..|++..+. .++.|+|.
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~----~~~~~afV~f~~~~~A~~A~~~l~~~~i~-~g~~l~v~   82 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLG-ENHHLRVS   82 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS----SSTTCEEEEESSHHHHHHHHHHHTTCBSS-SSCBCEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee----cccceeEEEECCHHHHHHHHHhccCCEec-CCCEEEEE
Confidence            46889999999999999999999999999988877654    35789999999999999999999998874 35889998


Q ss_pred             cccc
Q 013141          193 WATF  196 (449)
Q Consensus       193 ~~~~  196 (449)
                      |++.
T Consensus        83 ~sk~   86 (88)
T d2adca2          83 FSKS   86 (88)
T ss_dssp             ECSS
T ss_pred             eCCC
Confidence            8864

>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=99.66  E-value=2.4e-16  Score=118.94  Aligned_cols=77  Identities=23%  Similarity=0.507  Sum_probs=71.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeec
Q 013141          207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVA  286 (449)
Q Consensus       207 ~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~  286 (449)
                      ..++|||+|||.++++++|+++|+ .||.|.+|+++++      +|||||+|.+.++|++|+..|++..|.|+.|+|+|+
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~-~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~a   89 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFS-PFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG   89 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHH-HHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHH-HhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            457899999999999999999995 9999999999865      789999999999999999999999999999999999


Q ss_pred             CCCC
Q 013141          287 TPKK  290 (449)
Q Consensus       287 ~~~~  290 (449)
                      +++.
T Consensus        90 k~~p   93 (96)
T d1x4ga1          90 KESP   93 (96)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7653

>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=99.65  E-value=7e-17  Score=119.71  Aligned_cols=79  Identities=13%  Similarity=0.147  Sum_probs=67.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      +...+|||+|||++++++||+++|+.||.+.+..++.+..+++++|+|||+|.+.++|.+|++.||+..+.  ++.|+|.
T Consensus         7 p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~--gr~i~v~   84 (86)
T d2cqpa1           7 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIG--SRKVKLV   84 (86)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEET--TEECEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEEC--CEEEEEE
Confidence            34567999999999999999999999999877544454568999999999999999999999999999995  4556654


Q ss_pred             c
Q 013141          193 W  193 (449)
Q Consensus       193 ~  193 (449)
                      +
T Consensus        85 l   85 (86)
T d2cqpa1          85 L   85 (86)
T ss_dssp             E
T ss_pred             E
Confidence            3

>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=99.65  E-value=1.6e-16  Score=118.21  Aligned_cols=70  Identities=26%  Similarity=0.438  Sum_probs=65.0

Q ss_pred             CcEEEEcCCCCCCCHhHH---HhhccccCceEEEEEeCC---------CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEE
Q 013141          327 NATIFVGALDSDVSDEDL---REPFSQFGEILSVKIPVG---------KGCGFVQFANRKDAEVALQKLQGTAIGKQTVR  394 (449)
Q Consensus       327 ~~~l~V~nlp~~~t~~~L---~~~f~~~G~v~~v~i~~~---------~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~  394 (449)
                      .++|||+|||+++++++|   +++|++||.|.+|.++++         +++|||+|.+.++|.+|++.|||..|+|+.|+
T Consensus         8 ~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~lk   87 (89)
T d2cpia1           8 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLK   87 (89)
T ss_dssp             SSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEEE
Confidence            467999999999999999   789999999999999863         27999999999999999999999999999999


Q ss_pred             EE
Q 013141          395 LS  396 (449)
Q Consensus       395 v~  396 (449)
                      |+
T Consensus        88 vS   89 (89)
T d2cpia1          88 AS   89 (89)
T ss_dssp             EE
T ss_pred             EC
Confidence            85

>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=99.64  E-value=4e-17  Score=121.97  Aligned_cols=83  Identities=18%  Similarity=0.429  Sum_probs=74.7

Q ss_pred             ccCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEE
Q 013141          204 EACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRI  283 (449)
Q Consensus       204 ~~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  283 (449)
                      .+....+|||+|||+++|+++|+++|+ .||.|..+.++.+ .+++++|||||+|.+.++|.+|++ |++..+.|+.|+|
T Consensus         9 ~~~~~~~ifV~nL~~~~te~~l~~~F~-~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V   85 (91)
T d1fjeb1           9 ESTTPFNLFIGNLNPNKSVAELKVAIS-ELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKL   85 (91)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHH-HHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEE
T ss_pred             CCCCCcEEEEeCccCcchHHHHHHHHh-cCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEE
Confidence            345667999999999999999999995 9999999888655 678999999999999999999995 9999999999999


Q ss_pred             eecCCC
Q 013141          284 DVATPK  289 (449)
Q Consensus       284 ~~~~~~  289 (449)
                      ++++.+
T Consensus        86 ~~ak~k   91 (91)
T d1fjeb1          86 EKPKGR   91 (91)
T ss_dssp             ECCCCS
T ss_pred             EecCCC
Confidence            998754

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=2.3e-16  Score=122.12  Aligned_cols=79  Identities=25%  Similarity=0.309  Sum_probs=71.4

Q ss_pred             CCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeC--CCcEEEEEecCHHHHHHHHHHhcCCee--CCeEEEEEecC
Q 013141          324 ESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPV--GKGCGFVQFANRKDAEVALQKLQGTAI--GKQTVRLSWGR  399 (449)
Q Consensus       324 ~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~--~~g~afV~F~~~~~A~~A~~~l~g~~~--~g~~l~v~~~~  399 (449)
                      ..+..+|||+|||+.+|+++|+++|++||.|.+|.+.+  ++++|||+|.+.++|.+|++.||+..|  .++.|+|.|++
T Consensus         4 ~s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~   83 (108)
T d2adba1           4 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK   83 (108)
T ss_dssp             CCCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEECS
T ss_pred             CCCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeCCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEecC
Confidence            34567899999999999999999999999999998875  468999999999999999999999998  57899999998


Q ss_pred             CCC
Q 013141          400 NPG  402 (449)
Q Consensus       400 ~~~  402 (449)
                      ...
T Consensus        84 ~~~   86 (108)
T d2adba1          84 LTS   86 (108)
T ss_dssp             SCS
T ss_pred             Ccc
Confidence            754

>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=99.64  E-value=4.9e-16  Score=114.41  Aligned_cols=78  Identities=17%  Similarity=0.152  Sum_probs=71.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeec
Q 013141          207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVA  286 (449)
Q Consensus       207 ~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~  286 (449)
                      ..++|||+|||.++|+++|+++|+ .||.|..+.+.++. +++++|||||+|.+.++|.+|+ ++++..+.|+.|.|.+.
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~-~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al-~~~~~~~~g~~l~v~~~   81 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLE-DKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFV-ETPGQKYKETDLLILFK   81 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHT-TSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHH-TCCCCEETTEECEEEEG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHH-Hhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHH-HHCCCEECCEEEEEEEc
Confidence            357899999999999999999995 99999999998874 7899999999999999999999 58999999999999986


Q ss_pred             C
Q 013141          287 T  287 (449)
Q Consensus       287 ~  287 (449)
                      .
T Consensus        82 ~   82 (85)
T d1zh5a2          82 D   82 (85)
T ss_dssp             G
T ss_pred             C
Confidence            4

>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=99.64  E-value=4.4e-16  Score=121.02  Aligned_cols=76  Identities=18%  Similarity=0.307  Sum_probs=68.1

Q ss_pred             CceEEEcCCCC-CCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccccc
Q 013141          115 TKTIWIGDLFH-WMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNW  193 (449)
Q Consensus       115 ~~~l~v~nLp~-~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~  193 (449)
                      +++|||+|||+ .+|+++|+++|+.||.|.+|+|++++     +|||||+|.+.++|.+|++.|++..+.  ++.|++.|
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~-----kg~afV~f~~~~~A~~ai~~lng~~l~--g~~l~v~~   74 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLH--GKPIRITL   74 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCS--SSBCEEEC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-----cceEEEEECCHHHHHHHHHHhCCCEEC--CEEEEEEE
Confidence            67999999965 59999999999999999999998874     589999999999999999999999995  46888888


Q ss_pred             cccC
Q 013141          194 ATFS  197 (449)
Q Consensus       194 ~~~~  197 (449)
                      ++..
T Consensus        75 s~~~   78 (109)
T d2adca1          75 SKHQ   78 (109)
T ss_dssp             CSCC
T ss_pred             CCCC
Confidence            7644

>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=3.4e-16  Score=119.75  Aligned_cols=83  Identities=18%  Similarity=0.172  Sum_probs=70.7

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      ......+|||+|||+++|++||+++|..||. .+|.++.+. +++.+|||||+|.+.++|++|++ +|+..|.  ++.|+
T Consensus        11 ~~~~~~~v~v~nLp~~~te~dl~~~F~~~~~-~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~--gR~I~   85 (102)
T d1weza_          11 QSTTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQ--HRYVE   85 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSS--SSCCE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHhccCc-ceeeeEEec-CCcceEEEEEEECCHHHHHHHHH-cCCCEEC--CEEEE
Confidence            3456679999999999999999999999984 578888875 58999999999999999999995 8999995  46788


Q ss_pred             ccccccCC
Q 013141          191 LNWATFSG  198 (449)
Q Consensus       191 ~~~~~~~~  198 (449)
                      |.++....
T Consensus        86 V~~s~~~~   93 (102)
T d1weza_          86 LFLNSTAG   93 (102)
T ss_dssp             EEEECCCC
T ss_pred             EEEcCCCC
Confidence            87776543

>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=99.64  E-value=1.9e-16  Score=123.60  Aligned_cols=77  Identities=21%  Similarity=0.232  Sum_probs=68.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      +..++|||+|||+++++++|+++|+.||.|.+|.|.+      .+|||||+|.+.++|.+|++.||+..+.  ++.|+|+
T Consensus         8 r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~------~kg~afV~f~~~~~A~~A~~~lng~~~~--gr~l~v~   79 (111)
T d1whxa_           8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFH--HVPLYLE   79 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSS--SSBCEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec------cCceEEEEEcCHHHHHHHHHHHcCCccC--CCeEEEE
Confidence            4567999999999999999999999999999998743      4689999999999999999999999995  5788888


Q ss_pred             ccccC
Q 013141          193 WATFS  197 (449)
Q Consensus       193 ~~~~~  197 (449)
                      |+...
T Consensus        80 ~a~~~   84 (111)
T d1whxa_          80 WAPIG   84 (111)
T ss_dssp             EEETT
T ss_pred             ECCCC
Confidence            87644

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.64  E-value=2.6e-16  Score=120.24  Aligned_cols=79  Identities=15%  Similarity=0.156  Sum_probs=71.4

Q ss_pred             CCCcEEEEcCCCCCC-CH----hHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 013141          325 SNNATIFVGALDSDV-SD----EDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGR  399 (449)
Q Consensus       325 ~~~~~l~V~nlp~~~-t~----~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  399 (449)
                      ...++|||.||+.++ ++    ++|+++|+.||.|.++.+++++++|||+|.+.++|.+|++.|||..|.|+.|+|.|++
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   82 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQ   82 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCC
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecCCCEEEEEECCHHHHHHHHHHhcccccCCCEeEEeecc
Confidence            346789999999886 33    5688999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 013141          400 NPGN  403 (449)
Q Consensus       400 ~~~~  403 (449)
                      ....
T Consensus        83 ~~~~   86 (104)
T d1weya_          83 TLHI   86 (104)
T ss_dssp             CSSC
T ss_pred             cCCC
Confidence            7543

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=3.6e-16  Score=119.61  Aligned_cols=80  Identities=21%  Similarity=0.348  Sum_probs=69.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC-----CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 013141          323 GESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-----KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSW  397 (449)
Q Consensus       323 ~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~-----~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  397 (449)
                      ......+|||+|||+++|++||+++|+.||. ..|.++.+     +++|||+|.+.++|.+|++ ||+..|+|+.|+|.|
T Consensus        11 ~~~~~~~v~v~nLp~~~te~dl~~~F~~~~~-~~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~   88 (102)
T d1weza_          11 QSTTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFL   88 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHhccCc-ceeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEE
Confidence            4456679999999999999999999999974 45666543     6899999999999999986 899999999999999


Q ss_pred             cCCCCCC
Q 013141          398 GRNPGNK  404 (449)
Q Consensus       398 ~~~~~~~  404 (449)
                      ++.....
T Consensus        89 s~~~~~~   95 (102)
T d1weza_          89 NSTAGTS   95 (102)
T ss_dssp             ECCCCCC
T ss_pred             cCCCCCC
Confidence            9876533

>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=99.64  E-value=2.7e-16  Score=119.01  Aligned_cols=84  Identities=15%  Similarity=0.288  Sum_probs=74.2

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhhCCC-eeEEEEeecC-CCCCcceEEEEEeCCHHHHHHHHHHhCC--ceecCcceEE
Q 013141          208 DLSIFVGDLAPDVTDSILQETFSSKYPS-VKGAKVIIDS-NTGRTKGYGFVRFGDENERSRAMTEMNG--VYCSSRPMRI  283 (449)
Q Consensus       208 ~~~l~v~~lp~~~t~~~l~~~f~~~~g~-v~~i~~~~~~-~~~~~~g~afV~f~~~~~A~~A~~~l~g--~~~~g~~i~v  283 (449)
                      +++|||+|||.++|+++|+++|+ .||+ |.++.++++. .+++++|||||+|.+.++|.+|++.|++  ..+.|+.|+|
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~-~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V   79 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIA-KVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAV   79 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHH-HHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHH-HhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEE
Confidence            46899999999999999999996 8996 8999999885 4688999999999999999999999864  4568999999


Q ss_pred             eecCCCCCC
Q 013141          284 DVATPKKAS  292 (449)
Q Consensus       284 ~~~~~~~~~  292 (449)
                      +|++++...
T Consensus        80 ~~A~p~~~~   88 (96)
T d2disa1          80 DWAEPEIDV   88 (96)
T ss_dssp             EESCSSCST
T ss_pred             EEcCCCCCC
Confidence            999886553

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=2.4e-16  Score=117.16  Aligned_cols=81  Identities=20%  Similarity=0.256  Sum_probs=70.0

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      ...++++|||+|||+++++++|+++|++||.|.++++.+++      +||||+|.+.++|++|++.+++..+...+++++
T Consensus         4 ~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~~------~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~   77 (88)
T d2cq1a1           4 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGK------NQAFLELATEEAAITMVNYYSAVTPHLRNQPIY   77 (88)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETTT------TEEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcccccccccccccc------eEEEEEeCCHHHHHHHHHHHccCCCccCCCEEE
Confidence            45789999999999999999999999999999999988654      699999999999999999876544334678899


Q ss_pred             ccccccC
Q 013141          191 LNWATFS  197 (449)
Q Consensus       191 ~~~~~~~  197 (449)
                      +.|++..
T Consensus        78 v~~sk~~   84 (88)
T d2cq1a1          78 IQYSNHK   84 (88)
T ss_dssp             EEECSCS
T ss_pred             EEECCCC
Confidence            9888644

>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=99.64  E-value=4.2e-16  Score=115.08  Aligned_cols=77  Identities=26%  Similarity=0.498  Sum_probs=71.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeec
Q 013141          207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVA  286 (449)
Q Consensus       207 ~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~  286 (449)
                      ..++|||+|||.++++++|+++|+ .||.|.++.+.++      ++||||+|.+.++|.+|++.||+..|.|+.|+|+++
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~-~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A   79 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFE-KYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFA   79 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTS-TTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHH-HhCCceEeeeecc------cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            346799999999999999999995 9999999999865      679999999999999999999999999999999999


Q ss_pred             CCCC
Q 013141          287 TPKK  290 (449)
Q Consensus       287 ~~~~  290 (449)
                      ....
T Consensus        80 ~~~~   83 (86)
T d2cpja1          80 CHSA   83 (86)
T ss_dssp             SCCS
T ss_pred             CCcC
Confidence            8764

>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=99.64  E-value=3.1e-16  Score=112.47  Aligned_cols=70  Identities=19%  Similarity=0.276  Sum_probs=65.1

Q ss_pred             cEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC----CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 013141          328 ATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG----KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWG  398 (449)
Q Consensus       328 ~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~----~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~  398 (449)
                      ++|||+|||+++++++|+++|+.||.|..|++.++    +++|||+|++.++|.+|+. +|+..|+|+.|.|+.+
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 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccccceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            47999999999999999999999999999999864    5799999999999999985 8999999999999865

>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=99.63  E-value=1.9e-16  Score=117.82  Aligned_cols=77  Identities=17%  Similarity=0.295  Sum_probs=69.7

Q ss_pred             CCceEEEcCCCCCCCHHHH---HHHHhhhCCCeeEEEEeecCCCCCc---ceEEEEEeCCHHHHHHHHHHhCCceecCcc
Q 013141          207 SDLSIFVGDLAPDVTDSIL---QETFSSKYPSVKGAKVIIDSNTGRT---KGYGFVRFGDENERSRAMTEMNGVYCSSRP  280 (449)
Q Consensus       207 ~~~~l~v~~lp~~~t~~~l---~~~f~~~~g~v~~i~~~~~~~~~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~  280 (449)
                      ..++|||+|||+++++++|   +++|+ .||.|.++.+++++.++.+   +|||||+|.+.++|.+|++.|||..+.|+.
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~-~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~   85 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFG-KFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRT   85 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTT-TTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhc-ccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEE
Confidence            3468999999999999999   67896 9999999999999776654   499999999999999999999999999999


Q ss_pred             eEEe
Q 013141          281 MRID  284 (449)
Q Consensus       281 i~v~  284 (449)
                      |+++
T Consensus        86 lkvS   89 (89)
T d2cpia1          86 LKAS   89 (89)
T ss_dssp             EEEE
T ss_pred             EEEC
Confidence            9985

>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=99.63  E-value=2.1e-16  Score=115.05  Aligned_cols=77  Identities=27%  Similarity=0.491  Sum_probs=69.1

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCc-eecCcceEEeecC
Q 013141          209 LSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGV-YCSSRPMRIDVAT  287 (449)
Q Consensus       209 ~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~-~~~g~~i~v~~~~  287 (449)
                      ++|||+|||.++|+++|+++|+ .||.|..+.+.+.      +|||||+|.+.++|.+|++.|||. .+.|+.|+|+++.
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~-~~G~i~~~~~~~~------rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~   74 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFG-DRKLPLAGQVLLK------SGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSV   74 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHH-HTTCCCSSCEEEE------TTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECC
T ss_pred             CEEEEECCCCCCCHHHHHHHHH-HhCcEEEeEEecc------cceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcC
Confidence            4799999999999999999995 9999988777654      789999999999999999999986 6999999999999


Q ss_pred             CCCCC
Q 013141          288 PKKAS  292 (449)
Q Consensus       288 ~~~~~  292 (449)
                      ++..+
T Consensus        75 ~k~~r   79 (80)
T d2cqha1          75 SKKLR   79 (80)
T ss_dssp             CCCCC
T ss_pred             CcCcC
Confidence            87653

>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=99.63  E-value=2.8e-16  Score=116.40  Aligned_cols=79  Identities=19%  Similarity=0.287  Sum_probs=70.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeec
Q 013141          207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVA  286 (449)
Q Consensus       207 ~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~  286 (449)
                      ..++|||+|||+++++++|+++|+ .|+.+....++.+..++.++|+|||+|.+.++|++|++.||+..+.|++|+|+++
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~-~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFY-GYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTT-TSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHh-hcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            356799999999999999999995 9999977544444577999999999999999999999999999999999999874

>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=99.63  E-value=9.9e-17  Score=114.53  Aligned_cols=71  Identities=27%  Similarity=0.509  Sum_probs=67.9

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceE
Q 013141          211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMR  282 (449)
Q Consensus       211 l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  282 (449)
                      |||+|||+++|+++|+++|+ .||.|..+++.+++.++.++|+|||+|.+.++|++|++.|||..|.|+.++
T Consensus         1 lyV~nLp~~~te~~l~~~F~-~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQ-PYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTST-TTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHh-hhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            79999999999999999995 999999999999999999999999999999999999999999999998764

>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=99.63  E-value=2.8e-16  Score=116.43  Aligned_cols=70  Identities=16%  Similarity=0.201  Sum_probs=62.3

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcccccccc
Q 013141          117 TIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLNWAT  195 (449)
Q Consensus       117 ~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~~~~  195 (449)
                      +|||+|||+++++++|+++|+.||.|.++++.++       |||||+|.+.++|++||+.|++..+.+  +.+++.+..
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g--~~i~v~~~~   71 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRS--HEGETAYIR   71 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCC--TTSCCCBCE
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhccccccccccc-------ceeeEEeCCHHHHHHHHHHhCCCEECC--cEeEEeEEe
Confidence            6999999999999999999999999999998654       799999999999999999999999955  555555554

>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=9.6e-16  Score=115.96  Aligned_cols=76  Identities=14%  Similarity=0.200  Sum_probs=66.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      ...++|||+|||++++++||+++|+.||.|++|++.+       +|||||+|.+.++|++||+.||+..+.+  +.+++.
T Consensus        13 ~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g--~~i~v~   83 (98)
T d1wg4a_          13 RSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRS--HEGETS   83 (98)
T ss_dssp             SCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEEC--TTSCEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCC--eEEEEE
Confidence            4567899999999999999999999999999999864       3799999999999999999999999954  566666


Q ss_pred             ccccC
Q 013141          193 WATFS  197 (449)
Q Consensus       193 ~~~~~  197 (449)
                      +....
T Consensus        84 ~~~~~   88 (98)
T d1wg4a_          84 YIRVY   88 (98)
T ss_dssp             EEEEE
T ss_pred             EEecC
Confidence            65543

>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=99.62  E-value=5.1e-16  Score=117.51  Aligned_cols=76  Identities=21%  Similarity=0.409  Sum_probs=66.1

Q ss_pred             CCCCceEEEcCCC-CCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          112 NDETKTIWIGDLF-HWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       112 ~~~~~~l~v~nLp-~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      ....++|||+||| ..+++++|+++|++||.|++|+|.        +|||||+|.+.++|++|++.||+..+  .++.|+
T Consensus        12 ~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~--------rg~aFV~f~~~~~A~~Ai~~lng~~~--~g~~l~   81 (98)
T d1wf2a_          12 RSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH--------KGFAFVQYVNERNARAAVAGEDGRMI--AGQVLD   81 (98)
T ss_dssp             SSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE--------TEEEEEEESSHHHHHHHHHTTTTCEE--TTEECE
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe--------CCeEEEEECCHHHHHHHHHHcCCCEE--CCEEEE
Confidence            3456789999997 578899999999999999999983        48999999999999999999999999  457888


Q ss_pred             ccccccC
Q 013141          191 LNWATFS  197 (449)
Q Consensus       191 ~~~~~~~  197 (449)
                      |.|+...
T Consensus        82 V~~a~~~   88 (98)
T d1wf2a_          82 INLAAEP   88 (98)
T ss_dssp             EEETTSC
T ss_pred             EEECCCC
Confidence            8888643

>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=99.62  E-value=1.1e-15  Score=117.46  Aligned_cols=86  Identities=16%  Similarity=0.190  Sum_probs=77.2

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEe
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRID  284 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  284 (449)
                      .....+|||+|||+++|+++|+++|. .+|.|....++.+..++.++|+|||+|.+.++|++|+ ++++..|.+|.|+|.
T Consensus        12 ~~~~~~v~v~nLP~~~te~dI~~~F~-~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~-~~~~~~i~gR~i~V~   89 (104)
T d1wg5a_          12 TANDGFVRLRGLPFGCSKEEIVQFFS-GLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKAL-KKHKERIGHRYIEIF   89 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTT-TCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHH-TTTTCCSSSSCCEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHH-hcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHH-hhCCCEEcceEEEEE
Confidence            44566899999999999999999995 9999988777777788999999999999999999999 599999999999999


Q ss_pred             ecCCCCCC
Q 013141          285 VATPKKAS  292 (449)
Q Consensus       285 ~~~~~~~~  292 (449)
                      ++..+...
T Consensus        90 ~~~~~~~~   97 (104)
T d1wg5a_          90 KSSRAEVR   97 (104)
T ss_dssp             EECTTTSC
T ss_pred             ECCHHHhc
Confidence            99887543

>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=99.61  E-value=8e-16  Score=116.29  Aligned_cols=81  Identities=17%  Similarity=0.364  Sum_probs=72.4

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEe
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRID  284 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  284 (449)
                      ..+.++|||+|||+++|+++|+++|. .||.|..+.     .++.+++||||+|.+.++|++|++.||+..|.|+.|+|.
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~-~~g~v~~~~-----~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~   86 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFE-DALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLY   86 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHC-SEEEECCEE-----ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHH-hcccceeee-----ecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34568999999999999999999995 999876654     357889999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 013141          285 VATPKKA  291 (449)
Q Consensus       285 ~~~~~~~  291 (449)
                      |+.++..
T Consensus        87 ~a~~k~~   93 (96)
T d1fjca_          87 YTGEKGG   93 (96)
T ss_dssp             ECSSSCC
T ss_pred             EeCCCCC
Confidence            9998754

>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=99.61  E-value=2.6e-15  Score=110.97  Aligned_cols=78  Identities=21%  Similarity=0.423  Sum_probs=70.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeec
Q 013141          207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVA  286 (449)
Q Consensus       207 ~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~  286 (449)
                      ..++|||+|||+++++++|+++|+ .||.|..+.+.+      ++|||||+|.+.++|.+|+..|++..|.|+.|+|+|+
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~-~~g~i~~~~~~~------~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~a   79 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFN-NIKPGAVERVKK------IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLA   79 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHH-TTSTTCEEEEEE------CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhc-ccceeeeEEEcc------ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            346899999999999999999995 999998887743      4789999999999999999999999999999999999


Q ss_pred             CCCCC
Q 013141          287 TPKKA  291 (449)
Q Consensus       287 ~~~~~  291 (449)
                      .++..
T Consensus        80 kP~~~   84 (86)
T d2cpda1          80 KPVDK   84 (86)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            87654

>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=99.61  E-value=1e-15  Score=111.07  Aligned_cols=75  Identities=17%  Similarity=0.343  Sum_probs=68.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEee
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV  285 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  285 (449)
                      ...++|||+|++  +|+++|+++|+ .||.|.++.+.++      +++|||+|.+.++|.+|++.||+..+.|+.|+|+|
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~-~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~   73 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFS-PFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNI   73 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHS-TTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEE
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHh-ccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEE
Confidence            356799999985  89999999995 9999999998754      67999999999999999999999999999999999


Q ss_pred             cCCC
Q 013141          286 ATPK  289 (449)
Q Consensus       286 ~~~~  289 (449)
                      ++++
T Consensus        74 a~~~   77 (79)
T d2bz2a1          74 ARKQ   77 (79)
T ss_dssp             CCSS
T ss_pred             ecCC
Confidence            9765

>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=99.60  E-value=6.9e-16  Score=115.37  Aligned_cols=81  Identities=22%  Similarity=0.426  Sum_probs=71.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHH----HHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceE
Q 013141          207 SDLSIFVGDLAPDVTDSILQE----TFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMR  282 (449)
Q Consensus       207 ~~~~l~v~~lp~~~t~~~l~~----~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  282 (449)
                      ++++|||+|||+++++++|++    +|+ .||+|.+|.+.+   ++.++|+|||+|.+.++|.+|++.+++..+.|+.|+
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~-~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~   77 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFS-RFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMR   77 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHG-GGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhc-ccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            568999999999999999865    575 999999988764   366789999999999999999999999999999999


Q ss_pred             EeecCCCCC
Q 013141          283 IDVATPKKA  291 (449)
Q Consensus       283 v~~~~~~~~  291 (449)
                      |.|++.+..
T Consensus        78 v~~ak~~~~   86 (91)
T d1nu4a_          78 IQYAKTDSD   86 (91)
T ss_dssp             EEECSSCCT
T ss_pred             EEEeCCCch
Confidence            999987643

>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=99.60  E-value=4.8e-16  Score=121.00  Aligned_cols=81  Identities=19%  Similarity=0.235  Sum_probs=68.9

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccc
Q 013141          111 TNDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      .....++|||+|||+++|++||+++|+.||.+..+.++.+..+|+++|||||+|.+.++|.+||+ +|+..|.+  +.|+
T Consensus        14 ~~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~g--R~i~   90 (112)
T d1wela1          14 PHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGN--RFIQ   90 (112)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTT--SCBE
T ss_pred             CCCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCC--EEEE
Confidence            34567799999999999999999999999998877677777789999999999999999999995 89999854  5555


Q ss_pred             cccc
Q 013141          191 LNWA  194 (449)
Q Consensus       191 ~~~~  194 (449)
                      |..+
T Consensus        91 V~~~   94 (112)
T d1wela1          91 VHPI   94 (112)
T ss_dssp             EEEE
T ss_pred             EEEc
Confidence            5433

>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=3e-15  Score=107.22  Aligned_cols=74  Identities=8%  Similarity=0.102  Sum_probs=67.6

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeec
Q 013141          209 LSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVA  286 (449)
Q Consensus       209 ~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~  286 (449)
                      ++|||+|||+++++++|+++|+ .||.|..+++..++..  .+++|||+|.+.++|.+|+ .+++..|+|+.|.|+..
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 TTVLVKNLPKSYNQNKVYKYFK-HCGPIIHVDVADSLKK--NFRFARIEFARYDGALAAI-TKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHG-GGSCEEEEEEEECTTS--SSEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHh-cCCceEEEEEEeeccc--cceEEEEEEcchHHhHHHH-HhcCcEECCEEEEEEEC
Confidence            4799999999999999999996 9999999999998653  3579999999999999998 68999999999999875

>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=99.59  E-value=3.7e-16  Score=119.96  Aligned_cols=79  Identities=11%  Similarity=0.055  Sum_probs=67.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCccccc
Q 013141          113 DETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPFRLN  192 (449)
Q Consensus       113 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~~~~  192 (449)
                      ....+|||+|||+++|+++|+++|..||.|..+.++.+..+|+++|||||+|.+.++|++||+ +++..|.+  +.|.|.
T Consensus         6 ~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~g--r~i~V~   82 (103)
T d2cpya1           6 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNG--REAFVH   82 (103)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETT--EEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECC--cEEEEE
Confidence            456789999999999999999999999998876666666789999999999999999999995 89988844  566665


Q ss_pred             cc
Q 013141          193 WA  194 (449)
Q Consensus       193 ~~  194 (449)
                      ++
T Consensus        83 ~~   84 (103)
T d2cpya1          83 VV   84 (103)
T ss_dssp             EE
T ss_pred             EC
Confidence            44

>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=2.5e-15  Score=113.92  Aligned_cols=79  Identities=14%  Similarity=0.218  Sum_probs=66.5

Q ss_pred             CCCCCceEEEcCCCCC-CCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHh--cCCCCCCCCC
Q 013141          111 TNDETKTIWIGDLFHW-MDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSY--SGSLMPNTDQ  187 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~-~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l--~~~~~~~~~~  187 (449)
                      ....+++|||+|||.+ +|+++|+++|+.||.|.+|.+++++      |+|||+|.+.++|.+|++.+  ++..+  .++
T Consensus        14 ~~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~k------~~afV~f~~~~~A~~Ai~~~~~~~~~~--~gr   85 (99)
T d1x4fa1          14 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMK------SQAFIEMETREDAMAMVDHCLKKALWF--QGR   85 (99)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETTT------TEEEEECSSHHHHHHHHHHHHHSCCCS--SSS
T ss_pred             CCCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeecC------CcEEEEecchHHHHHHHHHHhcCCceE--CCE
Confidence            3456789999999985 8999999999999999999998764      79999999999999999854  45455  568


Q ss_pred             cccccccccC
Q 013141          188 PFRLNWATFS  197 (449)
Q Consensus       188 ~~~~~~~~~~  197 (449)
                      .|+|.+++..
T Consensus        86 ~l~V~~s~~~   95 (99)
T d1x4fa1          86 CVKVDLSEKY   95 (99)
T ss_dssp             CCEEEEECSC
T ss_pred             EEEEEEcCCc
Confidence            8888887643

>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=99.58  E-value=2.7e-15  Score=111.14  Aligned_cols=77  Identities=16%  Similarity=0.241  Sum_probs=66.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeec
Q 013141          207 SDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVA  286 (449)
Q Consensus       207 ~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~  286 (449)
                      .+++|||+|||+++++++|+++|. .|| +..+.+      +..++||||+|.+.++|++|++.||+..+.|+.|+|+++
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~-~~G-~~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a   75 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLK-DYD-LKYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQ   75 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTC-SSC-CCCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHH-hcC-ceeeee------eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            457899999999999999999995 999 333333      345889999999999999999999999999999999999


Q ss_pred             CCCCC
Q 013141          287 TPKKA  291 (449)
Q Consensus       287 ~~~~~  291 (449)
                      ..+..
T Consensus        76 ~~~~~   80 (88)
T d1wg1a_          76 PTDAL   80 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            76543

>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=99.57  E-value=2.1e-15  Score=115.65  Aligned_cols=82  Identities=15%  Similarity=0.253  Sum_probs=72.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEee
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV  285 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  285 (449)
                      ....+|||+|||+++|+++|+++|. .||.|..+.++.+..+|.++|+|||+|.+.++|++|++ |++..|.|+.|.|.+
T Consensus         6 ~~~~~v~v~nLp~~~t~~~l~~~F~-~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~   83 (103)
T d2cpya1           6 SAKVCAHITNIPFSITKMDVLQFLE-GIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHV   83 (103)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTT-TSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHhhhhc-ccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEE
Confidence            3456899999999999999999995 99999876666666789999999999999999999995 999999999999998


Q ss_pred             cCCC
Q 013141          286 ATPK  289 (449)
Q Consensus       286 ~~~~  289 (449)
                      +...
T Consensus        84 ~~~~   87 (103)
T d2cpya1          84 VTLE   87 (103)
T ss_dssp             ECHH
T ss_pred             CCHH
Confidence            7543

>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=99.56  E-value=1.8e-15  Score=112.22  Aligned_cols=79  Identities=25%  Similarity=0.390  Sum_probs=69.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEee
Q 013141          206 CSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDV  285 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  285 (449)
                      ..+++|||+|||+++|+++|+++|+ .||.|.++++..     .+++||||+|.+.++|++|+.  ++..|.|+.|+|++
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~-~~G~v~~v~~~~-----~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~   74 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFS-QYGDVMDVFIPK-----PFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISN   74 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHST-TTSCCCEEECCS-----SCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHH-HcCCceEEEEee-----ccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEe
Confidence            3568999999999999999999995 999999987653     457899999999999999984  78899999999999


Q ss_pred             cCCCCCC
Q 013141          286 ATPKKAS  292 (449)
Q Consensus       286 ~~~~~~~  292 (449)
                      +.++...
T Consensus        75 a~~k~~~   81 (88)
T d1wf0a_          75 AEPKHNS   81 (88)
T ss_dssp             CCCCCCC
T ss_pred             CCCCCCC
Confidence            9877543

>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=99.55  E-value=1e-14  Score=104.33  Aligned_cols=71  Identities=21%  Similarity=0.354  Sum_probs=63.5

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecCCC
Q 013141          211 IFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATPK  289 (449)
Q Consensus       211 l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~~~  289 (449)
                      |||+|||+++++++|+++|+ .|| +..+.+      ++++|+|||+|.+.++|.+|++.||+..+.|++|+|+++...
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 ILIRGLPGDVTNQEVHDLLS-DYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTT-TSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHh-ccc-ccceee------cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            79999999999999999995 999 554444      346889999999999999999999999999999999999654

>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=99.55  E-value=2.8e-15  Score=111.13  Aligned_cols=80  Identities=14%  Similarity=0.156  Sum_probs=69.4

Q ss_pred             CCCCCceEEEcCCCCC-CCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcc
Q 013141          111 TNDETKTIWIGDLFHW-MDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPF  189 (449)
Q Consensus       111 ~~~~~~~l~v~nLp~~-~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~  189 (449)
                      ..+.+++|||+|||.. +|++||.++|++||.|.+|.+++++      ++|||+|.+.++|.+|++.++...+...++++
T Consensus         4 ~~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~k------~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l   77 (89)
T d1x4da1           4 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI------NEAFIEMATTEDAQAAVDYYTTTPALVFGKPV   77 (89)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS------SCEEEEESSHHHHHHHHHHHHHSCCEETTEEC
T ss_pred             CCCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccc------eEEEEEEcchhhHHHHHHHHhhCCCccCCceE
Confidence            4568999999999986 8899999999999999999998765      58999999999999999987655544467899


Q ss_pred             ccccccc
Q 013141          190 RLNWATF  196 (449)
Q Consensus       190 ~~~~~~~  196 (449)
                      +|.|++.
T Consensus        78 ~V~~s~~   84 (89)
T d1x4da1          78 RVHLSQK   84 (89)
T ss_dssp             EEEEECC
T ss_pred             EEEECCC
Confidence            9999863

>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=99.53  E-value=5.5e-15  Score=114.87  Aligned_cols=84  Identities=20%  Similarity=0.332  Sum_probs=74.7

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEe
Q 013141          205 ACSDLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRID  284 (449)
Q Consensus       205 ~~~~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  284 (449)
                      ....++|||+|||+++|+++|+++|+ .+|.+..+.++.+..+|.++|+|||+|.+.++|.+|+ .||+..|+|+.|.|.
T Consensus        15 ~~~~~~i~v~nLp~~~t~~di~~~F~-~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al-~~~~~~i~gR~i~V~   92 (112)
T d1wela1          15 HEAGFCVYLKGLPFEAENKHVIDFFK-KLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAAL-CRHKQYMGNRFIQVH   92 (112)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSC-SSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHH-TSCSBCSTTSCBEEE
T ss_pred             CCCCeEEEEecCCCcCcHHHHhhHHh-hccccccceeeecCcccceeeEEEEEECCHHHHHHHH-HcCCCcCCCEEEEEE
Confidence            44567999999999999999999995 9999987767766678999999999999999999999 599999999999999


Q ss_pred             ecCCCC
Q 013141          285 VATPKK  290 (449)
Q Consensus       285 ~~~~~~  290 (449)
                      .+..+.
T Consensus        93 ~~~~~~   98 (112)
T d1wela1          93 PITKKG   98 (112)
T ss_dssp             EECHHH
T ss_pred             EcChHH
Confidence            886653

>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=99.52  E-value=4.9e-16  Score=116.07  Aligned_cols=78  Identities=14%  Similarity=0.353  Sum_probs=65.3

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEE-----ecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCCCCCCCcc
Q 013141          115 TKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVI-----RNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLMPNTDQPF  189 (449)
Q Consensus       115 ~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~-----~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~~~~~~~~  189 (449)
                      .|+|||+|||+++|+++|+++|+.||.|.++.+.     .+..+++++|||||+|.+.++|++|++ ||+..+.+  +.|
T Consensus         1 aRrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~G--r~l   77 (90)
T d1u2fa_           1 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQG--QSL   77 (90)
T ss_dssp             CCEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSS--SCC
T ss_pred             CCEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECC--EEE
Confidence            3789999999999999999999999987666543     455677899999999999999999995 99999955  666


Q ss_pred             cccccc
Q 013141          190 RLNWAT  195 (449)
Q Consensus       190 ~~~~~~  195 (449)
                      +|.+++
T Consensus        78 ~V~r~k   83 (90)
T d1u2fa_          78 KIRRPH   83 (90)
T ss_dssp             CCBCTT
T ss_pred             EECCCC
Confidence            665443

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.51  E-value=1.5e-14  Score=112.45  Aligned_cols=73  Identities=25%  Similarity=0.370  Sum_probs=65.2

Q ss_pred             CcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCH-HHHHHHHHHhcCCeeCCeEEEEEecC
Q 013141          327 NATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANR-KDAEVALQKLQGTAIGKQTVRLSWGR  399 (449)
Q Consensus       327 ~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~-~~A~~A~~~l~g~~~~g~~l~v~~~~  399 (449)
                      ...+||+|||+++|+++|+++|++||.|.+|.|++++++|||+|.+. ++|..|+..|++..+.++.+.|.|..
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~   84 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEV   84 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEE
T ss_pred             CeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecCCceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEee
Confidence            45569999999999999999999999999999999999999999985 78999999999998887666666654

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.49  E-value=2.3e-14  Score=108.74  Aligned_cols=66  Identities=18%  Similarity=0.328  Sum_probs=60.7

Q ss_pred             CCCCcEEEEcC--CCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeC
Q 013141          324 ESNNATIFVGA--LDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIG  389 (449)
Q Consensus       324 ~~~~~~l~V~n--lp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~  389 (449)
                      ..++.+|+|.|  ||..+|+++|+++|++||.|.+|.+.+++++|||+|.+.++|.+|++.|||+.+.
T Consensus        15 ~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~k~~aFV~f~~~e~A~~A~~~lng~~i~   82 (101)
T d2cq2a1          15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVV   82 (101)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTTCSCEEEEESSHHHHHHHHHHTTTCEEE
T ss_pred             CCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccCccEEEEEECCHHHHHHHHHHhCCCCCC
Confidence            34467888855  9999999999999999999999999999999999999999999999999999873

>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=99.46  E-value=1.2e-15  Score=113.88  Aligned_cols=72  Identities=14%  Similarity=0.329  Sum_probs=63.4

Q ss_pred             cEEEEcCCCCCCCHhHHHhhccccCceEEEEEe-----------CCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEE
Q 013141          328 ATIFVGALDSDVSDEDLREPFSQFGEILSVKIP-----------VGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLS  396 (449)
Q Consensus       328 ~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~-----------~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~  396 (449)
                      ++|||+|||+++|+++|+++|+.||.|..+.+.           +++++|||+|.+.++|.+|++ |||..|.|+.|+|.
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            579999999999999999999999987665543           357999999999999999985 99999999999997


Q ss_pred             ecCC
Q 013141          397 WGRN  400 (449)
Q Consensus       397 ~~~~  400 (449)
                      ..+.
T Consensus        81 r~k~   84 (90)
T d1u2fa_          81 RPHD   84 (90)
T ss_dssp             CTTC
T ss_pred             CCCC
Confidence            5543

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.42  E-value=8.7e-14  Score=105.46  Aligned_cols=65  Identities=15%  Similarity=0.257  Sum_probs=58.7

Q ss_pred             CCCCceEEEcC--CCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhcCCCC
Q 013141          112 NDETKTIWIGD--LFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYSGSLM  182 (449)
Q Consensus       112 ~~~~~~l~v~n--Lp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~~~~~  182 (449)
                      ..++++|+|.|  ||+++|+++|+++|++||.|.+|.+++++      +||||+|.+.++|.+|++.||+..+
T Consensus        15 ~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~k------~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK------PYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTTC------SCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccCc------cEEEEEECCHHHHHHHHHHhCCCCC
Confidence            45678999955  99999999999999999999999887653      6999999999999999999999876

>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=99.42  E-value=9.4e-14  Score=105.80  Aligned_cols=79  Identities=10%  Similarity=0.086  Sum_probs=69.2

Q ss_pred             CCCceEEEcCCCCCC-C----HHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcc
Q 013141          206 CSDLSIFVGDLAPDV-T----DSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRP  280 (449)
Q Consensus       206 ~~~~~l~v~~lp~~~-t----~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~  280 (449)
                      ...++|||+||+.++ +    +++|+++|+ .||.|.++.+++      ++++|||+|.+.++|.+|++.|||..|.|+.
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~-~~G~i~~~~~~k------~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~   75 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFR-TYDKDTTFQYFK------SFKRVRINFSNPLSAADARLRLHKTEFLGKE   75 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHH-TTCSSCEEEEET------TTTEEEEECSSTTHHHHHHHTSTTSEETTEE
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhc-ccccceEEEEec------CCCEEEEEECCHHHHHHHHHHhcccccCCCE
Confidence            356789999999876 3    356899995 999999999974      3679999999999999999999999999999


Q ss_pred             eEEeecCCCCC
Q 013141          281 MRIDVATPKKA  291 (449)
Q Consensus       281 i~v~~~~~~~~  291 (449)
                      |+|.|+.+...
T Consensus        76 l~v~~a~~~~~   86 (104)
T d1weya_          76 MKLYFAQTLHI   86 (104)
T ss_dssp             CEEECCCCSSC
T ss_pred             eEEeecccCCC
Confidence            99999977654

>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=99.42  E-value=2.6e-13  Score=102.44  Aligned_cols=79  Identities=22%  Similarity=0.327  Sum_probs=68.5

Q ss_pred             CCCCcEEEEcCC--CCCC---------CHhHHHhhccccCceEEEEEeCC--CcEEEEEecCHHHHHHHHHHhcCCeeCC
Q 013141          324 ESNNATIFVGAL--DSDV---------SDEDLREPFSQFGEILSVKIPVG--KGCGFVQFANRKDAEVALQKLQGTAIGK  390 (449)
Q Consensus       324 ~~~~~~l~V~nl--p~~~---------t~~~L~~~f~~~G~v~~v~i~~~--~g~afV~F~~~~~A~~A~~~l~g~~~~g  390 (449)
                      ...+++|+|.||  |.++         .++||++.|++||.|..|.+..+  +|+|||+|.+.++|.+|+..|||+.|+|
T Consensus         5 ~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~~~G~~fV~f~~~e~A~~A~~~lng~~~~g   84 (99)
T d2dita1           5 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGG   84 (99)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEETT
T ss_pred             CCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCCCccEEEEEECCHHHHHHHHHHhCCcEECC
Confidence            345789999999  5432         23689999999999999999875  6999999999999999999999999999


Q ss_pred             eEEEEEecCCCC
Q 013141          391 QTVRLSWGRNPG  402 (449)
Q Consensus       391 ~~l~v~~~~~~~  402 (449)
                      +.|+|+|..+..
T Consensus        85 r~i~v~~~~g~~   96 (99)
T d2dita1          85 RQITAQAWDGTT   96 (99)
T ss_dssp             EECEEEECCSCC
T ss_pred             EEEEEEEeCCcC
Confidence            999999987653

>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=3e-13  Score=104.90  Aligned_cols=76  Identities=16%  Similarity=0.142  Sum_probs=64.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccH-HHHHHHHHHhcCCCCCCCCCccc
Q 013141          112 NDETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSR-AAAEKVLQSYSGSLMPNTDQPFR  190 (449)
Q Consensus       112 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~-~~A~~Al~~l~~~~~~~~~~~~~  190 (449)
                      ...+..+||+|||+++|+++|+++|++||+|.+|.|+++      +|||||+|.+. ++|..|+..+++..+.+....+.
T Consensus         8 ~~g~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~   81 (113)
T d1owxa_           8 KIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVT   81 (113)
T ss_dssp             CCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEE
T ss_pred             CCCCeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEEE
Confidence            345777899999999999999999999999999999865      48999999995 78999999999998866555554


Q ss_pred             ccc
Q 013141          191 LNW  193 (449)
Q Consensus       191 ~~~  193 (449)
                      +.+
T Consensus        82 ~~~   84 (113)
T d1owxa_          82 WEV   84 (113)
T ss_dssp             EEE
T ss_pred             Eee
Confidence            433

>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=99.40  E-value=1.4e-14  Score=110.48  Aligned_cols=71  Identities=18%  Similarity=0.252  Sum_probs=65.5

Q ss_pred             cEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC-----CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 013141          328 ATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG-----KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWG  398 (449)
Q Consensus       328 ~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~-----~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~  398 (449)
                      ..++|.++...+++++|+++|++||.|.+|+|+++     +|+|||+|.+.++|.+|++.|||+.|+|+.|+|+|+
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            35778888888999999999999999999999763     699999999999999999999999999999999986

>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=99.39  E-value=3e-13  Score=97.57  Aligned_cols=72  Identities=15%  Similarity=0.219  Sum_probs=63.5

Q ss_pred             CcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeE-EEEEecCC
Q 013141          327 NATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQT-VRLSWGRN  400 (449)
Q Consensus       327 ~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~-l~v~~~~~  400 (449)
                      .+.|+|.++|++.+++ |..+|++||.|.++++.+++++|||+|.+.++|.+||+ +||..|+|+. |.|....+
T Consensus         4 ~~wV~V~G~p~~~~~~-il~~F~~~G~I~~~~~~~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~~   76 (81)
T d1wwha1           4 DTWVTVFGFPQASASY-ILLQFAQYGNILKHVMSNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCID   76 (81)
T ss_dssp             GGEEEEECCCGGGHHH-HHHHHHTTSCEEEEEECSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCC
T ss_pred             ccEEEEECCChHHHHH-HHHHHHhhhhhheEEecCCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCCC
Confidence            4679999999998865 55689999999999999999999999999999999996 9999999975 56877654

>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=99.39  E-value=3.9e-14  Score=107.97  Aligned_cols=75  Identities=16%  Similarity=0.334  Sum_probs=69.3

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeec
Q 013141          210 SIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVA  286 (449)
Q Consensus       210 ~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~  286 (449)
                      .++|.++..++++++|+++|+ +||.|.+|+|+++ .++.++|+|||+|.+.++|.+|++.|||+.+.|+.|+|+++
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 DVEMQEHYDEFFEEVFTEMEE-KYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH-HTCCEEEEEECCS-SSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             hHHhhhhhhhhhHHHHHHHhc-cCCCEEEEEeecC-CCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            477788888899999999995 9999999999877 57999999999999999999999999999999999999886

>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=99.33  E-value=6e-13  Score=101.50  Aligned_cols=76  Identities=24%  Similarity=0.371  Sum_probs=66.1

Q ss_pred             CCCcEEEEcCC--CCCCC--------HhHHHhhccccCceEEEEEeCC--------CcEEEEEecCHHHHHHHHHHhcCC
Q 013141          325 SNNATIFVGAL--DSDVS--------DEDLREPFSQFGEILSVKIPVG--------KGCGFVQFANRKDAEVALQKLQGT  386 (449)
Q Consensus       325 ~~~~~l~V~nl--p~~~t--------~~~L~~~f~~~G~v~~v~i~~~--------~g~afV~F~~~~~A~~A~~~l~g~  386 (449)
                      +++++|.|.||  +..+.        .+||++.|++||.|.+|.|+++        .|++||+|.+.++|.+|+..|||+
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr   81 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   81 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSC
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCC
Confidence            35789999999  44432        3679999999999999999752        489999999999999999999999


Q ss_pred             eeCCeEEEEEecCC
Q 013141          387 AIGKQTVRLSWGRN  400 (449)
Q Consensus       387 ~~~g~~l~v~~~~~  400 (449)
                      .|+||.|+|.|...
T Consensus        82 ~f~gR~v~v~f~~~   95 (104)
T d1o0pa_          82 KFANRVVVTKYCDP   95 (104)
T ss_dssp             CSSSSCCEEEEECH
T ss_pred             EECCeEEEEEEcCH
Confidence            99999999999763

>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=99.25  E-value=1.1e-11  Score=93.33  Aligned_cols=81  Identities=14%  Similarity=0.237  Sum_probs=68.3

Q ss_pred             cCCCceEEEcCC--CCCCC---------HHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCC
Q 013141          205 ACSDLSIFVGDL--APDVT---------DSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNG  273 (449)
Q Consensus       205 ~~~~~~l~v~~l--p~~~t---------~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g  273 (449)
                      ...+++|+|.|+  |.++.         +++|++.|+ +||.|..+.+..+    ..+|++||+|.+.++|.+|+..|||
T Consensus         5 ~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~-~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~lng   79 (99)
T d2dita1           5 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECS-KFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDG   79 (99)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGG-GTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHSTT
T ss_pred             CCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhc-CcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhCC
Confidence            345679999998  54321         368889995 9999999988654    4579999999999999999999999


Q ss_pred             ceecCcceEEeecCCCC
Q 013141          274 VYCSSRPMRIDVATPKK  290 (449)
Q Consensus       274 ~~~~g~~i~v~~~~~~~  290 (449)
                      +.++|+.|+|++++.+.
T Consensus        80 ~~~~gr~i~v~~~~g~~   96 (99)
T d2dita1          80 RWFGGRQITAQAWDGTT   96 (99)
T ss_dssp             CEETTEECEEEECCSCC
T ss_pred             cEECCEEEEEEEeCCcC
Confidence            99999999999987764

>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=99.17  E-value=2.9e-11  Score=86.88  Aligned_cols=73  Identities=14%  Similarity=0.195  Sum_probs=61.1

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcc-eEEeec
Q 013141          208 DLSIFVGDLAPDVTDSILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRP-MRIDVA  286 (449)
Q Consensus       208 ~~~l~v~~lp~~~t~~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~-i~v~~~  286 (449)
                      ++.|+|+++|++.+++. .+.|+ .||+|.++.+.      +.++|+||+|.++++|++|+ .+||..|+|+. |.|...
T Consensus         4 ~~wV~V~G~p~~~~~~i-l~~F~-~~G~I~~~~~~------~~~~~~fV~f~~~~~A~~Al-~~nG~~~~g~~~vgV~~~   74 (81)
T d1wwha1           4 DTWVTVFGFPQASASYI-LLQFA-QYGNILKHVMS------NTGNWMHIRYQSKLQARKAL-SKDGRIFGESIMIGVKPC   74 (81)
T ss_dssp             GGEEEEECCCGGGHHHH-HHHHH-TTSCEEEEEEC------SSSSEEEEEESSHHHHHHHH-TTTTCEETTTEECEEEEC
T ss_pred             ccEEEEECCChHHHHHH-HHHHH-hhhhhheEEec------CCCCEEEEEEcccHHHHHHH-hcCCCeECCcEEEEEEeC
Confidence            46799999999988654 46795 99999999874      34789999999999999999 59999999985 568877


Q ss_pred             CCC
Q 013141          287 TPK  289 (449)
Q Consensus       287 ~~~  289 (449)
                      .++
T Consensus        75 ~~k   77 (81)
T d1wwha1          75 IDK   77 (81)
T ss_dssp             CCH
T ss_pred             CCh
Confidence            654

>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=99.16  E-value=1.9e-11  Score=92.97  Aligned_cols=82  Identities=17%  Similarity=0.191  Sum_probs=68.8

Q ss_pred             CCCceEEEcCC--CCCCC--------HHHHHHHHhhhCCCeeEEEEeecCCC--CCcceEEEEEeCCHHHHHHHHHHhCC
Q 013141          206 CSDLSIFVGDL--APDVT--------DSILQETFSSKYPSVKGAKVIIDSNT--GRTKGYGFVRFGDENERSRAMTEMNG  273 (449)
Q Consensus       206 ~~~~~l~v~~l--p~~~t--------~~~l~~~f~~~~g~v~~i~~~~~~~~--~~~~g~afV~f~~~~~A~~A~~~l~g  273 (449)
                      .+++.|.|.|+  +.++.        .++|++.|. +||.|.++.+.++..+  ....|++||+|.+.++|.+|+..|+|
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 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECS-KYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG   80 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHT-TTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSS
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhc-ccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCC
Confidence            35778999998  44432        357899995 9999999999887554  34568999999999999999999999


Q ss_pred             ceecCcceEEeecCC
Q 013141          274 VYCSSRPMRIDVATP  288 (449)
Q Consensus       274 ~~~~g~~i~v~~~~~  288 (449)
                      +.++||.|.+.+...
T Consensus        81 r~f~gR~v~v~f~~~   95 (104)
T d1o0pa_          81 RKFANRVVVTKYCDP   95 (104)
T ss_dssp             CCSSSSCCEEEEECH
T ss_pred             CEECCeEEEEEEcCH
Confidence            999999999999864

>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=97.83  E-value=3.6e-05  Score=50.85  Aligned_cols=59  Identities=27%  Similarity=0.358  Sum_probs=51.9

Q ss_pred             hHHHhhccccCceEEEEEeCC---CcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecCC
Q 013141          342 EDLREPFSQFGEILSVKIPVG---KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGRN  400 (449)
Q Consensus       342 ~~L~~~f~~~G~v~~v~i~~~---~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  400 (449)
                      +-|.+.|++++.|.++.|..-   .-.|-|...+..+|.-|+..||.+.|+.++|.|+++..
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~dg~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~~   72 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATG   72 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             HHHHHHHHhheeEEEEEEEeccCCcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEecC
Confidence            445578899999999999752   45899999999999999999999999999999999863

>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=97.73  E-value=3.4e-05  Score=53.77  Aligned_cols=55  Identities=25%  Similarity=0.450  Sum_probs=48.5

Q ss_pred             hHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 013141          342 EDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGR  399 (449)
Q Consensus       342 ~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  399 (449)
                      ++|.+.|..||+|.=|++.  .+..+|+|.+-++|.+|++ |++.++.|+.|+|+...
T Consensus        39 ~~Llq~l~~~GeViLvRFv--~d~mwVTF~dG~SAL~al~-l~g~~v~G~~l~It~~~   93 (95)
T d1ufwa_          39 TELMQTLGSYGTIVLVRIN--QGQMLVTFADSHSALSVLD-VDGMKVKGRAVKISGPS   93 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEE--TTEEEEECSCSHHHHHHHH-GGGSEETTEEEEEECCC
T ss_pred             HHHHHHHhhCCeEEEEEEe--CCeEEEEECCcHHHHHHhc-cCCeEEcceEEEEecCC
Confidence            5677889999999999998  4679999999999999986 89999999999998543

>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=97.64  E-value=8e-05  Score=52.94  Aligned_cols=67  Identities=9%  Similarity=0.122  Sum_probs=57.8

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcc--cEEEEEEccHHHHHHHHHHhcCCCC
Q 013141          116 KTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSE--GYGFVEFYSRAAAEKVLQSYSGSLM  182 (449)
Q Consensus       116 ~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~--g~afV~f~~~~~A~~Al~~l~~~~~  182 (449)
                      ++|.||.||+.+||+++.+.+...+.+........+.+-+..  .-|||.|.+.+++....+.+++..+
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            579999999999999999999999998888887766544432  3599999999999999999999876

>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=97.54  E-value=0.00013  Score=51.83  Aligned_cols=71  Identities=13%  Similarity=0.232  Sum_probs=59.9

Q ss_pred             cEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCC--------CcEEEEEecCHHHHHHHHHHhcCCeeCC-----eEEE
Q 013141          328 ATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVG--------KGCGFVQFANRKDAEVALQKLQGTAIGK-----QTVR  394 (449)
Q Consensus       328 ~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~--------~g~afV~F~~~~~A~~A~~~l~g~~~~g-----~~l~  394 (449)
                      ++|.|+.||+.+|++++.+.+...|.+....+..+        -.-|||.|.+.++.....+.++|+.|.+     ..-.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D~~g~~~~a~   81 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAI   81 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEcCCCCEeeeE
Confidence            57999999999999999999999999988877653        2679999999999999999999998853     2335


Q ss_pred             EEec
Q 013141          395 LSWG  398 (449)
Q Consensus       395 v~~~  398 (449)
                      |+||
T Consensus        82 VE~A   85 (91)
T d1uw4a_          82 VEFA   85 (91)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            5655

>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=96.99  E-value=0.00077  Score=46.81  Aligned_cols=55  Identities=16%  Similarity=0.327  Sum_probs=48.0

Q ss_pred             HHHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecC
Q 013141          223 SILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVAT  287 (449)
Q Consensus       223 ~~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~  287 (449)
                      ++|.+.|. .||+|.-|+++.+        ..+|+|.+-+.|.+|+ .+++.++.|+.|+|....
T Consensus        39 ~~Llq~l~-~~GeViLvRFv~d--------~mwVTF~dG~SAL~al-~l~g~~v~G~~l~It~~~   93 (95)
T d1ufwa_          39 TELMQTLG-SYGTIVLVRINQG--------QMLVTFADSHSALSVL-DVDGMKVKGRAVKISGPS   93 (95)
T ss_dssp             HHHHHHHH-HHSCCSEEEEETT--------EEEEECSCSHHHHHHH-HGGGSEETTEEEEEECCC
T ss_pred             HHHHHHHh-hCCeEEEEEEeCC--------eEEEEECCcHHHHHHh-ccCCeEEcceEEEEecCC
Confidence            47778885 9999999999866        5799999999999998 699999999999997543

>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=96.75  E-value=0.0044  Score=40.68  Aligned_cols=61  Identities=18%  Similarity=0.244  Sum_probs=50.4

Q ss_pred             HHHHHHhhhCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceecCcceEEeecCC
Q 013141          224 ILQETFSSKYPSVKGAKVIIDSNTGRTKGYGFVRFGDENERSRAMTEMNGVYCSSRPMRIDVATP  288 (449)
Q Consensus       224 ~l~~~f~~~~g~v~~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~~~~  288 (449)
                      .|.+.|. +++.|.++.+....+ +  .-.|-|...+..+|.-|+..|+...|+.++|.|.+++.
T Consensus        12 ~L~~~f~-~h~~V~sv~l~~~~d-g--~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~~   72 (73)
T d2dgxa1          12 LLQEAFA-RHGKVKSVELSPHTD-Y--QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATG   72 (73)
T ss_dssp             HHHHHHH-HHSCEEEEEECSCCS-T--TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             HHHHHHH-hheeEEEEEEEeccC-C--cEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEecC
Confidence            4456784 899999998875422 2  33689999999999999999999999999999998753

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.97  E-value=0.014  Score=41.13  Aligned_cols=61  Identities=20%  Similarity=0.329  Sum_probs=49.9

Q ss_pred             CCCCCCcEEEEcCCCCCCCHhHHHhhccccCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhc
Q 013141          322 DGESNNATIFVGALDSDVSDEDLREPFSQFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQ  384 (449)
Q Consensus       322 ~~~~~~~~l~V~nlp~~~t~~~L~~~f~~~G~v~~v~i~~~~g~afV~F~~~~~A~~A~~~l~  384 (449)
                      ++.+...-||.-..|......||.++|++||.|.=-.|  +...|||...+.++|..+++.++
T Consensus        10 d~~p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswI--ddTSa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          10 DLQPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWI--DDTSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCCCCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEE--ETTEEEEECSCHHHHHHHHHHHH
T ss_pred             CCCCCcceeEEEeCCcccchhHHHHHhcCCCceEEEEe--cCceEEEEecCHHHHHHHHHHhc
Confidence            34455567888899999999999999999998654444  45699999999999999887765

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.73  E-value=0.077  Score=37.19  Aligned_cols=57  Identities=12%  Similarity=0.131  Sum_probs=46.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCcEEEEEEecCCCCCcccEEEEEEccHHHHHHHHHHhc
Q 013141          114 ETKTIWIGDLFHWMDETFLHNCFSHTGQVVNVKVIRNKQTGQSEGYGFVEFYSRAAAEKVLQSYS  178 (449)
Q Consensus       114 ~~~~l~v~nLp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~  178 (449)
                      ...-||.-..|......||.++|++||.|. |..+.|.       .|||...+.+.|+.++..+.
T Consensus        14 ~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~-VswIddT-------Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          14 KRDHVLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDDT-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCSEEEEECCTTCCHHHHHHHHTTTCSCC-CEEEETT-------EEEEECSCHHHHHHHHHHHH
T ss_pred             CcceeEEEeCCcccchhHHHHHhcCCCceE-EEEecCc-------eEEEEecCHHHHHHHHHHhc
Confidence            444699999999999999999999999863 4444442       69999999999999986544