Psyllid ID: psy16184

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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---
Protein Sequence
MTQFLPPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFEDPKDTPPPTRVETREERLERRRRERAEQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGGTRRGGPDVNLKHSGREDNERERERYRLERERELAGGPPRARSGSNDRERERERRRSRSRERKRRTSRSRSRDRRRRRSRERIRDDDIEEVEFRPKDRSDRDRDRDRKRRRERENSEDRNERKRDRKERRKERERNNEEREEKVFIKQEPVDDYQEYDNYEDEASSV
Secondary Structure (PSIPRED)
ccccccHHHHHccccccccccccccccccccccccccccHHHHHHHcccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccEEEEEcccccccHHHHHHHHHHHccccEEEEEccccccccccEEEEEEccHHHHHHHHHHccccEEccEEEEEEEEcccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccHHHHHHHccccccccccccccccccccccccccHHHHHHHHccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccEEEEEEEcccccHHHHHHHHHHcccEEEEEEEEEcccccccEEEEEEEccHHHHHHHHHHccccEEcccEEEEEEEcccEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHcccccccccccccHHHHcccccc
Coil and Loop (DISEMBL)
mtqflppnllalfaprdpvpylppveklphekkthgySGIAAFLnefedpkdtppptrveTREERLERRRRERAEQVAYKLEQEIalwdpnsfpnatmdpfKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNkvtgkprgyAFIEYEHerdmhsaykhadgkkidgrrVLVDVERsrtvkgwlprrlggglggtrrggpdvnlkhsgredneRERERYRLERERelaggpprarsgsndreRERERRRSRSRErkrrtsrsrsRDRRRRRsrerirdddieevefrpkdrsdrdrdrdRKRRRERENSEDRNERKRDRKERRKERErnneereekvfikqepvddyqeydnyedeassv
Flexible Loop (DISEMBL)
mtqflppnllalfaprdpvPYLPPVEKLPHEKKTHGYSGIAAFLnefedpkdtppptrvetreerleRRRRERAEQVAYKLEqeialwdpnsfpNATMDPFKTLFIARVNYdtsesklrrefevygpikkivmvhnkvtgkpRGYAFIEYEHERDMHSaykhadgkkidgrrvlvdversrtvkgwlprrlggglggtrrggpdvnlkhsgrednerereryrlererelaggpprarsgsndrerererrrsrsrerkrrtsrsrsrdrrrrrsrerirdddieevefrpkdrsdrdrdrdrkrrrerensedrnerkrdrkerrkerernneereekvfikqepvddyqeydnyedeassv
Low Complexity Region (SEG)
MTQflppnllalfapRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFEDPKDtppptrvetreerlerrrreraeQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERSRTVKgwlprrlggglggtrrggPDVNLKHSGrednerereryrlerereLAGGPPRArsgsndrerererrrsrsrerkrrtsrsrsrdrrrrrsrerirdddieevefrPkdrsdrdrdrdrkrrrerensedrnerkrdrkerrkerernneereekVFIKQEPVddyqeydnyedeASSV
Disordered region (IsUnstruct)
********LLALFAPRDPVPYL*************GYSGIAAFL********************************VAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPRRLGG**************************************************************************************************************************************************************************
Disordered Region (DISOPRED)
MTQFLPPNLLALFAPRDPVPYLPPV***********YSGIAAFLNEFE************************************************TMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER****************************************************************************************************************************************************************************************
Disordered Region (DISEMBL)
MTQFLPPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFEDP***********************AEQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGGTRRGGPDVNLKH************YRLER**************************************************ERIRDDDIEEVEFR************************************************KVFIKQEPVDDYQEYDNYEDEASSV
Disordered Region (DISPRO)
**QFLPPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFEDPKDTPPPTRVETREERLERRRRERAEQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPRR*****************************************************************************************************************************************************************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
ooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MTQFLPPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFEDPKDTPPPTRVETREERLERRRRERAEQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGGTRRGGPDVNLKHSGREDNERERERYRLERERELAGGPPRARSGSNDRERERERRRSRSRERKRRTSRSRSRDRRRRRSRERIRDDDIEEVEFRPKDRSDRDRDRDRKRRRExxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxPVDDYQEYDNYEDEASSV
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	363	2.2.26 [Sep-21-2011]
P17133	448	U1 small nuclear ribonucl	yes	N/A	0.581	0.470	0.800	8e-81
Q62376	448	U1 small nuclear ribonucl	yes	N/A	0.608	0.493	0.761	6e-76
P08621	437	U1 small nuclear ribonucl	yes	N/A	0.608	0.505	0.761	7e-76
Q1RMR2	439	U1 small nuclear ribonucl	yes	N/A	0.608	0.503	0.761	1e-75
Q66II8	471	U1 small nuclear ribonucl	yes	N/A	0.597	0.460	0.766	2e-75
P09406	471	U1 small nuclear ribonucl	N/A	N/A	0.597	0.460	0.751	5e-74
Q42404	427	U1 small nuclear ribonucl	yes	N/A	0.710	0.604	0.492	4e-60
Q55FQ0	459	U1 small nuclear ribonucl	yes	N/A	0.575	0.455	0.439	3e-38
O13829	261	U1 small nuclear ribonucl	yes	N/A	0.517	0.720	0.484	4e-37
Q1LZH0	245	U11/U12 small nuclear rib	no	N/A	0.283	0.420	0.476	3e-20

>sp|P17133|RU17_DROME U1 small nuclear ribonucleoprotein 70 kDa OS=Drosophila melanogaster GN=snRNP-U1-70K PE=1 SV=2

 Score =  300 bits (769), Expect = 8e-81,   Method: Compositional matrix adjust.
 Identities = 169/211 (80%), Positives = 194/211 (91%)

Query: 1   MTQFLPPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFEDPKDTPPPTRVE 60
           MTQ+LPPNLLALFA R+P+P++PPV+KLPHEKK+ GY G+A F+ +FEDPKDTP P  VE
Sbjct: 1   MTQYLPPNLLALFAAREPIPFMPPVDKLPHEKKSRGYLGVAKFMADFEDPKDTPLPKTVE 60

Query: 61  TREERLERRRRERAEQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRR 120
           TR+ERLERRRRE+AEQVAYKLE+EIALWDP    NAT DPF+TLFIAR+NYDTSESKLRR
Sbjct: 61  TRQERLERRRREKAEQVAYKLEREIALWDPTEIKNATEDPFRTLFIARINYDTSESKLRR 120

Query: 121 EFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS 180
           EFE YGPIKKIV++H++ +GKP+GYAFIEYEHERDMH+AYKHADGKKID +RVLVDVER+
Sbjct: 121 EFEFYGPIKKIVLIHDQESGKPKGYAFIEYEHERDMHAAYKHADGKKIDSKRVLVDVERA 180

Query: 181 RTVKGWLPRRLGGGLGGTRRGGPDVNLKHSG 211
           RTVKGWLPRRLGGGLGGTRRGG DVN+KHSG
Sbjct: 181 RTVKGWLPRRLGGGLGGTRRGGNDVNIKHSG 211

Mediates the splicing of pre-mRNA by binding to the stem loop I region of U1-snRNA.
Drosophila melanogaster (taxid: 7227)

>sp|Q62376|RU17_MOUSE U1 small nuclear ribonucleoprotein 70 kDa OS=Mus musculus GN=Snrnp70 PE=1 SV=2

 Score =  284 bits (727), Expect = 6e-76,   Method: Compositional matrix adjust.
 Identities = 169/222 (76%), Positives = 193/222 (86%), Gaps = 1/222 (0%)

Query: 1   MTQFLPPNLLALFAPRDPVPYLPPVEKLPHEK-KTHGYSGIAAFLNEFEDPKDTPPPTRV 59
           MTQFLPPNLLALFAPRDP+PYLPP+EKLPHEK     Y GIA ++ EFEDP+D PPPTR 
Sbjct: 1   MTQFLPPNLLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRDAPPPTRA 60

Query: 60  ETREERLERRRRERAEQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLR 119
           ETREER+ER+RRE+ E+   ++E E+ +WDP++ PNA  D FKTLF+ARVNYDT+ESKLR
Sbjct: 61  ETREERMERKRREKIERRQQEVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLR 120

Query: 120 REFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 179
           REFEVYGPIK+I MV++K +GKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER
Sbjct: 121 REFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 180

Query: 180 SRTVKGWLPRRLGGGLGGTRRGGPDVNLKHSGREDNERERER 221
            RTVKGW PRRLGGGLGGTRRGG DVN++HSGR+D  R  ER
Sbjct: 181 GRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRYDER 222

Mediates the splicing of pre-mRNA by binding to the loop I region of U1-snRNA. The truncated isoform cannot bind U1-snRNA.

Mus musculus (taxid: 10090)

>sp|P08621|RU17_HUMAN U1 small nuclear ribonucleoprotein 70 kDa OS=Homo sapiens GN=SNRNP70 PE=1 SV=2

 Score =  284 bits (727), Expect = 7e-76,   Method: Compositional matrix adjust.
 Identities = 169/222 (76%), Positives = 193/222 (86%), Gaps = 1/222 (0%)

Query: 1   MTQFLPPNLLALFAPRDPVPYLPPVEKLPHEK-KTHGYSGIAAFLNEFEDPKDTPPPTRV 59
           MTQFLPPNLLALFAPRDP+PYLPP+EKLPHEK     Y GIA ++ EFEDP+D PPPTR 
Sbjct: 1   MTQFLPPNLLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRDAPPPTRA 60

Query: 60  ETREERLERRRRERAEQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLR 119
           ETREER+ER+RRE+ E+   ++E E+ +WDP++ PNA  D FKTLF+ARVNYDT+ESKLR
Sbjct: 61  ETREERMERKRREKIERRQQEVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLR 120

Query: 120 REFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 179
           REFEVYGPIK+I MV++K +GKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER
Sbjct: 121 REFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 180

Query: 180 SRTVKGWLPRRLGGGLGGTRRGGPDVNLKHSGREDNERERER 221
            RTVKGW PRRLGGGLGGTRRGG DVN++HSGR+D  R  ER
Sbjct: 181 GRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRYDER 222

Mediates the splicing of pre-mRNA by binding to the loop I region of U1-snRNA. The truncated isoforms cannot bind U1-snRNA.

Homo sapiens (taxid: 9606)

>sp|Q1RMR2|RU17_BOVIN U1 small nuclear ribonucleoprotein 70 kDa OS=Bos taurus GN=SNRNP70 PE=2 SV=1

 Score =  283 bits (725), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 169/222 (76%), Positives = 193/222 (86%), Gaps = 1/222 (0%)

Query: 1   MTQFLPPNLLALFAPRDPVPYLPPVEKLPHEKK-THGYSGIAAFLNEFEDPKDTPPPTRV 59
           MTQFLPPNLLALFAPRDP+PYLPP+EKLPHEK     Y GIA ++ EFEDP+D PPPTR 
Sbjct: 1   MTQFLPPNLLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRDAPPPTRA 60

Query: 60  ETREERLERRRRERAEQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLR 119
           ETREER+ER+RRE+ E+   ++E E+ +WDP++ PNA  D FKTLF+ARVNYDT+ESKLR
Sbjct: 61  ETREERMERKRREKIERRQQEVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLR 120

Query: 120 REFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 179
           REFEVYGPIK+I MV++K +GKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER
Sbjct: 121 REFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 180

Query: 180 SRTVKGWLPRRLGGGLGGTRRGGPDVNLKHSGREDNERERER 221
            RTVKGW PRRLGGGLGGTRRGG DVN++HSGR+D  R  ER
Sbjct: 181 GRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRYDER 222

Mediates the splicing of pre-mRNA by binding to the loop I region of U1-snRNA. The truncated isoforms cannot bind U1-snRNA.

Bos taurus (taxid: 9913)

>sp|Q66II8|RU17_XENTR U1 small nuclear ribonucleoprotein 70 kDa OS=Xenopus tropicalis GN=snrnp70 PE=2 SV=1

 Score =  283 bits (723), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 167/218 (76%), Positives = 189/218 (86%), Gaps = 1/218 (0%)

Query: 1   MTQFLPPNLLALFAPRDPVPYLPPVEKLPHEKK-THGYSGIAAFLNEFEDPKDTPPPTRV 59
           MTQFLPPNLLALFAPRDPVPYLPP++KLPHEK     Y GIA ++ EFEDP+D PPPTR 
Sbjct: 1   MTQFLPPNLLALFAPRDPVPYLPPLDKLPHEKHHNQPYCGIAPYIREFEDPRDAPPPTRA 60

Query: 60  ETREERLERRRRERAEQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLR 119
           ETREER+ER+RRE+ E+    +E E+ +WDP++  NA  D FKTLF+ARVNYDT+ESKLR
Sbjct: 61  ETREERMERKRREKIERRQQDVENELKIWDPHNDQNAQGDAFKTLFVARVNYDTTESKLR 120

Query: 120 REFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 179
           REFEVYGPIK+I MV+NK +GKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER
Sbjct: 121 REFEVYGPIKRIHMVYNKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 180

Query: 180 SRTVKGWLPRRLGGGLGGTRRGGPDVNLKHSGREDNER 217
            RTVKGW PRRLGGGLGGTRRGG DVN++HSGR+D  R
Sbjct: 181 GRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSR 218

Mediates the splicing of pre-mRNA by binding to the stem loop I region of U1-snRNA.

Xenopus tropicalis (taxid: 8364)

>sp|P09406|RU17_XENLA U1 small nuclear ribonucleoprotein 70 kDa OS=Xenopus laevis GN=snrnp70 PE=2 SV=1

 Score =  278 bits (710), Expect = 5e-74,   Method: Compositional matrix adjust.
 Identities = 166/221 (75%), Positives = 189/221 (85%), Gaps = 4/221 (1%)

Query: 1   MTQFLPPNLLALFAPRDPVPYLPPVEKLPHEKK-THGYSGIAAFLNEFEDPKDTPPPTRV 59
           MTQFLPPNLLALFAPRDPVPYLPP++KLPHEK     Y GIA ++ EFEDP+D PPPTR 
Sbjct: 1   MTQFLPPNLLALFAPRDPVPYLPPLDKLPHEKHHNQPYCGIAPYIREFEDPRDAPPPTRA 60

Query: 60  ETREERLERRRRERAEQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLR 119
           ETREER+ER+RRE+ E+    +E E+ +WDP++  NA  D FKTLF+ARVNYDT+ESKLR
Sbjct: 61  ETREERMERKRREKIERRQQDVENELKIWDPHNDQNAQGDAFKTLFVARVNYDTTESKLR 120

Query: 120 REFEVYGPIKKIVMVHNKVT---GKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD 176
           REFEVYGPIK+I +V+NK +   GKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD
Sbjct: 121 REFEVYGPIKRIHIVYNKGSEGSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD 180

Query: 177 VERSRTVKGWLPRRLGGGLGGTRRGGPDVNLKHSGREDNER 217
           VER RTVKGW PRRLGGGLGGTRRGG DVN++HSGR+D  R
Sbjct: 181 VERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSR 221

Mediates the splicing of pre-mRNA by binding to the stem loop I region of U1-snRNA.

Xenopus laevis (taxid: 8355)

>sp|Q42404|RU17_ARATH U1 small nuclear ribonucleoprotein 70 kDa OS=Arabidopsis thaliana GN=RNU1 PE=1 SV=1

 Score =  232 bits (591), Expect = 4e-60,   Method: Compositional matrix adjust.
 Identities = 134/272 (49%), Positives = 175/272 (64%), Gaps = 14/272 (5%)

Query: 5   LPPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFEDPKD---TPPPTRVET 61
           L  NLL LF PR P+ Y PP EK    +K   Y+G+A F++ F +P D    PP   VE 
Sbjct: 42  LTNNLLKLFEPRPPLEYKPPPEK----RKCPPYTGMAQFVSNFAEPGDPEYAPPKPEVEL 97

Query: 62  REERLERRRRERAEQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRRE 121
             ++ ER  + R E+   K  +++  +DPN+ PNAT DP+KTLF++R+NY++SESK++RE
Sbjct: 98  PSQKRERIHKLRLEKGVEKAAEDLKKYDPNNDPNATGDPYKTLFVSRLNYESSESKIKRE 157

Query: 122 FEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERSR 181
           FE YGPIK++ +V +++T KP+GYAFIEY H RDM +AYK ADG+KIDGRRVLVDVER R
Sbjct: 158 FESYGPIKRVHLVTDQLTNKPKGYAFIEYMHTRDMKAAYKQADGQKIDGRRVLVDVERGR 217

Query: 182 TVKGWLPRRLGGGLGGTRRGGPDVNL---KHSGREDNERERERYRLERERELAGGPPRAR 238
           TV  W PRRLGGGLG +R GG +  +   +  GR     E  R R ERE+    G  R R
Sbjct: 218 TVPNWRPRRLGGGLGTSRVGGGEEIVGEQQPQGRTSQSEEPSRPREEREKSREKGKERER 277

Query: 239 SGSNDRERERERRRSRSRERKRRTSRSRSRDR 270
           S    RE   E+ R RSR+R R     R RD+
Sbjct: 278 S----RELSHEQPRERSRDRPREDKHHRDRDQ 305

Mediates the splicing of pre-mRNA by binding to the loop I region of U1-snRNA.

Arabidopsis thaliana (taxid: 3702)

>sp|Q55FQ0|RU17_DICDI U1 small nuclear ribonucleoprotein 70 kDa OS=Dictyostelium discoideum GN=snrnp70 PE=3 SV=1

 Score =  159 bits (402), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 95/216 (43%), Positives = 133/216 (61%), Gaps = 7/216 (3%)

Query: 4   FLPPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFEDPKDTPPPTR--VET 61
           FLPPNL  +F PR P P        P       Y+G+  +L+ F DP +  P  +  +E 
Sbjct: 3   FLPPNLKIMFNPRHPPP----FLPPPPPSNLPPYTGLRDYLSIFTDPSNEEPFKKEHIEN 58

Query: 62  REERLERRRRERAEQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRRE 121
            EE+ E++R+ +  +   ++ + +  WDP S    T DP+KT+F++R++Y T++ KL  E
Sbjct: 59  LEEKREKKRKLKISENDERISKSLKAWDPYSNSETTGDPYKTIFVSRISYKTTQQKLEFE 118

Query: 122 FEVYGPIKKIVMVHNKVTG-KPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS 180
           F  +GPIK + +V +     K  GYAFIE+E ERDM +AYK ADG KID RR++VD+ER 
Sbjct: 119 FGQFGPIKSLFLVKDSNNPEKHTGYAFIEFERERDMKAAYKQADGMKIDDRRIVVDIERG 178

Query: 181 RTVKGWLPRRLGGGLGGTRRGGPDVNLKHSGREDNE 216
           R +K W PR+ GGGLG TR GG DVN   SGRE +E
Sbjct: 179 RVIKNWKPRKFGGGLGNTRAGGVDVNQTFSGREMSE 214

Mediates the splicing of pre-mRNA by binding to the stem loop I region of U1-snRNA.

Dictyostelium discoideum (taxid: 44689)

>sp|O13829|RU17_SCHPO U1 small nuclear ribonucleoprotein 70 kDa homolog OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=usp101 PE=1 SV=1

 Score =  155 bits (393), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 92/190 (48%), Positives = 127/190 (66%), Gaps = 2/190 (1%)

Query: 1   MTQFLPPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFEDPKDTPPPTRVE 60
           M + LP  LLALFAPR P+ YLPP++  P ++ T   SGIA +L   +       PT  E
Sbjct: 1   MAEKLPAPLLALFAPRPPLRYLPPMDVPPEKRSTPRVSGIAKYLKYAQSHDQQYHPT--E 58

Query: 61  TREERLERRRRERAEQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRR 120
           + EE+  R R E+ +Q   +L   I +WDP+   +   DP+KT+F++R++YDT ES + R
Sbjct: 59  SLEEKRLRLRDEKQKQQRERLRSMIKVWDPDHDRHVIGDPYKTMFLSRLSYDTKESDIER 118

Query: 121 EFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS 180
           EF  YGPI++I +V NKVTGK  GYAF+ +E ERD+  AYK + G  ++GRR++VDVER 
Sbjct: 119 EFTRYGPIERIRVVRNKVTGKSMGYAFVVFERERDLKVAYKASAGLMLNGRRIVVDVERG 178

Query: 181 RTVKGWLPRR 190
           RTVKGWLPR+
Sbjct: 179 RTVKGWLPRK 188

Involved in nuclear mRNA splicing (By similarity). Essential for growth.

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

>sp|Q1LZH0|U1SBP_BOVIN U11/U12 small nuclear ribonucleoprotein 35 kDa protein OS=Bos taurus GN=SNRNP35 PE=2 SV=1

 Score = 99.4 bits (246), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 50/105 (47%), Positives = 67/105 (63%), Gaps = 2/105 (1%)

Query: 85  IALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRG 144
           +A + PN     T DP  TLF+AR+N  T E KL+  F  YG I+++ +V + VTG  +G
Sbjct: 36  LARYTPNK--GVTGDPLLTLFVARLNLQTKEEKLKEVFSRYGDIRRLRLVRDLVTGFSKG 93

Query: 145 YAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPR 189
           YAFIEY+ ER +  AY+ ADG  ID   + VD E  RT+KGW+PR
Sbjct: 94  YAFIEYKDERSLLKAYRDADGLVIDQHEIFVDYELERTLKGWIPR 138

Bos taurus (taxid: 9913)

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	363
193657247	397	PREDICTED: u1 small nuclear ribonucleopr	0.922	0.843	0.622	2e-97
156547263	402	PREDICTED: U1 small nuclear ribonucleopr	0.581	0.524	0.881	3e-90
91078908	408	PREDICTED: similar to AGAP006755-PA isof	0.578	0.514	0.895	4e-90
427788187	449	Putative u1 small nuclear ribonucleoprot	0.608	0.492	0.833	3e-89
193662169	414	PREDICTED: u1 small nuclear ribonucleopr	0.581	0.509	0.867	8e-89
380019745	409	PREDICTED: U1 small nuclear ribonucleopr	0.581	0.515	0.872	2e-87
383866115	410	PREDICTED: U1 small nuclear ribonucleopr	0.581	0.514	0.872	2e-87
307173080	409	U1 small nuclear ribonucleoprotein 70 kD	0.581	0.515	0.857	5e-87
340715914	409	PREDICTED: u1 small nuclear ribonucleopr	0.581	0.515	0.867	7e-87
242003896	309	U1 small nuclear ribonucleoprotein 70 kD	0.581	0.682	0.862	9e-87

>gi|193657247|ref|XP_001947021.1| PREDICTED: u1 small nuclear ribonucleoprotein 70 kDa-like [Acyrthosiphon pisum]

 Score =  362 bits (929), Expect = 2e-97,   Method: Compositional matrix adjust.
 Identities = 234/376 (62%), Positives = 279/376 (74%), Gaps = 41/376 (10%)

Query: 1   MTQFLPPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFEDPKDTPPPTRVE 60
           MTQ+LP NLL LFAPRDP+PYLPPV KL HEKK  GYSG+ +F++ FEDPKDTPPPT +E
Sbjct: 1   MTQYLPHNLLTLFAPRDPIPYLPPVSKLSHEKKNRGYSGVGSFMDLFEDPKDTPPPTTIE 60

Query: 61  TREERLERRRRERAEQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRR 120
           T+E++LERRRRE+AEQVAYKLEQEIA W+P+S  NA  DPFKTLF+AR+NYDTSESKLRR
Sbjct: 61  TKEDKLERRRREKAEQVAYKLEQEIAAWNPHSDANAVTDPFKTLFVARINYDTSESKLRR 120

Query: 121 EFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS 180
           EFE+YG IKKIV+  NK+ GKPRGYAFIEYE+ERDM+SAYK+ADGKKIDGRRVLVDVER+
Sbjct: 121 EFELYGLIKKIVVTRNKIDGKPRGYAFIEYENERDMYSAYKYADGKKIDGRRVLVDVERA 180

Query: 181 RTVKGWLPRRLGGGLGGTRRGGPDVNLKHSGREDNERERERYRLERERELAGGPPRARSG 240
           RTVKGWLPRRLGGGLGGTRRGGP+VNL HSGREDNERERERY        A     + S 
Sbjct: 181 RTVKGWLPRRLGGGLGGTRRGGPEVNLIHSGREDNERERERY--------ARKMLISYSR 232

Query: 241 SNDRERERE-------------RRRSRSRERKRRTSRSRSRDRRRRRSRER----IRDDD 283
           + +R RER+             R RSR  ERK   S+S SR     RSR+R    +  D+
Sbjct: 233 TTERNRERDYYDRDGDREREPRRPRSRDHERKHHCSKSGSRKLHICRSRDRGPRDVEYDE 292

Query: 284 IEEVEFRPKDRSDRDRDRDRKRRRERENSEDRNERKRDRKERRKER-----------ERN 332
           +EEV         RD+D DRKR+R+R +S D  ER+++RKER   R           ++N
Sbjct: 293 VEEV----LGSKPRDKDPDRKRKRKRSHSRD-CERRKNRKERDHYRRDKSKDRCEKYDKN 347

Query: 333 NEEREEKVFIKQEPVD 348
           N ER++K+ IK+EPVD
Sbjct: 348 NSERDDKIHIKEEPVD 363

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|156547263|ref|XP_001602052.1| PREDICTED: U1 small nuclear ribonucleoprotein 70 kDa-like [Nasonia vitripennis]

 Score =  338 bits (866), Expect = 3e-90,   Method: Compositional matrix adjust.
 Identities = 186/211 (88%), Positives = 199/211 (94%)

Query: 1   MTQFLPPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFEDPKDTPPPTRVE 60
           MTQFLPPNLLALFAPRDP+PYLPPV KLPHEKK+ GY G+ AFLN FEDPKDTPPP RVE
Sbjct: 1   MTQFLPPNLLALFAPRDPIPYLPPVNKLPHEKKSAGYVGLGAFLNNFEDPKDTPPPVRVE 60

Query: 61  TREERLERRRRERAEQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRR 120
           TREERLERRRRER EQVAYKLEQEIA+WDP S PN T+DPFKTLF+AR+NYDTSESKLRR
Sbjct: 61  TREERLERRRRERNEQVAYKLEQEIAVWDPASIPNVTVDPFKTLFVARINYDTSESKLRR 120

Query: 121 EFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS 180
           EFEVYGP+KKIV++HN + GKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER+
Sbjct: 121 EFEVYGPVKKIVVIHNSINGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERA 180

Query: 181 RTVKGWLPRRLGGGLGGTRRGGPDVNLKHSG 211
           RTVKGWLPRRLGGGLGGTRRGGPDVN+KHSG
Sbjct: 181 RTVKGWLPRRLGGGLGGTRRGGPDVNIKHSG 211

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91078908|ref|XP_967303.1| PREDICTED: similar to AGAP006755-PA isoform 1 [Tribolium castaneum] gi|270003669|gb|EFA00117.1| hypothetical protein TcasGA2_TC002933 [Tribolium castaneum]

 Score =  337 bits (865), Expect = 4e-90,   Method: Compositional matrix adjust.
 Identities = 188/210 (89%), Positives = 201/210 (95%)

Query: 1   MTQFLPPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFEDPKDTPPPTRVE 60
           MTQFLPPNLLALFAPRDP+PYLPPV KLPHEKK+ GY G+ AFL EFEDPKDTPPPTRVE
Sbjct: 1   MTQFLPPNLLALFAPRDPIPYLPPVAKLPHEKKSRGYLGVGAFLKEFEDPKDTPPPTRVE 60

Query: 61  TREERLERRRRERAEQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRR 120
           TREER+ERRRRERAEQVAYKLEQEIA+WDPNS PN T+DPFKTLF+AR+NYDTSESKLRR
Sbjct: 61  TREERIERRRRERAEQVAYKLEQEIAVWDPNSAPNITVDPFKTLFVARINYDTSESKLRR 120

Query: 121 EFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS 180
           EFEVYGPIKKIV++HN V GKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER+
Sbjct: 121 EFEVYGPIKKIVLIHNSVNGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERA 180

Query: 181 RTVKGWLPRRLGGGLGGTRRGGPDVNLKHS 210
           RTVKGWLPRRLGGGLGGTRRGGP+VN+KHS
Sbjct: 181 RTVKGWLPRRLGGGLGGTRRGGPEVNIKHS 210

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|427788187|gb|JAA59545.1| Putative u1 small nuclear ribonucleoprotein 70 kda [Rhipicephalus pulchellus]

 Score =  334 bits (857), Expect = 3e-89,   Method: Compositional matrix adjust.
 Identities = 185/222 (83%), Positives = 206/222 (92%), Gaps = 1/222 (0%)

Query: 1   MTQFLPPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFEDPKDTPPPTRVE 60
           MTQ+LPPNLLALFAPRDP+PYLPP +KLPHEK    Y+G++ +LN FEDPKDTPPPTRVE
Sbjct: 1   MTQYLPPNLLALFAPRDPIPYLPPTDKLPHEKTQGTYTGVSQYLNLFEDPKDTPPPTRVE 60

Query: 61  TREERLERRRRERAEQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRR 120
           TREER+ER+RRE+AEQVAYKLEQ+IALWDP +  + T+DPFKTLF+AR+NYDTSESKLRR
Sbjct: 61  TREERIERKRREKAEQVAYKLEQDIALWDPYNNSSGTLDPFKTLFVARINYDTSESKLRR 120

Query: 121 EFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS 180
           EFEV+GPIKKIV+VHNK+TGKPRGYAF+EYEHERDMHSAYKHADGKKIDGRRVLVDVER 
Sbjct: 121 EFEVFGPIKKIVIVHNKITGKPRGYAFVEYEHERDMHSAYKHADGKKIDGRRVLVDVERG 180

Query: 181 RTVKGWLPRRLGGGLGGTRRGGPDVNLKHSGREDNERERERY 222
           RTVKGWLPRRLGGGLGGTRRGGPDVN KHSGRED+ R  ERY
Sbjct: 181 RTVKGWLPRRLGGGLGGTRRGGPDVNTKHSGREDS-RMDERY 221

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|193662169|ref|XP_001952270.1| PREDICTED: u1 small nuclear ribonucleoprotein 70 kDa-like [Acyrthosiphon pisum]

 Score =  333 bits (854), Expect = 8e-89,   Method: Compositional matrix adjust.
 Identities = 183/211 (86%), Positives = 201/211 (95%)

Query: 1   MTQFLPPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFEDPKDTPPPTRVE 60
           MTQFLPPNLLALFAPRDPVPYLPPV KLPHEKKT GY G+ +F++ FEDP+DTPPPT++E
Sbjct: 1   MTQFLPPNLLALFAPRDPVPYLPPVAKLPHEKKTRGYLGVGSFMDLFEDPEDTPPPTKIE 60

Query: 61  TREERLERRRRERAEQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRR 120
           TREERLERRRRE+AEQVAYKLEQEIALW+P+S  NAT DPFKTLF+AR+NYDTSESKLRR
Sbjct: 61  TREERLERRRREKAEQVAYKLEQEIALWEPHSVANATTDPFKTLFVARINYDTSESKLRR 120

Query: 121 EFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS 180
           EFE+YGPIKKIV+ HNK+ GKPRGYAFIEYE+ERDMHSAYKHADGKKIDGRRVLVDVER+
Sbjct: 121 EFELYGPIKKIVVTHNKIDGKPRGYAFIEYEYERDMHSAYKHADGKKIDGRRVLVDVERA 180

Query: 181 RTVKGWLPRRLGGGLGGTRRGGPDVNLKHSG 211
           RTVKGWLPRRLGGGLGGTRRGGP+VNLKHSG
Sbjct: 181 RTVKGWLPRRLGGGLGGTRRGGPEVNLKHSG 211

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380019745|ref|XP_003693763.1| PREDICTED: U1 small nuclear ribonucleoprotein 70 kDa-like [Apis florea]

 Score =  328 bits (842), Expect = 2e-87,   Method: Compositional matrix adjust.
 Identities = 184/211 (87%), Positives = 195/211 (92%)

Query: 1   MTQFLPPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFEDPKDTPPPTRVE 60
           MTQFLPPNLLALFAPRDP+PYLPPV KLPHEKK  GY G+  FL  FEDPKDTPPP RVE
Sbjct: 1   MTQFLPPNLLALFAPRDPIPYLPPVSKLPHEKKNGGYIGVGGFLKYFEDPKDTPPPVRVE 60

Query: 61  TREERLERRRRERAEQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRR 120
           TREERLERRRRERAEQVAYKLEQEIA+WDP   PN T DPFKTLF+AR+NYDTSESKLRR
Sbjct: 61  TREERLERRRRERAEQVAYKLEQEIAVWDPAGIPNVTADPFKTLFVARINYDTSESKLRR 120

Query: 121 EFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS 180
           EFEVYGP+KKIV++HN + GKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER+
Sbjct: 121 EFEVYGPVKKIVVIHNTINGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERA 180

Query: 181 RTVKGWLPRRLGGGLGGTRRGGPDVNLKHSG 211
           RTVKGWLPRRLGGGLGGTRRGGPDVN+KHSG
Sbjct: 181 RTVKGWLPRRLGGGLGGTRRGGPDVNIKHSG 211

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383866115|ref|XP_003708517.1| PREDICTED: U1 small nuclear ribonucleoprotein 70 kDa-like [Megachile rotundata]

 Score =  328 bits (842), Expect = 2e-87,   Method: Compositional matrix adjust.
 Identities = 184/211 (87%), Positives = 195/211 (92%)

Query: 1   MTQFLPPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFEDPKDTPPPTRVE 60
           MTQFLPPNLLALFAPRDP+PYLPPV KLPHEKK  GY G+  FL  FEDPKDTPPP RVE
Sbjct: 1   MTQFLPPNLLALFAPRDPIPYLPPVSKLPHEKKNGGYIGVGGFLKYFEDPKDTPPPVRVE 60

Query: 61  TREERLERRRRERAEQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRR 120
           TREERLERRRRERAEQVAYKLEQEIA+WDP   PN T DPFKTLF+AR+NYDTSESKLRR
Sbjct: 61  TREERLERRRRERAEQVAYKLEQEIAVWDPAGIPNVTADPFKTLFVARINYDTSESKLRR 120

Query: 121 EFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS 180
           EFEVYGP+KKIV++HN + GKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER+
Sbjct: 121 EFEVYGPVKKIVVIHNTINGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERA 180

Query: 181 RTVKGWLPRRLGGGLGGTRRGGPDVNLKHSG 211
           RTVKGWLPRRLGGGLGGTRRGGPDVN+KHSG
Sbjct: 181 RTVKGWLPRRLGGGLGGTRRGGPDVNIKHSG 211

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307173080|gb|EFN64210.1| U1 small nuclear ribonucleoprotein 70 kDa [Camponotus floridanus]

 Score =  327 bits (839), Expect = 5e-87,   Method: Compositional matrix adjust.
 Identities = 181/211 (85%), Positives = 193/211 (91%)

Query: 1   MTQFLPPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFEDPKDTPPPTRVE 60
           MTQFLPPNLLALFAPRDP+PYLPP  KLPHEKK  GY G+  FL  FEDPKDTPPP RVE
Sbjct: 1   MTQFLPPNLLALFAPRDPIPYLPPASKLPHEKKNSGYIGVGGFLKYFEDPKDTPPPVRVE 60

Query: 61  TREERLERRRRERAEQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRR 120
           TREERLERRRRERAEQVAYKLEQEIA+WDP    N T DPFKTLF+AR+NYDTSESKLRR
Sbjct: 61  TREERLERRRRERAEQVAYKLEQEIAVWDPAGISNVTADPFKTLFVARINYDTSESKLRR 120

Query: 121 EFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS 180
           EFEVYGP+KKIV++HN + GKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER+
Sbjct: 121 EFEVYGPVKKIVVIHNTINGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERA 180

Query: 181 RTVKGWLPRRLGGGLGGTRRGGPDVNLKHSG 211
           RTVKGWLPR+LGGGLGGTRRGGPDVN+KHSG
Sbjct: 181 RTVKGWLPRKLGGGLGGTRRGGPDVNIKHSG 211

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340715914|ref|XP_003396452.1| PREDICTED: u1 small nuclear ribonucleoprotein 70 kDa-like [Bombus terrestris] gi|350396793|ref|XP_003484667.1| PREDICTED: U1 small nuclear ribonucleoprotein 70 kDa-like [Bombus impatiens]

 Score =  327 bits (837), Expect = 7e-87,   Method: Compositional matrix adjust.
 Identities = 183/211 (86%), Positives = 195/211 (92%)

Query: 1   MTQFLPPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFEDPKDTPPPTRVE 60
           MTQFLPPNLLALFAPRDP+PYLPPV KLPHEKK  GY G+  FL  FE+PKDTPPP RVE
Sbjct: 1   MTQFLPPNLLALFAPRDPIPYLPPVSKLPHEKKNGGYIGVGGFLKYFEEPKDTPPPVRVE 60

Query: 61  TREERLERRRRERAEQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRR 120
           TREERLERRRRERAEQVAYKLEQEIA+WDP   PN T DPFKTLF+AR+NYDTSESKLRR
Sbjct: 61  TREERLERRRRERAEQVAYKLEQEIAVWDPAGIPNVTADPFKTLFVARINYDTSESKLRR 120

Query: 121 EFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS 180
           EFEVYGP+KKIV++HN + GKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER+
Sbjct: 121 EFEVYGPVKKIVVIHNTINGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERA 180

Query: 181 RTVKGWLPRRLGGGLGGTRRGGPDVNLKHSG 211
           RTVKGWLPRRLGGGLGGTRRGGPDVN+KHSG
Sbjct: 181 RTVKGWLPRRLGGGLGGTRRGGPDVNIKHSG 211

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242003896|ref|XP_002422903.1| U1 small nuclear ribonucleoprotein 70 kDa, putative [Pediculus humanus corporis] gi|212505785|gb|EEB10165.1| U1 small nuclear ribonucleoprotein 70 kDa, putative [Pediculus humanus corporis]

 Score =  326 bits (836), Expect = 9e-87,   Method: Compositional matrix adjust.
 Identities = 182/211 (86%), Positives = 197/211 (93%)

Query: 1   MTQFLPPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFEDPKDTPPPTRVE 60
           MTQFLPPNLLALFAPRDP+P+LPP +KLPHEKK  GY G+ AF+  FEDPKDTPPPTRVE
Sbjct: 1   MTQFLPPNLLALFAPRDPIPFLPPPDKLPHEKKNRGYQGVGAFIKYFEDPKDTPPPTRVE 60

Query: 61  TREERLERRRRERAEQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRR 120
           TR+ERLERRRRERAEQVAYKLEQEIA+WDP++ P AT DPFKTLF+AR+NYDTSE KLRR
Sbjct: 61  TRDERLERRRRERAEQVAYKLEQEIAVWDPHNIPIATGDPFKTLFVARINYDTSEFKLRR 120

Query: 121 EFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS 180
           EFEVYGPIKKIV+ HN + GKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER+
Sbjct: 121 EFEVYGPIKKIVVSHNTINGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERA 180

Query: 181 RTVKGWLPRRLGGGLGGTRRGGPDVNLKHSG 211
           RTVKGWLPRRLGGGLGGTRRGGPDVN+KHSG
Sbjct: 181 RTVKGWLPRRLGGGLGGTRRGGPDVNIKHSG 211

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

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	363
FB|FBgn0016978	448	snRNP-U1-70K "small ribonucleo	0.581	0.470	0.582	2.6e-63
UNIPROTKB|Q1RMR2	439	SNRNP70 "U1 small nuclear ribo	0.581	0.480	0.556	3.6e-57
UNIPROTKB|E2QRU8	386	SNRNP70 "Uncharacterized prote	0.581	0.546	0.556	3.6e-57
UNIPROTKB|F6V5G7	439	SNRNP70 "Uncharacterized prote	0.581	0.480	0.556	3.6e-57
UNIPROTKB|P08621	437	SNRNP70 "U1 small nuclear ribo	0.581	0.482	0.556	3.6e-57
UNIPROTKB|I3LNE5	452	SNRNP70 "Uncharacterized prote	0.581	0.466	0.556	3.6e-57
MGI|MGI:98341	448	Snrnp70 "small nuclear ribonuc	0.581	0.470	0.556	3.6e-57
UNIPROTKB|Q66II8	471	snrnp70 "U1 small nuclear ribo	0.581	0.447	0.556	1.6e-56
ZFIN|ZDB-GENE-040825-2	495	snrnp70 "small nuclear ribonuc	0.581	0.426	0.547	6.1e-55
UNIPROTKB|P09406	471	snrnp70 "U1 small nuclear ribo	0.581	0.447	0.544	9.9e-55

FB|FBgn0016978 snRNP-U1-70K "small ribonucleoprotein particle U1 subunit 70K" [Drosophila melanogaster (taxid:7227)]

 Score = 646 (232.5 bits), Expect = 2.6e-63, P = 2.6e-63
 Identities = 123/211 (58%), Positives = 145/211 (68%)

Query:     1 MTQXXXXXXXXXXXXRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFEDPKDXXXXXXXX 60
             MTQ            R+P+P++PPV+KLPHEKK+ GY G+A F+ +FEDPKD        
Sbjct:     1 MTQYLPPNLLALFAAREPIPFMPPVDKLPHEKKSRGYLGVAKFMADFEDPKDTPLPKTVE 60

Query:    61 XXXXXXXXXXXXXXXQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRR 120
                            QVAYKLE+EIALWDP    NAT DPF+TLFIAR+NYDTSESKLRR
Sbjct:    61 TRQERLERRRREKAEQVAYKLEREIALWDPTEIKNATEDPFRTLFIARINYDTSESKLRR 120

Query:   121 EFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS 180
             EFE YGPIKKIV++H++ +GKP+GYAFIEYEHERDMH+AYKHADGKKID +RVLVDVER+
Sbjct:   121 EFEFYGPIKKIVLIHDQESGKPKGYAFIEYEHERDMHAAYKHADGKKIDSKRVLVDVERA 180

Query:   181 RTVKXXXXXXXXXXXXXXXXXXPDVNLKHSG 211
             RTVK                   DVN+KHSG
Sbjct:   181 RTVKGWLPRRLGGGLGGTRRGGNDVNIKHSG 211

GO:0005692 "U11 snRNP" evidence=ISS

GO:0030532 "small nuclear ribonucleoprotein complex" evidence=ISS

GO:0030619 "U1 snRNA binding" evidence=NAS

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

GO:0003729 "mRNA binding" evidence=ISS;IDA

GO:0005685 "U1 snRNP" evidence=ISS

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

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=IC

GO:0005515 "protein binding" evidence=IPI

GO:0007052 "mitotic spindle organization" evidence=IMP

GO:0071011 "precatalytic spliceosome" evidence=IDA

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

GO:0022008 "neurogenesis" evidence=IMP

UNIPROTKB|Q1RMR2 SNRNP70 "U1 small nuclear ribonucleoprotein 70 kDa" [Bos taurus (taxid:9913)]

 Score = 588 (212.0 bits), Expect = 3.6e-57, P = 3.6e-57
 Identities = 118/212 (55%), Positives = 138/212 (65%)

Query:     1 MTQXXXXXXXXXXXXRDPVPYLPPVEKLPHEKK-THGYSGIAAFLNEFEDPKDXXXXXXX 59
             MTQ            RDP+PYLPP+EKLPHEK     Y GIA ++ EFEDP+D       
Sbjct:     1 MTQFLPPNLLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRDAPPPTRA 60

Query:    60 XXXXXXXXXXXXXXXXQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLR 119
                             +   ++E E+ +WDP++ PNA  D FKTLF+ARVNYDT+ESKLR
Sbjct:    61 ETREERMERKRREKIERRQQEVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLR 120

Query:   120 REFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 179
             REFEVYGPIK+I MV++K +GKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER
Sbjct:   121 REFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 180

Query:   180 SRTVKXXXXXXXXXXXXXXXXXXPDVNLKHSG 211
              RTVK                   DVN++HSG
Sbjct:   181 GRTVKGWRPRRLGGGLGGTRRGGADVNIRHSG 212

GO:0043484 "regulation of RNA splicing" evidence=ISS

GO:0005681 "spliceosomal complex" evidence=ISS

GO:0003723 "RNA binding" evidence=ISS

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

GO:0016607 "nuclear speck" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|E2QRU8 SNRNP70 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 588 (212.0 bits), Expect = 3.6e-57, P = 3.6e-57
 Identities = 118/212 (55%), Positives = 138/212 (65%)

Query:     1 MTQXXXXXXXXXXXXRDPVPYLPPVEKLPHEKK-THGYSGIAAFLNEFEDPKDXXXXXXX 59
             MTQ            RDP+PYLPP+EKLPHEK     Y GIA ++ EFEDP+D       
Sbjct:     1 MTQFLPPNLLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRDAPPPTRA 60

Query:    60 XXXXXXXXXXXXXXXXQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLR 119
                             +   ++E E+ +WDP++ PNA  D FKTLF+ARVNYDT+ESKLR
Sbjct:    61 ETREERMERKRREKIERRQQEVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLR 120

Query:   120 REFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 179
             REFEVYGPIK+I MV++K +GKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER
Sbjct:   121 REFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 180

Query:   180 SRTVKXXXXXXXXXXXXXXXXXXPDVNLKHSG 211
              RTVK                   DVN++HSG
Sbjct:   181 GRTVKGWRPRRLGGGLGGTRRGGADVNIRHSG 212

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|F6V5G7 SNRNP70 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 588 (212.0 bits), Expect = 3.6e-57, P = 3.6e-57
 Identities = 118/212 (55%), Positives = 138/212 (65%)

Query:     1 MTQXXXXXXXXXXXXRDPVPYLPPVEKLPHEKK-THGYSGIAAFLNEFEDPKDXXXXXXX 59
             MTQ            RDP+PYLPP+EKLPHEK     Y GIA ++ EFEDP+D       
Sbjct:     1 MTQFLPPNLLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRDAPPPTRA 60

Query:    60 XXXXXXXXXXXXXXXXQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLR 119
                             +   ++E E+ +WDP++ PNA  D FKTLF+ARVNYDT+ESKLR
Sbjct:    61 ETREERMERKRREKIERRQQEVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLR 120

Query:   120 REFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 179
             REFEVYGPIK+I MV++K +GKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER
Sbjct:   121 REFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 180

Query:   180 SRTVKXXXXXXXXXXXXXXXXXXPDVNLKHSG 211
              RTVK                   DVN++HSG
Sbjct:   181 GRTVKGWRPRRLGGGLGGTRRGGADVNIRHSG 212

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|P08621 SNRNP70 "U1 small nuclear ribonucleoprotein 70 kDa" [Homo sapiens (taxid:9606)]

 Score = 588 (212.0 bits), Expect = 3.6e-57, P = 3.6e-57
 Identities = 118/212 (55%), Positives = 138/212 (65%)

Query:     1 MTQXXXXXXXXXXXXRDPVPYLPPVEKLPHEKK-THGYSGIAAFLNEFEDPKDXXXXXXX 59
             MTQ            RDP+PYLPP+EKLPHEK     Y GIA ++ EFEDP+D       
Sbjct:     1 MTQFLPPNLLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRDAPPPTRA 60

Query:    60 XXXXXXXXXXXXXXXXQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLR 119
                             +   ++E E+ +WDP++ PNA  D FKTLF+ARVNYDT+ESKLR
Sbjct:    61 ETREERMERKRREKIERRQQEVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLR 120

Query:   120 REFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 179
             REFEVYGPIK+I MV++K +GKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER
Sbjct:   121 REFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 180

Query:   180 SRTVKXXXXXXXXXXXXXXXXXXPDVNLKHSG 211
              RTVK                   DVN++HSG
Sbjct:   181 GRTVKGWRPRRLGGGLGGTRRGGADVNIRHSG 212

GO:0000166 "nucleotide binding" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0003723 "RNA binding" evidence=IMP

GO:0043484 "regulation of RNA splicing" evidence=IMP

GO:0005681 "spliceosomal complex" evidence=IDA

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

GO:0006397 "mRNA processing" evidence=TAS

GO:0005634 "nucleus" evidence=IDA

GO:0005654 "nucleoplasm" evidence=TAS

GO:0008380 "RNA splicing" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

UNIPROTKB|I3LNE5 SNRNP70 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 588 (212.0 bits), Expect = 3.6e-57, P = 3.6e-57
 Identities = 118/212 (55%), Positives = 138/212 (65%)

Query:     1 MTQXXXXXXXXXXXXRDPVPYLPPVEKLPHEKK-THGYSGIAAFLNEFEDPKDXXXXXXX 59
             MTQ            RDP+PYLPP+EKLPHEK     Y GIA ++ EFEDP+D       
Sbjct:     1 MTQFLPPNLLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRDAPPPTRA 60

Query:    60 XXXXXXXXXXXXXXXXQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLR 119
                             +   ++E E+ +WDP++ PNA  D FKTLF+ARVNYDT+ESKLR
Sbjct:    61 ETREERMERKRREKIERRQQEVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLR 120

Query:   120 REFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 179
             REFEVYGPIK+I MV++K +GKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER
Sbjct:   121 REFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 180

Query:   180 SRTVKXXXXXXXXXXXXXXXXXXPDVNLKHSG 211
              RTVK                   DVN++HSG
Sbjct:   181 GRTVKGWRPRRLGGGLGGTRRGGADVNIRHSG 212

GO:0043484 "regulation of RNA splicing" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

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

GO:0000166 "nucleotide binding" evidence=IEA

MGI|MGI:98341 Snrnp70 "small nuclear ribonucleoprotein 70 (U1)" [Mus musculus (taxid:10090)]

 Score = 588 (212.0 bits), Expect = 3.6e-57, P = 3.6e-57
 Identities = 118/212 (55%), Positives = 138/212 (65%)

Query:     1 MTQXXXXXXXXXXXXRDPVPYLPPVEKLPHEKK-THGYSGIAAFLNEFEDPKDXXXXXXX 59
             MTQ            RDP+PYLPP+EKLPHEK     Y GIA ++ EFEDP+D       
Sbjct:     1 MTQFLPPNLLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRDAPPPTRA 60

Query:    60 XXXXXXXXXXXXXXXXQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLR 119
                             +   ++E E+ +WDP++ PNA  D FKTLF+ARVNYDT+ESKLR
Sbjct:    61 ETREERMERKRREKIERRQQEVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLR 120

Query:   120 REFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 179
             REFEVYGPIK+I MV++K +GKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER
Sbjct:   121 REFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 180

Query:   180 SRTVKXXXXXXXXXXXXXXXXXXPDVNLKHSG 211
              RTVK                   DVN++HSG
Sbjct:   181 GRTVKGWRPRRLGGGLGGTRRGGADVNIRHSG 212

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISO

GO:0005634 "nucleus" evidence=ISS

GO:0005681 "spliceosomal complex" evidence=ISO

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0043484 "regulation of RNA splicing" evidence=ISO

UNIPROTKB|Q66II8 snrnp70 "U1 small nuclear ribonucleoprotein 70 kDa" [Xenopus (Silurana) tropicalis (taxid:8364)]

 Score = 582 (209.9 bits), Expect = 1.6e-56, P = 1.6e-56
 Identities = 118/212 (55%), Positives = 136/212 (64%)

Query:     1 MTQXXXXXXXXXXXXRDPVPYLPPVEKLPHEKK-THGYSGIAAFLNEFEDPKDXXXXXXX 59
             MTQ            RDPVPYLPP++KLPHEK     Y GIA ++ EFEDP+D       
Sbjct:     1 MTQFLPPNLLALFAPRDPVPYLPPLDKLPHEKHHNQPYCGIAPYIREFEDPRDAPPPTRA 60

Query:    60 XXXXXXXXXXXXXXXXQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLR 119
                             +    +E E+ +WDP++  NA  D FKTLF+ARVNYDT+ESKLR
Sbjct:    61 ETREERMERKRREKIERRQQDVENELKIWDPHNDQNAQGDAFKTLFVARVNYDTTESKLR 120

Query:   120 REFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 179
             REFEVYGPIK+I MV+NK +GKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER
Sbjct:   121 REFEVYGPIKRIHMVYNKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 180

Query:   180 SRTVKXXXXXXXXXXXXXXXXXXPDVNLKHSG 211
              RTVK                   DVN++HSG
Sbjct:   181 GRTVKGWRPRRLGGGLGGTRRGGADVNIRHSG 212

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

GO:0003723 "RNA binding" evidence=ISS

GO:0005681 "spliceosomal complex" evidence=ISS

GO:0043484 "regulation of RNA splicing" evidence=ISS

ZFIN|ZDB-GENE-040825-2 snrnp70 "small nuclear ribonucleoprotein 70 (U1)" [Danio rerio (taxid:7955)]

 Score = 567 (204.7 bits), Expect = 6.1e-55, P = 6.1e-55
 Identities = 116/212 (54%), Positives = 133/212 (62%)

Query:     1 MTQXXXXXXXXXXXXRDPVPYLPPVEKLPHEKK-THGYSGIAAFLNEFEDPKDXXXXXXX 59
             MTQ            RDP+P+LP + KLPHEK     Y GIA F+  FEDP+D       
Sbjct:     1 MTQFLPPNLLALFAPRDPIPFLPQLGKLPHEKHHNQPYCGIAPFIRHFEDPRDAPPPTRA 60

Query:    60 XXXXXXXXXXXXXXXXQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLR 119
                             +    +E E+ LWDP++  NA  D FKTLF+AR+NYDT+ESKLR
Sbjct:    61 ETREERLERKRREKMERRQVVVEGELKLWDPHNDANAQGDAFKTLFVARINYDTTESKLR 120

Query:   120 REFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 179
             REFEVYGPIK+I +V+NK TGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER
Sbjct:   121 REFEVYGPIKRIYIVYNKKTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 180

Query:   180 SRTVKXXXXXXXXXXXXXXXXXXPDVNLKHSG 211
              RTVK                   DVN+KHSG
Sbjct:   181 GRTVKGWRPRRLGGGLGGTRRGGADVNIKHSG 212

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0060218 "hematopoietic stem cell differentiation" evidence=IMP

GO:0030529 "ribonucleoprotein complex" evidence=IEA

UNIPROTKB|P09406 snrnp70 "U1 small nuclear ribonucleoprotein 70 kDa" [Xenopus laevis (taxid:8355)]

 Score = 565 (203.9 bits), Expect = 9.9e-55, P = 9.9e-55
 Identities = 117/215 (54%), Positives = 136/215 (63%)

Query:     1 MTQXXXXXXXXXXXXRDPVPYLPPVEKLPHEKK-THGYSGIAAFLNEFEDPKDXXXXXXX 59
             MTQ            RDPVPYLPP++KLPHEK     Y GIA ++ EFEDP+D       
Sbjct:     1 MTQFLPPNLLALFAPRDPVPYLPPLDKLPHEKHHNQPYCGIAPYIREFEDPRDAPPPTRA 60

Query:    60 XXXXXXXXXXXXXXXXQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLR 119
                             +    +E E+ +WDP++  NA  D FKTLF+ARVNYDT+ESKLR
Sbjct:    61 ETREERMERKRREKIERRQQDVENELKIWDPHNDQNAQGDAFKTLFVARVNYDTTESKLR 120

Query:   120 REFEVYGPIKKIVMVHNKVT---GKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD 176
             REFEVYGPIK+I +V+NK +   GKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD
Sbjct:   121 REFEVYGPIKRIHIVYNKGSEGSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD 180

Query:   177 VERSRTVKXXXXXXXXXXXXXXXXXXPDVNLKHSG 211
             VER RTVK                   DVN++HSG
Sbjct:   181 VERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSG 215

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

GO:0003723 "RNA binding" evidence=ISS

GO:0005681 "spliceosomal complex" evidence=ISS

GO:0043484 "regulation of RNA splicing" evidence=ISS

---

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)
Q66II8	RU17_XENTR	No assigned EC number	0.7660	0.5977	0.4607	yes	N/A
Q62376	RU17_MOUSE	No assigned EC number	0.7612	0.6088	0.4933	yes	N/A
P08621	RU17_HUMAN	No assigned EC number	0.7612	0.6088	0.5057	yes	N/A
P17133	RU17_DROME	No assigned EC number	0.8009	0.5812	0.4709	yes	N/A
Q42404	RU17_ARATH	No assigned EC number	0.4926	0.7107	0.6042	yes	N/A
Q1RMR2	RU17_BOVIN	No assigned EC number	0.7612	0.6088	0.5034	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	363
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	4e-51
pfam12220	94	pfam12220, U1snRNP70_N, U1 small nuclear ribonucle	9e-35
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	1e-32
smart00360	73	smart00360, RRM, RNA recognition motif	4e-20
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	8e-17
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-16
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	9e-14
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	1e-13
PRK12678	672	PRK12678, PRK12678, transcription termination fact	2e-13
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	3e-13
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	9e-13
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	2e-12
PRK12678	672	PRK12678, PRK12678, transcription termination fact	1e-11
PRK12678	672	PRK12678, PRK12678, transcription termination fact	1e-11
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	1e-11
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	2e-11
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	3e-11
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	4e-11
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	5e-11
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	1e-10
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	1e-10
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	2e-10
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	2e-10
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	2e-10
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	2e-10
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	3e-10
PRK12678	672	PRK12678, PRK12678, transcription termination fact	5e-10
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	5e-10
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	6e-10
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	7e-10
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	8e-10
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	9e-10
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	9e-10
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	1e-09
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	1e-09
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	1e-09
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	2e-09
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	2e-09
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	2e-09
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	3e-09
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	4e-09
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	6e-09
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	6e-09
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	9e-09
PRK12678	672	PRK12678, PRK12678, transcription termination fact	1e-08
PRK12678	672	PRK12678, PRK12678, transcription termination fact	1e-08
PRK12678	672	PRK12678, PRK12678, transcription termination fact	1e-08
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	1e-08
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	2e-08
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	3e-08
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	4e-08
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	1e-07
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	2e-07
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	2e-07
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	2e-07
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	2e-07
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	2e-07
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	3e-07
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	3e-07
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	4e-07
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	4e-07
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	4e-07
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	6e-07
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	6e-07
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	7e-07
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	7e-07
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	8e-07
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	1e-06
PRK10811	1068	PRK10811, rne, ribonuclease E; Reviewed	1e-06
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	1e-06
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	2e-06
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	2e-06
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	2e-06
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	2e-06
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	2e-06
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	2e-06
cd12431	80	cd12431, RRM_ALKBH8, RNA recognition motif in alky	2e-06
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	3e-06
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	3e-06
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	3e-06
cd12646	77	cd12646, RRM_SRSF7, RNA recognition motif in verte	3e-06
cd12551	77	cd12551, RRM_II_PABPN1L, RNA recognition motif in	3e-06
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	4e-06
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	5e-06
cd12616	81	cd12616, RRM1_TIAR, RNA recognition motif 1 in nuc	5e-06
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	6e-06
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	7e-06
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	1e-05
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	1e-05
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	1e-05
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	2e-05
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	2e-05
cd12645	81	cd12645, RRM_SRSF3, RNA recognition motif in verte	2e-05
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	2e-05
cd12527	71	cd12527, RRM2_EAR1_like, RNA recognition motif 2 i	2e-05
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	2e-05
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	2e-05
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	2e-05
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	2e-05
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	2e-05
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	3e-05
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	3e-05
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	3e-05
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	3e-05
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	3e-05
cd12615	74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	3e-05
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	4e-05
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	4e-05
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	4e-05
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	4e-05
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	5e-05
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	6e-05
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	6e-05
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	7e-05
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	7e-05
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	7e-05
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	7e-05
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	7e-05
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	9e-05
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	1e-04
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	1e-04
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	1e-04
cd12550	76	cd12550, RRM_II_PABPN1, RNA recognition motif in t	1e-04
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	1e-04
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	1e-04
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	1e-04
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	1e-04
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	1e-04
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	2e-04
cd12267	77	cd12267, RRM_YRA1_MLO3, RNA recognition motif in y	2e-04
pfam02956	525	pfam02956, TT_ORF1, TT viral orf 1	2e-04
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	3e-04
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	3e-04
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	3e-04
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	3e-04
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	3e-04
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	4e-04
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	4e-04
cd12596	70	cd12596, RRM1_SRSF6, RNA recognition motif 1 in ve	4e-04
cd12584	80	cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in	5e-04
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	5e-04
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	7e-04
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	7e-04
cd12556	85	cd12556, RRM2_RBM15B, RNA recognition motif 2 in p	7e-04
cd12358	73	cd12358, RRM1_VICKZ, RNA recognition motif 1 in th	8e-04
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	8e-04
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	8e-04
pfam02956	525	pfam02956, TT_ORF1, TT viral orf 1	0.001
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	0.001
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	0.001
cd12482	79	cd12482, RRM1_hnRNPR, RNA recognition motif 1 in v	0.001
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	0.001
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	0.001
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	0.001
cd12364	81	cd12364, RRM_RDM1, RNA recognition motif of RAD52	0.001
pfam02724	583	pfam02724, CDC45, CDC45-like protein	0.001
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	0.002
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	0.002
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	0.002
cd12631	84	cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif	0.002
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	0.002
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	0.002
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	0.002
pfam02956	525	pfam02956, TT_ORF1, TT viral orf 1	0.003
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	0.003
cd12360	78	cd12360, RRM_cwf2, RNA recognition motif in yeast	0.003
cd12666	77	cd12666, RRM2_RAVER2, RNA recognition motif 2 in v	0.003
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	0.003
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	0.003
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	0.004
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	0.004
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	0.004
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	0.004
PRK00247	429	PRK00247, PRK00247, putative inner membrane protei	0.004
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	0.004
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	0.004

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

 Score =  165 bits (419), Expect = 4e-51
 Identities = 76/91 (83%), Positives = 85/91 (93%)

Query: 101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAY 160
           FKTLF+AR+NYDT+ESKLRREFE YGPIK+I +V +K TGKPRGYAFIE+EHERDM +AY
Sbjct: 1   FKTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAY 60

Query: 161 KHADGKKIDGRRVLVDVERSRTVKGWLPRRL 191
           K+ADGKKIDGRRVLVDVER RTVKGWLPRRL
Sbjct: 61  KYADGKKIDGRRVLVDVERGRTVKGWLPRRL 91

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|221466 pfam12220, U1snRNP70_N, U1 small nuclear ribonucleoprotein of 70kDa MW N terminal

 Score =  122 bits (309), Expect = 9e-35
 Identities = 52/94 (55%), Positives = 70/94 (74%)

Query: 1  MTQFLPPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFEDPKDTPPPTRVE 60
          MT  LPPNLLALFAPR P+PYLPP++K P ++KT+  +G+A +L+EF+D KD PPP   E
Sbjct: 1  MTDKLPPNLLALFAPRPPLPYLPPLDKAPEKRKTNPITGVAQYLSEFKDYKDEPPPEPTE 60

Query: 61 TREERLERRRRERAEQVAYKLEQEIALWDPNSFP 94
          T  E+ ER +RE+ E++  KLE+E+  WDPN  P
Sbjct: 61 TWLEKREREKREKKEKLEKKLEEELKEWDPNEDP 94

This domain is found in eukaryotes. This domain is about 90 amino acids in length. This domain is found associated with pfam00076. This domain is part of U1 snRNP, which is the pre-mRNA binding protein of the penta-snRNP spliceosome complex. It extends over a distance of 180 A from its RNA binding domain, wraps around the core domain of U1 snRNP consisting of the seven Sm proteins and finally contacts U1-C, which is crucial for 5'-splice-site recognition. Length = 94

>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 =  116 bits (294), Expect = 1e-32
 Identities = 47/93 (50%), Positives = 63/93 (67%)

Query: 99  DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHS 158
           DP+ TLF+ R++  T+E  LR  F  YG I+++ +V + VTG  +GYAF+EYEHERD   
Sbjct: 1   DPYLTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALR 60

Query: 159 AYKHADGKKIDGRRVLVDVERSRTVKGWLPRRL 191
           AY+ A    IDG  + VD ER RT+ GW+PRRL
Sbjct: 61  AYRDAHKLVIDGSEIFVDFERERTLPGWIPRRL 93

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|214636 smart00360, RRM, RNA recognition motif

 Score = 83.0 bits (206), Expect = 4e-20
 Identities = 29/73 (39%), Positives = 48/73 (65%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
           TLF+  +  DT+E +LR  F  +G ++ + +V +K TGK +G+AF+E+E E D   A + 
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 163 ADGKKIDGRRVLV 175
            +GK++DGR + V
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score = 73.8 bits (182), Expect = 8e-17
 Identities = 26/70 (37%), Positives = 43/70 (61%), Gaps = 1/70 (1%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           LF+  +  DT+E  L+  F  +GPI+ I +V    TG+ +G+AF+E+E E D   A +  
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIV-RDETGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 164 DGKKIDGRRV 173
           +GK++ GR +
Sbjct: 60  NGKELGGREL 69

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

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

 Score = 73.1 bits (180), Expect = 2e-16
 Identities = 27/73 (36%), Positives = 45/73 (61%), Gaps = 1/73 (1%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           LF+  +  DT+E  LR  F  +G I+ + +V +K  GK +G+AF+E+E   D   A +  
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDK-DGKSKGFAFVEFESPEDAEKALEAL 59

Query: 164 DGKKIDGRRVLVD 176
           +GK++DGR++ V 
Sbjct: 60  NGKELDGRKLKVS 72

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

>gnl|CDD|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 = 65.7 bits (161), Expect = 9e-14
 Identities = 20/77 (25%), Positives = 48/77 (62%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
            LF++ ++  T+E +L   F  +G +++++++ +  TG+ RG+ F+ +E   D  +A + 
Sbjct: 3   KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRD 62

Query: 163 ADGKKIDGRRVLVDVER 179
            +GK+++GR + V+  +
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|240681 cd12235, RRM_PPIL4, RNA recognition motif in peptidyl-prolyl cis-trans isomerase-like 4 (PPIase) and similar proteins

 Score = 65.0 bits (159), Expect = 1e-13
 Identities = 30/81 (37%), Positives = 43/81 (53%)

Query: 100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSA 159
           P   LF+ ++N  T++  L   F  +G IK   ++ +K TG    YAFIE+E + D   A
Sbjct: 2   PENVLFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEA 61

Query: 160 YKHADGKKIDGRRVLVDVERS 180
           Y   D   ID RR+ VD  +S
Sbjct: 62  YFKMDNVLIDDRRIHVDFSQS 82

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|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 70.7 bits (174), Expect = 2e-13
 Identities = 40/157 (25%), Positives = 56/157 (35%), Gaps = 8/157 (5%)

Query: 188 PRRLGGGLGGTRRGGPDVNLKHSGREDNERERERYRLERERELAGGPPRARSGSNDRERE 247
            R+ G G             + +  E+ +  R R   E  +  A    R R     R+ +
Sbjct: 142 ARKAGEGGEQPATEARADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGD 201

Query: 248 RERRRSRSRERKRRTSRSRS----RDRRRRRSRERIRDDDIEEVEFRPKDRSDRDRDRDR 303
              RR R  +  RR  R R     R  RRRR   R    D    +   +D  D +    R
Sbjct: 202 DRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGR 261

Query: 304 KRRRERENSEDRNERKRDRKERRKERERNNEEREEKV 340
           + RR R    DR+ R R   +   ERE    E +  V
Sbjct: 262 RGRRFR----DRDRRGRRGGDGGNEREPELREDDVLV 294

Length = 672

>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 = 63.8 bits (156), Expect = 3e-13
 Identities = 25/72 (34%), Positives = 41/72 (56%)

Query: 105 FIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHAD 164
           F+  + YD +E +L   F   GP+    +V ++ TGKP+GY F E+E      SA ++ +
Sbjct: 2   FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61

Query: 165 GKKIDGRRVLVD 176
           G + +GR + VD
Sbjct: 62  GYEFNGRALRVD 73

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

 Score = 62.6 bits (153), Expect = 9e-13
 Identities = 22/71 (30%), Positives = 41/71 (57%), Gaps = 1/71 (1%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
             +F+  + Y T++  LR+ F  +G I++ V++ ++ TGK RGY F+ ++ +     A K
Sbjct: 1   TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60

Query: 162 HADGKKIDGRR 172
             +   IDGR+
Sbjct: 61  DPN-PIIDGRK 70

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

 Score = 61.8 bits (151), Expect = 2e-12
 Identities = 24/72 (33%), Positives = 41/72 (56%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           L + ++  + ++  L+  F  YG +K + +  ++    PRGYA++E+E   D   A KH 
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 164 DGKKIDGRRVLV 175
           DG +IDG+ V V
Sbjct: 61  DGGQIDGQEVTV 72

This subfamily corresponds to the RRM of RNPS1 and its eukaryotic homologs. RNPS1, also termed RNA-binding protein prevalent during the S phase, or SR-related protein LDC2, was originally characterized as a general pre-mRNA splicing activator, which activates both constitutive and alternative splicing of pre-mRNA in vitro.It has been identified as a protein component of the splicing-dependent mRNP complex, or exon-exon junction complex (EJC), and is directly involved in mRNA surveillance. Furthermore, RNPS1 is a splicing regulator whose activator function is controlled in part by CK2 (casein kinase II) protein kinase phosphorylation. It can also function as a squamous-cell carcinoma antigen recognized by T cells-3 (SART3)-binding protein, and is involved in the regulation of mRNA splicing. RNPS1 contains an N-terminal serine-rich (S) domain, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and the C-terminal arginine/serine/proline-rich (RS/P) domain. . Length = 73

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 65.7 bits (161), Expect = 1e-11
 Identities = 32/129 (24%), Positives = 47/129 (36%), Gaps = 9/129 (6%)

Query: 210 SGREDNERERERYRLERERELAGGPPRARSGSNDRERERERRRSRSRERKRRTSRSRSRD 269
           +       E  R    R+    G  P   + ++  ER  E  R   R R  R  R    +
Sbjct: 127 ARERRERGEAARRGAARKAGEGGEQPATEARADAAERTEEEERDERRRRGDREDRQAEAE 186

Query: 270 RRRRRSRERIRDDDIEEVEFRPKDRSDRDRDRDRKRRRERENSEDRNERKRDRKERRKER 329
           R  R  RE    D          D  DR   R++  RRE     D  +R+  R+ R +  
Sbjct: 187 RGERGRREERGRDG---------DDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRD 237

Query: 330 ERNNEEREE 338
            R ++ RE+
Sbjct: 238 ARGDDNRED 246

Length = 672

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 65.7 bits (161), Expect = 1e-11
 Identities = 38/162 (23%), Positives = 49/162 (30%), Gaps = 10/162 (6%)

Query: 189 RRLGGGLGGTRRGGPDVNLKHSGREDNERERERYRLERERELAGGPPRARSGSNDRERER 248
           +       G             G E    E      ER  E      R R    DR+ E 
Sbjct: 126 QARERRERGEAARRGAARKAGEGGEQPATEARADAAERTEEEERDERRRRGDREDRQAEA 185

Query: 249 ERRRSRSRERKRRTSRSRSRDRRRRRSRERIRDDDIEEVEF--RPKDRSDRDRDRDRKRR 306
           ER     RE + R    R R  RR +   R      +  +   R + R  RD   D  R 
Sbjct: 186 ERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNRE 245

Query: 307 RERENSED--------RNERKRDRKERRKERERNNEEREEKV 340
              +   D        R  R RDR  R +       ERE ++
Sbjct: 246 DRGDRDGDDGEGRGGRRGRRFRDRDRRGRRGGDGGNEREPEL 287

Length = 672

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

 Score = 59.6 bits (145), Expect = 1e-11
 Identities = 24/79 (30%), Positives = 43/79 (54%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
           TLF+  + YDT++ +L   F   GPIK+  +V +K + K RG+ ++ +  E D   A + 
Sbjct: 1   TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEE 60

Query: 163 ADGKKIDGRRVLVDVERSR 181
               K  GR++ V+  + +
Sbjct: 61  KKKTKFGGRKIHVEFAKKK 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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 59.1 bits (144), Expect = 2e-11
 Identities = 23/70 (32%), Positives = 39/70 (55%), Gaps = 2/70 (2%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           L++  +    +E  LR  F  YG ++ + +V NK   +PRG+AF+E+    D  +A K  
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNK--DRPRGFAFVEFASPEDAEAALKKL 58

Query: 164 DGKKIDGRRV 173
           +G  +DGR +
Sbjct: 59  NGLVLDGRTL 68

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

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

 Score = 58.2 bits (141), Expect = 3e-11
 Identities = 23/75 (30%), Positives = 45/75 (60%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
           TLF+  +++   +  L+ EFE +G +    ++ ++ TG+ RG+ ++++E   D   A + 
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 163 ADGKKIDGRRVLVDV 177
            DGK++DGR + VD 
Sbjct: 61  MDGKELDGRPINVDF 75

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

 Score = 63.8 bits (155), Expect = 4e-11
 Identities = 32/112 (28%), Positives = 48/112 (42%), Gaps = 3/112 (2%)

Query: 244 RERERERRRSRSRERKRRTSRSRSRDRRRRRSRERIRDDDIEEVEFRPKDRSDRDRDRDR 303
           R+ E +R R +SR R R  S  R R R R RSR R R         R      R RDR R
Sbjct: 1   RDEEPDREREKSRGRDRDRSSERPRRRSRDRSRFRDRH---RRSRERSYREDSRPRDRRR 57

Query: 304 KRRRERENSEDRNERKRDRKERRKERERNNEEREEKVFIKQEPVDDYQEYDN 355
              R   +    + R+   + RR+ R   + E+  +    + P + +++ D 
Sbjct: 58  YDSRSPRSLRYSSVRRSRDRPRRRSRSVRSIEQHRRRLRDRSPSNQWRKDDK 109

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|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins

 Score = 57.9 bits (140), Expect = 5e-11
 Identities = 27/73 (36%), Positives = 46/73 (63%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           LFI  +++DT+E  L + F  YG I ++V+V ++ T + RG+ F+ +E+  D   A    
Sbjct: 3   LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62

Query: 164 DGKKIDGRRVLVD 176
           +GK +DGR++ VD
Sbjct: 63  NGKSVDGRQIRVD 75

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

 Score = 56.9 bits (138), Expect = 1e-10
 Identities = 27/65 (41%), Positives = 42/65 (64%)

Query: 112 DTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGR 171
            T+E  LR  F  YGPI+K+ +V+++ TG+ RG+ F+ +E   D   A +  +G +IDGR
Sbjct: 10  YTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEIDGR 69

Query: 172 RVLVD 176
           R+ VD
Sbjct: 70  RIRVD 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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 56.0 bits (136), Expect = 1e-10
 Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 5/60 (8%)

Query: 118 LRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV 177
           L + F  +G ++KI ++  K      G+AF+E+  E     A ++ +G    GR + VD 
Sbjct: 1   LYKLFSPFGNVEKIKLLKKK-----PGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDY 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|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 61.8 bits (150), Expect = 2e-10
 Identities = 34/125 (27%), Positives = 46/125 (36%), Gaps = 20/125 (16%)

Query: 212 REDNERERERYRLERERELAGGPPRARSGSNDRERERERRRSRSRERKRRTSRSRSRDRR 271
             + E+ R R R            R+      R R+R R R R R  + R+ R  SR R 
Sbjct: 6   DREREKSRGRDR-----------DRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRD 54

Query: 272 RRRSRERIRDDDIEEVEFRPKDRSDRDRDRDRKRRRERENSEDRNERKRDRKERRKERER 331
           RRR   R                S   R RDR RRR R        R+R R      + R
Sbjct: 55  RRRYDSRSPRSL---------RYSSVRRSRDRPRRRSRSVRSIEQHRRRLRDRSPSNQWR 105

Query: 332 NNEER 336
            ++++
Sbjct: 106 KDDKK 110

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|240758 cd12312, RRM_SRSF10_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins

 Score = 56.6 bits (137), Expect = 2e-10
 Identities = 23/75 (30%), Positives = 39/75 (52%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
            +L++  V   T    LRR F  YGPI  + +  +  T +PRG+A++++E  RD   A  
Sbjct: 1   TSLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALY 60

Query: 162 HADGKKIDGRRVLVD 176
           + D  +  GR + + 
Sbjct: 61  YLDRTRFLGREIEIQ 75

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

 Score = 57.7 bits (139), Expect = 2e-10
 Identities = 30/99 (30%), Positives = 52/99 (52%), Gaps = 3/99 (3%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           LFI  +++ T ++ LR  F  +G +    ++ ++ TG+ RG+ F+ +  E    +A    
Sbjct: 37  LFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEM 96

Query: 164 DGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGGTRRGG 202
           DGK+++GR + V+    R      PR  GGG G +  GG
Sbjct: 97  DGKELNGRHIRVNPANDRPSA---PRAYGGGGGYSGGGG 132

Length = 144

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

 Score = 55.9 bits (135), Expect = 2e-10
 Identities = 22/74 (29%), Positives = 44/74 (59%), Gaps = 1/74 (1%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
             LF++ + +  ++ +L + F+ +G +K + +V N+ +GKP+G A++EYE+E     A  
Sbjct: 3   HKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNR-SGKPKGLAYVEYENESSASQAVL 61

Query: 162 HADGKKIDGRRVLV 175
             DG +I  + + V
Sbjct: 62  KMDGTEIKEKTISV 75

This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 81

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

 Score = 55.9 bits (135), Expect = 3e-10
 Identities = 21/68 (30%), Positives = 36/68 (52%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           LF+  + Y   E  L + F  +G + ++ +  +K +GK +G+A++ +    D   AYK  
Sbjct: 5   LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKEL 64

Query: 164 DGKKIDGR 171
           DGK   GR
Sbjct: 65  DGKVFQGR 72

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|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 60.7 bits (148), Expect = 5e-10
 Identities = 25/124 (20%), Positives = 40/124 (32%)

Query: 216 ERERERYRLERERELAGGPPRARSGSNDRERERERRRSRSRERKRRTSRSRSRDRRRRRS 275
           E              A   P A      RER    RR  +R+      +  +  R     
Sbjct: 103 EAAPAARAAAAAAAEAASAPEAAQARERRERGEAARRGAARKAGEGGEQPATEARADAAE 162

Query: 276 RERIRDDDIEEVEFRPKDRSDRDRDRDRKRRRERENSEDRNERKRDRKERRKERERNNEE 335
           R    + D        +DR       +R RR ER    D  +R+  R++  +  ER   +
Sbjct: 163 RTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRD 222

Query: 336 REEK 339
             ++
Sbjct: 223 GGDR 226

Length = 672

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

 Score = 55.0 bits (133), Expect = 5e-10
 Identities = 25/70 (35%), Positives = 40/70 (57%), Gaps = 3/70 (4%)

Query: 109 VNY---DTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADG 165
           VNY   D ++ +LR  FE  GPI+   +V +++TG+  GY F++Y  E D   A    +G
Sbjct: 5   VNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNG 64

Query: 166 KKIDGRRVLV 175
            +I  +R+ V
Sbjct: 65  FEIRNKRLKV 74

This subfamily corresponds to the RRM1 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. This family also includes the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds to its own pre-mRNA and promotes female-specific alternative splicing. It contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 77

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

 Score = 54.7 bits (132), Expect = 6e-10
 Identities = 23/72 (31%), Positives = 41/72 (56%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           +++  ++++  E  +R+ F  +GPIK I M  + VT K +G+AF+EYE       A +  
Sbjct: 3   VYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQM 62

Query: 164 DGKKIDGRRVLV 175
           +G  + GR + V
Sbjct: 63  NGVMLGGRNIKV 74

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

 Score = 54.6 bits (132), Expect = 7e-10
 Identities = 21/56 (37%), Positives = 33/56 (58%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSA 159
           +++A V+ D SE  ++  FE +G IK   +  +  TGK +GY FIEYE+ +    A
Sbjct: 3   IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDA 58

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

 Score = 54.5 bits (132), Expect = 8e-10
 Identities = 21/77 (27%), Positives = 37/77 (48%), Gaps = 5/77 (6%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPR-----GYAFIEYEHERDM 156
            TLF+  +N+ T+E  L++ FE  G ++ + +   K    P      GY F+E++ +   
Sbjct: 1   TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAA 60

Query: 157 HSAYKHADGKKIDGRRV 173
             A K   G  +DG  +
Sbjct: 61  QKALKRLQGTVLDGHAL 77

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

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

 Score = 54.6 bits (132), Expect = 9e-10
 Identities = 26/73 (35%), Positives = 42/73 (57%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           ++I  + Y+ +E  +   F  YG I  I +V +K TGK +G+AF+ YE +R    A  + 
Sbjct: 12  IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71

Query: 164 DGKKIDGRRVLVD 176
           +G K+ GR + VD
Sbjct: 72  NGIKLLGRTIRVD 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|240835 cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 54.2 bits (131), Expect = 9e-10
 Identities = 20/75 (26%), Positives = 42/75 (56%), Gaps = 2/75 (2%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
            L +  +  + ++ + R     +G +++  +V+++ TG+ +GY F+EY   +      K+
Sbjct: 1   LLCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYA-SKASALKAKN 59

Query: 163 A-DGKKIDGRRVLVD 176
             DGK+I GR++ VD
Sbjct: 60  QLDGKQIGGRKLQVD 74

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

 Score = 54.2 bits (130), Expect = 1e-09
 Identities = 27/64 (42%), Positives = 43/64 (67%)

Query: 113 TSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRR 172
           T+E  LR  F  YGP+  + +V+++ TG+ RG+AF+ +E   D   A +HA+G ++DGRR
Sbjct: 11  TTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGMELDGRR 70

Query: 173 VLVD 176
           + VD
Sbjct: 71  IRVD 74

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|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 = 54.0 bits (130), Expect = 1e-09
 Identities = 24/73 (32%), Positives = 47/73 (64%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           +F+  + Y+ +E +L+  F   GP+    +V+++ TGKP+GY F EY+ +    SA ++ 
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 164 DGKKIDGRRVLVD 176
           +G +++GR++ VD
Sbjct: 61  NGYELNGRQLRVD 73

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

 Score = 53.7 bits (130), Expect = 1e-09
 Identities = 22/79 (27%), Positives = 42/79 (53%), Gaps = 2/79 (2%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
           T+ +  ++ D  E  LR  F  +GPI ++ +  +K TG+ RG+AF+ +    D   A + 
Sbjct: 1   TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60

Query: 163 ADGKKIDGRRVLVDVERSR 181
            +G   D   +++ VE ++
Sbjct: 61  LNGFGYD--NLILSVEWAK 77

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|240686 cd12240, RRM_NCBP2, RNA recognition motif found in nuclear cap-binding protein subunit 2 (CBP20) and similar proteins

 Score = 53.3 bits (129), Expect = 2e-09
 Identities = 24/73 (32%), Positives = 43/73 (58%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           L++  +++ T+E ++   F   G IK+I+M  ++ T  P G+ F+EY    D  +A K+ 
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60

Query: 164 DGKKIDGRRVLVD 176
           +G K+D R + VD
Sbjct: 61  NGTKLDDRIIRVD 73

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

 Score = 53.4 bits (129), Expect = 2e-09
 Identities = 24/82 (29%), Positives = 47/82 (57%), Gaps = 9/82 (10%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIK--KIVMVHNKVTGKPRGYAFIEYEHERD---- 155
           +T+FI  + +D +E +L+  F  +G +K  +IV   +K+TG  +G AF++++ +      
Sbjct: 1   RTVFIRNLPFDATEEELKELFSQFGEVKYARIVK--DKLTGHSKGTAFVKFKTKESAQKC 58

Query: 156 MHSAYKHADGK-KIDGRRVLVD 176
           + +A    D    +DGRR++V 
Sbjct: 59  LEAADNAEDSGLSLDGRRLIVT 80

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|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 = 53.1 bits (128), Expect = 2e-09
 Identities = 21/68 (30%), Positives = 36/68 (52%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           LF+  + + T+E +LR  FE +G I ++ +  +K T + +G+AF+ +        AY   
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 164 DGKKIDGR 171
           DG    GR
Sbjct: 62  DGSIFQGR 69

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

 Score = 52.8 bits (127), Expect = 3e-09
 Identities = 23/68 (33%), Positives = 36/68 (52%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           LFI  + Y  +E  L + F  YGP+ ++ +  +K+T KP+G+AF+ Y        A+   
Sbjct: 5   LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAEL 64

Query: 164 DGKKIDGR 171
           DG    GR
Sbjct: 65  DGTVFQGR 72

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

 Score = 52.6 bits (127), Expect = 4e-09
 Identities = 21/70 (30%), Positives = 37/70 (52%), Gaps = 1/70 (1%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           LFI  +++DT+E  LR  F  YG +   V++ + +TG+ RG+ F+ +     +      A
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLA-A 59

Query: 164 DGKKIDGRRV 173
               +DGR +
Sbjct: 60  KPHVLDGREI 69

This subfamily corresponds to the RRM1 in the hnRNP A subfamily which includes hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The hnRNP D subfamily includes hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus, plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this subfamily contain two putative RRMs and a glycine- and tyrosine-rich C-terminus. The family also contains DAZAP1 (Deleted in azoospermia-associated protein 1), RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins. They all harbor two RRMs. . Length = 72

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

 Score = 52.2 bits (126), Expect = 6e-09
 Identities = 19/77 (24%), Positives = 41/77 (53%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
            L++  + Y+ +E  L+  F  +G +    ++ ++ TG+ RG+ F+E E   + ++A + 
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 163 ADGKKIDGRRVLVDVER 179
            +G    GR + V+  R
Sbjct: 61  LNGTDFGGRTLTVNEAR 77

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

>gnl|CDD|240772 cd12326, RRM1_hnRNPA0, RNA recognition motif 1 found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 52.1 bits (125), Expect = 6e-09
 Identities = 25/80 (31%), Positives = 39/80 (48%), Gaps = 5/80 (6%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           LF+  +N  TS+S LRR F  YG + + V++ +  T + RG+ FI +    +   A + A
Sbjct: 5   LFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAME-A 63

Query: 164 DGKKIDGRRVLVDVERSRTV 183
               IDG      +E  R  
Sbjct: 64  QPHSIDG----NQIELKRAK 79

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

 Score = 51.3 bits (123), Expect = 9e-09
 Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 4/73 (5%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
           T++          S ++R FE  GP++K+ M+   V    + +AFI +E+      A + 
Sbjct: 1   TVYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTV----QPHAFITFENLEAAQLAIET 56

Query: 163 ADGKKIDGRRVLV 175
            +G  +DG  + V
Sbjct: 57  LNGASVDGNCIKV 69

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

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 56.5 bits (137), Expect = 1e-08
 Identities = 27/151 (17%), Positives = 39/151 (25%), Gaps = 7/151 (4%)

Query: 188 PRRLGGGLGGTRRGGPDVNLKHSGREDNERERERYRLERERELAGGPPRARSGSNDRERE 247
           P                     +     + E            A       +      RE
Sbjct: 73  PAAAARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQARERRE 132

Query: 248 RERRRSRSRERKRRTSRSRSRDRRRRRSRERIRDDDIEEVEFRPKDRSDRDRDRDRKRRR 307
           R     R   RK      +     R  + ER  ++          +R  R    DR+   
Sbjct: 133 RGEAARRGAARKAGEGGEQPATEARADAAERTEEE-------ERDERRRRGDREDRQAEA 185

Query: 308 ERENSEDRNERKRDRKERRKERERNNEEREE 338
           ER     R ER RD  +R +   R   +R E
Sbjct: 186 ERGERGRREERGRDGDDRDRRDRREQGDRRE 216

Length = 672

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 56.5 bits (137), Expect = 1e-08
 Identities = 28/143 (19%), Positives = 42/143 (29%), Gaps = 3/143 (2%)

Query: 198 TRRGGPDVNLKHSGREDNERERERYRLERERELAGGPPRARSGSNDRERERERRRSRSRE 257
            RR            +                 A     A + S     +   RR R   
Sbjct: 77  ARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQARERRERGEA 136

Query: 258 RKRRTSRSRSRDRRRRRSRERIRDDDIEEVEFRPKDRSDRDRDRDRKRRRERENSEDRNE 317
            +R  +R       +  +  R    +    E    +R  R    DR+   ER     R E
Sbjct: 137 ARRGAARKAGEGGEQPATEARADAAE-RTEEEERDERRRRGDREDRQAEAERGERGRREE 195

Query: 318 RKR--DRKERRKERERNNEEREE 338
           R R  D ++RR  RE+ +   E 
Sbjct: 196 RGRDGDDRDRRDRREQGDRREER 218

Length = 672

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 56.1 bits (136), Expect = 1e-08
 Identities = 17/114 (14%), Positives = 35/114 (30%), Gaps = 7/114 (6%)

Query: 225 ERERELAGGPPRARSGSNDRERERERRRSRSRERKRRTSRSRSRDRRRRRSRERIRDDDI 284
               +      R  +      R+      +     R  +  R+ +  R   R R   +D 
Sbjct: 122 PEAAQARERRERGEAARRGAARKAGEGGEQPATEARADAAERTEEEERDERRRRGDRED- 180

Query: 285 EEVEFRPKDRSDRDRDRDRKRRRERENSEDRNERKRDRKERRKERERNNEEREE 338
                  +  ++R     R+ R    +  DR +R+     R +   R+  +R  
Sbjct: 181 ------RQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRG 228

Length = 672

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

 Score = 51.4 bits (124), Expect = 1e-08
 Identities = 25/82 (30%), Positives = 40/82 (48%), Gaps = 5/82 (6%)

Query: 100 PFKTLFIARVNYDTSESKLRREFEVYG--PIKKIVMVHNKVTGKPRGYAFIEYEHERD-- 155
           P  TL +  ++  T+E  + +        PIK + ++ +K+TG  RG+AF+E+    D  
Sbjct: 1   PTNTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDAT 60

Query: 156 -MHSAYKHADGKKIDGRRVLVD 176
               A  + D   IDGR V V 
Sbjct: 61  QWMDALNNLDPFVIDGRVVRVS 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|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins

 Score = 50.8 bits (121), Expect = 2e-08
 Identities = 29/81 (35%), Positives = 49/81 (60%)

Query: 96  ATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERD 155
           A  DP   L +  ++  T+E  LR  F  YGPI  + +V+++ + + RG+AF+ +E+  D
Sbjct: 4   ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDD 63

Query: 156 MHSAYKHADGKKIDGRRVLVD 176
              A + A+G ++DGRR+ VD
Sbjct: 64  AKEAKERANGMELDGRRIRVD 84

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|240968 cd12524, RRM1_MEI2_like, RNA recognition motif 1 in plant Mei2-like proteins

 Score = 50.0 bits (120), Expect = 3e-08
 Identities = 19/74 (25%), Positives = 36/74 (48%), Gaps = 5/74 (6%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
           +TLF+  +N +  + +LR  FE +G I+ +         K RG+  + Y   R    A +
Sbjct: 2   RTLFVRNINSNVEDEELRALFEQFGDIRTLYT-----ACKHRGFIMVSYYDIRAARRAKR 56

Query: 162 HADGKKIDGRRVLV 175
              G ++ GR++ +
Sbjct: 57  ALQGTELGGRKLDI 70

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

 Score = 53.8 bits (128), Expect = 4e-08
 Identities = 43/210 (20%), Positives = 77/210 (36%), Gaps = 16/210 (7%)

Query: 99  DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHS 158
           +   TLF+  + YD +E  LR  F+ +GP+K++ +V ++ TGK RG+AF+E+E E     
Sbjct: 113 EENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEK 172

Query: 159 AYKHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGGTRRGGPDVNLKHSGREDNERE 218
           A +  +GK+++GR + V   +                   R      N   +        
Sbjct: 173 AIEELNGKELEGRPLRVQKAQPA--------------SQPRSELS--NNLDASFAKKLSR 216

Query: 219 RERYRLERERELAGGPPRARSGSNDRERERERRRSRSRERKRRTSRSRSRDRRRRRSRER 278
            +   LE+   L  G    ++   +     + R    R     +   +    R     E 
Sbjct: 217 GKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGNEA 276

Query: 279 IRDDDIEEVEFRPKDRSDRDRDRDRKRRRE 308
            +D          K    R   +   + R 
Sbjct: 277 SKDALESNSRGNKKKILGRGPRKAFSQPRL 306

Length = 306

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

 Score = 48.7 bits (116), Expect = 1e-07
 Identities = 24/79 (30%), Positives = 38/79 (48%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
           TLF+  + +  ++  L   F    PIK  V+V +  TG+ RGY F+ +    D   A   
Sbjct: 1   TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAK 60

Query: 163 ADGKKIDGRRVLVDVERSR 181
              KK+ GR + +D+   R
Sbjct: 61  LKNKKLHGRILRLDIAERR 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|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 52.6 bits (126), Expect = 2e-07
 Identities = 33/107 (30%), Positives = 43/107 (40%), Gaps = 13/107 (12%)

Query: 244 RERERERRRSRSRERKRRTSRSRSRDR---RRRRSRERIRDDDIEEVEFRPKDRSDRDRD 300
           R R+RER R R+  R+    R RSR R   R R  R R RD          + R  R R 
Sbjct: 1   RYRDRERGRLRNDTRRSDKGRERSRRRSRSRDRSRRRRDRD--------YYRGRRGRSRS 52

Query: 301 RDRKRRRERENSEDRNERKRDRKERRKERERNNEEREEK-VFIKQEP 346
           R    R  R   +    R   R  R  +      ER+++ VF+ Q  
Sbjct: 53  R-SPNRYYRPRGDRSYRRDDRRSGRNTKEPLTEAERDDRTVFVLQLA 98

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|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II polyadenylate-binding proteins

 Score = 47.7 bits (114), Expect = 2e-07
 Identities = 21/71 (29%), Positives = 43/71 (60%), Gaps = 1/71 (1%)

Query: 105 FIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHAD 164
           F+  V+Y T+  +L+  F+  G I +I ++ +K TG+P+G+A+IE+  +  + +A    +
Sbjct: 3   FVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENA-LLLN 61

Query: 165 GKKIDGRRVLV 175
             +  GR++ V
Sbjct: 62  ESEFRGRQIKV 72

This subfamily corresponds to the RRM of type II polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 2 (PABP-2 or PABPN1), embryonic polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and similar proteins. PABPs are highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. ePABP-2 is predominantly located in the cytoplasm and PABP-2 is located in the nucleus. In contrast to the type I PABPs containing four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), the type II PABPs contains a single highly-conserved RRM. This subfamily also includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C) gene encoding cytoplasmic mRNA-binding protein Rbp29 that binds preferentially to poly(A). Although not essential for cell viability, Rbp29 plays a role in modulating the expression of cytoplasmic mRNA. Like other type II PABPs, Rbp29 contains one RRM only. . Length = 73

>gnl|CDD|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 = 47.7 bits (114), Expect = 2e-07
 Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 6/75 (8%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
            TL+I  ++   +E  L+  FE YG I+ I M+       PRG A++  E  +D H A +
Sbjct: 3   TTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIP------PRGCAYVCMETRQDAHRALQ 56

Query: 162 HADGKKIDGRRVLVD 176
                K+ G+++ V 
Sbjct: 57  KLRNVKLAGKKIKVA 71

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|240770 cd12324, RRM_RBM8, RNA recognition motif in RNA-binding protein RBM8A, RBM8B nd similar proteins

 Score = 47.6 bits (114), Expect = 2e-07
 Identities = 22/73 (30%), Positives = 44/73 (60%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           +F+  V+ +  E  +  +F  +G IK + +  ++ TG  +GYA IEYE +++  +A +  
Sbjct: 9   IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 164 DGKKIDGRRVLVD 176
           +GK++ G+ + VD
Sbjct: 69  NGKELLGQTISVD 81

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

 Score = 47.3 bits (113), Expect = 2e-07
 Identities = 24/77 (31%), Positives = 41/77 (53%), Gaps = 3/77 (3%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKV---TGKPRGYAFIEYEHERDMHSA 159
            L+I  ++   +E  L + F  YG IKK   + +K     G+PRGY F+ +E + +   A
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 160 YKHADGKKIDGRRVLVD 176
            K  +GK   G++++V 
Sbjct: 61  LKSLNGKTALGKKLVVR 77

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|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 = 15/73 (20%), Positives = 34/73 (46%), Gaps = 1/73 (1%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
            LF+  + +     +L+  F  +G +K   +  +K TG  +GY F+ +     + +A + 
Sbjct: 1   KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK 60

Query: 163 ADGKKIDGRRVLV 175
                ++G ++ V
Sbjct: 61  -QKHILEGNKLQV 72

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

 Score = 52.0 bits (124), Expect = 3e-07
 Identities = 24/72 (33%), Positives = 43/72 (59%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           +++  ++++  E  +RR F+ +GPIK I M  +  TGK +G+AF+EYE       A +  
Sbjct: 110 VYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQM 169

Query: 164 DGKKIDGRRVLV 175
           +G+ + GR + V
Sbjct: 170 NGQMLGGRNIKV 181

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

 Score = 46.9 bits (112), Expect = 4e-07
 Identities = 21/66 (31%), Positives = 38/66 (57%), Gaps = 1/66 (1%)

Query: 111 YDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDG 170
           +  +E+ L++ F  +G + ++ +      GK +G+AF+++  + D   A K  +GKKI G
Sbjct: 9   FKCTEADLKKLFSPFGFVWEVTIPRKP-DGKKKGFAFVQFTSKADAEKAIKGVNGKKIKG 67

Query: 171 RRVLVD 176
           R V VD
Sbjct: 68  RPVAVD 73

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

 Score = 47.6 bits (113), Expect = 4e-07
 Identities = 17/61 (27%), Positives = 34/61 (55%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
           TLF+  + YD +E  L   F  +G ++  + V +K TG+ +G  F+ ++ +   ++  K+
Sbjct: 3   TLFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACLKN 62

Query: 163 A 163
           A
Sbjct: 63  A 63

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

 Score = 46.9 bits (112), Expect = 4e-07
 Identities = 18/69 (26%), Positives = 31/69 (44%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
           TL++  +     E+ +   F   G +  + ++ NK TGK  GY F+E+        A + 
Sbjct: 1   TLWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQS 60

Query: 163 ADGKKIDGR 171
            +GK I   
Sbjct: 61  LNGKPIPNT 69

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

 Score = 46.4 bits (110), Expect = 6e-07
 Identities = 20/74 (27%), Positives = 41/74 (55%), Gaps = 3/74 (4%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK-- 161
           +FI  +N++T++  LR  F  +G +    ++ +  TG+ RG+ F+ ++  + ++   K  
Sbjct: 1   MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKE 60

Query: 162 -HADGKKIDGRRVL 174
              DGK ID +R +
Sbjct: 61  HILDGKIIDPKRAI 74

This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition, steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway. It binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y. . Length = 76

>gnl|CDD|240846 cd12400, RRM_Nop6, RNA recognition motif in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and similar proteins

 Score = 46.2 bits (110), Expect = 6e-07
 Identities = 22/70 (31%), Positives = 35/70 (50%), Gaps = 4/70 (5%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK- 161
            LF+  + YDT+   L   F+  G    + ++ +K TGK +G AF+E++    M  A K 
Sbjct: 2   ILFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKL 61

Query: 162 ---HADGKKI 168
                 G+KI
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|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 46.1 bits (110), Expect = 7e-07
 Identities = 15/75 (20%), Positives = 36/75 (48%), Gaps = 4/75 (5%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVM---VHNKVTGKPRGYAFIEYEHERDMHSAY 160
           +++  +++   E  LR  F  +G ++ I +      K      G+AF+ ++      +A 
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62

Query: 161 KHADGKKIDGRRVLV 175
           +  +G ++ GR++ V
Sbjct: 63  Q-LNGTELGGRKISV 76

This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

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

 Score = 46.1 bits (110), Expect = 7e-07
 Identities = 25/69 (36%), Positives = 39/69 (56%), Gaps = 5/69 (7%)

Query: 112 DTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGR 171
             ++ +L  EFE YGP++ +      V   P G+AF+E+E  RD   A +  DG++I G 
Sbjct: 10  RATKRELEDEFEKYGPLRSVW-----VARNPPGFAFVEFEDPRDAEDAVRALDGRRICGN 64

Query: 172 RVLVDVERS 180
           RV V++ R 
Sbjct: 65  RVRVELSRG 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|240757 cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins

 Score = 45.7 bits (109), Expect = 8e-07
 Identities = 24/68 (35%), Positives = 39/68 (57%)

Query: 109 VNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKI 168
           + Y T+   LRR FE YG +  + +  ++ T + RG+AF+ +  +RD   A    DGK++
Sbjct: 6   LTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDGKEL 65

Query: 169 DGRRVLVD 176
           DGR + V 
Sbjct: 66  DGRELRVQ 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|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 45.3 bits (108), Expect = 1e-06
 Identities = 26/74 (35%), Positives = 43/74 (58%), Gaps = 2/74 (2%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
           T+F++ ++Y   E +LR+ F   G I  + +V N   GK +GYA++E+E+E  +  A K 
Sbjct: 1   TVFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYK-GKSKGYAYVEFENEESVQEALK- 58

Query: 163 ADGKKIDGRRVLVD 176
            D + I GR + V 
Sbjct: 59  LDRELIKGRPMFVS 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|236766 PRK10811, rne, ribonuclease E; Reviewed

 Score = 50.4 bits (121), Expect = 1e-06
 Identities = 29/125 (23%), Positives = 53/125 (42%), Gaps = 12/125 (9%)

Query: 234 PPRARSGSNDRERERERRRSRSRERKRRTSRSRSRDRRRRRSRERIRDDDIEEVEFRPKD 293
              A       ER+++RR+ R   R+ R  R  +RD R RR     R+++      R   
Sbjct: 590 EQPAPKAEAKPERQQDRRKPRQNNRRDRNERRDTRDNRTRREGRENREEN------RRNR 643

Query: 294 RSDRDRDRDRKRRRERENSEDRNERKRDRKERRKERE-RNNEER-----EEKVFIKQEPV 347
           R  + +  + +  ++ E +E    +   ++  R+ER+ R N+E+     E K    +E  
Sbjct: 644 RQAQQQTAETRESQQAEVTEKARTQDEQQQAPRRERQRRRNDEKRQAQQEAKALNVEEQS 703

Query: 348 DDYQE 352
               E
Sbjct: 704 VQETE 708

Length = 1068

>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 = 45.4 bits (108), Expect = 1e-06
 Identities = 20/71 (28%), Positives = 39/71 (54%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
           T++++ + +  + + L + F  YG + K+ +V +K T K +G AFI +    D H   K 
Sbjct: 3   TVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKA 62

Query: 163 ADGKKIDGRRV 173
            + K++ GR +
Sbjct: 63  LNNKELFGRTL 73

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

 Score = 49.5 bits (118), Expect = 2e-06
 Identities = 32/122 (26%), Positives = 43/122 (35%), Gaps = 21/122 (17%)

Query: 209 HSGREDNERERERYRLE---RERELAGGPPRARSGSNDRERERERRRSRSRERKRRTSRS 265
                 +ER R R R     R+R         R  S  R+R R   RS    R     RS
Sbjct: 15  RDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDSRSPRSLRYSSVRRS 74

Query: 266 RSRDRRRRRSRERIRDDDIEEVEFRPKDRSDRDRDRDRKRRRERENSEDRNERKRDRKER 325
           R R RRR RS   I                  ++ R R R R   N   ++++KR   + 
Sbjct: 75  RDRPRRRSRSVRSI------------------EQHRRRLRDRSPSNQWRKDDKKRSLWDI 116

Query: 326 RK 327
           + 
Sbjct: 117 KP 118

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

 Score = 45.3 bits (108), Expect = 2e-06
 Identities = 19/75 (25%), Positives = 38/75 (50%), Gaps = 1/75 (1%)

Query: 101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAY 160
           F  +++  +  D  + KL+  F  YG I     V     GK +G+ F+ +E+      A 
Sbjct: 1   FTNVYVKNLGEDMDDEKLKELFGKYGKITSAK-VMKDDEGKSKGFGFVNFENHEAAQKAV 59

Query: 161 KHADGKKIDGRRVLV 175
           +  +GK+++G+++ V
Sbjct: 60  EELNGKEVNGKKLYV 74

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|241003 cd12559, RRM_SRSF10, RNA recognition motif in serine/arginine-rich splicing factor 10 (SRSF10) and similar proteins

 Score = 45.3 bits (107), Expect = 2e-06
 Identities = 27/71 (38%), Positives = 42/71 (59%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
           +LF+  +  DT    LRREF  YGPI  + +  +  T +PRG+A++++E  RD   A  +
Sbjct: 2   SLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHN 61

Query: 163 ADGKKIDGRRV 173
            D K I GR++
Sbjct: 62  LDRKWICGRQI 72

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|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 45.0 bits (107), Expect = 2e-06
 Identities = 22/80 (27%), Positives = 38/80 (47%), Gaps = 5/80 (6%)

Query: 100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSA 159
           P   LFI       +E  LR  F  +G I+ I +V +K T + +G A++++        A
Sbjct: 2   PNSRLFIV-CGKSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARA 60

Query: 160 YKHADGKKIDGR----RVLV 175
            +  +GK + G     +VL+
Sbjct: 61  MEEMNGKCLGGDTKPLKVLI 80

This subfamily corresponds to the RRM1 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 81

>gnl|CDD|240677 cd12231, RRM2_U2AF65, RNA recognition motif 2 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 44.9 bits (107), Expect = 2e-06
 Identities = 16/48 (33%), Positives = 26/48 (54%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYE 151
           +FI  +    SE +++   E +G +K   +V +  TG  +GYAF EY 
Sbjct: 3   IFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYL 50

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

 Score = 44.8 bits (106), Expect = 2e-06
 Identities = 17/75 (22%), Positives = 37/75 (49%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
            ++I  + +   E +L++ F  +G +K + +  +K TG  + Y FI++ +      A K 
Sbjct: 1   VIYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKS 60

Query: 163 ADGKKIDGRRVLVDV 177
            +   + G+ + V V
Sbjct: 61  MNNYLLMGKVLQVHV 75

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

>gnl|CDD|240877 cd12431, RRM_ALKBH8, RNA recognition motif in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and similar proteins

 Score = 44.9 bits (107), Expect = 2e-06
 Identities = 20/56 (35%), Positives = 30/56 (53%), Gaps = 6/56 (10%)

Query: 114 SESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKID 169
           S  +L R FE YG ++ +VM      GKP  Y F+ Y    D  +AY   +GK+++
Sbjct: 16  SREELLRVFEKYGTVEDLVM----PPGKP--YCFVSYSSIEDAAAAYDALNGKELE 65

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

 Score = 48.4 bits (115), Expect = 3e-06
 Identities = 26/87 (29%), Positives = 35/87 (40%), Gaps = 2/87 (2%)

Query: 216 ERERERYRLERERELAGGPPRARSGSNDRERERERR-RSRSRERKRRTSRSRSRDRRRRR 274
           +RER R R    R    G  R+R  S  R+R R RR R   R R+ R+         R R
Sbjct: 4   DRERGRLR-NDTRRSDKGRERSRRRSRSRDRSRRRRDRDYYRGRRGRSRSRSPNRYYRPR 62

Query: 275 SRERIRDDDIEEVEFRPKDRSDRDRDR 301
                R DD        +  ++ +RD 
Sbjct: 63  GDRSYRRDDRRSGRNTKEPLTEAERDD 89

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

 Score = 44.2 bits (105), Expect = 3e-06
 Identities = 18/48 (37%), Positives = 30/48 (62%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYE 151
           LF+  +  D +E  LR  F  YG ++ + +V +K TGK RG+AF+ ++
Sbjct: 2   LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFD 49

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

 Score = 44.1 bits (105), Expect = 3e-06
 Identities = 19/69 (27%), Positives = 37/69 (53%), Gaps = 1/69 (1%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
            L ++ ++YD +E  L   F   G +KK+ + +++ +G+  G A + +E   D   A K 
Sbjct: 2   RLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDR-SGRSEGTADVVFEKREDAERAIKQ 60

Query: 163 ADGKKIDGR 171
            +G  +DG+
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|241090 cd12646, RRM_SRSF7, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 7 (SRSF7)

 Score = 44.2 bits (104), Expect = 3e-06
 Identities = 27/87 (31%), Positives = 44/87 (50%), Gaps = 11/87 (12%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           +++  +     + +L R F  YGP++ + +  N     P G+AF+E+E  RD   A +  
Sbjct: 2   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGL 56

Query: 164 DGKKIDGRRVLVDVERSRTVKGWLPRR 190
           DGK I G RV V++         +PRR
Sbjct: 57  DGKVICGSRVRVELSTG------MPRR 77

This subgroup corresponds to the RRM of SRSF7, also termed splicing factor 9G8, is a splicing regulatory serine/arginine (SR) protein that plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. SRSF7 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a CCHC-type zinc knuckle motif in its median region, and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 77

>gnl|CDD|240995 cd12551, RRM_II_PABPN1L, RNA recognition motif in vertebrate type II embryonic polyadenylate-binding protein 2 (ePABP-2)

 Score = 44.1 bits (104), Expect = 3e-06
 Identities = 23/78 (29%), Positives = 43/78 (55%), Gaps = 1/78 (1%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
           ++++  V+Y ++  +L   F   GPI ++ ++ +K +G P+GYA+IE+   RD   A   
Sbjct: 1   SVYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFA-TRDSVEAAVA 59

Query: 163 ADGKKIDGRRVLVDVERS 180
            D     GR + V  +R+
Sbjct: 60  LDESSFRGRVIKVLPKRT 77

This subgroup corresponds to the RRM of ePABP-2, also termed embryonic poly(A)-binding protein 2, or poly(A)-binding protein nuclear-like 1 (PABPN1L). ePABP-2 is a novel embryonic-specific cytoplasmic type II poly(A)-binding protein that is expressed during the early stages of vertebrate development and in adult ovarian tissue. It may play an important role in the poly(A) metabolism of stored mRNAs during early vertebrate development. ePABP-2 shows significant sequence similarity to the ubiquitously expressed nuclear polyadenylate-binding protein 2 (PABP-2 or PABPN1). Like PABP-2, ePABP-2 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, it possesses an acidic N-terminal domain predicted to form a coiled-coil and an arginine-rich C-terminal domain. . Length = 77

>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 = 4e-06
 Identities = 17/50 (34%), Positives = 31/50 (62%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHE 153
           +F+  ++ +T+E K+R  F  +G I +I +  +K T K RG+ FI ++ E
Sbjct: 2   IFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSE 51

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

 Score = 43.5 bits (103), Expect = 5e-06
 Identities = 26/72 (36%), Positives = 36/72 (50%), Gaps = 3/72 (4%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
           +TLFI  +   T+ S LR  FE +G I  I +   K  G P  YAFI+Y     +  A +
Sbjct: 3   RTLFIGNLEKTTTYSDLREAFERFGEIIDIDI--KKQGGNPA-YAFIQYADIASVVKAMR 59

Query: 162 HADGKKIDGRRV 173
             DG+ +   RV
Sbjct: 60  KMDGEYLGNNRV 71

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|241060 cd12616, RRM1_TIAR, RNA recognition motif 1 in nucleolysin TIAR and similar proteins

 Score = 44.0 bits (103), Expect = 5e-06
 Identities = 22/74 (29%), Positives = 38/74 (51%), Gaps = 2/74 (2%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
           TL++  ++ D +E  + + F   GP K   M+    +  P  Y F+E+   RD  +A   
Sbjct: 1   TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAAAALAA 58

Query: 163 ADGKKIDGRRVLVD 176
            +G+KI G+ V V+
Sbjct: 59  MNGRKILGKEVKVN 72

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

 Score = 47.8 bits (113), Expect = 6e-06
 Identities = 18/59 (30%), Positives = 30/59 (50%)

Query: 101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSA 159
           F  +++A V+ D SE+ ++  FE +G I K  +         +GY FIEY + +    A
Sbjct: 204 FNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEA 262

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|241095 cd12651, RRM2_SXL, RNA recognition motif 2 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 43.3 bits (102), Expect = 7e-06
 Identities = 21/68 (30%), Positives = 36/68 (52%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           L++  +    +E +LR+ FE YG I +  ++ +K TG PRG AF+ Y+   +  +A    
Sbjct: 3   LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSL 62

Query: 164 DGKKIDGR 171
           +G    G 
Sbjct: 63  NGTIPPGS 70

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

 Score = 43.4 bits (103), Expect = 1e-05
 Identities = 22/77 (28%), Positives = 36/77 (46%), Gaps = 6/77 (7%)

Query: 102 KTLFIARVNYD-TSESKLRREFEVYGPIK--KIVMVHNKVTGKPRGYAFIEYEHERDMHS 158
           + LF+ R+       S LR+ F   G     ++ +  N   G+PRG+AF+EY    D   
Sbjct: 3   RCLFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAPN---GQPRGFAFVEYATAEDAEE 59

Query: 159 AYKHADGKKIDGRRVLV 175
           A +  +G  + G  + V
Sbjct: 60  AQQALNGHSLQGSPIRV 76

This subfamily corresponds to the RRM3 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only. . Length = 92

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

 Score = 42.6 bits (101), Expect = 1e-05
 Identities = 16/51 (31%), Positives = 31/51 (60%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHE 153
            ++I  + +   E +LR+ F  +G + ++ +  +K TGK +GYAF+E+E  
Sbjct: 1   VVYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESP 51

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

 Score = 42.8 bits (101), Expect = 1e-05
 Identities = 20/75 (26%), Positives = 37/75 (49%), Gaps = 3/75 (4%)

Query: 109 VNY---DTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADG 165
           +NY     ++ + R  F   GP+K   +V +K TG   G+ F++Y+   D   A +  +G
Sbjct: 5   INYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLNG 64

Query: 166 KKIDGRRVLVDVERS 180
            ++  +R+ V   R 
Sbjct: 65  LQLQNKRIKVAYARP 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|241004 cd12560, RRM_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor 12 (SRSF12) and similar proteins

 Score = 42.3 bits (99), Expect = 2e-05
 Identities = 26/71 (36%), Positives = 41/71 (57%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
           +LF+  V   T    LRREF  YGPI  + +  +  T +PRG+A+I++E  RD   A  +
Sbjct: 2   SLFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYN 61

Query: 163 ADGKKIDGRRV 173
            + K + GR++
Sbjct: 62  LNRKWVCGRQI 72

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|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 = 41.9 bits (99), Expect = 2e-05
 Identities = 19/73 (26%), Positives = 39/73 (53%), Gaps = 2/73 (2%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKI-VMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
           LFI  +  + ++  L + F  +G +    V V +K TG+ + + F+ Y++     +A K 
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFV-DKNTGQSKCFGFVSYDNPESAQAAIKA 59

Query: 163 ADGKKIDGRRVLV 175
            +G ++ G+R+ V
Sbjct: 60  MNGFQVGGKRLKV 72

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

>gnl|CDD|241089 cd12645, RRM_SRSF3, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 3 (SRSF3)

 Score = 42.3 bits (99), Expect = 2e-05
 Identities = 22/74 (29%), Positives = 43/74 (58%), Gaps = 5/74 (6%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           +++  +  + ++++L R F  YGP++ + +  N     P G+AF+E+E  RD   A +  
Sbjct: 7   VYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVREL 61

Query: 164 DGKKIDGRRVLVDV 177
           DG+ + G RV V++
Sbjct: 62  DGRTLCGCRVRVEL 75

This subgroup corresponds to the RRM of SRSF3, also termed pre-mRNA-splicing factor SRp20, a splicing regulatory serine/arginine (SR) protein that modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation and tumor induction and maintenance. SRSF3 can shuttle between the nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 81

>gnl|CDD|241025 cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 42.0 bits (98), Expect = 2e-05
 Identities = 19/50 (38%), Positives = 30/50 (60%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYE 151
           K LF+  +  DT E  LR  FE YG I  I ++ ++ +GK RG+ F+ ++
Sbjct: 1   KKLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFD 50

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|240971 cd12527, RRM2_EAR1_like, RNA recognition motif 2 in terminal EAR1-like proteins

 Score = 41.7 bits (98), Expect = 2e-05
 Identities = 23/74 (31%), Positives = 39/74 (52%), Gaps = 5/74 (6%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
           TL I  ++   S   LR  F+VYG +K++     + T   R   F+E+   RD   A + 
Sbjct: 3   TLVIFNLDPTVSSETLRSIFQVYGDVKEL-----RETPCKREQRFVEFFDVRDAAKALRA 57

Query: 163 ADGKKIDGRRVLVD 176
            +GK+I G+ V+++
Sbjct: 58  MNGKEISGKPVVIE 71

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|241076 cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 42.0 bits (99), Expect = 2e-05
 Identities = 20/69 (28%), Positives = 33/69 (47%), Gaps = 1/69 (1%)

Query: 99  DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHS 158
           D  K LF+ ++  +  E  LR  FE +G I ++ ++ +K TG  +G AF+ Y        
Sbjct: 4   DAIK-LFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALK 62

Query: 159 AYKHADGKK 167
           A      +K
Sbjct: 63  AQSALHEQK 71

This subfamily corresponds to the RRM1 of CELF-3, CELF-4, CELF-5, CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In additiona to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 87

>gnl|CDD|241043 cd12599, RRM1_SF2_plant_like, RNA recognition motif 1 in plant pre-mRNA-splicing factor SF2 and similar proteins

 Score = 41.7 bits (98), Expect = 2e-05
 Identities = 27/75 (36%), Positives = 42/75 (56%), Gaps = 3/75 (4%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
           T+++  +  D  E ++   F  YGPI  I +   K+  +P GYAFIE+E  RD   A + 
Sbjct: 1   TVYVGNLPGDIREREVEDLFYKYGPIVDIDL---KLPPRPPGYAFIEFEDARDAEDAIRG 57

Query: 163 ADGKKIDGRRVLVDV 177
            DG   DG+R+ V++
Sbjct: 58  RDGYDFDGQRLRVEL 72

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|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 = 41.8 bits (99), Expect = 2e-05
 Identities = 18/65 (27%), Positives = 36/65 (55%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           LF+ ++    +E  +R  FE YG I+++ ++ +K TG+ +G AF+++    +   A +  
Sbjct: 2   LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEAL 61

Query: 164 DGKKI 168
            GK  
Sbjct: 62  HGKVT 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|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 = 41.5 bits (98), Expect = 2e-05
 Identities = 17/75 (22%), Positives = 39/75 (52%), Gaps = 4/75 (5%)

Query: 104 LFIARVNYDTSESKLR---REFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAY 160
           L++  + + T++  L     E  V   +K I    +K  GK +G+A++E+  E    +  
Sbjct: 1   LYVGNLTWWTTDEDLEGALAEAGVVD-VKSIKFFEHKANGKSKGFAYVEFASEAAAAAVK 59

Query: 161 KHADGKKIDGRRVLV 175
           +  +G++ +G++ +V
Sbjct: 60  EKLEGREFNGKKCVV 74

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

 Score = 41.8 bits (99), Expect = 2e-05
 Identities = 18/67 (26%), Positives = 29/67 (43%), Gaps = 13/67 (19%)

Query: 111 YDTSESKLRREFEVYGPIK--KIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKI 168
           YDT        F  +G I   K+    N   G  +GY F+ +E E     A +  +G  +
Sbjct: 20  YDT--------FSAFGNILSCKVATDEN---GGSKGYGFVHFETEEAAVRAIEKVNGMLL 68

Query: 169 DGRRVLV 175
           + ++V V
Sbjct: 69  NDKKVFV 75

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

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

 Score = 41.5 bits (98), Expect = 3e-05
 Identities = 20/78 (25%), Positives = 40/78 (51%), Gaps = 8/78 (10%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
           K L++  +   T+E +LR  F  YG ++++         K + YAF+ +E   D   A +
Sbjct: 2   KVLYVRNLPLSTTEEQLRELFSEYGEVERVK--------KIKDYAFVHFEERDDAVKAME 53

Query: 162 HADGKKIDGRRVLVDVER 179
             +GK+++G  + V + +
Sbjct: 54  EMNGKELEGSPIEVSLAK 71

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|240724 cd12278, RRM_eIF3B, RNA recognition motif in eukaryotic translation initiation factor 3 subunit B (eIF-3B) and similar proteins

 Score = 41.8 bits (99), Expect = 3e-05
 Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 3/61 (4%)

Query: 111 YDTSESKLRREFEVYGPIK--KIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKI 168
            +  +  LR+ F  +G  K   I M  ++ TGK +GYAF+E+    +   A K  +G K+
Sbjct: 17  LEKLKKVLRKIFSKFGVGKIVGIYMPVDE-TGKTKGYAFVEFATPEEAKEAVKALNGYKL 75

Query: 169 D 169
           D
Sbjct: 76  D 76

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

 Score = 41.6 bits (97), Expect = 3e-05
 Identities = 17/70 (24%), Positives = 38/70 (54%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           +F+  ++ + +   ++  F  +G I    +V +  TGK +GY F+ + ++ D  +A  H 
Sbjct: 4   VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63

Query: 164 DGKKIDGRRV 173
            G+ + GR++
Sbjct: 64  GGQWLGGRQI 73

This subgroup corresponds to the RRM2 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal, highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 80

>gnl|CDD|241020 cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins

 Score = 41.6 bits (98), Expect = 3e-05
 Identities = 19/70 (27%), Positives = 37/70 (52%), Gaps = 4/70 (5%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEH----ERDMHSA 159
           +FI  +++ T+   LR  F  +G IK+ +++ +  T + RG+ F+ +      ++ +   
Sbjct: 1   MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQG 60

Query: 160 YKHADGKKID 169
               DGKKID
Sbjct: 61  PHELDGKKID 70

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

 Score = 41.6 bits (98), Expect = 3e-05
 Identities = 21/70 (30%), Positives = 37/70 (52%), Gaps = 1/70 (1%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           LFI  ++Y+T++  L+  F  +G I   V++ +  T + RG+ F+ +        A  +A
Sbjct: 2   LFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFA-SASEVDAAMNA 60

Query: 164 DGKKIDGRRV 173
              K+DGR V
Sbjct: 61  RPHKVDGREV 70

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|241059 cd12615, RRM1_TIA1, RNA recognition motif 1 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 41.6 bits (97), Expect = 3e-05
 Identities = 20/74 (27%), Positives = 38/74 (51%), Gaps = 2/74 (2%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
           TL++  ++ D +E+ + + F   GP K   M+ +     P  Y F+E+   R   ++   
Sbjct: 1   TLYVGNLSRDVTEALILQLFSQIGPCKSCKMIMDTAGNDP--YCFVEFFEHRHAAASLAA 58

Query: 163 ADGKKIDGRRVLVD 176
            +G+KI G+ V V+
Sbjct: 59  MNGRKIMGKEVKVN 72

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|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 = 41.1 bits (97), Expect = 4e-05
 Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 14/75 (18%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
           T+++  + +  +E +L+R F  +G I+++ +  +K      GYAF+ +    D H A   
Sbjct: 2   TVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDK------GYAFVRF----DTHEAAAT 51

Query: 163 A----DGKKIDGRRV 173
           A    +G  I+G+ V
Sbjct: 52  AIVAVNGTSINGQTV 66

This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both TIA-1 and TIAR bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 73

>gnl|CDD|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 41.1 bits (96), Expect = 4e-05
 Identities = 19/50 (38%), Positives = 32/50 (64%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYE 151
           K +F+  +  DT E  LR  FE YG I+ I ++ ++ +GK RG+AF+ ++
Sbjct: 1   KKIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFD 50

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|240850 cd12404, RRM2_NCL, RNA recognition motif 2 in vertebrate nucleolin

 Score = 41.0 bits (96), Expect = 4e-05
 Identities = 22/75 (29%), Positives = 41/75 (54%), Gaps = 4/75 (5%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
           +TLF+  + Y+ +  +L+   EV+     I +   K  G  +G A+IE++ E +   A +
Sbjct: 4   RTLFVKNLPYNITVDELK---EVFEDAVDIRLPSGK-DGSSKGIAYIEFKTEAEAEKALE 59

Query: 162 HADGKKIDGRRVLVD 176
              G ++DGR ++VD
Sbjct: 60  EKQGAEVDGRSIVVD 74

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|240852 cd12406, RRM4_NCL, RNA recognition motif 4 in vertebrate nucleolin

 Score = 41.1 bits (96), Expect = 4e-05
 Identities = 24/80 (30%), Positives = 46/80 (57%), Gaps = 3/80 (3%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
           KTLF+  ++ DT+E  L+  F+  G I   + V ++ TG  +G+ F+++  E D  +A +
Sbjct: 1   KTLFVKGLSEDTTEETLKESFD--GSIAARI-VTDRDTGSSKGFGFVDFSSEEDAKAAKE 57

Query: 162 HADGKKIDGRRVLVDVERSR 181
             +  +IDG +V +D  + +
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|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 44.9 bits (106), Expect = 5e-05
 Identities = 21/134 (15%), Positives = 54/134 (40%), Gaps = 8/134 (5%)

Query: 212 REDNERERERYRLERERELAGGPPRARSGSNDRERERERRRSRSRERKRRTSRSRSRDRR 271
           ++  E+ +E  +  + +E A      +    ++E++ E  R R  E+KR   R++SR ++
Sbjct: 118 KKKKEKPKEEPKDRKPKEEAKEKRPPKEKEKEKEKKVEEPRDREEEKKRERVRAKSRPKK 177

Query: 272 RRRSRERIRDDDIEEVEFRPK--------DRSDRDRDRDRKRRRERENSEDRNERKRDRK 323
             + +   +  +  E E + +           + D + +R++  +     +      +  
Sbjct: 178 PPKKKPPNKKKEPPEEEKQRQAAREAVKGKPEEPDVNEEREKEEDDGKDRETTTSPMEED 237

Query: 324 ERRKERERNNEERE 337
           E R+  E +     
Sbjct: 238 ESRQSSEISRRSSS 251

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

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

 Score = 40.7 bits (96), Expect = 6e-05
 Identities = 20/64 (31%), Positives = 33/64 (51%)

Query: 112 DTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGR 171
           +  E  L   F  +G IK I +  +  T K RG+AF+E+E   D  +A  + +  ++ GR
Sbjct: 9   EVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNMNESELFGR 68

Query: 172 RVLV 175
            + V
Sbjct: 69  TIRV 72

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

>gnl|CDD|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast nucleolar protein 13 (Nop13p) and similar proteins

 Score = 40.5 bits (95), Expect = 6e-05
 Identities = 22/75 (29%), Positives = 46/75 (61%), Gaps = 3/75 (4%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           LF+  ++++T+E +LR  F   G I+++ M+  + +GK +G+AF+++E   ++  A    
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFE---EIEFATNAL 57

Query: 164 DGKKIDGRRVLVDVE 178
            GK ++GR + V+  
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|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 40.4 bits (95), Expect = 7e-05
 Identities = 18/70 (25%), Positives = 36/70 (51%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           +F+  ++ +     LR  F  +G I    +V +  TGK +GY F+ +  + D  +A +  
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 164 DGKKIDGRRV 173
           +G+ + GR +
Sbjct: 62  NGQWLGGRAI 71

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

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

 Score = 40.7 bits (96), Expect = 7e-05
 Identities = 23/86 (26%), Positives = 38/86 (44%), Gaps = 9/86 (10%)

Query: 88  WDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAF 147
           W  N F          +F+  +  + ++  L R F  Y   +K  +V +K TGK +GY F
Sbjct: 2   WPENDF---------RIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGF 52

Query: 148 IEYEHERDMHSAYKHADGKKIDGRRV 173
           + +    D   A K  +GK +  R +
Sbjct: 53  VSFSDPNDYLKAMKEMNGKYVGNRPI 78

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

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

 Score = 40.4 bits (95), Expect = 7e-05
 Identities = 24/76 (31%), Positives = 40/76 (52%), Gaps = 8/76 (10%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           ++I R+ Y   E  + R F+ YG I++I +          G+ F+E+E  RD   A    
Sbjct: 2   VYIGRLPYRARERDVERFFKGYGRIREINL--------KNGFGFVEFEDPRDADDAVYEL 53

Query: 164 DGKKIDGRRVLVDVER 179
           +GK++ G RV+V+  R
Sbjct: 54  NGKELCGERVIVEHAR 69

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|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related protein 7 (LARP7) and similar proteins

 Score = 40.4 bits (95), Expect = 7e-05
 Identities = 17/60 (28%), Positives = 31/60 (51%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
           T+++  +  + +   L+  F  YG +  + +   K TG  +G+AFIE+E   +   A KH
Sbjct: 1   TVYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKH 60

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|241024 cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 40.4 bits (94), Expect = 7e-05
 Identities = 19/50 (38%), Positives = 32/50 (64%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYE 151
           K +F+  +  DT E  LR  FE YG I+ I ++ ++ +GK RG+AF+ ++
Sbjct: 1   KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFD 50

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

 Score = 40.0 bits (94), Expect = 9e-05
 Identities = 21/63 (33%), Positives = 34/63 (53%), Gaps = 1/63 (1%)

Query: 114 SESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRV 173
            E KLR+ FE +G I  + + + K  GK R + F+ Y+ E +   A KH +   ID  ++
Sbjct: 13  KEDKLRKLFEAFGTITDVQLKYTK-DGKFRKFGFVGYKTEEEAQKALKHFNNSFIDTSKI 71

Query: 174 LVD 176
            V+
Sbjct: 72  TVE 74

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|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 43.3 bits (102), Expect = 1e-04
 Identities = 21/134 (15%), Positives = 54/134 (40%), Gaps = 5/134 (3%)

Query: 211 GREDNERERERYRLERERELAGGPPRARSGSNDRERERERRRS-----RSRERKRRTSRS 265
                E E+E+ +++ E++     P+        + E + +R      + +E+K    R 
Sbjct: 100 NESGKEEEKEKEQVKEEKKKKKEKPKEEPKDRKPKEEAKEKRPPKEKEKEKEKKVEEPRD 159

Query: 266 RSRDRRRRRSRERIRDDDIEEVEFRPKDRSDRDRDRDRKRRRERENSEDRNERKRDRKER 325
           R  +++R R R + R     + +   K +   + ++ R+  RE    +       + +E+
Sbjct: 160 REEEKKRERVRAKSRPKKPPKKKPPNKKKEPPEEEKQRQAAREAVKGKPEEPDVNEEREK 219

Query: 326 RKERERNNEEREEK 339
            ++  ++ E     
Sbjct: 220 EEDDGKDRETTTSP 233

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 40.3 bits (94), Expect = 1e-04
 Identities = 26/74 (35%), Positives = 40/74 (54%), Gaps = 5/74 (6%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           LF+  +  D  E  L   F  +GP++K  ++ +K TGK RG+ F+ ++   +  SA K A
Sbjct: 2   LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQ---NHDSADKAA 58

Query: 164 DGK--KIDGRRVLV 175
             K   I+G RV V
Sbjct: 59  VVKFHPINGHRVEV 72

This subgroup corresponds to the RRM2 of hnRNP A0, a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

>gnl|CDD|240786 cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in yeast nucleolar protein 3 (Npl3p) and similar proteins

 Score = 39.7 bits (93), Expect = 1e-04
 Identities = 21/72 (29%), Positives = 34/72 (47%), Gaps = 8/72 (11%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           L++     DTSES +R  F  YG +K++ M+ N        +AF+E+E       A    
Sbjct: 2   LYVRPFPPDTSESAIREIFSPYGAVKEVKMISN--------FAFVEFESLESAIRAKDSV 53

Query: 164 DGKKIDGRRVLV 175
            GK ++   + V
Sbjct: 54  HGKVLNNNPLYV 65

This subfamily corresponds to the RRM1 of Npl3p, also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. Npl3p is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein containing two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues. . Length = 67

>gnl|CDD|240994 cd12550, RRM_II_PABPN1, RNA recognition motif in type II polyadenylate-binding protein 2 (PABP-2) and similar proteins

 Score = 40.2 bits (94), Expect = 1e-04
 Identities = 17/77 (22%), Positives = 41/77 (53%), Gaps = 1/77 (1%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
           ++++  V+Y  +  +L   F   G + ++ ++ +K +G P+G+A+IE+  +++       
Sbjct: 1   SVYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFS-DKESVRTALA 59

Query: 163 ADGKKIDGRRVLVDVER 179
            D     GR++ V  +R
Sbjct: 60  LDESLFRGRQIKVMPKR 76

This subgroup corresponds to the RRM of PABP-2, also termed poly(A)-binding protein 2, or nuclear poly(A)-binding protein 1 (PABPN1), or poly(A)-binding protein II (PABII), which is a ubiquitously expressed type II nuclear poly(A)-binding protein that directs the elongation of mRNA poly(A) tails during pre-mRNA processing. Although PABP-2 binds poly(A) with high affinity and specificity as type I poly(A)-binding proteins, it contains only one highly conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, PABP-2 possesses an acidic N-terminal domain that is essential for the stimulation of PAP, and an arginine-rich C-terminal domain. . Length = 76

>gnl|CDD|240851 cd12405, RRM3_NCL, RNA recognition motif 3 in vertebrate nucleolin

 Score = 39.9 bits (93), Expect = 1e-04
 Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 5/72 (6%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
           K L +  ++Y  SE  L+  FE    I+   +  N   G+P+GYAF+E+E   D   A  
Sbjct: 2   KVLVVNNLSYSASEDSLQEVFEKATSIR---IPQNN--GRPKGYAFVEFESAEDAKEALN 56

Query: 162 HADGKKIDGRRV 173
             +  +I+GR +
Sbjct: 57  SCNNTEIEGRSI 68

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

 Score = 39.5 bits (93), Expect = 1e-04
 Identities = 14/46 (30%), Positives = 25/46 (54%)

Query: 126 GPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGR 171
           GP+  + +  ++VT   +GY F+E+  E D   A K  +  K+ G+
Sbjct: 23  GPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIMNMIKLYGK 68

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|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 = 39.4 bits (92), Expect = 1e-04
 Identities = 20/75 (26%), Positives = 36/75 (48%), Gaps = 9/75 (12%)

Query: 103 TLFIARVNYD-TSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
           TLF+   +   T E  + + FE +GP+ +  +         + +AF+E+E   D   A +
Sbjct: 1   TLFVVGFDPGTTREEDIEKLFEPFGPLVRCDI--------RKTFAFVEFEDSEDATKALE 52

Query: 162 HADGKKIDGRRVLVD 176
              G +IDG  + V+
Sbjct: 53  ALHGSRIDGSVLTVE 67

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|241053 cd12609, RRM2_CoAA, RNA recognition motif 2 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 39.5 bits (92), Expect = 1e-04
 Identities = 20/74 (27%), Positives = 39/74 (52%), Gaps = 8/74 (10%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           +F+  V+   +  +LR  FE +G + +   V        + YAF+  E E +  +A +  
Sbjct: 3   IFVGNVSATCTSDELRGLFEEFGRVVECDKV--------KDYAFVHMEREEEALAAIEAL 54

Query: 164 DGKKIDGRRVLVDV 177
           +GK++ GRR+ V++
Sbjct: 55  NGKEVKGRRINVEL 68

This subgroup corresponds to the RRM2 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs. . Length = 68

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

 Score = 39.3 bits (92), Expect = 1e-04
 Identities = 12/50 (24%), Positives = 32/50 (64%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHE 153
           +F+  ++ +T+E  +++ F  +G ++  +++ +K T + RG+ F+ +E E
Sbjct: 2   IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESE 51

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

 Score = 39.2 bits (92), Expect = 2e-04
 Identities = 19/68 (27%), Positives = 39/68 (57%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           L++  ++++ +E  LR  FE +G I+ + +  +  TG+ +GY FI++    D   A +  
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 164 DGKKIDGR 171
           +G ++ GR
Sbjct: 61  NGFELAGR 68

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|240713 cd12267, RRM_YRA1_MLO3, RNA recognition motif in yeast RNA annealing protein YRA1 (Yra1p), yeast mRNA export protein mlo3 and similar proteins

 Score = 38.9 bits (91), Expect = 2e-04
 Identities = 21/64 (32%), Positives = 36/64 (56%), Gaps = 2/64 (3%)

Query: 112 DTSESKLRREF-EVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDG 170
           D +E+++R  F    GPIK++++ +N+  GK  G A I ++   D   AY   +G+  DG
Sbjct: 10  DVTEAQIREYFVSQIGPIKRVLLSYNE-GGKSTGIANITFKRAGDATKAYDKFNGRIDDG 68

Query: 171 RRVL 174
            R +
Sbjct: 69  NRKM 72

This subfamily corresponds to the RRM of Yra1p and mlo3. Yra1p is an essential nuclear RNA-binding protein encoded by Saccharomyces cerevisiae YRA1 gene. It belongs to the evolutionarily conserved REF (RNA and export factor binding proteins) family of hnRNP-like proteins. Yra1p possesses potent RNA annealing activity and interacts with a number of proteins involved in nuclear transport and RNA processing. It binds to the mRNA export factor Mex67p/TAP and couples transcription to export in yeast. Yra1p is associated with Pse1p and Kap123p, two members of the beta-importin family, further mediating transport of Yra1p into the nucleus. In addition, the co-transcriptional loading of Yra1p is required for autoregulation. Yra1p consists of two highly conserved N- and C-terminal boxes and a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This subfamily includes RNA-annealing protein mlo3, also termed mRNA export protein mlo3, which has been identified in fission yeast as a protein that causes defects in chromosome segregation when overexpressed. It shows high sequence similarity with Yra1p. . Length = 77

>gnl|CDD|217301 pfam02956, TT_ORF1, TT viral orf 1

 Score = 42.6 bits (101), Expect = 2e-04
 Identities = 23/59 (38%), Positives = 27/59 (45%)

Query: 222 YRLERERELAGGPPRARSGSNDRERERERRRSRSRERKRRTSRSRSRDRRRRRSRERIR 280
               R R    G  R R     R R R RR  R R  +RR  R R R RRRRR R+++ 
Sbjct: 4   RWWRRRRRRWRGRRRRRRRRRARRRRRRRRVRRRRRGRRRRRRRRRRRRRRRRKRKKLI 62

TT virus (TTV), isolated initially from a Japanese patient with hepatitis of unknown aetiology, has since been found to infect both healthy and diseased individuals and numerous prevalence studies have raised questions about its role in unexplained hepatitis. ORF1 is a large 750 residue protein. The N-terminal half of this protein corresponds to the capsid protein. Length = 525

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

 Score = 38.9 bits (91), Expect = 3e-04
 Identities = 18/73 (24%), Positives = 37/73 (50%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           LF+  +++D  E  +   F  YG I  + +  +  +G+P+G+ ++E+  +    +A    
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 164 DGKKIDGRRVLVD 176
            G  + GR V +D
Sbjct: 61  GGTDLLGRPVRLD 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|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 38.9 bits (91), Expect = 3e-04
 Identities = 11/39 (28%), Positives = 26/39 (66%)

Query: 112 DTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEY 150
             +E  LR +F+ +G I+ + +V +K TG+ +G+ ++++
Sbjct: 11  SYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKF 49

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

 Score = 38.5 bits (90), Expect = 3e-04
 Identities = 20/75 (26%), Positives = 40/75 (53%), Gaps = 1/75 (1%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
           +TLF+  ++   +E  L   F   GP++  V +     GKP+ +AF+ ++HE  +  A +
Sbjct: 2   RTLFVGNLDARVTEEILYELFLQAGPLEG-VKIPKDPNGKPKSFAFVTFKHEVSVPYAIQ 60

Query: 162 HADGKKIDGRRVLVD 176
             +G ++ GR + + 
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|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 38.9 bits (91), Expect = 3e-04
 Identities = 19/75 (25%), Positives = 45/75 (60%), Gaps = 4/75 (5%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHE----RDMH 157
           K +F+  +  + +E+ LR+ F  +G + ++V++++    +PRG+ FI +E E    + ++
Sbjct: 3   KKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVVN 62

Query: 158 SAYKHADGKKIDGRR 172
             +   +GKK++ +R
Sbjct: 63  EHFHDINGKKVEVKR 77

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|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 38.6 bits (90), Expect = 3e-04
 Identities = 17/61 (27%), Positives = 38/61 (62%), Gaps = 1/61 (1%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           +F+  +++ T+E+ LR+ F  YG +K++ +V+++  G  +GY F+ +E + D     + A
Sbjct: 5   IFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDR-AGVSKGYGFVTFETQEDAQKILQEA 63

Query: 164 D 164
           +
Sbjct: 64  N 64

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

 Score = 38.1 bits (89), Expect = 4e-04
 Identities = 21/74 (28%), Positives = 35/74 (47%), Gaps = 7/74 (9%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIK--KIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
           L++  ++   +E  L   F   GPIK  K++  H         YAF+EY   R   +A +
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDP-----YAFVEYYDHRSAAAALQ 55

Query: 162 HADGKKIDGRRVLV 175
             +G+ I G+ + V
Sbjct: 56  TMNGRLILGQEIKV 69

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

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

 Score = 38.4 bits (90), Expect = 4e-04
 Identities = 18/79 (22%), Positives = 38/79 (48%), Gaps = 2/79 (2%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
           TLF+  +++   +  L   F+  G +   V +     G+ +G+  +E+  E     A + 
Sbjct: 1   TLFVGNLSWSAEQDDLEEFFKECGEVVD-VRIAQDDDGRSKGFGHVEFATEEGAQKALEK 59

Query: 163 ADGKKIDGRRVLVDVERSR 181
           + G+++ GR + VD+   R
Sbjct: 60  S-GEELLGREIRVDLATER 77

This subfamily corresponds to the RRM1 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 77

>gnl|CDD|241040 cd12596, RRM1_SRSF6, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 6 (SRSF6)

 Score = 38.0 bits (88), Expect = 4e-04
 Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 8/76 (10%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           ++I R++Y   E  ++R F  YG + +I +          GY F+E+E  RD   A    
Sbjct: 2   VYIGRLSYHVREKDIQRFFGGYGKLLEIDL--------KNGYGFVEFEDSRDADDAVYEL 53

Query: 164 DGKKIDGRRVLVDVER 179
           +GK + G RV+V+  R
Sbjct: 54  NGKDLCGERVIVEHAR 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|241028 cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 38.4 bits (89), Expect = 5e-04
 Identities = 19/55 (34%), Positives = 32/55 (58%)

Query: 99  DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHE 153
           DP K +F+  +N + +E K+R  F  +G I+ I +  +  T K RG+ FI ++ E
Sbjct: 2   DPVKKIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEE 56

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|240718 cd12272, RRM2_PHIP1, RNA recognition motif 2 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 37.8 bits (88), Expect = 5e-04
 Identities = 18/74 (24%), Positives = 39/74 (52%), Gaps = 2/74 (2%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
           T++I  + +D +E  +R  F+    I  + +  +K TG+ +G+  +++  E  + +A K 
Sbjct: 1   TVYIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLDAALK- 58

Query: 163 ADGKKIDGRRVLVD 176
            DG  + GR + + 
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|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 37.8 bits (87), Expect = 7e-04
 Identities = 22/73 (30%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAY 160
            + LFI  ++++T++  LR  FE +G +   V++ +  T + RG+ F+ Y    ++ +A 
Sbjct: 2   LRKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAM 61

Query: 161 KHADGKKIDGRRV 173
             A   K+DGR V
Sbjct: 62  -SARPHKVDGRVV 73

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

 Score = 37.9 bits (88), Expect = 7e-04
 Identities = 19/70 (27%), Positives = 39/70 (55%), Gaps = 4/70 (5%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           LF+  ++++T++  LRR F  YG +   V++ +K T + RG+ F++++    + +     
Sbjct: 2   LFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAGG 61

Query: 164 ----DGKKID 169
               DG+ ID
Sbjct: 62  PHTLDGRTID 71

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|241000 cd12556, RRM2_RBM15B, RNA recognition motif 2 in putative RNA binding motif protein 15B (RBM15B) from vertebrate

 Score = 37.6 bits (87), Expect = 7e-04
 Identities = 21/69 (30%), Positives = 39/69 (56%), Gaps = 1/69 (1%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
           + LFI  ++++ SE +LRR F+ YG I+++V +     G+   YAF+++++    H A  
Sbjct: 9   RNLFIGNLDHNVSEVELRRAFDKYGIIEEVV-IKRPARGQGGAYAFLKFQNLDMAHRAKV 67

Query: 162 HADGKKIDG 170
              G+ I  
Sbjct: 68  AMSGRVIGR 76

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|240804 cd12358, RRM1_VICKZ, RNA recognition motif 1 in the VICKZ family proteins

 Score = 37.4 bits (87), Expect = 8e-04
 Identities = 19/80 (23%), Positives = 39/80 (48%), Gaps = 8/80 (10%)

Query: 104 LFIARVNYDTSESKLRREFEVYG-PIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
           L+I  ++ D +ES LR+ FE +  P+  +++          GYAF++   +     A + 
Sbjct: 1   LYIGNLSSDVNESDLRQLFEEHKIPVSSVLVKKG-------GYAFVDCPDQSWADKAIEK 53

Query: 163 ADGKKIDGRRVLVDVERSRT 182
            +GK + G+ + V+    + 
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|241205 cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 37.7 bits (87), Expect = 8e-04
 Identities = 22/73 (30%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAY 160
            + LFI  ++++T++  LR  FE +G +   V++ +  T + RG+ F+ Y    ++ +A 
Sbjct: 2   LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAM 61

Query: 161 KHADGKKIDGRRV 173
             A   K+DGR V
Sbjct: 62  N-ARPHKVDGRVV 73

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

 Score = 37.5 bits (87), Expect = 8e-04
 Identities = 18/73 (24%), Positives = 39/73 (53%), Gaps = 4/73 (5%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEH----ERDMHSA 159
           +F+  +++DT++  L+  F  +G +    +  + VTG+ RG+ F+ ++     E+ +   
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60

Query: 160 YKHADGKKIDGRR 172
               DG+ ID +R
Sbjct: 61  EHKLDGRVIDPKR 73

This subfamily corresponds to the RRM1 in hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 74

>gnl|CDD|217301 pfam02956, TT_ORF1, TT viral orf 1

 Score = 40.3 bits (95), Expect = 0.001
 Identities = 28/66 (42%), Positives = 32/66 (48%), Gaps = 13/66 (19%)

Query: 244 RERERERRRSRSRERKRRTSRSRSRDRRRRRSRERIRDDDIEEVEFRPKDRSDRDRDRDR 303
             R R R R R R R+RR +R R R RRR R R R R             R  R R R R
Sbjct: 6   WRRRRRRWRGRRRRRRRRRARRRRR-RRRVRRRRRGR------------RRRRRRRRRRR 52

Query: 304 KRRRER 309
           +RRR+R
Sbjct: 53  RRRRKR 58

TT virus (TTV), isolated initially from a Japanese patient with hepatitis of unknown aetiology, has since been found to infect both healthy and diseased individuals and numerous prevalence studies have raised questions about its role in unexplained hepatitis. ORF1 is a large 750 residue protein. The N-terminal half of this protein corresponds to the capsid protein. Length = 525

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

 Score = 36.8 bits (86), Expect = 0.001
 Identities = 20/71 (28%), Positives = 38/71 (53%), Gaps = 9/71 (12%)

Query: 104 LFIARVNYD-TSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
           +F+  +N D  S+  L   F  YG I  I + H       +GY F+++++E D  +A   
Sbjct: 3   VFVGNLNTDKVSKEDLEEIFSKYGKILGISL-H-------KGYGFVQFDNEEDARAAVAG 54

Query: 163 ADGKKIDGRRV 173
            +G++I G+++
Sbjct: 55  ENGREIAGQKL 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|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 40.3 bits (94), Expect = 0.001
 Identities = 27/89 (30%), Positives = 43/89 (48%), Gaps = 7/89 (7%)

Query: 102 KTLFIARVNY---DTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHS 158
           KT  I  VNY     ++ ++R  F   G I+   +V +KVTG+  GY F+ Y    D   
Sbjct: 3   KTNLI--VNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEK 60

Query: 159 AYKHADGKKIDGRRVLVDVER--SRTVKG 185
           A    +G ++  + + V   R  S ++KG
Sbjct: 61  AVNSLNGLRLQNKTIKVSYARPSSDSIKG 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|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 37.3 bits (86), Expect = 0.001
 Identities = 20/65 (30%), Positives = 35/65 (53%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           +F+ ++  D  E +L   FE  GPI  + ++ + ++G+ RGYAFI +  +     A K  
Sbjct: 4   VFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAVKLC 63

Query: 164 DGKKI 168
           D  +I
Sbjct: 64  DNYEI 68

This subgroup corresponds to the RRM1 of hnRNP R, which is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. It is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, and in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; it binds RNA through its RRM domains. . Length = 79

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

 Score = 37.4 bits (86), Expect = 0.001
 Identities = 16/70 (22%), Positives = 38/70 (54%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           +F+  ++ + +   ++  F  +G I    +V +  TGK +GY F+ + ++ D  +A +  
Sbjct: 4   VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63

Query: 164 DGKKIDGRRV 173
            G+ + GR++
Sbjct: 64  GGQWLGGRQI 73

This subgroup corresponds to the RRM2 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1), and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 80

>gnl|CDD|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 = 0.001
 Identities = 21/73 (28%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAY 160
           F+ LFI  ++++T+E  LR  +E +G +   V++ +  + + RG+ F+ +    ++ +A 
Sbjct: 2   FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAM 61

Query: 161 KHADGKKIDGRRV 173
             A    IDGR V
Sbjct: 62  A-ARPHTIDGRVV 73

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

 Score = 36.8 bits (85), Expect = 0.001
 Identities = 18/73 (24%), Positives = 40/73 (54%), Gaps = 1/73 (1%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           L++  ++   +E  L++ F+V GP++ + ++ +K   K   Y F+EY    D   A +  
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDK-NNKGVNYGFVEYHQSHDAEIALQTL 59

Query: 164 DGKKIDGRRVLVD 176
           +G++I+   + V+
Sbjct: 60  NGRQIENNEIRVN 72

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|240810 cd12364, RRM_RDM1, RNA recognition motif of RAD52 motif-containing protein 1 (RDM1) and similar proteins

 Score = 37.0 bits (86), Expect = 0.001
 Identities = 19/81 (23%), Positives = 32/81 (39%), Gaps = 5/81 (6%)

Query: 102 KTLFIARVN--YDTSES--KLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMH 157
           KTL++  ++      E    L   F  +G +  + +  N     P  YAF+++   R   
Sbjct: 1   KTLYVWGISPKLTEEEIYESLCSAFSQFGLLYSVKVFPNAAVATPGFYAFVKFYSARAAS 60

Query: 158 SAYKHADGKK-IDGRRVLVDV 177
            A K  +GK    G  + V  
Sbjct: 61  RAQKACNGKWLFQGSPLKVRF 81

This subfamily corresponds to the RRM of RDM1, also termed RAD52 homolog B, a novel factor involved in the cellular response to the anti-cancer drug cisplatin in vertebrates. RDM1 contains a small RD motif that shares with the recombination and repair protein RAD52, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The RD motif is responsible for the acidic pH-dependent DNA-binding properties of RDM1. It interacts with ss- and dsDNA, and may act as a DNA-damage recognition factor by recognizing the distortions of the double helix caused by cisplatin-DNA adducts in vitro. In addition, due to the presence of RRM, RDM1 can bind to RNA as well as DNA. . Length = 81

>gnl|CDD|217203 pfam02724, CDC45, CDC45-like protein

 Score = 40.0 bits (94), Expect = 0.001
 Identities = 20/93 (21%), Positives = 31/93 (33%), Gaps = 15/93 (16%)

Query: 271 RRRRSRERIRDDDIEEVEFRPKDRSDRDRDRDRKRRRERENSEDRNERKRDRKERRKERE 330
           R     +   ++  EE E   K   D D D D       ++     ER  +R+ RR+E E
Sbjct: 121 RDLEEDDDDDEESDEEDEESSKSEDDEDDDDDD-----DDDDIATRERSLERRRRRREWE 175

Query: 331 RNNEEREEKVFIKQEPVDDYQEYDNYEDEASSV 363
               E E            Y +   Y   ++  
Sbjct: 176 EKRAELEF----------YYYQGTYYGTSSALT 198

CDC45 is an essential gene required for initiation of DNA replication in S. cerevisiae, forming a complex with MCM5/CDC46. Homologues of CDC45 have been identified in human, mouse and smut fungus among others. Length = 583

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

 Score = 36.4 bits (85), Expect = 0.002
 Identities = 13/52 (25%), Positives = 29/52 (55%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERD 155
           L++  ++ D +E+ L   F   GP+  I +  + +T +  GYA++ +++  D
Sbjct: 2   LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPAD 53

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

 Score = 36.4 bits (85), Expect = 0.002
 Identities = 19/79 (24%), Positives = 38/79 (48%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
            T+F+  +    S+  +R+  E  G +     V +  TGK + + F E+E       A +
Sbjct: 1   TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALR 60

Query: 162 HADGKKIDGRRVLVDVERS 180
             +G ++ G+++LV V+  
Sbjct: 61  LLNGLELGGKKLLVKVDAK 79

This subfamily corresponds to the RRM of RBM25, also termed Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein S164, or RNA-binding region-containing protein 7, an evolutionary-conserved splicing coactivator SRm160 (SR-related nuclear matrix protein of 160 kDa, )-interacting protein. RBM25 belongs to a family of RNA-binding proteins containing a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminus, a RE/RD-rich (ER) central region, and a C-terminal proline-tryptophan-isoleucine (PWI) motif. It localizes to the nuclear speckles and associates with multiple splicing components, including splicing cofactors SRm160/300, U snRNAs, assembled splicing complexes, and spliced mRNAs. It may play an important role in pre-mRNA processing by coupling splicing with mRNA 3'-end formation. Additional research indicates that RBM25 is one of the RNA-binding regulators that direct the alternative splicing of apoptotic factors. It can activate proapoptotic Bcl-xS 5'ss by binding to the exonic splicing enhancer, CGGGCA, and stabilize the pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1 snRNP-associated factor. . Length = 84

>gnl|CDD|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate Hu-antigen C (HuC)

 Score = 36.6 bits (84), Expect = 0.002
 Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 3/74 (4%)

Query: 109 VNY---DTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADG 165
           VNY   + ++ + +  F   G I+   +V +K+TG+  GY F+ Y    D   A    +G
Sbjct: 8   VNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINTLNG 67

Query: 166 KKIDGRRVLVDVER 179
            K+  + + V   R
Sbjct: 68  LKLQTKTIKVSYAR 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|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 = 36.7 bits (85), Expect = 0.002
 Identities = 13/54 (24%), Positives = 27/54 (50%), Gaps = 2/54 (3%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKP--RGYAFIEYEHERD 155
           +F+ ++    SE  LR  FE YG + +I ++ ++    P  +G  F+ +   + 
Sbjct: 4   MFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKA 57

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|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins

 Score = 36.1 bits (84), Expect = 0.002
 Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 3/72 (4%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           L++  + +  S  +L   F  YG I++I + + K T   RG AF+ YE   D  +A  H 
Sbjct: 5   LYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKET---RGTAFVVYEDIYDAKNACDHL 61

Query: 164 DGKKIDGRRVLV 175
            G  +  R ++V
Sbjct: 62  SGFNVANRYLVV 73

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|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 = 36.1 bits (84), Expect = 0.002
 Identities = 17/75 (22%), Positives = 40/75 (53%), Gaps = 1/75 (1%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
             L +  V ++ ++ +LR  F  +G +K + +   K  G  RG+AF+E+  +++  +A +
Sbjct: 1   TKLIVRNVPFEATKKELRELFSPFGQVKSVRLP-KKFDGSHRGFAFVEFVTKQEAQNAME 59

Query: 162 HADGKKIDGRRVLVD 176
                 + GR ++++
Sbjct: 60  ALKSTHLYGRHLVLE 74

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|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding protein 7 (RBM7)

 Score = 36.0 bits (83), Expect = 0.002
 Identities = 21/72 (29%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
           +TLF+  ++   +E  +   F   GP+ K+ +  +K  GKP+ +AF+ ++HE  +  A  
Sbjct: 2   RTLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDK-DGKPKQFAFVNFKHEVSVPYAMN 60

Query: 162 HADGKKIDGRRV 173
             +G K+ GR +
Sbjct: 61  LLNGIKLYGRPL 72

This subfamily corresponds to the RRM of RBM7, a ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. RBM7 interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20. It may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM7 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. . Length = 75

>gnl|CDD|217301 pfam02956, TT_ORF1, TT viral orf 1

 Score = 39.2 bits (92), Expect = 0.003
 Identities = 28/74 (37%), Positives = 34/74 (45%), Gaps = 18/74 (24%)

Query: 254 RSRERKRRTSRSRSRDRRRRRSRERIRDDDIEEVEFRPKDRSDRDRDRDRKRRRERENSE 313
           R   R+RR  R R R RRRRR+R R R                  R R R+RRR R    
Sbjct: 4   RWWRRRRRRWRGRRRRRRRRRARRRRR------------------RRRVRRRRRGRRRRR 45

Query: 314 DRNERKRDRKERRK 327
            R  R+R R+ +RK
Sbjct: 46  RRRRRRRRRRRKRK 59

TT virus (TTV), isolated initially from a Japanese patient with hepatitis of unknown aetiology, has since been found to infect both healthy and diseased individuals and numerous prevalence studies have raised questions about its role in unexplained hepatitis. ORF1 is a large 750 residue protein. The N-terminal half of this protein corresponds to the capsid protein. Length = 525

>gnl|CDD|240722 cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in Mei2-like proteins and terminal EAR1-like proteins

 Score = 35.7 bits (83), Expect = 0.003
 Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 5/74 (6%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
           TL +  ++   S+ +LR  F  +G +K I     + + K     F+E+   R   +A   
Sbjct: 3   TLLVFNLDSPISDQELRSLFSQFGEVKDIRETPLRPSQK-----FVEFYDIRAAEAALDA 57

Query: 163 ADGKKIDGRRVLVD 176
            +G+   G R+ V 
Sbjct: 58  LNGRPFLGGRLKVK 71

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

>gnl|CDD|240806 cd12360, RRM_cwf2, RNA recognition motif in yeast pre-mRNA-splicing factor Cwc2 and similar proteins

 Score = 35.7 bits (83), Expect = 0.003
 Identities = 15/56 (26%), Positives = 29/56 (51%), Gaps = 10/56 (17%)

Query: 102 KTLFIARVNYDTS----ESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHE 153
           +TL++  +   ++    E  LRR F  +G I+ I ++ +K      G AF+ Y++ 
Sbjct: 2   RTLYVGGIKAGSALKQIEEILRRHFGEWGDIEDIRVLPSK------GIAFVRYKYR 51

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

 Score = 35.6 bits (82), Expect = 0.003
 Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 4/59 (6%)

Query: 121 EFE----VYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLV 175
           EFE     YG I++  +V+++VTG  +GY F+EY  +     A     GK++    +  
Sbjct: 15  EFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKARLELLGKQLGESTLFA 73

This subgroup corresponds to the RRM2 of raver-2, a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It is present in vertebrates and shows high sequence homology to raver-1, a ubiquitously expressed co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. In contrast, raver-2 exerts a distinct spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Raver-2 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. Raver-2 binds to PTB through the SLLGEPP motif only, and binds to RNA through its RRMs. . Length = 77

>gnl|CDD|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 35.6 bits (82), Expect = 0.003
 Identities = 20/73 (27%), Positives = 39/73 (53%), Gaps = 8/73 (10%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           +F+  V+ DTS+ +LR  FE YG +    ++        R +AF+    E     A +  
Sbjct: 3   IFVGNVDEDTSQEELRALFEAYGAVLSCAVM--------RQFAFVHLRGEAAADRAIEEL 54

Query: 164 DGKKIDGRRVLVD 176
           +G+++ GR+++V+
Sbjct: 55  NGRELHGRKLVVE 67

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

 Score = 35.9 bits (82), Expect = 0.003
 Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 3/74 (4%)

Query: 109 VNY---DTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADG 165
           VNY   + ++ + R  F   G I+   +V +K+TG+  GY F+ Y   +D   A    +G
Sbjct: 7   VNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNG 66

Query: 166 KKIDGRRVLVDVER 179
            ++  + + V   R
Sbjct: 67  LRLQTKTIKVSYAR 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|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 38.7 bits (90), Expect = 0.004
 Identities = 23/116 (19%), Positives = 51/116 (43%), Gaps = 1/116 (0%)

Query: 225 ERERELAGGPPRARSGSNDRERERERRRSRSRERKRRTS-RSRSRDRRRRRSRERIRDDD 283
            +       P +     + +E E+E+ + +  ++K++   +   +DR+ +   +  R   
Sbjct: 85  SKGPAAKTKPAKEPKNESGKEEEKEKEQVKEEKKKKKEKPKEEPKDRKPKEEAKEKRPPK 144

Query: 284 IEEVEFRPKDRSDRDRDRDRKRRRERENSEDRNERKRDRKERRKERERNNEEREEK 339
            +E E   K    RDR+ ++KR R R  S  +   K+    ++KE     ++R+  
Sbjct: 145 EKEKEKEKKVEEPRDREEEKKRERVRAKSRPKKPPKKKPPNKKKEPPEEEKQRQAA 200

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|240927 cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 35.7 bits (82), Expect = 0.004
 Identities = 19/65 (29%), Positives = 34/65 (52%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           +F+ ++  D  E +L   FE  GPI  + ++ + +TG  RGYAF+ +  +     A K  
Sbjct: 4   IFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAVKLY 63

Query: 164 DGKKI 168
           +  +I
Sbjct: 64  NNHEI 68

This subgroup corresponds to the RRM1 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP, a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. Length = 79

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

 Score = 35.3 bits (82), Expect = 0.004
 Identities = 18/73 (24%), Positives = 35/73 (47%), Gaps = 3/73 (4%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKK-IVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
           L++  ++    + +LR EF  +G I    VM   K  G+ +G+ F+ +    +   A   
Sbjct: 4   LYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEK--GRSKGFGFVCFSSPEEATKAVTE 61

Query: 163 ADGKKIDGRRVLV 175
            +G+ I G+ + V
Sbjct: 62  MNGRIIGGKPLYV 74

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

 Score = 35.3 bits (82), Expect = 0.004
 Identities = 22/72 (30%), Positives = 34/72 (47%), Gaps = 8/72 (11%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           LF+  +   T+  +LR  FE YG + +  +V N        Y F+  E E D   A K  
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGTVTECDVVKN--------YGFVHMEEEEDAEDAIKAL 53

Query: 164 DGKKIDGRRVLV 175
           +G +  G+R+ V
Sbjct: 54  NGYEFMGKRINV 65

This subfamily corresponds to the RRM in CoAA (also known as RBM14 or PSP2) and RNA-binding protein 4 (RBM4). CoAA is a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner, and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. RBM4 is a ubiquitously expressed splicing factor with two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may also function as a translational regulator of stress-associated mRNAs as well as play a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RRMs, a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. This family also includes Drosophila RNA-binding protein lark (Dlark), a homolog of human RBM4. It plays an important role in embryonic development and in the circadian regulation of adult eclosion. Dlark shares high sequence similarity with RBM4 at the N-terminal region. However, Dlark has three proline-rich segments instead of three alanine-rich segments within the C-terminal region. . Length = 66

>gnl|CDD|178945 PRK00247, PRK00247, putative inner membrane protein translocase component YidC; Validated

 Score = 38.7 bits (90), Expect = 0.004
 Identities = 22/108 (20%), Positives = 39/108 (36%), Gaps = 10/108 (9%)

Query: 246 RERERRRSRSRERKRRTSRSRSRDRRRRRSRERIRDDDIEEVEFRPKDRSDRDRDRDRKR 305
           +E    +      K++  ++     RR R R  I      E+            + + K+
Sbjct: 284 KEHHAEQRAQYREKQKEKKAFLWTLRRNRLRMIITPWRAPEL---------HAENAEIKK 334

Query: 306 RRERENSEDRNERKRDRKERRK-ERERNNEEREEKVFIKQEPVDDYQE 352
            R  E +E +  +K   ++RR  ERE N E R+E+             
Sbjct: 335 TRTAEKNEAKARKKEIAQKRRAAEREINREARQERAAAMARARARRAA 382

Length = 429

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

 Score = 35.4 bits (82), Expect = 0.004
 Identities = 17/69 (24%), Positives = 35/69 (50%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
            +F+  +  D  ES L + F  +G +  + ++ +  T K +GY F+   +  + +SA   
Sbjct: 3   CIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIAS 62

Query: 163 ADGKKIDGR 171
            +G ++ GR
Sbjct: 63  LNGYRLGGR 71

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

>gnl|CDD|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 35.2 bits (82), Expect = 0.004
 Identities = 18/77 (23%), Positives = 36/77 (46%), Gaps = 5/77 (6%)

Query: 103 TLFIARVNY--DTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAY 160
           TL++   N+     +S +R  FE YG I  I     +   K R + ++++       +A 
Sbjct: 2   TLWVT--NFPPSFDQSDIRDLFEQYGEILSIRFPSLRF-NKTRRFCYVQFTSPESAAAAV 58

Query: 161 KHADGKKIDGRRVLVDV 177
              +GK  +G +++V +
Sbjct: 59  ALLNGKLGEGYKLVVKI 75

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	363
KOG0113|consensus	335		100.0
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.88
KOG0107|consensus	195		99.85
KOG0148|consensus	321		99.85
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.84
KOG4207|consensus	256		99.84
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.84
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.8
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.8
KOG0127|consensus	678		99.75
KOG0415|consensus	479		99.74
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.73
KOG0121|consensus	153		99.72
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.71
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.69
KOG0145|consensus	360		99.69
KOG0147|consensus	549		99.68
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.68
KOG0117|consensus	506		99.67
KOG0122|consensus	270		99.66
KOG4205|consensus	311		99.66
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.66
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.66
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.64
KOG0149|consensus	247		99.62
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.62
KOG0145|consensus	360		99.61
KOG0131|consensus	203		99.61
KOG0127|consensus	678		99.59
KOG0124|consensus	544		99.59
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.58
KOG0126|consensus	219		99.58
KOG0105|consensus	241		99.58
PLN03120	260	nucleic acid binding protein; Provisional	99.57
KOG0130|consensus	170		99.57
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.57
KOG0111|consensus	298		99.54
PLN03213	759	repressor of silencing 3; Provisional	99.53
KOG0144|consensus	510		99.53
KOG0125|consensus	376		99.52
KOG0123|consensus	369		99.51
KOG0131|consensus	203		99.51
KOG0148|consensus	321		99.5
PLN03121	243	nucleic acid binding protein; Provisional	99.5
smart00362	72	RRM_2 RNA recognition motif.	99.5
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.49
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.48
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.48
KOG0109|consensus	346		99.47
KOG0117|consensus	506		99.47
PF12220	94	U1snRNP70_N: U1 small nuclear ribonucleoprotein of	99.47
smart00360	71	RRM RNA recognition motif.	99.45
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.43
KOG0114|consensus	124		99.42
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.41
KOG0108|consensus	435		99.4
KOG0124|consensus	544		99.4
KOG4676|consensus	479		99.39
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.37
KOG0123|consensus	369		99.33
smart00361	70	RRM_1 RNA recognition motif.	99.32
KOG0110|consensus	725		99.31
KOG0146|consensus	371		99.31
KOG0144|consensus	510		99.29
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.29
KOG0109|consensus	346		99.29
KOG4661|consensus	940		99.25
KOG4212|consensus	608		99.19
KOG4208|consensus	214		99.14
KOG4676|consensus	479		99.1
KOG4206|consensus	221		99.1
KOG0116|consensus	419		99.09
KOG4205|consensus	311		99.04
KOG0132|consensus	894		99.04
KOG0153|consensus	377		98.96
KOG0106|consensus	216		98.95
KOG0110|consensus	725		98.93
KOG1548|consensus	382		98.93
KOG4209|consensus	231		98.91
KOG4212|consensus	608		98.89
KOG0226|consensus	290		98.87
KOG0147|consensus	549		98.87
KOG0533|consensus	243		98.86
KOG0106|consensus	216		98.86
KOG0146|consensus	371		98.78
KOG1457|consensus	284		98.77
KOG4454|consensus	267		98.75
KOG0151|consensus	877		98.68
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.66
KOG1995|consensus	351		98.61
KOG4660|consensus	549		98.61
KOG0120|consensus	500		98.57
KOG4206|consensus	221		98.48
KOG4210|consensus	285		98.44
KOG4211|consensus	510		98.31
COG5175	480	MOT2 Transcriptional repressor [Transcription]	98.26
KOG4849|consensus	498		98.26
KOG0120|consensus	500		98.23
KOG1190|consensus	492		98.22
KOG1548|consensus	382		98.22
KOG2416|consensus	718		98.2
KOG1457|consensus	284		98.18
KOG2202|consensus	260		98.09
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.04
KOG4211|consensus	510		97.91
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.9
KOG0129|consensus	520		97.86
KOG0128|consensus	881		97.84
KOG1365|consensus	508		97.76
KOG0112|consensus	975		97.7
KOG2314|consensus	698		97.63
KOG3152|consensus	278		97.63
KOG0105|consensus	241		97.62
KOG1855|consensus	484		97.52
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.49
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.41
KOG1190|consensus	492		97.39
KOG4307|consensus	944		97.36
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.32
KOG1456|consensus	494		97.32
KOG0129|consensus	520		97.27
KOG1456|consensus	494		97.19
COG0724	306	RNA-binding proteins (RRM domain) [General functio	97.13
KOG2068|consensus	327		96.97
KOG1996|consensus	378		96.94
KOG2253|consensus	668		96.77
KOG2193|consensus	584		96.63
KOG4368|consensus	757		96.61
KOG0112|consensus	975		96.51
KOG0115|consensus	275		96.49
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	96.46
KOG0128|consensus	881		96.43
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	96.3
KOG4207|consensus	256		96.27
KOG0113|consensus	335		96.15
KOG1365|consensus	508		96.06
KOG4454|consensus	267		95.82
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	95.79
KOG4307|consensus	944		95.65
KOG2135|consensus	526		95.6
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	95.06
KOG0149|consensus	247		95.02
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	95.01
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	94.96
KOG2548|consensus	653		94.83
KOG4574|consensus	1007		94.83
KOG4285|consensus	350		94.54
KOG4660|consensus	549		94.42
KOG2888|consensus	453		94.23
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	94.17
KOG4210|consensus	285		93.7
KOG0122|consensus	270		93.65
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	93.62
KOG2591|consensus	684		93.61
KOG2548|consensus	653		93.4
PLN03213	759	repressor of silencing 3; Provisional	93.18
KOG2318|consensus	650		92.76
KOG2888|consensus	453		92.39
KOG0151|consensus	877		92.19
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	92.05
KOG0125|consensus	376		91.68
KOG0108|consensus	435		91.58
KOG2193|consensus	584		91.28
KOG0804|consensus	493		90.3
KOG0111|consensus	298		89.56
KOG0126|consensus	219		88.47
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	88.02
smart00361	70	RRM_1 RNA recognition motif.	87.33
KOG0835|consensus	367		86.6
KOG4483|consensus	528		83.96
KOG0107|consensus	195		80.84

>KOG0113|consensus

Probab=100.00  E-value=5.4e-44  Score=314.31  Aligned_cols=200  Identities=73%  Similarity=1.239  Sum_probs=194.6

Q ss_pred             CCCCCChhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccCCCCCCCCCCCcccHHHHHHHHHHHHHHHHHHH
Q psy16184          1 MTQFLPPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFEDPKDTPPPTRVETREERLERRRRERAEQVAYK   80 (363)
Q Consensus         1 ~~~~~p~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (363)
                      ||++|||+|+.||+|.|||+++||+..+|+.+++..|+||..|+..++.+.++++++.++.....++.....+.++...+
T Consensus         1 M~~~lp~nllaLF~pRpPl~y~pP~d~~p~kr~~~~~tGvA~~~~~~~~~~d~p~~~p~~t~~e~~er~~~~k~e~~~~~   80 (335)
T KOG0113|consen    1 MTQFLPPNLLALFAPRPPLPYLPPTDKLPHKRKTNPYTGVAQYLSTFEDPKDAPPKFPVETPEEPLERGRREKTEKIPHK   80 (335)
T ss_pred             CCccCCccHHHhcCCCCCcccCCccccChhhccCCCcccHHHHHHhhcCcccCCCcCcccchhhHHHhhhhhhhhhhHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999989


Q ss_pred             HHHHHhhcCCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHH
Q psy16184         81 LEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAY  160 (363)
Q Consensus        81 ~~~~~~~~~p~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai  160 (363)
                      +...++.|+|..++++..+|.+||||+-|+++++|..|+..|..||.|+.|.|+.|+.||+++|||||+|+++.++..|+
T Consensus        81 ~~~~l~~wdP~~dp~a~gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AY  160 (335)
T KOG0113|consen   81 LERRLKLWDPNNDPNAIGDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAY  160 (335)
T ss_pred             HHHHHHhcCCCCCCcccCCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhCCceeCCEEEEEEeecccCCCCCCCCCCCCCCCCCCC
Q psy16184        161 KHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGGTRR  200 (363)
Q Consensus       161 ~~l~g~~i~g~~i~V~~a~~~~~~~~~~~~~~g~~g~~~~  200 (363)
                      ...+|..|+|+.|.|.+....++++|.|++.|||.||...
T Consensus       161 K~adG~~Idgrri~VDvERgRTvkgW~PRRLGGGLGg~r~  200 (335)
T KOG0113|consen  161 KDADGIKIDGRRILVDVERGRTVKGWLPRRLGGGLGGRRY  200 (335)
T ss_pred             HhccCceecCcEEEEEecccccccccccccccCCcCCccc
Confidence            9999999999999999999999999999999999998764

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.88  E-value=7.1e-23  Score=193.76  Aligned_cols=151  Identities=19%  Similarity=0.340  Sum_probs=121.9

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccC--CCCCCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHH
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFE--DPKDTPPPTRVETREERLERRRRERAEQVAYKLEQE   84 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (363)
                      .+|..+|..+++|..| -|+.++.|++++|| +||.|.++.+  .+...+....+..+.+.+...+              
T Consensus       122 ~~L~~lF~~~G~V~~v-~i~~d~~tg~srGy-aFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~a~--------------  185 (346)
T TIGR01659       122 RELYALFRTIGPINTC-RIMRDYKTGYSFGY-AFVDFGSEADSQRAIKNLNGITVRNKRLKVSYAR--------------  185 (346)
T ss_pred             HHHHHHHHhcCCEEEE-EEEecCCCCccCcE-EEEEEccHHHHHHHHHHcCCCccCCceeeeeccc--------------
Confidence            3589999999999888 46778899999999 9999977544  2333456666666555443211              


Q ss_pred             HhhcCCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhC
Q psy16184         85 IALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHAD  164 (363)
Q Consensus        85 ~~~~~p~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~  164 (363)
                           |    .......++|||+|||+.+|+++|+++|.+||.|..|.|+.++.|++++|||||+|.+.++|++||..||
T Consensus       186 -----p----~~~~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~ln  256 (346)
T TIGR01659       186 -----P----GGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALN  256 (346)
T ss_pred             -----c----cccccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhC
Confidence                 0    0011234689999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CceeCC--EEEEEEeecccC
Q psy16184        165 GKKIDG--RRVLVDVERSRT  182 (363)
Q Consensus       165 g~~i~g--~~i~V~~a~~~~  182 (363)
                      ++.|.+  +.|.|.++....
T Consensus       257 g~~~~g~~~~l~V~~a~~~~  276 (346)
T TIGR01659       257 NVIPEGGSQPLTVRLAEEHG  276 (346)
T ss_pred             CCccCCCceeEEEEECCccc
Confidence            999876  789999987643

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).

>KOG0107|consensus

Probab=99.85  E-value=1.2e-20  Score=155.13  Aligned_cols=79  Identities=30%  Similarity=0.640  Sum_probs=73.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      -.++||||||+..+++.+|+.+|..||.|..|+|..+     +.|||||+|+++.+|+.|+.+|+|..|+|..|.|+++.
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn-----PPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~   83 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN-----PPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELST   83 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec-----CCCceEEeccCcccHHHHHhhcCCccccCceEEEEeec
Confidence            3679999999999999999999999999999999775     47999999999999999999999999999999999997


Q ss_pred             ccCC
Q psy16184        180 SRTV  183 (363)
Q Consensus       180 ~~~~  183 (363)
                      ....
T Consensus        84 G~~r   87 (195)
T KOG0107|consen   84 GRPR   87 (195)
T ss_pred             CCcc
Confidence            7554

>KOG0148|consensus

Probab=99.85  E-value=4.9e-22  Score=173.54  Aligned_cols=160  Identities=21%  Similarity=0.342  Sum_probs=129.0

Q ss_pred             hhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccC--CCCCCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHH
Q psy16184          8 NLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFE--DPKDTPPPTRVETREERLERRRRERAEQVAYKLEQEI   85 (363)
Q Consensus         8 ~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   85 (363)
                      .|...|+|++-|..+. |.+|++|++++|| |||.|....+  .+...|...-+-.+.++...+.++-.+.-...+.   
T Consensus        78 ~lr~aF~pFGevS~ak-virD~~T~KsKGY-gFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATRKp~e~n~~~lt---  152 (321)
T KOG0148|consen   78 KLREAFAPFGEVSDAK-VIRDMNTGKSKGY-GFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATRKPSEMNGKPLT---  152 (321)
T ss_pred             HHHHHhccccccccce-EeecccCCcccce-eEEeccchHHHHHHHHHhCCeeeccceeeccccccCccccCCCCcc---
Confidence            5888999999999995 7779999999999 9999988655  5677888999988888877643322100000000   


Q ss_pred             hhcCCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCC
Q psy16184         86 ALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADG  165 (363)
Q Consensus        86 ~~~~p~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g  165 (363)
                          -...-+...+.+++||||||+..+|++.|+..|+.||.|.+|.|..+      +|||||.|.+.|.|..||..||+
T Consensus       153 ----fdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~------qGYaFVrF~tkEaAahAIv~mNn  222 (321)
T KOG0148|consen  153 ----FDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD------QGYAFVRFETKEAAAHAIVQMNN  222 (321)
T ss_pred             ----HHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc------cceEEEEecchhhHHHHHHHhcC
Confidence                00112334556889999999999999999999999999999999887      49999999999999999999999


Q ss_pred             ceeCCEEEEEEeecccC
Q psy16184        166 KKIDGRRVLVDVERSRT  182 (363)
Q Consensus       166 ~~i~g~~i~V~~a~~~~  182 (363)
                      ..|.|..+++.|-+...
T Consensus       223 tei~G~~VkCsWGKe~~  239 (321)
T KOG0148|consen  223 TEIGGQLVRCSWGKEGD  239 (321)
T ss_pred             ceeCceEEEEeccccCC
Confidence            99999999999987643

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

Probab=99.84  E-value=2.2e-21  Score=193.12  Aligned_cols=166  Identities=17%  Similarity=0.250  Sum_probs=130.0

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccC--CCCCCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHH
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFE--DPKDTPPPTRVETREERLERRRRERAEQVAYKLEQE   84 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (363)
                      .+|..+|.++|+|..+ -++.++.|++++|| +||.|.+...  .+...+....+.++.+.+......            
T Consensus       122 e~Lr~lF~~fG~I~sV-~I~~D~~TgkskGf-AFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~~~------------  187 (612)
T TIGR01645       122 DTIRRAFDPFGPIKSI-NMSWDPATGKHKGF-AFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNM------------  187 (612)
T ss_pred             HHHHHHHHccCCEEEE-EEeecCCCCCcCCe-EEEEeCcHHHHHHHHHhcCCeEEecceeeecccccc------------
Confidence            4689999999999988 46778999999999 9999988655  333456777777777665421000            


Q ss_pred             HhhcCCC-CCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHh
Q psy16184         85 IALWDPN-SFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA  163 (363)
Q Consensus        85 ~~~~~p~-~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l  163 (363)
                       ....+. ..........++|||+||++.+++++|+.+|+.||.|..|.|+.++.++.++|||||+|.+.++|..||..|
T Consensus       188 -p~a~~~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~am  266 (612)
T TIGR01645       188 -PQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASM  266 (612)
T ss_pred             -cccccccccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHh
Confidence             000000 000111224579999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCceeCCEEEEEEeecccCCCCCC
Q psy16184        164 DGKKIDGRRVLVDVERSRTVKGWL  187 (363)
Q Consensus       164 ~g~~i~g~~i~V~~a~~~~~~~~~  187 (363)
                      |+..|+|+.|.|.++...+...+.
T Consensus       267 Ng~elgGr~LrV~kAi~pP~~~~~  290 (612)
T TIGR01645       267 NLFDLGGQYLRVGKCVTPPDALLQ  290 (612)
T ss_pred             CCCeeCCeEEEEEecCCCccccCC
Confidence            999999999999999875544443

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.

>KOG4207|consensus

Probab=99.84  E-value=3.5e-20  Score=156.07  Aligned_cols=83  Identities=31%  Similarity=0.615  Sum_probs=79.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      +...+|.|-||.+.|+.++|..+|++||.|-+|.|+.|+.|..++|||||-|....+|+.|+++|+|.+|+|+.|.|++|
T Consensus        11 ~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~a   90 (256)
T KOG4207|consen   11 EGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMA   90 (256)
T ss_pred             ccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhh
Confidence            34568999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccc
Q psy16184        179 RSR  181 (363)
Q Consensus       179 ~~~  181 (363)
                      +..
T Consensus        91 ryg   93 (256)
T KOG4207|consen   91 RYG   93 (256)
T ss_pred             hcC
Confidence            753

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

Probab=99.84  E-value=7.8e-20  Score=152.18  Aligned_cols=84  Identities=26%  Similarity=0.576  Sum_probs=80.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      ..++|||+||++.+|+++|+++|.+||.|..|.|+.++.|++++|||||+|.+.++|+.||..||+..|+|+.|.|+++.
T Consensus        33 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a~  112 (144)
T PLN03134         33 MSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPAN  112 (144)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeCC
Confidence            46799999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             ccCC
Q psy16184        180 SRTV  183 (363)
Q Consensus       180 ~~~~  183 (363)
                      .+..
T Consensus       113 ~~~~  116 (144)
T PLN03134        113 DRPS  116 (144)
T ss_pred             cCCC
Confidence            6554

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

Probab=99.80  E-value=4.7e-20  Score=182.97  Aligned_cols=161  Identities=17%  Similarity=0.347  Sum_probs=123.6

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccC-CCCCCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHH
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFE-DPKDTPPPTRVETREERLERRRRERAEQVAYKLEQEI   85 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   85 (363)
                      .+|..+|..+|+|..+ -++.+..+++++|| +||.|.+... ..+..+....+.+..+.++....++...      ...
T Consensus       104 ~~l~~~F~~~G~v~~v-~i~~d~~~~~skg~-afVeF~~~e~A~~Al~l~g~~~~g~~i~v~~~~~~~~~~------~~~  175 (457)
T TIGR01622       104 RDLYEFFSKVGKVRDV-QCIKDRNSRRSKGV-AYVEFYDVESVIKALALTGQMLLGRPIIVQSSQAEKNRA------AKA  175 (457)
T ss_pred             HHHHHHHHhcCCeeEE-EEeecCCCCCcceE-EEEEECCHHHHHHHHHhCCCEECCeeeEEeecchhhhhh------hhc
Confidence            4689999999999887 45668889999999 9999988544 2233455566666555443321111100      000


Q ss_pred             hhcCCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCC
Q psy16184         86 ALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADG  165 (363)
Q Consensus        86 ~~~~p~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g  165 (363)
                      ..     ......+..++|||+|||..+|+++|.++|.+||.|..|.|+.+..+|.++|||||+|.+.++|..||..|||
T Consensus       176 ~~-----~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g  250 (457)
T TIGR01622       176 AT-----HQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNG  250 (457)
T ss_pred             cc-----ccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCC
Confidence            00     0011122368999999999999999999999999999999999998999999999999999999999999999


Q ss_pred             ceeCCEEEEEEeecc
Q psy16184        166 KKIDGRRVLVDVERS  180 (363)
Q Consensus       166 ~~i~g~~i~V~~a~~  180 (363)
                      ..|.|+.|.|.|+..
T Consensus       251 ~~i~g~~i~v~~a~~  265 (457)
T TIGR01622       251 FELAGRPIKVGYAQD  265 (457)
T ss_pred             cEECCEEEEEEEccC
Confidence            999999999999763

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.80  E-value=1.9e-20  Score=179.55  Aligned_cols=82  Identities=18%  Similarity=0.374  Sum_probs=78.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeecc
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS  180 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~  180 (363)
                      +.+|||+|||+.+++++|.++|++||.|..|.|+.|..|+.++|||||+|.+.++|..||..|||..|+|+.|.|.|+..
T Consensus       269 ~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~~  348 (352)
T TIGR01661       269 GYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTN  348 (352)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEccC
Confidence            34799999999999999999999999999999999999999999999999999999999999999999999999999876


Q ss_pred             cC
Q psy16184        181 RT  182 (363)
Q Consensus       181 ~~  182 (363)
                      +.
T Consensus       349 ~~  350 (352)
T TIGR01661       349 KA  350 (352)
T ss_pred             CC
Confidence            53

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

>KOG0127|consensus

Probab=99.75  E-value=8.1e-19  Score=166.47  Aligned_cols=172  Identities=23%  Similarity=0.367  Sum_probs=121.2

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccC--CCCCCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHH
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFE--DPKDTPPPTRVETREERLERRRRERAEQVAYKLEQE   84 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (363)
                      .+|..+|+..+||..| .|...+.+..++|| |||+|.-...  .+........++++.+.+..++.....+...+. +.
T Consensus        20 ~qL~e~FS~vGPik~~-~vVt~~gs~~~RGf-gfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~R~r~e~~~~~-e~   96 (678)
T KOG0127|consen   20 EQLEEFFSYVGPIKHA-VVVTNKGSSEKRGF-GFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKKRARSEEVEKG-EN   96 (678)
T ss_pred             hHHHHhhhcccCccee-EEecCCCcccccCc-cceeeehHhHHHHHHHHhhcCcccceecccccccccccchhcccc-cc
Confidence            4689999999999999 45557888999999 9999854332  222233444556655554432222111100000 00


Q ss_pred             HhhcCCCC--CCCC--CCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHH
Q psy16184         85 IALWDPNS--FPNA--TMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAY  160 (363)
Q Consensus        85 ~~~~~p~~--~~~~--~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai  160 (363)
                      .+...|..  .+..  ...+...|+|.||||.|...+|+.+|+.||.|..|.|+..+ .|+.+|||||+|....+|..||
T Consensus        97 ~~veK~~~q~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~-dgklcGFaFV~fk~~~dA~~Al  175 (678)
T KOG0127|consen   97 KAVEKPIEQKRPTKAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKK-DGKLCGFAFVQFKEKKDAEKAL  175 (678)
T ss_pred             hhhhcccccCCcchhhccCccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCC-CCCccceEEEEEeeHHHHHHHH
Confidence            00111111  1111  12346689999999999999999999999999999999765 5555699999999999999999


Q ss_pred             HHhCCceeCCEEEEEEeecccC
Q psy16184        161 KHADGKKIDGRRVLVDVERSRT  182 (363)
Q Consensus       161 ~~l~g~~i~g~~i~V~~a~~~~  182 (363)
                      ..||++.|+|++|-|.||-++.
T Consensus       176 ~~~N~~~i~gR~VAVDWAV~Kd  197 (678)
T KOG0127|consen  176 EFFNGNKIDGRPVAVDWAVDKD  197 (678)
T ss_pred             HhccCceecCceeEEeeecccc
Confidence            9999999999999999997754

>KOG0415|consensus

Probab=99.74  E-value=1.8e-17  Score=149.92  Aligned_cols=91  Identities=30%  Similarity=0.476  Sum_probs=84.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184         98 MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      .+|.+.|||..|++-||.++|.-+|+.||.|..|.|+.|..||.+..||||+|++.+++++|+-.|++..|+.+.|+|.|
T Consensus       236 ~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDF  315 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDF  315 (479)
T ss_pred             CCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeeh
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecccCCCCCCC
Q psy16184        178 ERSRTVKGWLP  188 (363)
Q Consensus       178 a~~~~~~~~~~  188 (363)
                      +.....-.|.+
T Consensus       316 SQSVsk~k~r~  326 (479)
T KOG0415|consen  316 SQSVSKVKYRQ  326 (479)
T ss_pred             hhhhhhhhccc
Confidence            98765544544

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.73  E-value=1.2e-18  Score=166.96  Aligned_cols=150  Identities=15%  Similarity=0.316  Sum_probs=119.6

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccC--CCCCCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHH
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFE--DPKDTPPPTRVETREERLERRRRERAEQVAYKLEQE   84 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (363)
                      .+|..+|..+|||..+ -|+.++.+++++|| +||.|.....  .+...+....+.++.+.++..               
T Consensus        18 ~~l~~~F~~~G~i~~v-~i~~d~~~g~s~g~-afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a---------------   80 (352)
T TIGR01661        18 EEIRSLFTSIGEIESC-KLVRDKVTGQSLGY-GFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYA---------------   80 (352)
T ss_pred             HHHHHHHHccCCEEEE-EEEEcCCCCccceE-EEEEECcHHHHHHHHhhcccEEECCeeEEEEee---------------
Confidence            4699999999999988 46778889999999 9999977543  223345555555554443321               


Q ss_pred             HhhcCCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhC
Q psy16184         85 IALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHAD  164 (363)
Q Consensus        85 ~~~~~p~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~  164 (363)
                          .|    .......++|||+|||..+++++|..+|..||.|..+.|+.+..++.++|||||+|.+.++|..||..||
T Consensus        81 ----~~----~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~  152 (352)
T TIGR01661        81 ----RP----SSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLN  152 (352)
T ss_pred             ----cc----cccccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhC
Confidence                00    1111235689999999999999999999999999999999988889999999999999999999999999


Q ss_pred             CceeCC--EEEEEEeeccc
Q psy16184        165 GKKIDG--RRVLVDVERSR  181 (363)
Q Consensus       165 g~~i~g--~~i~V~~a~~~  181 (363)
                      |..+.|  ..|.|.++...
T Consensus       153 g~~~~g~~~~i~v~~a~~~  171 (352)
T TIGR01661       153 GTTPSGCTEPITVKFANNP  171 (352)
T ss_pred             CCccCCCceeEEEEECCCC
Confidence            999877  67888888654

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

>KOG0121|consensus

Probab=99.72  E-value=1.3e-17  Score=130.22  Aligned_cols=80  Identities=24%  Similarity=0.519  Sum_probs=77.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeecc
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS  180 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~  180 (363)
                      ++|||||||++.|+|++|.++|+.||.|..|.|-.|+.+..+.|||||+|.+.++|..|+..+||+.|+.++|.|.|...
T Consensus        36 S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D~G  115 (153)
T KOG0121|consen   36 SCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWDAG  115 (153)
T ss_pred             cceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeecccc
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999754

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

Probab=99.71  E-value=5.3e-18  Score=172.44  Aligned_cols=164  Identities=16%  Similarity=0.302  Sum_probs=116.1

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccC--CCCCCCCCCCcc----cHHHHHHHHHHHHHH--HHH
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFE--DPKDTPPPTRVE----TREERLERRRRERAE--QVA   78 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~--~~~~~~~~~~~~----~~~~~~~~~~~~~~~--~~~   78 (363)
                      .+|..+|..+|.|..+. ++.+. ++.++|| +||.|.+...  .+...+....+.    +..+.+...+.....  ...
T Consensus       193 e~L~~~F~~fG~i~~~~-i~~~~-~g~~~G~-afV~F~~~e~A~~Av~~l~g~~i~~~~~g~~l~v~~a~~k~er~~~~~  269 (562)
T TIGR01628       193 DKLRELFAKFGEITSAA-VMKDG-SGRSRGF-AFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAEREAELR  269 (562)
T ss_pred             HHHHHHHHhcCCEEEEE-EEECC-CCCcccE-EEEEECCHHHHHHHHHHhCCcEecccccceeeEeecccChhhhHHHHH
Confidence            46889999999998873 44453 6889999 9999988544  222233444443    322211111000000  000


Q ss_pred             HHHHHHHhhcCCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHH
Q psy16184         79 YKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHS  158 (363)
Q Consensus        79 ~~~~~~~~~~~p~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~  158 (363)
                      .+.....       .........++|||+||++.+|+++|+++|+.||.|..|.|+.+ .+|.++|||||+|.+.++|.+
T Consensus       270 ~~~~~~~-------~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d-~~g~~~g~gfV~f~~~~~A~~  341 (562)
T TIGR01628       270 RKFEELQ-------QERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFSNPEEANR  341 (562)
T ss_pred             hhHHhhh-------hhhhcccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEEC-CCCCcCCeEEEEeCCHHHHHH
Confidence            0000000       00112234678999999999999999999999999999999998 689999999999999999999


Q ss_pred             HHHHhCCceeCCEEEEEEeeccc
Q psy16184        159 AYKHADGKKIDGRRVLVDVERSR  181 (363)
Q Consensus       159 Ai~~l~g~~i~g~~i~V~~a~~~  181 (363)
                      ||..|||..|+|+.|.|.+|..+
T Consensus       342 A~~~~~g~~~~gk~l~V~~a~~k  364 (562)
T TIGR01628       342 AVTEMHGRMLGGKPLYVALAQRK  364 (562)
T ss_pred             HHHHhcCCeeCCceeEEEeccCc
Confidence            99999999999999999998754

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

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

Probab=99.69  E-value=3.6e-17  Score=164.52  Aligned_cols=149  Identities=16%  Similarity=0.219  Sum_probs=103.2

Q ss_pred             CCCCCCCccccccccccC-CCCCCCCCCCcccHHHHHHHHHHHHHH-HHHHHHHH-----HHhhcCCCCCCCCCCCCCCe
Q psy16184         31 EKKTHGYSGIAAFLNEFE-DPKDTPPPTRVETREERLERRRRERAE-QVAYKLEQ-----EIALWDPNSFPNATMDPFKT  103 (363)
Q Consensus        31 t~~s~g~~g~v~f~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~-----~~~~~~p~~~~~~~~~~~~~  103 (363)
                      ..+.+|| +||.|.+..+ ..+.++....+.+..+.+......... +.......     ..................++
T Consensus       219 ~~~~kg~-afVeF~~~e~A~~Al~l~g~~~~g~~l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  297 (509)
T TIGR01642       219 INKEKNF-AFLEFRTVEEATFAMALDSIIYSNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDR  297 (509)
T ss_pred             ECCCCCE-EEEEeCCHHHHhhhhcCCCeEeeCceeEecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCE
Confidence            3567899 9999988555 233456666666654443321000000 00000000     00000000011112335679


Q ss_pred             EEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeecc
Q psy16184        104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS  180 (363)
Q Consensus       104 l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~  180 (363)
                      |||+|||+.+|+++|.++|..||.|..|.|+.+..+|.++|||||+|.+.++|..||..|||..|.|+.|.|.++..
T Consensus       298 l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~  374 (509)
T TIGR01642       298 IYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACV  374 (509)
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECcc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999864

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

>KOG0145|consensus

Probab=99.69  E-value=6.1e-18  Score=147.17  Aligned_cols=155  Identities=19%  Similarity=0.352  Sum_probs=119.8

Q ss_pred             CCCCChh-----hhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccC--CCCCCCCCCCcccHHHHHHHHHHHHH
Q psy16184          2 TQFLPPN-----LLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFE--DPKDTPPPTRVETREERLERRRRERA   74 (363)
Q Consensus         2 ~~~~p~~-----l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~   74 (363)
                      .+|||+.     |..||...+-|..|. +.+|..|+.+-|| |||.|+.+..  .+...++.-.+..+.+++..      
T Consensus        46 vNYLPQ~MTqdE~rSLF~SiGeiEScK-LvRDKitGqSLGY-GFVNYv~p~DAe~AintlNGLrLQ~KTIKVSy------  117 (360)
T KOG0145|consen   46 VNYLPQNMTQDELRSLFGSIGEIESCK-LVRDKITGQSLGY-GFVNYVRPKDAEKAINTLNGLRLQNKTIKVSY------  117 (360)
T ss_pred             eeecccccCHHHHHHHhhcccceeeee-eeecccccccccc-ceeeecChHHHHHHHhhhcceeeccceEEEEe------
Confidence            4567764     889999999999995 7789999999999 9999977543  11222222222222222211      


Q ss_pred             HHHHHHHHHHHhhcCCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHH
Q psy16184         75 EQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHER  154 (363)
Q Consensus        75 ~~~~~~~~~~~~~~~p~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~  154 (363)
                                   ..|    ........+|||.+||..+|..+|+++|++||.|..-.|+.|..||.++|.|||.|....
T Consensus       118 -------------ARP----Ss~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~  180 (360)
T KOG0145|consen  118 -------------ARP----SSDSIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRI  180 (360)
T ss_pred             -------------ccC----ChhhhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchh
Confidence                         111    112223458999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhCCceeCCE--EEEEEeeccc
Q psy16184        155 DMHSAYKHADGKKIDGR--RVLVDVERSR  181 (363)
Q Consensus       155 ~a~~Ai~~l~g~~i~g~--~i~V~~a~~~  181 (363)
                      +|+.||..|||..-.|.  +|.|+++...
T Consensus       181 EAe~AIk~lNG~~P~g~tepItVKFannP  209 (360)
T KOG0145|consen  181 EAEEAIKGLNGQKPSGCTEPITVKFANNP  209 (360)
T ss_pred             HHHHHHHhccCCCCCCCCCCeEEEecCCc
Confidence            99999999999876654  7999999754

>KOG0147|consensus

Probab=99.68  E-value=2.2e-17  Score=157.51  Aligned_cols=164  Identities=20%  Similarity=0.354  Sum_probs=125.4

Q ss_pred             ChhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccC-CCCCCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHH
Q psy16184          6 PPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFE-DPKDTPPPTRVETREERLERRRRERAEQVAYKLEQE   84 (363)
Q Consensus         6 p~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (363)
                      |=+|..||...++|-.+- +..+-.+++++|+ ++|.|.+... ..+.++.++.+.+..+.++.-.+++..         
T Consensus       193 pRdL~efFs~~gkVrdVr-iI~Dr~s~rskgi-~Yvef~D~~sVp~aiaLsGqrllg~pv~vq~sEaeknr---------  261 (549)
T KOG0147|consen  193 PRDLEEFFSIVGKVRDVR-IIGDRNSRRSKGI-AYVEFCDEQSVPLAIALSGQRLLGVPVIVQLSEAEKNR---------  261 (549)
T ss_pred             chhHHHHHHhhcCcceeE-eeccccchhhcce-eEEEEecccchhhHhhhcCCcccCceeEecccHHHHHH---------
Confidence            567999999999999884 4448889999999 9999987555 233456666665555444432222221         


Q ss_pred             HhhcCCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhC
Q psy16184         85 IALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHAD  164 (363)
Q Consensus        85 ~~~~~p~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~  164 (363)
                      .+...+.........|...||||||.+++++++|..+|+.||.|..|.++.|..||.++|||||+|.+.++|.+|+..||
T Consensus       262 ~a~~s~a~~~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~ln  341 (549)
T KOG0147|consen  262 AANASPALQGKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLN  341 (549)
T ss_pred             HHhccccccccccccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhc
Confidence            11111111112223344459999999999999999999999999999999998899999999999999999999999999


Q ss_pred             CceeCCEEEEEEeecc
Q psy16184        165 GKKIDGRRVLVDVERS  180 (363)
Q Consensus       165 g~~i~g~~i~V~~a~~  180 (363)
                      |.+|.|+.|+|.....
T Consensus       342 gfelAGr~ikV~~v~~  357 (549)
T KOG0147|consen  342 GFELAGRLIKVSVVTE  357 (549)
T ss_pred             cceecCceEEEEEeee
Confidence            9999999999987654

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

Probab=99.68  E-value=1.8e-17  Score=168.56  Aligned_cols=151  Identities=22%  Similarity=0.374  Sum_probs=119.7

Q ss_pred             ChhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccC--CCCCCCCCCCcccHHHHHHHHHHHHHHHHHHHHHH
Q psy16184          6 PPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFE--DPKDTPPPTRVETREERLERRRRERAEQVAYKLEQ   83 (363)
Q Consensus         6 p~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (363)
                      ..+|..+|..+|+|..+ -|+.+..|+++.|| +||.|.+...  .+...+....+.++.+.+....             
T Consensus        14 e~~L~~~F~~~G~v~~v-~v~~d~~t~~s~G~-afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~-------------   78 (562)
T TIGR01628        14 EAKLYDLFKPFGPVLSV-RVCRDSVTRRSLGY-GYVNFQNPADAERALETMNFKRLGGKPIRIMWSQ-------------   78 (562)
T ss_pred             HHHHHHHHHhcCCEEEE-EEEecCCCCCcceE-EEEEECCHHHHHHHHHHhCCCEECCeeEEeeccc-------------
Confidence            34699999999999887 47778999999999 9999988554  2333445555666555443211             


Q ss_pred             HHhhcCCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHh
Q psy16184         84 EIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA  163 (363)
Q Consensus        84 ~~~~~~p~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l  163 (363)
                              ..+........+|||+||+.++++++|.++|+.||.|..|.|+.+ .+|+++|||||+|.+.++|..||..|
T Consensus        79 --------~~~~~~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~-~~g~skg~afV~F~~~e~A~~Ai~~l  149 (562)
T TIGR01628        79 --------RDPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATD-ENGKSRGYGFVHFEKEESAKAAIQKV  149 (562)
T ss_pred             --------ccccccccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeec-CCCCcccEEEEEECCHHHHHHHHHHh
Confidence                    011111223458999999999999999999999999999999988 47889999999999999999999999


Q ss_pred             CCceeCCEEEEEEeecc
Q psy16184        164 DGKKIDGRRVLVDVERS  180 (363)
Q Consensus       164 ~g~~i~g~~i~V~~a~~  180 (363)
                      ||..+.|+.|.|.....
T Consensus       150 ng~~~~~~~i~v~~~~~  166 (562)
T TIGR01628       150 NGMLLNDKEVYVGRFIK  166 (562)
T ss_pred             cccEecCceEEEecccc
Confidence            99999999999976544

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

>KOG0117|consensus

Probab=99.67  E-value=2.8e-17  Score=152.92  Aligned_cols=170  Identities=24%  Similarity=0.454  Sum_probs=117.2

Q ss_pred             CCCCChhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccC--CCCCCCCCCCccc------------------
Q psy16184          2 TQFLPPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFE--DPKDTPPPTRVET------------------   61 (363)
Q Consensus         2 ~~~~p~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~--~~~~~~~~~~~~~------------------   61 (363)
                      ++.+..+|+-||...++|..| -+|++|.++.++|| .||+|.+..+  .+...+..++|..                  
T Consensus        93 rD~~EdeLvplfEkiG~I~el-RLMmD~~sG~nRGY-AFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~Svan~RLFiG  170 (506)
T KOG0117|consen   93 RDVFEDELVPLFEKIGKIYEL-RLMMDPFSGDNRGY-AFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCVSVANCRLFIG  170 (506)
T ss_pred             ccccchhhHHHHHhccceeeE-EEeecccCCCCcce-EEEEeecHHHHHHHHHHhhCccccCCCEeEEEEeeecceeEec
Confidence            355677899999999999999 58889999999999 9999988554  2222333332210                  


Q ss_pred             -------HHHHHHHHHH-HH------------------------------HHHHHHHH-HHHHhhcC---------CCCC
Q psy16184         62 -------REERLERRRR-ER------------------------------AEQVAYKL-EQEIALWD---------PNSF   93 (363)
Q Consensus        62 -------~~~~~~~~~~-~~------------------------------~~~~~~~~-~~~~~~~~---------p~~~   93 (363)
                             +.+.++..+. ..                              ++....++ .-....|.         |...
T Consensus       171 ~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwgn~~tVdWAep~~e  250 (506)
T KOG0117|consen  171 NIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIKLWGNAITVDWAEPEEE  250 (506)
T ss_pred             cCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCCceeecCCcceeeccCcccC
Confidence                   0111110000 00                              00000000 00001111         1111


Q ss_pred             CCC-CCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEE
Q psy16184         94 PNA-TMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRR  172 (363)
Q Consensus        94 ~~~-~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~  172 (363)
                      +.. .....+.|||.||+.+||++.|+++|..||.|..|+.+.|        ||||.|.+.++|.+|+..|||++|+|..
T Consensus       251 ~ded~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD--------YaFVHf~eR~davkAm~~~ngkeldG~~  322 (506)
T KOG0117|consen  251 PDEDTMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD--------YAFVHFAEREDAVKAMKETNGKELDGSP  322 (506)
T ss_pred             CChhhhhheeeeeeeccchhhhHHHHHHHHHhccceEEeecccc--------eeEEeecchHHHHHHHHHhcCceecCce
Confidence            111 1123568999999999999999999999999999999876        9999999999999999999999999999


Q ss_pred             EEEEeeccc
Q psy16184        173 VLVDVERSR  181 (363)
Q Consensus       173 i~V~~a~~~  181 (363)
                      |.|.+|++.
T Consensus       323 iEvtLAKP~  331 (506)
T KOG0117|consen  323 IEVTLAKPV  331 (506)
T ss_pred             EEEEecCCh
Confidence            999999874

>KOG0122|consensus

Probab=99.66  E-value=3.2e-16  Score=135.56  Aligned_cols=83  Identities=25%  Similarity=0.458  Sum_probs=79.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      +..++|-|.||+.++++++|+++|.+||.|..|.|..|+.||.++|||||+|.+.++|.+||..|||+-++.-.|.|+|+
T Consensus       187 ~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEws  266 (270)
T KOG0122|consen  187 DDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWS  266 (270)
T ss_pred             CccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEec
Confidence            35678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccc
Q psy16184        179 RSR  181 (363)
Q Consensus       179 ~~~  181 (363)
                      ++.
T Consensus       267 kP~  269 (270)
T KOG0122|consen  267 KPS  269 (270)
T ss_pred             CCC
Confidence            874

>KOG4205|consensus

Probab=99.66  E-value=1.7e-16  Score=146.29  Aligned_cols=158  Identities=20%  Similarity=0.354  Sum_probs=133.0

Q ss_pred             ChhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccC-CCCCCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHH
Q psy16184          6 PPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFE-DPKDTPPPTRVETREERLERRRRERAEQVAYKLEQE   84 (363)
Q Consensus         6 p~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (363)
                      ...|..+|..++-|..| .+|++|.|++++|| |||.|.+... .....+..+.|+++.++++++.....+         
T Consensus        20 ee~Lr~yf~~~Gev~d~-~vm~d~~t~rsrgF-gfv~f~~~~~v~~vl~~~~h~~dgr~ve~k~av~r~~~---------   88 (311)
T KOG4205|consen   20 EESLREYFSQFGEVTDC-VVMRDPSTGRSRGF-GFVTFATPEGVDAVLNARTHKLDGRSVEPKRAVSREDQ---------   88 (311)
T ss_pred             HHHHHHHhcccCceeeE-EEeccCCCCCcccc-cceecCCCcchheeecccccccCCccccceeccCcccc---------
Confidence            34688999999999999 79999999999999 9999986555 667778899999998888763221110         


Q ss_pred             HhhcCCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhC
Q psy16184         85 IALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHAD  164 (363)
Q Consensus        85 ~~~~~p~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~  164 (363)
                              ........+.+||||+||..+++.+|+++|.+||.|..+.|+.|..+..++||+||+|.+.+.+.+++. +.
T Consensus        89 --------~~~~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~  159 (311)
T KOG4205|consen   89 --------TKVGRHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QK  159 (311)
T ss_pred             --------cccccccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-cc
Confidence                    000111246799999999999999999999999999999999999999999999999999999999988 68


Q ss_pred             CceeCCEEEEEEeecccCC
Q psy16184        165 GKKIDGRRVLVDVERSRTV  183 (363)
Q Consensus       165 g~~i~g~~i~V~~a~~~~~  183 (363)
                      -+.|+|+.|.|..|.++..
T Consensus       160 f~~~~gk~vevkrA~pk~~  178 (311)
T KOG4205|consen  160 FHDFNGKKVEVKRAIPKEV  178 (311)
T ss_pred             eeeecCceeeEeeccchhh
Confidence            8999999999999988654

>PF00076 RRM_1: RNA recognition motif

Probab=99.66  E-value=5.9e-16  Score=112.44  Aligned_cols=70  Identities=39%  Similarity=0.755  Sum_probs=67.2

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEE
Q psy16184        104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVL  174 (363)
Q Consensus       104 l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~  174 (363)
                      |||+|||+.+|+++|.++|.+||.|..+.|..+ .++..+|||||+|.+.++|..|+..|||..|+|+.|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            799999999999999999999999999999887 6889999999999999999999999999999999885

(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 ....

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.66  E-value=3.8e-16  Score=148.01  Aligned_cols=83  Identities=25%  Similarity=0.443  Sum_probs=79.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184         98 MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      ....++|||+|||+++|+++|+++|..||.|+.|.|+.++.|++++|||||+|.++++|..||..||+..|.++.|.|.+
T Consensus       104 ~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~  183 (346)
T TIGR01659       104 NNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSY  183 (346)
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeec
Confidence            34578999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecc
Q psy16184        178 ERS  180 (363)
Q Consensus       178 a~~  180 (363)
                      +.+
T Consensus       184 a~p  186 (346)
T TIGR01659       184 ARP  186 (346)
T ss_pred             ccc
Confidence            865

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).

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

Probab=99.64  E-value=2.6e-15  Score=150.00  Aligned_cols=80  Identities=30%  Similarity=0.633  Sum_probs=76.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      ..++|||+||++.+++++|+++|.+||.|..|.|+.|+.|++++|||||+|.+.++|..||..|||..|.|+.|.|.+..
T Consensus       106 ~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~  185 (612)
T TIGR01645       106 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  185 (612)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecccc
Confidence            46799999999999999999999999999999999999999999999999999999999999999999999999998643

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.

>KOG0149|consensus

Probab=99.62  E-value=5.7e-16  Score=133.61  Aligned_cols=79  Identities=29%  Similarity=0.612  Sum_probs=74.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeecc
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS  180 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~  180 (363)
                      .++||||||+|.++.+.|+.+|++||+|.++.|+.|+.||+++|||||+|.+.++|..|++. .+-.|+|++..|++|.-
T Consensus        12 ~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcnlA~l   90 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCNLASL   90 (247)
T ss_pred             EEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccchhhh
Confidence            56899999999999999999999999999999999999999999999999999999999996 45789999999998753

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

Probab=99.62  E-value=6.5e-16  Score=153.96  Aligned_cols=77  Identities=22%  Similarity=0.515  Sum_probs=71.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhh--CCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVY--GPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~--G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      ..++|||+||++.+|+++|+++|+.|  |.|..|.++.        +||||+|.+.++|.+||..||+..|+|+.|.|.|
T Consensus       232 ~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~r--------gfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~  303 (578)
T TIGR01648       232 KVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIR--------DYAFVHFEDREDAVKAMDELNGKELEGSEIEVTL  303 (578)
T ss_pred             cccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeec--------CeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            35789999999999999999999999  9999998753        6999999999999999999999999999999999


Q ss_pred             ecccCCC
Q psy16184        178 ERSRTVK  184 (363)
Q Consensus       178 a~~~~~~  184 (363)
                      +++....
T Consensus       304 Akp~~~~  310 (578)
T TIGR01648       304 AKPVDKK  310 (578)
T ss_pred             ccCCCcc
Confidence            9886554

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.

>KOG0145|consensus

Probab=99.61  E-value=2.6e-16  Score=137.03  Aligned_cols=80  Identities=19%  Similarity=0.354  Sum_probs=76.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeecc
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS  180 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~  180 (363)
                      ..+|||-||.+++.+..|.++|.+||.|..|+|+.|..|.+++|||||++.+-++|..||..|||..+.++.|.|.+...
T Consensus       278 g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFKtn  357 (360)
T KOG0145|consen  278 GWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTN  357 (360)
T ss_pred             eeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEecC
Confidence            56899999999999999999999999999999999999999999999999999999999999999999999999998754

>KOG0131|consensus

Probab=99.61  E-value=3.1e-15  Score=124.07  Aligned_cols=149  Identities=24%  Similarity=0.389  Sum_probs=116.2

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccCCCCCCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFEDPKDTPPPTRVETREERLERRRRERAEQVAYKLEQEIA   86 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   86 (363)
                      +-|..||-+.+|+..+ -++++-.|....|| ||+.|.++...                          +.+-++-.+..
T Consensus        24 ~~l~EL~iqagpVv~i-~iPkDrv~~~~qGy-gF~Ef~~eeda--------------------------dYAikiln~Vk   75 (203)
T KOG0131|consen   24 ELLYELFIQAGPVVNL-HIPKDRVTQKHQGY-GFAEFRTEEDA--------------------------DYAIKILNMVK   75 (203)
T ss_pred             HHHHHHHHhcCceeee-ecchhhhcccccce-eEEEEechhhh--------------------------HHHHHHHHHHH
Confidence            3478899999999988 47788889999999 99999665421                          11222222333


Q ss_pred             hcCCC------CCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccE-EEEeccCCCCCcceEEEEEecCHHHHHHH
Q psy16184         87 LWDPN------SFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKK-IVMVHNKVTGKPRGYAFIEYEHERDMHSA  159 (363)
Q Consensus        87 ~~~p~------~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~-v~i~~d~~t~~~~g~afV~f~~~~~a~~A  159 (363)
                      .++-.      .......+.+.+|||+||.+.+++..|...|+.||.|.. -.|+.+..||.++|||||.|.+.+.+.+|
T Consensus        76 LYgrpIrv~kas~~~~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~a  155 (203)
T KOG0131|consen   76 LYGRPIRVNKASAHQKNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAA  155 (203)
T ss_pred             hcCceeEEEecccccccccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHH
Confidence            33211      111222334579999999999999999999999998764 47888989999999999999999999999


Q ss_pred             HHHhCCceeCCEEEEEEeecccCC
Q psy16184        160 YKHADGKKIDGRRVLVDVERSRTV  183 (363)
Q Consensus       160 i~~l~g~~i~g~~i~V~~a~~~~~  183 (363)
                      |..|||..++.++|.|.++..+..
T Consensus       156 i~s~ngq~l~nr~itv~ya~k~~~  179 (203)
T KOG0131|consen  156 IGSMNGQYLCNRPITVSYAFKKDT  179 (203)
T ss_pred             HHHhccchhcCCceEEEEEEecCC
Confidence            999999999999999999976543

>KOG0127|consensus

Probab=99.59  E-value=9.4e-16  Score=145.86  Aligned_cols=81  Identities=31%  Similarity=0.597  Sum_probs=75.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHh-----CC-ceeCCEEEE
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA-----DG-KKIDGRRVL  174 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l-----~g-~~i~g~~i~  174 (363)
                      ..+|||.|||+++|++.|.++|.+||+|..+.|+.++.|++++|.|||.|.++..|..||.+.     .| ..|+|+.|.
T Consensus       292 ~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR~Lk  371 (678)
T KOG0127|consen  292 GKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGRLLK  371 (678)
T ss_pred             cceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEeccEEe
Confidence            369999999999999999999999999999999999999999999999999999999999975     23 688999999


Q ss_pred             EEeeccc
Q psy16184        175 VDVERSR  181 (363)
Q Consensus       175 V~~a~~~  181 (363)
                      |..|-++
T Consensus       372 v~~Av~R  378 (678)
T KOG0127|consen  372 VTLAVTR  378 (678)
T ss_pred             eeeccch
Confidence            9998653

>KOG0124|consensus

Probab=99.59  E-value=2e-15  Score=137.21  Aligned_cols=158  Identities=19%  Similarity=0.307  Sum_probs=115.0

Q ss_pred             hhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccC--CCCCCCCCCCcccHHHHHHHH-HHHHHHHHHHHHHHH
Q psy16184          8 NLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFE--DPKDTPPPTRVETREERLERR-RRERAEQVAYKLEQE   84 (363)
Q Consensus         8 ~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~--~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~   84 (363)
                      -|...|.|+|||..+. +.+||.|++.+|| .||.|.-...  -+.+.++..-+.++-+++-+- ...+++..--.++++
T Consensus       129 tiR~AF~PFGPIKSIn-MSWDp~T~kHKgF-AFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPsNmpQAQpiID~vqee  206 (544)
T KOG0124|consen  129 TIRRAFDPFGPIKSIN-MSWDPATGKHKGF-AFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNMPQAQPIIDMVQEE  206 (544)
T ss_pred             HHHhhccCCCCcceee-cccccccccccce-EEEEEeCcHHHHHHHHHhccccccCccccccCCCCCcccchHHHHHHHH
Confidence            4677899999999994 8899999999999 5555533221  111223333333333322210 000111111111111


Q ss_pred             HhhcCCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhC
Q psy16184         85 IALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHAD  164 (363)
Q Consensus        85 ~~~~~p~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~  164 (363)
                      ..             ..+.|||..+.+++++++|+..|+.||+|..|.+..++.++.++||+||+|.+..+...||..||
T Consensus       207 Ak-------------~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMN  273 (544)
T KOG0124|consen  207 AK-------------KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMN  273 (544)
T ss_pred             HH-------------hhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcc
Confidence            11             24689999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CceeCCEEEEEEeecc
Q psy16184        165 GKKIDGRRVLVDVERS  180 (363)
Q Consensus       165 g~~i~g~~i~V~~a~~  180 (363)
                      =..|+|..|.|-.+-.
T Consensus       274 lFDLGGQyLRVGk~vT  289 (544)
T KOG0124|consen  274 LFDLGGQYLRVGKCVT  289 (544)
T ss_pred             hhhcccceEecccccC
Confidence            9999999999987654

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

Probab=99.58  E-value=1.4e-16  Score=160.21  Aligned_cols=171  Identities=15%  Similarity=0.175  Sum_probs=113.0

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccC--CCCCCCCCCCcccHHHHHHHHHHHHHHHHHHH----
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFE--DPKDTPPPTRVETREERLERRRRERAEQVAYK----   80 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----   80 (363)
                      .+|..+|+.+|+|..+ .+..++.++.++|| +||.|.+...  .+...+....+.+..+.++.............    
T Consensus       310 ~~l~~~f~~~G~i~~~-~~~~~~~~g~~~g~-afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~~~~~~~~~~~~~  387 (509)
T TIGR01642       310 DQIKELLESFGDLKAF-NLIKDIATGLSKGY-AFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVGANQATIDTSNGM  387 (509)
T ss_pred             HHHHHHHHhcCCeeEE-EEEecCCCCCcCeE-EEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccCCCCCCccccccc
Confidence            4588999999999887 45668889999999 9999977443  23334555555554333222110000000000    


Q ss_pred             --HHHHHhhcCCCCCCCCCCCCCCeEEEcCCCCCC----------CHHHHHHHHHhhCCccEEEEeccC---CCCCcceE
Q psy16184         81 --LEQEIALWDPNSFPNATMDPFKTLFIARVNYDT----------SESKLRREFEVYGPIKKIVMVHNK---VTGKPRGY  145 (363)
Q Consensus        81 --~~~~~~~~~p~~~~~~~~~~~~~l~V~nL~~~~----------t~~~L~~~F~~~G~i~~v~i~~d~---~t~~~~g~  145 (363)
                        +...... ...........++.+|+|.||...-          ..++|+++|.+||.|..|.|+.+.   .++...||
T Consensus       388 ~~~~~~~~~-~~~~~~~~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~~~~~~~~~~~~G~  466 (509)
T TIGR01642       388 APVTLLAKA-LSQSILQIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGK  466 (509)
T ss_pred             ccccccccc-chhhhccccCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeeccCcCCCcCCCcce
Confidence              0000000 0000111223467889999996321          236789999999999999998642   34566899


Q ss_pred             EEEEecCHHHHHHHHHHhCCceeCCEEEEEEeecc
Q psy16184        146 AFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS  180 (363)
Q Consensus       146 afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~  180 (363)
                      |||+|.+.++|++||..|||..|+|+.|.|.|...
T Consensus       467 ~fV~F~~~e~A~~A~~~lnGr~~~gr~v~~~~~~~  501 (509)
T TIGR01642       467 VFLEYADVRSAEKAMEGMNGRKFNDRVVVAAFYGE  501 (509)
T ss_pred             EEEEECCHHHHHHHHHHcCCCEECCeEEEEEEeCH
Confidence            99999999999999999999999999999999754

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

>KOG0126|consensus

Probab=99.58  E-value=1.6e-16  Score=131.58  Aligned_cols=81  Identities=32%  Similarity=0.541  Sum_probs=77.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      .+.-|||||||+.+|+.+|.-+|++||+|+.|.|+.|+.||+++||||+.|++..+..-|+..|||..|.|+.|.|.+..
T Consensus        34 dsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv~  113 (219)
T KOG0126|consen   34 DSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHVS  113 (219)
T ss_pred             cceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeecc
Confidence            35689999999999999999999999999999999999999999999999999999999999999999999999999865


Q ss_pred             c
Q psy16184        180 S  180 (363)
Q Consensus       180 ~  180 (363)
                      .
T Consensus       114 ~  114 (219)
T KOG0126|consen  114 N  114 (219)
T ss_pred             c
Confidence            4

>KOG0105|consensus

Probab=99.58  E-value=1.1e-14  Score=121.00  Aligned_cols=80  Identities=28%  Similarity=0.486  Sum_probs=71.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      ..++|||||||.+|.+.+|+++|-+||.|.+|.|...   ..+.+||||+|+++.+|+.||..-+|..++|..|.|+++.
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r---~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfpr   81 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNR---PGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPR   81 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccC---CCCCCeeEEEecCccchhhhhhcccccccCcceEEEEecc
Confidence            4679999999999999999999999999999998532   2345799999999999999999999999999999999997


Q ss_pred             ccC
Q psy16184        180 SRT  182 (363)
Q Consensus       180 ~~~  182 (363)
                      .-.
T Consensus        82 ggr   84 (241)
T KOG0105|consen   82 GGR   84 (241)
T ss_pred             CCC
Confidence            643

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.57  E-value=1.1e-14  Score=129.82  Aligned_cols=76  Identities=16%  Similarity=0.302  Sum_probs=70.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeecc
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS  180 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~  180 (363)
                      .++|||+||++.+|+++|+++|+.||.|..|.|+.+..   .+|||||+|.+.++|..||. |||..|.|+.|.|.++..
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccC
Confidence            56999999999999999999999999999999988753   46899999999999999996 999999999999999864

>KOG0130|consensus

Probab=99.57  E-value=5.9e-15  Score=116.45  Aligned_cols=84  Identities=27%  Similarity=0.444  Sum_probs=79.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      .....|||+++...+|+++|.+.|..||+|+.|.|-.|..||-.+|||+|+|++.+.|++||..|||..|.|..|.|.|+
T Consensus        70 VEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~  149 (170)
T KOG0130|consen   70 VEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWC  149 (170)
T ss_pred             eeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEE
Confidence            34678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccC
Q psy16184        179 RSRT  182 (363)
Q Consensus       179 ~~~~  182 (363)
                      ..+.
T Consensus       150 Fv~g  153 (170)
T KOG0130|consen  150 FVKG  153 (170)
T ss_pred             EecC
Confidence            7643

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.57  E-value=1.2e-14  Score=105.84  Aligned_cols=70  Identities=37%  Similarity=0.753  Sum_probs=64.8

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEE
Q psy16184        104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVL  174 (363)
Q Consensus       104 l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~  174 (363)
                      |||+|||+++++++|.++|..||.|..+.+..++. +..+|+|||+|.+.++|..|+..+++..|+|+.|.
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            79999999999999999999999999999999876 89999999999999999999999999999999884

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 ....

>KOG0111|consensus

Probab=99.54  E-value=5.2e-15  Score=126.01  Aligned_cols=85  Identities=24%  Similarity=0.479  Sum_probs=80.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      ...++||||+|...+|+.-|...|-+||.|..|.|+.|-.+++.+|||||+|...++|.+||..||+.+|.|+.|.|.+|
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~A   87 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLA   87 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeec
Confidence            34679999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccCC
Q psy16184        179 RSRTV  183 (363)
Q Consensus       179 ~~~~~  183 (363)
                      ++...
T Consensus        88 kP~ki   92 (298)
T KOG0111|consen   88 KPEKI   92 (298)
T ss_pred             CCccc
Confidence            98543

>PLN03213 repressor of silencing 3; Provisional

Probab=99.53  E-value=2.6e-14  Score=134.58  Aligned_cols=77  Identities=16%  Similarity=0.367  Sum_probs=71.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCH--HHHHHHHHHhCCceeCCEEEEEEe
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHE--RDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~--~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      ...+||||||++.+|+++|..+|..||.|..|.|+  +.||  +|||||+|.+.  .++.+||..|||..+.|+.|+|+.
T Consensus         9 ~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIp--RETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNK   84 (759)
T PLN03213          9 GGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFV--RTKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEK   84 (759)
T ss_pred             cceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEe--cccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEee
Confidence            35689999999999999999999999999999999  4567  89999999987  789999999999999999999999


Q ss_pred             ecc
Q psy16184        178 ERS  180 (363)
Q Consensus       178 a~~  180 (363)
                      |++
T Consensus        85 AKP   87 (759)
T PLN03213         85 AKE   87 (759)
T ss_pred             ccH
Confidence            875

>KOG0144|consensus

Probab=99.53  E-value=1.2e-14  Score=134.97  Aligned_cols=147  Identities=17%  Similarity=0.303  Sum_probs=108.8

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccCC--CCCC------CC--CCCcccHHHHHHHHHHHHHHH
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFED--PKDT------PP--PTRVETREERLERRRRERAEQ   76 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~~--~~~~------~~--~~~~~~~~~~~~~~~~~~~~~   76 (363)
                      -+|..+|++++-|-.+. |.+|..|+.++|+ =||.|....+.  +..+      ++  -+.|..+-..-          
T Consensus        49 ~dlr~lFe~yg~V~ein-l~kDk~t~~s~gc-CFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqvk~Ad~----------  116 (510)
T KOG0144|consen   49 KDLRELFEKYGNVYEIN-LIKDKSTGQSKGC-CFVKYYTRKEADEAINALHNQKTLPGMHHPVQVKYADG----------  116 (510)
T ss_pred             HHHHHHHHHhCceeEEE-eecccccCcccce-EEEEeccHHHHHHHHHHhhcccccCCCCcceeecccch----------
Confidence            47899999999988884 6779999999999 66666442210  0000      00  01111111110          


Q ss_pred             HHHHHHHHHhhcCCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHH
Q psy16184         77 VAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDM  156 (363)
Q Consensus        77 ~~~~~~~~~~~~~p~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a  156 (363)
                                       .........+||||-|+..+||.+|+++|.+||.|++|.|+.+. .+.++|||||+|.+.+.|
T Consensus       117 -----------------E~er~~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~-~~~sRGcaFV~fstke~A  178 (510)
T KOG0144|consen  117 -----------------ERERIVEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDP-DGLSRGCAFVKFSTKEMA  178 (510)
T ss_pred             -----------------hhhccccchhhhhhhccccccHHHHHHHHHhhCccchhhheecc-cccccceeEEEEehHHHH
Confidence                             11111335689999999999999999999999999999999984 799999999999999999


Q ss_pred             HHHHHHhCCce-eC--CEEEEEEeecccCC
Q psy16184        157 HSAYKHADGKK-ID--GRRVLVDVERSRTV  183 (363)
Q Consensus       157 ~~Ai~~l~g~~-i~--g~~i~V~~a~~~~~  183 (363)
                      ..||+.|||.. +.  ..+|.|.||.+...
T Consensus       179 ~~Aika~ng~~tmeGcs~PLVVkFADtqkd  208 (510)
T KOG0144|consen  179 VAAIKALNGTQTMEGCSQPLVVKFADTQKD  208 (510)
T ss_pred             HHHHHhhccceeeccCCCceEEEecccCCC
Confidence            99999999964 44  45899999987644

>KOG0125|consensus

Probab=99.52  E-value=4.5e-14  Score=127.05  Aligned_cols=82  Identities=23%  Similarity=0.497  Sum_probs=75.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184         98 MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      .+..+.|+|.|||+...+.||..+|.+||.|.+|.|+.+  .-.++|||||+|++.++|++|-+.|||..|.|++|.|..
T Consensus        93 ~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfN--ERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~  170 (376)
T KOG0125|consen   93 KDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFN--ERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNN  170 (376)
T ss_pred             CCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEec--cCCCCccceEEecChhhHHHHHHHhhcceeeceEEEEec
Confidence            344679999999999999999999999999999999986  355789999999999999999999999999999999999


Q ss_pred             eccc
Q psy16184        178 ERSR  181 (363)
Q Consensus       178 a~~~  181 (363)
                      |..+
T Consensus       171 ATar  174 (376)
T KOG0125|consen  171 ATAR  174 (376)
T ss_pred             cchh
Confidence            8764

>KOG0123|consensus

Probab=99.51  E-value=1.1e-14  Score=138.75  Aligned_cols=141  Identities=21%  Similarity=0.384  Sum_probs=116.0

Q ss_pred             CChhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccC--CCCCCCCCCCcccHHHHHHHHHHHHHHHHHHHHH
Q psy16184          5 LPPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFE--DPKDTPPPTRVETREERLERRRRERAEQVAYKLE   82 (363)
Q Consensus         5 ~p~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (363)
                      ..+.|..+|.+.+|+..+ -|.++. |  +-|| |+|.|.....  .+.++++...+.++.+++....            
T Consensus        11 ~e~~l~~~f~~~~~v~s~-rvc~d~-t--slgy-~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~------------   73 (369)
T KOG0123|consen   11 TEAMLFDKFSPAGPVLSI-RVCRDA-T--SLGY-AYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQ------------   73 (369)
T ss_pred             ChHHHHHHhcccCCceeE-EEeecC-C--ccce-EEEecCCHHHHHHHHHHcCCcccCCcEEEeehhc------------
Confidence            457899999999999988 477788 7  9999 9999977554  3444566666666666655411            


Q ss_pred             HHHhhcCCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHH
Q psy16184         83 QEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH  162 (363)
Q Consensus        83 ~~~~~~~p~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~  162 (363)
                                     .+ ...|||.||+..++...|.++|+.||.|..|++..+. .| ++|| ||+|++++.|.+||..
T Consensus        74 ---------------rd-~~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~-~g-~kg~-FV~f~~e~~a~~ai~~  134 (369)
T KOG0123|consen   74 ---------------RD-PSLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDE-NG-SKGY-FVQFESEESAKKAIEK  134 (369)
T ss_pred             ---------------cC-CceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcC-CC-ceee-EEEeCCHHHHHHHHHH
Confidence                           01 1129999999999999999999999999999999985 45 8999 9999999999999999


Q ss_pred             hCCceeCCEEEEEEeeccc
Q psy16184        163 ADGKKIDGRRVLVDVERSR  181 (363)
Q Consensus       163 l~g~~i~g~~i~V~~a~~~  181 (363)
                      |||..+.|+.|.|.....+
T Consensus       135 ~ng~ll~~kki~vg~~~~~  153 (369)
T KOG0123|consen  135 LNGMLLNGKKIYVGLFERK  153 (369)
T ss_pred             hcCcccCCCeeEEeeccch
Confidence            9999999999999887654

>KOG0131|consensus

Probab=99.51  E-value=2.2e-14  Score=119.07  Aligned_cols=82  Identities=28%  Similarity=0.416  Sum_probs=78.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184         98 MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      .++..|||||||+..++++.|.++|-++|.|..+.|+.|+.|...+|||||+|.++++|+-||..||...|-|++|.|..
T Consensus         6 rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~k   85 (203)
T KOG0131|consen    6 RNQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNK   85 (203)
T ss_pred             cCCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEe
Confidence            34567999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ec
Q psy16184        178 ER  179 (363)
Q Consensus       178 a~  179 (363)
                      +.
T Consensus        86 as   87 (203)
T KOG0131|consen   86 AS   87 (203)
T ss_pred             cc
Confidence            86

>KOG0148|consensus

Probab=99.50  E-value=5e-14  Score=123.69  Aligned_cols=82  Identities=20%  Similarity=0.483  Sum_probs=78.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeecc
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS  180 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~  180 (363)
                      ..-|||+.|...++-+.|++.|.+||+|.+++|+.|..|++++|||||.|.+.++|+.||..|||..|+++.|...||..
T Consensus        62 hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATR  141 (321)
T KOG0148|consen   62 HFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATR  141 (321)
T ss_pred             ceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeecccccc
Confidence            45799999999999999999999999999999999999999999999999999999999999999999999999999976


Q ss_pred             cC
Q psy16184        181 RT  182 (363)
Q Consensus       181 ~~  182 (363)
                      ++
T Consensus       142 Kp  143 (321)
T KOG0148|consen  142 KP  143 (321)
T ss_pred             Cc
Confidence            55

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.50  E-value=1.2e-13  Score=121.34  Aligned_cols=76  Identities=14%  Similarity=0.197  Sum_probs=69.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeecc
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS  180 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~  180 (363)
                      ..+|||+||++.+|+++|++||+.||.|..|.|+.+.   ...|||||+|.+++.|..||. |||..|.++.|.|..+..
T Consensus         5 g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~~~   80 (243)
T PLN03121          5 GYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRWGQ   80 (243)
T ss_pred             ceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeCcc
Confidence            5799999999999999999999999999999999874   445899999999999999996 999999999999998653

>smart00362 RRM_2 RNA recognition motif

Probab=99.50  E-value=1.8e-13  Score=98.82  Aligned_cols=72  Identities=35%  Similarity=0.717  Sum_probs=67.4

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEE
Q psy16184        103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD  176 (363)
Q Consensus       103 ~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~  176 (363)
                      +|||+|||..++.++|..+|..||.|..+.+..++  +.+.|+|||+|.+.+.|..|+..|++..|.|+.|.|.
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            58999999999999999999999999999998775  7788999999999999999999999999999999873

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

Probab=99.49  E-value=1.2e-13  Score=137.85  Aligned_cols=79  Identities=27%  Similarity=0.440  Sum_probs=72.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC-CEEEEEEe
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKID-GRRVLVDV  177 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~-g~~i~V~~  177 (363)
                      ...++|||+|||+++++++|.++|.+||.|..|.|+.| .+|.++|||||+|.+.++|+.||..||+..|. |+.|.|.+
T Consensus        56 ~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~  134 (578)
T TIGR01648        56 GRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCI  134 (578)
T ss_pred             CCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCccccccc
Confidence            34689999999999999999999999999999999999 79999999999999999999999999999885 77776665


Q ss_pred             e
Q psy16184        178 E  178 (363)
Q Consensus       178 a  178 (363)
                      +
T Consensus       135 S  135 (578)
T TIGR01648       135 S  135 (578)
T ss_pred             c
Confidence            4

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.

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

Probab=99.48  E-value=1.4e-13  Score=136.64  Aligned_cols=80  Identities=18%  Similarity=0.405  Sum_probs=76.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      +.++|||+|||+.+++++|.++|.+||.|..|.|+.++.++.++|||||+|.+.++|.+||. |+|..|.|+.|.|.++.
T Consensus        88 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~~~  166 (457)
T TIGR01622        88 DDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQSSQ  166 (457)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEeecc
Confidence            46799999999999999999999999999999999999999999999999999999999998 89999999999999865


Q ss_pred             c
Q psy16184        180 S  180 (363)
Q Consensus       180 ~  180 (363)
                      .
T Consensus       167 ~  167 (457)
T TIGR01622       167 A  167 (457)
T ss_pred             h
Confidence            4

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

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

Probab=99.48  E-value=1.3e-14  Score=144.68  Aligned_cols=152  Identities=16%  Similarity=0.229  Sum_probs=104.4

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccCCC--CC--CCCCCCcccHHHHHHHHHHHHHHHHHHHHH
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFEDP--KD--TPPPTRVETREERLERRRRERAEQVAYKLE   82 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~~~--~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (363)
                      .+|..+|+++|+|..+. ++      +++|| +||.|.+.....  ..  ...+..+.++.+.++.......        
T Consensus        17 ~~L~~~f~~fG~V~~v~-i~------~~k~~-afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s~~~~~--------   80 (481)
T TIGR01649        17 ADLVEALIPFGPVSYVM-ML------PGKRQ-ALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYSTSQEI--------   80 (481)
T ss_pred             HHHHHHHHhcCCeeEEE-EE------CCCCE-EEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEecCCccc--------
Confidence            46999999999999873 32      24678 899997754411  11  1245556665544433110000        


Q ss_pred             HHHhhcCCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHH
Q psy16184         83 QEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH  162 (363)
Q Consensus        83 ~~~~~~~p~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~  162 (363)
                         .................+|||+||++.+|+++|.++|+.||.|..|.|+.+.    ..|+|||+|.+.++|.+|+..
T Consensus        81 ---~~~~~~~~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~----~~~~afVef~~~~~A~~A~~~  153 (481)
T TIGR01649        81 ---KRDGNSDFDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKN----NVFQALVEFESVNSAQHAKAA  153 (481)
T ss_pred             ---ccCCCCcccCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecC----CceEEEEEECCHHHHHHHHHH
Confidence               0000000001111234579999999999999999999999999999997653    247999999999999999999


Q ss_pred             hCCceeCC--EEEEEEeeccc
Q psy16184        163 ADGKKIDG--RRVLVDVERSR  181 (363)
Q Consensus       163 l~g~~i~g--~~i~V~~a~~~  181 (363)
                      |||..|.|  ..|.|+|++..
T Consensus       154 Lng~~i~~~~~~l~v~~sk~~  174 (481)
T TIGR01649       154 LNGADIYNGCCTLKIEYAKPT  174 (481)
T ss_pred             hcCCcccCCceEEEEEEecCC
Confidence            99999965  58999998763

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).

>KOG0109|consensus

Probab=99.47  E-value=9.9e-15  Score=129.26  Aligned_cols=133  Identities=22%  Similarity=0.375  Sum_probs=104.3

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccC--CCCCCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHH
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFE--DPKDTPPPTRVETREERLERRRRERAEQVAYKLEQE   84 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (363)
                      ..|..||++++.|.-|..|..         | |||...+...  ++..++..-.+.+..|.++.                
T Consensus        17 ~elr~lFe~ygkVlECDIvKN---------Y-gFVHiEdktaaedairNLhgYtLhg~nInVea----------------   70 (346)
T KOG0109|consen   17 QELRSLFEQYGKVLECDIVKN---------Y-GFVHIEDKTAAEDAIRNLHGYTLHGVNINVEA----------------   70 (346)
T ss_pred             HHHHHHHHhhCceEeeeeecc---------c-ceEEeecccccHHHHhhcccceecceEEEEEe----------------
Confidence            458899999999999976653         7 8887654333  22333444445554444432                


Q ss_pred             HhhcCCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhC
Q psy16184         85 IALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHAD  164 (363)
Q Consensus        85 ~~~~~p~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~  164 (363)
                               .......+++|+||||.+.++.++|+..|.+||.|.+|.|+.|        |+||.|.-.++|..||..||
T Consensus        71 ---------SksKsk~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd--------y~fvh~d~~eda~~air~l~  133 (346)
T KOG0109|consen   71 ---------SKSKSKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD--------YAFVHFDRAEDAVEAIRGLD  133 (346)
T ss_pred             ---------ccccCCCccccccCCCCccccCHHHhhhhcccCCceeeeeecc--------eeEEEEeeccchHHHHhccc
Confidence                     1112345789999999999999999999999999999999875        99999999999999999999


Q ss_pred             CceeCCEEEEEEeecccC
Q psy16184        165 GKKIDGRRVLVDVERSRT  182 (363)
Q Consensus       165 g~~i~g~~i~V~~a~~~~  182 (363)
                      +.+|.|+.++|+++..+.
T Consensus       134 ~~~~~gk~m~vq~stsrl  151 (346)
T KOG0109|consen  134 NTEFQGKRMHVQLSTSRL  151 (346)
T ss_pred             ccccccceeeeeeecccc
Confidence            999999999999987643

>KOG0117|consensus

Probab=99.47  E-value=1.5e-13  Score=128.26  Aligned_cols=83  Identities=24%  Similarity=0.376  Sum_probs=76.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCcee-CCEEEEE
Q psy16184         97 TMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKI-DGRRVLV  175 (363)
Q Consensus        97 ~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i-~g~~i~V  175 (363)
                      .....+-||||.||.++.|++|.-+|++.|+|-++.|+.|+.+|.++|||||+|.+.+.|+.||..||+++| .|+.|.|
T Consensus        79 ~p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igv  158 (506)
T KOG0117|consen   79 PPPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGV  158 (506)
T ss_pred             CCCCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEE
Confidence            345578999999999999999999999999999999999999999999999999999999999999999988 5888777


Q ss_pred             Eeec
Q psy16184        176 DVER  179 (363)
Q Consensus       176 ~~a~  179 (363)
                      ..+.
T Consensus       159 c~Sv  162 (506)
T KOG0117|consen  159 CVSV  162 (506)
T ss_pred             EEee
Confidence            6543

>PF12220 U1snRNP70_N: U1 small nuclear ribonucleoprotein of 70kDa MW N terminal; InterPro: IPR022023 This domain is found in eukaryotes

Probab=99.47  E-value=2e-13  Score=104.80  Aligned_cols=93  Identities=55%  Similarity=0.972  Sum_probs=86.1

Q ss_pred             CCCCCChhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccCCCCCCCCCCCcccHHHHHHHHHHHHHHHHHHH
Q psy16184          1 MTQFLPPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFEDPKDTPPPTRVETREERLERRRRERAEQVAYK   80 (363)
Q Consensus         1 ~~~~~p~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (363)
                      ||.+|||+|+.||+|.|||.+++|+...|...+...|+||..|++.++....+.....++...+..++.+.++.++.+++
T Consensus         1 Mt~~lPp~ll~LF~PRPPL~y~pP~d~~p~~r~t~~itGvs~~l~~~~~~~~~~~~~~~et~~e~~~r~~~ek~~~~~~~   80 (94)
T PF12220_consen    1 MTSKLPPNLLALFAPRPPLPYLPPIDYPPEKRKTPPITGVSQYLSEFEDYKDEPPPEPTETKEERRERKRKEKKEKNEEK   80 (94)
T ss_pred             CcCcCCHHHHHHcCCCCCCCCCCccccCcccccCCCCCcHHHHHHHHhccccCCCCCCccCHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999888777899999999999888877778889999999999999999999999


Q ss_pred             HHHHHhhcCCCCC
Q psy16184         81 LEQEIALWDPNSF   93 (363)
Q Consensus        81 ~~~~~~~~~p~~~   93 (363)
                      +++++..|+|..+
T Consensus        81 l~~~l~~w~P~~D   93 (94)
T PF12220_consen   81 LEEELKEWDPHED   93 (94)
T ss_pred             HHHHHHhcCCCCC
Confidence            9999999999865

This domain is about 90 amino acids in length. This domain is found associated with PF00076 from PFAM. This domain is part of U1 snRNP, which is the pre-mRNA binding protein of the penta-snRNP spliceosome complex. It extends over a distance of 180 A from its RNA binding domain, wraps around the core domain of U1 snRNP consisting of the seven Sm proteins and finally contacts U1-C, which is crucial for 5'-splice-site recognition.

>smart00360 RRM RNA recognition motif

Probab=99.45  E-value=4.1e-13  Score=96.55  Aligned_cols=71  Identities=37%  Similarity=0.695  Sum_probs=67.1

Q ss_pred             EcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEE
Q psy16184        106 IARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD  176 (363)
Q Consensus       106 V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~  176 (363)
                      |+|||..+++++|..+|..||.|..+.|..++.++.++|||||+|.+.++|..|+..|++..|.|+.|.|.
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            68999999999999999999999999999887789999999999999999999999999999999998873

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

Probab=99.43  E-value=5.3e-13  Score=122.09  Aligned_cols=79  Identities=37%  Similarity=0.756  Sum_probs=76.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      .++|||+|||+.+|+++|.++|..||.|..|.|+.++.++.++|||||+|.+.++|..|+..|++..|.|+.|.|.++.
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~  193 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQ  193 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeeccc
Confidence            5899999999999999999999999999999999998899999999999999999999999999999999999999965

>KOG0114|consensus

Probab=99.42  E-value=9.7e-13  Score=99.35  Aligned_cols=79  Identities=27%  Similarity=0.455  Sum_probs=72.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      ..+..|||.|||+.+|.+++.++|.+||.|..|.|-.   +...+|-|||.|++..+|.+|+..|+|..++++.|.|-+.
T Consensus        16 evnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~---~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyy   92 (124)
T KOG0114|consen   16 EVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGN---TKETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYY   92 (124)
T ss_pred             hhheeEEEecCCccccHHHHHHHhhcccceEEEEecC---ccCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEec
Confidence            3467899999999999999999999999999999965   4456799999999999999999999999999999999987


Q ss_pred             cc
Q psy16184        179 RS  180 (363)
Q Consensus       179 ~~  180 (363)
                      .+
T Consensus        93 q~   94 (124)
T KOG0114|consen   93 QP   94 (124)
T ss_pred             CH
Confidence            65

>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=99.41  E-value=2e-12  Score=93.77  Aligned_cols=74  Identities=35%  Similarity=0.681  Sum_probs=68.6

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184        103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus       103 ~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      +|+|+|||+.+++++|.++|..||.|..+.+..++.+ .+.|+|||+|.+.++|..|+..+++..+.|..|.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~-~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDT-KSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCC-CcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            4899999999999999999999999999999887544 6789999999999999999999999999999999874

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).

>KOG0108|consensus

Probab=99.40  E-value=5.6e-13  Score=128.36  Aligned_cols=81  Identities=28%  Similarity=0.619  Sum_probs=78.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeeccc
Q psy16184        102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERSR  181 (363)
Q Consensus       102 ~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~~  181 (363)
                      +.|||||||+.+++++|..+|+..|.|..++++.|+.||+++|||||+|.+.+.|..|+..|||.++.|++|.|.|+...
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~   98 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNR   98 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeeccccc
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999999998754


Q ss_pred             C
Q psy16184        182 T  182 (363)
Q Consensus       182 ~  182 (363)
                      .
T Consensus        99 ~   99 (435)
T KOG0108|consen   99 K   99 (435)
T ss_pred             c
Confidence            3

>KOG0124|consensus

Probab=99.40  E-value=2.8e-13  Score=123.34  Aligned_cols=77  Identities=31%  Similarity=0.672  Sum_probs=74.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      .|.||||.|.+.+.++.|+..|..||.|+.|.+.+|+.|++++|||||+|+-++.|+-|++.|||..++|+.|+|..
T Consensus       113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgr  189 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGR  189 (544)
T ss_pred             hHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccC
Confidence            47899999999999999999999999999999999999999999999999999999999999999999999999984

>KOG4676|consensus

Probab=99.39  E-value=5e-13  Score=122.74  Aligned_cols=79  Identities=9%  Similarity=0.145  Sum_probs=65.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCC---CCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184        102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKV---TGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus       102 ~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~---t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      ..|.|.||.+++|.++|+.||..+|.|.++.|+.+..   .....-.|||.|.+...+..|.++.|.++|+-..|+|.+.
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQhLtntvfvdraliv~p~~   87 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQHLTNTVFVDRALIVRPYG   87 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhhhccceeeeeeEEEEecC
Confidence            3899999999999999999999999999999876321   2334568999999999999999977777777777777765


Q ss_pred             cc
Q psy16184        179 RS  180 (363)
Q Consensus       179 ~~  180 (363)
                      ..
T Consensus        88 ~~   89 (479)
T KOG4676|consen   88 DE   89 (479)
T ss_pred             CC
Confidence            54

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

Probab=99.37  E-value=2.3e-12  Score=128.45  Aligned_cols=78  Identities=23%  Similarity=0.381  Sum_probs=72.3

Q ss_pred             CCCCeEEEcCCCC-CCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184         99 DPFKTLFIARVNY-DTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus        99 ~~~~~l~V~nL~~-~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      .++++|||+||++ .+|+++|.++|+.||.|..|.|+.++     +|||||+|.+.++|..||..|||..|.|+.|.|.+
T Consensus       273 ~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~  347 (481)
T TIGR01649       273 GPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK-----KETALIEMADPYQAQLALTHLNGVKLFGKPLRVCP  347 (481)
T ss_pred             CCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEE
Confidence            4678999999998 69999999999999999999998763     69999999999999999999999999999999999


Q ss_pred             eccc
Q psy16184        178 ERSR  181 (363)
Q Consensus       178 a~~~  181 (363)
                      ++..
T Consensus       348 s~~~  351 (481)
T TIGR01649       348 SKQQ  351 (481)
T ss_pred             cccc
Confidence            8764

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

>KOG0123|consensus

Probab=99.33  E-value=1.2e-12  Score=125.07  Aligned_cols=167  Identities=22%  Similarity=0.387  Sum_probs=116.9

Q ss_pred             CChhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccC--CCCCCCCCCCcccHHHHHHHHHHH--HHHHHHHH
Q psy16184          5 LPPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFE--DPKDTPPPTRVETREERLERRRRE--RAEQVAYK   80 (363)
Q Consensus         5 ~p~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~   80 (363)
                      -...|..+|+..++|..+. ++.+. +++++|| |||.|.....  .+...+...........+.+.+..  ........
T Consensus       180 ~~~~l~~~f~~~g~i~s~~-v~~~~-~g~~~~~-gfv~f~~~e~a~~av~~l~~~~~~~~~~~V~~aqkk~e~~~~l~~~  256 (369)
T KOG0123|consen  180 TDEELKDLFSAYGSITSVA-VMRDS-IGKSKGF-GFVNFENPEDAKKAVETLNGKIFGDKELYVGRAQKKSEREAELKRK  256 (369)
T ss_pred             chHHHHHhhcccCcceEEE-EeecC-CCCCCCc-cceeecChhHHHHHHHhccCCcCCccceeecccccchhhHHHHhhh
Confidence            3458999999999999984 44444 4569999 9999988443  222233333333222222221110  00000000


Q ss_pred             HHHHHhhcCCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHH
Q psy16184         81 LEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAY  160 (363)
Q Consensus        81 ~~~~~~~~~p~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai  160 (363)
                      .....       .......+..+|||.||+..++.+.|..+|..||+|..+.|+.+ ..+.++||+||.|.+.++|..|+
T Consensus       257 ~~~~~-------~~~~~~~~~~nl~vknld~~~~~e~L~~~f~~~GeI~s~kv~~~-~~g~skG~gfV~fs~~eeA~~A~  328 (369)
T KOG0123|consen  257 FEQEF-------AKRSVSLQGANLYVKNLDETLSDEKLRKIFSSFGEITSAKVMVD-ENGKSKGFGFVEFSSPEEAKKAM  328 (369)
T ss_pred             hHhhh-------hhccccccccccccccCccccchhHHHHHHhcccceeeEEEEec-cCCCccceEEEEcCCHHHHHHHH
Confidence            00000       11112234668999999999999999999999999999999888 57999999999999999999999


Q ss_pred             HHhCCceeCCEEEEEEeecccC
Q psy16184        161 KHADGKKIDGRRVLVDVERSRT  182 (363)
Q Consensus       161 ~~l~g~~i~g~~i~V~~a~~~~  182 (363)
                      ..||+..|.++.|.|.++....
T Consensus       329 ~~~n~~~i~~k~l~vav~qr~~  350 (369)
T KOG0123|consen  329 TEMNGRLIGGKPLYVAVAQRKE  350 (369)
T ss_pred             HhhChhhhcCCchhhhHHhhhc
Confidence            9999999999999999987433

>smart00361 RRM_1 RNA recognition motif

Probab=99.32  E-value=7.8e-12  Score=91.04  Aligned_cols=61  Identities=30%  Similarity=0.558  Sum_probs=55.2

Q ss_pred             HHHHHHHHH----hhCCccEEE-EeccCCC--CCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEE
Q psy16184        115 ESKLRREFE----VYGPIKKIV-MVHNKVT--GKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLV  175 (363)
Q Consensus       115 ~~~L~~~F~----~~G~i~~v~-i~~d~~t--~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V  175 (363)
                      +++|.++|.    +||.|..|. |+.++.+  +.++|||||+|.+.++|.+|+..|||..|.|+.|.+
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            578888998    999999995 6666656  899999999999999999999999999999999976

>KOG0110|consensus

Probab=99.31  E-value=1.6e-13  Score=134.73  Aligned_cols=163  Identities=15%  Similarity=0.328  Sum_probs=118.6

Q ss_pred             CCChhhhhcCCCCCCCCCC-CCCCCCCCC-CCCCCCccccccccccC--CCCCCCCCCCcccHHHHHHHHHHHHHHHHHH
Q psy16184          4 FLPPNLLALFAPRDPVPYL-PPVEKLPHE-KKTHGYSGIAAFLNEFE--DPKDTPPPTRVETREERLERRRRERAEQVAY   79 (363)
Q Consensus         4 ~~p~~l~~~f~~~~pi~~~-~p~~~~p~t-~~s~g~~g~v~f~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   79 (363)
                      +-+.+|..+|...+.|..+ .+...+|.. -.|.|| |||.|.....  .+...+..+.+++..+.++.... +.     
T Consensus       527 Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGf-gFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~~-k~-----  599 (725)
T KOG0110|consen  527 TTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGF-GFVEFAKPESAQAALKALQGTVLDGHKLELKISEN-KP-----  599 (725)
T ss_pred             cchhHHHHHHHhcCeEEEEEEeccccccccccccce-eEEEecCHHHHHHHHHHhcCceecCceEEEEeccC-cc-----
Confidence            3456788889998887775 233344432 358899 9999988654  22334556777776665553110 00     


Q ss_pred             HHHHHHhhcCCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHH
Q psy16184         80 KLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSA  159 (363)
Q Consensus        80 ~~~~~~~~~~p~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~A  159 (363)
                           .......   .......++|+|.|||+.++-.+|+.+|..||.|..|.|+.-...+.++|||||+|-++.+|..|
T Consensus       600 -----~~~~gK~---~~~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA  671 (725)
T KOG0110|consen  600 -----ASTVGKK---KSKKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNA  671 (725)
T ss_pred             -----ccccccc---cccccccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHH
Confidence                 0000000   01112257899999999999999999999999999999987655677799999999999999999


Q ss_pred             HHHhCCceeCCEEEEEEeeccc
Q psy16184        160 YKHADGKKIDGRRVLVDVERSR  181 (363)
Q Consensus       160 i~~l~g~~i~g~~i~V~~a~~~  181 (363)
                      +.+|.++-|.|+.|+++||...
T Consensus       672 ~~al~STHlyGRrLVLEwA~~d  693 (725)
T KOG0110|consen  672 FDALGSTHLYGRRLVLEWAKSD  693 (725)
T ss_pred             HHhhcccceechhhheehhccc
Confidence            9999999999999999999753

>KOG0146|consensus

Probab=99.31  E-value=1.4e-12  Score=114.34  Aligned_cols=86  Identities=17%  Similarity=0.342  Sum_probs=81.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEE
Q psy16184         97 TMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD  176 (363)
Q Consensus        97 ~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~  176 (363)
                      ..+..|+|||-.||....+.+|..+|-.||.|+..++..|+.|+.+++|+||.|.++.+|+.||.+|||..|+=+.|+|.
T Consensus       281 eGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQ  360 (371)
T KOG0146|consen  281 EGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQ  360 (371)
T ss_pred             cCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhh
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecccC
Q psy16184        177 VERSRT  182 (363)
Q Consensus       177 ~a~~~~  182 (363)
                      +.+++.
T Consensus       361 LKRPkd  366 (371)
T KOG0146|consen  361 LKRPKD  366 (371)
T ss_pred             hcCccc
Confidence            987754

>KOG0144|consensus

Probab=99.29  E-value=7.5e-12  Score=116.54  Aligned_cols=82  Identities=27%  Similarity=0.510  Sum_probs=74.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCce-eCC--EEEEEE
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKK-IDG--RRVLVD  176 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~-i~g--~~i~V~  176 (363)
                      ..-+||||-||..++|.+|+.+|++||.|.+|.|++|+.|+.++|||||.|.+.++|.+|+.+||+.. |-|  .+|.|.
T Consensus        33 ~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqvk  112 (510)
T KOG0144|consen   33 SAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQVK  112 (510)
T ss_pred             hhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceeec
Confidence            34589999999999999999999999999999999999999999999999999999999999998864 444  578888


Q ss_pred             eeccc
Q psy16184        177 VERSR  181 (363)
Q Consensus       177 ~a~~~  181 (363)
                      +|...
T Consensus       113 ~Ad~E  117 (510)
T KOG0144|consen  113 YADGE  117 (510)
T ss_pred             ccchh
Confidence            88653

>PF13893 RRM_5: RNA recognition motif

Probab=99.29  E-value=1.6e-11  Score=85.24  Aligned_cols=56  Identities=32%  Similarity=0.661  Sum_probs=50.9

Q ss_pred             HHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184        118 LRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus       118 L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      |..+|++||.|..|.+....     .++|||+|.+.++|..|+..|||..|.|+.|.|.||
T Consensus         1 L~~~f~~fG~V~~i~~~~~~-----~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK-----RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS-----TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            67899999999999997653     589999999999999999999999999999999986

(a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....

>KOG0109|consensus

Probab=99.29  E-value=4.4e-12  Score=112.63  Aligned_cols=72  Identities=28%  Similarity=0.532  Sum_probs=68.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeeccc
Q psy16184        102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERSR  181 (363)
Q Consensus       102 ~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~~  181 (363)
                      .+|||||||..+++.+|+.+|++||+|.+|.|+++        ||||..++...|..||..|||..|+|..|.|+-++.+
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN--------YgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK   74 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKN--------YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK   74 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeecc--------cceEEeecccccHHHHhhcccceecceEEEEEecccc
Confidence            37999999999999999999999999999999875        9999999999999999999999999999999998876

>KOG4661|consensus

Probab=99.25  E-value=3.8e-11  Score=115.14  Aligned_cols=83  Identities=18%  Similarity=0.355  Sum_probs=77.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeecc
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS  180 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~  180 (363)
                      ..+|||.+|...|...+|+.+|++||.|+-.+|+++..+.-.++|+||++.+.++|.+||..||-++|.|+.|.|+.++.
T Consensus       405 gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaKN  484 (940)
T KOG4661|consen  405 GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAKN  484 (940)
T ss_pred             ccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeeccc
Confidence            46899999999999999999999999999999999988888899999999999999999999999999999999999876


Q ss_pred             cCC
Q psy16184        181 RTV  183 (363)
Q Consensus       181 ~~~  183 (363)
                      .+.
T Consensus       485 Ep~  487 (940)
T KOG4661|consen  485 EPG  487 (940)
T ss_pred             Ccc
Confidence            543

>KOG4212|consensus

Probab=99.19  E-value=6.3e-11  Score=110.51  Aligned_cols=79  Identities=20%  Similarity=0.469  Sum_probs=73.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHH-hhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        101 FKTLFIARVNYDTSESKLRREFE-VYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~-~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      .+.|||+|||+++.|.+|+++|. +.|+|+.|.|+.| .+|+++|||.|+|+++|.+++|++.||.+.+.|+.|.|+...
T Consensus        44 ~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D-~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~  122 (608)
T KOG4212|consen   44 DRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFD-ESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDH  122 (608)
T ss_pred             cceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecc-cCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccC
Confidence            45699999999999999999997 5799999999999 689999999999999999999999999999999999999765


Q ss_pred             c
Q psy16184        180 S  180 (363)
Q Consensus       180 ~  180 (363)
                      .
T Consensus       123 d  123 (608)
T KOG4212|consen  123 D  123 (608)
T ss_pred             c
Confidence            4

>KOG4208|consensus

Probab=99.14  E-value=9.1e-11  Score=99.78  Aligned_cols=81  Identities=20%  Similarity=0.343  Sum_probs=75.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhh-CCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVY-GPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~-G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      ...+||..||..+.+.+|..+|.+| |.|..+.+..++.||.++|||||+|++.+.|..|.+.||+..|.++.|.|.+-.
T Consensus        49 ~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~vmp  128 (214)
T KOG4208|consen   49 EGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHVMP  128 (214)
T ss_pred             ccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEEeC
Confidence            4579999999999999999999998 788888888999999999999999999999999999999999999999999876


Q ss_pred             cc
Q psy16184        180 SR  181 (363)
Q Consensus       180 ~~  181 (363)
                      +.
T Consensus       129 pe  130 (214)
T KOG4208|consen  129 PE  130 (214)
T ss_pred             ch
Confidence            54

>KOG4676|consensus

Probab=99.10  E-value=1.8e-11  Score=112.67  Aligned_cols=69  Identities=9%  Similarity=0.079  Sum_probs=56.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEE
Q psy16184        102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLV  175 (363)
Q Consensus       102 ~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V  175 (363)
                      .+|+|++|+..+...++.++|..+|+|....+.    .+...-+|.|+|....+...|+. ++|.++.-+...+
T Consensus       152 Rt~~v~sl~~~~~l~e~~e~f~r~Gev~ya~~a----sk~~s~~c~~sf~~qts~~halr-~~gre~k~qhsr~  220 (479)
T KOG4676|consen  152 RTREVQSLISAAILPESGESFERKGEVSYAHTA----SKSRSSSCSHSFRKQTSSKHALR-SHGRERKRQHSRR  220 (479)
T ss_pred             hhhhhhcchhhhcchhhhhhhhhcchhhhhhhh----ccCCCcchhhhHhhhhhHHHHHH-hcchhhhhhhhhh
Confidence            589999999999999999999999999988773    44456688899999999999998 5777776433333

>KOG4206|consensus

Probab=99.10  E-value=2.8e-10  Score=98.33  Aligned_cols=81  Identities=26%  Similarity=0.437  Sum_probs=73.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHH----HHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEE
Q psy16184         99 DPFKTLFIARVNYDTSESKLRR----EFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVL  174 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~----~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~  174 (363)
                      .++.||||.||+..+..++|+.    +|++||.|..|...   .|.+.+|-|||.|.+.+.|-.|+..|+|..+-|+.+.
T Consensus         7 ~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~---kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mr   83 (221)
T KOG4206|consen    7 NPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAF---KTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMR   83 (221)
T ss_pred             CCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEec---CCCCccCceEEEecChhHHHHHHHHhcCCcccCchhh
Confidence            4556999999999999988877    99999999998775   3788999999999999999999999999999999999


Q ss_pred             EEeecccC
Q psy16184        175 VDVERSRT  182 (363)
Q Consensus       175 V~~a~~~~  182 (363)
                      |.||+...
T Consensus        84 iqyA~s~s   91 (221)
T KOG4206|consen   84 IQYAKSDS   91 (221)
T ss_pred             eecccCcc
Confidence            99998754

>KOG0116|consensus

Probab=99.09  E-value=5.5e-10  Score=107.21  Aligned_cols=83  Identities=23%  Similarity=0.387  Sum_probs=70.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeecc
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS  180 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~  180 (363)
                      ..+|||.|||++++..+|+++|..||.|+...|..-...++..+||||+|.+...++.||.+ +-..|+++.|.|+..++
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek~~  366 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEKRP  366 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEeccc
Confidence            34699999999999999999999999999888855332344459999999999999999996 68899999999998876


Q ss_pred             cCCC
Q psy16184        181 RTVK  184 (363)
Q Consensus       181 ~~~~  184 (363)
                      ....
T Consensus       367 ~~~g  370 (419)
T KOG0116|consen  367 GFRG  370 (419)
T ss_pred             cccc
Confidence            5443

>KOG4205|consensus

Probab=99.04  E-value=1.3e-10  Score=107.49  Aligned_cols=82  Identities=28%  Similarity=0.548  Sum_probs=75.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      ..++||||+|+|.++++.|+.+|.+||+|.+|.|+.|+.++.++||+||+|.+.+.+..+|. ...+.|+|+.|.++.|.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~-~~~h~~dgr~ve~k~av   83 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLN-ARTHKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeec-ccccccCCccccceecc
Confidence            46799999999999999999999999999999999999999999999999999999999988 46688999999999887


Q ss_pred             ccC
Q psy16184        180 SRT  182 (363)
Q Consensus       180 ~~~  182 (363)
                      +..
T Consensus        84 ~r~   86 (311)
T KOG4205|consen   84 SRE   86 (311)
T ss_pred             Ccc
Confidence            643

>KOG0132|consensus

Probab=99.04  E-value=6.3e-10  Score=110.54  Aligned_cols=77  Identities=23%  Similarity=0.466  Sum_probs=72.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeecc
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS  180 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~  180 (363)
                      ++|||||+|+..+++.+|..+|+.||+|..|.++.      ++|||||.+....+|.+||.+|+.+.|.++.|+|.|+..
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~------~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g  494 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIP------PRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVG  494 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeecc------CCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeecc
Confidence            67999999999999999999999999999999876      469999999999999999999999999999999999987


Q ss_pred             cCC
Q psy16184        181 RTV  183 (363)
Q Consensus       181 ~~~  183 (363)
                      +..
T Consensus       495 ~G~  497 (894)
T KOG0132|consen  495 KGP  497 (894)
T ss_pred             CCc
Confidence            544

>KOG0153|consensus

Probab=98.96  E-value=1.6e-09  Score=98.80  Aligned_cols=75  Identities=27%  Similarity=0.474  Sum_probs=67.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHH-hCCceeCCEEEEEEee
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH-ADGKKIDGRRVLVDVE  178 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~-l~g~~i~g~~i~V~~a  178 (363)
                      ...+|||+||...+++.+|.++|.+||+|..|.++..      .++|||+|.+.++|+.|... +|...|+|..|.|.|.
T Consensus       227 ~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~------~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg  300 (377)
T KOG0153|consen  227 SIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR------KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWG  300 (377)
T ss_pred             ceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc------cccceeeehhhHHHHHHHHhhcceeeecceEEEEEeC
Confidence            3569999999999999999999999999999999764      47999999999999988765 5667899999999998


Q ss_pred             cc
Q psy16184        179 RS  180 (363)
Q Consensus       179 ~~  180 (363)
                      .+
T Consensus       301 ~~  302 (377)
T KOG0153|consen  301 RP  302 (377)
T ss_pred             CC
Confidence            87

>KOG0106|consensus

Probab=98.95  E-value=1.2e-09  Score=95.40  Aligned_cols=72  Identities=33%  Similarity=0.655  Sum_probs=67.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeeccc
Q psy16184        102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERSR  181 (363)
Q Consensus       102 ~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~~  181 (363)
                      ..||||+||+.+.+.+|+.||..||.|..|.|..        ||+||+|.+..+|..||..||+..|+|-.+.|+|+...
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~--------gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~   73 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMKN--------GFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGK   73 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceeec--------ccceeccCchhhhhcccchhcCceecceeeeeeccccc
Confidence            3699999999999999999999999999998853        79999999999999999999999999999999998753

>KOG0110|consensus

Probab=98.93  E-value=2.2e-09  Score=106.02  Aligned_cols=78  Identities=23%  Similarity=0.462  Sum_probs=69.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCC---CCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184        102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVT---GKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus       102 ~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t---~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      ++|||.||++.+|.+.|..+|..+|.|..|.|...+..   -.+.|||||+|.+.++|+.|+..|+|+.|+|..|.|.++
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            34999999999999999999999999999988654322   135699999999999999999999999999999999998


Q ss_pred             c
Q psy16184        179 R  179 (363)
Q Consensus       179 ~  179 (363)
                      .
T Consensus       596 ~  596 (725)
T KOG0110|consen  596 E  596 (725)
T ss_pred             c
Confidence            7

>KOG1548|consensus

Probab=98.93  E-value=3.8e-09  Score=96.30  Aligned_cols=85  Identities=16%  Similarity=0.287  Sum_probs=75.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhhCCcc--------EEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC
Q psy16184         98 MDPFKTLFIARVNYDTSESKLRREFEVYGPIK--------KIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKID  169 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~--------~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~  169 (363)
                      ...++.|||.|||.++|.+++.++|++||-|.        .|+|..+. .|+.+|-|+|.|...+++.-||..|++..|.
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 PKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDN-QGKLKGDALCCYIKRESVELAIKILDEDELR  209 (382)
T ss_pred             cccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecC-CCCccCceEEEeecccHHHHHHHHhCccccc
Confidence            44566799999999999999999999999775        56777774 5999999999999999999999999999999


Q ss_pred             CEEEEEEeecccCC
Q psy16184        170 GRRVLVDVERSRTV  183 (363)
Q Consensus       170 g~~i~V~~a~~~~~  183 (363)
                      |+.|.|+.|+-...
T Consensus       210 g~~~rVerAkfq~K  223 (382)
T KOG1548|consen  210 GKKLRVERAKFQMK  223 (382)
T ss_pred             CcEEEEehhhhhhc
Confidence            99999999875443

>KOG4209|consensus

Probab=98.91  E-value=2.5e-09  Score=95.57  Aligned_cols=83  Identities=25%  Similarity=0.543  Sum_probs=78.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184         98 MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      ......|||+|+.+.+|.++|+.+|+.||.|..|.|+.++.+++++|||||+|.+.+.+..||. ||+..|.|..|.|.+
T Consensus        98 ~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~  176 (231)
T KOG4209|consen   98 EVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTL  176 (231)
T ss_pred             ccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceeee
Confidence            3456799999999999999999999999999999999999999999999999999999999999 999999999999999


Q ss_pred             eccc
Q psy16184        178 ERSR  181 (363)
Q Consensus       178 a~~~  181 (363)
                      ....
T Consensus       177 ~r~~  180 (231)
T KOG4209|consen  177 KRTN  180 (231)
T ss_pred             eeee
Confidence            8765

>KOG4212|consensus

Probab=98.89  E-value=3e-09  Score=99.48  Aligned_cols=75  Identities=21%  Similarity=0.371  Sum_probs=68.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      ...|+|||.|||+++||+.|++-|..||.|..+.|+.   .|+.+|  .|.|.++++|+.|+..|||..|+|+.|.|.|.
T Consensus       534 rKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadime---~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I~V~y~  608 (608)
T KOG4212|consen  534 RKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIME---NGKSKG--VVRFFSPEDAERACALMNGSRLDGRNIKVTYF  608 (608)
T ss_pred             ccccEEEEecCCccccHHHHHHHHHhccceehhhhhc---cCCccc--eEEecCHHHHHHHHHHhccCcccCceeeeeeC
Confidence            4578999999999999999999999999999999954   577776  89999999999999999999999999999873

>KOG0226|consensus

Probab=98.87  E-value=2.8e-09  Score=93.32  Aligned_cols=78  Identities=22%  Similarity=0.462  Sum_probs=73.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      ...||.|.|...++.+.|-..|.+|-.....+++.++.||+++||+||.|.+..++..|+..|||..++.+.|.+--+
T Consensus       190 DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS  267 (290)
T KOG0226|consen  190 DFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKS  267 (290)
T ss_pred             cceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhh
Confidence            358999999999999999999999999999999999999999999999999999999999999999999999877644

>KOG0147|consensus

Probab=98.87  E-value=2.5e-09  Score=102.97  Aligned_cols=76  Identities=16%  Similarity=0.232  Sum_probs=59.7

Q ss_pred             CCCCeEEEcCCCC--CCC--------HHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCcee
Q psy16184         99 DPFKTLFIARVNY--DTS--------ESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKI  168 (363)
Q Consensus        99 ~~~~~l~V~nL~~--~~t--------~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i  168 (363)
                      .++.++.+.|+=.  ..|        .++|.+...+||.|.+|.|..+     +-||.||.|.+.+.|..|+.+|||.+|
T Consensus       441 i~t~C~lL~nMFdpstete~n~d~eI~edV~Eec~k~g~v~hi~vd~n-----s~g~VYvrc~s~~~A~~a~~alhgrWF  515 (549)
T KOG0147|consen  441 IPTQCLLLSNMFDPSTETEPNWDQEIREDVIEECGKHGKVCHIFVDKN-----SAGCVYVRCPSAEAAGTAVKALHGRWF  515 (549)
T ss_pred             CccHHHHHhhcCCcccccCcchhhHHHHHHHHHHHhcCCeeEEEEccC-----CCceEEEecCcHHHHHHHHHHHhhhhh
Confidence            4455677777521  111        2566677799999999888543     349999999999999999999999999


Q ss_pred             CCEEEEEEeec
Q psy16184        169 DGRRVLVDVER  179 (363)
Q Consensus       169 ~g~~i~V~~a~  179 (363)
                      .|+.|.+.|-.
T Consensus       516 ~gr~Ita~~~~  526 (549)
T KOG0147|consen  516 AGRMITAKYLP  526 (549)
T ss_pred             ccceeEEEEee
Confidence            99999999864

>KOG0533|consensus

Probab=98.86  E-value=1e-08  Score=91.44  Aligned_cols=81  Identities=20%  Similarity=0.443  Sum_probs=74.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeecc
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS  180 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~  180 (363)
                      ..+|+|.||++.|++++|+++|..||.+..+.|..++ +|.+.|.|-|.|...++|..|++.|||+.|+|..|.+.....
T Consensus        83 ~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~~  161 (243)
T KOG0533|consen   83 STKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIISS  161 (243)
T ss_pred             cceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEecC
Confidence            4689999999999999999999999999999888884 899999999999999999999999999999999999998765


Q ss_pred             cC
Q psy16184        181 RT  182 (363)
Q Consensus       181 ~~  182 (363)
                      ..
T Consensus       162 ~~  163 (243)
T KOG0533|consen  162 PS  163 (243)
T ss_pred             cc
Confidence            43

>KOG0106|consensus

Probab=98.86  E-value=1.2e-09  Score=95.33  Aligned_cols=141  Identities=20%  Similarity=0.329  Sum_probs=91.8

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccC--CCCCCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHH
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFE--DPKDTPPPTRVETREERLERRRRERAEQVAYKLEQE   84 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (363)
                      -+|..||..+|-|..+. +.        .|| +||.|.+.-.  ++.-.+....+.+..+.++..+...-.+        
T Consensus        16 ~d~E~~f~~yg~~~d~~-mk--------~gf-~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~~~~~--------   77 (216)
T KOG0106|consen   16 RDVERFFKGYGKIPDAD-MK--------NGF-GFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGKRRGR--------   77 (216)
T ss_pred             hHHHHHHhhccccccce-ee--------ccc-ceeccCchhhhhcccchhcCceecceeeeeeccccccccc--------
Confidence            46889999999999883 22        356 5666654322  3333333444433332222211100000        


Q ss_pred             HhhcCCCC----CCCCC---CCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHH
Q psy16184         85 IALWDPNS----FPNAT---MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMH  157 (363)
Q Consensus        85 ~~~~~p~~----~~~~~---~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~  157 (363)
                        ...+..    +....   ....+.|+|.||+..+.+.+|..+|.++|.+....+        ..+++||+|.+.++|.
T Consensus        78 --g~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--------~~~~~~v~Fs~~~da~  147 (216)
T KOG0106|consen   78 --GRPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--------RRNFAFVEFSEQEDAK  147 (216)
T ss_pred             --CCCCCCCccchhhccCCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhh--------hccccceeehhhhhhh
Confidence              001111    11111   223567899999999999999999999999955444        2479999999999999


Q ss_pred             HHHHHhCCceeCCEEEEE
Q psy16184        158 SAYKHADGKKIDGRRVLV  175 (363)
Q Consensus       158 ~Ai~~l~g~~i~g~~i~V  175 (363)
                      .||..|++..|.++.|.|
T Consensus       148 ra~~~l~~~~~~~~~l~~  165 (216)
T KOG0106|consen  148 RALEKLDGKKLNGRRISV  165 (216)
T ss_pred             hcchhccchhhcCceeee
Confidence            999999999999999999

>KOG0146|consensus

Probab=98.78  E-value=1.3e-08  Score=89.63  Aligned_cols=80  Identities=21%  Similarity=0.472  Sum_probs=71.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCcee-C--CEEEEEE
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKI-D--GRRVLVD  176 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i-~--g~~i~V~  176 (363)
                      ..++||||-|...-.|++++.+|..||.|.+|.+...+ .|.++|||||.|.+.-+|+.||..|||... -  ...|.|+
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~-dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK   96 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGP-DGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVK   96 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCC-CCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEE
Confidence            46799999999999999999999999999999998774 788999999999999999999999999653 3  3478999


Q ss_pred             eecc
Q psy16184        177 VERS  180 (363)
Q Consensus       177 ~a~~  180 (363)
                      ++..
T Consensus        97 ~ADT  100 (371)
T KOG0146|consen   97 FADT  100 (371)
T ss_pred             eccc
Confidence            9865

>KOG1457|consensus

Probab=98.77  E-value=6.1e-08  Score=83.48  Aligned_cols=84  Identities=17%  Similarity=0.284  Sum_probs=68.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEe-ccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC---CEEEEE
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMV-HNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKID---GRRVLV  175 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~-~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~---g~~i~V  175 (363)
                      ..+||||.+||.++...+|..+|..|--.+.+.|. .++...-.+-+|||+|.+...|.+|+.+|||+.|+   +..|+|
T Consensus        33 ~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhi  112 (284)
T KOG1457|consen   33 AVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHI  112 (284)
T ss_pred             ccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeEe
Confidence            36799999999999999999999998655555553 33322334579999999999999999999999985   789999


Q ss_pred             EeecccCC
Q psy16184        176 DVERSRTV  183 (363)
Q Consensus       176 ~~a~~~~~  183 (363)
                      ++|+..+.
T Consensus       113 ElAKSNtK  120 (284)
T KOG1457|consen  113 ELAKSNTK  120 (284)
T ss_pred             eehhcCcc
Confidence            99987543

>KOG4454|consensus

Probab=98.75  E-value=3.2e-09  Score=90.97  Aligned_cols=78  Identities=17%  Similarity=0.291  Sum_probs=70.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeecc
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS  180 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~  180 (363)
                      ..||||+||...++++-|.++|-+.|.|..|.|+.++ .+..+ ||||.|.++.++.-|++.|||..+.+..|.|.+-.+
T Consensus         9 drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~-d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r~G   86 (267)
T KOG4454|consen    9 DRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQ-DQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLRCG   86 (267)
T ss_pred             hhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCc-cCCCc-eeeeecccccchhhhhhhcccchhccchhhcccccC
Confidence            4699999999999999999999999999999998774 56666 999999999999999999999999999999987554

>KOG0151|consensus

Probab=98.68  E-value=4.4e-08  Score=96.75  Aligned_cols=84  Identities=17%  Similarity=0.325  Sum_probs=74.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCC---CCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEE
Q psy16184         98 MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVT---GKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVL  174 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t---~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~  174 (363)
                      .+.+++|||+||++.++++.|...|..||+|..|+|+.....   ....-||||.|-+..+|+.|+..|+|..|.+..++
T Consensus       171 DP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K  250 (877)
T KOG0151|consen  171 DPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMK  250 (877)
T ss_pred             CCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeee
Confidence            345678999999999999999999999999999999876422   33466999999999999999999999999999999


Q ss_pred             EEeeccc
Q psy16184        175 VDVERSR  181 (363)
Q Consensus       175 V~~a~~~  181 (363)
                      +-|+++.
T Consensus       251 ~gWgk~V  257 (877)
T KOG0151|consen  251 LGWGKAV  257 (877)
T ss_pred             ecccccc
Confidence            9998653

>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=2.2e-07  Score=71.26  Aligned_cols=79  Identities=18%  Similarity=0.233  Sum_probs=70.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhh--CCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC----CEEEEE
Q psy16184        102 KTLFIARVNYDTSESKLRREFEVY--GPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKID----GRRVLV  175 (363)
Q Consensus       102 ~~l~V~nL~~~~t~~~L~~~F~~~--G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~----g~~i~V  175 (363)
                      +||.|.|||...|.++|.+++...  |....+.++.|..++-+.|||||.|.+++.|..-...++|..+.    .+.+.|
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            589999999999999999988754  77888899999999999999999999999999999999998774    667888


Q ss_pred             Eeecc
Q psy16184        176 DVERS  180 (363)
Q Consensus       176 ~~a~~  180 (363)
                      .+|+-
T Consensus        82 ~yAri   86 (97)
T PF04059_consen   82 SYARI   86 (97)
T ss_pred             ehhHh
Confidence            88854

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG1995|consensus

Probab=98.61  E-value=1.1e-07  Score=87.61  Aligned_cols=86  Identities=28%  Similarity=0.344  Sum_probs=78.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhhCCcc--------EEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC
Q psy16184         98 MDPFKTLFIARVNYDTSESKLRREFEVYGPIK--------KIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKID  169 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~--------~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~  169 (363)
                      .....+|||-+|+..+++.+|.++|.+||.|.        .|+|.+++.|+.++|-|.|+|.+...|++||.-+++..+.
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            34566999999999999999999999999875        5678889999999999999999999999999999999999


Q ss_pred             CEEEEEEeecccCC
Q psy16184        170 GRRVLVDVERSRTV  183 (363)
Q Consensus       170 g~~i~V~~a~~~~~  183 (363)
                      |..|+|.+|..++.
T Consensus       143 gn~ikvs~a~~r~~  156 (351)
T KOG1995|consen  143 GNTIKVSLAERRTG  156 (351)
T ss_pred             CCCchhhhhhhccC
Confidence            99999999876653

>KOG4660|consensus

Probab=98.61  E-value=3.9e-08  Score=95.07  Aligned_cols=77  Identities=30%  Similarity=0.436  Sum_probs=68.2

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEE
Q psy16184         93 FPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRR  172 (363)
Q Consensus        93 ~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~  172 (363)
                      ++.....+..+|+|-|||..|++++|..+|+.||+|..|..     |-...|.+||+|.+..+|+.|+.+||+..|.|+.
T Consensus        67 np~~~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~-----t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~  141 (549)
T KOG4660|consen   67 NPSEKDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRE-----TPNKRGIVFVEFYDVRDAERALKALNRREIAGKR  141 (549)
T ss_pred             CCCcccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhc-----ccccCceEEEEEeehHhHHHHHHHHHHHHhhhhh
Confidence            44444556789999999999999999999999999999766     4446799999999999999999999999999999


Q ss_pred             EE
Q psy16184        173 VL  174 (363)
Q Consensus       173 i~  174 (363)
                      |.
T Consensus       142 ~k  143 (549)
T KOG4660|consen  142 IK  143 (549)
T ss_pred             hc
Confidence            88

>KOG0120|consensus

Probab=98.57  E-value=6.1e-08  Score=94.45  Aligned_cols=82  Identities=21%  Similarity=0.465  Sum_probs=77.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      ...+.|||+|||..+++.++.+++..||.+....++.+..+|.++||||.+|.+......|+..|||..+.++.|+|..|
T Consensus       287 ~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A  366 (500)
T KOG0120|consen  287 DSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRA  366 (500)
T ss_pred             cccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehh
Confidence            34678999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             cc
Q psy16184        179 RS  180 (363)
Q Consensus       179 ~~  180 (363)
                      -.
T Consensus       367 ~~  368 (500)
T KOG0120|consen  367 IV  368 (500)
T ss_pred             hc
Confidence            65

>KOG4206|consensus

Probab=98.48  E-value=8.7e-08  Score=83.05  Aligned_cols=162  Identities=17%  Similarity=0.241  Sum_probs=104.0

Q ss_pred             hhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccC--CCCCCCCCCCcccHHHHHHHHHHHHHHHHH-------
Q psy16184          8 NLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFE--DPKDTPPPTRVETREERLERRRRERAEQVA-------   78 (363)
Q Consensus         8 ~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------   78 (363)
                      .|..||+++|.|..+-+.    .|.+.+|- .||.|.+...  .+..++.+-.+-++..+++.++....--.+       
T Consensus        29 sL~~LFsqfG~ildI~a~----kt~KmRGQ-A~VvFk~~~~As~A~r~l~gfpFygK~mriqyA~s~sdii~~~~~~~v~  103 (221)
T KOG4206|consen   29 SLYLLFSQFGKILDISAF----KTPKMRGQ-AFVVFKETEAASAALRALQGFPFYGKPMRIQYAKSDSDIIAQAPGTFVE  103 (221)
T ss_pred             HHHHHHHhhCCeEEEEec----CCCCccCc-eEEEecChhHHHHHHHHhcCCcccCchhheecccCccchhhccCceecc
Confidence            478899999976654222    25677787 5666655222  223345555555555555443221100000       


Q ss_pred             -------HHHH-------HHHh------hcCCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCC
Q psy16184         79 -------YKLE-------QEIA------LWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKV  138 (363)
Q Consensus        79 -------~~~~-------~~~~------~~~p~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~  138 (363)
                             +...       ....      ...|..-+.....+..+||+.|||..++.+.|..+|.+|.-...|.++... 
T Consensus       104 ~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~~~~~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~-  182 (221)
T KOG4206|consen  104 KEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFLAQMAPPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPR-  182 (221)
T ss_pred             ccCccccccccccCCcccccccccccccccCCCCccccCCCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCC-
Confidence                   0000       0000      000000012235677899999999999999999999999999999887653 


Q ss_pred             CCCcceEEEEEecCHHHHHHHHHHhCCceeC-CEEEEEEeec
Q psy16184        139 TGKPRGYAFIEYEHERDMHSAYKHADGKKID-GRRVLVDVER  179 (363)
Q Consensus       139 t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~-g~~i~V~~a~  179 (363)
                          .+.|||+|.+...|..|..+|.+..|- ...+.|.++.
T Consensus       183 ----~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~a~  220 (221)
T KOG4206|consen  183 ----SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITFAK  220 (221)
T ss_pred             ----CceeEEecchhhhhHHHhhhhccceeccCceEEecccC
Confidence                589999999999999999999998886 7778887764

>KOG4210|consensus

Probab=98.44  E-value=9e-08  Score=88.42  Aligned_cols=84  Identities=18%  Similarity=0.493  Sum_probs=76.4

Q ss_pred             CCCCeEE-EcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184         99 DPFKTLF-IARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus        99 ~~~~~l~-V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      .+..++| |+||+..++.++|..+|..+|.|..+.++.++.++.++|||||.|.+...+..|+.. +...|.+..|.|..
T Consensus       182 ~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~  260 (285)
T KOG4210|consen  182 GPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEE  260 (285)
T ss_pred             CccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCccccccc
Confidence            3455666 999999999999999999999999999999999999999999999999999999986 88999999999999


Q ss_pred             ecccCC
Q psy16184        178 ERSRTV  183 (363)
Q Consensus       178 a~~~~~  183 (363)
                      ..+...
T Consensus       261 ~~~~~~  266 (285)
T KOG4210|consen  261 DEPRPK  266 (285)
T ss_pred             CCCCcc
Confidence            877544

>KOG4211|consensus

Probab=98.31  E-value=2.1e-06  Score=82.12  Aligned_cols=78  Identities=21%  Similarity=0.358  Sum_probs=67.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeecc
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS  180 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~  180 (363)
                      ...|-+.+|||++|+++|.+||+.|+ |..+.+++  .+|++.|-|||+|.+++++++||+ .+-..+..+.|.|-.+..
T Consensus        10 ~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r--~~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~~~   85 (510)
T KOG4211|consen   10 AFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPR--RNGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTAGG   85 (510)
T ss_pred             ceEEEecCCCccccHHHHHHHHhcCc-eeEEEEec--cCCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEccCC
Confidence            45688899999999999999999995 77766655  589999999999999999999999 588888899999988765


Q ss_pred             cC
Q psy16184        181 RT  182 (363)
Q Consensus       181 ~~  182 (363)
                      ..
T Consensus        86 ~e   87 (510)
T KOG4211|consen   86 AE   87 (510)
T ss_pred             cc
Confidence            44

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=98.26  E-value=6.2e-06  Score=75.27  Aligned_cols=93  Identities=19%  Similarity=0.342  Sum_probs=70.1

Q ss_pred             cCCCCCCCCCCCCCCeEEEcCCCCCCCHHH----H--HHHHHhhCCccEEEEeccCCC-CCcce--EEEEEecCHHHHHH
Q psy16184         88 WDPNSFPNATMDPFKTLFIARVNYDTSESK----L--RREFEVYGPIKKIVMVHNKVT-GKPRG--YAFIEYEHERDMHS  158 (363)
Q Consensus        88 ~~p~~~~~~~~~~~~~l~V~nL~~~~t~~~----L--~~~F~~~G~i~~v~i~~d~~t-~~~~g--~afV~f~~~~~a~~  158 (363)
                      .+-....+....+.+-|||-+|++.+..++    |  .++|.+||.|..|.|-..... ....+  -.||+|.+.++|..
T Consensus       101 ~nrkhlsniRVvQKNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAar  180 (480)
T COG5175         101 QNRKHLSNIRVVQKNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAAR  180 (480)
T ss_pred             ccccccccceeeecceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHH
Confidence            333445556666778899999998886655    3  579999999998877432101 11122  34999999999999


Q ss_pred             HHHHhCCceeCCEEEEEEeecc
Q psy16184        159 AYKHADGKKIDGRRVLVDVERS  180 (363)
Q Consensus       159 Ai~~l~g~~i~g~~i~V~~a~~  180 (363)
                      ||..++|..++|+.|+..|...
T Consensus       181 cIa~vDgs~~DGr~lkatYGTT  202 (480)
T COG5175         181 CIAEVDGSLLDGRVLKATYGTT  202 (480)
T ss_pred             HHHHhccccccCceEeeecCch
Confidence            9999999999999999998654

>KOG4849|consensus

Probab=98.26  E-value=1.9e-06  Score=78.92  Aligned_cols=75  Identities=16%  Similarity=0.357  Sum_probs=67.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhhC--CccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEE
Q psy16184        102 KTLFIARVNYDTSESKLRREFEVYG--PIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD  176 (363)
Q Consensus       102 ~~l~V~nL~~~~t~~~L~~~F~~~G--~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~  176 (363)
                      .++|||||-|++|.++|.+.+...|  .|.++++..+..+|+++|||+|...+...+++.++.|....|.|+.-.|-
T Consensus        81 ~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~  157 (498)
T KOG4849|consen   81 YCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVL  157 (498)
T ss_pred             EEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeee
Confidence            4799999999999999999998777  57778888899999999999999999999999999999999999865554

>KOG0120|consensus

Probab=98.23  E-value=6.3e-07  Score=87.47  Aligned_cols=170  Identities=14%  Similarity=0.217  Sum_probs=96.2

Q ss_pred             hhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccC--CCCCCCCCCCcccHHHHHHHHHHHHHH-HHHHHHHHH
Q psy16184          8 NLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFE--DPKDTPPPTRVETREERLERRRRERAE-QVAYKLEQE   84 (363)
Q Consensus         8 ~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~   84 (363)
                      .+..+...++||..+. +..+..++.++|| .|..|++..-  .+.+.+....+....+.++.+-..+.. .....+.+.
T Consensus       305 q~~Ell~~fg~lk~f~-lv~d~~~g~skg~-af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~~~~~~~~~~~~~  382 (500)
T KOG0120|consen  305 QVKELLDSFGPLKAFR-LVKDSATGNSKGF-AFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGASNANVNFNISQS  382 (500)
T ss_pred             HHHHHHHhcccchhhe-eecccccccccce-eeeeeeCCcchhhhhcccchhhhcCceeEeehhhccchhccccCCcccc
Confidence            4566677778888774 4457778999999 5555555333  244445554444333222221100000 000000000


Q ss_pred             HhhcCCCCCCCCCCCCCCeEEEcCCC--CCC-CH-------HHHHHHHHhhCCccEEEEeccC---CCCCcceEEEEEec
Q psy16184         85 IALWDPNSFPNATMDPFKTLFIARVN--YDT-SE-------SKLRREFEVYGPIKKIVMVHNK---VTGKPRGYAFIEYE  151 (363)
Q Consensus        85 ~~~~~p~~~~~~~~~~~~~l~V~nL~--~~~-t~-------~~L~~~F~~~G~i~~v~i~~d~---~t~~~~g~afV~f~  151 (363)
                      ....-+.........++..|.+.|+-  ..+ .+       ++|+.-+.+||.|..|.|+.+-   ...-..|..||+|.
T Consensus       383 ~~~~i~~~~~q~~g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefa  462 (500)
T KOG0120|consen  383 QVPGIPLLMTQMAGIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFA  462 (500)
T ss_pred             ccccchhhhcccCCCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEec
Confidence            00000000112233445556555542  111 22       2344456789999999997762   22335688999999


Q ss_pred             CHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        152 HERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       152 ~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      +.++++.|+++|+|..|+|+.|...|..
T Consensus       463 s~ed~qrA~~~L~GrKF~nRtVvtsYyd  490 (500)
T KOG0120|consen  463 DTEDSQRAMEELTGRKFANRTVVASYYD  490 (500)
T ss_pred             ChHHHHHHHHHccCceeCCcEEEEEecC
Confidence            9999999999999999999999998864

>KOG1190|consensus

Probab=98.22  E-value=4.4e-06  Score=78.10  Aligned_cols=77  Identities=22%  Similarity=0.434  Sum_probs=69.3

Q ss_pred             CCeEEEcCCCC-CCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        101 FKTLFIARVNY-DTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       101 ~~~l~V~nL~~-~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      ++.|.|.||.. .+|.+.|..+|..||.|..|+|..++     +--|+|+|.+...|+-|+++|+|+.|.|+.|.|.+++
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nk-----kd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SK  371 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNK-----KDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSK  371 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecC-----CcceeeeecchhHHHHHHHHhhcceecCceEEEeecc
Confidence            57899999975 58999999999999999999998864     3579999999999999999999999999999999987


Q ss_pred             ccC
Q psy16184        180 SRT  182 (363)
Q Consensus       180 ~~~  182 (363)
                      -..
T Consensus       372 H~~  374 (492)
T KOG1190|consen  372 HTN  374 (492)
T ss_pred             Ccc
Confidence            543

>KOG1548|consensus

Probab=98.22  E-value=1.5e-05  Score=73.13  Aligned_cols=99  Identities=18%  Similarity=0.434  Sum_probs=75.5

Q ss_pred             HHHHHHHhhcCCCCCCCCCCCCCCeEEEcCCC----CCCC-------HHHHHHHHHhhCCccEEEEeccCCCCCcceEEE
Q psy16184         79 YKLEQEIALWDPNSFPNATMDPFKTLFIARVN----YDTS-------ESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAF  147 (363)
Q Consensus        79 ~~~~~~~~~~~p~~~~~~~~~~~~~l~V~nL~----~~~t-------~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~af  147 (363)
                      +++++.+-.|.|...........++|.|.||=    +..+       .++|.+-..+||.|..|.|.    ..++.|.+-
T Consensus       243 ~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~----d~hPdGvvt  318 (382)
T KOG1548|consen  243 KKQQQKLLDWRPDRDDPSKARADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVY----DRHPDGVVT  318 (382)
T ss_pred             HHHHHhhcccCCCccccccccCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEe----ccCCCceeE
Confidence            34445555667766444445567899999973    2233       34566668899999999884    245789999


Q ss_pred             EEecCHHHHHHHHHHhCCceeCCEEEEEEeeccc
Q psy16184        148 IEYEHERDMHSAYKHADGKKIDGRRVLVDVERSR  181 (363)
Q Consensus       148 V~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~~  181 (363)
                      |.|.+.+.|..||+.|+|..|+|++|...+....
T Consensus       319 V~f~n~eeA~~ciq~m~GR~fdgRql~A~i~DG~  352 (382)
T KOG1548|consen  319 VSFRNNEEADQCIQTMDGRWFDGRQLTASIWDGK  352 (382)
T ss_pred             EEeCChHHHHHHHHHhcCeeecceEEEEEEeCCc
Confidence            9999999999999999999999999999987543

>KOG2416|consensus

Probab=98.20  E-value=1.8e-06  Score=84.10  Aligned_cols=78  Identities=13%  Similarity=0.261  Sum_probs=66.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHH-hhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCcee---CCEEE
Q psy16184         98 MDPFKTLFIARVNYDTSESKLRREFE-VYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKI---DGRRV  173 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~~~F~-~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i---~g~~i  173 (363)
                      ..+++.|||.||-.-+|.-+|+.++. .+|.|..++|  |+    .+..|||.|.+.++|.+.+.+|||+.+   +++.|
T Consensus       441 ~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~Wm--Dk----IKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L  514 (718)
T KOG2416|consen  441 KEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWM--DK----IKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHL  514 (718)
T ss_pred             CCccceEeeecccccchHHHHHHHHhhccCchHHHHH--HH----hhcceeEecccHHHHHHHHHHHhccccCCCCCcee
Confidence            34578999999999999999999999 5677777743  32    467999999999999999999999875   78899


Q ss_pred             EEEeeccc
Q psy16184        174 LVDVERSR  181 (363)
Q Consensus       174 ~V~~a~~~  181 (363)
                      .|.|....
T Consensus       515 ~adf~~~d  522 (718)
T KOG2416|consen  515 IADFVRAD  522 (718)
T ss_pred             Eeeecchh
Confidence            99998653

>KOG1457|consensus

Probab=98.18  E-value=1.8e-06  Score=74.60  Aligned_cols=65  Identities=22%  Similarity=0.330  Sum_probs=54.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCcee
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKI  168 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i  168 (363)
                      .+.||||.||..+||+++|+.+|+.|--..-++|..  ..  ...+|||+|++.+.|..|+..|.|..|
T Consensus       209 acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~--~~--g~~vaf~~~~~~~~at~am~~lqg~~~  273 (284)
T KOG1457|consen  209 ACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRA--RG--GMPVAFADFEEIEQATDAMNHLQGNLL  273 (284)
T ss_pred             hhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEec--CC--CcceEeecHHHHHHHHHHHHHhhccee
Confidence            356899999999999999999999997666666632  12  235899999999999999999988766

>KOG2202|consensus

Probab=98.09  E-value=1e-05  Score=71.51  Aligned_cols=64  Identities=19%  Similarity=0.418  Sum_probs=53.5

Q ss_pred             HHHHHHH-hhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeeccc
Q psy16184        117 KLRREFE-VYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERSR  181 (363)
Q Consensus       117 ~L~~~F~-~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~~  181 (363)
                      +|...|. +||+|..+.|..+ ..-+..|-+||.|...++|++|+..||+..|.|++|..++....
T Consensus        84 d~f~E~~~kygEiee~~Vc~N-l~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pvT  148 (260)
T KOG2202|consen   84 DVFTELEDKYGEIEELNVCDN-LGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPVT  148 (260)
T ss_pred             HHHHHHHHHhhhhhhhhhhcc-cchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCcC
Confidence            4444445 8999999977544 45667899999999999999999999999999999999987654

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=98.04  E-value=1.2e-05  Score=58.94  Aligned_cols=68  Identities=18%  Similarity=0.346  Sum_probs=47.3

Q ss_pred             CeEEEcCCCCCCCHHH----HHHHHHhhC-CccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEE
Q psy16184        102 KTLFIARVNYDTSESK----LRREFEVYG-PIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD  176 (363)
Q Consensus       102 ~~l~V~nL~~~~t~~~----L~~~F~~~G-~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~  176 (363)
                      ..|||.|||.+.....    |+.++..|| .|..|.          .+.|+|.|.+.+.|..|+..|+|..+.|..|.|.
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            3699999999988765    456666776 565541          2689999999999999999999999999999999


Q ss_pred             eec
Q psy16184        177 VER  179 (363)
Q Consensus       177 ~a~  179 (363)
                      +..
T Consensus        73 ~~~   75 (90)
T PF11608_consen   73 FSP   75 (90)
T ss_dssp             SS-
T ss_pred             EcC
Confidence            974

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG4211|consensus

Probab=97.91  E-value=3.5e-05  Score=73.93  Aligned_cols=79  Identities=16%  Similarity=0.261  Sum_probs=65.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccE-EEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKK-IVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~-v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      +...|-+.+||+.||+++|.+||+..-.|.. |.++.+ ..+.+.|-|||.|++.+.|++||.. |...|..+-|.|-.+
T Consensus       102 ~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d-~rgR~tGEAfVqF~sqe~ae~Al~r-hre~iGhRYIEvF~S  179 (510)
T KOG4211|consen  102 NDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMD-QRGRPTGEAFVQFESQESAEIALGR-HRENIGHRYIEVFRS  179 (510)
T ss_pred             CCceEEecCCCccCcHHHHHHHhcCCcccccceeeecc-CCCCcccceEEEecCHHHHHHHHHH-HHHhhccceEEeehh
Confidence            4568999999999999999999997655544 445555 4677999999999999999999995 778899999999876


Q ss_pred             cc
Q psy16184        179 RS  180 (363)
Q Consensus       179 ~~  180 (363)
                      .-
T Consensus       180 s~  181 (510)
T KOG4211|consen  180 SR  181 (510)
T ss_pred             HH
Confidence            43

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation

Probab=97.90  E-value=1.4e-05  Score=62.73  Aligned_cols=70  Identities=16%  Similarity=0.330  Sum_probs=44.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCc-----eeCCEEEEEE
Q psy16184        102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGK-----KIDGRRVLVD  176 (363)
Q Consensus       102 ~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~-----~i~g~~i~V~  176 (363)
                      +.|+|.|++..++.++|+++|..||.|..|.+...      -.-|||-|.+.+.|+.|+..+...     .|.+..+.+.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G------~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~   75 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRG------DTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLE   75 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCC------CCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEE
Confidence            57899999999999999999999999999988553      248999999999999999876433     5566555555


Q ss_pred             e
Q psy16184        177 V  177 (363)
Q Consensus       177 ~  177 (363)
                      +
T Consensus        76 v   76 (105)
T PF08777_consen   76 V   76 (105)
T ss_dssp             -
T ss_pred             E
Confidence            4

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG0129|consensus

Probab=97.86  E-value=4.7e-05  Score=73.51  Aligned_cols=69  Identities=16%  Similarity=0.308  Sum_probs=63.8

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHHHHH-hhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHH
Q psy16184         94 PNATMDPFKTLFIARVNYDTSESKLRREFE-VYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH  162 (363)
Q Consensus        94 ~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~-~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~  162 (363)
                      .+...++.+|||||+||--+|.++|..+|. -||.|..|-|-+|+.-+-++|-|-|+|.+..+..+||.+
T Consensus       363 ~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  363 HNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             cCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            455667899999999999999999999999 799999999999988889999999999999999999985

>KOG0128|consensus

Probab=97.84  E-value=7.4e-06  Score=83.10  Aligned_cols=135  Identities=19%  Similarity=0.234  Sum_probs=101.8

Q ss_pred             CChhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccCCCCCCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHH
Q psy16184          5 LPPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFEDPKDTPPPTRVETREERLERRRRERAEQVAYKLEQE   84 (363)
Q Consensus         5 ~p~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (363)
                      +-++|...|.+.+.+.++- +.-.-.+++.+|+ +++.|+......+.      |...-...                  
T Consensus       680 ~~~dl~~~~~~~~~~e~vq-i~~h~n~~~~rG~-~Y~~F~~~~~~~aa------V~f~d~~~------------------  733 (881)
T KOG0128|consen  680 SEEDLSERFSPSGTIEVVQ-IVIHKNEKRFRGK-AYVEFLKPEHAGAA------VAFRDSCF------------------  733 (881)
T ss_pred             cCchhhhhcCccchhhhHH-HHHHhhccccccc-eeeEeecCCchhhh------hhhhhhhh------------------
Confidence            4578888888888888773 3334456888899 77777654321110      00000000                  


Q ss_pred             HhhcCCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhC
Q psy16184         85 IALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHAD  164 (363)
Q Consensus        85 ~~~~~p~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~  164 (363)
                                    -....|||.|+|+..|.+.|+.+|..+|.++.+.++.. ..|+++|.|||.|.++.+|..++..+.
T Consensus       734 --------------~gK~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~-r~gkpkg~a~v~y~~ea~~s~~~~s~d  798 (881)
T KOG0128|consen  734 --------------FGKISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTV-RAGKPKGKARVDYNTEADASRKVASVD  798 (881)
T ss_pred             --------------hhhhhhheeCCCCCCchHHHHhhccccCCccccchhhh-hccccccceeccCCCcchhhhhcccch
Confidence                          00237999999999999999999999999999988776 479999999999999999999999888


Q ss_pred             CceeCCEEEEEEeecc
Q psy16184        165 GKKIDGRRVLVDVERS  180 (363)
Q Consensus       165 g~~i~g~~i~V~~a~~  180 (363)
                      ...+.-..+.|..+.+
T Consensus       799 ~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  799 VAGKRENNGEVQVSNP  814 (881)
T ss_pred             hhhhhhcCccccccCC
Confidence            8888888888888665

>KOG1365|consensus

Probab=97.76  E-value=5.1e-05  Score=70.55  Aligned_cols=79  Identities=19%  Similarity=0.259  Sum_probs=68.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCC-ccE--EEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGP-IKK--IVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~-i~~--v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      ..+|-+.+||+.++.++|..||..|.. |..  |+|+.+ ..|.+.|-|||+|.+.+.|.+|....+.+....+.|.|-.
T Consensus       280 kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N-~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp  358 (508)
T KOG1365|consen  280 KDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLN-GQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFP  358 (508)
T ss_pred             CCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEc-CCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEee
Confidence            458999999999999999999999863 443  778777 5799999999999999999999999888888899998887


Q ss_pred             ecc
Q psy16184        178 ERS  180 (363)
Q Consensus       178 a~~  180 (363)
                      +..
T Consensus       359 ~S~  361 (508)
T KOG1365|consen  359 CSV  361 (508)
T ss_pred             ccH
Confidence            653

>KOG0112|consensus

Probab=97.70  E-value=5.4e-05  Score=77.40  Aligned_cols=78  Identities=32%  Similarity=0.532  Sum_probs=67.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC--EEEE
Q psy16184         97 TMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDG--RRVL  174 (363)
Q Consensus        97 ~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g--~~i~  174 (363)
                      ...+++.|||++|..++....|...|..||.|..|.+-.    |  .-||||.|++...|+.|++.|-|..|+|  +.|.
T Consensus       451 kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~h----g--q~yayi~yes~~~aq~a~~~~rgap~G~P~~r~r  524 (975)
T KOG0112|consen  451 KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRH----G--QPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLR  524 (975)
T ss_pred             ccccceeeccCCCCCCChHHHHHHHhhccCcceeeeccc----C--CcceeeecccCccchhhHHHHhcCcCCCCCcccc
Confidence            345678999999999999999999999999999887732    2  3599999999999999999999999976  5689


Q ss_pred             EEeecc
Q psy16184        175 VDVERS  180 (363)
Q Consensus       175 V~~a~~  180 (363)
                      |.++..
T Consensus       525 vdla~~  530 (975)
T KOG0112|consen  525 VDLASP  530 (975)
T ss_pred             cccccC
Confidence            998865

>KOG2314|consensus

Probab=97.63  E-value=0.00015  Score=70.60  Aligned_cols=76  Identities=24%  Similarity=0.406  Sum_probs=61.2

Q ss_pred             CCeEEEcCCCCCCC------HHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC-CEEE
Q psy16184        101 FKTLFIARVNYDTS------ESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKID-GRRV  173 (363)
Q Consensus       101 ~~~l~V~nL~~~~t------~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~-g~~i  173 (363)
                      ...|+|.|+|.--.      ..-|..+|+++|+|..+.++.+..+| .+||.|++|.+..+|+.|+..|||+.|+ ...+
T Consensus        58 D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~gg-tkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf  136 (698)
T KOG2314|consen   58 DSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGG-TKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTF  136 (698)
T ss_pred             ceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCC-eeeEEEEEecChhhHHHHHHhcccceecccceE
Confidence            45789999985322      23456789999999999999886555 9999999999999999999999999885 4455


Q ss_pred             EEEe
Q psy16184        174 LVDV  177 (363)
Q Consensus       174 ~V~~  177 (363)
                      .|..
T Consensus       137 ~v~~  140 (698)
T KOG2314|consen  137 FVRL  140 (698)
T ss_pred             Eeeh
Confidence            5554

>KOG3152|consensus

Probab=97.63  E-value=3.9e-05  Score=67.79  Aligned_cols=72  Identities=13%  Similarity=0.284  Sum_probs=61.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCC--------CCcce----EEEEEecCHHHHHHHHHHhCCcee
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVT--------GKPRG----YAFIEYEHERDMHSAYKHADGKKI  168 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t--------~~~~g----~afV~f~~~~~a~~Ai~~l~g~~i  168 (363)
                      +-.||++|||+.+....|+++|..||.|-.|.|.....+        |.+..    -|.|+|.+...|..+...||+..|
T Consensus        74 ~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~I  153 (278)
T KOG3152|consen   74 TGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTPI  153 (278)
T ss_pred             ceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCcc
Confidence            458999999999999999999999999999998654433        33332    267999999999999999999999


Q ss_pred             CCEE
Q psy16184        169 DGRR  172 (363)
Q Consensus       169 ~g~~  172 (363)
                      +|+.
T Consensus       154 ggkk  157 (278)
T KOG3152|consen  154 GGKK  157 (278)
T ss_pred             CCCC
Confidence            9875

>KOG0105|consensus

Probab=97.62  E-value=0.00057  Score=57.67  Aligned_cols=61  Identities=18%  Similarity=0.257  Sum_probs=56.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC
Q psy16184        102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKID  169 (363)
Q Consensus       102 ~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~  169 (363)
                      ..|.|.+||+..+|++|++++...|.|....+..|       |++.|+|...++++-||..|....+.
T Consensus       116 ~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD-------g~GvV~~~r~eDMkYAvr~ld~~~~~  176 (241)
T KOG0105|consen  116 YRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD-------GVGVVEYLRKEDMKYAVRKLDDQKFR  176 (241)
T ss_pred             eeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc-------cceeeeeeehhhHHHHHHhhcccccc
Confidence            47999999999999999999999999999999887       69999999999999999999887654

>KOG1855|consensus

Probab=97.52  E-value=8.2e-05  Score=70.24  Aligned_cols=70  Identities=23%  Similarity=0.311  Sum_probs=57.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEecc---CCC--CC--------cceEEEEEecCHHHHHHHHHHhC
Q psy16184         98 MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHN---KVT--GK--------PRGYAFIEYEHERDMHSAYKHAD  164 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d---~~t--~~--------~~g~afV~f~~~~~a~~Ai~~l~  164 (363)
                      .-+.++|.+.|||.+-.-+.|.++|..||.|..|.|+..   +.+  +.        .+-+|||+|...+.|.+|.+.||
T Consensus       228 el~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~  307 (484)
T KOG1855|consen  228 ELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLN  307 (484)
T ss_pred             ccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhc
Confidence            347899999999999888999999999999999999654   222  21        24589999999999999999886


Q ss_pred             Cce
Q psy16184        165 GKK  167 (363)
Q Consensus       165 g~~  167 (363)
                      ...
T Consensus       308 ~e~  310 (484)
T KOG1855|consen  308 PEQ  310 (484)
T ss_pred             hhh
Confidence            543

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=97.49  E-value=0.00025  Score=48.21  Aligned_cols=52  Identities=17%  Similarity=0.390  Sum_probs=42.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHH
Q psy16184        102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAY  160 (363)
Q Consensus       102 ~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai  160 (363)
                      +.|-|.+.+....+ .|..+|..||+|..+.+..      ...+.||.|.+..+|++||
T Consensus         2 ~wI~V~Gf~~~~~~-~vl~~F~~fGeI~~~~~~~------~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAE-EVLEHFASFGEIVDIYVPE------STNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHH-HHHHHHHhcCCEEEEEcCC------CCcEEEEEECCHHHHHhhC
Confidence            46889999987664 4555999999999988852      2359999999999999985

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=97.41  E-value=0.00081  Score=55.17  Aligned_cols=74  Identities=16%  Similarity=0.350  Sum_probs=53.1

Q ss_pred             CCCCCeEEEcCCC-----C-CCCH---HHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCcee
Q psy16184         98 MDPFKTLFIARVN-----Y-DTSE---SKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKI  168 (363)
Q Consensus        98 ~~~~~~l~V~nL~-----~-~~t~---~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i  168 (363)
                      ++|..||.|.=+.     . ...+   .+|.+.|..||+|.-|+++.+        .-+|+|.+-.+|.+|+. |+|..|
T Consensus        24 GPpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals-~dg~~v   94 (146)
T PF08952_consen   24 GPPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALS-LDGIQV   94 (146)
T ss_dssp             --TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHH-GCCSEE
T ss_pred             CCCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHc-cCCcEE
Confidence            3445577776554     1 1222   367788899999998888653        67899999999999999 899999


Q ss_pred             CCEEEEEEeecc
Q psy16184        169 DGRRVLVDVERS  180 (363)
Q Consensus       169 ~g~~i~V~~a~~  180 (363)
                      +|+.|.|.+..+
T Consensus        95 ~g~~l~i~LKtp  106 (146)
T PF08952_consen   95 NGRTLKIRLKTP  106 (146)
T ss_dssp             TTEEEEEEE---
T ss_pred             CCEEEEEEeCCc
Confidence            999999998654

; PDB: 1UFW_A 2DNR_A.

>KOG1190|consensus

Probab=97.39  E-value=0.00035  Score=65.71  Aligned_cols=79  Identities=20%  Similarity=0.226  Sum_probs=65.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCE-EEEEE
Q psy16184         98 MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGR-RVLVD  176 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~-~i~V~  176 (363)
                      -+|+.+|.+.|||..+++++|+.+|..-|-........    ++.+-+|++.+.+.+.|..|+..|+.+.+++. .|.|.
T Consensus       411 ~PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff----~kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvS  486 (492)
T KOG1190|consen  411 FPPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFF----QKDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVS  486 (492)
T ss_pred             CCchhheeeccCCcccchhHHHHhhhcCCceEEeeeec----CCCcceeecccCChhHhhhhccccccccCCCCceEEEE
Confidence            35677999999999999999999999988664443322    33456999999999999999999999998766 89999


Q ss_pred             eecc
Q psy16184        177 VERS  180 (363)
Q Consensus       177 ~a~~  180 (363)
                      |++.
T Consensus       487 FSks  490 (492)
T KOG1190|consen  487 FSKS  490 (492)
T ss_pred             eecc
Confidence            9864

>KOG4307|consensus

Probab=97.36  E-value=0.00068  Score=67.74  Aligned_cols=75  Identities=21%  Similarity=0.378  Sum_probs=64.4

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184        103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus       103 ~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      .|-|.|+|+.++-++|.+||.-|-.+-.-.++.-...|.+.|-|.|.|++.++|..|...|++..|..++|.|.+
T Consensus       869 V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~nd~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  869 VLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             EEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            788899999999999999999997654333333336799999999999999999999999999999999998864

>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=97.32  E-value=0.0011  Score=51.35  Aligned_cols=77  Identities=16%  Similarity=0.180  Sum_probs=51.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccC-------CCCCcceEEEEEecCHHHHHHHHHHhCCceeCCE-E
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNK-------VTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGR-R  172 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~-------~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~-~  172 (363)
                      .+-|.|-+.|+. ....|..+|++||.|.+..-+...       .......+..|+|.+..+|.+||. -||..|.|. .
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            346888899987 557788899999999876411000       001123588999999999999999 599999885 5


Q ss_pred             EEEEeec
Q psy16184        173 VLVDVER  179 (363)
Q Consensus       173 i~V~~a~  179 (363)
                      |-|.+.+
T Consensus        84 vGV~~~~   90 (100)
T PF05172_consen   84 VGVKPCD   90 (100)
T ss_dssp             EEEEE-H
T ss_pred             EEEEEcH
Confidence            5677764

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.

>KOG1456|consensus

Probab=97.32  E-value=0.0013  Score=61.28  Aligned_cols=81  Identities=17%  Similarity=0.268  Sum_probs=71.2

Q ss_pred             CCCCCCeEEEcCCCCC-CCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEE
Q psy16184         97 TMDPFKTLFIARVNYD-TSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLV  175 (363)
Q Consensus        97 ~~~~~~~l~V~nL~~~-~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V  175 (363)
                      ...+.+.+.|-+|... ++-+.|..+|-.||.|..|+++.-+     .|-|.|++.+...++.|+..||+..+-|.+|.|
T Consensus       283 g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk-----~gtamVemgd~~aver~v~hLnn~~lfG~kl~v  357 (494)
T KOG1456|consen  283 GGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK-----PGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNV  357 (494)
T ss_pred             CCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc-----cceeEEEcCcHHHHHHHHHHhccCccccceEEE
Confidence            3446788999999865 5778999999999999999998764     489999999999999999999999999999999


Q ss_pred             EeecccC
Q psy16184        176 DVERSRT  182 (363)
Q Consensus       176 ~~a~~~~  182 (363)
                      .+++...
T Consensus       358 ~~SkQ~~  364 (494)
T KOG1456|consen  358 CVSKQNF  364 (494)
T ss_pred             eeccccc
Confidence            9987643

>KOG0129|consensus

Probab=97.27  E-value=0.00043  Score=67.07  Aligned_cols=63  Identities=22%  Similarity=0.538  Sum_probs=49.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccC---CCCCcce---EEEEEecCHHHHHHHHHHhC
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNK---VTGKPRG---YAFIEYEHERDMHSAYKHAD  164 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~---~t~~~~g---~afV~f~~~~~a~~Ai~~l~  164 (363)
                      +++||||+||+.++|+.|...|..||.+. |.++...   .--.++|   |+|+.|+++.++...|.++.
T Consensus       259 S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~  327 (520)
T KOG0129|consen  259 SRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACS  327 (520)
T ss_pred             ccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHh
Confidence            67999999999999999999999999764 4444211   1122456   99999999999988777653

>KOG1456|consensus

Probab=97.19  E-value=0.0013  Score=61.23  Aligned_cols=77  Identities=19%  Similarity=0.314  Sum_probs=62.2

Q ss_pred             CCCeEEEc--CCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC-C-EEEEE
Q psy16184        100 PFKTLFIA--RVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKID-G-RRVLV  175 (363)
Q Consensus       100 ~~~~l~V~--nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~-g-~~i~V  175 (363)
                      ++..|.++  |--+.+|.+-|..+....|.|..|.|...  +|   --|.|+|++.+.|++|.++|||..|- | ..|+|
T Consensus       119 pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk--ng---VQAmVEFdsv~~AqrAk~alNGADIYsGCCTLKI  193 (494)
T KOG1456|consen  119 PNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK--NG---VQAMVEFDSVEVAQRAKAALNGADIYSGCCTLKI  193 (494)
T ss_pred             CCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec--cc---eeeEEeechhHHHHHHHhhcccccccccceeEEE
Confidence            44555555  44467899999999999999999988653  22   36999999999999999999999774 3 47899


Q ss_pred             Eeeccc
Q psy16184        176 DVERSR  181 (363)
Q Consensus       176 ~~a~~~  181 (363)
                      +||++.
T Consensus       194 eyAkP~  199 (494)
T KOG1456|consen  194 EYAKPT  199 (494)
T ss_pred             EecCcc
Confidence            999874

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

Probab=97.13  E-value=4.5e-05  Score=69.28  Aligned_cols=154  Identities=16%  Similarity=0.217  Sum_probs=94.6

Q ss_pred             CChhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccC--CCCCCCCCCCcccHHHHHHHHHH--HHHHHHHHH
Q psy16184          5 LPPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFE--DPKDTPPPTRVETREERLERRRR--ERAEQVAYK   80 (363)
Q Consensus         5 ~p~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~--~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~   80 (363)
                      -..+|..+|..++++..+ .+..+..++.++|| +||.|.....  .+...+....+.++.+.+.....  .........
T Consensus       128 ~~~~l~~~F~~~g~~~~~-~~~~d~~~~~~~g~-~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~  205 (306)
T COG0724         128 TEEDLRELFKKFGPVKRV-RLVRDRETGKSRGF-AFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNN  205 (306)
T ss_pred             CHHHHHHHHHhcCceeEE-EeeeccccCccCce-EEEEecCHHHHHHHHHHcCCCeECCceeEeeccccccccccccccc
Confidence            346799999999999776 46667789999999 9999988544  33344555666666655554221  000000000


Q ss_pred             HHHHHhhcCCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHH
Q psy16184         81 LEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAY  160 (363)
Q Consensus        81 ~~~~~~~~~p~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai  160 (363)
                       ......................++++|++..++...+..+|..+|.+..+.+...........+.++.+.....+..++
T Consensus       206 -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  284 (306)
T COG0724         206 -LDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGNEASKDALESN  284 (306)
T ss_pred             -cchhhhccccccccccccccceeeccccccccchhHHHHhccccccceeeeccCCCCCcccccccccchhHHHhhhhhh
Confidence             0000000011122233445678999999999999999999999999977777655444444455555555444444444


Q ss_pred             H
Q psy16184        161 K  161 (363)
Q Consensus       161 ~  161 (363)
                      .
T Consensus       285 ~  285 (306)
T COG0724         285 S  285 (306)
T ss_pred             c
Confidence            4

>KOG2068|consensus

Probab=96.97  E-value=0.0006  Score=62.94  Aligned_cols=86  Identities=21%  Similarity=0.359  Sum_probs=64.9

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHH---HHHHHhhCCccEEEEeccCC--CCC-cceEEEEEecCHHHHHHHHHHhCCceeC
Q psy16184         96 ATMDPFKTLFIARVNYDTSESKL---RREFEVYGPIKKIVMVHNKV--TGK-PRGYAFIEYEHERDMHSAYKHADGKKID  169 (363)
Q Consensus        96 ~~~~~~~~l~V~nL~~~~t~~~L---~~~F~~~G~i~~v~i~~d~~--t~~-~~g~afV~f~~~~~a~~Ai~~l~g~~i~  169 (363)
                      .......-+||-+|+..+..+.+   .++|.+||.|..|.+-.++.  .+. ...-+||+|...++|..||..++|..++
T Consensus        72 ~rvVqknlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~d  151 (327)
T KOG2068|consen   72 VRVVQKNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDD  151 (327)
T ss_pred             chhhhhhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhh
Confidence            33345567999999988755444   35899999999998876552  111 1223899999999999999999999999


Q ss_pred             CEEEEEEeeccc
Q psy16184        170 GRRVLVDVERSR  181 (363)
Q Consensus       170 g~~i~V~~a~~~  181 (363)
                      |+.|+..+...+
T Consensus       152 g~~lka~~gttk  163 (327)
T KOG2068|consen  152 GRALKASLGTTK  163 (327)
T ss_pred             hhhhHHhhCCCc
Confidence            999877776543

>KOG1996|consensus

Probab=96.94  E-value=0.0027  Score=57.40  Aligned_cols=64  Identities=19%  Similarity=0.317  Sum_probs=51.4

Q ss_pred             HHHHHHHHhhCCccEEEEeccCCCCCcce-EEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        116 SKLRREFEVYGPIKKIVMVHNKVTGKPRG-YAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       116 ~~L~~~F~~~G~i~~v~i~~d~~t~~~~g-~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      +++.+.+.+||.|..|.|...+....... --||+|...++|.+|+..|||..|+|+.+..-|..
T Consensus       301 de~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn  365 (378)
T KOG1996|consen  301 DETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYN  365 (378)
T ss_pred             HHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheecc
Confidence            45667788999999998876653333322 47999999999999999999999999998776643

>KOG2253|consensus

Probab=96.77  E-value=0.0022  Score=64.09  Aligned_cols=70  Identities=17%  Similarity=0.273  Sum_probs=62.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      +..+|||+||...+..+-+..++..||.|..+..+.         |||+.|..+..+..|+..|+-..++|..+.+...
T Consensus        39 ~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~~d  108 (668)
T KOG2253|consen   39 PRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---------FGFCEFLKHIGDLRASRLLTELNIDDQKLIENVD  108 (668)
T ss_pred             CCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---------hcccchhhHHHHHHHHHHhcccCCCcchhhccch
Confidence            456999999999999999999999999998876643         9999999999999999999999999998887764

>KOG2193|consensus

Probab=96.63  E-value=0.0019  Score=61.12  Aligned_cols=73  Identities=23%  Similarity=0.401  Sum_probs=58.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhhC-CccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCc-eeCCEEEEEEeec
Q psy16184        102 KTLFIARVNYDTSESKLRREFEVYG-PIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGK-KIDGRRVLVDVER  179 (363)
Q Consensus       102 ~~l~V~nL~~~~t~~~L~~~F~~~G-~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~-~i~g~~i~V~~a~  179 (363)
                      ..||++||.+.++..+|..+|...- ....-.|+.       .||+||.+.+..-|.+|++.|+|. ++.|+.+.|++.-
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            4799999999999999999997541 111112222       489999999999999999999986 6899999999876


Q ss_pred             cc
Q psy16184        180 SR  181 (363)
Q Consensus       180 ~~  181 (363)
                      ++
T Consensus        75 ~k   76 (584)
T KOG2193|consen   75 PK   76 (584)
T ss_pred             hH
Confidence            54

>KOG4368|consensus

Probab=96.61  E-value=0.0026  Score=62.38  Aligned_cols=8  Identities=25%  Similarity=0.779  Sum_probs=3.5

Q ss_pred             CCCCCCcc
Q psy16184         32 KKTHGYSG   39 (363)
Q Consensus        32 ~~s~g~~g   39 (363)
                      +...||.|
T Consensus       351 ~~~pg~pG  358 (757)
T KOG4368|consen  351 RGDPGWNG  358 (757)
T ss_pred             CCCCCCCC
Confidence            33444444

>KOG0112|consensus

Probab=96.51  E-value=0.00087  Score=68.85  Aligned_cols=79  Identities=19%  Similarity=0.309  Sum_probs=66.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      .+.+||+|||+..+++.+|+..|..+|.|..|.|-..+ -+.-..||||.|.+...+..|+..|.+..|....+.+-+..
T Consensus       371 atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~-~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG~  449 (975)
T KOG0112|consen  371 ATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPH-IKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLGQ  449 (975)
T ss_pred             hhhhhhhcCcccchhhhhhhhhhhhhccccccccccCC-CCcccchhhhhhhccccCcccchhhcCCccccCcccccccc
Confidence            46799999999999999999999999999999995542 23445699999999999999999999888876676666664

>KOG0115|consensus

Probab=96.49  E-value=0.0036  Score=55.68  Aligned_cols=78  Identities=22%  Similarity=0.393  Sum_probs=63.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCC----ceeCCEEEEEEe
Q psy16184        102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADG----KKIDGRRVLVDV  177 (363)
Q Consensus       102 ~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g----~~i~g~~i~V~~  177 (363)
                      ..|||.||+..+..+.|...|..||.|....++.| ..++..+-++|.|...-.|.+|+..++-    ..+.+.++.|..
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD-~r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~~~~~~~~p~~VeP  110 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVD-DRGKPTREGIVEFAKKPNARKAARRCREGGFGGTTGGRPVGVEP  110 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeec-ccccccccchhhhhcchhHHHHHHHhccCccccCCCCCccCCCh
Confidence            58999999999999999999999999987777666 4688889999999999999999987632    234566666665


Q ss_pred             ecc
Q psy16184        178 ERS  180 (363)
Q Consensus       178 a~~  180 (363)
                      ...
T Consensus       111 ~eq  113 (275)
T KOG0115|consen  111 MEQ  113 (275)
T ss_pred             hhc
Confidence            543

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=96.46  E-value=0.022  Score=39.79  Aligned_cols=55  Identities=15%  Similarity=0.203  Sum_probs=45.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhh---CCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHh
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVY---GPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA  163 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~---G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l  163 (363)
                      ..+|+|.||. +++.++|+.+|..|   .....|.++.|.       -|-|.|.+.+.|..||.+|
T Consensus         5 peavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    5 PEAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            3489999996 47889999999998   235578888774       6889999999999999865

>KOG0128|consensus

Probab=96.43  E-value=0.00018  Score=73.37  Aligned_cols=67  Identities=22%  Similarity=0.338  Sum_probs=58.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCcee
Q psy16184        102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKI  168 (363)
Q Consensus       102 ~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i  168 (363)
                      +++||.||++.+.+.+|...|..+|.|..+.|.....++..+|+|||+|..++.+.+||....++.+
T Consensus       668 ~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~  734 (881)
T KOG0128|consen  668 IKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFF  734 (881)
T ss_pred             HHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhh
Confidence            4799999999999999999999999988888876667899999999999999999999985444433

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=96.30  E-value=0.015  Score=42.93  Aligned_cols=54  Identities=11%  Similarity=0.259  Sum_probs=41.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhC
Q psy16184        102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHAD  164 (363)
Q Consensus       102 ~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~  164 (363)
                      ...||+ +|..+...+|.++|+.||.|. |.++.|       .-|||...+.+.|..|+..+.
T Consensus        10 HVFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~d-------TSAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen   10 HVFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWIND-------TSAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             CEEEEE---TT--HHHHHHHCCCCCCEE-EEEECT-------TEEEEEECCCHHHHHHHHHHT
T ss_pred             eEEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcC-------CcEEEEeecHHHHHHHHHHhc
Confidence            456666 999999999999999999885 555555       389999999999999988775

; 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.

>KOG4207|consensus

Probab=96.27  E-value=0.00061  Score=58.54  Aligned_cols=62  Identities=19%  Similarity=0.294  Sum_probs=50.4

Q ss_pred             CCChhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccc--CCCCCCCCCCCcccHHHHHH
Q psy16184          4 FLPPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEF--EDPKDTPPPTRVETREERLE   67 (363)
Q Consensus         4 ~~p~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~--~~~~~~~~~~~~~~~~~~~~   67 (363)
                      +-|.+|..+|+.+|-|..+ -|.+++.|+.++|| +||-|-..-  +++.+++.+..++++++.++
T Consensus        25 Tspd~LrrvFekYG~vgDV-yIPrdr~Tr~sRgF-aFVrf~~k~daedA~damDG~~ldgRelrVq   88 (256)
T KOG4207|consen   25 TSPDDLRRVFEKYGRVGDV-YIPRDRYTRQSRGF-AFVRFHDKRDAEDALDAMDGAVLDGRELRVQ   88 (256)
T ss_pred             CCHHHHHHHHHHhCcccce-ecccccccccccce-eEEEeeecchHHHHHHhhcceeeccceeeeh
Confidence            4678899999999999998 68999999999999 888886643  35666777777777776654

>KOG0113|consensus

Probab=96.15  E-value=0.015  Score=52.94  Aligned_cols=37  Identities=16%  Similarity=0.292  Sum_probs=30.9

Q ss_pred             CChhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCcccccc
Q psy16184          5 LPPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAF   43 (363)
Q Consensus         5 ~p~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f   43 (363)
                      -...|...|..++||.-+ -|..+..|++|+|| +||.|
T Consensus       114 ~EskLrreF~~YG~Ikri-rlV~d~vTgkskGY-AFIey  150 (335)
T KOG0113|consen  114 SESKLRREFEKYGPIKRI-RLVRDKVTGKSKGY-AFIEY  150 (335)
T ss_pred             cHHHHHHHHHhcCcceeE-EEeeecccCCccce-EEEEe
Confidence            345688999999999998 57779999999999 66666

>KOG1365|consensus

Probab=96.06  E-value=0.017  Score=54.26  Aligned_cols=72  Identities=19%  Similarity=0.333  Sum_probs=54.8

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhh----CCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEE
Q psy16184        103 TLFIARVNYDTSESKLRREFEVY----GPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD  176 (363)
Q Consensus       103 ~l~V~nL~~~~t~~~L~~~F~~~----G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~  176 (363)
                      .|-+.+||+++|+.++.+||..-    |.+..|.++.. .+|+..|-|||.|..+++|+.||.. |...|+-+.|.|-
T Consensus       163 ivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~r-pdgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYIElF  238 (508)
T KOG1365|consen  163 IVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTR-PDGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYIELF  238 (508)
T ss_pred             EEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEEC-CCCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHHHHH
Confidence            46667999999999999999732    34445555554 3789999999999999999999985 5555555555443

>KOG4454|consensus

Probab=95.82  E-value=0.0013  Score=56.98  Aligned_cols=65  Identities=22%  Similarity=0.381  Sum_probs=55.0

Q ss_pred             eEEEcC----CCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCcee
Q psy16184        103 TLFIAR----VNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKI  168 (363)
Q Consensus       103 ~l~V~n----L~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i  168 (363)
                      +++.||    |...++++.+...|+..|.|..+.+..+. .|.++.|+||+|......-.|+....+..+
T Consensus        82 ~~r~G~shapld~r~~~ei~~~v~s~a~p~~~~R~~~~~-d~rnrn~~~~~~qr~~~~P~~~~~y~~l~~  150 (267)
T KOG4454|consen   82 TLRCGNSHAPLDERVTEEILYEVFSQAGPIEGVRIPTDN-DGRNRNFGFVTYQRLCAVPFALDLYQGLEL  150 (267)
T ss_pred             ccccCCCcchhhhhcchhhheeeecccCCCCCccccccc-cCCccCccchhhhhhhcCcHHhhhhcccCc
Confidence            677787    78889999999999999999999998774 588899999999988888888876665544

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=95.79  E-value=0.053  Score=44.17  Aligned_cols=76  Identities=13%  Similarity=0.288  Sum_probs=56.8

Q ss_pred             CCCCCCCeEEEcCCCCCCC-HH---HHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCE
Q psy16184         96 ATMDPFKTLFIARVNYDTS-ES---KLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGR  171 (363)
Q Consensus        96 ~~~~~~~~l~V~nL~~~~t-~~---~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~  171 (363)
                      ...+|..||.|.=|..++. .+   .|...++.||+|..|.+.-       +--|.|.|.+..+|=.|+.+++. ..-|.
T Consensus        81 ~kepPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cG-------rqsavVvF~d~~SAC~Av~Af~s-~~pgt  152 (166)
T PF15023_consen   81 TKEPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCG-------RQSAVVVFKDITSACKAVSAFQS-RAPGT  152 (166)
T ss_pred             CCCCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecC-------CceEEEEehhhHHHHHHHHhhcC-CCCCc
Confidence            3456677899986665552 23   4455677899999998842       24799999999999999999875 56777


Q ss_pred             EEEEEeec
Q psy16184        172 RVLVDVER  179 (363)
Q Consensus       172 ~i~V~~a~  179 (363)
                      .+.+.|-.
T Consensus       153 m~qCsWqq  160 (166)
T PF15023_consen  153 MFQCSWQQ  160 (166)
T ss_pred             eEEeeccc
Confidence            88887754

>KOG4307|consensus

Probab=95.65  E-value=0.013  Score=58.93  Aligned_cols=78  Identities=17%  Similarity=0.071  Sum_probs=64.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccE-EEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKK-IVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~-v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      .+..|||-.||..+++.++..+|...-.|++ |.|..- -+++..+.|||.|..++.+..|+..-+.+.++.+.|.|.-.
T Consensus       433 ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~-P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si  511 (944)
T KOG4307|consen  433 AGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRL-PTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSI  511 (944)
T ss_pred             ccceEEeccCCccccccchhhhhhhhhhhhheeEeccC-CcccccchhhheeccccccchhhhcccccccCceEEEeech
Confidence            3568999999999999999999998877777 655444 47888999999999988888888765666677788888754

>KOG2135|consensus

Probab=95.60  E-value=0.0079  Score=57.86  Aligned_cols=73  Identities=15%  Similarity=0.279  Sum_probs=59.3

Q ss_pred             CeEEEcCCCCCC-CHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeecc
Q psy16184        102 KTLFIARVNYDT-SESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS  180 (363)
Q Consensus       102 ~~l~V~nL~~~~-t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~  180 (363)
                      +.|-+.-+++.+ |..+|..+|.+||+|..|.|-..      .-.|.|+|.+..+|-.|.. .++..|+++.|+|-|-++
T Consensus       373 s~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~------~~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~whnp  445 (526)
T KOG2135|consen  373 SPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS------SLHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWHNP  445 (526)
T ss_pred             chhhhhccCCCCchHhhhhhhhhhcCccccccccCc------hhhheeeeeccccccchhc-cccceecCceeEEEEecC
Confidence            344455555554 56899999999999999988543      3479999999999988887 699999999999999876


Q ss_pred             c
Q psy16184        181 R  181 (363)
Q Consensus       181 ~  181 (363)
                      .
T Consensus       446 s  446 (526)
T KOG2135|consen  446 S  446 (526)
T ss_pred             C
Confidence            3

>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=95.06  E-value=0.11  Score=37.80  Aligned_cols=67  Identities=21%  Similarity=0.319  Sum_probs=40.3

Q ss_pred             eEEEc-CCCCCCCHHHHHHHHHhhCC-----ccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEE
Q psy16184        103 TLFIA-RVNYDTSESKLRREFEVYGP-----IKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD  176 (363)
Q Consensus       103 ~l~V~-nL~~~~t~~~L~~~F~~~G~-----i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~  176 (363)
                      +|||. +--..++..+|..+|...+.     |-.|.|..        .|+||+-.. +.|..++..|++..+.|+.|.|+
T Consensus         2 rl~in~Gr~dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~--------~~S~vev~~-~~a~~v~~~l~~~~~~gk~v~ve   72 (74)
T PF03880_consen    2 RLFINVGRKDGLTPRDIVGAICNEAGIPGRDIGRIDIFD--------NFSFVEVPE-EVAEKVLEALNGKKIKGKKVRVE   72 (74)
T ss_dssp             EEEES-SGGGT--HHHHHHHHHTCTTB-GGGEEEEEE-S--------S-EEEEE-T-T-HHHHHHHHTT--SSS----EE
T ss_pred             EEEEEcccccCCCHHHHHHHHHhccCCCHHhEEEEEEee--------eEEEEEECH-HHHHHHHHHhcCCCCCCeeEEEE
Confidence            45553 33456888999999887654     44677744        399999865 57888999999999999999998


Q ss_pred             ee
Q psy16184        177 VE  178 (363)
Q Consensus       177 ~a  178 (363)
                      .|
T Consensus        73 ~A   74 (74)
T PF03880_consen   73 RA   74 (74)
T ss_dssp             E-
T ss_pred             EC
Confidence            75

; PDB: 2G0C_A 3MOJ_B.

>KOG0149|consensus

Probab=95.02  E-value=0.0027  Score=55.76  Aligned_cols=60  Identities=15%  Similarity=0.192  Sum_probs=47.4

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccC-CCCCCCCCCCcccHHHHHHH
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFE-DPKDTPPPTRVETREERLER   68 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~-~~~~~~~~~~~~~~~~~~~~   68 (363)
                      ..|..+|..+|-|..+ .|.-|-.|++|+|| |||+|.+... .-+.+.+.+.|+++......
T Consensus        27 ~~l~~yFeqfGeI~ea-vvitd~~t~rskGy-GfVTf~d~~aa~rAc~dp~piIdGR~aNcnl   87 (247)
T KOG0149|consen   27 ETLRRYFEQFGEIVEA-VVITDKNTGRSKGY-GFVTFRDAEAATRACKDPNPIIDGRKANCNL   87 (247)
T ss_pred             HHHHHHHHHhCceEEE-EEEeccCCccccce-eeEEeecHHHHHHHhcCCCCcccccccccch
Confidence            3588999999999988 45568999999999 9999998665 33455666778888766554

>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=95.01  E-value=0.023  Score=48.86  Aligned_cols=80  Identities=14%  Similarity=0.132  Sum_probs=50.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHh-hCCc---cEEEEeccC--CCCCcceEEEEEecCHHHHHHHHHHhCCceeC---C-
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEV-YGPI---KKIVMVHNK--VTGKPRGYAFIEYEHERDMHSAYKHADGKKID---G-  170 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~-~G~i---~~v~i~~d~--~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~---g-  170 (363)
                      ..+|.|.+||+.+|++++.+.+.. ++..   ..+......  .......-|||.|.+.+++..-+..++|+.|.   | 
T Consensus         7 ~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~kg~   86 (176)
T PF03467_consen    7 GTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSKGN   86 (176)
T ss_dssp             --EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TTS-
T ss_pred             CceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCCCC
Confidence            458999999999999999886665 5544   233211111  11223457999999999999999999997763   2 


Q ss_pred             -EEEEEEeecc
Q psy16184        171 -RRVLVDVERS  180 (363)
Q Consensus       171 -~~i~V~~a~~  180 (363)
                       ....|++|--
T Consensus        87 ~~~~~VE~Apy   97 (176)
T PF03467_consen   87 EYPAVVEFAPY   97 (176)
T ss_dssp             EEEEEEEE-SS
T ss_pred             CcceeEEEcch
Confidence             3456777654

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=94.96  E-value=0.26  Score=38.85  Aligned_cols=75  Identities=16%  Similarity=0.171  Sum_probs=52.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhh-CCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC---EEEEEE
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVY-GPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDG---RRVLVD  176 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~-G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g---~~i~V~  176 (363)
                      +..+.+...|+.++.+.|..+.+.+ ..|..+.|+.+.  ..++-.++|.|.+...|..-+..+||+.++.   ..++|-
T Consensus        13 ~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~--~pnrymVLikF~~~~~Ad~Fy~~fNGk~FnslEpE~Chvv   90 (110)
T PF07576_consen   13 STLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDG--TPNRYMVLIKFRDQESADEFYEEFNGKPFNSLEPETCHVV   90 (110)
T ss_pred             ceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCC--CCceEEEEEEECCHHHHHHHHHHhCCCccCCCCCceeEEE
Confidence            3445555666666667776665555 357788888763  2355679999999999999999999987653   344444


Q ss_pred             e
Q psy16184        177 V  177 (363)
Q Consensus       177 ~  177 (363)
                      +
T Consensus        91 f   91 (110)
T PF07576_consen   91 F   91 (110)
T ss_pred             E
Confidence            4

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG2548|consensus

Probab=94.83  E-value=0.0071  Score=58.78  Aligned_cols=10  Identities=0%  Similarity=0.156  Sum_probs=4.7

Q ss_pred             cCHHHHHHHH
Q psy16184        151 EHERDMHSAY  160 (363)
Q Consensus       151 ~~~~~a~~Ai  160 (363)
                      .+.++|.++.
T Consensus       235 kdkeea~a~k  244 (653)
T KOG2548|consen  235 KDKEEAKAQK  244 (653)
T ss_pred             hhHHHHHHHH
Confidence            4455554443

>KOG4574|consensus

Probab=94.83  E-value=0.094  Score=54.12  Aligned_cols=74  Identities=14%  Similarity=0.200  Sum_probs=64.4

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCcee--CCEEEEEEeecc
Q psy16184        103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKI--DGRRVLVDVERS  180 (363)
Q Consensus       103 ~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i--~g~~i~V~~a~~  180 (363)
                      +.++.|.+-..+...|..+|..||.|..++.+.+-      ..|.|+|.+.+.|..|+.+|+|+.+  .|.+..|.+|+.
T Consensus       300 ~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~------N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~  373 (1007)
T KOG4574|consen  300 KQSLENNAVNLTSSSLATLCSDYGSVASAWTLRDL------NMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKT  373 (1007)
T ss_pred             hhhhhcccccchHHHHHHHHHhhcchhhheecccc------cchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEeccc
Confidence            56677888888999999999999999999887763      5899999999999999999999864  688899999986


Q ss_pred             cC
Q psy16184        181 RT  182 (363)
Q Consensus       181 ~~  182 (363)
                      .+
T Consensus       374 ~~  375 (1007)
T KOG4574|consen  374 LP  375 (1007)
T ss_pred             cc
Confidence            54

>KOG4285|consensus

Probab=94.54  E-value=0.12  Score=47.32  Aligned_cols=66  Identities=20%  Similarity=0.229  Sum_probs=49.2

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEE-EEEEe
Q psy16184        104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRR-VLVDV  177 (363)
Q Consensus       104 l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~-i~V~~  177 (363)
                      |-|-++++..+ ..|..+|.+||.|......      ..-.|-+|.|.+..+|.+||.. ||+.|+|.. |-|..
T Consensus       200 VTVfGFppg~~-s~vL~~F~~cG~Vvkhv~~------~ngNwMhirYssr~~A~KALsk-ng~ii~g~vmiGVkp  266 (350)
T KOG4285|consen  200 VTVFGFPPGQV-SIVLNLFSRCGEVVKHVTP------SNGNWMHIRYSSRTHAQKALSK-NGTIIDGDVMIGVKP  266 (350)
T ss_pred             EEEeccCccch-hHHHHHHHhhCeeeeeecC------CCCceEEEEecchhHHHHhhhh-cCeeeccceEEeeee
Confidence            44557776543 5677899999999776443      2234899999999999999994 999998865 44554

>KOG4660|consensus

Probab=94.42  E-value=0.067  Score=52.73  Aligned_cols=81  Identities=22%  Similarity=0.242  Sum_probs=63.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHH-hhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCcee---C-CEEEE
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFE-VYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKI---D-GRRVL  174 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~-~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i---~-g~~i~  174 (363)
                      +-+++.|.|++...|...|...-. ..|.-..+.++.|-.+..+.|||||-|.+.+.+..+++++||+..   + .+.+.
T Consensus       387 ~rtt~~iknipNK~T~~ml~~~d~~~~gtYDFlYLPiDF~nkcNvGYAFINm~sp~ai~~F~kAFnGk~W~~FnS~Kia~  466 (549)
T KOG4660|consen  387 PRTTLMIKNIPNKYTSKMLLAADEKNKGTYDFLYLPIDFKNKCNVGYAFINMTSPEAIIRFYKAFNGKKWEKFNSEKIAS  466 (549)
T ss_pred             chhhhHhhccCchhhHHhhhhhhccccCccceEEeccccccccccceeEEeecCHHHHHHHHHHHcCCchhhhcceeeee
Confidence            356788889988877776655543 357777888888888888999999999999999999999999743   3 45567


Q ss_pred             EEeecc
Q psy16184        175 VDVERS  180 (363)
Q Consensus       175 V~~a~~  180 (363)
                      |.||+-
T Consensus       467 itYArI  472 (549)
T KOG4660|consen  467 ITYARI  472 (549)
T ss_pred             eehhhh
Confidence            777753

>KOG2888|consensus

Probab=94.23  E-value=0.011  Score=54.39  Aligned_cols=9  Identities=33%  Similarity=0.962  Sum_probs=4.8

Q ss_pred             ceEEEEEec
Q psy16184        143 RGYAFIEYE  151 (363)
Q Consensus       143 ~g~afV~f~  151 (363)
                      .||-||-|.
T Consensus       160 lGFmYiRYt  168 (453)
T KOG2888|consen  160 LGFMYIRYT  168 (453)
T ss_pred             heeeEEeec
Confidence            355555554

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

Probab=94.17  E-value=0.0035  Score=52.12  Aligned_cols=39  Identities=23%  Similarity=0.252  Sum_probs=33.2

Q ss_pred             ChhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          6 PPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         6 p~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      ..+|..+|.++++|..+ .+..++.|++++|| +||.|.+.
T Consensus        48 e~~L~~~F~~~G~I~~v-~i~~d~~tg~~kGf-aFV~F~~~   86 (144)
T PLN03134         48 DASLRDAFAHFGDVVDA-KVIVDRETGRSRGF-GFVNFNDE   86 (144)
T ss_pred             HHHHHHHHhcCCCeEEE-EEEecCCCCCcceE-EEEEECCH
Confidence            35799999999999998 46678899999999 99999654

>KOG4210|consensus

Probab=93.70  E-value=0.055  Score=50.21  Aligned_cols=82  Identities=15%  Similarity=0.151  Sum_probs=67.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      ..+++||+++.+.+.+.++..+|..+|.+..+.+........++|+++|.|...+.+..||.......+.+..+...+..
T Consensus        87 ~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~~  166 (285)
T KOG4210|consen   87 SSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLNT  166 (285)
T ss_pred             ccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCcccc
Confidence            46789999999999999999999999988887776666678889999999999999999999543356777776666654


Q ss_pred             cc
Q psy16184        180 SR  181 (363)
Q Consensus       180 ~~  181 (363)
                      ..
T Consensus       167 ~~  168 (285)
T KOG4210|consen  167 RR  168 (285)
T ss_pred             cc
Confidence            43

>KOG0122|consensus

Probab=93.65  E-value=0.019  Score=50.83  Aligned_cols=39  Identities=18%  Similarity=0.371  Sum_probs=33.9

Q ss_pred             ChhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          6 PPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         6 p~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .++|..||-+++||.-+ -|.++..||.++|| +||+|...
T Consensus       203 E~dL~eLf~~fg~i~rv-ylardK~TG~~kGF-AFVtF~sR  241 (270)
T KOG0122|consen  203 EDDLEELFRPFGPITRV-YLARDKETGLSKGF-AFVTFESR  241 (270)
T ss_pred             hhHHHHHhhccCcccee-EEEEccccCcccce-EEEEEecH
Confidence            46799999999999988 57789999999999 88888543

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=93.62  E-value=0.25  Score=42.77  Aligned_cols=61  Identities=16%  Similarity=0.266  Sum_probs=45.4

Q ss_pred             CHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhC--CceeCCEEEEEEeecc
Q psy16184        114 SESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHAD--GKKIDGRRVLVDVERS  180 (363)
Q Consensus       114 t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~--g~~i~g~~i~V~~a~~  180 (363)
                      ....|+.+|..|+.+..+.++..      -+=..|.|.+.+.|..|...|+  +..|.|..|.|.++..
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s------FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~   70 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS------FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQP   70 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT------TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC------CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccc
Confidence            34789999999998888777553      3468899999999999999999  9999999999999854

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.

>KOG2591|consensus

Probab=93.61  E-value=0.08  Score=52.16  Aligned_cols=68  Identities=18%  Similarity=0.290  Sum_probs=53.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHh--hCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCC--ceeCCEEEEE
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEV--YGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADG--KKIDGRRVLV  175 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~--~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g--~~i~g~~i~V  175 (363)
                      -|.|+|.-||..+-.++|+.+|..  |-.++.|.+..+       .-=||+|++..+|+.|+..|..  +.|.|++|..
T Consensus       175 RcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N-------~nWyITfesd~DAQqAykylreevk~fqgKpImA  246 (684)
T KOG2591|consen  175 RCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHN-------DNWYITFESDTDAQQAYKYLREEVKTFQGKPIMA  246 (684)
T ss_pred             eeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeec-------CceEEEeecchhHHHHHHHHHHHHHhhcCcchhh
Confidence            356788999999999999999984  678888888554       2468999999999999887743  3456665543

>KOG2548|consensus

Probab=93.40  E-value=0.033  Score=54.32  Aligned_cols=18  Identities=22%  Similarity=0.405  Sum_probs=7.4

Q ss_pred             hhhcCCCCCCCCCCCCCC
Q psy16184          9 LLALFAPRDPVPYLPPVE   26 (363)
Q Consensus         9 l~~~f~~~~pi~~~~p~~   26 (363)
                      ++..|...--|-++|+|.
T Consensus        73 ~idrFDvRAhLdhi~~vd   90 (653)
T KOG2548|consen   73 QIDRFDVRAHLDHIPEVD   90 (653)
T ss_pred             hhhhhhhHhhhccCCccC
Confidence            344444444444444333

>PLN03213 repressor of silencing 3; Provisional

Probab=93.18  E-value=0.015  Score=56.23  Aligned_cols=61  Identities=18%  Similarity=0.211  Sum_probs=44.9

Q ss_pred             ChhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc----cCCCCCCCCCCCcccHHHHHHHHHHH
Q psy16184          6 PPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE----FEDPKDTPPPTRVETREERLERRRRE   72 (363)
Q Consensus         6 p~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~   72 (363)
                      ..+|..+|+++|.|..+..+   -.|+  +|| +||.|...    +..+...+....+.|+.+++.+++..
T Consensus        24 EDDLravFSeFGsVkdVEIp---RETG--RGF-AFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAKP~   88 (759)
T PLN03213         24 RDDLLKIFSPMGTVDAVEFV---RTKG--RSF-AYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAKEH   88 (759)
T ss_pred             HHHHHHHHHhcCCeeEEEEe---cccC--Cce-EEEEecCCcHHHHHHHHHHhcCCeecCceeEEeeccHH
Confidence            35799999999999987533   3456  999 99999875    22455678888888887777654433

>KOG2318|consensus

Probab=92.76  E-value=0.53  Score=46.85  Aligned_cols=80  Identities=20%  Similarity=0.363  Sum_probs=61.9

Q ss_pred             CCCCCeEEEcCCCCC-CCHHHHHHHHHhh----CCccEEEEeccC----------CCCC---------------------
Q psy16184         98 MDPFKTLFIARVNYD-TSESKLRREFEVY----GPIKKIVMVHNK----------VTGK---------------------  141 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~-~t~~~L~~~F~~~----G~i~~v~i~~d~----------~t~~---------------------  141 (363)
                      ..+++.|-|.||.|. +...+|..+|..|    |.|..|.|....          .+|.                     
T Consensus       171 ~~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeFGkeRM~eEeV~GP~~el~~~~e~~~~s~sD~ee~  250 (650)
T KOG2318|consen  171 GEETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEFGKERMKEEEVHGPPKELFKPVEEYKESESDDEEE  250 (650)
T ss_pred             ccccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhhhHHHhhhhcccCChhhhccccccCcccccchhhh
Confidence            456789999999987 6789999999987    689999885421          1122                     


Q ss_pred             ----------------cceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184        142 ----------------PRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus       142 ----------------~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                                      ..-||.|+|.+.+.|.+.+..|+|.+|..-...+.+
T Consensus       251 ~~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~DL  302 (650)
T KOG2318|consen  251 EDVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSANKLDL  302 (650)
T ss_pred             hhHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccceeee
Confidence                            112799999999999999999999999765555554

>KOG2888|consensus

Probab=92.39  E-value=0.04  Score=50.79  Aligned_cols=10  Identities=30%  Similarity=0.471  Sum_probs=4.5

Q ss_pred             HHHHHHHHhh
Q psy16184        116 SKLRREFEVY  125 (363)
Q Consensus       116 ~~L~~~F~~~  125 (363)
                      .+|..+|+.|
T Consensus       172 ~dLw~WyEpy  181 (453)
T KOG2888|consen  172 ADLWDWYEPY  181 (453)
T ss_pred             hHHHHHhhhh
Confidence            3444444444

>KOG0151|consensus

Probab=92.19  E-value=0.15  Score=51.73  Aligned_cols=12  Identities=25%  Similarity=0.639  Sum_probs=7.0

Q ss_pred             eeCCEEEEEEee
Q psy16184        167 KIDGRRVLVDVE  178 (363)
Q Consensus       167 ~i~g~~i~V~~a  178 (363)
                      .|+|.+|.++..
T Consensus       632 ~ldgipm~~e~~  643 (877)
T KOG0151|consen  632 DLDGIPMMVETK  643 (877)
T ss_pred             cccCceeeeeec
Confidence            356666666643

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=92.05  E-value=1.6  Score=45.36  Aligned_cols=69  Identities=12%  Similarity=0.057  Sum_probs=50.4

Q ss_pred             EEEc-CCCCCCCHHHHHHHHHhhCCc-----cEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184        104 LFIA-RVNYDTSESKLRREFEVYGPI-----KKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus       104 l~V~-nL~~~~t~~~L~~~F~~~G~i-----~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      +||. +-...++..+|..++..-+.|     -.|.|..        .|.||+... ..|...+..|++..|.|+.|.|+.
T Consensus       489 ~~~~~g~~~~~~~~~~~~~i~~~~~~~~~~ig~i~i~~--------~~s~v~~~~-~~~~~~~~~~~~~~~~~~~~~~~~  559 (629)
T PRK11634        489 YRIEVGRDDGVEVRHIVGAIANEGDISSRYIGNIKLFA--------SHSTIELPK-GMPGEVLQHFTRTRILNKPMNMQL  559 (629)
T ss_pred             EEEecccccCCCHHHHHHHHHhhcCCChhhCCcEEEeC--------CceEEEcCh-hhHHHHHHHhccccccCCceEEEE
Confidence            4442 234567888888888766544     3556643        499999864 567888888999999999999998


Q ss_pred             eccc
Q psy16184        178 ERSR  181 (363)
Q Consensus       178 a~~~  181 (363)
                      +...
T Consensus       560 ~~~~  563 (629)
T PRK11634        560 LGDA  563 (629)
T ss_pred             CCCC
Confidence            7543

>KOG0125|consensus

Probab=91.68  E-value=0.0086  Score=55.10  Aligned_cols=59  Identities=22%  Similarity=0.320  Sum_probs=45.6

Q ss_pred             ChhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccC--CCCCCCCCCCcccHHHHHHH
Q psy16184          6 PPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFE--DPKDTPPPTRVETREERLER   68 (363)
Q Consensus         6 p~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~--~~~~~~~~~~~~~~~~~~~~   68 (363)
                      -|||..+|..+|+|..+-.|-   +..-|+|| |||+|.+...  .+-.++-...|+++.|++..
T Consensus       110 dpDL~aMF~kfG~VldVEIIf---NERGSKGF-GFVTmen~~dadRARa~LHgt~VEGRkIEVn~  170 (376)
T KOG0125|consen  110 DPDLRAMFEKFGKVLDVEIIF---NERGSKGF-GFVTMENPADADRARAELHGTVVEGRKIEVNN  170 (376)
T ss_pred             CccHHHHHHhhCceeeEEEEe---ccCCCCcc-ceEEecChhhHHHHHHHhhcceeeceEEEEec
Confidence            489999999999999885444   46789999 9999977544  33446777788888777654

>KOG0108|consensus

Probab=91.58  E-value=0.01  Score=58.03  Aligned_cols=65  Identities=18%  Similarity=0.275  Sum_probs=49.6

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccC--CCCCCCCCCCcccHHHHHHHHHHHH
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFE--DPKDTPPPTRVETREERLERRRRER   73 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~   73 (363)
                      ..|..+|+..+||..+. +..|+.||+++|| ||+.|.+...  .+...++..++.++..++..+...+
T Consensus        33 ~~l~~~~~~~g~v~s~~-~v~D~~tG~~~G~-~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~~   99 (435)
T KOG0108|consen   33 EQLLSIFSGVGPVLSFR-LVYDRETGKPKGF-GFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNRK   99 (435)
T ss_pred             HHHHHHHhccCccceee-ecccccCCCcCce-eeEecCchhhHHHHHHhcCCcccCCceEEeecccccc
Confidence            45889999999999884 6779999999999 9999988555  3344577778877776666544433

>KOG2193|consensus

Probab=91.28  E-value=0.0093  Score=56.57  Aligned_cols=76  Identities=13%  Similarity=0.215  Sum_probs=63.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      ++++-|.|+|+...++.|..++.+||.|..|..+.   |.--....-|+|.+.+.+..||..|||..|....+.|.|-.
T Consensus        80 srk~Qirnippql~wevld~Ll~qyg~ve~~eqvn---t~~etavvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~YiP  155 (584)
T KOG2193|consen   80 SRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVN---TDSETAVVNVTYSAQQQHRQAIHKLNGPQLENQHLKVGYIP  155 (584)
T ss_pred             hhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhc---cchHHHHHHHHHHHHHHHHHHHHhhcchHhhhhhhhcccCc
Confidence            45688999999999999999999999999887632   22223455689999999999999999999999999888753

>KOG0804|consensus

Probab=90.30  E-value=0.93  Score=43.88  Aligned_cols=68  Identities=21%  Similarity=0.308  Sum_probs=56.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhh-CCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVY-GPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDG  170 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~-G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g  170 (363)
                      +..|+|-.+|..+|--+|..|+..| -.|.++.|+.|..  -++=.++|.|.+.++|...+..+||..|+.
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~--pnrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGM--PNRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCC--CceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            6789999999999999999999876 4788999998532  223358999999999999999999987753

>KOG0111|consensus

Probab=89.56  E-value=0.07  Score=46.54  Aligned_cols=57  Identities=19%  Similarity=0.266  Sum_probs=43.5

Q ss_pred             hhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccC--CCCCCCCCCCcccHHHHHH
Q psy16184          9 LLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFE--DPKDTPPPTRVETREERLE   67 (363)
Q Consensus         9 l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~--~~~~~~~~~~~~~~~~~~~   67 (363)
                      |...|-|++-|..+ .++.|..+.+-+|| |||.|.....  .+.+.+...++-++.+++.
T Consensus        27 LhaAFIPFGDI~dI-qiPlDyesqkHRgF-gFVefe~aEDAaaAiDNMnesEL~GrtirVN   85 (298)
T KOG0111|consen   27 LHAAFIPFGDIKDI-QIPLDYESQKHRGF-GFVEFEEAEDAAAAIDNMNESELFGRTIRVN   85 (298)
T ss_pred             HHhccccccchhhc-ccccchhcccccce-eEEEeeccchhHHHhhcCchhhhcceeEEEe
Confidence            67889999999988 57778899999999 9999977554  3455666666666655443

>KOG0126|consensus

Probab=88.47  E-value=0.052  Score=46.01  Aligned_cols=61  Identities=11%  Similarity=0.215  Sum_probs=44.8

Q ss_pred             CChhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccC--CCCCCCCCCCcccHHHHHH
Q psy16184          5 LPPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFE--DPKDTPPPTRVETREERLE   67 (363)
Q Consensus         5 ~p~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~--~~~~~~~~~~~~~~~~~~~   67 (363)
                      -..+|+.+|+++|-|..+. +++|-.||+|+|| .|..|.+.-.  -+.+++++..|.++++++.
T Consensus        48 tEgDil~VFSqyGe~vdin-LiRDk~TGKSKGF-aFLcYEDQRSTILAVDN~NGiki~gRtirVD  110 (219)
T KOG0126|consen   48 TEGDILCVFSQYGEIVDIN-LIRDKKTGKSKGF-AFLCYEDQRSTILAVDNLNGIKILGRTIRVD  110 (219)
T ss_pred             cCCcEEEEeeccCceEEEE-EEecCCCCcccce-EEEEecCccceEEEEeccCCceecceeEEee
Confidence            3567899999999999884 8889999999999 3333333222  3566778888888776653

>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=88.02  E-value=3.2  Score=29.43  Aligned_cols=55  Identities=11%  Similarity=0.332  Sum_probs=43.1

Q ss_pred             CCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEE
Q psy16184        112 DTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLV  175 (363)
Q Consensus       112 ~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V  175 (363)
                      .++-++|+..+..|+- .  .|..++     .| =||.|.+..+|+.|+...+|..+.+..|.+
T Consensus        11 ~~~v~d~K~~Lr~y~~-~--~I~~d~-----tG-fYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRW-D--RIRDDR-----TG-FYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCCc-c--eEEecC-----CE-EEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            4678999999999973 2  343443     23 379999999999999999999988877765

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>smart00361 RRM_1 RNA recognition motif

Probab=87.33  E-value=0.031  Score=40.15  Aligned_cols=40  Identities=10%  Similarity=-0.044  Sum_probs=29.0

Q ss_pred             hhhhhcCC----CCCCCCCCCCCCCCCCC--CCCCCCcccccccccc
Q psy16184          7 PNLLALFA----PRDPVPYLPPVEKLPHE--KKTHGYSGIAAFLNEF   47 (363)
Q Consensus         7 ~~l~~~f~----~~~pi~~~~p~~~~p~t--~~s~g~~g~v~f~~~~   47 (363)
                      .+|..+|.    .+|+|..+.-+..++.+  +.++|| +||.|.+..
T Consensus         3 ~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~-~fV~f~~~~   48 (70)
T smart00361        3 EDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGN-VYITFERSE   48 (70)
T ss_pred             hhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEE-EEEEECCHH
Confidence            46778888    99999876423334444  889999 999997654

>KOG0835|consensus

Probab=86.60  E-value=1.2  Score=41.50  Aligned_cols=6  Identities=33%  Similarity=1.032  Sum_probs=2.7

Q ss_pred             EEEEec
Q psy16184        146 AFIEYE  151 (363)
Q Consensus       146 afV~f~  151 (363)
                      .||-|.
T Consensus       176 v~vry~  181 (367)
T KOG0835|consen  176 VFVRYS  181 (367)
T ss_pred             eeeecC
Confidence            444443

>KOG4483|consensus

Probab=83.96  E-value=8.2  Score=37.00  Aligned_cols=56  Identities=18%  Similarity=0.102  Sum_probs=47.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCC-ccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHH
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGP-IKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH  162 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~-i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~  162 (363)
                      -.+.|-|-|+|...-.++|...|..|+. --.|.|+-|.       .||..|.+...|..||..
T Consensus       390 lpHVlEIydfp~efkteDll~~f~~yq~kgfdIkWvDdt-------halaVFss~~~AaeaLt~  446 (528)
T KOG4483|consen  390 LPHVLEIYDFPDEFKTEDLLKAFETYQNKGFDIKWVDDT-------HALAVFSSVNRAAEALTL  446 (528)
T ss_pred             ccceeEeccCchhhccHHHHHHHHHhhcCCceeEEeecc-------eeEEeecchHHHHHHhhc
Confidence            4568899999999988999999999974 4567777764       899999999999999984

>KOG0107|consensus

Probab=80.84  E-value=4.5  Score=34.40  Aligned_cols=12  Identities=17%  Similarity=0.437  Sum_probs=7.8

Q ss_pred             CCeEEEcCCCCC
Q psy16184        101 FKTLFIARVNYD  112 (363)
Q Consensus       101 ~~~l~V~nL~~~  112 (363)
                      ...|||.-.|+.
T Consensus        37 lrsvWvArnPPG   48 (195)
T KOG0107|consen   37 LRSVWVARNPPG   48 (195)
T ss_pred             ceeEEEeecCCC
Confidence            457888766654

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	363
3pgw_S	437	Crystal Structure Of Human U1 Snrnp Length = 437		5e-59
3cw1_K	216	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		7e-59
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		1e-09
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		1e-09
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		3e-09
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		6e-09
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		8e-09
2fc8_A	102	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		2e-08
2dnm_A	103	Solution Structure Of Rna Binding Domain In Srp46 S		2e-08
2cqc_A	95	Solution Structure Of The Rna Recognition Motif In		3e-08
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		4e-08
2lea_A	135	Solution Structure Of Human Srsf2 (Sc35) Rrm Length		3e-07
2kn4_A	158	The Structure Of The Rrm Domain Of Sc35 Length = 15		3e-07
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		8e-07
2hvz_A	101	Solution Structure Of The Rrm Domain Of Sr Rich Fac		8e-07
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		2e-06
1whw_A	99	Solution Structure Of The N-Terminal Rna Binding Do		2e-06
2i2y_A	150	Solution Structure Of The Rrm Of Srp20 Bound To The		2e-06
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		2e-06
2i38_A	150	Solution Structure Of The Rrm Of Srp20 Length = 150		2e-06
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		3e-06
1h2t_Z	156	Structure Of The Human Nuclear Cap-Binding-Complex		1e-05
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		1e-05
2cq0_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		1e-05
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		1e-05
1hl6_A	165	A Novel Mode Of Rbd-Protein Recognition In The Y14-		2e-05
1oo0_B	110	Crystal Structure Of The Drosophila Mago Nashi-Y14		3e-05
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		4e-05
2dgs_A	99	Solution Structure Of The Second Rna Binding Domain		4e-05
2j0q_D	109	The Crystal Structure Of The Exon Junction Complex		4e-05
2jwn_A	124	Solution Nmr Structure Of The Protease-Resistent Do		5e-05
1p27_B	106	Crystal Structure Of The Human Y14MAGOH COMPLEX Len		5e-05
2xb2_D	90	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		5e-05
2j0s_D	89	The Crystal Structure Of The Exon Junction Complex		6e-05
3ex7_B	126	The Crystal Structure Of Ejc In Its Transition Stat		6e-05
1h6k_Z	98	Nuclear Cap Binding Complex Length = 98		7e-05
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		7e-05
2hyi_B	91	Structure Of The Human Exon Junction Complex With A		8e-05
4a8x_A	88	Structure Of The Core Asap Complex Length = 88		1e-04
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		1e-04
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		1e-04
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		1e-04
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		1e-04
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		1e-04
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		1e-04
2x1a_A	97	Structure Of Rna15 Rrm With Rna Bound (G) Length =		1e-04
1x4b_A	116	Solution Structure Of Rrm Domain In Heterogeneous N		1e-04
2x1f_A	96	Structure Of Rna15 Rrm With Bound Rna (Gu) Length =		1e-04
2do4_A	100	Solution Structure Of The Rna Binding Domain Of Squ		2e-04
2km8_B	84	Interdomain Rrm Packing Contributes To Rna Recognit		3e-04
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		3e-04
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		4e-04
2fc9_A	101	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		4e-04

>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp Length = 437

Iteration: 1
 Score =  224 bits (571), Expect = 5e-59,   Method: Compositional matrix adjust.
 Identities = 118/212 (55%), Positives = 138/212 (65%), Gaps = 1/212 (0%)
Query: 1   MTQXXXXXXXXXXXXRDPVPYLPPVEKLPHEKK-THGYSGIAAFLNEFEDPKDXXXXXXX 59
           MTQ            RDP+PYLPP+EKLPHEK     Y GIA ++ EFEDP+D       
Sbjct: 1   MTQFLPPNLLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRDAPPPTRA 60
Query: 60  XXXXXXXXXXXXXXXXQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLR 119
                           +   ++E E+ +WDP++ PNA  D FKTLF+ARVNYDT+ESKLR
Sbjct: 61  ETREERMERKRREKIERRQQEVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLR 120
Query: 120 REFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 179
           REFEVYGPIK+I MV++K +GKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER
Sbjct: 121 REFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 180
Query: 180 SRTVKXXXXXXXXXXXXXXXXXXPDVNLKHSG 211
            RTVK                   DVN++HSG
Sbjct: 181 GRTVKGWRPRRLGGGLGGTRRGGADVNIRHSG 212

>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 216

Iteration: 1
 Score =  224 bits (570), Expect = 7e-59,   Method: Compositional matrix adjust.
 Identities = 118/212 (55%), Positives = 138/212 (65%), Gaps = 1/212 (0%)
Query: 1   MTQXXXXXXXXXXXXRDPVPYLPPVEKLPHEKK-THGYSGIAAFLNEFEDPKDXXXXXXX 59
           MTQ            RDP+PYLPP+EKLPHEK     Y GIA ++ EFEDP+D       
Sbjct: 1   MTQFLPPNLLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRDAPPPTRA 60
Query: 60  XXXXXXXXXXXXXXXXQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLR 119
                           +   ++E E+ +WDP++ PNA  D FKTLF+ARVNYDT+ESKLR
Sbjct: 61  ETREERMERKRREKIERRQQEVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLR 120
Query: 120 REFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 179
           REFEVYGPIK+I MV++K +GKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER
Sbjct: 121 REFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 180
Query: 180 SRTVKXXXXXXXXXXXXXXXXXXPDVNLKHSG 211
            RTVK                   DVN++HSG
Sbjct: 181 GRTVKGWRPRRLGGGLGGTRRGGADVNIRHSG 212

>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 = 61.2 bits (147), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 24/76 (31%), Positives = 47/76 (61%)
Query: 101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAY 160
            +++F+  + Y+ +E +L+  F   GP+    +V+++ TGKP+GY F EY+ +    SA 
Sbjct: 8   LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAM 67
Query: 161 KHADGKKIDGRRVLVD 176
           ++ +G++  GR + VD
Sbjct: 68  RNLNGREFSGRALRVD 83

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 60.8 bits (146), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 26/73 (35%), Positives = 46/73 (63%)
Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           LF+  +++DT+E  L + F  YG I ++V+V ++ T + RG+ F+ +E+  D   A    
Sbjct: 15  LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 164 DGKKIDGRRVLVD 176
           +GK +DGR++ VD
Sbjct: 75  NGKSVDGRQIRVD 87

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 59.3 bits (142), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 29/81 (35%), Positives = 49/81 (60%)
Query: 96  ATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERD 155
           A  DP   L +  ++  T+E  LR  F  YGPI  + +V+++ + + RG+AF+ +E+  D
Sbjct: 7   ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDD 66
Query: 156 MHSAYKHADGKKIDGRRVLVD 176
              A + A+G ++DGRR+ VD
Sbjct: 67  AKEAKERANGMELDGRRIRVD 87

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 58.5 bits (140), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 28/78 (35%), Positives = 48/78 (61%)
Query: 99  DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHS 158
           DP   L +  ++  T+E  LR  F  YGPI  + +V+++ + + RG+AF+ +E+  D   
Sbjct: 44  DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 103
Query: 159 AYKHADGKKIDGRRVLVD 176
           A + A+G ++DGRR+ VD
Sbjct: 104 AKERANGMELDGRRIRVD 121

>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2 Beta Protein In Complex With Rna (Gaagaa) Length = 99

Iteration: 1
 Score = 57.8 bits (138), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 29/81 (35%), Positives = 49/81 (60%)
Query: 96  ATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERD 155
           A  DP   L +  ++  T+E  LR  F  YGPI  + +V+++ + + RG+AF+ +E+  D
Sbjct: 10  ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDD 69
Query: 156 MHSAYKHADGKKIDGRRVLVD 176
              A + A+G ++DGRR+ VD
Sbjct: 70  AKEAKERANGMELDGRRIRVD 90

>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 102

Iteration: 1
 Score = 57.0 bits (136), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 28/86 (32%), Positives = 51/86 (59%), Gaps = 3/86 (3%)
Query: 91  NSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEY 150
           +S PNA   P KTLF+  ++ DT+E  L+  F+  G ++  + V ++ TG  +G+ F+++
Sbjct: 5   SSGPNARSQPSKTLFVKGLSEDTTEETLKESFD--GSVRARI-VTDRETGSSKGFGFVDF 61
Query: 151 EHERDMHSAYKHADGKKIDGRRVLVD 176
             E D  +A +  +  +IDG +V +D
Sbjct: 62  NSEEDAKAAKEAMEDGEIDGNKVTLD 87

>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing Factor Length = 103

Iteration: 1
 Score = 56.6 bits (135), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 30/82 (36%), Positives = 42/82 (51%)
Query: 98  MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMH 157
           +D   TL +  + Y TS   LRR FE YG +  + +     T  PRG+AF+ +   RD  
Sbjct: 10  VDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQ 69
Query: 158 SAYKHADGKKIDGRRVLVDVER 179
            A    DG ++DGR + V V R
Sbjct: 70  DAEAAMDGAELDGRELRVQVAR 91

>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In ArginineSERINE-Rich Splicing Factor 10 Length = 95

Iteration: 1
 Score = 56.2 bits (134), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 28/80 (35%), Positives = 48/80 (60%)
Query: 96  ATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERD 155
           A  DP   L +  ++  T+E  LR  F  YGPI  + +V+++ + + RG+AF+ +E+  D
Sbjct: 10  ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDD 69
Query: 156 MHSAYKHADGKKIDGRRVLV 175
              A + A+G ++DGRR+ V
Sbjct: 70  AKEAKERANGMELDGRRIRV 89

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 55.5 bits (132), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 26/73 (35%), Positives = 47/73 (64%), Gaps = 1/73 (1%)
Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           LFI  +N +T+E  L+  F  +GPI +++++ ++ T K RG+AFI +E+  D  +A K  
Sbjct: 10  LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDM 68
Query: 164 DGKKIDGRRVLVD 176
           +GK + G+ + V+
Sbjct: 69  NGKSLHGKAIKVE 81

>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm Length = 135

Iteration: 1
 Score = 52.8 bits (125), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 26/79 (32%), Positives = 42/79 (53%)
Query: 101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAY 160
             +L +  + Y TS   LRR FE YG +  + +  ++ T + RG+AF+ +  +RD   A 
Sbjct: 47  MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAM 106
Query: 161 KHADGKKIDGRRVLVDVER 179
              DG  +DGR + V + R
Sbjct: 107 DAMDGAVLDGRELRVQMAR 125

>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35 Length = 158

Iteration: 1
 Score = 52.8 bits (125), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 26/77 (33%), Positives = 42/77 (54%)
Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
           +L +  + Y TS   LRR FE YG +  + +  ++ T + RG+AF+ +  +RD   A   
Sbjct: 72  SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 131
Query: 163 ADGKKIDGRRVLVDVER 179
            DG  +DGR + V + R
Sbjct: 132 MDGAVLDGRELRVQMAR 148

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 51.2 bits (121), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 27/84 (32%), Positives = 45/84 (53%), Gaps = 3/84 (3%)
Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           +FI  +N+DT+E  LR  F  YG +  + ++ +  TG+ RG+ F+ +E    +    K  
Sbjct: 6   MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65
Query: 164 ---DGKKIDGRRVLVDVERSRTVK 184
              DGK ID +R +   E+ +T K
Sbjct: 66  HILDGKVIDPKRAIPRDEQDKTGK 89

>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8 Length = 101

Iteration: 1
 Score = 51.2 bits (121), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 40/74 (54%), Gaps = 5/74 (6%)
Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           +++  +     + +L R F  YGP++ + +  N     P G+AF+E+E  RD   A +  
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGL 57
Query: 164 DGKKIDGRRVLVDV 177
           DGK I G RV V++
Sbjct: 58  DGKVICGSRVRVEL 71

>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 = 50.4 bits (119), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/75 (30%), Positives = 39/75 (52%)
Query: 101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAY 160
           F  +++A V+ D S+  ++  FE +G IK   +  +  TGK +GY FIEYE  +    A 
Sbjct: 109 FNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAV 168
Query: 161 KHADGKKIDGRRVLV 175
              +   + G+ + V
Sbjct: 169 SSXNLFDLGGQYLRV 183

>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain From Hypothetical Protein Bab23448 Length = 99

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/72 (31%), Positives = 39/72 (54%)
Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           LF+  ++Y +SE  L + F  YGP+ ++    + +T KP+G+AF+ +        AY   
Sbjct: 11  LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 164 DGKKIDGRRVLV 175
           DG+   GR + V
Sbjct: 71  DGQVFQGRMLHV 82

>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna Cauc Length = 150

Iteration: 1
 Score = 50.1 bits (118), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 22/74 (29%), Positives = 43/74 (58%), Gaps = 5/74 (6%)
Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           +++  +  + ++++L R F  YGP++ + +  N     P G+AF+E+E  RD   A +  
Sbjct: 76  VYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVREL 130
Query: 164 DGKKIDGRRVLVDV 177
           DG+ + G RV V++
Sbjct: 131 DGRTLCGCRVRVEL 144

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 50.1 bits (118), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/75 (30%), Positives = 39/75 (52%)
Query: 101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAY 160
           F  +++A V+ D S+  ++  FE +G IK   +  +  TGK +GY FIEYE  +    A 
Sbjct: 110 FNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAV 169
Query: 161 KHADGKKIDGRRVLV 175
              +   + G+ + V
Sbjct: 170 SSMNLFDLGGQYLRV 184

>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20 Length = 150

Iteration: 1
 Score = 50.1 bits (118), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 22/74 (29%), Positives = 43/74 (58%), Gaps = 5/74 (6%)
Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           +++  +  + ++++L R F  YGP++ + +  N     P G+AF+E+E  RD   A +  
Sbjct: 76  VYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRDL 130
Query: 164 DGKKIDGRRVLVDV 177
           DG+ + G RV V++
Sbjct: 131 DGRTLCGCRVRVEL 144

>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 = 49.3 bits (116), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 23/72 (31%), Positives = 39/72 (54%)
Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           +++  + Y+  E  +R+ F  +GPIK I M  + VT K +G+AF+EYE       A +  
Sbjct: 31  VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 164 DGKKIDGRRVLV 175
           +   + GR + V
Sbjct: 91  NSVMLGGRNIKV 102

>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 = 47.8 bits (112), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 22/74 (29%), Positives = 42/74 (56%)
Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
           TL++  +++ T+E ++   F   G IKKI+M  +K+     G+ F+EY    D  +A ++
Sbjct: 41  TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 100
Query: 163 ADGKKIDGRRVLVD 176
            +G ++D R +  D
Sbjct: 101 INGTRLDDRIIRTD 114

>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna- Binding Region Containing Protein 1 Length = 116

Iteration: 1
 Score = 47.8 bits (112), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 25/77 (32%), Positives = 44/77 (57%), Gaps = 1/77 (1%)
Query: 101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAY 160
           F  +F+  + Y T+++ LR+ FE +G I++ V++ ++ TGK RGY F+          A 
Sbjct: 17  FTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERAC 76
Query: 161 KHADGKKIDGRRVLVDV 177
           K  +   IDGR+  V++
Sbjct: 77  KDPN-PIIDGRKANVNL 92

>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 3 Subunit 4 Length = 103

Iteration: 1
 Score = 47.4 bits (111), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 26/91 (28%), Positives = 47/91 (51%), Gaps = 2/91 (2%)
Query: 91  NSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEY 150
           +S PN   D   T+ +  ++ DT E+ L+  F  +G I +I +  +K TG+ +G+AFI +
Sbjct: 5   SSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISF 64
Query: 151 EHERDMHSAYKHADGKKIDGRRVLVDVERSR 181
               D   A     G   D   ++++VE ++
Sbjct: 65  HRREDAARAIAGVSGFGYD--HLILNVEWAK 93

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 47.0 bits (110), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 23/82 (28%), Positives = 42/82 (51%)
Query: 99  DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHS 158
           D  + L +  +     E +LR+ FE YGPI+ + +V ++ T + RGY F++++       
Sbjct: 40  DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQ 99
Query: 159 AYKHADGKKIDGRRVLVDVERS 180
           A    +G  I  +R+ V +  S
Sbjct: 100 AIAGLNGFNILNKRLKVALAAS 121

>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago Complex Length = 165

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 23/73 (31%), Positives = 43/73 (58%)
Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           LF+  ++ +  E +++ +F  YG IK I +  ++ TG  +GYA +EYE  +   +A +  
Sbjct: 75  LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 164 DGKKIDGRRVLVD 176
           +G +I G+ + VD
Sbjct: 135 NGAEIMGQTIQVD 147

>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex Length = 110

Iteration: 1
 Score = 46.2 bits (108), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 23/73 (31%), Positives = 43/73 (58%)
Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           LF+  ++ +  E +++ +F  YG IK I +  ++ TG  +GYA +EYE  +   +A +  
Sbjct: 29  LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 164 DGKKIDGRRVLVD 176
           +G +I G+ + VD
Sbjct: 89  NGAEIMGQTIQVD 101

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 45.8 bits (107), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 21/72 (29%), Positives = 40/72 (55%)
Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           L++  ++++ +E  LR  FE +G I  IV++ +  TG+ +GY FI +        A +  
Sbjct: 8   LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 164 DGKKIDGRRVLV 175
           +G ++ GR + V
Sbjct: 68  NGFELAGRPMRV 79

>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In Daz- Associated Protein 1 Length = 99

Iteration: 1
 Score = 45.8 bits (107), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 20/73 (27%), Positives = 44/73 (60%), Gaps = 4/73 (5%)
Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSA---- 159
           +F+  + ++  E++LR  F+ +G + ++VM+++    +PRG+ FI +E E+ +  A    
Sbjct: 13  IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMH 72
Query: 160 YKHADGKKIDGRR 172
           +    GKK++ +R
Sbjct: 73  FHDIMGKKVEVKR 85

>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 109

Iteration: 1
 Score = 45.4 bits (106), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 22/73 (30%), Positives = 42/73 (57%)
Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           LF+  V+ + +E  +  +F  YG IK I +  ++ TG  +GY  +EYE  ++  +A +  
Sbjct: 10  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 164 DGKKIDGRRVLVD 176
           +G+ + G+ + VD
Sbjct: 70  NGQDLMGQPISVD 82

>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of Xenopus Laevis Epabp2 Length = 124

Iteration: 1
 Score = 45.4 bits (106), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 22/74 (29%), Positives = 40/74 (54%), Gaps = 1/74 (1%)
Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
           +++++  V+Y ++   L   F   G I +I ++ +K +G P+GYA+IE+  ER+   A  
Sbjct: 37  RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFA-ERNSVDAAV 95
Query: 162 HADGKKIDGRRVLV 175
             D     GR + V
Sbjct: 96  AMDETVFRGRTIKV 109

>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX Length = 106

Iteration: 1
 Score = 45.4 bits (106), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 22/73 (30%), Positives = 42/73 (57%)
Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           LF+  V+ + +E  +  +F  YG IK I +  ++ TG  +GY  +EYE  ++  +A +  
Sbjct: 26  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 164 DGKKIDGRRVLVD 176
           +G+ + G+ + VD
Sbjct: 86  NGQDLMGQPISVD 98

>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd Machinery Length = 90

Iteration: 1
 Score = 45.4 bits (106), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 22/73 (30%), Positives = 42/73 (57%)
Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           LF+  V+ + +E  +  +F  YG IK I +  ++ TG  +GY  +EYE  ++  +A +  
Sbjct: 10  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 164 DGKKIDGRRVLVD 176
           +G+ + G+ + VD
Sbjct: 70  NGQDLMGQPISVD 82

>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2 A Resolution Length = 89

Iteration: 1
 Score = 45.1 bits (105), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 22/73 (30%), Positives = 42/73 (57%)
Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           LF+  V+ + +E  +  +F  YG IK I +  ++ TG  +GY  +EYE  ++  +A +  
Sbjct: 10  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 164 DGKKIDGRRVLVD 176
           +G+ + G+ + VD
Sbjct: 70  NGQDLMGQPISVD 82

>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State Length = 126

Iteration: 1
 Score = 45.1 bits (105), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 22/73 (30%), Positives = 42/73 (57%)
Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           LF+  V+ + +E  +  +F  YG IK I +  ++ TG  +GY  +EYE  ++  +A +  
Sbjct: 25  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 164 DGKKIDGRRVLVD 176
           +G+ + G+ + VD
Sbjct: 85  NGQDLMGQPISVD 97

>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex Length = 98

Iteration: 1
 Score = 45.1 bits (105), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 22/74 (29%), Positives = 42/74 (56%), Gaps = 1/74 (1%)
Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
           TL++  +++ T+E ++   F   G IKKI+M  +K+     G+ F+EY    D  +A ++
Sbjct: 20  TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMK-TACGFCFVEYYSRADAENAMRY 78
Query: 163 ADGKKIDGRRVLVD 176
            +G ++D R +  D
Sbjct: 79  INGTRLDDRIIRTD 92

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 45.1 bits (105), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 24/92 (26%), Positives = 47/92 (51%), Gaps = 1/92 (1%)
Query: 91  NSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEY 150
           N+    +  P + L++  ++++ +E  LR  FE +G I+ I ++ +  TG+ +GY FI +
Sbjct: 17  NNLQKGSAGPMR-LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITF 75
Query: 151 EHERDMHSAYKHADGKKIDGRRVLVDVERSRT 182
                   A +  +G ++ GR + V     RT
Sbjct: 76  SDSECAKKALEQLNGFELAGRPMKVGHVTERT 107

>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A Trapped Dead-Box Helicase Bound To Rna Length = 91

Iteration: 1
 Score = 44.7 bits (104), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 22/73 (30%), Positives = 42/73 (57%)
Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           LF+  V+ + +E  +  +F  YG IK I +  ++ TG  +GY  +EYE  ++  +A +  
Sbjct: 12  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 164 DGKKIDGRRVLVD 176
           +G+ + G+ + VD
Sbjct: 72  NGQDLMGQPISVD 84

>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex Length = 88

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 26/78 (33%), Positives = 42/78 (53%), Gaps = 2/78 (2%)
Query: 97  TMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVM-VHNKVTGKPRGYAFIEYEHERD 155
           +M P K + I R+  + ++  +   F  YG IK I M V        +GYA++E+E+  +
Sbjct: 1   SMKPTK-VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDE 59
Query: 156 MHSAYKHADGKKIDGRRV 173
              A KH DG +IDG+ +
Sbjct: 60  AEKALKHMDGGQIDGQEI 77

>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 = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 22/75 (29%), Positives = 43/75 (57%), Gaps = 1/75 (1%)
Query: 99  DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHS 158
           +  + LFI  ++++T++  LR  FE +G +   V++ +  T + RG+ F+ Y    ++ +
Sbjct: 10  EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 69
Query: 159 AYKHADGKKIDGRRV 173
           A  +A   K+DGR V
Sbjct: 70  AM-NARPHKVDGRVV 83

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 22/75 (29%), Positives = 43/75 (57%), Gaps = 1/75 (1%)
Query: 99  DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHS 158
           +  + LFI  ++++T++  LR  FE +G +   V++ +  T + RG+ F+ Y    ++ +
Sbjct: 11  EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 70
Query: 159 AYKHADGKKIDGRRV 173
           A  +A   K+DGR V
Sbjct: 71  AM-NARPHKVDGRVV 84

>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 = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 22/75 (29%), Positives = 43/75 (57%), Gaps = 1/75 (1%)
Query: 99  DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHS 158
           +  + LFI  ++++T++  LR  FE +G +   V++ +  T + RG+ F+ Y    ++ +
Sbjct: 12  EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 71
Query: 159 AYKHADGKKIDGRRV 173
           A  +A   K+DGR V
Sbjct: 72  AM-NARPHKVDGRVV 85

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 22/75 (29%), Positives = 43/75 (57%), Gaps = 1/75 (1%)
Query: 99  DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHS 158
           +  + LFI  ++++T++  LR  FE +G +   V++ +  T + RG+ F+ Y    ++ +
Sbjct: 11  EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 70
Query: 159 AYKHADGKKIDGRRV 173
           A  +A   K+DGR V
Sbjct: 71  AM-NARPHKVDGRVV 84

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 22/75 (29%), Positives = 43/75 (57%), Gaps = 1/75 (1%)
Query: 99  DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHS 158
           +  + LFI  ++++T++  LR  FE +G +   V++ +  T + RG+ F+ Y    ++ +
Sbjct: 4   EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 63
Query: 159 AYKHADGKKIDGRRV 173
           A  +A   K+DGR V
Sbjct: 64  AM-NARPHKVDGRVV 77

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 22/75 (29%), Positives = 43/75 (57%), Gaps = 1/75 (1%)
Query: 99  DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHS 158
           +  + LFI  ++++T++  LR  FE +G +   V++ +  T + RG+ F+ Y    ++ +
Sbjct: 9   EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 68
Query: 159 AYKHADGKKIDGRRV 173
           A  +A   K+DGR V
Sbjct: 69  AM-NARPHKVDGRVV 82

>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G) Length = 97

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 19/72 (26%), Positives = 39/72 (54%)
Query: 100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSA 159
           P + +++  + YD +E ++       GP+  + M+ +  TG+ +GYAFIE+       SA
Sbjct: 2   PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 61
Query: 160 YKHADGKKIDGR 171
            ++ +G ++  R
Sbjct: 62  VRNLNGYQLGSR 73

>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear Ribonucleaoproteins A2B1 Length = 116

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/75 (28%), Positives = 42/75 (56%), Gaps = 1/75 (1%)
Query: 99  DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHS 158
           + F+ LFI  ++++T+E  LR  +E +G +   V++ +  + + RG+ F+ +    ++ +
Sbjct: 25  EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDA 84
Query: 159 AYKHADGKKIDGRRV 173
           A   A    IDGR V
Sbjct: 85  AM-AARPHSIDGRVV 98

>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu) Length = 96

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 19/72 (26%), Positives = 39/72 (54%)
Query: 100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSA 159
           P + +++  + YD +E ++       GP+  + M+ +  TG+ +GYAFIE+       SA
Sbjct: 1   PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60
Query: 160 YKHADGKKIDGR 171
            ++ +G ++  R
Sbjct: 61  VRNLNGYQLGSR 72

>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous Cell Carcinoma Antigen Recognized By T Cells 3 Length = 100

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 23/77 (29%), Positives = 41/77 (53%), Gaps = 1/77 (1%)
Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           LFI+ + +  ++ +L    + +G +K + +V N+  GKP+G A++EYE+E     A    
Sbjct: 20  LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKM 78
Query: 164 DGKKIDGRRVLVDVERS 180
           DG  I    + V +  S
Sbjct: 79  DGMTIKENIIKVAISNS 95

>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 = 43.1 bits (100), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 19/72 (26%), Positives = 39/72 (54%)
Query: 100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSA 159
           P + +++  + YD +E ++       GP+  + M+ +  TG+ +GYAFIE+       SA
Sbjct: 3   PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 62
Query: 160 YKHADGKKIDGR 171
            ++ +G ++  R
Sbjct: 63  VRNLNGYQLGSR 74

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 42.7 bits (99), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 22/75 (29%), Positives = 42/75 (56%), Gaps = 1/75 (1%)
Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
           + L++  ++   +E  L++ F+V GPI  I ++ +K   K   YAF+EY    D + A +
Sbjct: 1   RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQ 59
Query: 162 HADGKKIDGRRVLVD 176
             +GK+I+   V ++
Sbjct: 60  TLNGKQIENNIVKIN 74

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 42.4 bits (98), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 17/73 (23%), Positives = 39/73 (53%)
Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           +F+  ++ + +   ++  F  +G I    +V +  TGK +GY F+ + ++ D  +A  H 
Sbjct: 18  VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 164 DGKKIDGRRVLVD 176
            G+ + GR++  +
Sbjct: 78  GGQWLGGRQIRTN 90

>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 101

Iteration: 1
 Score = 42.4 bits (98), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 25/80 (31%), Positives = 42/80 (52%), Gaps = 4/80 (5%)
Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
           KTL ++ ++Y  +E  L+  FE    IK    V     GK +GYAFIE+    D   A  
Sbjct: 16  KTLVLSNLSYSATEETLQEVFEKATFIK----VPQNQNGKSKGYAFIEFASFEDAKEALN 71
Query: 162 HADGKKIDGRRVLVDVERSR 181
             + ++I+GR + ++++  R
Sbjct: 72  SCNKREIEGRAIRLELQGPR 91

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	363
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	6e-28
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	7e-24
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	1e-23
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	2e-21
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	2e-20
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	1e-19
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	6e-19
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	7e-18
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	1e-17
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	7e-17
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	1e-16
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-16
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	3e-16
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	3e-16
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	4e-16
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	7e-16
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	7e-16
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	1e-15
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	2e-15
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	2e-15
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	2e-15
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-15
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	8e-12
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	2e-15
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	3e-15
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	3e-15
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	3e-15
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	3e-15
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	4e-15
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	5e-15
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	5e-15
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	7e-15
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	7e-15
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	7e-15
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	7e-15
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	2e-14
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	3e-14
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	1e-08
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	5e-14
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	6e-14
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	1e-13
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	1e-13
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	1e-13
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	4e-08
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-13
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-08
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	8e-07
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	2e-13
1x4e_A	85	RNA binding motif, single-stranded interacting pro	2e-13
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	2e-13
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	3e-13
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	3e-13
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	3e-13
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	8e-08
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	4e-13
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	4e-13
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	5e-13
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	5e-13
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	9e-13
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	9e-13
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-12
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	1e-12
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	1e-12
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	2e-12
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-12
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	8e-10
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	3e-12
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	3e-12
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-11
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	3e-12
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	3e-12
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-12
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-09
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	4e-08
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	4e-12
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	4e-12
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	5e-12
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	8e-12
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	7e-12
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	8e-12
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	8e-12
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	9e-12
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-11
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	7e-06
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	2e-11
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	2e-11
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	2e-11
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	2e-11
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	2e-11
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	2e-11
2dis_A	109	Unnamed protein product; structural genomics, RRM	3e-11
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	3e-11
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	3e-11
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	3e-11
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	5e-11
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	3e-11
2div_A	99	TRNA selenocysteine associated protein; structural	3e-11
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	3e-11
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	3e-11
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	3e-11
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-11
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-07
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	4e-11
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	5e-11
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	5e-11
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	9e-07
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	5e-11
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	6e-11
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	6e-11
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	8e-11
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	9e-11
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	1e-10
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	1e-10
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	1e-10
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	2e-10
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	2e-10
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	2e-10
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	2e-10
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	2e-10
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	2e-10
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	2e-10
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-10
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	4e-10
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	5e-10
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	6e-10
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	6e-10
1x5p_A	97	Negative elongation factor E; structure genomics,	7e-10
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	7e-10
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	9e-10
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	1e-09
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-09
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	5e-07
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	2e-09
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	2e-09
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	3e-09
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	3e-09
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	4e-09
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	4e-09
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	4e-09
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	4e-09
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	5e-09
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	6e-09
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	1e-05
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	9e-09
1x5o_A	114	RNA binding motif, single-stranded interacting pro	1e-08
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	2e-08
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	2e-08
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	3e-08
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	3e-08
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	4e-08
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	4e-08
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	5e-07
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	4e-08
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	5e-08
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	1e-07
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	7e-08
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	8e-08
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	9e-08
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	1e-07
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	1e-07
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-07
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-05
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	3e-07
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-07
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	7e-07
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	8e-07
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	9e-07
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	9e-07
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	2e-06
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	2e-06
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	2e-06
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	3e-06
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	3e-06
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	4e-06
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	5e-06
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	8e-06
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	8e-06
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-05
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	2e-05
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	3e-05
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	3e-05
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	4e-05
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	4e-05
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	2e-04
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	3e-04
1qzv_F	154	Plant photosystem I: subunit PSAF; photosynthesis,	4e-05
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	1e-04
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	2e-04
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	3e-04
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	4e-04
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	6e-04
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	7e-04

>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 =  104 bits (261), Expect = 6e-28
 Identities = 27/101 (26%), Positives = 46/101 (45%), Gaps = 4/101 (3%)

Query: 90  PNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIE 149
            +S  +      KTL ++ ++Y  +E  L+  FE    IK    V     GK +GYAFIE
Sbjct: 4   GSSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFIK----VPQNQNGKSKGYAFIE 59

Query: 150 YEHERDMHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPRR 190
           +    D   A    + ++I+GR + ++++  R      P  
Sbjct: 60  FASFEDAKEALNSCNKREIEGRAIRLELQGPRGSPNSGPSS 100

>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 =  101 bits (251), Expect = 7e-24
 Identities = 189/340 (55%), Positives = 223/340 (65%), Gaps = 1/340 (0%)

Query: 1   MTQFLPPNLLALFAPRDPVPYLPPVEKLPHEKK-THGYSGIAAFLNEFEDPKDTPPPTRV 59
           MTQFLPPNLLALFAPRDP+PYLPP+EKLPHEK     Y GIA ++ EFEDP+D PPPTR 
Sbjct: 1   MTQFLPPNLLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRDAPPPTRA 60

Query: 60  ETREERLERRRRERAEQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLR 119
           ETREER+ER+RRE+ E+   ++E E+ +WDP++ PNA  D FKTLF+ARVNYDT+ESKLR
Sbjct: 61  ETREERMERKRREKIERRQQEVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLR 120

Query: 120 REFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 179
           REFEVYGPIK+I MV++K +GKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER
Sbjct: 121 REFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 180

Query: 180 SRTVKGWLPRRLGGGLGGTRRGGPDVNLKHSGREDNERERERYRLERERELAGGPPRARS 239
            RTVKGW PRRLGGGLGGTRRGG DVN++HSGR+D  R  ER              R R 
Sbjct: 181 GRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRYDERPGPSPLPHRDRDRDRERE 240

Query: 240 GSNDRERERERRRSRSRERKRRTSRSRSRDRRRRRSRERIRDDDIEEVEFRPKDRSDRDR 299
                    + R  R    + R  RSRSRD+  RR       D   + + R     +R R
Sbjct: 241 RRERSRERDKERERRRSRSRDRRRRSRSRDKEERRRSRERSKDKDRDRKRRSSRSRERAR 300

Query: 300 DRDRKRRRERENSEDRNERKRDRKERRKERERNNEEREEK 339
               ++   R    D  E          +        +  
Sbjct: 301 RERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGP 340

>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 = 93.1 bits (232), Expect = 1e-23
 Identities = 29/101 (28%), Positives = 52/101 (51%), Gaps = 3/101 (2%)

Query: 90  PNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIE 149
            +S PNA   P KTLF+  ++ DT+E  L+  F       +  +V ++ TG  +G+ F++
Sbjct: 4   GSSGPNARSQPSKTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFGFVD 60

Query: 150 YEHERDMHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPRR 190
           +  E D  +A +  +  +IDG +V +D  + +   G  P  
Sbjct: 61  FNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGEGGSGPSS 101

>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 = 86.9 bits (216), Expect = 2e-21
 Identities = 31/96 (32%), Positives = 43/96 (44%)

Query: 94  PNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHE 153
               +D   TL +  + Y TS   LRR FE YG +  + +     T  PRG+AF+ +   
Sbjct: 6   SGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDR 65

Query: 154 RDMHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPR 189
           RD   A    DG ++DGR + V V R        P 
Sbjct: 66  RDAQDAEAAMDGAELDGRELRVQVARYGRRDLSGPS 101

>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 = 84.2 bits (209), Expect = 2e-20
 Identities = 30/92 (32%), Positives = 51/92 (55%)

Query: 89  DPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFI 148
             +S   A  DP   L +  ++  T+E  LR  F  YGPI  + +V+++ + + RG+AF+
Sbjct: 3   SGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFV 62

Query: 149 EYEHERDMHSAYKHADGKKIDGRRVLVDVERS 180
            +E+  D   A + A+G ++DGRR+ V    S
Sbjct: 63  YFENVDDAKEAKERANGMELDGRRIRVSGPSS 94

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 82.0 bits (203), Expect = 1e-19
 Identities = 18/88 (20%), Positives = 34/88 (38%), Gaps = 6/88 (6%)

Query: 99  DPFKTLFIARVNYDTSESKLRREFEVYG--PIKKIVMVHNKVTGKPRGYAFIEYEHERDM 156
               T+ +  +   T    +      Y    +  I ++ +K T + RG+AF++     D 
Sbjct: 7   HHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDA 66

Query: 157 HSAYKHADGK----KIDGRRVLVDVERS 180
               +         KIDG+ + VD  +S
Sbjct: 67  SQLLQILQSLHPPLKIDGKTIGVDFAKS 94

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 80.1 bits (198), Expect = 6e-19
 Identities = 17/96 (17%), Positives = 38/96 (39%)

Query: 100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSA 159
           P K +  AR+N +  E+ L+     YG ++++ ++ +  T K  G A + +   R     
Sbjct: 5   PLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKET 64

Query: 160 YKHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGL 195
            K+     + G  +   ++     +      +  G 
Sbjct: 65  VKNLHLTSVMGNIIHAQLDIKGQQRMKYYELIVNGS 100

>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 = 76.9 bits (190), Expect = 7e-18
 Identities = 21/88 (23%), Positives = 41/88 (46%), Gaps = 5/88 (5%)

Query: 94  PNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHE 153
            +  +   +TL    ++++ +E +L+  FE    I+ +        GK +G A+IE++ E
Sbjct: 9   TSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSE 63

Query: 154 RDMHSAYKHADGKKIDGRRVLVDVERSR 181
            D     +   G +IDGR V +     +
Sbjct: 64  ADAEKNLEEKQGAEIDGRSVSLYYTGEK 91

>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 = 77.5 bits (191), Expect = 1e-17
 Identities = 29/94 (30%), Positives = 52/94 (55%)

Query: 88  WDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAF 147
              +    A  DP   L +  ++  T+E  LR  F  YGPI  + +V+++ + + RG+AF
Sbjct: 33  GSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAF 92

Query: 148 IEYEHERDMHSAYKHADGKKIDGRRVLVDVERSR 181
           + +E+  D   A + A+G ++DGRR+ VD   ++
Sbjct: 93  VYFENVDDAKEAKERANGMELDGRRIRVDFSITK 126

>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 = 74.2 bits (183), Expect = 7e-17
 Identities = 20/86 (23%), Positives = 43/86 (50%)

Query: 100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSA 159
           P + +++  + YD +E ++       GP+  + M+ +  TG+ +GYAFIE+       SA
Sbjct: 1   PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60

Query: 160 YKHADGKKIDGRRVLVDVERSRTVKG 185
            ++ +G ++  R +      +  + G
Sbjct: 61  VRNLNGYQLGSRFLKCGYSSNSDISG 86

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 75.2 bits (185), Expect = 1e-16
 Identities = 19/89 (21%), Positives = 40/89 (44%)

Query: 88  WDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAF 147
              +     +    + L++  +  +  +  L   F  +G I  I +  +  T K RG+AF
Sbjct: 50  SGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAF 109

Query: 148 IEYEHERDMHSAYKHADGKKIDGRRVLVD 176
           +E+E   D  +A  + +  ++ GR + V+
Sbjct: 110 VEFELAEDAAAAIDNMNESELFGRTIRVN 138

>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 = 73.4 bits (181), Expect = 2e-16
 Identities = 30/106 (28%), Positives = 53/106 (50%), Gaps = 5/106 (4%)

Query: 91  NSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEY 150
           +S  +        LF+  +++DT+E  L + F  YG I ++V+V ++ T + RG+ F+ +
Sbjct: 2   SSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTF 61

Query: 151 EHERDMHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLG 196
           E+  D   A    +GK +DGR++ VD     +       R G   G
Sbjct: 62  ENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSS-----DNRSGPSSG 102

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 72.6 bits (179), Expect = 3e-16
 Identities = 17/87 (19%), Positives = 40/87 (45%)

Query: 90  PNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIE 149
            +           T++++ + +  + + L R F  YG + K+ ++ +K T K +G AFI 
Sbjct: 5   SSGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFIL 64

Query: 150 YEHERDMHSAYKHADGKKIDGRRVLVD 176
           +  +    +  +  + K++ GR +   
Sbjct: 65  FLDKDSAQNCTRAINNKQLFGRVIKAS 91

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 72.7 bits (179), Expect = 3e-16
 Identities = 26/96 (27%), Positives = 45/96 (46%), Gaps = 1/96 (1%)

Query: 90  PNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIE 149
              F  +T      LFI+ + +  ++ +L    + +G +K + +V N+  GKP+G A++E
Sbjct: 6   SGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVE 64

Query: 150 YEHERDMHSAYKHADGKKIDGRRVLVDVERSRTVKG 185
           YE+E     A    DG  I    + V +  S    G
Sbjct: 65  YENESQASQAVMKMDGMTIKENIIKVAISNSGPSSG 100

>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 = 72.3 bits (178), Expect = 4e-16
 Identities = 26/94 (27%), Positives = 44/94 (46%)

Query: 89  DPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFI 148
             +S PN   D   T+ +  ++ DT E+ L+  F  +G I +I +  +K TG+ +G+AFI
Sbjct: 3   SGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFI 62

Query: 149 EYEHERDMHSAYKHADGKKIDGRRVLVDVERSRT 182
            +    D   A     G   D   + V+  +  T
Sbjct: 63  SFHRREDAARAIAGVSGFGYDHLILNVEWAKPST 96

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 71.7 bits (176), Expect = 7e-16
 Identities = 19/74 (25%), Positives = 30/74 (40%), Gaps = 5/74 (6%)

Query: 111 YDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDG 170
               +  L   F   G +  +    ++ TGK +G+ F+E     D     K   GK++D 
Sbjct: 22  VPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDL 81

Query: 171 RRVLV-----DVER 179
           +  L      DVER
Sbjct: 82  KHRLFLYTMKDVER 95

>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 = 72.0 bits (177), Expect = 7e-16
 Identities = 30/108 (27%), Positives = 54/108 (50%), Gaps = 1/108 (0%)

Query: 96  ATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERD 155
              D    LFI  +N +T+E  L+  F  +GPI +++++ ++ T K RG+AFI +E+  D
Sbjct: 2   VEADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPAD 60

Query: 156 MHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGGTRRGGP 203
             +A K  +GK + G+ + V+  +  + +    RR           G 
Sbjct: 61  AKNAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSRNRSPSGS 108

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score = 70.3 bits (173), Expect = 1e-15
 Identities = 22/83 (26%), Positives = 40/83 (48%), Gaps = 1/83 (1%)

Query: 100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKV-TGKPRGYAFIEYEHERDMHS 158
               + I R+  + ++  +   F  YG IK I M   ++     +GYA++E+E+  +   
Sbjct: 3   KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEK 62

Query: 159 AYKHADGKKIDGRRVLVDVERSR 181
           A KH DG +IDG+ +      + 
Sbjct: 63  ALKHMDGGQIDGQEITATAVLAP 85

>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 = 71.7 bits (176), Expect = 2e-15
 Identities = 29/112 (25%), Positives = 49/112 (43%), Gaps = 5/112 (4%)

Query: 90  PNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIE 149
           P +  N   D  + L +  +     E +LR+ FE YGPI+ + +V ++ T + RGY F++
Sbjct: 31  PPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVK 90

Query: 150 YEHERDMHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGGTRRG 201
           ++       A    +G  I  +R+ V +  S        R    G  G   G
Sbjct: 91  FQSGSSAQQAIAGLNGFNILNKRLKVALAASGH-----QRPGIAGAVGDGNG 137

>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 = 70.4 bits (173), Expect = 2e-15
 Identities = 29/102 (28%), Positives = 52/102 (50%), Gaps = 3/102 (2%)

Query: 96  ATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERD 155
           A     +++F+  + Y+ +E +L+  F   GP+    +V+++ TGKP+GY F EY+ +  
Sbjct: 3   AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQET 62

Query: 156 MHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGG 197
             SA ++ +G++  GR + VD   S   K         G G 
Sbjct: 63  ALSAMRNLNGREFSGRALRVDNAASEKNK---EELKSLGTGA 101

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 70.4 bits (173), Expect = 2e-15
 Identities = 24/93 (25%), Positives = 45/93 (48%)

Query: 89  DPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFI 148
           D +            LF+  V+ + +E  +  +F  YG IK I +  ++ TG  +GY  +
Sbjct: 11  DGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLV 70

Query: 149 EYEHERDMHSAYKHADGKKIDGRRVLVDVERSR 181
           EYE  ++  +A +  +G+ + G+ + VD    R
Sbjct: 71  EYETYKEAQAAMEGLNGQDLMGQPISVDWCFVR 103

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 73.5 bits (181), Expect = 2e-15
 Identities = 25/112 (22%), Positives = 46/112 (41%)

Query: 89  DPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFI 148
              +     +     +++  + Y+  E  +R+ F  +GPIK I M  + VT K +G+AF+
Sbjct: 16  GSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFV 75

Query: 149 EYEHERDMHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGGTRR 200
           EYE       A +  +   + GR + V    +      +  +L        R
Sbjct: 76  EYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNR 127

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 63.1 bits (154), Expect = 8e-12
 Identities = 23/83 (27%), Positives = 39/83 (46%)

Query: 94  PNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHE 153
                  F  +++A V+ D S+  ++  FE +G IK   +  +  TGK +GY FIEYE  
Sbjct: 118 LAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKA 177

Query: 154 RDMHSAYKHADGKKIDGRRVLVD 176
           +    A    +   + G+ + V 
Sbjct: 178 QSSQDAVSSMNLFDLGGQYLRVG 200

>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 = 70.0 bits (172), Expect = 2e-15
 Identities = 19/87 (21%), Positives = 40/87 (45%), Gaps = 1/87 (1%)

Query: 90  PNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIE 149
            +    A  +  +T+F+  +     E  L   F   GP+ K+ +  ++  GKP+ + F+ 
Sbjct: 5   SSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVC 63

Query: 150 YEHERDMHSAYKHADGKKIDGRRVLVD 176
           ++H   +  A    +G ++ GR + V 
Sbjct: 64  FKHPESVSYAIALLNGIRLYGRPINVS 90

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 69.9 bits (172), Expect = 3e-15
 Identities = 22/103 (21%), Positives = 45/103 (43%), Gaps = 3/103 (2%)

Query: 92  SFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYE 151
           S  +      + L++  +  +  +  L   F  +G I  I +  +  T K RG+AF+E+E
Sbjct: 3   SGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFE 62

Query: 152 HERDMHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGG 194
              D  +A  + +  ++ GR + V++ +   +K         G
Sbjct: 63  LAEDAAAAIDNMNESELFGRTIRVNLAKPMRIK---ESGPSSG 102

>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 = 71.8 bits (176), Expect = 3e-15
 Identities = 29/142 (20%), Positives = 57/142 (40%), Gaps = 5/142 (3%)

Query: 45  NEFEDPKDTPPPTRVETREERLERRRRERAEQVAYKLEQEIALWDPNSFPNATMDP---- 100
            EFE  +D          + +  + R   ++    +                   P    
Sbjct: 11  EEFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSV 70

Query: 101 -FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSA 159
               LF+  ++ +  E +++ +F  YG IK I +  ++ TG  +GYA +EYE  +   +A
Sbjct: 71  EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 130

Query: 160 YKHADGKKIDGRRVLVDVERSR 181
            +  +G +I G+ + VD    +
Sbjct: 131 KEALNGAEIMGQTIQVDWCFVK 152

>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 = 70.1 bits (172), Expect = 3e-15
 Identities = 24/102 (23%), Positives = 46/102 (45%), Gaps = 6/102 (5%)

Query: 94  PNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHE 153
             + +   KT+FI  +++D+ E  L    + +G +K + +V +  T   +G AF ++  +
Sbjct: 8   LPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQ 67

Query: 154 RDMHSAYKHAD------GKKIDGRRVLVDVERSRTVKGWLPR 189
                    A       G K+DGR++ VD+  +R      P 
Sbjct: 68  EAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAASGPS 109

>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 = 71.4 bits (175), Expect = 3e-15
 Identities = 25/136 (18%), Positives = 56/136 (41%), Gaps = 6/136 (4%)

Query: 46  EFEDPKDTPPPTRVETREERLERRRRERAEQVAYKLEQEIALWDPNSFPNATMDPFKTLF 105
           E  D        +    +  ++           + + +       +   ++     K ++
Sbjct: 19  EAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCK-VY 77

Query: 106 IARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADG 165
           +  +  + ++++L R F  YGP++ + +  N     P G+AF+E+E  RD   A +  DG
Sbjct: 78  VGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDG 132

Query: 166 KKIDGRRVLVDVERSR 181
           + + G RV V++    
Sbjct: 133 RTLCGCRVRVELSNGE 148

>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 = 69.6 bits (171), Expect = 4e-15
 Identities = 23/80 (28%), Positives = 40/80 (50%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
             LF+  ++Y +SE  L + F  YGP+ ++    + +T KP+G+AF+ +        AY 
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 162 HADGKKIDGRRVLVDVERSR 181
             DG+   GR + V     +
Sbjct: 69  EVDGQVFQGRMLHVLPSTIK 88

>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 = 69.6 bits (171), Expect = 5e-15
 Identities = 25/90 (27%), Positives = 44/90 (48%)

Query: 92  SFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYE 151
           S P +  +   T+++  ++   SE  L   F   GP+    M  ++VTG+ +GY F+E+ 
Sbjct: 6   SGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFL 65

Query: 152 HERDMHSAYKHADGKKIDGRRVLVDVERSR 181
            E D   A K  D  K+ G+ + V+   + 
Sbjct: 66  SEEDADYAIKIMDMIKLYGKPIRVNKASAH 95

>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 = 68.7 bits (169), Expect = 5e-15
 Identities = 19/75 (25%), Positives = 38/75 (50%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
           + L++  +  +  +  L   F  +G I  I +  +  T K RG+AF+E+E   D  +A  
Sbjct: 8   RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67

Query: 162 HADGKKIDGRRVLVD 176
           + +  ++ GR + V+
Sbjct: 68  NMNESELFGRTIRVN 82

>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 = 70.6 bits (173), Expect = 7e-15
 Identities = 30/136 (22%), Positives = 59/136 (43%), Gaps = 11/136 (8%)

Query: 94  PNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHE 153
               +    TL++  +++ T+E ++   F   G IKKI+M  +K+     G+ F+EY   
Sbjct: 32  QEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSR 91

Query: 154 RDMHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGGTRRGGPDVNLKHSGRE 213
            D  +A ++ +G ++D R +  D +          R+ G G  G +        +   R+
Sbjct: 92  ADAENAMRYINGTRLDDRIIRTDWDAGFKE----GRQYGRGRSGGQV-------RDEYRQ 140

Query: 214 DNERERERYRLERERE 229
           D +  R  Y    + +
Sbjct: 141 DYDAGRGGYGKLAQNQ 156

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 68.9 bits (169), Expect = 7e-15
 Identities = 30/103 (29%), Positives = 47/103 (45%), Gaps = 11/103 (10%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           +++  +     + +L R F  YGP++ + +  N     P G+AF+E+E  RD   A +  
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGL 57

Query: 164 DGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGGTRRGGPDVN 206
           DGK I G RV V++          PRR        RR   +V 
Sbjct: 58  DGKVICGSRVRVELSTGM------PRRSRFDRPPARRKLLEVL 94

>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 = 68.9 bits (169), Expect = 7e-15
 Identities = 23/82 (28%), Positives = 44/82 (53%)

Query: 100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSA 159
               LF+  ++ +  E +++ +F  YG IK I +  ++ TG  +GYA +EYE  +   +A
Sbjct: 25  EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 84

Query: 160 YKHADGKKIDGRRVLVDVERSR 181
            +  +G +I G+ + VD    +
Sbjct: 85  KEALNGAEIMGQTIQVDWCFVK 106

>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 = 68.4 bits (168), Expect = 7e-15
 Identities = 21/86 (24%), Positives = 39/86 (45%), Gaps = 6/86 (6%)

Query: 100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSA 159
           P   L++  +  +TS + L REF+ +G I+ I  V      K   +A+I+YE      +A
Sbjct: 16  PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHV------KGDSFAYIQYESLDAAQAA 69

Query: 160 YKHADGKKIDGRRVLVDVERSRTVKG 185
                G  + G    + V+ +++   
Sbjct: 70  CAKMRGFPLGGPDRRLRVDFAKSGPS 95

>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 = 67.2 bits (165), Expect = 2e-14
 Identities = 23/87 (26%), Positives = 42/87 (48%)

Query: 99  DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHS 158
                L++  ++++ +E  LR  FE +G I  IV++ +  TG+ +GY FI +        
Sbjct: 3   SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARR 62

Query: 159 AYKHADGKKIDGRRVLVDVERSRTVKG 185
           A +  +G ++ GR + V     R   G
Sbjct: 63  ALEQLNGFELAGRPMRVGHVTERLDGG 89

>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 = 69.7 bits (171), Expect = 3e-14
 Identities = 24/107 (22%), Positives = 46/107 (42%)

Query: 70  RRERAEQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIK 129
           RR    Q    + +  +++ P        D    LFI  +    ++ +++     +GP+K
Sbjct: 83  RRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLK 142

Query: 130 KIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD 176
              +V +  TG  +GYAF EY        A    +G ++  +++LV 
Sbjct: 143 AFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQ 189

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 53.5 bits (129), Expect = 1e-08
 Identities = 11/83 (13%), Positives = 29/83 (34%), Gaps = 6/83 (7%)

Query: 99  DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVM-----VHNKVTGKPRGYAFIEYEHE 153
              + L++  + +  +E  +   F     +  +       V      + + +AF+E+   
Sbjct: 2   AMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 61

Query: 154 RDMHSAYKHADGKKIDGRRVLVD 176
            +   A    DG    G+ + + 
Sbjct: 62  DETTQAMA-FDGIIFQGQSLKIR 83

>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 = 66.6 bits (163), Expect = 5e-14
 Identities = 25/101 (24%), Positives = 49/101 (48%), Gaps = 1/101 (0%)

Query: 82  EQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGK 141
              +A    N+    +  P + L++  ++++ +E  LR  FE +G I+ I ++ +  TG+
Sbjct: 8   HSHMAAAMANNLQKGSAGPMR-LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGR 66

Query: 142 PRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERSRT 182
            +GY FI +        A +  +G ++ GR + V     RT
Sbjct: 67  SKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERT 107

>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 = 66.5 bits (163), Expect = 6e-14
 Identities = 28/98 (28%), Positives = 47/98 (47%), Gaps = 1/98 (1%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           +F+  + Y T+++ LR+ FE +G I++ V++ ++ TGK RGY F+          A K  
Sbjct: 20  IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK-D 78

Query: 164 DGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGGTRRG 201
               IDGR+  V++         L      G+ G   G
Sbjct: 79  PNPIIDGRKANVNLAYLGAKPRSLQTGFAIGVSGPSSG 116

>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 = 66.2 bits (162), Expect = 1e-13
 Identities = 18/83 (21%), Positives = 41/83 (49%)

Query: 99  DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHS 158
           +P K L++  ++   +E  L   F  +   K   +    +TG+ RG AFI + ++     
Sbjct: 23  EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQ 82

Query: 159 AYKHADGKKIDGRRVLVDVERSR 181
           A    +G K+ G+ ++++  +++
Sbjct: 83  ALHLVNGYKLYGKILVIEFGKNK 105

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 65.9 bits (161), Expect = 1e-13
 Identities = 18/74 (24%), Positives = 32/74 (43%), Gaps = 7/74 (9%)

Query: 111 YDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDG 170
            +  ++ + + F  +G I        +  GK +GY F+EY        A K+ADG K+D 
Sbjct: 31  LEKLKNVIHKIFSKFGKITNDFY--PEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDK 88

Query: 171 RRVLV-----DVER 179
           +         D ++
Sbjct: 89  QHTFRVNLFTDFDK 102

>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 = 67.2 bits (165), Expect = 1e-13
 Identities = 20/75 (26%), Positives = 35/75 (46%)

Query: 101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAY 160
              L +  +  D ++ +L   F   GPI    ++ +  TG   GYAF+++  E D   A 
Sbjct: 3   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62

Query: 161 KHADGKKIDGRRVLV 175
           K  +G  +  +R+ V
Sbjct: 63  KVLNGITVRNKRLKV 77

>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 = 51.4 bits (124), Expect = 4e-08
 Identities = 17/68 (25%), Positives = 33/68 (48%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           L++  +    ++ +L   F  YG I +  ++ +K+TG+PRG AF+ Y    +   A    
Sbjct: 92  LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 151

Query: 164 DGKKIDGR 171
           +    +G 
Sbjct: 152 NNVIPEGG 159

>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 = 69.6 bits (171), Expect = 1e-13
 Identities = 16/77 (20%), Positives = 34/77 (44%)

Query: 100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSA 159
               L +A +    ++ +       +G +++  +V+++ TG+ +GY F EY  +     A
Sbjct: 94  TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARA 153

Query: 160 YKHADGKKIDGRRVLVD 176
                GK +  R + V 
Sbjct: 154 KSDLLGKPLGPRTLYVH 170

>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 = 55.0 bits (133), Expect = 1e-08
 Identities = 16/92 (17%), Positives = 31/92 (33%), Gaps = 2/92 (2%)

Query: 94  PNATMDPFKTLFIARVNYDTSES-KLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEH 152
               +   + L + R+    ++   L R            +   +  G+ +G+A +EYE 
Sbjct: 177 LTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYET 235

Query: 153 ERDMHSAYKHADGKKIDGRRVLVDVERSRTVK 184
                 A + ADG  + G  + V         
Sbjct: 236 AEMAEEAQQQADGLSLGGSHLRVSFCAPGPPG 267

>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 = 48.8 bits (117), Expect = 8e-07
 Identities = 10/81 (12%), Positives = 27/81 (33%), Gaps = 7/81 (8%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
           + + I  +  D +  ++      Y        +      K +G AF+   +     +A  
Sbjct: 23  RKILIRGLPGDVTNQEVHDLLSDYE-------LKYCFVDKYKGTAFVTLLNGEQAEAAIN 75

Query: 162 HADGKKIDGRRVLVDVERSRT 182
                ++  R + V ++ +  
Sbjct: 76  AFHQSRLRERELSVQLQPTDA 96

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 64.3 bits (157), Expect = 2e-13
 Identities = 17/64 (26%), Positives = 29/64 (45%), Gaps = 2/64 (3%)

Query: 111 YDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDG 170
            +  ++ + + F  +G I        +  GK +GY F+EY        A K+ADG K+D 
Sbjct: 17  LEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDK 74

Query: 171 RRVL 174
           +   
Sbjct: 75  QHTF 78

>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 = 64.1 bits (157), Expect = 2e-13
 Identities = 15/77 (19%), Positives = 30/77 (38%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           L+I  +   T++  L +  + YG I     + +K T K +GY F++++       A    
Sbjct: 8   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67

Query: 164 DGKKIDGRRVLVDVERS 180
               +  +        S
Sbjct: 68  KASGVQAQMAKQSGPSS 84

>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 = 66.0 bits (161), Expect = 2e-13
 Identities = 31/133 (23%), Positives = 54/133 (40%), Gaps = 1/133 (0%)

Query: 49  DPKDTPPPTRVETREERLERRRRERAEQVAYKLEQEIALWDPNSFPNATMDPFKTLFIAR 108
           +  D     +V  +         E     A K          +   +  ++   +L +  
Sbjct: 19  EAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEG-SHHHHHHMDVEGMTSLKVDN 77

Query: 109 VNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKI 168
           + Y TS   LRR FE YG +  + +  ++ T + RG+AF+ +  +RD   A    DG  +
Sbjct: 78  LTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVL 137

Query: 169 DGRRVLVDVERSR 181
           DGR + V + R  
Sbjct: 138 DGRELRVQMARYG 150

>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 = 64.6 bits (158), Expect = 3e-13
 Identities = 18/90 (20%), Positives = 39/90 (43%), Gaps = 8/90 (8%)

Query: 95  NATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHER 154
           ++ M   K LF+  +    +E  L + F  +G ++++         K + YAFI ++   
Sbjct: 5   SSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVK--------KLKDYAFIHFDERD 56

Query: 155 DMHSAYKHADGKKIDGRRVLVDVERSRTVK 184
               A +  +GK ++G  + +   +    K
Sbjct: 57  GAVKAMEEMNGKDLEGENIEIVFAKPPDQK 86

>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 = 64.7 bits (158), Expect = 3e-13
 Identities = 22/114 (19%), Positives = 50/114 (43%), Gaps = 6/114 (5%)

Query: 90  PNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIE 149
            +     T + F  +F+  ++ + +   ++  F  +G I    +V +  TGK +GY F+ 
Sbjct: 5   SSGQKKDTSNHFH-VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVS 63

Query: 150 YEHERDMHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGGTRRGGP 203
           + ++ D  +A +   G+ + GR++  +    +      P         T++ GP
Sbjct: 64  FFNKWDAENAIQQMGGQWLGGRQIRTNWATRKP-----PAPKSTYESNTKQSGP 112

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 66.1 bits (162), Expect = 3e-13
 Identities = 17/73 (23%), Positives = 35/73 (47%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
            L +  +  + ++ + R  F   G I+   +V +K+TG+  GY F+ Y   +D   A   
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 163 ADGKKIDGRRVLV 175
            +G ++  + + V
Sbjct: 64  LNGLRLQTKTIKV 76

>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 = 50.6 bits (122), Expect = 8e-08
 Identities = 18/68 (26%), Positives = 35/68 (51%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           L+++ +    ++ +L + F  YG I    ++ ++VTG  RG  FI ++   +   A K  
Sbjct: 91  LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150

Query: 164 DGKKIDGR 171
           +G+K  G 
Sbjct: 151 NGQKPSGA 158

>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 = 63.8 bits (156), Expect = 4e-13
 Identities = 19/94 (20%), Positives = 42/94 (44%), Gaps = 3/94 (3%)

Query: 88  WDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAF 147
            +     + +  PF  LFI  +N + S ++L+           + +V +  TG  R + +
Sbjct: 5   LEDPVEGSESTTPF-NLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGY 62

Query: 148 IEYEHERDMHSAYKHADGKKIDGRRVLVDVERSR 181
           +++E   D+  A +   G K+ G  + ++  + R
Sbjct: 63  VDFESAEDLEKALE-LTGLKVFGNEIKLEKPKGR 95

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Length = 229

 Score = 67.1 bits (163), Expect = 4e-13
 Identities = 17/139 (12%), Positives = 44/139 (31%), Gaps = 2/139 (1%)

Query: 67  ERRRRERAEQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYG 126
               R+  + +   +  ++      +           L+I  + + T++  L       G
Sbjct: 34  APEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLG 93

Query: 127 P--IKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERSRTVK 184
              I +I    N+  G+ +G+A +    E            +++ G+  +V     + + 
Sbjct: 94  VNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLS 153

Query: 185 GWLPRRLGGGLGGTRRGGP 203
            +  +       G   G  
Sbjct: 154 QFEMQSRKTTQSGQMSGEG 172

>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 = 64.3 bits (157), Expect = 5e-13
 Identities = 29/116 (25%), Positives = 51/116 (43%), Gaps = 5/116 (4%)

Query: 89  DPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFI 148
           D +            LF+  V+ + +E  +  +F  YG IK I +  ++ TG  +GY  +
Sbjct: 10  DGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLV 69

Query: 149 EYEHERDMHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGGTRRGGPD 204
           EYE  ++  +A +  +G+ + G+ + VD    R      P +     G  R   PD
Sbjct: 70  EYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRG-----PPKGKRRGGRRRSRSPD 120

>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 = 63.5 bits (155), Expect = 5e-13
 Identities = 18/83 (21%), Positives = 35/83 (42%), Gaps = 8/83 (9%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIK--------KIVMVHNKVTGKPRGYAFIEYEHE 153
            T+F+  +  + +   +   F+  G IK         I +  ++ TGK +G A + ++  
Sbjct: 14  NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 73

Query: 154 RDMHSAYKHADGKKIDGRRVLVD 176
               +A    DGK+  G  + V 
Sbjct: 74  PSAKAAIDWFDGKEFSGNPIKVS 96

>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 = 62.5 bits (153), Expect = 9e-13
 Identities = 17/80 (21%), Positives = 44/80 (55%), Gaps = 1/80 (1%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
           +++++  V+Y  +  +L   F   G + ++ ++ +K +G P+G+A+IE+  +  + ++  
Sbjct: 7   RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA 66

Query: 162 HADGKKIDGRRVLVDVERSR 181
             D     GR++ V  +R+ 
Sbjct: 67  L-DESLFRGRQIKVIPKRTN 85

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Length = 106

 Score = 63.1 bits (154), Expect = 9e-13
 Identities = 22/89 (24%), Positives = 38/89 (42%), Gaps = 3/89 (3%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           LFI ++  +  E  L+  FE +G I ++ ++ ++ TG  +G AF+ Y        A    
Sbjct: 16  LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSAL 75

Query: 164 DGKKI---DGRRVLVDVERSRTVKGWLPR 189
             +K      R + V    S +  G  P 
Sbjct: 76  HEQKTLPGMNRPIQVKPADSESRGGSGPS 104

>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 = 62.1 bits (152), Expect = 1e-12
 Identities = 17/78 (21%), Positives = 36/78 (46%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           LF+  +N +  +  LR  F+ +       ++ +  TG  RGY F+ +  + D  +A    
Sbjct: 4   LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63

Query: 164 DGKKIDGRRVLVDVERSR 181
            G+ ++GR + ++     
Sbjct: 64  QGQDLNGRPLRINWAAKL 81

>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 = 62.2 bits (152), Expect = 1e-12
 Identities = 16/84 (19%), Positives = 41/84 (48%)

Query: 98  MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMH 157
           +     +F+  ++ + + + +   F  +G I    +V +  TGK +GY F+ + ++ D  
Sbjct: 3   LGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAE 62

Query: 158 SAYKHADGKKIDGRRVLVDVERSR 181
           +A +   G+ + GR++  +    +
Sbjct: 63  NAIQQMGGQWLGGRQIRTNWATRK 86

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 63.2 bits (154), Expect = 1e-12
 Identities = 27/88 (30%), Positives = 45/88 (51%)

Query: 94  PNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHE 153
           P   ++   +L +  + Y TS   LRR FE YG +  + +  ++ T + RG+AF+ +  +
Sbjct: 40  PPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDK 99

Query: 154 RDMHSAYKHADGKKIDGRRVLVDVERSR 181
           RD   A    DG  +DGR + V + R  
Sbjct: 100 RDAEDAMDAMDGAVLDGRELRVQMARYG 127

>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 = 62.3 bits (152), Expect = 2e-12
 Identities = 23/80 (28%), Positives = 35/80 (43%), Gaps = 6/80 (7%)

Query: 97  TMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDM 156
           TM   K L++  +   TSE  + +EF    P         +   K R YAF+ + +  D 
Sbjct: 11  TMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGA------VERVKKIRDYAFVHFSNREDA 64

Query: 157 HSAYKHADGKKIDGRRVLVD 176
             A K  +GK +DG  + V 
Sbjct: 65  VEAMKALNGKVLDGSPIEVT 84

>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 = 63.8 bits (156), Expect = 2e-12
 Identities = 19/85 (22%), Positives = 37/85 (43%)

Query: 92  SFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYE 151
                 +     LFI  +    ++ +++     +GP+K   +V +  TG  +GYAF EY 
Sbjct: 85  PHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYV 144

Query: 152 HERDMHSAYKHADGKKIDGRRVLVD 176
                  A    +G ++  +++LV 
Sbjct: 145 DINVTDQAIAGLNGMQLGDKKLLVQ 169

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 56.5 bits (137), Expect = 8e-10
 Identities = 11/79 (13%), Positives = 29/79 (36%), Gaps = 6/79 (7%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVM-----VHNKVTGKPRGYAFIEYEHERDM 156
           + L++  + +  +E  +   F     +  +       V      + + +AF+E+    + 
Sbjct: 5   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64

Query: 157 HSAYKHADGKKIDGRRVLV 175
             A    DG    G+ + +
Sbjct: 65  TQAMA-FDGIIFQGQSLKI 82

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 61.0 bits (149), Expect = 3e-12
 Identities = 13/70 (18%), Positives = 37/70 (52%), Gaps = 1/70 (1%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           +FI  +++ T++  LR  F  +G +K+ +++ + +T + RG+ F+ +  +  +       
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-Q 61

Query: 164 DGKKIDGRRV 173
              ++D + +
Sbjct: 62  SRHELDSKTI 71

>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 = 63.4 bits (155), Expect = 3e-12
 Identities = 17/88 (19%), Positives = 38/88 (43%), Gaps = 2/88 (2%)

Query: 94  PNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHE 153
             +       LFI  +N + S ++L+           + +V +  TG  R + ++++E  
Sbjct: 6   EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESA 64

Query: 154 RDMHSAYKHADGKKIDGRRVLVDVERSR 181
            D+  A +   G K+ G  + ++  + R
Sbjct: 65  EDLEKALE-LTGLKVFGNEIKLEKPKGR 91

>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 = 61.9 bits (151), Expect = 1e-11
 Identities = 26/94 (27%), Positives = 45/94 (47%), Gaps = 5/94 (5%)

Query: 83  QEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKP 142
            EI L  P    +  +   +TL    ++++ +E +L+  FE      +I +V     GK 
Sbjct: 81  NEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDAL---EIRLVSQ--DGKS 135

Query: 143 RGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD 176
           +G A+IE++ E D     +   G +IDGR V + 
Sbjct: 136 KGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLY 169

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 63.0 bits (153), Expect = 3e-12
 Identities = 15/92 (16%), Positives = 40/92 (43%), Gaps = 2/92 (2%)

Query: 95  NATMDPFKTLFIARVNYDTSESKLRREFEVYGP--IKKIVMVHNKVTGKPRGYAFIEYEH 152
           +   +    +++   ++ T++ +L +     G   + ++    N+  G+ +GYA +    
Sbjct: 49  SGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVAS 108

Query: 153 ERDMHSAYKHADGKKIDGRRVLVDVERSRTVK 184
           E  +H   +   GK ++G +V V     + + 
Sbjct: 109 ENSVHKLLELLPGKVLNGEKVDVRPATRQNLS 140

>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 = 60.6 bits (148), Expect = 3e-12
 Identities = 16/70 (22%), Positives = 33/70 (47%), Gaps = 1/70 (1%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           +F+  ++ DT E K+R  F  +G ++ I +  +  T K RG+ FI ++ E  +    +  
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-K 60

Query: 164 DGKKIDGRRV 173
               +   + 
Sbjct: 61  KYHNVGLSKC 70

>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 = 65.4 bits (160), Expect = 3e-12
 Identities = 12/79 (15%), Positives = 31/79 (39%)

Query: 101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAY 160
             TL++       ++  +R   +    +   + + +      R +A+I+   + D     
Sbjct: 117 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCV 176

Query: 161 KHADGKKIDGRRVLVDVER 179
           +  +G KI+G  ++  V  
Sbjct: 177 EKLNGLKIEGYTLVTKVSN 195

>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 = 56.1 bits (136), Expect = 3e-09
 Identities = 14/81 (17%), Positives = 33/81 (40%), Gaps = 3/81 (3%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
           T+ +  +    +++K+ + F+  GPI  + +  +    K   +A IE+       +A   
Sbjct: 43  TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFRFARIEFARYDGALAAITK 100

Query: 163 ADGKKIDGRRVLVDVERSRTV 183
              K +    ++V      T+
Sbjct: 101 -THKVVGQNEIIVSHLTECTL 120

>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 = 53.1 bits (128), Expect = 4e-08
 Identities = 17/83 (20%), Positives = 35/83 (42%), Gaps = 3/83 (3%)

Query: 96  ATMDPFKTLFIARVNYD-TSESKLRREFEVYGPIKKI-VMVHNKVTGKPRGYAFIEYEHE 153
           +     + + I  ++ +   E+ LR  FE +G I+KI +    K        AF+ +E++
Sbjct: 205 SATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENK 264

Query: 154 RDMHSAYKHADGKKIDGRRVLVD 176
                A +  +   +  R + V 
Sbjct: 265 DSAERALQ-MNRSLLGNREISVS 286

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 60.2 bits (147), Expect = 4e-12
 Identities = 14/73 (19%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           +F+  ++ +T+   ++  FE +G +   +++ +K T + RG+ F+ +E E  +    +  
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-I 60

Query: 164 DGKKIDGRRVLVD 176
              +I+ + V   
Sbjct: 61  HFHEINNKMVECK 73

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 61.6 bits (150), Expect = 4e-12
 Identities = 24/109 (22%), Positives = 41/109 (37%), Gaps = 11/109 (10%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIK--------KIVMVHNKVTGKPRGYAFIEYEHE 153
            T+F+  +  + +   +   F+  G IK         I +  ++ TGK +G A + ++  
Sbjct: 8   NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 67

Query: 154 RDMHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGGTRRGG 202
               +A    DGK+  G  + V     R       R  G G GG     
Sbjct: 68  PSAKAAIDWFDGKEFSGNPIKVSFATRRADF---NRGGGNGRGGLEHHH 113

>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 = 62.5 bits (153), Expect = 5e-12
 Identities = 18/94 (19%), Positives = 37/94 (39%), Gaps = 2/94 (2%)

Query: 89  DPN-SFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAF 147
           DP  + P    D    +F+  +  D    +    F  +G I    ++ +K TG+ RG+ F
Sbjct: 74  DPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGF 133

Query: 148 IEYEHERDMHSAYKHADGKKIDGRRVLVDVERSR 181
           + Y+    +    ++        R++ +     R
Sbjct: 134 VTYDSADAVDRVCQN-KFIDFKDRKIEIKRAEPR 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 = 61.8 bits (151), Expect = 8e-12
 Identities = 21/80 (26%), Positives = 38/80 (47%), Gaps = 2/80 (2%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
             +FI  +N+DT+E  LR  F  YG +  + ++ +  TG+ RG+ F+ +E    +    K
Sbjct: 4   CKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK 63

Query: 162 HADGKKIDGRRVLVDVERSR 181
                 +DG+ +       R
Sbjct: 64  --TQHILDGKVIDPKRAIPR 81

>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 = 60.4 bits (147), Expect = 7e-12
 Identities = 16/95 (16%), Positives = 41/95 (43%), Gaps = 2/95 (2%)

Query: 89  DPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNK-VTGKPRGYAF 147
             +S           + +  + +  ++ ++R  F  +G +K + +      TG  RG+ F
Sbjct: 3   SGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGF 62

Query: 148 IEYEHERDMHSAYKH-ADGKKIDGRRVLVDVERSR 181
           +++  ++D   A+        + GRR++++   S 
Sbjct: 63  VDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSE 97

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 60.3 bits (147), Expect = 8e-12
 Identities = 22/88 (25%), Positives = 46/88 (52%), Gaps = 2/88 (2%)

Query: 94  PNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHE 153
            ++     K +F+  + ++  E++LR  F+ +G + ++VM+++    +PRG+ FI +E E
Sbjct: 4   GSSGSKSNK-IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDE 62

Query: 154 RDMHSAYKHADGKKIDGRRVLVDVERSR 181
           + +  A        I G++V V     R
Sbjct: 63  QSVDQAVN-MHFHDIMGKKVEVKRAEPR 89

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 59.9 bits (146), Expect = 8e-12
 Identities = 18/96 (18%), Positives = 39/96 (40%), Gaps = 14/96 (14%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
             LFI  +  + +E ++R  FE YG + +  ++        + Y F+  E +     A +
Sbjct: 9   VKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIR 60

Query: 162 HADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGG 197
           +    K+ G  + V+  +++       +   G   G
Sbjct: 61  NLHHYKLHGVNINVEASKNK------SKASSGPSSG 90

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 60.0 bits (146), Expect = 9e-12
 Identities = 20/94 (21%), Positives = 36/94 (38%), Gaps = 6/94 (6%)

Query: 91  NSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEY 150
           +S    T      LF+  +  D +E ++R+ FE YG   ++ +       K +G+ FI  
Sbjct: 5   SSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH------KDKGFGFIRL 58

Query: 151 EHERDMHSAYKHADGKKIDGRRVLVDVERSRTVK 184
           E       A    D   + G+++ V         
Sbjct: 59  ETRTLAEIAKVELDNMPLRGKQLRVRFACHSASL 92

>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 = 62.7 bits (153), Expect = 1e-11
 Identities = 21/80 (26%), Positives = 40/80 (50%)

Query: 94  PNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHE 153
           P+A   P  +L++  ++ D +E+ L  +F   GPI  I +  + +T +  GYA++ ++  
Sbjct: 8   PSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQP 67

Query: 154 RDMHSAYKHADGKKIDGRRV 173
            D   A    +   I G+ V
Sbjct: 68  ADAERALDTMNFDVIKGKPV 87

>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 = 45.3 bits (108), Expect = 7e-06
 Identities = 20/94 (21%), Positives = 37/94 (39%), Gaps = 6/94 (6%)

Query: 94  PNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIK--KIVMVHNKVTGKPRGYAFIEYE 151
           P+        +FI  ++       L   F  +G I   K+V          +GY F+ +E
Sbjct: 96  PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVV----CDENGSKGYGFVHFE 151

Query: 152 HERDMHSAYKHADGKKIDGRRVLVDVERSRTVKG 185
            +     A +  +G  ++ R+V V   +SR  + 
Sbjct: 152 TQEAAERAIEKMNGMLLNDRKVFVGRFKSRKERE 185

>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 = 59.1 bits (144), Expect = 2e-11
 Identities = 14/80 (17%), Positives = 30/80 (37%), Gaps = 2/80 (2%)

Query: 104 LFIARVNYDTSESKLRREFEVYGP--IKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
           L+I  + + T++  L       G   I +I    N+  G+ +G+A +    E        
Sbjct: 4   LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63

Query: 162 HADGKKIDGRRVLVDVERSR 181
               +++ G+  +V      
Sbjct: 64  LLPKRELHGQNPVVTPSNKL 83

>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 = 59.2 bits (144), Expect = 2e-11
 Identities = 19/93 (20%), Positives = 45/93 (48%), Gaps = 2/93 (2%)

Query: 89  DPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFI 148
             +S  + +    K L ++ + +   +  LR+ F  +G I  + ++ N+     +G+ F+
Sbjct: 3   SGSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFV 60

Query: 149 EYEHERDMHSAYKHADGKKIDGRRVLVDVERSR 181
            +E+  D   A +   G  ++GR++ V+   +R
Sbjct: 61  TFENSADADRAREKLHGTVVEGRKIEVNNATAR 93

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 58.8 bits (143), Expect = 2e-11
 Identities = 24/96 (25%), Positives = 40/96 (41%), Gaps = 14/96 (14%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
             L +  ++   +  +LR +FE YGP+ +  +V        + YAF+  E   D   A +
Sbjct: 11  TKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAVEAIR 62

Query: 162 HADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGG 197
             D  +  G+R+ V +  SR       R   G   G
Sbjct: 63  GLDNTEFQGKRMHVQLSTSR------LRTASGPSSG 92

>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 = 59.6 bits (145), Expect = 2e-11
 Identities = 12/80 (15%), Positives = 38/80 (47%), Gaps = 1/80 (1%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
           +T+F  ++        L   F   G ++ + ++ ++ + + +G A++E+   + +  A  
Sbjct: 26  RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG 85

Query: 162 HADGKKIDGRRVLVDVERSR 181
              G+++ G  ++V   ++ 
Sbjct: 86  -LTGQRLLGVPIIVQASQAE 104

>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 = 59.3 bits (144), Expect = 2e-11
 Identities = 21/78 (26%), Positives = 38/78 (48%), Gaps = 3/78 (3%)

Query: 99  DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHS 158
           +  + L+I  + Y  +  ++   F  YGPI++I +     T + RG A++ YE   D  +
Sbjct: 6   EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYEDIFDAKN 62

Query: 159 AYKHADGKKIDGRRVLVD 176
           A  H  G  +  R ++V 
Sbjct: 63  AVDHLSGFNVSNRYLVVL 80

>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 = 58.3 bits (142), Expect = 2e-11
 Identities = 16/70 (22%), Positives = 35/70 (50%), Gaps = 1/70 (1%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           +F+  +++DTS+  L+  F  +G +    +  +  TG+ RG+ FI ++    +       
Sbjct: 14  MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-Q 72

Query: 164 DGKKIDGRRV 173
              ++DGR +
Sbjct: 73  KEHRLDGRVI 82

>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 = 59.0 bits (143), Expect = 3e-11
 Identities = 19/78 (24%), Positives = 31/78 (39%), Gaps = 4/78 (5%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHN--KVTGKPRGYAFIEYEHERDMHSAY 160
            LFI  +       ++  E          V+V+       K RG+AF+EYE  R    A 
Sbjct: 10  RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 69

Query: 161 K--HADGKKIDGRRVLVD 176
           +       ++ G ++ VD
Sbjct: 70  RKLMPGRIQLWGHQIAVD 87

>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 = 59.3 bits (144), Expect = 3e-11
 Identities = 21/80 (26%), Positives = 42/80 (52%), Gaps = 1/80 (1%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
           +++++  V+Y ++   L   F   G I +I ++ +K +G P+GYA+IE+     + +A  
Sbjct: 37  RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVA 96

Query: 162 HADGKKIDGRRVLVDVERSR 181
             D     GR + V  +R+ 
Sbjct: 97  -MDETVFRGRTIKVLPKRTN 115

>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 = 58.8 bits (143), Expect = 3e-11
 Identities = 23/86 (26%), Positives = 35/86 (40%), Gaps = 3/86 (3%)

Query: 100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKP---RGYAFIEYEHERDM 156
               LFI  +N+ T+E  L+  F   G IK   +   K         G+ F+EY+     
Sbjct: 4   GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQA 63

Query: 157 HSAYKHADGKKIDGRRVLVDVERSRT 182
             A K   G  +DG ++ V +    T
Sbjct: 64  QKALKQLQGHTVDGHKLEVRISERAT 89

>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 = 61.2 bits (149), Expect = 3e-11
 Identities = 24/83 (28%), Positives = 44/83 (53%), Gaps = 1/83 (1%)

Query: 99  DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHS 158
           +  + LFI  ++++T++  LR  FE +G +   V++ +  T + RG+ F+ Y    ++ +
Sbjct: 11  EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 70

Query: 159 AYKHADGKKIDGRRVLVDVERSR 181
           A   A   K+DGR V      SR
Sbjct: 71  AMN-ARPHKVDGRVVEPKRAVSR 92

>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 = 60.4 bits (147), Expect = 5e-11
 Identities = 25/112 (22%), Positives = 49/112 (43%), Gaps = 9/112 (8%)

Query: 90  PNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIE 149
            +S         K +F+  +  DT E  LR  FE YG I+ I ++ ++ +GK RG+AF+ 
Sbjct: 93  EDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVT 152

Query: 150 YEHERDMHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGGTRRG 201
           ++    +           ++G     +V ++      L ++       ++RG
Sbjct: 153 FDDHDSVDKIVIQ-KYHTVNGHN--CEVRKA------LSKQEMASASSSQRG 195

>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 = 58.7 bits (142), Expect = 3e-11
 Identities = 15/98 (15%), Positives = 34/98 (34%), Gaps = 8/98 (8%)

Query: 89  DPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFI 148
             +S  +  +     + +  +     E+ L    E +G I  ++M+  K        A +
Sbjct: 3   SGSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFK------RQALV 56

Query: 149 EYEHERDMHSAYKHADGKK--IDGRRVLVDVERSRTVK 184
           E+E+          A      I G++   +   S+ + 
Sbjct: 57  EFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRIT 94

>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 = 58.5 bits (142), Expect = 3e-11
 Identities = 16/83 (19%), Positives = 34/83 (40%), Gaps = 1/83 (1%)

Query: 94  PNATMDPFKTLFIARVNYDTSESKLRREFEVYG-PIKKIVMVHNKVTGKPRGYAFIEYEH 152
            + +     +L++  +     E+ + R F   G  +  + ++ N++TG P GY F+E+  
Sbjct: 2   SSGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFAD 61

Query: 153 ERDMHSAYKHADGKKIDGRRVLV 175
                      +GK + G     
Sbjct: 62  LATAEKCLHKINGKPLPGATPAK 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 = 58.4 bits (142), Expect = 3e-11
 Identities = 22/95 (23%), Positives = 42/95 (44%), Gaps = 14/95 (14%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
             +F+  V+   +  +LR  FE  G + +  +V        + YAF+  E E D  +A  
Sbjct: 10  WKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEADAKAAIA 61

Query: 162 HADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLG 196
             +GK++ G+R+ V++           ++ G   G
Sbjct: 62  QLNGKEVKGKRINVELSTKG------QKKSGPSSG 90

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 58.4 bits (142), Expect = 3e-11
 Identities = 18/90 (20%), Positives = 45/90 (50%), Gaps = 4/90 (4%)

Query: 92  SFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYE 151
           S P   + P  T+F+  ++    E+++R  F  YG +K++ ++ ++ TG  +GY F+ + 
Sbjct: 1   SLPEGKIMP-NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFY 58

Query: 152 HERDMHSAYKHADGKKIDGRRVLVDVERSR 181
           ++ D+    +        G+++ +     +
Sbjct: 59  NDVDVQKIVE--SQINFHGKKLKLGPAIRK 86

>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 = 58.4 bits (142), Expect = 3e-11
 Identities = 16/93 (17%), Positives = 34/93 (36%), Gaps = 2/93 (2%)

Query: 89  DPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFI 148
             +S     +     L +  + + T+E  L+  F  +G +  + +  +  TG  +G+ F+
Sbjct: 3   SGSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFV 62

Query: 149 EYEHERDMHSAYKHADGKKIDGRRVLVDVERSR 181
            +                 IDGR     +  S+
Sbjct: 63  RFTEYETQVKVMS--QRHMIDGRWCDCKLPNSK 93

>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 = 60.2 bits (147), Expect = 4e-11
 Identities = 22/75 (29%), Positives = 42/75 (56%), Gaps = 1/75 (1%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
           + L++  ++   +E  L++ F+V GPI  I ++ +K   K   YAF+EY    D + A +
Sbjct: 1   RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQ 59

Query: 162 HADGKKIDGRRVLVD 176
             +GK+I+   V ++
Sbjct: 60  TLNGKQIENNIVKIN 74

>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 = 49.8 bits (120), Expect = 1e-07
 Identities = 18/84 (21%), Positives = 39/84 (46%)

Query: 94  PNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHE 153
             ++ D    LF+  +N +  +  LR  F+ +       ++ +  TG  RGY F+ +  +
Sbjct: 80  QQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQ 139

Query: 154 RDMHSAYKHADGKKIDGRRVLVDV 177
            D  +A     G+ ++GR + ++ 
Sbjct: 140 DDAQNAMDSMQGQDLNGRPLRINW 163

>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 = 58.5 bits (142), Expect = 4e-11
 Identities = 24/88 (27%), Positives = 36/88 (40%), Gaps = 3/88 (3%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
            +++  +  D     +   F  YG I+ I +   K       +AF+E+E  RD   A   
Sbjct: 24  RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL---KNRRGGPPFAFVEFEDPRDAEDAVYG 80

Query: 163 ADGKKIDGRRVLVDVERSRTVKGWLPRR 190
            DG   DG R+ V+  RS    G  P  
Sbjct: 81  RDGYDYDGYRLRVEFPRSGRGTGSGPSS 108

>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 = 58.0 bits (141), Expect = 5e-11
 Identities = 22/87 (25%), Positives = 40/87 (45%), Gaps = 2/87 (2%)

Query: 90  PNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIE 149
            +S         +TL++  ++ D +E  + + F   GP K   M+    +     Y F+E
Sbjct: 4   GSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVE 61

Query: 150 YEHERDMHSAYKHADGKKIDGRRVLVD 176
           +   RD  +A    +G+KI G+ V V+
Sbjct: 62  FYEHRDAAAALAAMNGRKILGKEVKVN 88

>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 = 59.9 bits (146), Expect = 5e-11
 Identities = 19/91 (20%), Positives = 36/91 (39%), Gaps = 8/91 (8%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKP--RGYAFIEYEHERDMHSAY 160
            +F+ +V    SE  LR  FE YG + +I ++ ++    P  +G  F+ +   +    A 
Sbjct: 5   KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64

Query: 161 KHADGKKIDGRRVLV------DVERSRTVKG 185
                 K+             D E++  V+ 
Sbjct: 65  NALHNMKVLPGMHHPIQMKPADSEKNNAVED 95

>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 = 47.6 bits (114), Expect = 9e-07
 Identities = 15/65 (23%), Positives = 29/65 (44%), Gaps = 1/65 (1%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           LFI  ++   +E+ +R  F  +G I++  ++     G  RG AF+ +       +A K  
Sbjct: 98  LFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAM 156

Query: 164 DGKKI 168
              + 
Sbjct: 157 HQAQT 161

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 58.5 bits (142), Expect = 5e-11
 Identities = 15/78 (19%), Positives = 39/78 (50%), Gaps = 4/78 (5%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIK--KIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
           LFI  +  + +++ L   F  +G +   K+ +  +K T   + + F+ +++      A K
Sbjct: 43  LFIYHLPQEFTDTDLASTFLPFGNVISAKVFI--DKQTSLSKCFGFVSFDNPDSAQVAIK 100

Query: 162 HADGKKIDGRRVLVDVER 179
             +G ++  +R+ V +++
Sbjct: 101 AMNGFQVGTKRLKVQLKK 118

>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 = 57.6 bits (140), Expect = 6e-11
 Identities = 19/85 (22%), Positives = 42/85 (49%), Gaps = 1/85 (1%)

Query: 89  DPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFI 148
             +   N+  D    LF+  +++ T++  LR  F  YG +   V++ +K T + RG+ F+
Sbjct: 4   GSSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFV 63

Query: 149 EYEHERDMHSAYKHADGKKIDGRRV 173
           +++    + +    +    +DGR +
Sbjct: 64  KFKDPNCVGTVLA-SRPHTLDGRNI 87

>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 = 58.2 bits (141), Expect = 6e-11
 Identities = 22/87 (25%), Positives = 39/87 (44%), Gaps = 8/87 (9%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIK--------KIVMVHNKVTGKPRGYAFIEYEHER 154
            +++  +N   +   L   F+  G +K         I +  +K TGKP+G A + YE   
Sbjct: 17  AIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPP 76

Query: 155 DMHSAYKHADGKKIDGRRVLVDVERSR 181
              +A +  DGK   G ++ V + R +
Sbjct: 77  TAKAAVEWFDGKDFQGSKLKVSLARKK 103

>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 = 57.7 bits (140), Expect = 8e-11
 Identities = 15/78 (19%), Positives = 39/78 (50%), Gaps = 1/78 (1%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           +FI  +++ T++  LR  F  +G +K+ +++ + +T + RG+ F+ +  +  +       
Sbjct: 28  MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-Q 86

Query: 164 DGKKIDGRRVLVDVERSR 181
              ++D + +   V   R
Sbjct: 87  SRHELDSKTIDPKVAFPR 104

>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 = 57.8 bits (140), Expect = 9e-11
 Identities = 19/112 (16%), Positives = 39/112 (34%), Gaps = 1/112 (0%)

Query: 90  PNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIE 149
            +S             I  + +  ++  + +  E     +  V V     G+  G A ++
Sbjct: 4   GSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQ 63

Query: 150 YEHERDMHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGGTRRG 201
           +++E D   + +    KK++GR   V V     ++         G  G   G
Sbjct: 64  FKNEDDARKSER-LHRKKLNGREAFVHVVTLEDMREIEKNPPAQGKSGPSSG 114

>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 = 56.4 bits (137), Expect = 1e-10
 Identities = 15/80 (18%), Positives = 39/80 (48%), Gaps = 1/80 (1%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
           + +++  + Y  +  +++  F  +G +  + +++++ T KP+G+ F+E + E  +  A  
Sbjct: 2   RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEE-SVSEAIA 60

Query: 162 HADGKKIDGRRVLVDVERSR 181
             D     GR + V     +
Sbjct: 61  KLDNTDFMGRTIRVTEANPK 80

>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 = 56.9 bits (138), Expect = 1e-10
 Identities = 20/82 (24%), Positives = 43/82 (52%), Gaps = 1/82 (1%)

Query: 96  ATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERD 155
           A ++    L ++ +++  S++ ++  F  +G +KK   VH   +G+  G A + +E + D
Sbjct: 24  AGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKK-AAVHYDRSGRSLGTADVHFERKAD 82

Query: 156 MHSAYKHADGKKIDGRRVLVDV 177
              A K  +G  +DGR + + +
Sbjct: 83  ALKAMKQYNGVPLDGRPMNIQL 104

>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 = 56.4 bits (137), Expect = 2e-10
 Identities = 22/86 (25%), Positives = 38/86 (44%), Gaps = 5/86 (5%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPI---KKIVMVHNKVTGKPRGYAFIEYEHERDMHSA 159
            +FI  ++ +  E  L   F  +G I    KI+   +  TG  +GYAFI +       +A
Sbjct: 7   GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMR--DPDTGNSKGYAFINFASFDASDAA 64

Query: 160 YKHADGKKIDGRRVLVDVERSRTVKG 185
            +  +G+ +  R + V     +  KG
Sbjct: 65  IEAMNGQYLCNRPITVSYAFKKDSKG 90

>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 = 55.7 bits (135), Expect = 2e-10
 Identities = 17/73 (23%), Positives = 34/73 (46%), Gaps = 7/73 (9%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
            TL++  +    +E+ LR  F  +G I+ I +V  +        AFI++   +    A +
Sbjct: 13  TTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQ------QCAFIQFATRQAAEVAAE 66

Query: 162 H-ADGKKIDGRRV 173
              +   ++GRR+
Sbjct: 67  KSFNKLIVNGRRL 79

>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 = 56.1 bits (136), Expect = 2e-10
 Identities = 18/98 (18%), Positives = 41/98 (41%), Gaps = 13/98 (13%)

Query: 89  DPNSFPNATMDPFKTLFIARVNYDTSESKLRRE----FEVYGPIKKIVMVHNKVTGKPRG 144
            P + PN       T++I  +N    + +L++     F  +G I  I++     + K RG
Sbjct: 2   VPETRPN------HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILV---SRSLKMRG 52

Query: 145 YAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERSRT 182
            AF+ ++      +A +   G     + + +   ++ +
Sbjct: 53  QAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDS 90

>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 = 56.1 bits (136), Expect = 2e-10
 Identities = 17/85 (20%), Positives = 34/85 (40%), Gaps = 7/85 (8%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
             L+I  ++   +   LR+ F          +          GYAF++Y  +     A +
Sbjct: 9   NKLYIGNLSPAVTADDLRQLFGDRK------LPLAGQVLLKSGYAFVDYPDQNWAIRAIE 62

Query: 162 HADGK-KIDGRRVLVDVERSRTVKG 185
              GK ++ G+ + VD   S+ ++ 
Sbjct: 63  TLSGKVELHGKIMEVDYSVSKKLRS 87

>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 = 56.6 bits (137), Expect = 2e-10
 Identities = 18/80 (22%), Positives = 41/80 (51%), Gaps = 4/80 (5%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIK--KIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
           LFI  +  +  +  L + F  +G +   K+ +  +K T   + + F+ Y++     +A +
Sbjct: 28  LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFI--DKQTNLSKCFGFVSYDNPVSAQAAIQ 85

Query: 162 HADGKKIDGRRVLVDVERSR 181
             +G +I  +R+ V ++RS+
Sbjct: 86  SMNGFQIGMKRLKVQLKRSK 105

>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 = 56.5 bits (137), Expect = 2e-10
 Identities = 23/92 (25%), Positives = 45/92 (48%), Gaps = 1/92 (1%)

Query: 90  PNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIE 149
           P        + F+ LFI  ++++T+E  LR  +E +G +   V++ +  + + RG+ F+ 
Sbjct: 16  PLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVT 75

Query: 150 YEHERDMHSAYKHADGKKIDGRRVLVDVERSR 181
           +    ++ +A   A    IDGR V      +R
Sbjct: 76  FSSMAEVDAAMA-ARPHSIDGRVVEPKRAVAR 106

>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 = 55.8 bits (135), Expect = 2e-10
 Identities = 15/86 (17%), Positives = 33/86 (38%)

Query: 90  PNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIE 149
            +S  ++       + +  + +  S  ++   F  Y  I   V +     G P G A + 
Sbjct: 4   GSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVA 63

Query: 150 YEHERDMHSAYKHADGKKIDGRRVLV 175
           +E   +  +A    + + I  R+V +
Sbjct: 64  FESRDEATAAVIDLNDRPIGSRKVKL 89

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 55.8 bits (135), Expect = 3e-10
 Identities = 14/79 (17%), Positives = 26/79 (32%), Gaps = 6/79 (7%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
           T +I  + +  +E+ L   F+ +G I              +G  FI+Y+           
Sbjct: 29  TAYIGNIPHFATEADLIPLFQNFGFILDFKH------YPEKGCCFIKYDTHEQAAVCIVA 82

Query: 163 ADGKKIDGRRVLVDVERSR 181
                  GR +     + R
Sbjct: 83  LANFPFQGRNLRTGWGKER 101

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 54.9 bits (133), Expect = 4e-10
 Identities = 16/84 (19%), Positives = 39/84 (46%), Gaps = 8/84 (9%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKV---TGKPRGYAFIEYEHERDMHS 158
             +F+  + +D +   L+ +F   G +     ++  +    GK +G   +++E       
Sbjct: 9   CQIFVRNLPFDFTWKMLKDKFNECGHV-----LYADIKMENGKSKGCGVVKFESPEVAER 63

Query: 159 AYKHADGKKIDGRRVLVDVERSRT 182
           A +  +G K+ GR + V ++R+ +
Sbjct: 64  ACRMMNGMKLSGREIDVRIDRNAS 87

>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 = 55.5 bits (134), Expect = 5e-10
 Identities = 21/95 (22%), Positives = 40/95 (42%), Gaps = 14/95 (14%)

Query: 103 TLFIARVNYD-TSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
            +FI  +N     +S +   F  YG +    +         +GYAF++Y +ER   +A  
Sbjct: 29  RVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVL 80

Query: 162 HADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLG 196
             +G+ + G+ + +++          P R G   G
Sbjct: 81  GENGRVLAGQTLDINMAGEPK-----PDRSGPSSG 110

>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 = 55.0 bits (133), Expect = 6e-10
 Identities = 15/87 (17%), Positives = 33/87 (37%)

Query: 90  PNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIE 149
            +S  ++       + +  + +  S  ++   F  Y  I   V +     G P G A + 
Sbjct: 4   GSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVA 63

Query: 150 YEHERDMHSAYKHADGKKIDGRRVLVD 176
           +E   +  +A    + + I  R+V + 
Sbjct: 64  FESRDEATAAVIDLNDRPIGSRKVKLV 90

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 54.5 bits (132), Expect = 6e-10
 Identities = 18/85 (21%), Positives = 39/85 (45%), Gaps = 9/85 (10%)

Query: 98  MDPFKTLFIARVNY-DTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDM 156
           + P   LFI  +   + S+  L R F  YG I +I +           + FI++++ + +
Sbjct: 7   IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSV 58

Query: 157 HSAYKHADGKKIDGRRVLVDVERSR 181
             A +    +   G++++++V  S 
Sbjct: 59  RDAIECESQEMNFGKKLILEVSSSN 83

>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 = 54.6 bits (132), Expect = 7e-10
 Identities = 20/94 (21%), Positives = 37/94 (39%), Gaps = 9/94 (9%)

Query: 92  SFPNATMDPFK-TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEY 150
           S           TL++     D + + LR  F  +G I  + M        PR  AF+ Y
Sbjct: 5   SSGERRAPRKGNTLYVY--GEDMTPTLLRGAFSPFGNIIDLSM------DPPRNCAFVTY 56

Query: 151 EHERDMHSAYKHADGKKIDGRRVLVDVERSRTVK 184
           E       A    +G +++  ++ V++ R + + 
Sbjct: 57  EKMESADQAVAELNGTQVESVQLKVNIARKQPML 90

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 55.0 bits (133), Expect = 7e-10
 Identities = 19/109 (17%), Positives = 36/109 (33%), Gaps = 8/109 (7%)

Query: 73  RAEQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIV 132
            +    +     +                  LF+     D  ES+L   F  +GP+K++ 
Sbjct: 3   SSHHHHHHSSGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVK 62

Query: 133 MVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERSR 181
           +          G+AF+E+E       A +   GK    + + V   +  
Sbjct: 63  I--------LNGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLP 103

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 54.6 bits (132), Expect = 9e-10
 Identities = 18/83 (21%), Positives = 41/83 (49%), Gaps = 2/83 (2%)

Query: 99  DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHS 158
              K L ++ + +   +  LR+ F  +G I  + ++ N+     +G+ F+ +E+  D   
Sbjct: 27  SQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADR 84

Query: 159 AYKHADGKKIDGRRVLVDVERSR 181
           A +   G  ++GR++ V+   +R
Sbjct: 85  AREKLHGTVVEGRKIEVNNATAR 107

>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 = 54.7 bits (132), Expect = 1e-09
 Identities = 19/87 (21%), Positives = 41/87 (47%), Gaps = 1/87 (1%)

Query: 96  ATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERD 155
             ++    L ++ +++  S++ ++  F  +G +KK   V    +G+  G A + +E   D
Sbjct: 30  EGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKK-AAVDYDRSGRSLGTADVHFERRAD 88

Query: 156 MHSAYKHADGKKIDGRRVLVDVERSRT 182
              A K   G  +DGR + + +  S+ 
Sbjct: 89  ALKAMKQYKGVPLDGRPMDIQLVASQI 115

>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 = 56.9 bits (137), Expect = 1e-09
 Identities = 16/98 (16%), Positives = 39/98 (39%), Gaps = 6/98 (6%)

Query: 88  WDPNSFPNATMDPFKTLFIARVNYDT-SESKLRREFEVYGPIKKIVMVHNKVTGKPRGYA 146
               + P         L ++ +N +  +   L   F VYG ++++     K+    +  A
Sbjct: 21  MGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRV-----KILFNKKENA 75

Query: 147 FIEYEHERDMHSAYKHADGKKIDGRRVLVDVERSRTVK 184
            ++         A  H +G K+ G+ + + + + + V+
Sbjct: 76  LVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQ 113

>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 = 49.2 bits (117), Expect = 5e-07
 Identities = 15/86 (17%), Positives = 24/86 (27%), Gaps = 4/86 (4%)

Query: 89  DPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFI 148
             +        P  TL ++ +    SE  L+  F   G + K          K R  A I
Sbjct: 139 PGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFK----FFQKDRKMALI 194

Query: 149 EYEHERDMHSAYKHADGKKIDGRRVL 174
           +     +   A        +     L
Sbjct: 195 QMGSVEEAVQALIDLHNHDLGENHHL 220

>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 = 53.8 bits (130), Expect = 2e-09
 Identities = 18/91 (19%), Positives = 35/91 (38%), Gaps = 1/91 (1%)

Query: 100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSA 159
           P  T F+  + YD +E  ++  F         +        + +G+ + E+E    + SA
Sbjct: 14  PPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSA 73

Query: 160 YKHADGKKIDGRRVLVDVERSRTVKGWLPRR 190
               + + +  +R+ VDV      K   P  
Sbjct: 74  LS-LNEESLGNKRIRVDVADQAQDKDSGPSS 103

>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 = 53.7 bits (129), Expect = 2e-09
 Identities = 14/80 (17%), Positives = 34/80 (42%), Gaps = 6/80 (7%)

Query: 103 TLFIARVNYDTSESKLRREFEV---YGPIKKIVMVHNKVTGK---PRGYAFIEYEHERDM 156
            +F+  ++   ++ ++ +  E    +G I K+V+ ++        P   A++ Y    D 
Sbjct: 17  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 76

Query: 157 HSAYKHADGKKIDGRRVLVD 176
             A +  +   +DGR +   
Sbjct: 77  LRAIQCVNNVVVDGRTLKAS 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 = 52.7 bits (127), Expect = 3e-09
 Identities = 17/79 (21%), Positives = 36/79 (45%), Gaps = 9/79 (11%)

Query: 104 LFIARVNYDT-SESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
           LFI  +     S+  L R F  YG I +I +           + FI++++ + +  A + 
Sbjct: 25  LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEX 76

Query: 163 ADGKKIDGRRVLVDVERSR 181
              +   G++++++V  S 
Sbjct: 77  ESQEMNFGKKLILEVSSSN 95

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 53.4 bits (128), Expect = 3e-09
 Identities = 18/113 (15%), Positives = 39/113 (34%), Gaps = 7/113 (6%)

Query: 74  AEQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRRE----FEVYGPIK 129
            E  A K E++              +P + + I  +N +  + KL+          G I 
Sbjct: 2   KETAAAKFERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDIL 61

Query: 130 KIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERSRT 182
            IV+    ++    G A+I +  +    +  +   G    G  +++    +  
Sbjct: 62  DIVV---DLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQ 111

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 52.5 bits (126), Expect = 4e-09
 Identities = 18/96 (18%), Positives = 30/96 (31%), Gaps = 5/96 (5%)

Query: 89  DPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFI 148
            P S P         +++  +  D   S L+R     G +             PR  AF+
Sbjct: 7   GPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVP-----LRLTWQGPRRRAFL 61

Query: 149 EYEHERDMHSAYKHADGKKIDGRRVLVDVERSRTVK 184
            Y        A     G ++    + V + R +  K
Sbjct: 62  HYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQRDK 97

>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 = 53.1 bits (128), Expect = 4e-09
 Identities = 22/111 (19%), Positives = 41/111 (36%), Gaps = 1/111 (0%)

Query: 91  NSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEY 150
           +S          T+F+A ++Y     KL+  F + G + +   +     GK RG   + +
Sbjct: 5   SSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVR-ADILEDKDGKSRGIGTVTF 63

Query: 151 EHERDMHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGGTRRG 201
           E   +   A    +G+ +  R + V ++     KG           G   G
Sbjct: 64  EQSIEAVQAISMFNGQLLFDRPMHVKMDERALPKGDFFPPERPQQSGPSSG 114

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 52.7 bits (127), Expect = 4e-09
 Identities = 20/98 (20%), Positives = 43/98 (43%), Gaps = 8/98 (8%)

Query: 100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSA 159
           P  T ++  + ++T +  +   F+    I+ + +V +K T K +G+ ++E++    +  A
Sbjct: 14  PPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEA 72

Query: 160 YKHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGG 197
               DG  +  R + VD+   R       +   G   G
Sbjct: 73  LT-YDGALLGDRSLRVDIAEGR------KQDKSGPSSG 103

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 52.3 bits (126), Expect = 4e-09
 Identities = 14/92 (15%), Positives = 33/92 (35%), Gaps = 6/92 (6%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
           +++F++        ++L   F  +GP+  +VM  +K       +A +E        +   
Sbjct: 9   RSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDK-----GVFAIVEMGDVGAREAVLS 63

Query: 162 HADGKKIDGRRVLVDVERSRTVKGWLPRRLGG 193
                 + G R+ V     +  +    +   G
Sbjct: 64  Q-SQHSLGGHRLRVRPREQKEFQSPASKSPKG 94

>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 = 52.6 bits (127), Expect = 5e-09
 Identities = 19/82 (23%), Positives = 34/82 (41%), Gaps = 6/82 (7%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIK--KIVMVHNKVTGKPRGYAFIEYEHERDMHSA 159
             +FI  ++       L   F  +G I   K+V          +GY F+ +E +     A
Sbjct: 6   GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD----ENGSKGYGFVHFETQEAAERA 61

Query: 160 YKHADGKKIDGRRVLVDVERSR 181
            +  +G  ++ R+V V   +SR
Sbjct: 62  IEKMNGMLLNDRKVFVGRFKSR 83

>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 = 55.7 bits (133), Expect = 6e-09
 Identities = 16/93 (17%), Positives = 38/93 (40%), Gaps = 7/93 (7%)

Query: 94  PNATMDPFKTLFIARVNYDTSESKLRRE----FEVYGPIKKIVMVHNKVTGKPRGYAFIE 149
                 P  T++I  +N    + +L++     F  +G I  I++     + K RG AF+ 
Sbjct: 2   AVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVI 58

Query: 150 YEHERDMHSAYKHADGKKIDGRRVLVDVERSRT 182
           ++      +A +   G     + + +   ++ +
Sbjct: 59  FKEVSSATNALRSMQGFPFYDKPMRIQYAKTDS 91

>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 = 45.6 bits (107), Expect = 1e-05
 Identities = 24/159 (15%), Positives = 47/159 (29%), Gaps = 5/159 (3%)

Query: 16  RDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFEDPKDTPPPTRVETREERLERRRRERAE 75
           +  V        +   +                      PP                +  
Sbjct: 122 KKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIP 181

Query: 76  QVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVH 135
             A   +Q +    P + P +   P   LF+  +  +T+E  L   F  +   K++ +V 
Sbjct: 182 PGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVP 241

Query: 136 NKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVL 174
            +        AF+E+++E    +A     G KI     +
Sbjct: 242 GR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAM 275

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 51.7 bits (124), Expect = 9e-09
 Identities = 15/79 (18%), Positives = 29/79 (36%), Gaps = 8/79 (10%)

Query: 100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSA 159
               + I  +     E+ L    + +GPI  +V++        +  A +E+E      +A
Sbjct: 20  ASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVM------PKKRQALVEFEDVLGACNA 73

Query: 160 YKHADGK--KIDGRRVLVD 176
             +A      I G    V+
Sbjct: 74  VNYAADNQIYIAGHPAFVN 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 = 51.5 bits (124), Expect = 1e-08
 Identities = 15/82 (18%), Positives = 29/82 (35%), Gaps = 3/82 (3%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKI-VMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
           L+I+ +     E +L    + +G +    ++  +  +G  RG  F   E      +   H
Sbjct: 28  LYISNLPLSMDEQELENMLKPFGQVISTRILRDS--SGTSRGVGFARMESTEKCEAVIGH 85

Query: 163 ADGKKIDGRRVLVDVERSRTVK 184
            +GK I     +         K
Sbjct: 86  FNGKFIKTPPGVSAPTEPLLCK 107

>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 = 50.7 bits (122), Expect = 2e-08
 Identities = 17/82 (20%), Positives = 33/82 (40%), Gaps = 1/82 (1%)

Query: 100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSA 159
           P  T F+  + YD +E  ++  F         +        + +G+ + E+E    + SA
Sbjct: 18  PPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSA 77

Query: 160 YKHADGKKIDGRRVLVDVERSR 181
               + + +  RR+ VDV    
Sbjct: 78  LS-LNEESLGNRRIRVDVADQA 98

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 52.5 bits (126), Expect = 2e-08
 Identities = 21/115 (18%), Positives = 51/115 (44%), Gaps = 1/115 (0%)

Query: 68  RRRRERAEQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGP 127
            R    +       + +  L+D        ++    L ++ +++  S++ ++  F  +G 
Sbjct: 55  NRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGT 114

Query: 128 IKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERSRT 182
           +KK  + +++ +G+  G A + +E   D   A K   G  +DGR + + +  S+ 
Sbjct: 115 LKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQI 168

>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 = 50.4 bits (121), Expect = 3e-08
 Identities = 16/93 (17%), Positives = 33/93 (35%), Gaps = 6/93 (6%)

Query: 90  PNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIE 149
                N +     T++   +    ++  +R+ F  +G I +I +   K      GY+F+ 
Sbjct: 14  FEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK------GYSFVR 67

Query: 150 YEHERDMHSAYKHADGKKIDGRRVLVDVERSRT 182
           +        A    +G  I+G  V     +   
Sbjct: 68  FSTHESAAHAIVSVNGTTIEGHVVKCYWGKESP 100

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 50.1 bits (120), Expect = 3e-08
 Identities = 10/75 (13%), Positives = 22/75 (29%), Gaps = 3/75 (4%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
           + L I  +        L      YG ++    V+            + Y  +     A  
Sbjct: 16  RKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET---AVVNVTYSSKDQARQALD 72

Query: 162 HADGKKIDGRRVLVD 176
             +G +++   + V 
Sbjct: 73  KLNGFQLENFTLKVA 87

>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 = 49.9 bits (120), Expect = 4e-08
 Identities = 15/91 (16%), Positives = 40/91 (43%), Gaps = 6/91 (6%)

Query: 96  ATMDPFKTLFIARVNYDTSESKLRREFEVYGPIK--KIVMVHNKVTGKPRGYAFIEYEHE 153
            T      L++  ++    + +LR+ F  +G I   K++M      G+ +G+ F+ +   
Sbjct: 10  ITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME----GGRSKGFGFVCFSSP 65

Query: 154 RDMHSAYKHADGKKIDGRRVLVDVERSRTVK 184
            +   A    +G+ +  + + V + + +  +
Sbjct: 66  EEATKAVTEMNGRIVATKPLYVALAQRKEER 96

>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 = 51.8 bits (124), Expect = 4e-08
 Identities = 16/84 (19%), Positives = 39/84 (46%), Gaps = 6/84 (7%)

Query: 102 KTLFIARVNYDT-SESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAY 160
             L ++ +N +  +   L   F VYG ++++ ++ NK     +  A ++         A 
Sbjct: 4   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAM 58

Query: 161 KHADGKKIDGRRVLVDVERSRTVK 184
            H +G K+ G+ + + + + + V+
Sbjct: 59  SHLNGHKLHGKPIRITLSKHQNVQ 82

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 48.7 bits (116), Expect = 5e-07
 Identities = 16/86 (18%), Positives = 25/86 (29%), Gaps = 4/86 (4%)

Query: 89  DPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFI 148
             +        P  TL ++ +    SE  L+  F   G + K      K   K R  A I
Sbjct: 108 PGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVK----GFKFFQKDRKMALI 163

Query: 149 EYEHERDMHSAYKHADGKKIDGRRVL 174
           +     +   A        +     L
Sbjct: 164 QMGSVEEAVQALIDLHNHDLGENHHL 189

>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 = 49.8 bits (119), Expect = 4e-08
 Identities = 14/96 (14%), Positives = 36/96 (37%), Gaps = 8/96 (8%)

Query: 91  NSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEY 150
           +S       P + L I ++  + +E+++      +G +  I+M+  K        AF+E 
Sbjct: 5   SSGDKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGK------NQAFLEL 58

Query: 151 EHERDMHSAYKHADGKK--IDGRRVLVDVERSRTVK 184
             E    +   +       +  + + +     + +K
Sbjct: 59  ATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKELK 94

>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 = 52.0 bits (124), Expect = 5e-08
 Identities = 20/119 (16%), Positives = 44/119 (36%), Gaps = 6/119 (5%)

Query: 102 KTLFIARVNYD-TSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAY 160
             L +  ++    +  ++   F +YG ++K+  + +K      G A +E      +  A 
Sbjct: 5   PVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDRAI 59

Query: 161 KHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGGTRRGGPDVNLKHSGREDNERER 219
            H +   + G+++ V V +   +       L  G    +      N + S  E   + R
Sbjct: 60  THLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNR 118

>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 = 50.5 bits (120), Expect = 1e-07
 Identities = 7/87 (8%), Positives = 21/87 (24%)

Query: 90  PNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIE 149
             +  N    P   L       + +E       +  G  +   +       +      +E
Sbjct: 112 EQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLE 171

Query: 150 YEHERDMHSAYKHADGKKIDGRRVLVD 176
           ++ + D        +  ++        
Sbjct: 172 WDSKSDALETLGFLNHYQMKNPNGPYP 198

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 49.1 bits (117), Expect = 7e-08
 Identities = 15/90 (16%), Positives = 37/90 (41%), Gaps = 8/90 (8%)

Query: 97  TMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDM 156
           +  P + + I ++  D +E ++      +G +  ++M+  K        AFIE   E   
Sbjct: 12  SGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK------NQAFIEMNTEEAA 65

Query: 157 HSA--YKHADGKKIDGRRVLVDVERSRTVK 184
           ++   Y  +    + G+ + +     + +K
Sbjct: 66  NTMVNYYTSVTPVLRGQPIYIQFSNHKELK 95

>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 = 49.0 bits (117), Expect = 8e-08
 Identities = 8/75 (10%), Positives = 29/75 (38%), Gaps = 6/75 (8%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
             +    +   T  ++++  F  +G + ++++       +    A +E+    +   A++
Sbjct: 11  TVILAKNLPAGTLAAEIQETFSRFGSLGRVLL------PEGGITAIVEFLEPLEARKAFR 64

Query: 162 HADGKKIDGRRVLVD 176
           H    K     + ++
Sbjct: 65  HLAYSKFHHVPLYLE 79

>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 = 48.4 bits (116), Expect = 9e-08
 Identities = 16/73 (21%), Positives = 30/73 (41%), Gaps = 7/73 (9%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           +F+ R   D +E +LR  F  YG +  +      +    R +AF+ +  ++   S     
Sbjct: 8   VFVGRCTGDMTEDELREFFSQYGDVMDVF-----IPKPFRAFAFVTFADDQIAQSLCG-- 60

Query: 164 DGKKIDGRRVLVD 176
           +   I G  V + 
Sbjct: 61  EDLIIKGISVHIS 73

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 48.8 bits (116), Expect = 1e-07
 Identities = 17/80 (21%), Positives = 33/80 (41%), Gaps = 8/80 (10%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIK--KIVMVHNKVTGKPRGYAFIEYEHERDMH-- 157
           + +F+  +  D  E ++   F  +GP+         +K    P+GYAF+ ++ E  +   
Sbjct: 9   RKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQAL 68

Query: 158 -SAYKHADGK---KIDGRRV 173
             A    DGK    +    +
Sbjct: 69  IDACLEEDGKLYLCVSSPTI 88

>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 = 48.4 bits (116), Expect = 1e-07
 Identities = 15/65 (23%), Positives = 30/65 (46%), Gaps = 1/65 (1%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           LF+  +N   SE  + R F+ +G I +  ++     G  +G AF+++    +  +A    
Sbjct: 18  LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHAL 76

Query: 164 DGKKI 168
            G + 
Sbjct: 77  HGSQT 81

>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 = 50.5 bits (121), Expect = 2e-07
 Identities = 19/82 (23%), Positives = 31/82 (37%), Gaps = 6/82 (7%)

Query: 94  PNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHE 153
              T      LF+  +  D +E   +R FE YG   ++ +       + RG+ FI  E  
Sbjct: 15  GEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFIN------RDRGFGFIRLESR 68

Query: 154 RDMHSAYKHADGKKIDGRRVLV 175
                A    DG  +  R + +
Sbjct: 69  TLAEIAKAELDGTILKSRPLRI 90

>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 = 44.7 bits (106), Expect = 2e-05
 Identities = 27/161 (16%), Positives = 51/161 (31%), Gaps = 30/161 (18%)

Query: 99  DPFKTLFIARVNYDTSESKLRREFEVYGPIKKI-VMVHNKVTGKPRGYAFIEYEHERDMH 157
                L +  ++   S   L + F  +GP++K  V+V +   G+  G  F+E+  +    
Sbjct: 94  THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD--RGRATGKGFVEFAAKPPAR 151

Query: 158 SAYKHADGKKI----DGRRVLVDVERSRTVKGWLPRRLGGGLGGTRRGGP---------D 204
            A +             R V+V+       +  LP +L        +             
Sbjct: 152 KALERCGDGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLMQKTQQYHKEREQPPRFAQPGT 211

Query: 205 VNLKHSGRE--------------DNERERERYRLERERELA 231
              +++ R               D      + +LE E E A
Sbjct: 212 FEFEYASRWKALDEMEKQQREQVDRNIREAKEKLEAEMEAA 252

>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 = 47.6 bits (113), Expect = 3e-07
 Identities = 16/71 (22%), Positives = 29/71 (40%), Gaps = 8/71 (11%)

Query: 100 PFKTLFIARVN--YDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMH 157
             ++L +A        S ++L    E  G +  ++M  NK       Y+F  Y    +  
Sbjct: 24  ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK------PYSFARYRTTEESK 77

Query: 158 SAYKHADGKKI 168
            AY   +GK++
Sbjct: 78  RAYVTLNGKEV 88

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 47.6 bits (113), Expect = 3e-07
 Identities = 15/91 (16%), Positives = 37/91 (40%), Gaps = 8/91 (8%)

Query: 96  ATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERD 155
           +   P + + I ++  D +E ++      +G +  ++M+  K        AFIE   E  
Sbjct: 26  SAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK------NQAFIEMNTEEA 79

Query: 156 MHSA--YKHADGKKIDGRRVLVDVERSRTVK 184
            ++   Y  +    + G+ + +     + +K
Sbjct: 80  ANTMVNYYTSVTPVLRGQPIYIQFSNHKELK 110

>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 = 47.1 bits (112), Expect = 7e-07
 Identities = 19/88 (21%), Positives = 37/88 (42%), Gaps = 5/88 (5%)

Query: 99  DPFKTLFIARVNYDTSESKLRREFEVYGPI-----KKIVMVHNKVTGKPRGYAFIEYEHE 153
           +P   +++  +     E  L+  F  Y        + +  +     G+ +G AFI   +E
Sbjct: 43  EPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNE 102

Query: 154 RDMHSAYKHADGKKIDGRRVLVDVERSR 181
           +    A K A+G  + G+ ++V   RS 
Sbjct: 103 KAAAKALKEANGYVLFGKPMVVQFARSA 130

>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 = 45.9 bits (109), Expect = 8e-07
 Identities = 11/86 (12%), Positives = 32/86 (37%), Gaps = 1/86 (1%)

Query: 99  DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHS 158
                + +  + +  S+ ++ + F     +   + +     G+  G AF+++  +     
Sbjct: 13  ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEK 72

Query: 159 AYKHADGKKIDGRRVLVDVERSRTVK 184
           A K    ++I  R + +       V+
Sbjct: 73  ALKK-HKERIGHRYIEIFKSSRAEVR 97

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 47.9 bits (113), Expect = 9e-07
 Identities = 16/146 (10%), Positives = 41/146 (28%), Gaps = 2/146 (1%)

Query: 30  HEKKTHGYSGIAAFLNEFEDPKDTPPPTRVETREERLERRRRERAEQVAYKLEQEIALWD 89
             K   G+  +   +      + T     +     + +    E +E              
Sbjct: 38  QIKLDEGWVPLEIMIKFNRLNRLTTDFNVIVEALSKSKAELMEISEDKTKIRRSPSKPLP 97

Query: 90  PNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIE 149
             +         ++++I     D +   ++   E  G +  I M         +G  F+ 
Sbjct: 98  EVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVV 156

Query: 150 YEHERDMHSAYKHADGKKIDGRRVLV 175
           ++         +   G+K     +L+
Sbjct: 157 FDSIESAKKFVE-TPGQKYKETDLLI 181

>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 = 45.3 bits (108), Expect = 9e-07
 Identities = 14/78 (17%), Positives = 31/78 (39%), Gaps = 7/78 (8%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           +F+ R   D +  +L++ F  YG +  +      +    R +AF+ +  ++   S     
Sbjct: 14  VFVGRCTEDMTAEELQQFFCQYGEVVDVF-----IPKPFRAFAFVTFADDKVAQSLCG-- 66

Query: 164 DGKKIDGRRVLVDVERSR 181
           +   I G  V +     +
Sbjct: 67  EDLIIKGISVHISNAEPK 84

>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 = 44.6 bits (106), Expect = 2e-06
 Identities = 19/87 (21%), Positives = 37/87 (42%), Gaps = 3/87 (3%)

Query: 99  DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHS 158
               T+ +    ++ +E  +        P   I +V N   G   GY F+++ +E ++  
Sbjct: 8   TTCHTVKLRGAPFNVTEKNVMEFLAPLKP-VAIRIVRNA-HGNKTGYIFVDFSNEEEVKQ 65

Query: 159 AYKHADGKKIDGRRVLVDVERSRTVKG 185
           A K  + + + GR + V  E+S    G
Sbjct: 66  ALK-CNREYMGGRYIEVFREKSGPSSG 91

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 45.8 bits (108), Expect = 2e-06
 Identities = 13/79 (16%), Positives = 29/79 (36%), Gaps = 4/79 (5%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           + +  + Y  +   L + F  +G + KI+          +  A ++Y        A    
Sbjct: 31  IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSL 86

Query: 164 DGKKIDGRRVLVDVERSRT 182
           DG+ I      + ++ S+ 
Sbjct: 87  DGQNIYNACCTLRIDFSKL 105

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 44.7 bits (106), Expect = 2e-06
 Identities = 11/74 (14%), Positives = 27/74 (36%), Gaps = 2/74 (2%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
           ++++I     D +   ++   E  G +  I M         +G  F+ ++         +
Sbjct: 12  RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE 70

Query: 162 HADGKKIDGRRVLV 175
              G+K     +L+
Sbjct: 71  -TPGQKYKETDLLI 83

>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 = 44.3 bits (105), Expect = 3e-06
 Identities = 7/84 (8%), Positives = 29/84 (34%), Gaps = 7/84 (8%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
             + +  +  D++  ++    + Y        +      + +  AF+   +     +A +
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNAIQ 58

Query: 162 HADGKKIDGRRVLVDVERSRTVKG 185
                   G+ ++V ++ +  +  
Sbjct: 59  MFHQYSFRGKDLIVQLQPTDALLC 82

>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 = 45.9 bits (108), Expect = 3e-06
 Identities = 13/79 (16%), Positives = 29/79 (36%), Gaps = 4/79 (5%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           + +  + Y  +   L + F  +G + KI+          +  A ++Y        A    
Sbjct: 49  IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSL 104

Query: 164 DGKKIDGRRVLVDVERSRT 182
           DG+ I      + ++ S+ 
Sbjct: 105 DGQNIYNACCTLRIDFSKL 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 = 44.8 bits (106), Expect = 4e-06
 Identities = 11/83 (13%), Positives = 32/83 (38%), Gaps = 1/83 (1%)

Query: 94  PNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHE 153
             +  +    +++  + ++     +   F+    ++  + +     GK  G  F+E+ +E
Sbjct: 18  SRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNE 77

Query: 154 RDMHSAYKHADGKKIDGRRVLVD 176
            D  +A      + +  R + V 
Sbjct: 78  ADYKAALCR-HKQYMGNRFIQVH 99

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 44.0 bits (104), Expect = 5e-06
 Identities = 15/108 (13%), Positives = 34/108 (31%), Gaps = 3/108 (2%)

Query: 90  PNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIE 149
            +  P         + +  + +   E+ +R  F     +  + ++ +   G+  G   ++
Sbjct: 5   SSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKDH-VGRNNGNGLVK 62

Query: 150 YEHERDMHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGG 197
           +   +D   A K  +   +  R V V     R           G   G
Sbjct: 63  FLSPQDTFEALKR-NRMLMIQRYVEVSPATERQWVAAGGHITSGPSSG 109

>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 = 43.8 bits (103), Expect = 8e-06
 Identities = 17/115 (14%), Positives = 38/115 (33%), Gaps = 5/115 (4%)

Query: 90  PNSFPNATMDPFKTLFIARVNYDTSESKLRR---EFEVYGPIKKIVMVHNKVTGKPRGYA 146
                         + +  + +  S   ++    +  ++  +  +  ++ +  G+  G A
Sbjct: 6   SGMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTR-EGRQSGEA 64

Query: 147 FIEYEHERDMHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGGTRRG 201
           F+E E E D+  A K  D + +  R + V       +   L         G   G
Sbjct: 65  FVELESEDDVKLALKK-DRESMGHRYIEVFKSHRTEMDWVLKHSGPNSASGPSSG 118

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 43.9 bits (103), Expect = 8e-06
 Identities = 16/95 (16%), Positives = 30/95 (31%), Gaps = 7/95 (7%)

Query: 90  PNSFPNATMDPFKTLFIARVN--YDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAF 147
                +      K L ++  N  Y  +   L       G +++IV+            A 
Sbjct: 12  RPGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRN-----GIQAM 66

Query: 148 IEYEHERDMHSAYKHADGKKIDGRRVLVDVERSRT 182
           +E+E       A    +G  I      + +E +R 
Sbjct: 67  VEFESVLCAQKAKAALNGADIYAGCCTLKIEYARP 101

>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 = 42.9 bits (101), Expect = 2e-05
 Identities = 11/86 (12%), Positives = 31/86 (36%), Gaps = 1/86 (1%)

Query: 90  PNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIE 149
                +A       + +  + +  ++ ++ + F     +   + +     GK  G AF++
Sbjct: 31  GRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQ 90

Query: 150 YEHERDMHSAYKHADGKKIDGRRVLV 175
           +  +     A      ++I  R + V
Sbjct: 91  FASQELAEKALGK-HKERIGHRYIEV 115

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 46.0 bits (108), Expect = 2e-05
 Identities = 37/285 (12%), Positives = 73/285 (25%), Gaps = 104/285 (36%)

Query: 4   FLPPNLLALFAPRDPVPYLP-PVEKLPHEKKTHG---YSGIAAFLNEFEDPKDTPPPTRV 59
             P  + +L        YL    + LP E  T      S IA  + +             
Sbjct: 298 LTPDEVKSLLLK-----YLDCRPQDLPREVLTTNPRRLSIIAESIRDGLA---------- 342

Query: 60  ETREERLERRRRERAEQVAYKLEQEIALWDPNS----------FPNATMDPFKTLFIARV 109
                  +  +    +++   +E  + + +P            FP +   P   L +   
Sbjct: 343 -----TWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWF 397

Query: 110 NYDTSE-----SKLRRE------------------FEVYGPIKKIVMVHNKVTGKPRGYA 146
           +   S+     +KL +                    E+   ++    +H  +      Y 
Sbjct: 398 DVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDH---YN 454

Query: 147 FIEYEHERDM-----------HSAYKHADGKKIDG-----RRVLVDVERSRTVKGWLPRR 190
             +     D+           H  + H    +        R V +D         +L ++
Sbjct: 455 IPKTFDSDDLIPPYLDQYFYSHIGH-HLKNIEHPERMTLFRMVFLDF-------RFLEQK 506

Query: 191 LGGGLGGTRRGGPDVNLKHSGRE-------------DNERERERY 222
           +       R      N   S                DN+ + ER 
Sbjct: 507 I-------RHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERL 544

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 42.6 bits (100), Expect = 2e-05
 Identities = 11/90 (12%), Positives = 32/90 (35%), Gaps = 4/90 (4%)

Query: 89  DPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIK---KIVMVHNKVTGKPRGY 145
                   + +    + +  + +  +  ++   F  + PI    + ++      G+P G 
Sbjct: 11  SNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGD 70

Query: 146 AFIEYEHERDMHSAYKHADGKKIDGRRVLV 175
           AF+ +  E    +A +      +  R + +
Sbjct: 71  AFVLFACEEYAQNALRK-HKDLLGKRYIEL 99

>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 = 41.5 bits (97), Expect = 3e-05
 Identities = 14/87 (16%), Positives = 37/87 (42%), Gaps = 7/87 (8%)

Query: 103 TLFIARVNYDTSESKLRRE----FEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHS 158
            + ++ ++Y  S  +L++     F  +G +K + +  +      +  A ++ E+ +D   
Sbjct: 11  DVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHT---DYQLKAVVQMENLQDAIG 67

Query: 159 AYKHADGKKIDGRRVLVDVERSRTVKG 185
           A       KI  +++LV +    +   
Sbjct: 68  AVNSLHRYKIGSKKILVSLATGASGPS 94

>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 = 41.6 bits (98), Expect = 3e-05
 Identities = 16/91 (17%), Positives = 33/91 (36%), Gaps = 3/91 (3%)

Query: 99  DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHS 158
                + +  + Y  +E+ +   F    P++  V +     G+  G A +E+    D  +
Sbjct: 13  TTGHCVHMRGLPYRATENDIYNFFSPLNPMR--VHIEIGPDGRVTGEADVEFATHEDAVA 70

Query: 159 AYKHADGKKIDGRRVLVDVERSRTVKGWLPR 189
           A    D   +  R V + +  +    G  P 
Sbjct: 71  AMA-KDKANMQHRYVELFLNSTAGTSGSGPS 100

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 41.9 bits (98), Expect = 4e-05
 Identities = 15/88 (17%), Positives = 28/88 (31%), Gaps = 3/88 (3%)

Query: 90  PNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVH--NKVTGKPRGYAF 147
            +            + +  + +  S   ++              VH      G+  G AF
Sbjct: 33  GSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAF 92

Query: 148 IEYEHERDMHSAYKHADGKKIDGRRVLV 175
           +E   E D+  A K  D + +  R + V
Sbjct: 93  VELGSEDDVKMALKK-DRESMGHRYIEV 119

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C} Length = 579

 Score = 44.4 bits (105), Expect = 4e-05
 Identities = 14/92 (15%), Positives = 31/92 (33%)

Query: 187 LPRRLGGGLGGTRRGGPDVNLKHSGREDNERERERYRLERERELAGGPPRARSGSNDRER 246
           + RR    LG +R        +       +   + Y  + + E++    +  +  +    
Sbjct: 487 VSRRFLDKLGLSRSPIGKAMFEIRDYSSRDGNNKSYDYDDDSEISFRGNKNYNNRSQNRD 546

Query: 247 ERERRRSRSRERKRRTSRSRSRDRRRRRSRER 278
             +    RS   +R  SRS  ++    R+   
Sbjct: 547 YDDEPFRRSNNNRRSFSRSNDKNNYSSRNSNI 578

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C} Length = 579

 Score = 42.1 bits (99), Expect = 2e-04
 Identities = 17/106 (16%), Positives = 32/106 (30%), Gaps = 2/106 (1%)

Query: 165 GKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGGTRRGGPDVNLKHSGREDNERERERYRL 224
           G  ++  ++ + V R    K  L R   G      R     +  +   + ++     +R 
Sbjct: 475 GVLLNDPQLKIPVSRRFLDKLGLSRSPIGKAMFEIRDYSSRDGNNKSYDYDDDSEISFRG 534

Query: 225 ERERELAGGPPRARSGSNDRERERERRRSRSRERKRRTSRSRSRDR 270
            +                   R    RRS SR   +    SR+ + 
Sbjct: 535 NKNYN--NRSQNRDYDDEPFRRSNNNRRSFSRSNDKNNYSSRNSNI 578

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C} Length = 579

 Score = 41.7 bits (98), Expect = 3e-04
 Identities = 13/82 (15%), Positives = 24/82 (29%)

Query: 199 RRGGPDVNLKHSGREDNERERERYRLERERELAGGPPRARSGSNDRERERERRRSRSRER 258
               P        R+ + R+      + + +        ++ +N  +          R  
Sbjct: 497 LSRSPIGKAMFEIRDYSSRDGNNKSYDYDDDSEISFRGNKNYNNRSQNRDYDDEPFRRSN 556

Query: 259 KRRTSRSRSRDRRRRRSRERIR 280
             R S SRS D+    SR    
Sbjct: 557 NNRRSFSRSNDKNNYSSRNSNI 578

>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant photosynthetic reaction center, peripheral antenna; HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1 Length = 154

 Score = 42.2 bits (98), Expect = 4e-05
 Identities = 10/32 (31%), Positives = 16/32 (50%), Gaps = 6/32 (18%)

Query: 72 ERAEQVAYKLEQEIALWDPNSFP----NATMD 99
          E+  Q   KL+  + L+  +S P     ATM+
Sbjct: 18 EK--QALKKLQASLKLYADDSAPALAIKATME 47

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 40.0 bits (94), Expect = 1e-04
 Identities = 17/71 (23%), Positives = 32/71 (45%), Gaps = 2/71 (2%)

Query: 103 TLFIARVNYDTSESKLRREF-EVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
           +LF+  +  D  +  L   F +VY   +   +V ++ TG  +GY F+++  E +   A  
Sbjct: 11  SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALT 69

Query: 162 HADGKKIDGRR 172
              G    G +
Sbjct: 70  ECQGAVGLGSK 80

>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 = 39.1 bits (91), Expect = 2e-04
 Identities = 17/80 (21%), Positives = 27/80 (33%), Gaps = 3/80 (3%)

Query: 98  MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVH--NKVTGKPRGYAFIEYEHERD 155
           +D    +    + +  +   +   F           +H      GK RG A IE E E+D
Sbjct: 8   VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQD 67

Query: 156 MHSAYKHADGKKIDGRRVLV 175
           +  A        +  R V V
Sbjct: 68  VQKA-LEKHRMYMGQRYVEV 86

>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 = 38.8 bits (90), Expect = 3e-04
 Identities = 22/92 (23%), Positives = 39/92 (42%), Gaps = 9/92 (9%)

Query: 89  DPNSFPNATMDPFKTLFIARVNYD-TSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAF 147
            P+   +   +  + + ++ + +   S+S + +  E YG IK  +++  K        AF
Sbjct: 13  KPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMK------SQAF 66

Query: 148 IEYEHERDMHSAYKHADGK--KIDGRRVLVDV 177
           IE E   D  +   H   K     GR V VD+
Sbjct: 67  IEMETREDAMAMVDHCLKKALWFQGRCVKVDL 98

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 41.4 bits (97), Expect = 4e-04
 Identities = 15/118 (12%), Positives = 50/118 (42%), Gaps = 1/118 (0%)

Query: 236 RARSGSNDRERERERRRSRSRERKRRTSRSRSRDRRRRRSRERIRDDDIEEVEFRPKDRS 295
             R     + ++ E +R++ R++K          +  +   E+    +  + E      +
Sbjct: 852 VTRQEEEMQAKDEELQRTKERQQKAEAELKELEQKHTQLCEEKNLLQEKLQAETELYAEA 911

Query: 296 DRDRDRDRKRRRERENSEDRNERKRDRKERR-KERERNNEEREEKVFIKQEPVDDYQE 352
           +  R R   +++E E      E + + +E R ++ +   ++ ++++   +E +++ + 
Sbjct: 912 EEMRVRLAAKKQELEEILHEMEARIEEEEERSQQLQAEKKKMQQQMLDLEEQLEEEEA 969

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3 Length = 104

 Score = 37.9 bits (88), Expect = 6e-04
 Identities = 10/65 (15%), Positives = 27/65 (41%), Gaps = 1/65 (1%)

Query: 112 DTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGR 171
           +  E       E YG ++++  V + +     G  ++++  E D   A    + +  +G+
Sbjct: 38  EFFEEVFTEMEEKYGEVEEMN-VCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQ 96

Query: 172 RVLVD 176
            +  +
Sbjct: 97  PIHAE 101

>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 = 38.7 bits (90), Expect = 7e-04
 Identities = 13/85 (15%), Positives = 30/85 (35%), Gaps = 3/85 (3%)

Query: 89  DPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFI 148
             +S           + +  + Y  +E+ +   F    P++  V +     G+  G A +
Sbjct: 34  SGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVR--VHIEIGPDGRVTGEADV 91

Query: 149 EYEHERDMHSAYKHADGKKIDGRRV 173
           E+    +  +A    D   +  R +
Sbjct: 92  EFATHEEAVAAMSK-DRANMQHRYI 115

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	363
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	100.0
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.87
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.85
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.84
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.84
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.84
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.84
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.84
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.84
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.83
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.83
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.83
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.83
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.83
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.83
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.83
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.83
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.83
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.82
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.82
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.82
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.82
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.82
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.82
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.82
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.82
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.82
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.82
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.82
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.82
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.82
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.82
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.82
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.81
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.81
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.81
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.81
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.81
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.81
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.81
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.81
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.81
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.81
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.81
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.81
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.81
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.81
2div_A	99	TRNA selenocysteine associated protein; structural	99.8
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.8
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.8
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.8
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.8
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.8
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.8
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.8
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.8
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.8
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.8
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.8
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.79
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.79
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.79
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.79
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.79
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.79
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.79
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.79
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.79
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.79
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.79
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.79
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.79
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.79
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.79
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.79
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.78
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.78
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.78
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.78
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.78
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.78
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.78
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.78
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.77
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.77
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.77
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.77
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.77
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.77
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.77
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.77
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.77
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.77
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.77
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.77
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.77
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.77
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.77
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.77
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.77
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.76
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.76
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.76
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.76
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.76
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.76
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.76
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.76
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.76
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.76
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.76
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.76
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.76
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.76
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.75
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.75
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.75
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.75
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.75
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.75
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.61
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.75
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.75
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.75
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.74
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.74
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.74
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.74
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.74
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.74
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.74
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.74
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.74
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.74
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.74
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.73
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.73
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.73
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.73
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.73
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.73
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.73
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.73
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.73
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.73
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.73
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.73
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.73
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.72
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.72
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.72
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.72
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.72
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.72
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.72
1x5p_A	97	Negative elongation factor E; structure genomics,	99.71
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.7
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.7
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.7
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.7
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.69
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.69
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.69
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.69
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.69
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.69
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.68
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.68
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.68
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.68
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.68
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.67
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.66
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.66
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.66
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.66
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.65
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.65
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.65
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.65
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.64
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.64
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.64
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.63
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.62
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.62
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.6
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.59
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.59
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.58
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.58
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.57
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.56
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.54
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.53
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.51
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.51
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.51
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.5
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.44
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.43
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.43
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.42
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.38
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.22
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.22
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.19
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	99.08
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.88
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.59
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.87
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.54
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.54
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.51
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.2
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.16
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	97.11
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	96.81
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.43
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	95.88
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	95.74
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	94.46
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	95.37
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	95.14
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	94.93
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	94.83
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	94.7
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	94.65
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	94.57
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	94.33
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	94.01
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	93.96
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	93.95
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	93.85
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	93.51
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	92.99
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	92.78
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	92.75
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	92.65
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	92.56
1x4e_A	85	RNA binding motif, single-stranded interacting pro	92.53
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	92.43
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	92.4
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	92.29
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	92.2
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	92.14
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	92.07
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	91.92
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	91.89
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	91.71
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	91.68
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	91.59
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	91.37
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	91.19
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	91.18
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	90.96
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	90.84
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	90.76
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	90.66
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	90.65
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	90.62
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	90.59
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	90.18
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	90.06
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	89.96
2div_A	99	TRNA selenocysteine associated protein; structural	89.92
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	89.88
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	89.85
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	89.77
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	89.71
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	89.64
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	89.63
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	89.53
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	89.48
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	89.47
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	89.41
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	89.38
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	89.17
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	89.04
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	88.81
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	88.74
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	88.62
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	88.58
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	88.57
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	88.42
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	88.35
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	87.71
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	87.54
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	87.47
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	87.28
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	86.96
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	86.61
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	86.58
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	86.14
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	86.0
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	85.84
2dis_A	109	Unnamed protein product; structural genomics, RRM	85.83
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	85.46
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	85.43
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	85.36
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	84.97
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	84.93
1x5o_A	114	RNA binding motif, single-stranded interacting pro	84.67
2g0c_A	76	ATP-dependent RNA helicase DBPA; RNA recognition m	84.36
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	84.16
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	83.88
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	82.87
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	82.67
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	82.25
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	82.03
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	81.92
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	81.05
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	80.59
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	80.49
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	80.19
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	80.13
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	80.1
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	80.04

>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=100.00  E-value=9.1e-47  Score=368.45  Aligned_cols=212  Identities=78%  Similarity=1.322  Sum_probs=181.1

Q ss_pred             CCCCCChhhhhcCCCCCCCCCCCCCCCCCCCC-CCCCCccccccccccCCCCCCCCCCCcccHHHHHHHHHHHHHHHHHH
Q psy16184          1 MTQFLPPNLLALFAPRDPVPYLPPVEKLPHEK-KTHGYSGIAAFLNEFEDPKDTPPPTRVETREERLERRRRERAEQVAY   79 (363)
Q Consensus         1 ~~~~~p~~l~~~f~~~~pi~~~~p~~~~p~t~-~s~g~~g~v~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   79 (363)
                      ||++|||+|+.||+|.|||++|+|+...|... ...+|+||..|+..++....++....++...+..+.++.++.++.+.
T Consensus         1 mt~~lPp~L~~lF~p~pPl~~~~P~~~~p~~~~~~~~~~gia~~~~~f~~~~~~~~~~~~e~~~~~~~~~~~~k~~~~~~   80 (437)
T 3pgw_S            1 MTQFLPPNLLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRDAPPPTRAETREERMERKRREKIERRQQ   80 (437)
T ss_pred             CCCcCCccHHHhcCCCCCCcCCCCcccccccccCCCCcccHHHHHHhhcCcccccccccccCHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999988777544 78889899989888887766666666777777666666667777777


Q ss_pred             HHHHHHhhcCCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHH
Q psy16184         80 KLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSA  159 (363)
Q Consensus        80 ~~~~~~~~~~p~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~A  159 (363)
                      ++...+..|.|...+.....+.++|||+|||+.||+++|..+|.+||.|..|.|+.++.|++++|||||+|.+.++|.+|
T Consensus        81 ~~~~~~~~~~p~~~~~~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~A  160 (437)
T 3pgw_S           81 EVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSA  160 (437)
T ss_pred             HHHHhhhhcCCcccccccCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHH
Confidence            77778888888888888888899999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhCCceeCCEEEEEEeecccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q psy16184        160 YKHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGGTRRGGPDVNLKHSGR  212 (363)
Q Consensus       160 i~~l~g~~i~g~~i~V~~a~~~~~~~~~~~~~~g~~g~~~~~~~~~~~~~~~~  212 (363)
                      |..|||+.|+|+.|.|.|+.+.....|.+...+||.|++.+++...+....++
T Consensus       161 i~~lng~~i~gr~i~V~~a~~~~~~~~~~~~~ggG~gg~~~gg~~~~~~~~gr  213 (437)
T 3pgw_S          161 YKHADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGR  213 (437)
T ss_pred             HHHcCCCEECCEEEEEEEeCCCCCCCCCCCCcCCCCCCCCCCCCccccccccc
Confidence            99999999999999999999999888988777776666555554444333333

>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=99.87  E-value=5.7e-22  Score=153.94  Aligned_cols=82  Identities=21%  Similarity=0.437  Sum_probs=78.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      .+.++|||+|||+.+|+++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+||..|||..|.|+.|.|.||
T Consensus        17 ~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~A   96 (99)
T 4fxv_A           17 FQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYA   96 (99)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            34679999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cc
Q psy16184        179 RS  180 (363)
Q Consensus       179 ~~  180 (363)
                      +|
T Consensus        97 kP   98 (99)
T 4fxv_A           97 RP   98 (99)
T ss_dssp             CB
T ss_pred             eC
Confidence            75

>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=99.85  E-value=1.7e-23  Score=177.50  Aligned_cols=149  Identities=18%  Similarity=0.334  Sum_probs=113.3

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccCCCCCCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFEDPKDTPPPTRVETREERLERRRRERAEQVAYKLEQEIA   86 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   86 (363)
                      .+|..+|+++|+|..+ -++.++.++.++|| +||.|.+...........+.+.++.+.+...                 
T Consensus        18 ~~l~~~F~~~G~i~~v-~i~~~~~~g~~~g~-afV~f~~~~~a~~A~~~~~~~~g~~i~v~~~-----------------   78 (167)
T 2cjk_A           18 DNLREYFGKYGTVTDL-KIMKDPATGRSRGF-GFLSFEKPSSVDEVVKTQHILDGKVIDPKRA-----------------   78 (167)
T ss_dssp             HHHHHHHTTTCCEEEE-ECCCCTTTSSCCSC-EEEEESSTHHHHHHHHSCCEETTEECCCEEC-----------------
T ss_pred             HHHHHHHHhCCCEEEE-EEEECCCCCCccce-EEEEEccHHHHHHHHhcccccCCeEcccccc-----------------
Confidence            4589999999999888 46678889999999 9999976432110000011122211111000                 


Q ss_pred             hcCCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCc
Q psy16184         87 LWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGK  166 (363)
Q Consensus        87 ~~~p~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~  166 (363)
                            .+.....+.++|||+|||+.+|+++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+|+. ||+.
T Consensus        79 ------~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~  151 (167)
T 2cjk_A           79 ------IPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFI  151 (167)
T ss_dssp             ------CCHHHHHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEE
T ss_pred             ------cchhhccCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCE
Confidence                  000001125699999999999999999999999999999999998899999999999999999999998 8999


Q ss_pred             eeCCEEEEEEeeccc
Q psy16184        167 KIDGRRVLVDVERSR  181 (363)
Q Consensus       167 ~i~g~~i~V~~a~~~  181 (363)
                      .|+|+.|.|.+|.++
T Consensus       152 ~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A          152 DFKDRKIEIKRAEPR  166 (167)
T ss_dssp             CSSSSCEEEEECCCC
T ss_pred             EeCCeEEEEeecCCC
Confidence            999999999999764

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.84  E-value=8e-21  Score=150.30  Aligned_cols=82  Identities=20%  Similarity=0.295  Sum_probs=79.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      .+.++|||+||++.+|+++|.++|++||.|..|.|+.++.|+.++|||||+|.+.++|++||..|||..|+|+.|.|.++
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a   83 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLD   83 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cc
Q psy16184        179 RS  180 (363)
Q Consensus       179 ~~  180 (363)
                      ..
T Consensus        84 ~~   85 (110)
T 3s8s_A           84 IK   85 (110)
T ss_dssp             ST
T ss_pred             CC
Confidence            64

>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=99.84  E-value=4.7e-23  Score=179.32  Aligned_cols=157  Identities=22%  Similarity=0.371  Sum_probs=113.3

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccCC-CCCCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHH
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFED-PKDTPPPTRVETREERLERRRRERAEQVAYKLEQEI   85 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   85 (363)
                      .+|..+|.++|+|..+ .++.++.++.++|| +||.|.+.... .+.......+.++.+.+.......            
T Consensus        28 ~~l~~~F~~~G~i~~v-~i~~~~~~g~~~g~-afV~f~~~~~A~~A~~~~~~~~~g~~l~v~~~~~~~------------   93 (196)
T 1l3k_A           28 ESLRSHFEQWGTLTDC-VVMRDPNTKRSRGF-GFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSRE------------   93 (196)
T ss_dssp             HHHHHHHGGGSCEEEE-EEEECTTTCCEEEE-EEEEESSHHHHHHHHHTCSCEETTEECEEEECCC--------------
T ss_pred             HHHHHHHHhCCCEEEE-EEEEcCCCCCccce-EEEEeCCHHHHHHHHhcCCCEECCEEeeeecccCcc------------
Confidence            4689999999999887 46678889999999 99999774331 111112223332221111100000            


Q ss_pred             hhcCCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCC
Q psy16184         86 ALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADG  165 (363)
Q Consensus        86 ~~~~p~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g  165 (363)
                           .........+.++|||+|||+.+|+++|.++|+.||.|..|.|+.+..++.++|||||+|.+.++|.+||.. ++
T Consensus        94 -----~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~  167 (196)
T 1l3k_A           94 -----DSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KY  167 (196)
T ss_dssp             --------------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SC
T ss_pred             -----cccccccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CC
Confidence                 000011123467999999999999999999999999999999999988999999999999999999999985 89


Q ss_pred             ceeCCEEEEEEeecccCC
Q psy16184        166 KKIDGRRVLVDVERSRTV  183 (363)
Q Consensus       166 ~~i~g~~i~V~~a~~~~~  183 (363)
                      ..|+|+.|.|.++.++..
T Consensus       168 ~~~~G~~i~v~~a~~k~~  185 (196)
T 1l3k_A          168 HTVNGHNCEVRKALSKQE  185 (196)
T ss_dssp             CEETTEECEEEECC----
T ss_pred             cEECCEEEEEEecCChhH
Confidence            999999999999987654

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.84  E-value=2.2e-20  Score=154.00  Aligned_cols=89  Identities=26%  Similarity=0.487  Sum_probs=82.7

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEE
Q psy16184         96 ATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLV  175 (363)
Q Consensus        96 ~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V  175 (363)
                      ....+.++|||+|||+.+|+++|.++|..||.|..|.|+.++.++.++|||||+|.+.++|.+||..|||..|.|+.|.|
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            34456789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecccCCC
Q psy16184        176 DVERSRTVK  184 (363)
Q Consensus       176 ~~a~~~~~~  184 (363)
                      .++......
T Consensus       117 ~~a~~~~~~  125 (139)
T 1u6f_A          117 ALAASGHQR  125 (139)
T ss_dssp             EESSCCCCC
T ss_pred             EECCCCCCC
Confidence            999876543

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.84  E-value=1.1e-22  Score=179.73  Aligned_cols=163  Identities=20%  Similarity=0.355  Sum_probs=115.6

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccCC--CCCCCCCCCcccHHHHHHHHHHHH-HHHHHHHHHH
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFED--PKDTPPPTRVETREERLERRRRER-AEQVAYKLEQ   83 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~   83 (363)
                      .+|..+|..+++|..+ -+..++.++.++|| +||.|.+....  +...+....+.++.+.+....... ..........
T Consensus        43 ~~l~~~f~~~G~i~~v-~i~~~~~~g~~~g~-afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~  120 (216)
T 2qfj_A           43 DTIRQAFAPFGPIKSI-DMSWDSVTMKHKGF-AFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAE  120 (216)
T ss_dssp             HHHHHHHGGGSCEEEE-EECCC-CC-CCCSE-EEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCSCCGGGHHHHHHHHH
T ss_pred             HHHHHHHHhCCCEEEE-EEeecCCCCccCce-EEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCCCccccchhhhhhhc
Confidence            4689999999999887 45667888999999 99999774331  111112222222111110000000 0000000000


Q ss_pred             HHhhcCCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHh
Q psy16184         84 EIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA  163 (363)
Q Consensus        84 ~~~~~~p~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l  163 (363)
                                   .....++|||+|||..+|+++|.++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+||..|
T Consensus       121 -------------~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l  187 (216)
T 2qfj_A          121 -------------EARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM  187 (216)
T ss_dssp             -------------HHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHH
T ss_pred             -------------ccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHc
Confidence                         0123579999999999999999999999999999999999889999999999999999999999999


Q ss_pred             CCceeCCEEEEEEeecccCCC
Q psy16184        164 DGKKIDGRRVLVDVERSRTVK  184 (363)
Q Consensus       164 ~g~~i~g~~i~V~~a~~~~~~  184 (363)
                      ||..|+|+.|.|.++.+....
T Consensus       188 ~g~~~~g~~i~V~~a~~~~~~  208 (216)
T 2qfj_A          188 NLFDLGGQYLRVGKAVTPPMP  208 (216)
T ss_dssp             TTCBCSSSBCEEEECSSCSST
T ss_pred             cCCEeCCcEEEEEEecCCCCC
Confidence            999999999999999876543

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.84  E-value=5.8e-21  Score=145.87  Aligned_cols=82  Identities=20%  Similarity=0.428  Sum_probs=76.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhC-CccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHh-CCceeCCEEEEEEee
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYG-PIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA-DGKKIDGRRVLVDVE  178 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G-~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l-~g~~i~g~~i~V~~a  178 (363)
                      +++|||+|||+.+|+++|+++|++|| .|..|.|+.++.||.++|||||+|.+.++|.+||..| |+..|+|+.|.|+++
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a   80 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYS   80 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEc
Confidence            46899999999999999999999999 8999999999999999999999999999999999987 466899999999999


Q ss_pred             cccC
Q psy16184        179 RSRT  182 (363)
Q Consensus       179 ~~~~  182 (363)
                      .++.
T Consensus        81 ~~~~   84 (91)
T 2lxi_A           81 DPKP   84 (91)
T ss_dssp             CSCC
T ss_pred             CCCC
Confidence            8754

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=5.6e-20  Score=146.81  Aligned_cols=86  Identities=29%  Similarity=0.561  Sum_probs=80.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEE
Q psy16184         97 TMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD  176 (363)
Q Consensus        97 ~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~  176 (363)
                      ...+.++|||+|||+.+|+++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|++||..||+ .|.|+.|.|.
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~   91 (116)
T 2cqd_A           13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVN   91 (116)
T ss_dssp             CSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEE
Confidence            445678999999999999999999999999999999999999999999999999999999999999998 8999999999


Q ss_pred             eecccCC
Q psy16184        177 VERSRTV  183 (363)
Q Consensus       177 ~a~~~~~  183 (363)
                      ++.....
T Consensus        92 ~a~~~~~   98 (116)
T 2cqd_A           92 LAYLGAK   98 (116)
T ss_dssp             ESTTTCC
T ss_pred             EcccCCC
Confidence            9976543

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.83  E-value=3.1e-20  Score=144.71  Aligned_cols=89  Identities=22%  Similarity=0.421  Sum_probs=82.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEE
Q psy16184         97 TMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD  176 (363)
Q Consensus        97 ~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~  176 (363)
                      ...+.++|||+|||+.+|+++|.++|.+||.|..|.|+.++.++.++|||||+|.+.++|.+||..||+..|.|+.|.|.
T Consensus         8 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   87 (102)
T 2cqb_A            8 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN   87 (102)
T ss_dssp             SCCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            34567899999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             eecccCCCC
Q psy16184        177 VERSRTVKG  185 (363)
Q Consensus       177 ~a~~~~~~~  185 (363)
                      ++.+.....
T Consensus        88 ~a~~~~~~~   96 (102)
T 2cqb_A           88 LAKPMRIKE   96 (102)
T ss_dssp             ECCCCCCCC
T ss_pred             eCCCCCCCC
Confidence            998765543

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.83  E-value=6.1e-23  Score=181.77  Aligned_cols=150  Identities=20%  Similarity=0.350  Sum_probs=109.9

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccCCC--CCCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHH
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFEDP--KDTPPPTRVETREERLERRRRERAEQVAYKLEQE   84 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (363)
                      .+|..+|.++|+|..+ -|+.++.|++++|| +||.|.+.....  ...+....+.++.+.+                  
T Consensus        30 ~~L~~~F~~~G~I~~v-~i~~d~~tg~~~G~-afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~------------------   89 (213)
T 4f02_A           30 AMLYEKFSPAGPILSI-RVCRDMITRRSLGY-AYVNFQQPADAERALDTMNFDVIKGKPVRI------------------   89 (213)
T ss_dssp             HHHHHHHGGGSCEEEE-EEEECTTTCCEEEE-EEEEESSHHHHHHHHHHHTTCEETTEECEE------------------
T ss_pred             HHHHHHHHhhCCEEEE-EEecccCCCCcccc-ccceeCCHHHHHHHHHHhhhhhcCCccccc------------------
Confidence            3589999999999988 46778899999999 999986543100  0000011110000000                  


Q ss_pred             HhhcCCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhC
Q psy16184         85 IALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHAD  164 (363)
Q Consensus        85 ~~~~~p~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~  164 (363)
                         ...............+|||+|||+.+|+++|.++|..||.|..|.|+.+.  +.++|||||+|.+.++|.+||..||
T Consensus        90 ---~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~--~~~~g~~fV~f~~~~~a~~Ai~~ln  164 (213)
T 4f02_A           90 ---MWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMN  164 (213)
T ss_dssp             ---EECCCCTHHHHHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESSHHHHHHHHHHHT
T ss_pred             ---ccccccccccccccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC--CCCceEEEEEeCCHHHHHHHHHHhC
Confidence               00000000111235689999999999999999999999999999999874  4579999999999999999999999


Q ss_pred             CceeCCEEEEEEeeccc
Q psy16184        165 GKKIDGRRVLVDVERSR  181 (363)
Q Consensus       165 g~~i~g~~i~V~~a~~~  181 (363)
                      |..|+|+.|.|.++.++
T Consensus       165 g~~~~g~~i~V~~a~~~  181 (213)
T 4f02_A          165 GMLLNDRKVFVGRFKSR  181 (213)
T ss_dssp             TCEETTEECEEEECCCH
T ss_pred             CCEECCEEEEEEEcCCC
Confidence            99999999999999764

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.83  E-value=3.1e-20  Score=142.75  Aligned_cols=85  Identities=26%  Similarity=0.509  Sum_probs=80.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      .+.++|||+|||+.+|+++|.++|.+||.|..|.|+.++.++.++|||||+|.+.++|.+||..|||..|.|+.|.|.++
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            35789999999999999999999999999999999999989999999999999999999999999999999999999999


Q ss_pred             cccCC
Q psy16184        179 RSRTV  183 (363)
Q Consensus       179 ~~~~~  183 (363)
                      .++..
T Consensus        83 ~~~~~   87 (95)
T 2dnz_A           83 TERLD   87 (95)
T ss_dssp             SCCCC
T ss_pred             ccccC
Confidence            87554

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.83  E-value=4.6e-20  Score=142.07  Aligned_cols=85  Identities=21%  Similarity=0.382  Sum_probs=80.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEE-EEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKI-VMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v-~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      .+.++|||+|||+.+|+++|..+|.+||.|..| .|+.++.++.++|||||+|.+.++|.+||..|||..|.|+.|.|.+
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 9999988999999999999999999999999999999999999999


Q ss_pred             ecccCC
Q psy16184        178 ERSRTV  183 (363)
Q Consensus       178 a~~~~~  183 (363)
                      +.+...
T Consensus        83 a~~~~~   88 (96)
T 1x5t_A           83 AFKKDS   88 (96)
T ss_dssp             SCCCCC
T ss_pred             ecccCC
Confidence            987554

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.83  E-value=4.7e-20  Score=143.99  Aligned_cols=89  Identities=27%  Similarity=0.436  Sum_probs=82.9

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEE
Q psy16184         95 NATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVL  174 (363)
Q Consensus        95 ~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~  174 (363)
                      .....+.++|||+|||+.+|+++|.++|.+||.|..|.|+.++.++.++|||||+|.+.++|.+||..|||..|.|+.|.
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   88 (103)
T 2cq0_A            9 NRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILN   88 (103)
T ss_dssp             CCCCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEE
Confidence            34456688999999999999999999999999999999999988999999999999999999999999999999999999


Q ss_pred             EEeecccCC
Q psy16184        175 VDVERSRTV  183 (363)
Q Consensus       175 V~~a~~~~~  183 (363)
                      |.++.+...
T Consensus        89 v~~a~~~~~   97 (103)
T 2cq0_A           89 VEWAKPSTN   97 (103)
T ss_dssp             EEESSCCCC
T ss_pred             EEECCCCCC
Confidence            999987544

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.83  E-value=3.9e-22  Score=168.48  Aligned_cols=149  Identities=17%  Similarity=0.305  Sum_probs=110.3

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccCCC--CCCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHH
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFEDP--KDTPPPTRVETREERLERRRRERAEQVAYKLEQE   84 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (363)
                      .+|..+|.++|+|..+. +..++ +++++|| +||.|.+.....  ...+....+.+..+.+                  
T Consensus        15 ~~l~~~f~~~G~i~~v~-i~~~~-~~~~~g~-afV~f~~~~~a~~A~~~l~~~~~~g~~i~v------------------   73 (166)
T 3md3_A           15 DILKQYFQVGGPIANIK-IMIDK-NNKNVNY-AFVEYHQSHDANIALQTLNGKQIENNIVKI------------------   73 (166)
T ss_dssp             HHHHHHHGGGSCEEEEE-EECCC-C-CCEEE-EEEEESSHHHHHHHHHHHTTCEETTEECEE------------------
T ss_pred             HHHHHHHHhcCCeEEEE-EEECC-CCCCCCE-EEEEeCCHHHHHHHHHHcCCCccCCCeeEE------------------
Confidence            56999999999988763 44444 4678999 899885533100  0011111111110000                  


Q ss_pred             HhhcCCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhC
Q psy16184         85 IALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHAD  164 (363)
Q Consensus        85 ~~~~~p~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~  164 (363)
                         ............+.++|||+|||+.+|+++|.++|+.||.|..+.|+.++.+|.++|||||+|.+.++|.+|+..||
T Consensus        74 ---~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~  150 (166)
T 3md3_A           74 ---NWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQ  150 (166)
T ss_dssp             ---EECCCCCCCCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHT
T ss_pred             ---EEcCCCCCCCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhC
Confidence               00111222334567899999999999999999999999999999999998999999999999999999999999999


Q ss_pred             CceeCCEEEEEEeec
Q psy16184        165 GKKIDGRRVLVDVER  179 (363)
Q Consensus       165 g~~i~g~~i~V~~a~  179 (363)
                      |..|+|+.|.|.||+
T Consensus       151 g~~~~g~~i~v~~a~  165 (166)
T 3md3_A          151 GQDLNGRPLRINWAA  165 (166)
T ss_dssp             TCEETTEECEEEESC
T ss_pred             CCccCCcEEEEEecC
Confidence            999999999999985

>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=99.83  E-value=7.6e-20  Score=145.79  Aligned_cols=87  Identities=20%  Similarity=0.328  Sum_probs=81.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEE
Q psy16184         97 TMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD  176 (363)
Q Consensus        97 ~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~  176 (363)
                      ...+.++|||+|||+.+|+++|+++|..||.|..|.|+.++.++.++|||||+|.+.++|.+||..||+..|.|+.|.|.
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~  100 (115)
T 2cpz_A           21 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQ  100 (115)
T ss_dssp             CCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34467899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             eecccCC
Q psy16184        177 VERSRTV  183 (363)
Q Consensus       177 ~a~~~~~  183 (363)
                      ++.+...
T Consensus       101 ~a~~~~~  107 (115)
T 2cpz_A          101 LKRSKND  107 (115)
T ss_dssp             CCCCSCC
T ss_pred             EcCCCCc
Confidence            9987654

>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=99.83  E-value=4.4e-20  Score=139.47  Aligned_cols=83  Identities=19%  Similarity=0.456  Sum_probs=77.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      .+.++|||+|||+.+|+++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|..||..|||..|+|+.|.|.++
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   83 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA   83 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEec
Confidence            34679999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             ccc
Q psy16184        179 RSR  181 (363)
Q Consensus       179 ~~~  181 (363)
                      .++
T Consensus        84 ~~k   86 (87)
T 3bs9_A           84 TRK   86 (87)
T ss_dssp             C--
T ss_pred             CCC
Confidence            764

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.83  E-value=1.2e-20  Score=145.03  Aligned_cols=81  Identities=22%  Similarity=0.417  Sum_probs=75.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCC--ccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCc----eeCCEEE
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGP--IKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGK----KIDGRRV  173 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~--i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~----~i~g~~i  173 (363)
                      .-.||||+|||+.+|+++|.++|++||.  |..|.|+.|+.||.++|||||+|.+.++|.+||..|||.    .|+|+.|
T Consensus         8 ~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i   87 (95)
T 2lkz_A            8 HMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTI   87 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEE
T ss_pred             ccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEE
Confidence            3569999999999999999999999994  779999999999999999999999999999999999996    5999999


Q ss_pred             EEEeecc
Q psy16184        174 LVDVERS  180 (363)
Q Consensus       174 ~V~~a~~  180 (363)
                      .|+||+.
T Consensus        88 ~V~~Aks   94 (95)
T 2lkz_A           88 GVDFAKS   94 (95)
T ss_dssp             EEEECCC
T ss_pred             EEEEccC
Confidence            9999964

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.82  E-value=1.9e-19  Score=143.38  Aligned_cols=88  Identities=18%  Similarity=0.430  Sum_probs=82.2

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEE
Q psy16184         96 ATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLV  175 (363)
Q Consensus        96 ~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V  175 (363)
                      ....+.++|||+|||+.+|+++|+++|..||.|..|.|+.++.++.++|||||+|.+.++|++||..|||..|.|+.|.|
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            34456789999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             EeecccCC
Q psy16184        176 DVERSRTV  183 (363)
Q Consensus       176 ~~a~~~~~  183 (363)
                      .|+.+...
T Consensus        90 ~~a~~~~~   97 (115)
T 2dgo_A           90 NWATRKPP   97 (115)
T ss_dssp             EESSCCCC
T ss_pred             EEccCCCC
Confidence            99987544

>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=99.82  E-value=5.4e-20  Score=144.12  Aligned_cols=89  Identities=26%  Similarity=0.388  Sum_probs=82.7

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEE
Q psy16184         95 NATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVL  174 (363)
Q Consensus        95 ~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~  174 (363)
                      .....+.++|||+|||+.+|+++|.++|.+||.|..|.|+.++.++.++|||||+|.+.++|.+||..||+..|.|+.|.
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   88 (105)
T 1x5u_A            9 ISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIR   88 (105)
T ss_dssp             CCCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCE
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEE
Confidence            34455688999999999999999999999999999999999988999999999999999999999999999999999999


Q ss_pred             EEeecccCC
Q psy16184        175 VDVERSRTV  183 (363)
Q Consensus       175 V~~a~~~~~  183 (363)
                      |.++.+...
T Consensus        89 v~~a~~~~~   97 (105)
T 1x5u_A           89 VNKASAHNK   97 (105)
T ss_dssp             EEETTTTSC
T ss_pred             EEECCCCCc
Confidence            999987543

>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=99.82  E-value=6.9e-20  Score=141.93  Aligned_cols=85  Identities=27%  Similarity=0.529  Sum_probs=80.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      .+.++|||+|||+.+|+++|.++|.+||.|..|.|+.++.++.++|||||+|.+.++|..||..|||..|.|+.|.|.++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   85 (99)
T 1whw_A            6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            45789999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             cccCC
Q psy16184        179 RSRTV  183 (363)
Q Consensus       179 ~~~~~  183 (363)
                      .+...
T Consensus        86 ~~~~~   90 (99)
T 1whw_A           86 TIKKE   90 (99)
T ss_dssp             CCCST
T ss_pred             CCCcc
Confidence            87654

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.82  E-value=3.2e-20  Score=144.94  Aligned_cols=87  Identities=34%  Similarity=0.589  Sum_probs=81.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEE
Q psy16184         97 TMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD  176 (363)
Q Consensus        97 ~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~  176 (363)
                      ...+.++|||+|||+.+|+++|.++|.+||.|..|.|+.++.++.++|||||+|.+.++|++||..|||..|+|+.|.|.
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            34567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecccCC
Q psy16184        177 VERSRTV  183 (363)
Q Consensus       177 ~a~~~~~  183 (363)
                      ++.....
T Consensus        89 ~a~~~~~   95 (103)
T 2dnm_A           89 VARYGRR   95 (103)
T ss_dssp             ECSSCCS
T ss_pred             ECCcCCC
Confidence            9987543

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.82  E-value=5.9e-20  Score=142.38  Aligned_cols=86  Identities=26%  Similarity=0.501  Sum_probs=80.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184         98 MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      ..+.++|||+|||+.+|+++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|.+||. ||+..|+|+.|.|.+
T Consensus         7 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~~   85 (99)
T 2dgs_A            7 GSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVKR   85 (99)
T ss_dssp             CSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEEE
Confidence            3467899999999999999999999999999999999999999999999999999999999999 999999999999999


Q ss_pred             ecccCCC
Q psy16184        178 ERSRTVK  184 (363)
Q Consensus       178 a~~~~~~  184 (363)
                      +.++...
T Consensus        86 a~~~~~~   92 (99)
T 2dgs_A           86 AEPRDSK   92 (99)
T ss_dssp             CCCCCCC
T ss_pred             CCCCccc
Confidence            9876543

>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=99.82  E-value=7e-20  Score=154.09  Aligned_cols=86  Identities=26%  Similarity=0.449  Sum_probs=81.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184         98 MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      ..+.++|||+|||+.+|+++|.++|.+||.|..|.|+.++.++.++|||||+|.+.++|++||..||++.|.|+.|.|.|
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            34678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecccCC
Q psy16184        178 ERSRTV  183 (363)
Q Consensus       178 a~~~~~  183 (363)
                      +.+...
T Consensus       116 a~~~~~  121 (156)
T 1h2v_Z          116 DAGFKE  121 (156)
T ss_dssp             ESCCCT
T ss_pred             CCCCCC
Confidence            987543

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=7.6e-20  Score=142.50  Aligned_cols=87  Identities=30%  Similarity=0.581  Sum_probs=81.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEE
Q psy16184         97 TMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD  176 (363)
Q Consensus        97 ~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~  176 (363)
                      ...+.++|||+|||+.+|+++|.++|.+||.|..|.|+.++.++.++|||||+|.+.++|..||..||+..|.|+.|.|.
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            34567899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             eecccCC
Q psy16184        177 VERSRTV  183 (363)
Q Consensus       177 ~a~~~~~  183 (363)
                      ++.+...
T Consensus        88 ~a~~~~~   94 (102)
T 1x5s_A           88 QAGKSSD   94 (102)
T ss_dssp             EEECCCC
T ss_pred             ECCCCCC
Confidence            9987554

>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=99.82  E-value=2.6e-20  Score=150.92  Aligned_cols=86  Identities=27%  Similarity=0.434  Sum_probs=81.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184         98 MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      ..+.++|||+|||+.+|+++|.++|.+||.|..|.|+.++.++.++|||||+|.+.++|++||..|||..|+|+.|.|.+
T Consensus        19 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   98 (126)
T 3ex7_B           19 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW   98 (126)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEE
Confidence            34578999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ecccCC
Q psy16184        178 ERSRTV  183 (363)
Q Consensus       178 a~~~~~  183 (363)
                      +.+...
T Consensus        99 a~~~~~  104 (126)
T 3ex7_B           99 CFVRGP  104 (126)
T ss_dssp             SEESSS
T ss_pred             ecCCCC
Confidence            987654

>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=99.82  E-value=9.2e-20  Score=145.65  Aligned_cols=85  Identities=32%  Similarity=0.604  Sum_probs=79.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184         98 MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      ..+.++|||+|||+.+|+++|.++|++||.|..|.|+.+. ++.++|||||+|.+.++|++||..|||..|+|+.|.|.+
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~   82 (116)
T 2fy1_A            4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQ   82 (116)
T ss_dssp             TCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3457899999999999999999999999999999999997 999999999999999999999999999999999999999


Q ss_pred             ecccCC
Q psy16184        178 ERSRTV  183 (363)
Q Consensus       178 a~~~~~  183 (363)
                      +++...
T Consensus        83 a~~~~~   88 (116)
T 2fy1_A           83 AKKPSF   88 (116)
T ss_dssp             CCCSSC
T ss_pred             CCCCCC
Confidence            987543

>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=99.82  E-value=6.5e-20  Score=137.25  Aligned_cols=81  Identities=21%  Similarity=0.447  Sum_probs=77.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeecc
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS  180 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~  180 (363)
                      +++|||+|||+.+++++|.++|.+||.|..|.|+.++.++.++|||||+|.+.++|..|+..|||..|+|+.|.|.++.+
T Consensus         1 t~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~   80 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK   80 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCc
Confidence            36899999999999999999999999999999999989999999999999999999999999999999999999999976


Q ss_pred             c
Q psy16184        181 R  181 (363)
Q Consensus       181 ~  181 (363)
                      +
T Consensus        81 ~   81 (83)
T 3md1_A           81 L   81 (83)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.82  E-value=3.9e-22  Score=169.11  Aligned_cols=147  Identities=20%  Similarity=0.365  Sum_probs=111.5

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccCCC--CCCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHH
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFEDP--KDTPPPTRVETREERLERRRRERAEQVAYKLEQE   84 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (363)
                      .+|..+|.++|+|..+ .+..++.++.++|| +||.|.+.....  ...+....+.+..+.+                  
T Consensus        18 ~~l~~~f~~~G~i~~v-~i~~~~~~~~~~g~-afV~f~~~~~A~~a~~~l~~~~~~g~~l~v------------------   77 (168)
T 1b7f_A           18 RELYALFRAIGPINTC-RIMRDYKTGYSYGY-AFVDFTSEMDSQRAIKVLNGITVRNKRLKV------------------   77 (168)
T ss_dssp             HHHHHHHHTTSCEEEE-ECCEETTTTEECSE-EEEEESSHHHHHHHHHHHTTCEETTEECEE------------------
T ss_pred             HHHHHHHHhcCCeeEE-EEEEeCCCCccceE-EEEEECCHHHHHHHHHhcCCCEeCCcEEEE------------------
Confidence            4699999999999887 45667788999999 899885542100  0000111111100000                  


Q ss_pred             HhhcCCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhC
Q psy16184         85 IALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHAD  164 (363)
Q Consensus        85 ~~~~~p~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~  164 (363)
                        .+   ..+.....+.++|||+|||..+|+++|.++|++||.|..|.|+.+..++.++|||||+|.+.++|.+|+..||
T Consensus        78 --~~---~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~  152 (168)
T 1b7f_A           78 --SY---ARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALN  152 (168)
T ss_dssp             --EE---CCCCSSTTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHT
T ss_pred             --Ee---cCCCcccCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhc
Confidence              00   0122233457899999999999999999999999999999999998899999999999999999999999999


Q ss_pred             CceeCC--EEEEEEee
Q psy16184        165 GKKIDG--RRVLVDVE  178 (363)
Q Consensus       165 g~~i~g--~~i~V~~a  178 (363)
                      |..|.|  +.|.|.||
T Consensus       153 g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          153 NVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             TCCCTTCSSCCEEEEC
T ss_pred             CCEecCCCeEEEEEeC
Confidence            999988  99999986

>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=99.82  E-value=6e-20  Score=138.06  Aligned_cols=81  Identities=23%  Similarity=0.452  Sum_probs=77.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      .+.++|||+|||+.+++++|.++|.+||.|..|.|+.++.++.++|||||+|.+.++|..|+..|||..|+|+.|.|.++
T Consensus         5 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   84 (85)
T 3mdf_A            5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   84 (85)
T ss_dssp             CCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            45789999999999999999999999999999999999889999999999999999999999999999999999999997


Q ss_pred             c
Q psy16184        179 R  179 (363)
Q Consensus       179 ~  179 (363)
                      +
T Consensus        85 k   85 (85)
T 3mdf_A           85 K   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=9.9e-20  Score=139.85  Aligned_cols=85  Identities=34%  Similarity=0.556  Sum_probs=80.1

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEE
Q psy16184         96 ATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLV  175 (363)
Q Consensus        96 ~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V  175 (363)
                      ....+.++|||+|||+.+|+++|.++|.+||.|..|.|+.++.++.++|||||+|.+.++|.+||..|||..|+|+.|.|
T Consensus        10 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   89 (95)
T 2cqc_A           10 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   89 (95)
T ss_dssp             CSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            34456789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             Eeecc
Q psy16184        176 DVERS  180 (363)
Q Consensus       176 ~~a~~  180 (363)
                      .+++.
T Consensus        90 ~~a~~   94 (95)
T 2cqc_A           90 SGPSS   94 (95)
T ss_dssp             ECCSC
T ss_pred             EecCC
Confidence            99864

>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=99.82  E-value=8.8e-20  Score=140.61  Aligned_cols=83  Identities=23%  Similarity=0.492  Sum_probs=79.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      |+++|||+|||+.+++++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.++.
T Consensus         1 P~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   80 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSS   80 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcC
Confidence            46899999999999999999999999999999999998899999999999999999999999999999999999999997


Q ss_pred             ccC
Q psy16184        180 SRT  182 (363)
Q Consensus       180 ~~~  182 (363)
                      +..
T Consensus        81 ~~~   83 (96)
T 2x1f_A           81 NSD   83 (96)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            653

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.82  E-value=8.3e-20  Score=141.22  Aligned_cols=85  Identities=27%  Similarity=0.474  Sum_probs=79.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCC---CCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEE
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKV---TGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLV  175 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~---t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V  175 (363)
                      .+.++|||+|||+.+|+++|.++|++||.|..|.|+.++.   |+.++|||||+|.+.++|.+||..|||..|.|+.|.|
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            4578999999999999999999999999999999998876   6689999999999999999999999999999999999


Q ss_pred             EeecccCC
Q psy16184        176 DVERSRTV  183 (363)
Q Consensus       176 ~~a~~~~~  183 (363)
                      .++.+...
T Consensus        83 ~~a~~~~~   90 (98)
T 2cpf_A           83 RISERATK   90 (98)
T ss_dssp             ECSSCSSC
T ss_pred             EEccCCCC
Confidence            99987554

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.81  E-value=1.4e-19  Score=141.38  Aligned_cols=86  Identities=21%  Similarity=0.456  Sum_probs=79.7

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEE
Q psy16184         96 ATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLV  175 (363)
Q Consensus        96 ~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V  175 (363)
                      ....+.++|||+|||+.+|+++|.++|.+|| |..|.|+.++.++.++|||||+|.+.++|.+|| .||+..|.|+.|.|
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            3445678999999999999999999999997 999999999999999999999999999999999 79999999999999


Q ss_pred             EeecccCC
Q psy16184        176 DVERSRTV  183 (363)
Q Consensus       176 ~~a~~~~~  183 (363)
                      .++.+...
T Consensus        88 ~~a~~~~~   95 (103)
T 2dng_A           88 DIAEGRKQ   95 (103)
T ss_dssp             EECCCCCC
T ss_pred             EEecCCCC
Confidence            99987544

>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=99.81  E-value=1.6e-19  Score=142.77  Aligned_cols=87  Identities=26%  Similarity=0.466  Sum_probs=81.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhC------CceeCC
Q psy16184         97 TMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHAD------GKKIDG  170 (363)
Q Consensus        97 ~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~------g~~i~g  170 (363)
                      ...+.++|||+|||+.+|+++|.++|..||.|..|.|+.++.++.++|||||+|.+.++|.+||..||      +..|+|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g   90 (111)
T 1x4h_A           11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG   90 (111)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS
T ss_pred             cCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcC
Confidence            34567899999999999999999999999999999999999999999999999999999999999999      999999


Q ss_pred             EEEEEEeecccCC
Q psy16184        171 RRVLVDVERSRTV  183 (363)
Q Consensus       171 ~~i~V~~a~~~~~  183 (363)
                      +.|.|.++.++..
T Consensus        91 ~~l~v~~a~~~~~  103 (111)
T 1x4h_A           91 RQLKVDLAVTRDE  103 (111)
T ss_dssp             CEEEEECCCCCCC
T ss_pred             EEEEEEECCCCcc
Confidence            9999999987544

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.81  E-value=1.5e-19  Score=140.35  Aligned_cols=85  Identities=28%  Similarity=0.489  Sum_probs=79.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEE
Q psy16184         97 TMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD  176 (363)
Q Consensus        97 ~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~  176 (363)
                      ...+.++|||+|||+.+|+++|.++|.+||.|..|.|+.++ ++.++|||||+|.+.++|.+||..|||..|+|+.|.|.
T Consensus        13 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   91 (100)
T 2do4_A           13 TSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVA   91 (100)
T ss_dssp             SCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999997 99999999999999999999999999999999999999


Q ss_pred             eecccC
Q psy16184        177 VERSRT  182 (363)
Q Consensus       177 ~a~~~~  182 (363)
                      ++.+..
T Consensus        92 ~a~~~~   97 (100)
T 2do4_A           92 ISNSGP   97 (100)
T ss_dssp             ECCCCS
T ss_pred             ECCCCC
Confidence            998754

>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=99.81  E-value=1.5e-20  Score=143.17  Aligned_cols=82  Identities=17%  Similarity=0.339  Sum_probs=73.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhhC--CccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        102 KTLFIARVNYDTSESKLRREFEVYG--PIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       102 ~~l~V~nL~~~~t~~~L~~~F~~~G--~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      .+|||+|||+.+|+++|+++|++||  .|..|.|+.++.+|.++|||||+|.+.++|.+||..|||..|+|+.|.|.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            4799999999999999999999999  99999999999999999999999999999999999999999999999999998


Q ss_pred             ccCC
Q psy16184        180 SRTV  183 (363)
Q Consensus       180 ~~~~  183 (363)
                      +...
T Consensus        82 ~~~~   85 (90)
T 3p5t_L           82 KLEH   85 (90)
T ss_dssp             ----
T ss_pred             CCcc
Confidence            7544

>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=99.81  E-value=1.2e-19  Score=142.31  Aligned_cols=88  Identities=23%  Similarity=0.354  Sum_probs=81.4

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCcee---CCEE
Q psy16184         96 ATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKI---DGRR  172 (363)
Q Consensus        96 ~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i---~g~~  172 (363)
                      ....+.++|||+|||+.+|+++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|.+||..||+..|   .|+.
T Consensus         8 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~   87 (106)
T 2dgp_A            8 MKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRP   87 (106)
T ss_dssp             CCCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCce
Confidence            3445678999999999999999999999999999999999999999999999999999999999999999988   8999


Q ss_pred             EEEEeecccCC
Q psy16184        173 VLVDVERSRTV  183 (363)
Q Consensus       173 i~V~~a~~~~~  183 (363)
                      |.|.++.+...
T Consensus        88 l~v~~a~~~~~   98 (106)
T 2dgp_A           88 IQVKPADSESR   98 (106)
T ss_dssp             CEEEECCCCSC
T ss_pred             EEEEECCcccc
Confidence            99999987543

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.81  E-value=1.3e-19  Score=142.43  Aligned_cols=88  Identities=17%  Similarity=0.479  Sum_probs=81.7

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEecc-CCCCCcceEEEEEecCHHHHHHHHHHh-CCceeCCEEE
Q psy16184         96 ATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHN-KVTGKPRGYAFIEYEHERDMHSAYKHA-DGKKIDGRRV  173 (363)
Q Consensus        96 ~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d-~~t~~~~g~afV~f~~~~~a~~Ai~~l-~g~~i~g~~i  173 (363)
                      ....+.++|||+|||+.+|+++|+++|.+||.|..|.|+.+ +.++.++|||||+|.+.++|.+||..| |+..|.|+.|
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            34456789999999999999999999999999999999998 789999999999999999999999999 9999999999


Q ss_pred             EEEeecccCC
Q psy16184        174 LVDVERSRTV  183 (363)
Q Consensus       174 ~V~~a~~~~~  183 (363)
                      .|.++.+...
T Consensus        90 ~v~~a~~~~~   99 (107)
T 2cph_A           90 VLEWADSEVT   99 (107)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEeCCCCCC
Confidence            9999987544

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.81  E-value=1.3e-19  Score=138.94  Aligned_cols=83  Identities=20%  Similarity=0.411  Sum_probs=78.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEE
Q psy16184         97 TMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD  176 (363)
Q Consensus        97 ~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~  176 (363)
                      ...+.++|||+|||+.+++++|.++|.+||.|..|.|+.++.++.++|||||+|.+.++|..||..||+..|.|+.|.|.
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   91 (94)
T 2e5h_A           12 LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKAS   91 (94)
T ss_dssp             CCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            34567899999999999999999999999999999999999899999999999999999999999999999999999999


Q ss_pred             eec
Q psy16184        177 VER  179 (363)
Q Consensus       177 ~a~  179 (363)
                      ||+
T Consensus        92 ~ak   94 (94)
T 2e5h_A           92 IAI   94 (94)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            984

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.81  E-value=1.1e-19  Score=140.88  Aligned_cols=84  Identities=21%  Similarity=0.355  Sum_probs=79.2

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccE--------EEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCce
Q psy16184         96 ATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKK--------IVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKK  167 (363)
Q Consensus        96 ~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~--------v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~  167 (363)
                      ....+.++|||+|||+.+|+++|+++|++||.|..        |.|+.++.+|.++|||||+|.+.++|..||..|||..
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~   87 (99)
T 2la6_A            8 HSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKE   87 (99)
T ss_dssp             CSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCB
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCE
Confidence            34456789999999999999999999999999999        9999999999999999999999999999999999999


Q ss_pred             eCCEEEEEEeec
Q psy16184        168 IDGRRVLVDVER  179 (363)
Q Consensus       168 i~g~~i~V~~a~  179 (363)
                      |.|+.|.|.+|+
T Consensus        88 ~~g~~l~V~~A~   99 (99)
T 2la6_A           88 FSGNPIKVSFAT   99 (99)
T ss_dssp             SSSSBCEEEECC
T ss_pred             eCCcEEEEEecC
Confidence            999999999974

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.81  E-value=1.1e-19  Score=141.86  Aligned_cols=88  Identities=15%  Similarity=0.422  Sum_probs=81.0

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEE
Q psy16184         95 NATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVL  174 (363)
Q Consensus        95 ~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~  174 (363)
                      .....+.++|||+|||+.+|+++|.++|.+||.|..|.|+.+  ++.++|||||+|.+.++|.+||..||+..|.|+.|.
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   86 (103)
T 2d9p_A            9 RITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLY   86 (103)
T ss_dssp             CCCCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCE
T ss_pred             ccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEE
Confidence            344457889999999999999999999999999999999987  899999999999999999999999999999999999


Q ss_pred             EEeecccCCC
Q psy16184        175 VDVERSRTVK  184 (363)
Q Consensus       175 V~~a~~~~~~  184 (363)
                      |.++.+....
T Consensus        87 V~~a~~~~~~   96 (103)
T 2d9p_A           87 VALAQRKEER   96 (103)
T ss_dssp             EEECSSCCCC
T ss_pred             EEEecccccC
Confidence            9999876543

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=1.9e-19  Score=143.04  Aligned_cols=87  Identities=25%  Similarity=0.404  Sum_probs=81.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCcc--------EEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCcee
Q psy16184         97 TMDPFKTLFIARVNYDTSESKLRREFEVYGPIK--------KIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKI  168 (363)
Q Consensus        97 ~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~--------~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i  168 (363)
                      ...+.++|||+|||+.+|+++|+++|.+||.|.        .|.|+.++.++.++|||||+|.+.++|.+||..|||..|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   90 (113)
T 2cpe_A           11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   90 (113)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCcc
Confidence            345678999999999999999999999999999        699999989999999999999999999999999999999


Q ss_pred             CCEEEEEEeecccCC
Q psy16184        169 DGRRVLVDVERSRTV  183 (363)
Q Consensus       169 ~g~~i~V~~a~~~~~  183 (363)
                      .|+.|.|.++.+...
T Consensus        91 ~g~~l~V~~a~~~~~  105 (113)
T 2cpe_A           91 QGSKLKVSLARKKPP  105 (113)
T ss_dssp             TTEECEEECSSCCCC
T ss_pred             CCCEEEEEECCCCCC
Confidence            999999999987544

>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=99.81  E-value=1.5e-19  Score=141.40  Aligned_cols=85  Identities=20%  Similarity=0.391  Sum_probs=79.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEE
Q psy16184         97 TMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVT-GKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLV  175 (363)
Q Consensus        97 ~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t-~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V  175 (363)
                      ...+.++|||+|||+.+|+++|.++|..|| |..|.|+.++.+ +.++|||||+|.+.++|.+|| .||+..|.|+.|.|
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            345678999999999999999999999999 999999999887 999999999999999999999 89999999999999


Q ss_pred             EeecccCC
Q psy16184        176 DVERSRTV  183 (363)
Q Consensus       176 ~~a~~~~~  183 (363)
                      .++.++..
T Consensus        89 ~~a~~~~~   96 (104)
T 1wi8_A           89 DVADQAQD   96 (104)
T ss_dssp             EECCCCCC
T ss_pred             EEccCCCC
Confidence            99987544

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=9.9e-20  Score=142.88  Aligned_cols=85  Identities=27%  Similarity=0.446  Sum_probs=80.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184         98 MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      ..+.++|||+|||+.+|+++|.++|+.||.|..|.|+.++.++.++|||||+|.+.++|.+||..|||..|.|+.|.|.+
T Consensus        20 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   99 (106)
T 1p27_B           20 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW   99 (106)
T ss_dssp             BTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEe
Confidence            34568999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecccC
Q psy16184        178 ERSRT  182 (363)
Q Consensus       178 a~~~~  182 (363)
                      +.++.
T Consensus       100 a~~~~  104 (106)
T 1p27_B          100 CFVRG  104 (106)
T ss_dssp             SEESS
T ss_pred             ecCCC
Confidence            98754

>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=99.81  E-value=5.2e-19  Score=138.02  Aligned_cols=88  Identities=20%  Similarity=0.474  Sum_probs=79.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEE
Q psy16184         97 TMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD  176 (363)
Q Consensus        97 ~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~  176 (363)
                      ...+.++|||+|||+.+|+++|.++|.+||.|..|.|+.++.  .++|||||+|.+.++|.+||..||+..|+|+.|.|.
T Consensus        11 ~~~~~~~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           11 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN   88 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            345678999999999999999999999999999999998753  388999999999999999999999999999999999


Q ss_pred             eecccCCCCC
Q psy16184        177 VERSRTVKGW  186 (363)
Q Consensus       177 ~a~~~~~~~~  186 (363)
                      ++.+.....+
T Consensus        89 ~a~~~~~~~~   98 (103)
T 2cq3_A           89 NATARVMTNS   98 (103)
T ss_dssp             ECCSSCCCCC
T ss_pred             EcccCCCCCC
Confidence            9988765544

>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=99.81  E-value=7.2e-22  Score=167.00  Aligned_cols=147  Identities=19%  Similarity=0.353  Sum_probs=109.9

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccCCC--CCCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHH
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFEDP--KDTPPPTRVETREERLERRRRERAEQVAYKLEQE   84 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (363)
                      .+|..+|..+|+|..+ .+..++.++.++|| +||.|.+.....  ...+....+.+..+.+                  
T Consensus        17 ~~l~~~f~~~G~i~~v-~~~~~~~~~~~~g~-afV~f~~~~~A~~a~~~l~~~~~~g~~l~v------------------   76 (167)
T 1fxl_A           17 EEFRSLFGSIGEIESC-KLVRDKITGQSLGY-GFVNYIDPKDAEKAINTLNGLRLQTKTIKV------------------   76 (167)
T ss_dssp             HHHHHHHHTTSCEEEE-EEEECTTTCCEEEE-EEEEESSHHHHHHHHHHHTTCEETTEECEE------------------
T ss_pred             HHHHHHHHhcCCeEEE-EEEeCCCCCcceeE-EEEEECCHHHHHHHHHHcCCCccCCceEEE------------------
Confidence            4689999999999887 45667788999999 899885532100  0001111111100000                  


Q ss_pred             HhhcCCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhC
Q psy16184         85 IALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHAD  164 (363)
Q Consensus        85 ~~~~~p~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~  164 (363)
                        .+   ..+.....+.++|||+|||..+|+++|.++|.+||.|..+.|+.+..+|.++|||||+|.+.++|.+|+..||
T Consensus        77 --~~---~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~  151 (167)
T 1fxl_A           77 --SY---ARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLN  151 (167)
T ss_dssp             --EE---CCCCCGGGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHT
T ss_pred             --Ee---cCCCcccCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhc
Confidence              00   0111223356799999999999999999999999999999999998899999999999999999999999999


Q ss_pred             CceeCCEE--EEEEee
Q psy16184        165 GKKIDGRR--VLVDVE  178 (363)
Q Consensus       165 g~~i~g~~--i~V~~a  178 (363)
                      |..|.|+.  |.|.||
T Consensus       152 g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          152 GQKPSGATEPITVKFA  167 (167)
T ss_dssp             TCCCTTCSSCCEEEEC
T ss_pred             CCccCCCccceEEEeC
Confidence            99999965  888875

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=1.9e-19  Score=139.40  Aligned_cols=84  Identities=19%  Similarity=0.400  Sum_probs=79.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhhCCcc-EEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEE----
Q psy16184         98 MDPFKTLFIARVNYDTSESKLRREFEVYGPIK-KIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRR----  172 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~-~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~----  172 (363)
                      ..+.++|||+|||+.+|+++|.++|.+||.|. .|.|+.++.++.++|||||+|.+.++|++||..|||..|.|+.    
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            34678999999999999999999999999999 9999999999999999999999999999999999999999999    


Q ss_pred             EEEEeeccc
Q psy16184        173 VLVDVERSR  181 (363)
Q Consensus       173 i~V~~a~~~  181 (363)
                      |.|.|+.+.
T Consensus        86 l~v~~a~~~   94 (99)
T 2div_A           86 FKLNYATYS   94 (99)
T ss_dssp             CCEEETTCC
T ss_pred             EEEeecCCC
Confidence            999998764

>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=99.80  E-value=2.1e-19  Score=142.03  Aligned_cols=85  Identities=27%  Similarity=0.435  Sum_probs=80.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184         98 MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      ..+.++|||+|||+.+|+++|..+|.+||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.+
T Consensus        23 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  102 (110)
T 1oo0_B           23 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW  102 (110)
T ss_dssp             BTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            34578999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ecccC
Q psy16184        178 ERSRT  182 (363)
Q Consensus       178 a~~~~  182 (363)
                      +.+..
T Consensus       103 a~~~~  107 (110)
T 1oo0_B          103 CFVKG  107 (110)
T ss_dssp             SEESS
T ss_pred             cccCC
Confidence            98754

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.80  E-value=9.8e-19  Score=139.00  Aligned_cols=85  Identities=21%  Similarity=0.355  Sum_probs=79.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEE
Q psy16184         97 TMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD  176 (363)
Q Consensus        97 ~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~  176 (363)
                      ...+.++|||+|||+.+|+++|+++|.+||.|..|.|+.++ ++.++|||||+|.+.++|..||..||++.|+|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   89 (114)
T 2do0_A           11 AGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVK   89 (114)
T ss_dssp             CCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEE
Confidence            34567899999999999999999999999999999999986 69999999999999999999999999999999999999


Q ss_pred             eecccC
Q psy16184        177 VERSRT  182 (363)
Q Consensus       177 ~a~~~~  182 (363)
                      ++....
T Consensus        90 ~a~~~~   95 (114)
T 2do0_A           90 MDERAL   95 (114)
T ss_dssp             ECSCCC
T ss_pred             EcccCC
Confidence            997543

>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=99.80  E-value=3.4e-19  Score=139.52  Aligned_cols=86  Identities=19%  Similarity=0.364  Sum_probs=79.9

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC---EEE
Q psy16184         97 TMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDG---RRV  173 (363)
Q Consensus        97 ~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g---~~i  173 (363)
                      ...+.++|||+|||+.+|+++|.++|.+||.|..|.|+.++ ++.++|||||+|.+.++|.+||..|||..|.|   +.|
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            34567899999999999999999999999999999999987 89999999999999999999999999999998   999


Q ss_pred             EEEeecccCC
Q psy16184        174 LVDVERSRTV  183 (363)
Q Consensus       174 ~V~~a~~~~~  183 (363)
                      .|.++.+...
T Consensus        90 ~V~~a~~~~~   99 (105)
T 2dnh_A           90 VVKFADTDKE   99 (105)
T ss_dssp             EEEESCSSCC
T ss_pred             EEEECccCcc
Confidence            9999987554

>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=99.80  E-value=1.7e-19  Score=142.21  Aligned_cols=85  Identities=25%  Similarity=0.484  Sum_probs=80.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEE
Q psy16184         97 TMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD  176 (363)
Q Consensus        97 ~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~  176 (363)
                      ...+.++|||+|||+.+|+++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|.|+.|.|.
T Consensus        22 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~  101 (108)
T 2jrs_A           22 GSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVG  101 (108)
T ss_dssp             SCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeccc
Q psy16184        177 VERSR  181 (363)
Q Consensus       177 ~a~~~  181 (363)
                      ++.++
T Consensus       102 ~a~~k  106 (108)
T 2jrs_A          102 HVTER  106 (108)
T ss_dssp             CSCSS
T ss_pred             EcccC
Confidence            99765

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.80  E-value=3.3e-20  Score=144.26  Aligned_cols=82  Identities=18%  Similarity=0.301  Sum_probs=78.3

Q ss_pred             CCCeEEEcCCCC------CCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC-EE
Q psy16184        100 PFKTLFIARVNY------DTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDG-RR  172 (363)
Q Consensus       100 ~~~~l~V~nL~~------~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g-~~  172 (363)
                      ..++|||+|||+      .+++++|.++|++||.|..|.|+.++.||.++|||||+|.+.++|.+||..|||..|.| +.
T Consensus         5 ~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~   84 (100)
T 3ns6_A            5 SDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHR   84 (100)
T ss_dssp             GGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCB
T ss_pred             cCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeE
Confidence            367999999999      99999999999999999999999999999999999999999999999999999999999 99


Q ss_pred             EEEEeeccc
Q psy16184        173 VLVDVERSR  181 (363)
Q Consensus       173 i~V~~a~~~  181 (363)
                      |.|.++.+.
T Consensus        85 l~V~~a~~~   93 (100)
T 3ns6_A           85 LFLYTMKDV   93 (100)
T ss_dssp             CEEEESHHH
T ss_pred             EEEEECchh
Confidence            999999753

>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=99.80  E-value=1.2e-18  Score=135.93  Aligned_cols=85  Identities=25%  Similarity=0.426  Sum_probs=77.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEE
Q psy16184         97 TMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD  176 (363)
Q Consensus        97 ~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~  176 (363)
                      ...+.++|||+|||+.+|+++|.++|.+||.|..|.|+.++.+  ++|||||+|.+.++|.+||..||+..|.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2cqi_A           11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVN   88 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCC--CCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEE
Confidence            4456789999999999999999999999999999999988543  68999999999999999999999999999999999


Q ss_pred             eecccCC
Q psy16184        177 VERSRTV  183 (363)
Q Consensus       177 ~a~~~~~  183 (363)
                      ++.+...
T Consensus        89 ~a~~~~~   95 (103)
T 2cqi_A           89 WATTPSS   95 (103)
T ss_dssp             ECCCTTC
T ss_pred             ECCCCcc
Confidence            9987543

>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=99.80  E-value=4.4e-19  Score=139.39  Aligned_cols=81  Identities=21%  Similarity=0.463  Sum_probs=77.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184         98 MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      ..+.++|||+|||+.+|+++|.++|.+||.|..|.|+.++ ++.++|||||+|.+.++|++||..|||..|.|+.|.|.+
T Consensus        26 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~  104 (107)
T 3ulh_A           26 VETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL  104 (107)
T ss_dssp             CCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            4567899999999999999999999999999999999997 999999999999999999999999999999999999999


Q ss_pred             ec
Q psy16184        178 ER  179 (363)
Q Consensus       178 a~  179 (363)
                      +.
T Consensus       105 a~  106 (107)
T 3ulh_A          105 VT  106 (107)
T ss_dssp             EC
T ss_pred             eC
Confidence            85

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A

Probab=99.80  E-value=3.9e-19  Score=134.28  Aligned_cols=80  Identities=20%  Similarity=0.456  Sum_probs=75.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184         98 MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      ..+.++|||+|||+.+|+++|.++|++||.|..|.|+.++.++.++|||||+|.+.++|.+||. +++..|+|+.|.|++
T Consensus         8 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~~   86 (87)
T 3s7r_A            8 EEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPKK   86 (87)
T ss_dssp             CSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEEe
Confidence            3467899999999999999999999999999999999999999999999999999999999997 588999999999997


Q ss_pred             e
Q psy16184        178 E  178 (363)
Q Consensus       178 a  178 (363)
                      |
T Consensus        87 A   87 (87)
T 3s7r_A           87 A   87 (87)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.80  E-value=2.6e-19  Score=139.95  Aligned_cols=84  Identities=21%  Similarity=0.398  Sum_probs=79.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHh-hCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCce-eCCEEEEEE
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEV-YGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKK-IDGRRVLVD  176 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~-~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~-i~g~~i~V~  176 (363)
                      .+.++|||+|||+.+|+++|.++|.+ ||.|..|.|+.++ ++.++|||||+|.+.++|.+||..||+.. |+|+.|.|.
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~   85 (104)
T 2dhg_A            7 GPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLS   85 (104)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEE
Confidence            46789999999999999999999999 9999999999998 99999999999999999999999999999 999999999


Q ss_pred             eecccCC
Q psy16184        177 VERSRTV  183 (363)
Q Consensus       177 ~a~~~~~  183 (363)
                      ++.+...
T Consensus        86 ~a~~~~~   92 (104)
T 2dhg_A           86 VAIPKAS   92 (104)
T ss_dssp             BCCCCCS
T ss_pred             EccCCCc
Confidence            9976543

>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=99.80  E-value=2.7e-19  Score=135.35  Aligned_cols=82  Identities=27%  Similarity=0.511  Sum_probs=77.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCC-cceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGK-PRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~-~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      ..++|||+|||+.+|+++|.++|.+||.|..|.|+.+..++. ++|||||+|.+.++|.+|+..|||..|+|+.|.|.++
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            367999999999999999999999999999999999877766 8999999999999999999999999999999999999


Q ss_pred             ccc
Q psy16184        179 RSR  181 (363)
Q Consensus       179 ~~~  181 (363)
                      .+.
T Consensus        83 ~~~   85 (88)
T 4a8x_A           83 LAP   85 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            764

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=3e-19  Score=139.90  Aligned_cols=87  Identities=22%  Similarity=0.481  Sum_probs=81.1

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEE
Q psy16184         96 ATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLV  175 (363)
Q Consensus        96 ~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V  175 (363)
                      ....+.++|||+|||+.+|+++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|.+||.. |++.|+|+.|.|
T Consensus        11 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V   89 (105)
T 2dh8_A           11 SGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDP   89 (105)
T ss_dssp             CCSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEE
Confidence            3455678999999999999999999999999999999999999999999999999999999999998 999999999999


Q ss_pred             EeecccCC
Q psy16184        176 DVERSRTV  183 (363)
Q Consensus       176 ~~a~~~~~  183 (363)
                      .++.++..
T Consensus        90 ~~a~~~~~   97 (105)
T 2dh8_A           90 KPCTPRGM   97 (105)
T ss_dssp             CCSCCSSC
T ss_pred             EEccCCCC
Confidence            99987554

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A

Probab=99.79  E-value=3.3e-19  Score=142.15  Aligned_cols=80  Identities=23%  Similarity=0.460  Sum_probs=74.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeecc
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS  180 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~  180 (363)
                      ..+|||+|||+.+|+++|.++|++||.|..|.|+.+.  +.++|||||+|.+.++|+.||..|||..|+|+.|.|.++.+
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~   82 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   82 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSC
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            5689999999999999999999999999999999885  45789999999999999999999999999999999999876


Q ss_pred             cC
Q psy16184        181 RT  182 (363)
Q Consensus       181 ~~  182 (363)
                      ..
T Consensus        83 ~~   84 (115)
T 4f25_A           83 RK   84 (115)
T ss_dssp             CC
T ss_pred             cc
Confidence            43

>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=99.79  E-value=2.9e-19  Score=141.53  Aligned_cols=89  Identities=16%  Similarity=0.322  Sum_probs=80.1

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHH---HHHHhhCCccEEEEeccCCCC---CcceEEEEEecCHHHHHHHHHHhCCcee
Q psy16184         95 NATMDPFKTLFIARVNYDTSESKLR---REFEVYGPIKKIVMVHNKVTG---KPRGYAFIEYEHERDMHSAYKHADGKKI  168 (363)
Q Consensus        95 ~~~~~~~~~l~V~nL~~~~t~~~L~---~~F~~~G~i~~v~i~~d~~t~---~~~g~afV~f~~~~~a~~Ai~~l~g~~i  168 (363)
                      .....+.++|||+|||+.+++++|.   ++|.+||.|..|.|+.++.++   .++|||||+|.+.++|++||..|||..|
T Consensus         9 ~~r~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~   88 (111)
T 2cpi_A            9 SVRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVV   88 (111)
T ss_dssp             CCCCCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEE
T ss_pred             cccccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEE
Confidence            3445567899999999999999999   999999999999999887654   5569999999999999999999999999


Q ss_pred             CCEEEEEEeecccCC
Q psy16184        169 DGRRVLVDVERSRTV  183 (363)
Q Consensus       169 ~g~~i~V~~a~~~~~  183 (363)
                      +|+.|.|.++.++..
T Consensus        89 ~gr~l~V~~a~~k~~  103 (111)
T 2cpi_A           89 DGRTLKASLGTTKYC  103 (111)
T ss_dssp             TTEEEEEESCCCCSC
T ss_pred             CCEEEEEEecccccc
Confidence            999999999987653

>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=99.79  E-value=3.2e-19  Score=137.91  Aligned_cols=85  Identities=16%  Similarity=0.222  Sum_probs=79.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEE
Q psy16184         97 TMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD  176 (363)
Q Consensus        97 ~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~  176 (363)
                      .....++|||+|||+.+|+++|+++|.+||.|..+.++.++.++.++|||||+|.+.++|++||..|||..|.|+.|.|+
T Consensus        11 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~   90 (98)
T 2cqp_A           11 GKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLV   90 (98)
T ss_dssp             CCCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            34456899999999999999999999999999988888888899999999999999999999999999999999999999


Q ss_pred             eeccc
Q psy16184        177 VERSR  181 (363)
Q Consensus       177 ~a~~~  181 (363)
                      ++...
T Consensus        91 ~a~~~   95 (98)
T 2cqp_A           91 LGSGP   95 (98)
T ss_dssp             ESSCS
T ss_pred             EcCCC
Confidence            98653

>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=99.79  E-value=1.7e-18  Score=135.16  Aligned_cols=78  Identities=21%  Similarity=0.492  Sum_probs=72.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      .+.++|||+|||+.+|+++|+++|.+||.|..|.|+        +|||||+|.+.++|.+||..||+..|.|+.|.|.++
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   80 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFA   80 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEc
Confidence            457899999999999999999999999999999986        369999999999999999999999999999999999


Q ss_pred             cccCCC
Q psy16184        179 RSRTVK  184 (363)
Q Consensus       179 ~~~~~~  184 (363)
                      .+....
T Consensus        81 ~~~~~~   86 (103)
T 2dgu_A           81 KPPDQK   86 (103)
T ss_dssp             CCCCCC
T ss_pred             CCCccc
Confidence            876543

>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=99.79  E-value=1.3e-18  Score=137.31  Aligned_cols=84  Identities=25%  Similarity=0.392  Sum_probs=76.2

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEE
Q psy16184         96 ATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLV  175 (363)
Q Consensus        96 ~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V  175 (363)
                      ....+.++|||+|||+.+|+++|+++|.+||.|..|.|+.   ++.++|||||+|.+.++|++||..||+..|+|+.|.|
T Consensus        17 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   93 (109)
T 1x4a_A           17 PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN---RRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRV   93 (109)
T ss_dssp             CCCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECC---SSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEE---CCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEE
Confidence            3445678999999999999999999999999999999965   4568999999999999999999999999999999999


Q ss_pred             EeecccC
Q psy16184        176 DVERSRT  182 (363)
Q Consensus       176 ~~a~~~~  182 (363)
                      .++++..
T Consensus        94 ~~a~~~~  100 (109)
T 1x4a_A           94 EFPRSGR  100 (109)
T ss_dssp             ECCCCCC
T ss_pred             EEcccCC
Confidence            9997754

>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=99.79  E-value=8.4e-19  Score=135.14  Aligned_cols=81  Identities=17%  Similarity=0.255  Sum_probs=75.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHH----HHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEE
Q psy16184        100 PFKTLFIARVNYDTSESKLR----REFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLV  175 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~----~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V  175 (363)
                      ..++|||+|||+.+++++|+    ++|.+||.|..|.|+.++.+   +|||||+|.+.++|.+||..|||..|+|+.|.|
T Consensus         8 ~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V   84 (96)
T 2dgx_A            8 NGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILV   84 (96)
T ss_dssp             SCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            46799999999999999999    99999999999999988755   789999999999999999999999999999999


Q ss_pred             EeecccCC
Q psy16184        176 DVERSRTV  183 (363)
Q Consensus       176 ~~a~~~~~  183 (363)
                      .++.+...
T Consensus        85 ~~a~~~~~   92 (96)
T 2dgx_A           85 SLATGASG   92 (96)
T ss_dssp             EECCCSSC
T ss_pred             EEcCCCCC
Confidence            99977543

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.79  E-value=3.6e-19  Score=149.63  Aligned_cols=82  Identities=18%  Similarity=0.372  Sum_probs=77.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhC--CccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYG--PIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G--~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      ..++|||+|||+++|+++|.++|..||  .|..|.|+.|+.+|.++|||||+|.+.++|.+||..|||..|+|+.|.|.+
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~  133 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRP  133 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEE
Confidence            357999999999999999999999999  999999999999999999999999999999999999999999999999999


Q ss_pred             eccc
Q psy16184        178 ERSR  181 (363)
Q Consensus       178 a~~~  181 (363)
                      +.+.
T Consensus       134 a~~~  137 (156)
T 3n9u_C          134 ATRQ  137 (156)
T ss_dssp             CCHH
T ss_pred             cCCC
Confidence            9764

>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=99.79  E-value=4.8e-19  Score=134.30  Aligned_cols=80  Identities=21%  Similarity=0.592  Sum_probs=76.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeecc
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS  180 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~  180 (363)
                      .++|||+|||+.+|+++|.++|.+||.|..|.|+.++.++.++|||||+|.+.++|.+|+ .|||..|.|+.|.|.++++
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~~   84 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKRT   84 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEccC
Confidence            469999999999999999999999999999999999889999999999999999999999 8999999999999999876


Q ss_pred             c
Q psy16184        181 R  181 (363)
Q Consensus       181 ~  181 (363)
                      .
T Consensus        85 ~   85 (89)
T 3ucg_A           85 N   85 (89)
T ss_dssp             T
T ss_pred             C
Confidence            3

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.79  E-value=1.6e-18  Score=136.50  Aligned_cols=78  Identities=17%  Similarity=0.239  Sum_probs=72.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC-----EEE
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDG-----RRV  173 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g-----~~i  173 (363)
                      ...++|||+|||+.+|+++|+++|.+||.|..|.|+.+       |||||+|.+.++|++||..||+..|.|     +.|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i   85 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI   85 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEE
Confidence            35789999999999999999999999999999999875       899999999999999999999999999     999


Q ss_pred             EEEeecccCC
Q psy16184        174 LVDVERSRTV  183 (363)
Q Consensus       174 ~V~~a~~~~~  183 (363)
                      .|+++.++..
T Consensus        86 ~V~~a~~~~~   95 (108)
T 1x4c_A           86 RVKVDGPRSP   95 (108)
T ss_dssp             EEEESSCCSC
T ss_pred             EEEeCCCCCC
Confidence            9999987543

>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=99.79  E-value=1.6e-18  Score=135.26  Aligned_cols=86  Identities=17%  Similarity=0.380  Sum_probs=79.1

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEE
Q psy16184         96 ATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLV  175 (363)
Q Consensus        96 ~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V  175 (363)
                      ....+.++|||+|||+.+|+++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|.+||.  +++.|+|+.|.|
T Consensus        10 ~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v   87 (103)
T 2cqg_A           10 RAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDC   87 (103)
T ss_dssp             CCCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEE
T ss_pred             CccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEE
Confidence            344567899999999999999999999999999999999999899999999999999999999998  478999999999


Q ss_pred             EeecccCC
Q psy16184        176 DVERSRTV  183 (363)
Q Consensus       176 ~~a~~~~~  183 (363)
                      .++.++..
T Consensus        88 ~~a~~~~~   95 (103)
T 2cqg_A           88 KLPNSKQS   95 (103)
T ss_dssp             ECCCTTCC
T ss_pred             EecCCCCc
Confidence            99987544

>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=99.79  E-value=9.7e-21  Score=161.17  Aligned_cols=147  Identities=18%  Similarity=0.323  Sum_probs=107.9

Q ss_pred             hhhhhcCCCCCCCCCCC-----CCCCCCCCCCCCCCccccccccccC-CCCCCCCCCCcccHHHHHHHHHHHHHHHHHHH
Q psy16184          7 PNLLALFAPRDPVPYLP-----PVEKLPHEKKTHGYSGIAAFLNEFE-DPKDTPPPTRVETREERLERRRRERAEQVAYK   80 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~-----p~~~~p~t~~s~g~~g~v~f~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (363)
                      .+|..+|.+++.+.-+.     ++. ...++.++|| +||.|.+... ..+..+....+.++.+.+..            
T Consensus        19 ~~l~~~F~~~g~~~g~~~~~~~~v~-~~~~~~~~g~-afV~f~~~~~A~~A~~~~~~~~~g~~i~v~~------------   84 (172)
T 2g4b_A           19 EAMMDFFNAQMRLGGLTQAPGNPVL-AVQINQDKNF-AFLEFRSVDETTQAMAFDGIIFQGQSLKIRR------------   84 (172)
T ss_dssp             HHHHHHHHHHHHHTTCCSSSSCSEE-EEEEETTTTE-EEEEESSHHHHHHHGGGTTCEETTEECEEEC------------
T ss_pred             HHHHHHHHHHhhhcccccCCCCcee-eeEecCCCCE-EEEEeCCHHHHHHHHHhCCcEecCceeeecC------------
Confidence            45888898884322210     111 2234678999 9999976543 11113344444443222211            


Q ss_pred             HHHHHhhcCCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHH
Q psy16184         81 LEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAY  160 (363)
Q Consensus        81 ~~~~~~~~~p~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai  160 (363)
                               +  .........++|||+|||+.+|+++|.++|.+||.|..|.|+.++.+|.++|||||+|.+.++|.+|+
T Consensus        85 ---------~--~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~  153 (172)
T 2g4b_A           85 ---------P--HDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI  153 (172)
T ss_dssp             ---------C--SSCCCCTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHH
T ss_pred             ---------C--cccCCCCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHH
Confidence                     1  11112234689999999999999999999999999999999999889999999999999999999999


Q ss_pred             HHhCCceeCCEEEEEEee
Q psy16184        161 KHADGKKIDGRRVLVDVE  178 (363)
Q Consensus       161 ~~l~g~~i~g~~i~V~~a  178 (363)
                      ..|||..|+|+.|.|.+|
T Consensus       154 ~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A          154 AGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             HHHTTCEETTEECEEEEC
T ss_pred             HHcCCCEECCeEEEEEeC
Confidence            999999999999999997

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=2.7e-19  Score=142.83  Aligned_cols=82  Identities=26%  Similarity=0.542  Sum_probs=77.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeecc
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS  180 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~  180 (363)
                      .++|||+|||+.+|+++|+++|..||.|..|.|+.++.++.++|||||+|.+.++|.+||.. |+..|+|+.|.|.++.+
T Consensus        27 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a~~  105 (116)
T 1x4b_A           27 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAVA  105 (116)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCSS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECCC
Confidence            57999999999999999999999999999999999999999999999999999999999997 99999999999999987


Q ss_pred             cCC
Q psy16184        181 RTV  183 (363)
Q Consensus       181 ~~~  183 (363)
                      +..
T Consensus       106 ~~~  108 (116)
T 1x4b_A          106 REE  108 (116)
T ss_dssp             CCC
T ss_pred             Ccc
Confidence            543

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.79  E-value=3.4e-19  Score=142.62  Aligned_cols=82  Identities=17%  Similarity=0.331  Sum_probs=77.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184         98 MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      ..+.++|||+|||+.+|+++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|..||..|||..|+|+.|.|+|
T Consensus        37 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~  116 (118)
T 2khc_A           37 GPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQL  116 (118)
T ss_dssp             CCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            34578999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ec
Q psy16184        178 ER  179 (363)
Q Consensus       178 a~  179 (363)
                      ++
T Consensus       117 ak  118 (118)
T 2khc_A          117 KK  118 (118)
T ss_dssp             C-
T ss_pred             cC
Confidence            74

>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=99.79  E-value=5e-19  Score=135.96  Aligned_cols=82  Identities=23%  Similarity=0.454  Sum_probs=76.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184         98 MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      ..+.++|||+|||+.+++++|.++|.+||.|..|.|+.++. +.++|||||+|.+.++|.+||..||+..|.|+.|.|.+
T Consensus        13 ~~~~~~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           13 EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSG   91 (95)
T ss_dssp             TTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEE
Confidence            34578999999999999999999999999999999999874 89999999999999999999999999999999999999


Q ss_pred             ecc
Q psy16184        178 ERS  180 (363)
Q Consensus       178 a~~  180 (363)
                      ++.
T Consensus        92 a~~   94 (95)
T 2ywk_A           92 PSS   94 (95)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            853

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A

Probab=99.79  E-value=2.6e-19  Score=145.74  Aligned_cols=87  Identities=33%  Similarity=0.573  Sum_probs=81.6

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEE
Q psy16184         96 ATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLV  175 (363)
Q Consensus        96 ~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V  175 (363)
                      ....+.++|||+|||+.+|+++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|++||..|||..|+|+.|.|
T Consensus        41 ~~~~~~~~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           41 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV  120 (129)
T ss_dssp             SCCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            34557889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecccC
Q psy16184        176 DVERSRT  182 (363)
Q Consensus       176 ~~a~~~~  182 (363)
                      .|+.++.
T Consensus       121 ~~a~~~~  127 (129)
T 2kxn_B          121 DFSITKR  127 (129)
T ss_dssp             SCCSSSS
T ss_pred             EEecCCC
Confidence            9997643

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=6e-19  Score=137.34  Aligned_cols=81  Identities=16%  Similarity=0.312  Sum_probs=73.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhC--CceeCCEEEEE
Q psy16184         98 MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHAD--GKKIDGRRVLV  175 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~--g~~i~g~~i~V  175 (363)
                      ..+.++|||+|||+.+|+++|+++|++||.|..|.|+.+      +|||||+|.+.++|..||..|+  +..|.|+.|.|
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V   86 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI   86 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCB
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            446789999999999999999999999999999999875      6999999999999999999886  47899999999


Q ss_pred             EeecccCCC
Q psy16184        176 DVERSRTVK  184 (363)
Q Consensus       176 ~~a~~~~~~  184 (363)
                      .|++.+...
T Consensus        87 ~~A~~~~~~   95 (105)
T 1sjq_A           87 QFSNHKELK   95 (105)
T ss_dssp             CCCSSSSCC
T ss_pred             EEcCCCCCC
Confidence            999876543

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A

Probab=99.78  E-value=7.3e-19  Score=149.28  Aligned_cols=86  Identities=27%  Similarity=0.423  Sum_probs=80.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184         98 MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      ..+.++|||+|||+.+|+++|..+|.+||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|.|+.|.|.|
T Consensus        69 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  148 (165)
T 1rk8_A           69 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW  148 (165)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            34577999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecccCC
Q psy16184        178 ERSRTV  183 (363)
Q Consensus       178 a~~~~~  183 (363)
                      +.+...
T Consensus       149 a~~~~~  154 (165)
T 1rk8_A          149 CFVKGP  154 (165)
T ss_dssp             SEECC-
T ss_pred             ecCCCC
Confidence            987543

>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=99.78  E-value=1.9e-19  Score=143.29  Aligned_cols=81  Identities=15%  Similarity=0.371  Sum_probs=77.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeecc
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS  180 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~  180 (363)
                      .++|||+|||+.+|+++|.++|..||.|..|.|+.++.++.++|||||+|.+.++|.+|| .|||+.|+|+.|.|.++.+
T Consensus        25 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~  103 (114)
T 2cq4_A           25 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQA  103 (114)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEecCC
Confidence            569999999999999999999999999999999999999999999999999999999999 8999999999999999976


Q ss_pred             cC
Q psy16184        181 RT  182 (363)
Q Consensus       181 ~~  182 (363)
                      ..
T Consensus       104 ~~  105 (114)
T 2cq4_A          104 EK  105 (114)
T ss_dssp             HH
T ss_pred             Cc
Confidence            43

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.78  E-value=2.4e-19  Score=146.31  Aligned_cols=86  Identities=16%  Similarity=0.320  Sum_probs=79.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccE--EEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCc----eeCC
Q psy16184         97 TMDPFKTLFIARVNYDTSESKLRREFEVYGPIKK--IVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGK----KIDG  170 (363)
Q Consensus        97 ~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~--v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~----~i~g  170 (363)
                      ...+.++|||+|||+.+|+++|.++|.+||.|..  |.|+.++.||.++|||||+|.+. +|.+||..|||.    .|+|
T Consensus        19 ~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~g   97 (131)
T 2m2b_A           19 SENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDG   97 (131)
T ss_dssp             CSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGG
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCC
Confidence            3456789999999999999999999999999966  99999999999999999999999 999999999999    9999


Q ss_pred             EEEEEEeecccCC
Q psy16184        171 RRVLVDVERSRTV  183 (363)
Q Consensus       171 ~~i~V~~a~~~~~  183 (363)
                      +.|.|.++.+...
T Consensus        98 r~l~V~~a~~~~~  110 (131)
T 2m2b_A           98 KTINVEFAKGSKR  110 (131)
T ss_dssp             CCCCCEECCCSCC
T ss_pred             EEEEEEECCCCCC
Confidence            9999999987543

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=2.4e-19  Score=140.07  Aligned_cols=80  Identities=14%  Similarity=0.214  Sum_probs=75.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      .+.++|||+|||+.+|+++|.++|++||.|..|.|+.++. |.++|||||+|.+.++|.+||. ||++.|+|+.|.|.++
T Consensus         9 ~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~   86 (103)
T 1s79_A            9 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFK   86 (103)
T ss_dssp             SGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEc
Confidence            3467999999999999999999999999999999999976 9999999999999999999999 8999999999999997


Q ss_pred             cc
Q psy16184        179 RS  180 (363)
Q Consensus       179 ~~  180 (363)
                      ..
T Consensus        87 ~~   88 (103)
T 1s79_A           87 DD   88 (103)
T ss_dssp             HH
T ss_pred             hH
Confidence            64

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.78  E-value=7.7e-19  Score=138.66  Aligned_cols=85  Identities=18%  Similarity=0.420  Sum_probs=76.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEE
Q psy16184         97 TMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD  176 (363)
Q Consensus        97 ~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~  176 (363)
                      ...+.++|||+|||+.+|+++|..+|..||.|..|.|+.++.+|.++|||||+|.+.++|.+||..+ +..|+|+.|.|.
T Consensus        21 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~   99 (109)
T 2rs2_A           21 MGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPK   99 (109)
T ss_dssp             -----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEE
Confidence            3446789999999999999999999999999999999999999999999999999999999999975 599999999999


Q ss_pred             eecccC
Q psy16184        177 VERSRT  182 (363)
Q Consensus       177 ~a~~~~  182 (363)
                      ++.++.
T Consensus       100 ~a~~~~  105 (109)
T 2rs2_A          100 VAFPRR  105 (109)
T ss_dssp             ECCCCC
T ss_pred             EccCCC
Confidence            997654

>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=99.78  E-value=3.2e-19  Score=137.02  Aligned_cols=80  Identities=18%  Similarity=0.248  Sum_probs=76.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      +.++|||+|||+.+|+++|+++|.+||.|..+.|+.++.++.++|||||+|.+.++|++||..||+..|.|+.|.|+++.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a~   93 (95)
T 2ek1_A           14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPS   93 (95)
T ss_dssp             -CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEecc
Confidence            46899999999999999999999999999999999988899999999999999999999999999999999999999875

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.78  E-value=7.2e-19  Score=142.40  Aligned_cols=82  Identities=17%  Similarity=0.318  Sum_probs=74.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHH----HHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEE
Q psy16184         98 MDPFKTLFIARVNYDTSESKLR----REFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRV  173 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~----~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i  173 (363)
                      ..+.++|||+|||+.+++++|+    ++|++||.|..|.|..   ++.++|||||+|.+.++|..||..|||..|.|+.|
T Consensus        26 ~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l  102 (127)
T 2a3j_A           26 TEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPL  102 (127)
T ss_dssp             CSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEE
Confidence            4567899999999999999875    7999999999988753   68899999999999999999999999999999999


Q ss_pred             EEEeecccC
Q psy16184        174 LVDVERSRT  182 (363)
Q Consensus       174 ~V~~a~~~~  182 (363)
                      .|.|+....
T Consensus       103 ~V~~a~~~~  111 (127)
T 2a3j_A          103 VITFSETPQ  111 (127)
T ss_dssp             EEEECCCCC
T ss_pred             EEEEccCcc
Confidence            999997643

>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=99.78  E-value=2.9e-19  Score=142.31  Aligned_cols=83  Identities=16%  Similarity=0.262  Sum_probs=77.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhhCCc-cEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEE
Q psy16184         98 MDPFKTLFIARVNYDTSESKLRREFEVYGPI-KKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD  176 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i-~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~  176 (363)
                      ..+.++|||+|||+.+|+++|+++|..||.| ..|.|+.++ ++.++|||||+|.+.++|.+||.. |+..|+|+.|.|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~   89 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVH   89 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEE
Confidence            4457899999999999999999999999999 899999998 999999999999999999999996 9999999999999


Q ss_pred             eecccC
Q psy16184        177 VERSRT  182 (363)
Q Consensus       177 ~a~~~~  182 (363)
                      ++....
T Consensus        90 ~a~~~~   95 (114)
T 2cpy_A           90 VVTLED   95 (114)
T ss_dssp             EECHHH
T ss_pred             ECCHHH
Confidence            997654

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=2.6e-18  Score=130.87  Aligned_cols=81  Identities=21%  Similarity=0.372  Sum_probs=76.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      ...++|||+|||+.+|+++|+++|..| .|..|.|+.+ .+|.++|||||+|.+.++|.+||. ||+..|+|+.|.|.++
T Consensus         8 ~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~a   84 (91)
T 2dgw_A            8 TTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFRE   84 (91)
T ss_dssp             CCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEEE
T ss_pred             CCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEEC
Confidence            456899999999999999999999999 9999999998 789999999999999999999999 9999999999999999


Q ss_pred             cccC
Q psy16184        179 RSRT  182 (363)
Q Consensus       179 ~~~~  182 (363)
                      .+..
T Consensus        85 ~~~~   88 (91)
T 2dgw_A           85 KSGP   88 (91)
T ss_dssp             SSCC
T ss_pred             CcCC
Confidence            7653

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.77  E-value=1.3e-20  Score=163.98  Aligned_cols=172  Identities=15%  Similarity=0.256  Sum_probs=113.6

Q ss_pred             hhhhhcCCCCCCCCCCCC----CCCCCCCCCCCCCccccccccccC-CCCCCCCCCCcccHHHHHHHHHHHHHHHHHHHH
Q psy16184          7 PNLLALFAPRDPVPYLPP----VEKLPHEKKTHGYSGIAAFLNEFE-DPKDTPPPTRVETREERLERRRRERAEQVAYKL   81 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p----~~~~p~t~~s~g~~g~v~f~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (363)
                      .+|..+|..++.|.-+.+    ......++.++|| +||.|.+... ..+..+....+.++.+.+........   ....
T Consensus        19 ~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~~~~g~-afV~F~~~~~A~~Al~l~g~~~~g~~i~v~~~~~~~~---~~~~   94 (198)
T 2yh0_A           19 EAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNF-AFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQP---LPGM   94 (198)
T ss_dssp             HHHHHHHHHHHHHHTCCSSSSCSEEEEEEETTTTE-EEEEESCSHHHHHHGGGTTEEETTEEEEEECCCCCCC---CCCS
T ss_pred             HHHHHHHHHHHhhcccccCCCCceEEeEecCCCCE-EEEEeCCHHHHHHHHHhcCCEEcCceEEEeCCCCCCC---CCCC
Confidence            458889998853332210    1112345778999 9999977543 11113444444443322211000000   0000


Q ss_pred             HHHHhhcCCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHH
Q psy16184         82 EQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK  161 (363)
Q Consensus        82 ~~~~~~~~p~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~  161 (363)
                      ........|.........+.++|||+|||+.+|+++|.++|.+||.|..|.|+.++.++.++|||||+|.+.++|..||.
T Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~  174 (198)
T 2yh0_A           95 SENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA  174 (198)
T ss_dssp             SSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHH
T ss_pred             cCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHH
Confidence            00000000000111223567899999999999999999999999999999999998899999999999999999999999


Q ss_pred             HhCCceeCCEEEEEEeecccC
Q psy16184        162 HADGKKIDGRRVLVDVERSRT  182 (363)
Q Consensus       162 ~l~g~~i~g~~i~V~~a~~~~  182 (363)
                      .|||..|+|+.|.|.++.+..
T Consensus       175 ~l~g~~~~g~~l~v~~a~~~~  195 (198)
T 2yh0_A          175 GLNGMQLGDKKLLVQRASVGA  195 (198)
T ss_dssp             HHTTCEETTEECEEEESCCCC
T ss_pred             HcCCCEECCEEEEEEECCCCC
Confidence            999999999999999997754

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.77  E-value=1.1e-18  Score=133.19  Aligned_cols=82  Identities=20%  Similarity=0.396  Sum_probs=76.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      .+.++|||+|||+.+|+++|+++|.+||.|..|.|+.+  ++.++|||||+|.+.++|.+||..||+..|+|+.|.|.++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a   83 (92)
T 2dgv_A            6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRID   83 (92)
T ss_dssp             SSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            45789999999999999999999999999999999874  7899999999999999999999999999999999999999


Q ss_pred             cccC
Q psy16184        179 RSRT  182 (363)
Q Consensus       179 ~~~~  182 (363)
                      .+..
T Consensus        84 ~~~~   87 (92)
T 2dgv_A           84 RNAS   87 (92)
T ss_dssp             SCCS
T ss_pred             CCCC
Confidence            7754

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=2.2e-18  Score=134.11  Aligned_cols=86  Identities=29%  Similarity=0.554  Sum_probs=77.5

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEE
Q psy16184         95 NATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVL  174 (363)
Q Consensus        95 ~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~  174 (363)
                      .....+.++|||+|||+.+|+++|+++|..|   ..|.|+.++.++.++|||||+|.+.++|++||..||++.|.|+.|.
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~---~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   85 (102)
T 2fc8_A            9 NARSQPSKTLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVT   85 (102)
T ss_dssp             SSSSCCCSSEEEECCCTTCCHHHHHHTSTTC---SEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCccCHHHHHHHhcCC---eEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEE
Confidence            3445678899999999999999999999976   3678888888999999999999999999999999999999999999


Q ss_pred             EEeecccCC
Q psy16184        175 VDVERSRTV  183 (363)
Q Consensus       175 V~~a~~~~~  183 (363)
                      |.+++++..
T Consensus        86 V~~a~~~~~   94 (102)
T 2fc8_A           86 LDWAKPKGE   94 (102)
T ss_dssp             EEECCCCCS
T ss_pred             EEEecCCCC
Confidence            999987543

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.77  E-value=1.7e-18  Score=129.02  Aligned_cols=74  Identities=12%  Similarity=0.165  Sum_probs=70.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      .+.-|||+||++.+|+++|+++|.+||+|..+.|+.      ++|||||+|.+.++|.+|+..||+..|.|+.|.|++|.
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 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            366899999999999999999999999999999965      57999999999999999999999999999999999984

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=5.8e-19  Score=137.93  Aligned_cols=82  Identities=30%  Similarity=0.669  Sum_probs=78.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeecc
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS  180 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~  180 (363)
                      .++|||+|||+.+|+++|.++|.+||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|.|+.|.|.++.+
T Consensus         8 ~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   87 (104)
T 1p1t_A            8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             ccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCCC
Confidence            57999999999999999999999999999999999988999999999999999999999999999999999999999976


Q ss_pred             cC
Q psy16184        181 RT  182 (363)
Q Consensus       181 ~~  182 (363)
                      ..
T Consensus        88 ~~   89 (104)
T 1p1t_A           88 EK   89 (104)
T ss_dssp             TT
T ss_pred             cc
Confidence            43

>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=99.77  E-value=1.6e-19  Score=140.35  Aligned_cols=85  Identities=21%  Similarity=0.401  Sum_probs=74.8

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccC-CCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEE
Q psy16184         95 NATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNK-VTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRV  173 (363)
Q Consensus        95 ~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~-~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i  173 (363)
                      .......++|||+|||+.+|+++|.++|+.|| |..|.|+.++ .+|.++|||||+|.+.++|.+|| .|||..|+|+.|
T Consensus        13 ~~~~~~~~~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           13 RLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRI   90 (100)
T ss_dssp             -------CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCC
T ss_pred             cCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEE
Confidence            33445678999999999999999999999999 9999999987 68999999999999999999999 799999999999


Q ss_pred             EEEeeccc
Q psy16184        174 LVDVERSR  181 (363)
Q Consensus       174 ~V~~a~~~  181 (363)
                      .|.++.+.
T Consensus        91 ~V~~a~~~   98 (100)
T 2j76_E           91 RVDVADQA   98 (100)
T ss_dssp             CCEECCCS
T ss_pred             EEEeccCC
Confidence            99999764

>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=99.77  E-value=3.4e-18  Score=132.80  Aligned_cols=84  Identities=14%  Similarity=0.243  Sum_probs=74.8

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHh--CCceeCCEEE
Q psy16184         96 ATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA--DGKKIDGRRV  173 (363)
Q Consensus        96 ~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l--~g~~i~g~~i  173 (363)
                      ....++++|||+|||+.+|+++|.++|.+||.|..|.|+.+      +|||||+|.+.++|..||..|  ++..|.|+.|
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            34457889999999999999999999999999999999765      699999999999999999977  5788999999


Q ss_pred             EEEeecccCCCC
Q psy16184        174 LVDVERSRTVKG  185 (363)
Q Consensus       174 ~V~~a~~~~~~~  185 (363)
                      .|.|+.......
T Consensus        84 ~V~~a~~~~~~~   95 (101)
T 2cq1_A           84 YIQYSNHKELKT   95 (101)
T ss_dssp             EEEECSCSSCCC
T ss_pred             EEEEcCcccCcC
Confidence            999998766543

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.77  E-value=3.6e-19  Score=130.62  Aligned_cols=75  Identities=19%  Similarity=0.453  Sum_probs=72.4

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184        103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus       103 ~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      +|||+|||+.+|+++|.++|++||.|..|.|+.++.++.++|||||+|.+.++|++|+. ||+..|+|+.|.|.+|
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            59999999999999999999999999999999998899999999999999999999998 9999999999999875

>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=99.77  E-value=2.1e-18  Score=135.93  Aligned_cols=85  Identities=20%  Similarity=0.261  Sum_probs=78.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCC-ccEEEEe-ccCCCCCcceEEEEEecCHHHHHHHHHHhC--CceeCCEEEE
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGP-IKKIVMV-HNKVTGKPRGYAFIEYEHERDMHSAYKHAD--GKKIDGRRVL  174 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~-i~~v~i~-~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~--g~~i~g~~i~  174 (363)
                      .+.++|||+|||+.+|+++|.++|..||. |..|.|+ .+..++.++|||||+|.+.++|..||..||  +..|+|+.|.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~   85 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIA   85 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCE
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEE
Confidence            45789999999999999999999999998 9999998 788889999999999999999999999996  5899999999


Q ss_pred             EEeecccCC
Q psy16184        175 VDVERSRTV  183 (363)
Q Consensus       175 V~~a~~~~~  183 (363)
                      |.|+.+...
T Consensus        86 V~~a~~~~~   94 (109)
T 2dis_A           86 VDWAEPEID   94 (109)
T ss_dssp             EEESCSSCS
T ss_pred             EEEcCCCCC
Confidence            999987543

>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=99.77  E-value=4.4e-19  Score=141.24  Aligned_cols=87  Identities=21%  Similarity=0.372  Sum_probs=75.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184         98 MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      ..+.++|||+|||+.+|+++|.++|..||.|..|.+..+..++.++|||||+|.+.++|..||..|||..|.|+.|.|.+
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~  101 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF  101 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            45678999999999999999999999999995433322223788999999999999999999999999999999999999


Q ss_pred             ecccCCC
Q psy16184        178 ERSRTVK  184 (363)
Q Consensus       178 a~~~~~~  184 (363)
                      +.+....
T Consensus       102 a~~~~~~  108 (115)
T 2cpx_A          102 GKNKKQR  108 (115)
T ss_dssp             CCCCSCC
T ss_pred             ccCCCCC
Confidence            9876543

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=99.77  E-value=2.8e-18  Score=144.40  Aligned_cols=85  Identities=31%  Similarity=0.602  Sum_probs=80.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184         98 MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      ..+.++|||+|||+.+|+++|.++|+.||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|.|+.|.|.+
T Consensus        67 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  146 (158)
T 2kn4_A           67 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM  146 (158)
T ss_dssp             CCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            34578999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ecccC
Q psy16184        178 ERSRT  182 (363)
Q Consensus       178 a~~~~  182 (363)
                      +.+..
T Consensus       147 a~~~~  151 (158)
T 2kn4_A          147 ARYGR  151 (158)
T ss_dssp             ECCSS
T ss_pred             CCCCC
Confidence            98754

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=1.8e-18  Score=136.59  Aligned_cols=85  Identities=21%  Similarity=0.497  Sum_probs=77.8

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEE
Q psy16184         95 NATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVL  174 (363)
Q Consensus        95 ~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~  174 (363)
                      .....+.++|||+|||..+|+++|.++|++||.|..|.|+.++  +.++|||||+|.+.++|.+|+..|||..|+|+.|.
T Consensus        23 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~  100 (109)
T 2err_A           23 TENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIE  100 (109)
T ss_dssp             CSCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECE
T ss_pred             ccCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            3445567899999999999999999999999999999999874  45899999999999999999999999999999999


Q ss_pred             EEeeccc
Q psy16184        175 VDVERSR  181 (363)
Q Consensus       175 V~~a~~~  181 (363)
                      |.++.++
T Consensus       101 V~~a~~~  107 (109)
T 2err_A          101 VNNATAR  107 (109)
T ss_dssp             EEECCCS
T ss_pred             EEECCCC
Confidence            9999765

>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=99.77  E-value=8.8e-21  Score=161.66  Aligned_cols=151  Identities=17%  Similarity=0.244  Sum_probs=106.9

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCC--CCCCCccccccccccCCC--CCCCCCCCcccHHHHHHHHHHHHHHHHHHHHH
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEK--KTHGYSGIAAFLNEFEDP--KDTPPPTRVETREERLERRRRERAEQVAYKLE   82 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~--~s~g~~g~v~f~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (363)
                      .+|..+|.++|+|..+ .++.++.++  +++|| +||.|.+.....  ...+....+....                   
T Consensus        18 ~~l~~~F~~~G~i~~v-~i~~~~~~~~~~~~g~-afV~f~~~~~A~~A~~~l~~~~~~~~~-------------------   76 (175)
T 3nmr_A           18 KDLRELFEQYGAVYEI-NVLRDRSQNPPQSKGC-CFVTFYTRKAALEAQNALHNMKVLPGM-------------------   76 (175)
T ss_dssp             HHHHHHHHTTSCEEEE-EEEEECSSSSCEEEEE-EEEEESSHHHHHHHHHHHTTTCCCTTC-------------------
T ss_pred             HHHHHHHHhCCCEEEE-EEEecCCCCCCCcceE-EEEEECCHHHHHHHHHHhcCcEEccCC-------------------
Confidence            4589999999999887 456677776  89999 899985542100  0000000000000                   


Q ss_pred             HHHhhcCCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHH
Q psy16184         83 QEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH  162 (363)
Q Consensus        83 ~~~~~~~p~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~  162 (363)
                      .......+.........+.++|||+|||+.+|+++|+++|++||.|..|.|+.+. +|.++|||||+|.+.++|.+||..
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~-~g~~~g~afV~f~~~~~A~~A~~~  155 (175)
T 3nmr_A           77 HHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKA  155 (175)
T ss_dssp             SSCCEEEECGGGCCSCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHH
T ss_pred             ccceEEccccccccccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECC-CCCEEEEEEEEECCHHHHHHHHHH
Confidence            0000000000111122356799999999999999999999999999999999885 689999999999999999999999


Q ss_pred             hCCceeC---CEEEEEEeec
Q psy16184        163 ADGKKID---GRRVLVDVER  179 (363)
Q Consensus       163 l~g~~i~---g~~i~V~~a~  179 (363)
                      |||..+.   |++|.|.||.
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            9998776   4999999973

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.77  E-value=3.6e-18  Score=137.91  Aligned_cols=85  Identities=21%  Similarity=0.426  Sum_probs=79.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184         98 MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      ..+.++|||+|||+.+++++|.++|..||.|..|.|+.+. +|.++|||||+|.+.++|..||..|||..|.|+.|.|.+
T Consensus        32 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  110 (124)
T 2kt5_A           32 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL  110 (124)
T ss_dssp             CSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            4567899999999999999999999999999999999997 999999999999999999999999999999999999999


Q ss_pred             ecccCC
Q psy16184        178 ERSRTV  183 (363)
Q Consensus       178 a~~~~~  183 (363)
                      |.....
T Consensus       111 a~~~~~  116 (124)
T 2kt5_A          111 VASQID  116 (124)
T ss_dssp             ECCTTC
T ss_pred             eCCCCC
Confidence            977543

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.77  E-value=2e-18  Score=139.30  Aligned_cols=80  Identities=26%  Similarity=0.602  Sum_probs=76.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeecc
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS  180 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~  180 (363)
                      .++|||+|||+.+|+++|.++|.+||.|..|.|+.++.++.++|||||+|.+.++|..|| .|||..|+|+.|.|.+++.
T Consensus        36 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~  114 (124)
T 2jwn_A           36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRT  114 (124)
T ss_dssp             HTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESSC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCC
Confidence            359999999999999999999999999999999999889999999999999999999999 7999999999999999975


Q ss_pred             c
Q psy16184        181 R  181 (363)
Q Consensus       181 ~  181 (363)
                      .
T Consensus       115 ~  115 (124)
T 2jwn_A          115 N  115 (124)
T ss_dssp             C
T ss_pred             C
Confidence            4

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=1.6e-19  Score=135.82  Aligned_cols=81  Identities=17%  Similarity=0.296  Sum_probs=76.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      .+.++|||+|||+.+++++|.++|.+||.|..|.|+.++.++.++|||||+|.+.++|..||..|||..|.|+.|.|.++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~   82 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGP   82 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCC
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999988765


Q ss_pred             c
Q psy16184        179 R  179 (363)
Q Consensus       179 ~  179 (363)
                      .
T Consensus        83 ~   83 (85)
T 1x4e_A           83 S   83 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.76  E-value=3e-19  Score=159.61  Aligned_cols=82  Identities=17%  Similarity=0.339  Sum_probs=77.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhC--CccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYG--PIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G--~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      ..++|||+||++.||+++|+++|.+||  .|..|.|+.++.|++++|||||+|.+.++|++||..||++.|+|+.|.|.+
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            467999999999999999999999999  999999999999999999999999999999999999999999999999999


Q ss_pred             eccc
Q psy16184        178 ERSR  181 (363)
Q Consensus       178 a~~~  181 (363)
                      +...
T Consensus       147 a~~~  150 (229)
T 3q2s_C          147 VNKQ  150 (229)
T ss_dssp             CCHH
T ss_pred             CCCC
Confidence            8753

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.76  E-value=1.8e-18  Score=134.38  Aligned_cols=79  Identities=18%  Similarity=0.235  Sum_probs=71.9

Q ss_pred             CCCCCCeEEEcCCCC-CCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCC--ceeCCEEE
Q psy16184         97 TMDPFKTLFIARVNY-DTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADG--KKIDGRRV  173 (363)
Q Consensus        97 ~~~~~~~l~V~nL~~-~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g--~~i~g~~i  173 (363)
                      ...+.++|||+|||+ .+|+++|.++|.+||.|..|.|+.+      +|||||+|.+.++|..||..||+  ..|.|+.|
T Consensus        11 ~~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l   84 (102)
T 1x4d_A           11 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPV   84 (102)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEEC
T ss_pred             CCCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECCcEE
Confidence            445788999999999 9999999999999999999999875      48999999999999999999886  46999999


Q ss_pred             EEEeeccc
Q psy16184        174 LVDVERSR  181 (363)
Q Consensus       174 ~V~~a~~~  181 (363)
                      .|.+++..
T Consensus        85 ~V~~a~~~   92 (102)
T 1x4d_A           85 RVHLSQKY   92 (102)
T ss_dssp             EEEEECCC
T ss_pred             EEEECCCC
Confidence            99999853

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=3.3e-18  Score=132.97  Aligned_cols=83  Identities=29%  Similarity=0.491  Sum_probs=74.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEE
Q psy16184         97 TMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD  176 (363)
Q Consensus        97 ~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~  176 (363)
                      ...+.++|||+|||+.+|+++|+++|.+||.|   .|+.+ .++.++|||||+|.+.++|++||..||+..|.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   86 (101)
T 2fc9_A           11 WSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLE   86 (101)
T ss_dssp             CSCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEE
Confidence            34467899999999999999999999999977   56666 689999999999999999999999999999999999999


Q ss_pred             eecccCC
Q psy16184        177 VERSRTV  183 (363)
Q Consensus       177 ~a~~~~~  183 (363)
                      ++.+...
T Consensus        87 ~a~~~~~   93 (101)
T 2fc9_A           87 LQGPRGS   93 (101)
T ss_dssp             ECSSCCC
T ss_pred             EcCCCCC
Confidence            9987543

>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=99.76  E-value=1.3e-18  Score=135.57  Aligned_cols=82  Identities=15%  Similarity=0.197  Sum_probs=74.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184         98 MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      ..+.++|||+|||+.+|+++|+++|..|| |..|.|+.++ +++++|||||+|.+.++|++||. ||+..|+|+.|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G-~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~   88 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFL   88 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcC-ceEEEEEECC-CCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEE
Confidence            34568999999999999999999999999 4599999997 89999999999999999999995 799999999999999


Q ss_pred             ecccC
Q psy16184        178 ERSRT  182 (363)
Q Consensus       178 a~~~~  182 (363)
                      +....
T Consensus        89 ~~~~~   93 (102)
T 1wez_A           89 NSTAG   93 (102)
T ss_dssp             ECCCC
T ss_pred             CCCCC
Confidence            87543

>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=99.76  E-value=5e-21  Score=163.59  Aligned_cols=145  Identities=21%  Similarity=0.278  Sum_probs=103.4

Q ss_pred             hhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccCC-CCCCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy16184          8 NLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFED-PKDTPPPTRVETREERLERRRRERAEQVAYKLEQEIA   86 (363)
Q Consensus         8 ~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   86 (363)
                      +|..+|..++++..+  +..++.++.++|| +||.|.+.... .+.++....+.++.+.+.                   
T Consensus        29 ~l~~~f~~~g~~~~~--~~~~~~~~~~~g~-afV~f~~~~~a~~A~~l~g~~~~g~~l~v~-------------------   86 (175)
T 1fje_B           29 ELKVAISELFAKNDL--AVVDVRTGTNRKF-GYVDFESAEDLEKALELTGLKVFGNEIKLE-------------------   86 (175)
T ss_dssp             HHHHHHHHHHHHHTC--CCCEEEEETTTTE-EEEEESSHHHHHHHHHGGGEEETTEEEEEE-------------------
T ss_pred             HHHHHHHHhCCcceE--EEEECCCCccccE-EEEEECCHHHHHHHHhcCCCEeCCeEEEEe-------------------
Confidence            466778887766552  3446678999999 99999654310 000111111111111110                   


Q ss_pred             hcCCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCc
Q psy16184         87 LWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGK  166 (363)
Q Consensus        87 ~~~p~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~  166 (363)
                        .+.........+.++|||+|||+.+|+++|.++|..||.|..+     ..++.++|||||+|.+.++|.+||..|||.
T Consensus        87 --~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~  159 (175)
T 1fje_B           87 --KPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGA  159 (175)
T ss_dssp             --CCCCSSCSTTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----CSSSSCCSEEEEECSSHHHHHHHHHHHTEE
T ss_pred             --cCCCccccccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----cCCCCCceEEEEEECCHHHHHHHHHHhCCC
Confidence              1111122233457899999999999999999999999988665     468899999999999999999999999999


Q ss_pred             eeCCEEEEEEeeccc
Q psy16184        167 KIDGRRVLVDVERSR  181 (363)
Q Consensus       167 ~i~g~~i~V~~a~~~  181 (363)
                      .|+|+.|.|.|+.++
T Consensus       160 ~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          160 EIDGRSVSLYYTGEK  174 (175)
T ss_dssp             EETTEEEEEEECSSC
T ss_pred             EECCeEEEEEecCCC
Confidence            999999999999764

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.76  E-value=1.3e-18  Score=136.45  Aligned_cols=82  Identities=23%  Similarity=0.345  Sum_probs=75.4

Q ss_pred             CCCCCCeEEEcCCCCCC------CHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC
Q psy16184         97 TMDPFKTLFIARVNYDT------SESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDG  170 (363)
Q Consensus        97 ~~~~~~~l~V~nL~~~~------t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g  170 (363)
                      .....++|||+|||+.+      |+++|..+|++||.|..|.|+  ..+|.++|||||+|.+.++|..||..|||..|.|
T Consensus        11 ~~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g   88 (105)
T 2nlw_A           11 ADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDK   88 (105)
T ss_dssp             CCSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECST
T ss_pred             CCCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCC
Confidence            33457899999999999      789999999999999999998  3689999999999999999999999999999999


Q ss_pred             E-EEEEEeecc
Q psy16184        171 R-RVLVDVERS  180 (363)
Q Consensus       171 ~-~i~V~~a~~  180 (363)
                      + .|.|.++..
T Consensus        89 ~~~l~V~~a~~   99 (105)
T 2nlw_A           89 QHTFRVNLFTD   99 (105)
T ss_dssp             TCEEEEECSCC
T ss_pred             CceEEEEEcch
Confidence            8 999999864

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.76  E-value=3.5e-18  Score=140.70  Aligned_cols=81  Identities=23%  Similarity=0.438  Sum_probs=76.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184         98 MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      ..+.++|||+|||+.+|+++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|.+||..|||..|.|+.|.|.+
T Consensus        60 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  139 (140)
T 2ku7_A           60 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL  139 (140)
T ss_dssp             CSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEEC
T ss_pred             CCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            34678999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             e
Q psy16184        178 E  178 (363)
Q Consensus       178 a  178 (363)
                      |
T Consensus       140 A  140 (140)
T 2ku7_A          140 A  140 (140)
T ss_dssp             -
T ss_pred             C
Confidence            6

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.76  E-value=3.3e-18  Score=131.84  Aligned_cols=79  Identities=20%  Similarity=0.318  Sum_probs=72.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCce--eCCEEEE
Q psy16184         97 TMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKK--IDGRRVL  174 (363)
Q Consensus        97 ~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~--i~g~~i~  174 (363)
                      ...|+++|||+|||+.+|+++|.++|++||.|..|.|+..      +|||||+|.+.++|.+||..||+..  |.|+.|.
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            3457889999999999999999999999999999999753      6999999999999999999999875  8899999


Q ss_pred             EEeeccc
Q psy16184        175 VDVERSR  181 (363)
Q Consensus       175 V~~a~~~  181 (363)
                      |++++.+
T Consensus        91 V~~S~~k   97 (100)
T 3r27_A           91 VNYSTSQ   97 (100)
T ss_dssp             EEECSCS
T ss_pred             EEecccc
Confidence            9999764

>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=99.76  E-value=3.2e-19  Score=135.69  Aligned_cols=81  Identities=19%  Similarity=0.505  Sum_probs=74.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeeccc
Q psy16184        102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERSR  181 (363)
Q Consensus       102 ~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~~  181 (363)
                      ++|||+|||+.+++++|.++|++||.|..|.|+.++.++.++|||||+|.+.+ |..|+..|||..|+|+.|.|.+|.+.
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~   80 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPK   80 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC---
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            58999999999999999999999999999999999989999999999999999 99999999999999999999999875


Q ss_pred             CC
Q psy16184        182 TV  183 (363)
Q Consensus       182 ~~  183 (363)
                      ..
T Consensus        81 ~~   82 (90)
T 2ki2_A           81 KS   82 (90)
T ss_dssp             --
T ss_pred             CC
Confidence            44

>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=99.76  E-value=3.8e-18  Score=136.06  Aligned_cols=83  Identities=16%  Similarity=0.317  Sum_probs=74.8

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCC--ceeCCEEE
Q psy16184         96 ATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADG--KKIDGRRV  173 (363)
Q Consensus        96 ~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g--~~i~g~~i  173 (363)
                      ....++++|||+|||+.+|+++|+++|++||.|..|.|+.+      +|||||+|.+.++|.+||..|++  ..|.|+.|
T Consensus        26 ~~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l   99 (119)
T 2ad9_A           26 SAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPI   99 (119)
T ss_dssp             SCSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEE
Confidence            34457889999999999999999999999999999999875      69999999999999999998874  68999999


Q ss_pred             EEEeecccCCC
Q psy16184        174 LVDVERSRTVK  184 (363)
Q Consensus       174 ~V~~a~~~~~~  184 (363)
                      .|.+++.+...
T Consensus       100 ~V~~a~~k~~~  110 (119)
T 2ad9_A          100 YIQFSNHKELK  110 (119)
T ss_dssp             EEEECSSSSCC
T ss_pred             EEEEccCCCCC
Confidence            99999876554

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.76  E-value=5.9e-19  Score=130.00  Aligned_cols=76  Identities=18%  Similarity=0.501  Sum_probs=73.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184        102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus       102 ~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      ++|||+|||+.+|+++|.++|++||.|..|.|+.++.++.++|||||+|.+.++|.+|+..|+ ..|+|+.|.|++|
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            479999999999999999999999999999999998899999999999999999999999999 9999999999987

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=3.8e-18  Score=129.75  Aligned_cols=77  Identities=21%  Similarity=0.460  Sum_probs=72.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      .+.++|||+|||+.+|+++|.++|.+||.|..|.|+        +|||||+|.+.++|.+||..||+..|+|+.|.|.++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   77 (90)
T 2dnq_A            6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEAS   77 (90)
T ss_dssp             SCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECS
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEEC
Confidence            457899999999999999999999999999999996        489999999999999999999999999999999999


Q ss_pred             cccCC
Q psy16184        179 RSRTV  183 (363)
Q Consensus       179 ~~~~~  183 (363)
                      .+...
T Consensus        78 ~~~~~   82 (90)
T 2dnq_A           78 KNKSK   82 (90)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            87554

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.76  E-value=3.8e-18  Score=134.80  Aligned_cols=78  Identities=10%  Similarity=0.056  Sum_probs=71.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhC-CccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYG-PIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G-~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      ..++|||+|||+.+|+++|+++|.+|| .|..|.|+.    ..++|||||+|.+.++|++||..|||..|+|+.|.|.++
T Consensus        27 ~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~----~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a  102 (111)
T 2jvr_A           27 KRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNT----RDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERD  102 (111)
T ss_dssp             CCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSS----CSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEc----CCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            467999999999999999999999999 999998853    347899999999999999999999999999999999998


Q ss_pred             ccc
Q psy16184        179 RSR  181 (363)
Q Consensus       179 ~~~  181 (363)
                      ...
T Consensus       103 ~~~  105 (111)
T 2jvr_A          103 DNP  105 (111)
T ss_dssp             CC-
T ss_pred             CCC
Confidence            653

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.76  E-value=9.2e-19  Score=143.63  Aligned_cols=87  Identities=30%  Similarity=0.582  Sum_probs=81.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEE
Q psy16184         97 TMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD  176 (363)
Q Consensus        97 ~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~  176 (363)
                      ...+.++|||+|||+.+|+++|.++|+.||.|..|.|+.++.++.++|||||+|.+.++|++||..|||..|.|+.|.|.
T Consensus        43 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~  122 (135)
T 2lea_A           43 DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQ  122 (135)
T ss_dssp             SGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34457899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             eecccCC
Q psy16184        177 VERSRTV  183 (363)
Q Consensus       177 ~a~~~~~  183 (363)
                      ++++...
T Consensus       123 ~a~~~~~  129 (135)
T 2lea_A          123 MARYGRP  129 (135)
T ss_dssp             ECCCCCC
T ss_pred             ECCCCCC
Confidence            9986543

>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=99.75  E-value=4e-20  Score=170.47  Aligned_cols=153  Identities=16%  Similarity=0.234  Sum_probs=114.4

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccCC--CCCCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHH
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFED--PKDTPPPTRVETREERLERRRRERAEQVAYKLEQE   84 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (363)
                      .+|..+|.++|+|..+ .+..++.++.++|| +||.|.+....  +...+....+.++.+.+.                 
T Consensus       110 ~~l~~~f~~~G~i~~~-~i~~~~~~g~~~g~-afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~-----------------  170 (284)
T 3smz_A          110 QQFEELVRPFGSLERC-FLVYSERTGQSKGY-GFAEYMKKDSAARAKSDLLGKPLGPRTLYVH-----------------  170 (284)
T ss_dssp             HHHHHHHGGGSCEEEE-EEEECTTTCCEEEE-EEEEESSHHHHHHHHHHHTTCEETTEECEEE-----------------
T ss_pred             HHHHHHHHhcCCeeEE-EEEeeCCCCccceE-EEEEECCHHHHHHHHHHhCCCEeCCcEEEEE-----------------
Confidence            4689999999998877 35667888999999 99999664320  000111111111111110                 


Q ss_pred             HhhcCCCCCCCCCCCCCCeEEEcCCCCCC-CHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHh
Q psy16184         85 IALWDPNSFPNATMDPFKTLFIARVNYDT-SESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA  163 (363)
Q Consensus        85 ~~~~~p~~~~~~~~~~~~~l~V~nL~~~~-t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l  163 (363)
                         +...........+.++|||+|||+.+ |+++|.++|+.||.|..|.|+.+. +|.++|||||+|.+.++|.+|+..|
T Consensus       171 ---~a~~~~~~~~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l  246 (284)
T 3smz_A          171 ---WTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQA  246 (284)
T ss_dssp             ---ECCGGGCCTTTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECS-SCCEEEEEEEECSSHHHHHHHHHHH
T ss_pred             ---ECCCCCCCcccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECC-CCCcccEEEEEeCCHHHHHHHHHHh
Confidence               00011112233467899999999995 999999999999999999999886 8999999999999999999999999


Q ss_pred             CCceeCCEEEEEEeecccC
Q psy16184        164 DGKKIDGRRVLVDVERSRT  182 (363)
Q Consensus       164 ~g~~i~g~~i~V~~a~~~~  182 (363)
                      ||..|+|+.|.|.|+.+..
T Consensus       247 ~g~~~~g~~l~v~~a~~~~  265 (284)
T 3smz_A          247 DGLSLGGSHLRVSFCAPGP  265 (284)
T ss_dssp             TTCEETTEECEEEECCSSS
T ss_pred             CCCccCCeEEEEEEecCCC
Confidence            9999999999999997654

>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=99.75  E-value=5.6e-18  Score=130.67  Aligned_cols=80  Identities=29%  Similarity=0.498  Sum_probs=73.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC--CEEEE
Q psy16184         97 TMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKID--GRRVL  174 (363)
Q Consensus        97 ~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~--g~~i~  174 (363)
                      ...+.++|||+|||+.+|+++|.++|.+||.|..|.|+.+      +|||||+|.+.++|++||..||+..|.  |+.|.
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            3456789999999999999999999999999999999754      689999999999999999999999999  99999


Q ss_pred             EEeecccC
Q psy16184        175 VDVERSRT  182 (363)
Q Consensus       175 V~~a~~~~  182 (363)
                      |.++.++.
T Consensus        87 V~~a~~~~   94 (97)
T 1why_A           87 VDFAKSGP   94 (97)
T ss_dssp             EEECCCCC
T ss_pred             EEECCCCC
Confidence            99998754

>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=99.75  E-value=2.4e-20  Score=172.74  Aligned_cols=152  Identities=14%  Similarity=0.196  Sum_probs=105.2

Q ss_pred             hhhhhcCCCCC-CCCCCCCCCCCCCCCCCCCCccccccccccCC--CCCCCCCCCcccHHHHHHHHHHHHHHHHHHHHHH
Q psy16184          7 PNLLALFAPRD-PVPYLPPVEKLPHEKKTHGYSGIAAFLNEFED--PKDTPPPTRVETREERLERRRRERAEQVAYKLEQ   83 (363)
Q Consensus         7 ~~l~~~f~~~~-pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (363)
                      .+|..+|.++| +|..+. +..++. +.++|| +||.|.+....  +...+....+.++.+.+..               
T Consensus       132 ~~l~~~f~~~G~~i~~v~-i~~~~~-~~~~g~-afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~---------------  193 (292)
T 2ghp_A          132 RNIRDLLQDINVVALSIR-LPSLRF-NTSRRF-AYIDVTSKEDARYCVEKLNGLKIEGYTLVTKV---------------  193 (292)
T ss_dssp             HHHHHHHHHTTCCCCEEE-CC--------CCE-EEEECSSHHHHHHHHHHHTTCEETTEECEEEE---------------
T ss_pred             HHHHHHHHHhCCCeEEEE-EEeCCC-CCcceE-EEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE---------------
Confidence            46899999999 888773 444443 789999 99998664321  1111222222222111110               


Q ss_pred             HHhhcCCCCCC---CCCCCCCCeEEEcCCCCC-CCHHHHHHHHHhhCCccEEEEeccCC-CCCcceEEEEEecCHHHHHH
Q psy16184         84 EIALWDPNSFP---NATMDPFKTLFIARVNYD-TSESKLRREFEVYGPIKKIVMVHNKV-TGKPRGYAFIEYEHERDMHS  158 (363)
Q Consensus        84 ~~~~~~p~~~~---~~~~~~~~~l~V~nL~~~-~t~~~L~~~F~~~G~i~~v~i~~d~~-t~~~~g~afV~f~~~~~a~~  158 (363)
                          ..|....   .....+.++|||+|||+. +|+++|.++|..||.|..|.|+.+.. ||.++|||||+|.+.++|.+
T Consensus       194 ----a~~~~~~~~~~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~  269 (292)
T 2ghp_A          194 ----SNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAER  269 (292)
T ss_dssp             ----CCCC---------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHH
T ss_pred             ----CCCCcccccccccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHH
Confidence                0011000   022345789999999999 99999999999999999999998876 69999999999999999999


Q ss_pred             HHHHhCCceeCCEEEEEEeeccc
Q psy16184        159 AYKHADGKKIDGRRVLVDVERSR  181 (363)
Q Consensus       159 Ai~~l~g~~i~g~~i~V~~a~~~  181 (363)
                      || .|||..|.|+.|.|.|+.++
T Consensus       270 A~-~l~g~~~~g~~i~V~~a~~k  291 (292)
T 2ghp_A          270 AL-QMNRSLLGNREISVSLADKK  291 (292)
T ss_dssp             HG-GGTTEEETTEEEEEEECCCC
T ss_pred             HH-HhcCCEECCcEEEEEEecCC
Confidence            99 99999999999999999764

>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=99.75  E-value=9.1e-18  Score=132.38  Aligned_cols=78  Identities=18%  Similarity=0.367  Sum_probs=73.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      +.++|||+|||+.+|+++|..+|.+||.|..|.|+.+      +|||||+|.+.++|..||..|||..|.|+.|.|.|+.
T Consensus        24 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   97 (109)
T 1x4g_A           24 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGK   97 (109)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecC
Confidence            4679999999999999999999999999999999875      6999999999999999999999999999999999998


Q ss_pred             ccCC
Q psy16184        180 SRTV  183 (363)
Q Consensus       180 ~~~~  183 (363)
                      +...
T Consensus        98 ~~~~  101 (109)
T 1x4g_A           98 ESPD  101 (109)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            7554

>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=99.75  E-value=3.7e-18  Score=135.69  Aligned_cols=82  Identities=18%  Similarity=0.351  Sum_probs=76.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCcee--------C
Q psy16184         98 MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKI--------D  169 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i--------~  169 (363)
                      ..+.++|||+|||+.+|+++|..+|..||.|..|.|+.++ ++.++|||||+|.+.++|..||..|||..|        .
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~  100 (114)
T 1x5o_A           22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAP  100 (114)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCC
Confidence            3457899999999999999999999999999999999997 999999999999999999999999999999        6


Q ss_pred             CEEEEEEeecc
Q psy16184        170 GRRVLVDVERS  180 (363)
Q Consensus       170 g~~i~V~~a~~  180 (363)
                      +++|.|.|+.+
T Consensus       101 ~~~l~v~~a~p  111 (114)
T 1x5o_A          101 TEPLLCKFSGP  111 (114)
T ss_dssp             SSCBEEEECCC
T ss_pred             CCceeEEccCC
Confidence            78899999875

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=3.9e-18  Score=133.39  Aligned_cols=83  Identities=13%  Similarity=0.213  Sum_probs=76.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccE-EEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKK-IVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~-v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      ...++|||+|||+.+|+++|+++|.+||.|.. |.|+.+ .+|.++|||||+|.+.++|.+||.. |+..|+|+.|.|.+
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~~   90 (104)
T 1wg5_A           13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIFK   90 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEEE
Confidence            45789999999999999999999999999987 888888 7999999999999999999999996 99999999999999


Q ss_pred             ecccCC
Q psy16184        178 ERSRTV  183 (363)
Q Consensus       178 a~~~~~  183 (363)
                      +.....
T Consensus        91 ~~~~~~   96 (104)
T 1wg5_A           91 SSRAEV   96 (104)
T ss_dssp             ECTTTS
T ss_pred             CCHHHH
Confidence            876543

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.61  E-value=7.6e-20  Score=146.06  Aligned_cols=85  Identities=22%  Similarity=0.362  Sum_probs=79.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccE--------EEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKK--------IVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDG  170 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~--------v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g  170 (363)
                      .+.++|||+|||+.+++++|.++|.+||.|..        |.|+.++.++.++|||||+|.+.++|.+||..|||..|.|
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   84 (116)
T 2lcw_A            5 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSG   84 (116)
Confidence            35679999999999999999999999999998        8999998899999999999999999999999999999999


Q ss_pred             EEEEEEeecccCC
Q psy16184        171 RRVLVDVERSRTV  183 (363)
Q Consensus       171 ~~i~V~~a~~~~~  183 (363)
                      +.|.|.++.++..
T Consensus        85 ~~l~V~~a~~~~~   97 (116)
T 2lcw_A           85 NPIKVSFATRRAD   97 (116)
Confidence            9999999987543

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=2e-17  Score=128.07  Aligned_cols=78  Identities=27%  Similarity=0.535  Sum_probs=71.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhh--CCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEE
Q psy16184         98 MDPFKTLFIARVNYDTSESKLRREFEVY--GPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLV  175 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~--G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V  175 (363)
                      ..+.++|||+|||+.+|+++|+.+|.+|  |.|..|.++        +|||||+|.+.++|.+||..|||..|.|+.|.|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   83 (99)
T 2cpd_A           12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEV   83 (99)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEE
T ss_pred             cCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            4467899999999999999999999999  999998874        579999999999999999999999999999999


Q ss_pred             EeecccCC
Q psy16184        176 DVERSRTV  183 (363)
Q Consensus       176 ~~a~~~~~  183 (363)
                      .++.+...
T Consensus        84 ~~a~~~~~   91 (99)
T 2cpd_A           84 TLAKPVDK   91 (99)
T ss_dssp             ECCCCCCC
T ss_pred             EECCCCCC
Confidence            99987543

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=1.9e-17  Score=126.40  Aligned_cols=78  Identities=27%  Similarity=0.481  Sum_probs=72.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184         98 MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      ..+.++|||+|||+.+|+++|+++|++||.|..|.|+.        +||||+|.+.++|.+||..||+..|.|+.|.|.+
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   78 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQL   78 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS--------SEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEE
Confidence            45678999999999999999999999999999999964        4999999999999999999999999999999999


Q ss_pred             ecccCC
Q psy16184        178 ERSRTV  183 (363)
Q Consensus       178 a~~~~~  183 (363)
                      +.+...
T Consensus        79 a~~~~~   84 (92)
T 2dgt_A           79 STSRLR   84 (92)
T ss_dssp             SSCCCS
T ss_pred             ccCCCC
Confidence            977543

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.75  E-value=4.4e-18  Score=136.26  Aligned_cols=81  Identities=17%  Similarity=0.212  Sum_probs=76.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCC---ccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEE
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGP---IKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLV  175 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~---i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V  175 (363)
                      ...++|||+|||+.+|+++|+++|..||.   |..|.|+.++. |+++|||||+|.+.++|.+||. ||++.|+|+.|.|
T Consensus        15 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V   92 (118)
T 2db1_A           15 GEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDRESMGHRYIEV   92 (118)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEE
Confidence            45689999999999999999999999999   89999999875 9999999999999999999999 9999999999999


Q ss_pred             Eeeccc
Q psy16184        176 DVERSR  181 (363)
Q Consensus       176 ~~a~~~  181 (363)
                      .++...
T Consensus        93 ~~a~~~   98 (118)
T 2db1_A           93 FKSHRT   98 (118)
T ss_dssp             EEECHH
T ss_pred             EECCHH
Confidence            998654

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.74  E-value=8.3e-19  Score=136.36  Aligned_cols=82  Identities=21%  Similarity=0.361  Sum_probs=75.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      .+.++|||+|||+.+|+++|.++|..||.|.. .++.+..++.++|||||+|.+.++|.+||. |||..|.|+.|.|.++
T Consensus        15 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~a   92 (101)
T 1fj7_A           15 TTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   92 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEc
Confidence            45789999999999999999999999999988 666777789999999999999999999999 9999999999999999


Q ss_pred             cccC
Q psy16184        179 RSRT  182 (363)
Q Consensus       179 ~~~~  182 (363)
                      .++.
T Consensus        93 ~~~~   96 (101)
T 1fj7_A           93 KGRD   96 (101)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            7644

>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=99.74  E-value=7.5e-18  Score=128.87  Aligned_cols=78  Identities=22%  Similarity=0.382  Sum_probs=70.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCC-ccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCC-ceeCCEEEEEE
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGP-IKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADG-KKIDGRRVLVD  176 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~-i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g-~~i~g~~i~V~  176 (363)
                      .+.++|||+|||+.+|+++|+++|.+||. |..+.|.       ++|||||+|.+.++|.+||..||| ..|+|+.|.|.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~   78 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVD   78 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEE
Confidence            45789999999999999999999999999 6666663       469999999999999999999999 99999999999


Q ss_pred             eecccCC
Q psy16184        177 VERSRTV  183 (363)
Q Consensus       177 ~a~~~~~  183 (363)
                      ++.+...
T Consensus        79 ~a~~~~~   85 (93)
T 2cqh_A           79 YSVSKKL   85 (93)
T ss_dssp             ECCCCCC
T ss_pred             EccCccc
Confidence            9987544

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.74  E-value=7.5e-18  Score=132.73  Aligned_cols=79  Identities=24%  Similarity=0.436  Sum_probs=72.3

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEE
Q psy16184         96 ATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLV  175 (363)
Q Consensus        96 ~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V  175 (363)
                      ....+.++|||+|||+.+|+++|.++|.+||.|..|.|+        +|||||+|.+.++|.+||..|||..|+|+.|.|
T Consensus        26 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V   97 (108)
T 2jvo_A           26 EGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEV   97 (108)
T ss_dssp             --CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEE
Confidence            344567899999999999999999999999999999997        589999999999999999999999999999999


Q ss_pred             EeecccC
Q psy16184        176 DVERSRT  182 (363)
Q Consensus       176 ~~a~~~~  182 (363)
                      .++.+..
T Consensus        98 ~~a~~~~  104 (108)
T 2jvo_A           98 VYSKLPA  104 (108)
T ss_dssp             ESCSCCC
T ss_pred             EEecCCC
Confidence            9997644

>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=99.74  E-value=1.6e-18  Score=127.00  Aligned_cols=75  Identities=23%  Similarity=0.454  Sum_probs=71.9

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184        103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus       103 ~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      +|||+|||+.+|+++|.++|++||.|..|.|+.++.++.++|||||+|.+.++|..||. +++..|.|+.|.|.+|
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~-~~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHT-TSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHH-hCCCeECCEEEEEEEC
Confidence            59999999999999999999999999999999999999999999999999999999999 5999999999999875

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.74  E-value=7.4e-18  Score=130.01  Aligned_cols=81  Identities=17%  Similarity=0.327  Sum_probs=72.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEE
Q psy16184         97 TMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD  176 (363)
Q Consensus        97 ~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~  176 (363)
                      .....++|||+|||+.+|+++|+.+|.+||.|. +.|+.    +.++|||||+|.+.++|+.||..|||..|+|+.|.|.
T Consensus        15 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~----~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   89 (97)
T 2e5j_A           15 GAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTW----QGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVA   89 (97)
T ss_dssp             SSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEE----ETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEc----CCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            344578999999999999999999999999997 66654    4578999999999999999999999999999999999


Q ss_pred             eecccC
Q psy16184        177 VERSRT  182 (363)
Q Consensus       177 ~a~~~~  182 (363)
                      ++.+..
T Consensus        90 ~a~~~~   95 (97)
T 2e5j_A           90 LARQQR   95 (97)
T ss_dssp             ECCCCC
T ss_pred             EcCCCC
Confidence            997643

>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=99.74  E-value=1.2e-17  Score=129.01  Aligned_cols=79  Identities=22%  Similarity=0.403  Sum_probs=71.2

Q ss_pred             CCCCCCCCeEEEcCCCC-CCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEE
Q psy16184         95 NATMDPFKTLFIARVNY-DTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRV  173 (363)
Q Consensus        95 ~~~~~~~~~l~V~nL~~-~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i  173 (363)
                      .....+.++|||+|||+ .+++++|..+|++||.|..|.|.        +|||||+|.+.++|.+||..|||..|+|+.|
T Consensus        16 ~~~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l   87 (97)
T 2xnq_A           16 PRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKL   87 (97)
T ss_dssp             ---CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEEC
T ss_pred             cCCCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            34455688999999998 99999999999999999999983        6899999999999999999999999999999


Q ss_pred             EEEeeccc
Q psy16184        174 LVDVERSR  181 (363)
Q Consensus       174 ~V~~a~~~  181 (363)
                      .|++++..
T Consensus        88 ~V~~a~~~   95 (97)
T 2xnq_A           88 ILEVSSSN   95 (97)
T ss_dssp             EEEECCCC
T ss_pred             EEEecCCC
Confidence            99998753

>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=99.74  E-value=1.2e-18  Score=140.75  Aligned_cols=82  Identities=13%  Similarity=0.272  Sum_probs=75.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      .+.++|||+|||+.+|+++|.++|..||.|..+.++.+..+|.++|||||+|.+.++|.+||. ||+..|+|+.|.|.++
T Consensus        23 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~a  101 (124)
T 1wel_A           23 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPI  101 (124)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEEC
Confidence            456899999999999999999999999999986666776799999999999999999999999 9999999999999998


Q ss_pred             ccc
Q psy16184        179 RSR  181 (363)
Q Consensus       179 ~~~  181 (363)
                      ...
T Consensus       102 ~~~  104 (124)
T 1wel_A          102 TKK  104 (124)
T ss_dssp             CHH
T ss_pred             CHH
Confidence            764

>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=99.74  E-value=1e-17  Score=130.83  Aligned_cols=80  Identities=16%  Similarity=0.279  Sum_probs=72.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCC--ceeCCEEEEE
Q psy16184         98 MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADG--KKIDGRRVLV  175 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g--~~i~g~~i~V  175 (363)
                      ..+.++|||+|||+.+|+++|+++|++||.|..|.|+.+      +|||||+|.+.++|.+||..|++  ..|.|+.|.|
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V   85 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFF   85 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            456789999999999999999999999999999999764      69999999999999999998865  4599999999


Q ss_pred             EeecccCC
Q psy16184        176 DVERSRTV  183 (363)
Q Consensus       176 ~~a~~~~~  183 (363)
                      .|+..+..
T Consensus        86 ~~a~~~~~   93 (104)
T 1wex_A           86 NYSTSKRI   93 (104)
T ss_dssp             EECSSSSC
T ss_pred             EEccCccc
Confidence            99987543

>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=99.74  E-value=4e-18  Score=131.38  Aligned_cols=82  Identities=20%  Similarity=0.374  Sum_probs=74.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHH----HHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEE
Q psy16184         98 MDPFKTLFIARVNYDTSESKLR----REFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRV  173 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~----~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i  173 (363)
                      ..++++|||+|||+.+++++|.    ++|.+||.|..|.|+.   ++.++|||||+|.+.++|..|+..|||..|.|+.|
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   81 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPM   81 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEE
Confidence            3467899999999999999999    9999999999998873   57788999999999999999999999999999999


Q ss_pred             EEEeecccC
Q psy16184        174 LVDVERSRT  182 (363)
Q Consensus       174 ~V~~a~~~~  182 (363)
                      .|.++.+..
T Consensus        82 ~v~~a~~~~   90 (97)
T 1nu4_A           82 RIQYAKTDS   90 (97)
T ss_dssp             EEEECSSCC
T ss_pred             EEEEccCCC
Confidence            999997643

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.74  E-value=3.7e-18  Score=131.47  Aligned_cols=77  Identities=23%  Similarity=0.461  Sum_probs=71.3

Q ss_pred             CCCCeEEEcCCCC-CCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184         99 DPFKTLFIARVNY-DTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus        99 ~~~~~l~V~nL~~-~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      .+.++|||+|||+ .+|+++|..+|.+||.|..|.|.        +|||||+|.+.++|..||..|||..|.|+.|.|.+
T Consensus         8 ~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   79 (96)
T 2kvi_A            8 PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEV   79 (96)
T ss_dssp             -CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEE
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEE
Confidence            4678999999999 99999999999999999999994        58999999999999999999999999999999999


Q ss_pred             ecccCC
Q psy16184        178 ERSRTV  183 (363)
Q Consensus       178 a~~~~~  183 (363)
                      +.+...
T Consensus        80 a~~~~~   85 (96)
T 2kvi_A           80 SSSNAR   85 (96)
T ss_dssp             EECCCC
T ss_pred             cCcCCC
Confidence            987543

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.74  E-value=7.8e-18  Score=130.81  Aligned_cols=76  Identities=32%  Similarity=0.661  Sum_probs=72.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeeccc
Q psy16184        102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERSR  181 (363)
Q Consensus       102 ~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~~  181 (363)
                      ++|||+|||+.+|+++|.++|++||.|..|.|+.+     ++|||||+|.+.++|.+||..|||..|.|+.|.|.++.+.
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   75 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGM   75 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCC
Confidence            48999999999999999999999999999999876     6799999999999999999999999999999999999875


Q ss_pred             C
Q psy16184        182 T  182 (363)
Q Consensus       182 ~  182 (363)
                      .
T Consensus        76 ~   76 (101)
T 2hvz_A           76 P   76 (101)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=2.6e-17  Score=125.08  Aligned_cols=76  Identities=26%  Similarity=0.468  Sum_probs=71.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      .+.++|||+|||+.+|+++|..+|.+||.|..|.|+.        +||||+|.+.++|..||..|||..|+|+.|.|.++
T Consensus         7 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   78 (90)
T 2dnp_A            7 GNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELS   78 (90)
T ss_dssp             CCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESCHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            4578999999999999999999999999999999964        49999999999999999999999999999999999


Q ss_pred             cccC
Q psy16184        179 RSRT  182 (363)
Q Consensus       179 ~~~~  182 (363)
                      .+..
T Consensus        79 ~~~~   82 (90)
T 2dnp_A           79 TKGQ   82 (90)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7753

>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=99.73  E-value=1.7e-17  Score=124.54  Aligned_cols=75  Identities=25%  Similarity=0.481  Sum_probs=70.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHh-CCceeCCEEEEEEe
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA-DGKKIDGRRVLVDV  177 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l-~g~~i~g~~i~V~~  177 (363)
                      .+.++|||+|||+.+|+++|.++|.+||.|..|.|+.+      +|||||+|.+.++|..|+..| |+..|+|+.|.|.|
T Consensus        10 ~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~   83 (85)
T 2ytc_A           10 KTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKW   83 (85)
T ss_dssp             SSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEE
T ss_pred             CCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEe
Confidence            45789999999999999999999999999999999864      699999999999999999998 99999999999999


Q ss_pred             ec
Q psy16184        178 ER  179 (363)
Q Consensus       178 a~  179 (363)
                      ++
T Consensus        84 ak   85 (85)
T 2ytc_A           84 GR   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            74

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=7.4e-18  Score=132.76  Aligned_cols=78  Identities=15%  Similarity=0.256  Sum_probs=72.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeecc
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS  180 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~  180 (363)
                      ..+|||+|||+.+|+++|+++|..| .|..|.|+.++. |+++|||||+|.+.++|.+|| .||+..|+|+.|.|..+..
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~-g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~~   92 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATE   92 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECCH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCc
Confidence            4699999999999999999999999 899999999964 999999999999999999999 5999999999999998865


Q ss_pred             c
Q psy16184        181 R  181 (363)
Q Consensus       181 ~  181 (363)
                      .
T Consensus        93 ~   93 (109)
T 2dnn_A           93 R   93 (109)
T ss_dssp             H
T ss_pred             c
Confidence            3

>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=99.73  E-value=1.6e-17  Score=128.62  Aligned_cols=81  Identities=22%  Similarity=0.402  Sum_probs=74.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEE
Q psy16184         97 TMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD  176 (363)
Q Consensus        97 ~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~  176 (363)
                      ...+.++|||+|||+.+|+++|+.+|.+||.|..|.|+.+      +|||||+|.+.++|.+||..|||..|.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~   84 (99)
T 2cpj_A           11 TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVR   84 (99)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEE
Confidence            3456789999999999999999999999999999999864      6999999999999999999999999999999999


Q ss_pred             eecccCC
Q psy16184        177 VERSRTV  183 (363)
Q Consensus       177 ~a~~~~~  183 (363)
                      ++.+...
T Consensus        85 ~a~~~~~   91 (99)
T 2cpj_A           85 FACHSAS   91 (99)
T ss_dssp             ESSCCSC
T ss_pred             EcCCCCC
Confidence            9987543

>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=99.73  E-value=4.8e-18  Score=139.15  Aligned_cols=81  Identities=16%  Similarity=0.179  Sum_probs=76.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCC---ccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEE
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGP---IKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLV  175 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~---i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V  175 (363)
                      ...++|||+|||+.+|+++|+++|+.||.   |..|.|+.++. |+++|||||+|.+.++|++||. ||+..|+|+.|.|
T Consensus        42 ~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~V  119 (136)
T 2hgl_A           42 GEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEV  119 (136)
T ss_dssp             CTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEE
Confidence            35679999999999999999999999999   89999999976 9999999999999999999999 9999999999999


Q ss_pred             Eeeccc
Q psy16184        176 DVERSR  181 (363)
Q Consensus       176 ~~a~~~  181 (363)
                      .++...
T Consensus       120 ~~a~~~  125 (136)
T 2hgl_A          120 FKSHRT  125 (136)
T ss_dssp             EECCHH
T ss_pred             EECChH
Confidence            998653

>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=99.73  E-value=4.2e-19  Score=163.47  Aligned_cols=76  Identities=22%  Similarity=0.388  Sum_probs=71.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC-CEEEEEEe
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKID-GRRVLVDV  177 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~-g~~i~V~~  177 (363)
                      .+.++|||+|||..+|+++|.++|..||.|..|.|+.+.     +|||||+|.+.++|.+||..|||..|. |+.|.|.|
T Consensus       205 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~  279 (282)
T 3pgw_A          205 PPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISF  279 (282)
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEE
Confidence            356889999999999999999999999999999998653     589999999999999999999999999 99999999


Q ss_pred             ec
Q psy16184        178 ER  179 (363)
Q Consensus       178 a~  179 (363)
                      ++
T Consensus       280 ak  281 (282)
T 3pgw_A          280 AK  281 (282)
T ss_pred             ec
Confidence            85

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.73  E-value=2.1e-18  Score=128.50  Aligned_cols=72  Identities=26%  Similarity=0.434  Sum_probs=67.6

Q ss_pred             CeEEEcCCCCCC------CHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCE-EEE
Q psy16184        102 KTLFIARVNYDT------SESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGR-RVL  174 (363)
Q Consensus       102 ~~l~V~nL~~~~------t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~-~i~  174 (363)
                      ++|||+|||+.+      |+++|..+|++||.|..|.|+  +.+|.++|||||+|.+.++|..||..|||..|+|+ .|.
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~   79 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFR   79 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEE
Confidence            689999999999      789999999999999999987  36899999999999999999999999999999999 887


Q ss_pred             E
Q psy16184        175 V  175 (363)
Q Consensus       175 V  175 (363)
                      |
T Consensus        80 V   80 (81)
T 2krb_A           80 V   80 (81)
T ss_dssp             C
T ss_pred             e
Confidence            6

>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=99.73  E-value=1.1e-18  Score=143.47  Aligned_cols=82  Identities=12%  Similarity=0.186  Sum_probs=74.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      ...++|||+|||+.+|+++|+++|.+|| |..|.|+.++. ++++|||||+|.+.++|++|| .||+..|.|+.|.|.++
T Consensus        44 ~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a  120 (139)
T 2hgn_A           44 TTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLN  120 (139)
T ss_dssp             -CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEEC
Confidence            3467999999999999999999999999 77999999975 999999999999999999999 68999999999999998


Q ss_pred             cccCC
Q psy16184        179 RSRTV  183 (363)
Q Consensus       179 ~~~~~  183 (363)
                      .....
T Consensus       121 ~~~~~  125 (139)
T 2hgn_A          121 STTGA  125 (139)
T ss_dssp             CCSCC
T ss_pred             CCCCC
Confidence            76543

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.73  E-value=1.1e-17  Score=129.87  Aligned_cols=75  Identities=17%  Similarity=0.265  Sum_probs=70.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      ..++|||+|||+.+|+++|..+|..||.|..|.|+.      ++|||||+|.+.++|..||..|||..|+|+.|.|.|++
T Consensus        26 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   99 (101)
T 2la4_A           26 RVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP------EKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGK   99 (101)
T ss_dssp             SCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCC
T ss_pred             CCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEecc
Confidence            357999999999999999999999999999999973      47999999999999999999999999999999999987


Q ss_pred             c
Q psy16184        180 S  180 (363)
Q Consensus       180 ~  180 (363)
                      +
T Consensus       100 ~  100 (101)
T 2la4_A          100 E  100 (101)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.73  E-value=2.9e-17  Score=129.68  Aligned_cols=75  Identities=23%  Similarity=0.469  Sum_probs=70.0

Q ss_pred             CCCCeEEEcCCCCC-CCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184         99 DPFKTLFIARVNYD-TSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus        99 ~~~~~l~V~nL~~~-~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      .+.++|||+|||+. +|+++|+++|.+||.|..|.|        ++|||||+|.+.++|+.||..||+..|+|+.|.|.+
T Consensus        25 ~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   96 (110)
T 1wf1_A           25 SINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINM   96 (110)
T ss_dssp             TCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            34589999999999 999999999999999999999        468999999999999999999999999999999999


Q ss_pred             eccc
Q psy16184        178 ERSR  181 (363)
Q Consensus       178 a~~~  181 (363)
                      +...
T Consensus        97 a~~~  100 (110)
T 1wf1_A           97 AGEP  100 (110)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            9753

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.73  E-value=1.2e-17  Score=143.19  Aligned_cols=84  Identities=21%  Similarity=0.443  Sum_probs=79.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184         98 MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      ..+.++|||+|||+.+|+++|+++|.+||.|..|.|+.++ ++.++|||||+|.+.++|.+||..|||..|+|+.|.|.|
T Consensus        85 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~  163 (177)
T 2f3j_A           85 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL  163 (177)
T ss_dssp             CTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3467899999999999999999999999999999999997 999999999999999999999999999999999999999


Q ss_pred             ecccC
Q psy16184        178 ERSRT  182 (363)
Q Consensus       178 a~~~~  182 (363)
                      +....
T Consensus       164 a~~~~  168 (177)
T 2f3j_A          164 VASQI  168 (177)
T ss_dssp             ESSGG
T ss_pred             ecCCC
Confidence            97654

>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=99.73  E-value=5.7e-18  Score=134.95  Aligned_cols=74  Identities=16%  Similarity=0.249  Sum_probs=66.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEE-----EE
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRR-----VL  174 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~-----i~  174 (363)
                      ..++|||+|||+.+|+++|+++|.+||.|..|.|+.+       |||||+|.+.++|++||..|||..|+|+.     |.
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~   87 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIR   87 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEE
Confidence            3579999999999999999999999999999999765       89999999999999999999999999998     66


Q ss_pred             EEeecc
Q psy16184        175 VDVERS  180 (363)
Q Consensus       175 V~~a~~  180 (363)
                      |..+.+
T Consensus        88 v~~~~~   93 (115)
T 3beg_B           88 VKVDGP   93 (115)
T ss_dssp             EEECC-
T ss_pred             eccCCC
Confidence            666554

>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=8.3e-18  Score=132.62  Aligned_cols=82  Identities=23%  Similarity=0.299  Sum_probs=72.8

Q ss_pred             CCCCCCeEEEcCCCCC-CCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhC--CceeCCEEE
Q psy16184         97 TMDPFKTLFIARVNYD-TSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHAD--GKKIDGRRV  173 (363)
Q Consensus        97 ~~~~~~~l~V~nL~~~-~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~--g~~i~g~~i  173 (363)
                      ...++++|||+|||+. +|+++|.++|.+||.|..|.|+.      .+|||||+|.+.++|..||..||  +..|.|+.|
T Consensus        21 ~~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~------~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l   94 (112)
T 1x4f_A           21 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCV   94 (112)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCC
T ss_pred             cCCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhccCCceECCEEE
Confidence            3557889999999998 99999999999999999999975      36999999999999999999886  456999999


Q ss_pred             EEEeecccCCC
Q psy16184        174 LVDVERSRTVK  184 (363)
Q Consensus       174 ~V~~a~~~~~~  184 (363)
                      .|.++......
T Consensus        95 ~V~~a~~~~~~  105 (112)
T 1x4f_A           95 KVDLSEKYKKL  105 (112)
T ss_dssp             EEEEECSCSSS
T ss_pred             EEEECcccccc
Confidence            99999875543

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.72  E-value=2.5e-17  Score=126.23  Aligned_cols=78  Identities=17%  Similarity=0.381  Sum_probs=69.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      ..++|||+|||+.+|+++|..+|.+||.|..|  +.++.++.   ||||+|.+.++|.+||. |||..|+|+.|.|.++.
T Consensus         7 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a~   80 (94)
T 2e5g_A            7 GLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPRE   80 (94)
T ss_dssp             TCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECC
Confidence            46799999999999999999999999999987  45555665   99999999999999999 99999999999999886


Q ss_pred             ccCC
Q psy16184        180 SRTV  183 (363)
Q Consensus       180 ~~~~  183 (363)
                      ....
T Consensus        81 ~~~~   84 (94)
T 2e5g_A           81 QKEF   84 (94)
T ss_dssp             CSCC
T ss_pred             cCCC
Confidence            5443

>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=99.72  E-value=1.5e-17  Score=132.31  Aligned_cols=81  Identities=25%  Similarity=0.441  Sum_probs=74.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      .++++|||+|||+.+|+++|..+|+.||.|..|.|+.+   +.++|||||+|.+.++|..||..|||..|+|+.|.|.++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   82 (115)
T 3lqv_A            6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYY   82 (115)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEe
Confidence            45789999999999999999999999999999999865   456899999999999999999999999999999999999


Q ss_pred             cccC
Q psy16184        179 RSRT  182 (363)
Q Consensus       179 ~~~~  182 (363)
                      .+..
T Consensus        83 ~~~~   86 (115)
T 3lqv_A           83 NANR   86 (115)
T ss_dssp             CHHH
T ss_pred             cCCh
Confidence            7643

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.72  E-value=2.1e-17  Score=145.99  Aligned_cols=83  Identities=23%  Similarity=0.440  Sum_probs=77.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184         98 MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      ..|.++|||+|||+.+|+++|.++|++||.|..|.|+.++.|+.++|||||+|.+.++|..||..||+..+.|+.|.|.+
T Consensus        12 ~~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~   91 (213)
T 4f02_A           12 SYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMW   91 (213)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCccccccc
Confidence            34678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecc
Q psy16184        178 ERS  180 (363)
Q Consensus       178 a~~  180 (363)
                      +..
T Consensus        92 ~~~   94 (213)
T 4f02_A           92 SQR   94 (213)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            864

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.72  E-value=9.2e-18  Score=129.11  Aligned_cols=80  Identities=26%  Similarity=0.477  Sum_probs=72.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184         98 MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      ..+.++|||+|||+.+|+++|..+|..||.|..+     ..++.++|||||+|.+.++|.+||..|||..|.|+.|.|.+
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   87 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY   87 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            3467899999999999999999999999988766     25788999999999999999999999999999999999999


Q ss_pred             ecccC
Q psy16184        178 ERSRT  182 (363)
Q Consensus       178 a~~~~  182 (363)
                      +.++.
T Consensus        88 a~~~~   92 (96)
T 1fjc_A           88 TGEKG   92 (96)
T ss_dssp             CSSSC
T ss_pred             cCCCC
Confidence            97643

>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=99.72  E-value=3.8e-18  Score=134.20  Aligned_cols=82  Identities=22%  Similarity=0.210  Sum_probs=76.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhhCC---ccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEE
Q psy16184         98 MDPFKTLFIARVNYDTSESKLRREFEVYGP---IKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVL  174 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~---i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~  174 (363)
                      ....++|||+|||+.+|+++|.++|..||.   |..|.|+.++. |.++|||||+|.+.++|.+||. ||+..|+|+.|.
T Consensus         8 ~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~   85 (107)
T 2lmi_A            8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVE   85 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCC
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEE
Confidence            345789999999999999999999999988   89999999976 9999999999999999999999 999999999999


Q ss_pred             EEeeccc
Q psy16184        175 VDVERSR  181 (363)
Q Consensus       175 V~~a~~~  181 (363)
                      |.++.+.
T Consensus        86 V~~a~~~   92 (107)
T 2lmi_A           86 VYEINNE   92 (107)
T ss_dssp             CEECCHH
T ss_pred             EEECCHH
Confidence            9998754

>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=99.72  E-value=4.5e-18  Score=140.87  Aligned_cols=85  Identities=22%  Similarity=0.352  Sum_probs=74.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEE--Ee---ccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEE
Q psy16184         98 MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIV--MV---HNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRR  172 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~--i~---~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~  172 (363)
                      ..++++|||+|||+.+|+++|..+|..||.|..|.  ++   ....++.++|||||+|.+.++|.+||..|||..|.|+.
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            45678999999999999999999999999998741  11   11247889999999999999999999999999999999


Q ss_pred             EEEEeecccC
Q psy16184        173 VLVDVERSRT  182 (363)
Q Consensus       173 i~V~~a~~~~  182 (363)
                      |.|.++++..
T Consensus       122 l~V~~a~~~~  131 (143)
T 3egn_A          122 MVVQFARSAR  131 (143)
T ss_dssp             CEEEECCCSC
T ss_pred             EEEEECCCCC
Confidence            9999997643

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.72  E-value=1.4e-17  Score=132.41  Aligned_cols=78  Identities=18%  Similarity=0.274  Sum_probs=71.5

Q ss_pred             CeEEEcCC----CCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecC----HHH----HHHHHH--HhCCce
Q psy16184        102 KTLFIARV----NYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEH----ERD----MHSAYK--HADGKK  167 (363)
Q Consensus       102 ~~l~V~nL----~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~----~~~----a~~Ai~--~l~g~~  167 (363)
                      ++|||+||    |+.|++.+|+++|+.||+|..|.++.|+.||.++|||||+|.+    ++.    |..||.  .|||..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            58999999    9999999999999999999999999999999999999999995    333    788888  789999


Q ss_pred             eCCEEEEEEeec
Q psy16184        168 IDGRRVLVDVER  179 (363)
Q Consensus       168 i~g~~i~V~~a~  179 (363)
                      |+|+.|.|.+..
T Consensus        83 I~Gr~irV~ln~   94 (136)
T 2j8a_A           83 IMGFKFEVILNK   94 (136)
T ss_dssp             ETTEEEEEEECC
T ss_pred             ecCcEEEEEECc
Confidence            999999999864

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=1.1e-16  Score=123.44  Aligned_cols=78  Identities=24%  Similarity=0.442  Sum_probs=71.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184         98 MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      ..+.++|||+||  .+|+++|+.+|.+||.|..|.|.      .++|||||+|.+.++|.+||..|||..|.|+.|.|.+
T Consensus        12 ~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~   83 (97)
T 1x5p_A           12 PRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNI   83 (97)
T ss_dssp             CCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEEC
T ss_pred             CCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            446789999996  89999999999999999999985      3579999999999999999999999999999999999


Q ss_pred             ecccCC
Q psy16184        178 ERSRTV  183 (363)
Q Consensus       178 a~~~~~  183 (363)
                      +.+...
T Consensus        84 a~~~~~   89 (97)
T 1x5p_A           84 ARKQPM   89 (97)
T ss_dssp             CSSCCC
T ss_pred             CCCCCC
Confidence            987554

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=1.9e-17  Score=133.19  Aligned_cols=80  Identities=16%  Similarity=0.247  Sum_probs=73.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCc----cEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEE
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPI----KKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLV  175 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i----~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V  175 (363)
                      ..++|||+|||+.+|+++|+++|++||.|    ..|.|+.+ .+|+++|||||+|.+.++|++||.. |+..|.|+.|.|
T Consensus        22 ~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d-~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~V   99 (123)
T 2dha_A           22 NQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTY-PDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIEL   99 (123)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEEC-TTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEEC-CCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEEE
Confidence            35799999999999999999999999975    68999988 5899999999999999999999995 999999999999


Q ss_pred             Eeeccc
Q psy16184        176 DVERSR  181 (363)
Q Consensus       176 ~~a~~~  181 (363)
                      ..+...
T Consensus       100 ~~a~~~  105 (123)
T 2dha_A          100 FRSTAA  105 (123)
T ss_dssp             EEECHH
T ss_pred             EECCHH
Confidence            988653

>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=99.70  E-value=4.9e-17  Score=128.31  Aligned_cols=81  Identities=17%  Similarity=0.328  Sum_probs=72.1

Q ss_pred             CCCCCCCeEEE--cCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCcee-----
Q psy16184         96 ATMDPFKTLFI--ARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKI-----  168 (363)
Q Consensus        96 ~~~~~~~~l~V--~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i-----  168 (363)
                      ....|+.+|||  |||++.+|+++|+++|++||.|..|.|+.+      +|||||+|.+.++|++|+..|||..|     
T Consensus        20 ~~~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~------rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg   93 (114)
T 2cq2_A           20 TVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVVDDLG   93 (114)
T ss_dssp             CCSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEECTTS
T ss_pred             CCCCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHhCCCEEccccC
Confidence            33456889999  779999999999999999999999988643      69999999999999999999999998     


Q ss_pred             CCEEEEEEeecccC
Q psy16184        169 DGRRVLVDVERSRT  182 (363)
Q Consensus       169 ~g~~i~V~~a~~~~  182 (363)
                      .|.+|.|.++...+
T Consensus        94 ~g~~l~v~~a~~~p  107 (114)
T 2cq2_A           94 QKITLYLNFVEKVQ  107 (114)
T ss_dssp             CEEECEEEEESCCC
T ss_pred             CCcEEEEEecccCc
Confidence            78999999997543

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.70  E-value=1.4e-17  Score=129.69  Aligned_cols=80  Identities=19%  Similarity=0.498  Sum_probs=75.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      +.++|||+|||+.+|+++|..+|..||.|..|.|+.++ ++.++|||||+|.+.++|.+||.  ++..|+|+.|.|.++.
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a~   84 (102)
T 2xs2_A            8 MPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPAI   84 (102)
T ss_dssp             EEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEECC
Confidence            46799999999999999999999999999999999998 99999999999999999999998  9999999999999987


Q ss_pred             ccC
Q psy16184        180 SRT  182 (363)
Q Consensus       180 ~~~  182 (363)
                      .+.
T Consensus        85 ~~~   87 (102)
T 2xs2_A           85 RKQ   87 (102)
T ss_dssp             ECC
T ss_pred             cCc
Confidence            643

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=99.70  E-value=5.2e-17  Score=135.53  Aligned_cols=80  Identities=28%  Similarity=0.601  Sum_probs=74.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEE
Q psy16184         97 TMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD  176 (363)
Q Consensus        97 ~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~  176 (363)
                      ...+.++|||+|||+.+|+++|.++|.+||.|..|.|+.+     ++|||||+|.+.++|..||..|||..|.|+.|.|.
T Consensus        69 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  143 (150)
T 2i2y_A           69 SCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVE  143 (150)
T ss_dssp             SSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            3456789999999999999999999999999999999876     57999999999999999999999999999999999


Q ss_pred             eeccc
Q psy16184        177 VERSR  181 (363)
Q Consensus       177 ~a~~~  181 (363)
                      ++.++
T Consensus       144 ~a~~~  148 (150)
T 2i2y_A          144 LSNGE  148 (150)
T ss_dssp             ECCCC
T ss_pred             EcCCC
Confidence            99764

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.69  E-value=4.5e-17  Score=128.89  Aligned_cols=76  Identities=11%  Similarity=0.220  Sum_probs=70.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeecc
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS  180 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~  180 (363)
                      .++|||+|||+.+|+++|+.+|.+||.|..|.|+.      .+|||||+|.+.++|..||..|||..|.|+.|.|+|+..
T Consensus        10 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   83 (111)
T 1whx_A           10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPI   83 (111)
T ss_dssp             EEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEET
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCC
Confidence            57999999999999999999999999999998864      468999999999999999999999999999999999976


Q ss_pred             cC
Q psy16184        181 RT  182 (363)
Q Consensus       181 ~~  182 (363)
                      ..
T Consensus        84 ~~   85 (111)
T 1whx_A           84 GV   85 (111)
T ss_dssp             TT
T ss_pred             Cc
Confidence            43

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.69  E-value=6.8e-17  Score=124.20  Aligned_cols=79  Identities=13%  Similarity=0.159  Sum_probs=71.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEE-EEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKI-VMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v-~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      ...++|||+|||+.+|+++|..+|.+||.|..| .|+.++.++    .|||+|.+.++|..||..|||..|.|+.|.|.+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~----~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   88 (96)
T 2e44_A           13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETA----VVNVTYSSKDQARQALDKLNGFQLENFTLKVAY   88 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSE----EEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEE
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCC----EEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            346899999999999999999999999999999 587775443    499999999999999999999999999999999


Q ss_pred             eccc
Q psy16184        178 ERSR  181 (363)
Q Consensus       178 a~~~  181 (363)
                      +.+.
T Consensus        89 a~~~   92 (96)
T 2e44_A           89 IPDE   92 (96)
T ss_dssp             CCCC
T ss_pred             cCcc
Confidence            9875

>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=99.69  E-value=2e-18  Score=151.73  Aligned_cols=78  Identities=9%  Similarity=0.170  Sum_probs=70.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCc--cEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCE----E
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPI--KKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGR----R  172 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i--~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~----~  172 (363)
                      .|+++|||+|||+.+|+++|+++|++||.|  ..|.|+.+.  +..+|||||+|.+.++|..||..|||..|.|.    +
T Consensus       121 ~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p  198 (205)
T 3tyt_A          121 HPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYP  198 (205)
T ss_dssp             CCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSC
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcc
Confidence            467899999999999999999999999999  899998764  55679999999999999999999999999887    5


Q ss_pred             EEEEee
Q psy16184        173 VLVDVE  178 (363)
Q Consensus       173 i~V~~a  178 (363)
                      +.|+++
T Consensus       199 ~~vk~~  204 (205)
T 3tyt_A          199 YTLKLC  204 (205)
T ss_dssp             EECEEE
T ss_pred             eEEEec
Confidence            777775

>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=99.69  E-value=3.2e-17  Score=151.00  Aligned_cols=138  Identities=17%  Similarity=0.278  Sum_probs=105.6

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccCCC--CCCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHH
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFEDP--KDTPPPTRVETREERLERRRRERAEQVAYKLEQE   84 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (363)
                      .+|..+|..+| |..+. +      ++++|| +||.|.+.....  ...+....+.+                       
T Consensus        37 ~~l~~~F~~~G-i~~~~-~------~~~~g~-afV~f~~~~~A~~A~~~l~~~~~~g-----------------------   84 (284)
T 3smz_A           37 QEVHDLLSDYE-LKYCF-V------DKYKGT-AFVTLLNGEQAEAAINAFHQSRLRE-----------------------   84 (284)
T ss_dssp             HHHHHHTTTSC-EEEEE-E------ETTTTE-EEEEESSHHHHHHHHHHHTTCEETT-----------------------
T ss_pred             HHHHHHHHHcC-CEEEE-E------ecCCCE-EEEEeCCHHHHHHHHHHcCCCeeCC-----------------------
Confidence            46999999999 66552 2      678899 899985543100  00001111111                       


Q ss_pred             HhhcCCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhC
Q psy16184         85 IALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHAD  164 (363)
Q Consensus        85 ~~~~~p~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~  164 (363)
                            ....-....+.++|||+|||+.+|+++|.++|..||.|..|.|+.+..+|.++|||||+|.+.++|..|+..||
T Consensus        85 ------~~i~v~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~  158 (284)
T 3smz_A           85 ------RELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLL  158 (284)
T ss_dssp             ------EECEEEECCCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHT
T ss_pred             ------eEEEEEecCCCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhC
Confidence                  00001112346799999999999999999999999999999999998899999999999999999999999999


Q ss_pred             CceeCCEEEEEEeecccC
Q psy16184        165 GKKIDGRRVLVDVERSRT  182 (363)
Q Consensus       165 g~~i~g~~i~V~~a~~~~  182 (363)
                      |..|+|+.|.|.++.+..
T Consensus       159 ~~~~~g~~i~v~~a~~~~  176 (284)
T 3smz_A          159 GKPLGPRTLYVHWTDAGQ  176 (284)
T ss_dssp             TCEETTEECEEEECCGGG
T ss_pred             CCEeCCcEEEEEECCCCC
Confidence            999999999999997654

>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=99.69  E-value=1.4e-16  Score=134.22  Aligned_cols=81  Identities=22%  Similarity=0.461  Sum_probs=77.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeecc
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS  180 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~  180 (363)
                      .++|||+|||+.+|+++|.++|+.||.|..|.|+.++.+|.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.+
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~   81 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCC
Confidence            57999999999999999999999999999999999988999999999999999999999999999999999999999875


Q ss_pred             c
Q psy16184        181 R  181 (363)
Q Consensus       181 ~  181 (363)
                      .
T Consensus        82 ~   82 (167)
T 1fxl_A           82 S   82 (167)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.69  E-value=1.6e-18  Score=160.34  Aligned_cols=141  Identities=15%  Similarity=0.171  Sum_probs=102.4

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccCC-CCCCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHH
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFED-PKDTPPPTRVETREERLERRRRERAEQVAYKLEQEI   85 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   85 (363)
                      .+|..+|..+|+|..+. +..++.  .++|| +||.|.+.... .+..+....+.++.+.+                   
T Consensus        56 ~~l~~~F~~~G~i~~v~-i~~~~~--~~~g~-afV~f~~~~~A~~A~~~~~~~~~g~~i~v-------------------  112 (292)
T 2ghp_A           56 NKVYKYFKHCGPIIHVD-VADSLK--KNFRF-ARIEFARYDGALAAITKTHKVVGQNEIIV-------------------  112 (292)
T ss_dssp             HHHHHHHGGGSCEEEEE-EEECTT--SSSEE-EEEEESSHHHHHHHHTTTTCEETTEECEE-------------------
T ss_pred             HHHHHHHHhcCCeEEEE-EEECCC--CCcEE-EEEEECCHHHHHHHHHhCCcEeCCcEEEE-------------------
Confidence            46999999999998773 444443  25799 89998664321 01112222222211111                   


Q ss_pred             hhcCCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhhC-CccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhC
Q psy16184         86 ALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYG-PIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHAD  164 (363)
Q Consensus        86 ~~~~p~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G-~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~  164 (363)
                                 .....++|||+|||+.+|+++|.++|..|| .|..|.|+.+.. +.++|||||+|.+.++|..||..||
T Consensus       113 -----------~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~  180 (292)
T 2ghp_A          113 -----------SHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRF-NTSRRFAYIDVTSKEDARYCVEKLN  180 (292)
T ss_dssp             -----------EECCSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHHHHHHHHHHT
T ss_pred             -----------EECCCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCC-CCcceEEEEEECCHHHHHHHHHHhC
Confidence                       112477999999999999999999999999 999999988864 8889999999999999999999999


Q ss_pred             CceeCCEEEEEEeecccC
Q psy16184        165 GKKIDGRRVLVDVERSRT  182 (363)
Q Consensus       165 g~~i~g~~i~V~~a~~~~  182 (363)
                      |..|.|+.|.|.++.+..
T Consensus       181 g~~~~g~~l~v~~a~~~~  198 (292)
T 2ghp_A          181 GLKIEGYTLVTKVSNPLE  198 (292)
T ss_dssp             TCEETTEECEEEECCCC-
T ss_pred             CCEeCCcEEEEEECCCCc
Confidence            999999999999987643

>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=99.68  E-value=1.1e-16  Score=135.38  Aligned_cols=83  Identities=25%  Similarity=0.434  Sum_probs=78.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      +.++|||+|||+.+|+++|.++|+.||.|..|.|+.++.+|.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   81 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR   81 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecC
Confidence            46899999999999999999999999999999999998899999999999999999999999999999999999999987


Q ss_pred             ccC
Q psy16184        180 SRT  182 (363)
Q Consensus       180 ~~~  182 (363)
                      +..
T Consensus        82 ~~~   84 (168)
T 1b7f_A           82 PGG   84 (168)
T ss_dssp             CCS
T ss_pred             CCc
Confidence            643

>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=99.68  E-value=1.2e-16  Score=120.82  Aligned_cols=76  Identities=11%  Similarity=0.214  Sum_probs=70.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      ..++|||+|||+.+++++|+++|.+| .|..|.|.      .++|||||+|.+.++|..||..|||..|.|+.|.|+++.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~   76 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcC
Confidence            46799999999999999999999999 99999985      468999999999999999999999999999999999986


Q ss_pred             ccC
Q psy16184        180 SRT  182 (363)
Q Consensus       180 ~~~  182 (363)
                      ...
T Consensus        77 ~~~   79 (88)
T 1wg1_A           77 TDA   79 (88)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            543

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.68  E-value=5.5e-18  Score=147.70  Aligned_cols=78  Identities=19%  Similarity=0.279  Sum_probs=72.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhC-CccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC-CEEEEEE
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYG-PIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKID-GRRVLVD  176 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G-~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~-g~~i~V~  176 (363)
                      .+.++|||+|||..+|+++|.++|..|| .|..|.|+.+     .+|||||+|.+.++|.+|+..|||..|+ |+.|.|.
T Consensus       118 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~  192 (198)
T 1qm9_A          118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVS  192 (198)
T ss_dssp             CCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST-----TSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEE
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC-----CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEE
Confidence            4588999999999999999999999999 9999999654     2699999999999999999999999999 9999999


Q ss_pred             eeccc
Q psy16184        177 VERSR  181 (363)
Q Consensus       177 ~a~~~  181 (363)
                      |+++.
T Consensus       193 ~a~~~  197 (198)
T 1qm9_A          193 FSKST  197 (198)
T ss_dssp             EECCC
T ss_pred             eeccc
Confidence            99763

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.68  E-value=1.8e-16  Score=119.21  Aligned_cols=75  Identities=20%  Similarity=0.331  Sum_probs=66.6

Q ss_pred             CCCCe-EEEcCCCCCCCHHH----HHHHHHhh-CCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEE
Q psy16184         99 DPFKT-LFIARVNYDTSESK----LRREFEVY-GPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRR  172 (363)
Q Consensus        99 ~~~~~-l~V~nL~~~~t~~~----L~~~F~~~-G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~  172 (363)
                      +|+.| |||+|||+.+++++    |.++|.+| |.|..|       |+   |||||.|.+.++|..|++.|||..|.|++
T Consensus         6 ~p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~   75 (96)
T 2diu_A            6 SGCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFGNR   75 (96)
T ss_dssp             CCSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSC
T ss_pred             CCcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCCce
Confidence            45666 99999999999987    55899999 599887       33   99999999999999999999999999999


Q ss_pred             EEEEeecccCC
Q psy16184        173 VLVDVERSRTV  183 (363)
Q Consensus       173 i~V~~a~~~~~  183 (363)
                      |.|.+|+....
T Consensus        76 i~v~~A~~~sd   86 (96)
T 2diu_A           76 IIVSFTPKNRE   86 (96)
T ss_dssp             CEEESSCCSCC
T ss_pred             EEEEecCCCcc
Confidence            99999987543

>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=99.68  E-value=3.8e-17  Score=131.84  Aligned_cols=80  Identities=15%  Similarity=0.177  Sum_probs=72.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCcc--EEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEE
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIK--KIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD  176 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~--~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~  176 (363)
                      ...++|||+|||+.+|+++|+++|+.| .|.  .|.|+.++. |.++|||||+|.+.++|.+||. +++..|+|+.|.|.
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~-~~~~~l~gR~I~V~  116 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALG-KHKERIGHRYIEVF  116 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHT-TTTCCBTTBCCCCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHH-HCCCEECCEEEEEE
Confidence            456799999999999999999999999 677  899999976 9999999999999999999999 57899999999999


Q ss_pred             eeccc
Q psy16184        177 VERSR  181 (363)
Q Consensus       177 ~a~~~  181 (363)
                      ++...
T Consensus       117 ~a~~~  121 (126)
T 2hgm_A          117 KSSQE  121 (126)
T ss_dssp             EECHH
T ss_pred             ECCHH
Confidence            88653

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.67  E-value=2.8e-16  Score=124.91  Aligned_cols=78  Identities=21%  Similarity=0.410  Sum_probs=68.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCC---CCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEE
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVT---GKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLV  175 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t---~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V  175 (363)
                      ...++|||+|||+.+|+++|+++|.+||.|. +.++.+..+   |.++|||||+|.+.++|++||..|+  .|+|+.|.|
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~   82 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYLC   82 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEEe
Confidence            3468999999999999999999999999999 888888777   7999999999999999999999984  377777777


Q ss_pred             Eeec
Q psy16184        176 DVER  179 (363)
Q Consensus       176 ~~a~  179 (363)
                      ..+.
T Consensus        83 ~~~~   86 (114)
T 2dnl_A           83 VSSP   86 (114)
T ss_dssp             ECCS
T ss_pred             ccCC
Confidence            6544

>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=99.66  E-value=6.9e-17  Score=147.20  Aligned_cols=140  Identities=18%  Similarity=0.261  Sum_probs=102.0

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccCCCCCCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFEDPKDTPPPTRVETREERLERRRRERAEQVAYKLEQEIA   86 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   86 (363)
                      .+|..+|.++|+|..+. +      .+++|| +||.|.+....                 +.         +. ......
T Consensus        37 ~~l~~~F~~~G~i~~v~-i------~~~kg~-afV~f~~~~~A-----------------~~---------A~-~~l~g~   81 (261)
T 3sde_A           37 EDFKRLFERYGEPSEVF-I------NRDRGF-GFIRLESRTLA-----------------EI---------AK-AELDGT   81 (261)
T ss_dssp             HHHHHHTGGGCCCSEEE-E------ETTTTE-EEEECSSHHHH-----------------HH---------HH-HHHTTC
T ss_pred             HHHHHHHHhcCCEEEEE-E------eCCCcE-EEEEECCHHHH-----------------HH---------HH-HHcCCc
Confidence            45899999999988763 2      346799 88988553210                 00         00 000000


Q ss_pred             hcCCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhC-C
Q psy16184         87 LWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHAD-G  165 (363)
Q Consensus        87 ~~~p~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~-g  165 (363)
                      ........-....+..+|||+|||+.+|+++|.++|..||.|..|.|+.+ .+|.++|||||+|.+.++|.+||..|| +
T Consensus        82 ~i~g~~l~v~~a~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~~~  160 (261)
T 3sde_A           82 ILKSRPLRIRFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGDG  160 (261)
T ss_dssp             EETTEECEEEECCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE-TTSCEEEEEEEEESSHHHHHHHHHHHHHS
T ss_pred             EECCceeEeeecccCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeC-CCCCcCcEEEEEeCCHHHHHHHHHHhcCC
Confidence            01100011111234679999999999999999999999999999999999 589999999999999999999999994 5


Q ss_pred             ceeC---CEEEEEEeecccC
Q psy16184        166 KKID---GRRVLVDVERSRT  182 (363)
Q Consensus       166 ~~i~---g~~i~V~~a~~~~  182 (363)
                      ..+.   +++|.|.++....
T Consensus       161 ~~~~~~~~r~i~v~~~~~~~  180 (261)
T 3sde_A          161 AFLLTTTPRPVIVEPMEQFD  180 (261)
T ss_dssp             CEESSSSCCBCEEEECCCEE
T ss_pred             eEEecCCCceEEEeeccccC
Confidence            5555   9999999997643

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.66  E-value=3.9e-16  Score=126.00  Aligned_cols=77  Identities=17%  Similarity=0.341  Sum_probs=70.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceE-EEEEecCHHHHHHHHHHhCCceeCC--EEEEEEe
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGY-AFIEYEHERDMHSAYKHADGKKIDG--RRVLVDV  177 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~-afV~f~~~~~a~~Ai~~l~g~~i~g--~~i~V~~  177 (363)
                      ...|||+||++.+|+++|.++|++||.|..|.|+..     .+|| |||+|.+.++|..|+..|||..|.|  +.|.|+|
T Consensus        28 VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~-----~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~  102 (130)
T 3zzy_A           28 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF  102 (130)
T ss_dssp             EEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE-----TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEE
T ss_pred             eEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC-----CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEe
Confidence            457889999999999999999999999999988754     3688 9999999999999999999999988  9999999


Q ss_pred             ecccC
Q psy16184        178 ERSRT  182 (363)
Q Consensus       178 a~~~~  182 (363)
                      ++...
T Consensus       103 ak~~~  107 (130)
T 3zzy_A          103 SKLTS  107 (130)
T ss_dssp             CSCSS
T ss_pred             cCCCc
Confidence            98754

>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=99.66  E-value=2.7e-16  Score=119.32  Aligned_cols=75  Identities=20%  Similarity=0.398  Sum_probs=62.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCce--eCCEEEEEE
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKK--IDGRRVLVD  176 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~--i~g~~i~V~  176 (363)
                      .+.++|||+|||+++|+++|+++|++||.|..|.|+.+     ++|||||+|.+.++|.+    |++..  +.|+.|.|.
T Consensus         9 ~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~   79 (89)
T 3d2w_A            9 HHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS----LCGEDLIIKGISVHIS   79 (89)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEE
Confidence            45789999999999999999999999999999999874     68999999999999883    45554  569999999


Q ss_pred             eecccC
Q psy16184        177 VERSRT  182 (363)
Q Consensus       177 ~a~~~~  182 (363)
                      ++.++.
T Consensus        80 ~a~~k~   85 (89)
T 3d2w_A           80 NAEPKH   85 (89)
T ss_dssp             ECC---
T ss_pred             EcCCCC
Confidence            997643

>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=99.66  E-value=3e-16  Score=131.37  Aligned_cols=78  Identities=17%  Similarity=0.298  Sum_probs=70.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC--EEEEEEee
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDG--RRVLVDVE  178 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g--~~i~V~~a  178 (363)
                      ..+|||+||++.+|+++|+++|++||.|..|.|...    .++|||||+|.+.++|..|+..|||..|.|  +.|.|+|+
T Consensus        46 vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k----~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~A  121 (164)
T 1sjr_A           46 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS  121 (164)
T ss_dssp             EEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES----SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEEC
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC----CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEe
Confidence            457999999999999999999999999999998643    257899999999999999999999999965  99999999


Q ss_pred             cccC
Q psy16184        179 RSRT  182 (363)
Q Consensus       179 ~~~~  182 (363)
                      ++..
T Consensus       122 k~~~  125 (164)
T 1sjr_A          122 KLTS  125 (164)
T ss_dssp             SSSS
T ss_pred             cCCc
Confidence            8754

>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=99.65  E-value=4.3e-16  Score=135.04  Aligned_cols=82  Identities=28%  Similarity=0.584  Sum_probs=77.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      .+.++|||+|||+.+|+++|.++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+||.. ++..|.|+.|.|.++
T Consensus        11 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~~~   89 (196)
T 1l3k_A           11 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRA   89 (196)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeeecc
Confidence            4578999999999999999999999999999999999999999999999999999999999985 999999999999998


Q ss_pred             ccc
Q psy16184        179 RSR  181 (363)
Q Consensus       179 ~~~  181 (363)
                      ...
T Consensus        90 ~~~   92 (196)
T 1l3k_A           90 VSR   92 (196)
T ss_dssp             CC-
T ss_pred             cCc
Confidence            654

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.65  E-value=7.4e-16  Score=120.48  Aligned_cols=82  Identities=21%  Similarity=0.250  Sum_probs=73.5

Q ss_pred             CCCCeEEEcCCCC-----CCCHHHHHHHHHhhCCccEEEEeccCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCEE
Q psy16184         99 DPFKTLFIARVNY-----DTSESKLRREFEVYGPIKKIVMVHNKVT-GKPRGYAFIEYEHERDMHSAYKHADGKKIDGRR  172 (363)
Q Consensus        99 ~~~~~l~V~nL~~-----~~t~~~L~~~F~~~G~i~~v~i~~d~~t-~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~  172 (363)
                      .++++|+|.||..     ..++++|+++|++||.|..|.|+.++.+ +.++|||||+|.+.++|.+|+..|||..|+|+.
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            4678999999963     2378999999999999999999988654 688999999999999999999999999999999


Q ss_pred             EEEEeecc
Q psy16184        173 VLVDVERS  180 (363)
Q Consensus       173 i~V~~a~~  180 (363)
                      |.|.++..
T Consensus        86 i~v~~a~~   93 (105)
T 2pe8_A           86 VKACFYNL   93 (105)
T ss_dssp             CEEEECCH
T ss_pred             EEEEEcCH
Confidence            99999865

>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=99.65  E-value=2.1e-16  Score=119.50  Aligned_cols=78  Identities=21%  Similarity=0.358  Sum_probs=66.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      .+.++|||+|||+.+|+++|+++|.+||.|..|.|+.+     ++|||||+|.+.++|++|+..  ...+.|..|.|.++
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~~--~~~~~g~~l~v~~a   75 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGE--DLIIKGISVHISNA   75 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTTC--EEEETTEEEEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhcC--CceeCCEEEEEEec
Confidence            35689999999999999999999999999999999764     689999999999999865332  35569999999999


Q ss_pred             cccCC
Q psy16184        179 RSRTV  183 (363)
Q Consensus       179 ~~~~~  183 (363)
                      .++..
T Consensus        76 ~~~~~   80 (88)
T 1wf0_A           76 EPKHN   80 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            77543

>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=99.65  E-value=9.6e-18  Score=149.91  Aligned_cols=78  Identities=19%  Similarity=0.279  Sum_probs=71.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhC-CccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC-CEEEEEE
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYG-PIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKID-GRRVLVD  176 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G-~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~-g~~i~V~  176 (363)
                      .+.++|||+|||+.+|+++|.++|..|| .|..|.|+.+     .+|||||+|.+.++|.+||..|||..|. |+.|.|.
T Consensus       149 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~  223 (229)
T 2adc_A          149 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVS  223 (229)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS-----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEE
T ss_pred             CCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC-----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEE
Confidence            4578999999999999999999999999 9999999653     3689999999999999999999999999 9999999


Q ss_pred             eeccc
Q psy16184        177 VERSR  181 (363)
Q Consensus       177 ~a~~~  181 (363)
                      |+++.
T Consensus       224 ~a~~~  228 (229)
T 2adc_A          224 FSKST  228 (229)
T ss_dssp             ECSSC
T ss_pred             EecCC
Confidence            99763

>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=99.64  E-value=5.6e-16  Score=116.66  Aligned_cols=71  Identities=17%  Similarity=0.443  Sum_probs=66.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhh----C-------CccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCcee
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVY----G-------PIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKI  168 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~----G-------~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i  168 (363)
                      +.++|||+|||+.+|+++|+++|.+|    |       .|..+.++.+      +|||||+|.+.++|.+|| .|||..|
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~l~g~~~   77 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDGIIF   77 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-hcCCCEE
Confidence            46799999999999999999999999    8       8999998754      699999999999999999 8999999


Q ss_pred             CCEEEEEEe
Q psy16184        169 DGRRVLVDV  177 (363)
Q Consensus       169 ~g~~i~V~~  177 (363)
                      .|+.|.|+.
T Consensus        78 ~g~~l~V~r   86 (87)
T 2hzc_A           78 QGQSLKIRR   86 (87)
T ss_dssp             TTEECEEEC
T ss_pred             CCeEEEEeC
Confidence            999999974

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.64  E-value=5.9e-16  Score=124.33  Aligned_cols=74  Identities=20%  Similarity=0.270  Sum_probs=67.2

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceE-EEEEecCHHHHHHHHHHhCCceeCC--EEEEEEeec
Q psy16184        103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGY-AFIEYEHERDMHSAYKHADGKKIDG--RRVLVDVER  179 (363)
Q Consensus       103 ~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~-afV~f~~~~~a~~Ai~~l~g~~i~g--~~i~V~~a~  179 (363)
                      .|||+||++.+|+++|.++|++||.|..|.|+..      .|| |||+|.+.++|..|+..|||..|.|  +.|.|++|+
T Consensus        27 ~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~------~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak  100 (124)
T 2e5i_A           27 LLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR------NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYAR  100 (124)
T ss_dssp             EEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES------SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCS
T ss_pred             EEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEec
Confidence            4689999999999999999999999999999642      286 9999999999999999999999988  699999998


Q ss_pred             ccC
Q psy16184        180 SRT  182 (363)
Q Consensus       180 ~~~  182 (363)
                      +..
T Consensus       101 ~~~  103 (124)
T 2e5i_A          101 PTR  103 (124)
T ss_dssp             CSC
T ss_pred             CCc
Confidence            754

>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=99.64  E-value=6.7e-16  Score=135.59  Aligned_cols=79  Identities=16%  Similarity=0.285  Sum_probs=73.0

Q ss_pred             CCCCeEEEcCCC-CCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184         99 DPFKTLFIARVN-YDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus        99 ~~~~~l~V~nL~-~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      .++++|||+||+ +.+|+++|.++|++||.|..|.|+.+     .+|||||+|.+.++|..||..|||..|.|+.|.|.+
T Consensus         2 ~~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   76 (205)
T 3tyt_A            2 ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCV   76 (205)
T ss_dssp             CCCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT-----STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC-----CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEE
Confidence            357899999999 89999999999999999999999875     379999999999999999999999999999999999


Q ss_pred             ecccC
Q psy16184        178 ERSRT  182 (363)
Q Consensus       178 a~~~~  182 (363)
                      ++...
T Consensus        77 s~~~~   81 (205)
T 3tyt_A           77 SKQPA   81 (205)
T ss_dssp             CSCSC
T ss_pred             ccCCc
Confidence            97543

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.62  E-value=1.6e-15  Score=127.65  Aligned_cols=80  Identities=28%  Similarity=0.512  Sum_probs=74.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeeccc
Q psy16184        102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERSR  181 (363)
Q Consensus       102 ~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~~  181 (363)
                      ++|||+|||+.+|+++|.++|++||.|..|.|+.++ ++.++|||||+|.+.++|..|+..|||..|.|+.|.|.++...
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~   79 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQS   79 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCC-C-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECC-CCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCC
Confidence            489999999999999999999999999999999886 5779999999999999999999999999999999999998764


Q ss_pred             C
Q psy16184        182 T  182 (363)
Q Consensus       182 ~  182 (363)
                      .
T Consensus        80 ~   80 (166)
T 3md3_A           80 Q   80 (166)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.62  E-value=9.3e-16  Score=135.03  Aligned_cols=80  Identities=29%  Similarity=0.572  Sum_probs=73.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeecc
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS  180 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~  180 (363)
                      .++|||+|||+.+|+++|.++|..||.|..|.|+.++.++.++|||||+|.+.++|.+||..||+..|.|+.|.|.++..
T Consensus        28 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~  107 (216)
T 2qfj_A           28 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSN  107 (216)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCSC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCCC
Confidence            46999999999999999999999999999999999988999999999999999999999999999999999999988754

>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=99.60  E-value=3e-15  Score=130.09  Aligned_cols=78  Identities=14%  Similarity=0.241  Sum_probs=71.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeecc
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS  180 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~  180 (363)
                      .++|||+|||+.+|+++|.++|++||.|..|.|+.+. ++.++|||||+|.+.++|.+||..+ +..|+|+.|.|.++..
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDD  186 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETTT
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhHH
Confidence            4699999999999999999999999999999999885 5899999999999999999999865 5699999999998764

>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=99.59  E-value=2.9e-15  Score=127.21  Aligned_cols=82  Identities=20%  Similarity=0.340  Sum_probs=74.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCC--CcceEEEEEecCHHHHHHHHHHhCCceeC---CEEEE
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTG--KPRGYAFIEYEHERDMHSAYKHADGKKID---GRRVL  174 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~--~~~g~afV~f~~~~~a~~Ai~~l~g~~i~---g~~i~  174 (363)
                      ..++|||+|||+.+|+++|.++|.+||.|..|.|+.++.++  .++|||||+|.+.++|..|+..||+..+.   +..|.
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            36799999999999999999999999999999999998777  89999999999999999999999998776   67788


Q ss_pred             EEeeccc
Q psy16184        175 VDVERSR  181 (363)
Q Consensus       175 V~~a~~~  181 (363)
                      |.++...
T Consensus        82 ~~~~~~~   88 (175)
T 3nmr_A           82 MKPADSE   88 (175)
T ss_dssp             EEECGGG
T ss_pred             Ecccccc
Confidence            8887654

>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=99.59  E-value=1.7e-15  Score=127.84  Aligned_cols=79  Identities=25%  Similarity=0.531  Sum_probs=74.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      +.++|||+|||+.+|+++|.++|+.||.|..|.|+.++.+|.++|||||+|.+.++|..||..  +..|+|+.|.|.++.
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~v~~~~   79 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHILDGKVIDPKRAI   79 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEETTEECCCEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--ccccCCeEccccccc
Confidence            357999999999999999999999999999999999988999999999999999999999994  679999999999876


Q ss_pred             c
Q psy16184        180 S  180 (363)
Q Consensus       180 ~  180 (363)
                      +
T Consensus        80 ~   80 (167)
T 2cjk_A           80 P   80 (167)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.58  E-value=6.1e-15  Score=135.52  Aligned_cols=82  Identities=20%  Similarity=0.376  Sum_probs=75.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHH----HHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEE
Q psy16184         98 MDPFKTLFIARVNYDTSESKLR----REFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRV  173 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~----~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i  173 (363)
                      ..+.++|||+|||+.+|+++|+    ++|..||.|..|.|+.   ++.++|||||+|.+.++|..||..|||..|.|+.|
T Consensus         6 ~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   82 (282)
T 3pgw_A            6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPM   82 (282)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEE
Confidence            4568899999999999999966    8999999999999875   78899999999999999999999999999999999


Q ss_pred             EEEeecccC
Q psy16184        174 LVDVERSRT  182 (363)
Q Consensus       174 ~V~~a~~~~  182 (363)
                      .|.|+....
T Consensus        83 ~v~~a~~~~   91 (282)
T 3pgw_A           83 RIQYAKTDS   91 (282)
T ss_pred             EEEEeccCc
Confidence            999997643

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.58  E-value=2.4e-15  Score=134.14  Aligned_cols=79  Identities=20%  Similarity=0.357  Sum_probs=70.5

Q ss_pred             CCCCeEEEcCCCCCC---------CHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCcee-
Q psy16184         99 DPFKTLFIARVNYDT---------SESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKI-  168 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~---------t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i-  168 (363)
                      ...++|||+||+..+         ++++|..+|++||.|..|.|+.+      +|||||+|.+.++|+.|+.+|||..| 
T Consensus       132 ~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~------kG~AFV~F~~~~~Ae~A~~am~g~~l~  205 (240)
T 3u1l_A          132 KKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES------KNCGFVKFKYQANAEFAKEAMSNQTLL  205 (240)
T ss_dssp             CCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHHHTTCCCC
T ss_pred             cCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC------CCEEEEEeCCHHHHHHHHHHhCCCEEe
Confidence            457899999999998         79999999999999999999864      69999999999999999999999999 


Q ss_pred             -----------CCEEEEEEeecccCC
Q psy16184        169 -----------DGRRVLVDVERSRTV  183 (363)
Q Consensus       169 -----------~g~~i~V~~a~~~~~  183 (363)
                                 .|+.|.|.||...+.
T Consensus       206 ~~~~~e~~~~~~gr~L~V~wA~~~pn  231 (240)
T 3u1l_A          206 LPSDKEWDDRREGTGLLVKWANEDPD  231 (240)
T ss_dssp             CTTSTTGGGGGGSCCCEEEECC----
T ss_pred             ccccccccccCCCCEEEEEEccCCCC
Confidence                       899999999986543

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.57  E-value=2.3e-14  Score=113.41  Aligned_cols=83  Identities=19%  Similarity=0.368  Sum_probs=70.9

Q ss_pred             CCCCCCeEEEcCCCCCCC-----------HHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCC
Q psy16184         97 TMDPFKTLFIARVNYDTS-----------ESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADG  165 (363)
Q Consensus        97 ~~~~~~~l~V~nL~~~~t-----------~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g  165 (363)
                      ...++++|+|.||.....           +++|.++|++||.|..|.| .++   .++|||||+|.+.++|.+||..|||
T Consensus        11 ~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~lng   86 (112)
T 2dit_A           11 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLDG   86 (112)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHSTT
T ss_pred             CCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcCC
Confidence            445688999999954432           5899999999999999966 443   3789999999999999999999999


Q ss_pred             ceeCCEEEEEEeecccCC
Q psy16184        166 KKIDGRRVLVDVERSRTV  183 (363)
Q Consensus       166 ~~i~g~~i~V~~a~~~~~  183 (363)
                      ..|+|+.|.|.++.+...
T Consensus        87 ~~~~gr~l~v~~a~~~~~  104 (112)
T 2dit_A           87 RWFGGRQITAQAWDGTTD  104 (112)
T ss_dssp             CEETTEECEEEECCSCCC
T ss_pred             CEECCcEEEEEEeCCCCC
Confidence            999999999999977543

>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=99.56  E-value=5.9e-15  Score=131.68  Aligned_cols=80  Identities=19%  Similarity=0.397  Sum_probs=74.3

Q ss_pred             CCCCCCeEEEcCCCC-CCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEE
Q psy16184         97 TMDPFKTLFIARVNY-DTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLV  175 (363)
Q Consensus        97 ~~~~~~~l~V~nL~~-~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V  175 (363)
                      ...++++|||+|||+ .+|+++|.++|+.||.|..|.|+.++     +|||||+|.+.++|.+||..|||..|.|+.|.|
T Consensus        30 ~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v  104 (229)
T 2adc_A           30 AGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRI  104 (229)
T ss_dssp             GCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEE
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            345688999999999 99999999999999999999998774     789999999999999999999999999999999


Q ss_pred             Eeeccc
Q psy16184        176 DVERSR  181 (363)
Q Consensus       176 ~~a~~~  181 (363)
                      .++...
T Consensus       105 ~~a~~~  110 (229)
T 2adc_A          105 TLSKHQ  110 (229)
T ss_dssp             ECCSCC
T ss_pred             EEecCc
Confidence            999764

>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=99.54  E-value=2e-14  Score=112.30  Aligned_cols=82  Identities=21%  Similarity=0.262  Sum_probs=71.4

Q ss_pred             CCCCeEEEcCCC--CCC--------CHHHHHHHHHhhCCccEEEEeccCCC--CCcceEEEEEecCHHHHHHHHHHhCCc
Q psy16184         99 DPFKTLFIARVN--YDT--------SESKLRREFEVYGPIKKIVMVHNKVT--GKPRGYAFIEYEHERDMHSAYKHADGK  166 (363)
Q Consensus        99 ~~~~~l~V~nL~--~~~--------t~~~L~~~F~~~G~i~~v~i~~d~~t--~~~~g~afV~f~~~~~a~~Ai~~l~g~  166 (363)
                      .|++.|.|.||-  ..+        .+++|+++|++||.|..|.|+.+..+  +.++|||||+|.+.++|.+|+..|||.
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            468899999983  333        23789999999999999999988654  467999999999999999999999999


Q ss_pred             eeCCEEEEEEeecc
Q psy16184        167 KIDGRRVLVDVERS  180 (363)
Q Consensus       167 ~i~g~~i~V~~a~~  180 (363)
                      .|+|+.|.|.++..
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            99999999999864

>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=99.53  E-value=5.6e-15  Score=125.77  Aligned_cols=83  Identities=20%  Similarity=0.350  Sum_probs=73.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEE
Q psy16184         97 TMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD  176 (363)
Q Consensus        97 ~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~  176 (363)
                      ...+.++|||+|||+.+|+++|+++|..||.|.. .++.+..++.++|||||+|.+.++|.+||+ |||..|.|+.|.|.
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v~   86 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLE   86 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEEe
Confidence            3446789999999999999999999999998776 334555678899999999999999999995 99999999999999


Q ss_pred             eeccc
Q psy16184        177 VERSR  181 (363)
Q Consensus       177 ~a~~~  181 (363)
                      ++...
T Consensus        87 ~~~~~   91 (175)
T 1fje_B           87 KPKGR   91 (175)
T ss_dssp             CCCCS
T ss_pred             cCCCc
Confidence            98764

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.51  E-value=1.7e-14  Score=125.50  Aligned_cols=77  Identities=19%  Similarity=0.435  Sum_probs=72.1

Q ss_pred             CCeEEEcCCCC-CCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        101 FKTLFIARVNY-DTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       101 ~~~l~V~nL~~-~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      .++|||+|||+ .+|+++|.++|+.||.|..|.|+.++     +|||||+|.+.++|..||..|||..|.|+.|.|.++.
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~   77 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   77 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECC
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEec
Confidence            57999999999 99999999999999999999998764     7899999999999999999999999999999999997


Q ss_pred             ccC
Q psy16184        180 SRT  182 (363)
Q Consensus       180 ~~~  182 (363)
                      ...
T Consensus        78 ~~~   80 (198)
T 1qm9_A           78 HQN   80 (198)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            643

>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=99.51  E-value=8.1e-15  Score=114.38  Aligned_cols=73  Identities=14%  Similarity=0.352  Sum_probs=64.8

Q ss_pred             EEcCCCCCCCHHHHHHHH------------HhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEE
Q psy16184        105 FIARVNYDTSESKLRREF------------EVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRR  172 (363)
Q Consensus       105 ~V~nL~~~~t~~~L~~~F------------~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~  172 (363)
                      .+.||++.+++++|+++|            ++||.|..|.|+.+. +++++|||||+|.+.++|.+|+..|||..|+|+.
T Consensus        19 ~~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~-~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~   97 (104)
T 1jmt_A           19 SADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQP   97 (104)
T ss_dssp             --CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEE
T ss_pred             ccCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCC-CCCccEEEEEEECCHHHHHHHHHHHCCCEECCEE
Confidence            367788888888887776            999999999999875 5789999999999999999999999999999999


Q ss_pred             EEEEee
Q psy16184        173 VLVDVE  178 (363)
Q Consensus       173 i~V~~a  178 (363)
                      |.|.++
T Consensus        98 i~v~~s  103 (104)
T 1jmt_A           98 IHAELS  103 (104)
T ss_dssp             CCEEEC
T ss_pred             EEEEEc
Confidence            999986

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A

Probab=99.51  E-value=4.4e-14  Score=112.54  Aligned_cols=81  Identities=17%  Similarity=0.358  Sum_probs=71.2

Q ss_pred             CCCeEEEcCCCC--C---CCHHHHHHHHHhhCCccEEEEeccCC----CCCcceEEEEEecCHHHHHHHHHHhCCceeCC
Q psy16184        100 PFKTLFIARVNY--D---TSESKLRREFEVYGPIKKIVMVHNKV----TGKPRGYAFIEYEHERDMHSAYKHADGKKIDG  170 (363)
Q Consensus       100 ~~~~l~V~nL~~--~---~t~~~L~~~F~~~G~i~~v~i~~d~~----t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g  170 (363)
                      ++++|+|.||-.  .   -.+++|++.|++||.|..|.|+.+..    ++.++|||||+|.+.++|.+|+..|||..|+|
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            478999999842  1   23689999999999999999998764    45778999999999999999999999999999


Q ss_pred             EEEEEEeecc
Q psy16184        171 RRVLVDVERS  180 (363)
Q Consensus       171 ~~i~V~~a~~  180 (363)
                      +.|.|.++..
T Consensus        99 R~i~v~~~~~  108 (118)
T 3ue2_A           99 RKVVAEVYDQ  108 (118)
T ss_dssp             EECEEEEECH
T ss_pred             cEEEEEEcCh
Confidence            9999999864

>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=99.50  E-value=8.3e-14  Score=126.73  Aligned_cols=77  Identities=23%  Similarity=0.413  Sum_probs=71.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184         98 MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      ..+.++|||+|||+.+|+++|..+|..||.|..|.|..+      +|||||+|.+.++|..||..|||..|.|+.|.|.+
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~   92 (261)
T 3sde_A           19 YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRF   92 (261)
T ss_dssp             SCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CcEEEEEECCHHHHHHHHHHcCCcEECCceeEeee
Confidence            345679999999999999999999999999999999654      69999999999999999999999999999999999


Q ss_pred             ecc
Q psy16184        178 ERS  180 (363)
Q Consensus       178 a~~  180 (363)
                      +.+
T Consensus        93 a~~   95 (261)
T 3sde_A           93 ATH   95 (261)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            865

>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=99.44  E-value=3e-13  Score=114.50  Aligned_cols=75  Identities=16%  Similarity=0.402  Sum_probs=66.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhh----C-------CccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCcee
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVY----G-------PIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKI  168 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~----G-------~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i  168 (363)
                      +.++|||+|||+.+|+++|.++|++|    |       .|..+.+..      ++|||||+|.+.++|.+|| .|||..|
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~------~~g~afV~f~~~~~A~~A~-~~~~~~~   75 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ------DKNFAFLEFRSVDETTQAM-AFDGIIF   75 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEET------TTTEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecC------CCCEEEEEeCCHHHHHHHH-HhCCcEe
Confidence            46799999999999999999999999    6       666666644      4799999999999999999 7999999


Q ss_pred             CCEEEEEEeeccc
Q psy16184        169 DGRRVLVDVERSR  181 (363)
Q Consensus       169 ~g~~i~V~~a~~~  181 (363)
                      .|+.|.|.++...
T Consensus        76 ~g~~i~v~~~~~~   88 (172)
T 2g4b_A           76 QGQSLKIRRPHDY   88 (172)
T ss_dssp             TTEECEEECCSSC
T ss_pred             cCceeeecCCccc
Confidence            9999999987653

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.43  E-value=8.5e-13  Score=101.88  Aligned_cols=76  Identities=17%  Similarity=0.203  Sum_probs=63.5

Q ss_pred             CCeEEEcCCC-------CCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEE
Q psy16184        101 FKTLFIARVN-------YDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRV  173 (363)
Q Consensus       101 ~~~l~V~nL~-------~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i  173 (363)
                      ...|.|.-..       ..+|+++|+++|.+||.|..|.|+     +.++|||||+|.+.++|..||..+++  +.|+.|
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l   82 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEVG--LVDNPL   82 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBC
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeE
Confidence            4466665433       468999999999999999999997     35789999999999999999997554  679999


Q ss_pred             EEEeecccCC
Q psy16184        174 LVDVERSRTV  183 (363)
Q Consensus       174 ~V~~a~~~~~  183 (363)
                      .|.|+.+...
T Consensus        83 ~V~~a~~~~~   92 (100)
T 2d9o_A           83 KISWLEGQPQ   92 (100)
T ss_dssp             EEECSSCCCC
T ss_pred             EEEEccCCCC
Confidence            9999977543

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.43  E-value=3.8e-13  Score=116.56  Aligned_cols=75  Identities=15%  Similarity=0.357  Sum_probs=65.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhC-----------CccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCcee
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYG-----------PIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKI  168 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G-----------~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i  168 (363)
                      ..++|||+|||+.+|+++|.++|..||           .|..+.+      +.++|||||+|.+.++|.+|| .|||..|
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~------~~~~g~afV~F~~~~~A~~Al-~l~g~~~   75 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDKNFAFLEFRSVDETTQAM-AFDGIIF   75 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE------ETTTTEEEEEESCSHHHHHHG-GGTTEEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe------cCCCCEEEEEeCCHHHHHHHH-HhcCCEE
Confidence            367999999999999999999999994           4455544      445799999999999999999 7999999


Q ss_pred             CCEEEEEEeeccc
Q psy16184        169 DGRRVLVDVERSR  181 (363)
Q Consensus       169 ~g~~i~V~~a~~~  181 (363)
                      .|+.|.|.++...
T Consensus        76 ~g~~i~v~~~~~~   88 (198)
T 2yh0_A           76 QGQSLKIRRPHDY   88 (198)
T ss_dssp             TTEEEEEECCCCC
T ss_pred             cCceEEEeCCCCC
Confidence            9999999998764

>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=99.42  E-value=4e-13  Score=125.99  Aligned_cols=80  Identities=19%  Similarity=0.359  Sum_probs=68.0

Q ss_pred             CCCCCCCCCeEEEcC--CCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC--
Q psy16184         94 PNATMDPFKTLFIAR--VNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKID--  169 (363)
Q Consensus        94 ~~~~~~~~~~l~V~n--L~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~--  169 (363)
                      ......|+.+|||||  |++.+|+++|+++|++||+|..|.|+.      .+|||||+|.+.++|++||..|||..+.  
T Consensus        11 v~~~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~   84 (345)
T 3tht_A           11 IETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDD   84 (345)
T ss_dssp             CCCCSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEECT
T ss_pred             ceecCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCccccc
Confidence            344566889999999  578999999999999999999987754      4699999999999999999999999883  


Q ss_pred             -CE--EEEEEeec
Q psy16184        170 -GR--RVLVDVER  179 (363)
Q Consensus       170 -g~--~i~V~~a~  179 (363)
                       |+  .|.|.++.
T Consensus        85 ~g~~~~ly~~~~~   97 (345)
T 3tht_A           85 LGQKITLYLNFVE   97 (345)
T ss_dssp             TSCEEECEEEECS
T ss_pred             cCCceEEEEEEee
Confidence             44  57777764

>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=99.38  E-value=2.5e-12  Score=101.68  Aligned_cols=78  Identities=10%  Similarity=0.121  Sum_probs=66.7

Q ss_pred             CCCCeEEEcCCCCCC----------CHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCcee
Q psy16184         99 DPFKTLFIARVNYDT----------SESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKI  168 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~----------t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i  168 (363)
                      .+++.|.|.||-...          .+++|++.|++||.|..|.|+.+.    .+|||||+|.+.++|.+|+..|||..|
T Consensus         5 ~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~f   80 (114)
T 3s6e_A            5 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRWF   80 (114)
T ss_dssp             CCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCEE
T ss_pred             CCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCEE
Confidence            357789999974321          236889999999999999997653    589999999999999999999999999


Q ss_pred             CCEEEEEEeecc
Q psy16184        169 DGRRVLVDVERS  180 (363)
Q Consensus       169 ~g~~i~V~~a~~  180 (363)
                      +|+.|.|.++..
T Consensus        81 ~GR~i~v~~~~~   92 (114)
T 3s6e_A           81 AGKMITAAYVPL   92 (114)
T ss_dssp             TTEECEEEEECH
T ss_pred             CCEEEEEEEEcH
Confidence            999999999864

>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=99.22  E-value=4.1e-11  Score=116.67  Aligned_cols=24  Identities=8%  Similarity=0.163  Sum_probs=12.8

Q ss_pred             EEEEEecCHHHHHHHHHH--hCCcee
Q psy16184        145 YAFIEYEHERDMHSAYKH--ADGKKI  168 (363)
Q Consensus       145 ~afV~f~~~~~a~~Ai~~--l~g~~i  168 (363)
                      +.|........|..+|..  |+|..|
T Consensus       149 V~F~~~e~A~~Ai~~lng~~i~gr~i  174 (437)
T 3pgw_S          149 IEYEHERDMHSAYKHADGKKIDGRRV  174 (437)
T ss_pred             EeeccHHHHHHHHHHcCCCEECCEEE
Confidence            445555666666655442  455444

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.22  E-value=3.9e-11  Score=89.35  Aligned_cols=74  Identities=12%  Similarity=0.260  Sum_probs=63.2

Q ss_pred             CCCCCeEEEcCCC----CCCCH----HHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC
Q psy16184         98 MDPFKTLFIARVN----YDTSE----SKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKID  169 (363)
Q Consensus        98 ~~~~~~l~V~nL~----~~~t~----~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~  169 (363)
                      .+|..||+|.-++    .++..    .+|.+.|.+||.|..++|+.+        .+||+|.+.++|.+||. |||..|+
T Consensus         4 GPpd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d--------~~fVtF~d~~sAlaAi~-mnG~~v~   74 (91)
T 2dnr_A            4 GSSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVED--------KMWVTFLEGSSALNVLS-LNGKELL   74 (91)
T ss_dssp             CCSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSS--------SEEEEESSHHHHHHGGG-GTTCEET
T ss_pred             CCCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecC--------CEEEEECChHHHHHHHh-cCCeEeC
Confidence            4566788888776    23333    678999999999999999876        48999999999999999 9999999


Q ss_pred             CEEEEEEeecc
Q psy16184        170 GRRVLVDVERS  180 (363)
Q Consensus       170 g~~i~V~~a~~  180 (363)
                      |+.|+|+++.+
T Consensus        75 Gr~LkV~lkt~   85 (91)
T 2dnr_A           75 NRTITIALKSP   85 (91)
T ss_dssp             TEEEEEEECCC
T ss_pred             CeEEEEEeCCC
Confidence            99999999865

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.19  E-value=3.3e-11  Score=95.52  Aligned_cols=79  Identities=19%  Similarity=0.123  Sum_probs=69.5

Q ss_pred             CCCCCCCeEEEcCCCCC-CCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecC-HHHHHHHHHHhC--CceeCCE
Q psy16184         96 ATMDPFKTLFIARVNYD-TSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEH-ERDMHSAYKHAD--GKKIDGR  171 (363)
Q Consensus        96 ~~~~~~~~l~V~nL~~~-~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~-~~~a~~Ai~~l~--g~~i~g~  171 (363)
                      ...++++.|||+||++. ++.++|+++|++||.|..|.|+.+..      .|||.|.+ ..+|..|+..||  +..|.|.
T Consensus        13 ~~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g~   86 (121)
T 1owx_A           13 LEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRNK   86 (121)
T ss_dssp             CSCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTSS
T ss_pred             ccccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeCc
Confidence            34567889999999999 99999999999999999999988753      69999999 899999999995  7889998


Q ss_pred             EEEEEeecc
Q psy16184        172 RVLVDVERS  180 (363)
Q Consensus       172 ~i~V~~a~~  180 (363)
                      .+.+++...
T Consensus        87 ~~~~evL~G   95 (121)
T 1owx_A           87 EVTWEVLEG   95 (121)
T ss_dssp             SEEEEECCH
T ss_pred             EEEEEECCC
Confidence            888887543

>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=99.08  E-value=4.2e-10  Score=84.14  Aligned_cols=74  Identities=16%  Similarity=0.236  Sum_probs=63.1

Q ss_pred             CCCCCCeEEEcCCCCC-----CCH----HHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCce
Q psy16184         97 TMDPFKTLFIARVNYD-----TSE----SKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKK  167 (363)
Q Consensus        97 ~~~~~~~l~V~nL~~~-----~t~----~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~  167 (363)
                      ..+|..||+|.-++..     +..    .+|.+.|.+||+|..++|+.++        +||+|.+.++|.+||. |||..
T Consensus        11 ~GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~-ldG~~   81 (95)
T 1ufw_A           11 QGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDGMK   81 (95)
T ss_dssp             CCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGGSE
T ss_pred             cCCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHh-cCCee
Confidence            4556779999988743     222    5689999999999999998873        9999999999999999 99999


Q ss_pred             eCCEEEEEEeec
Q psy16184        168 IDGRRVLVDVER  179 (363)
Q Consensus       168 i~g~~i~V~~a~  179 (363)
                      |+|+.|+|.+..
T Consensus        82 v~Gr~L~V~~k~   93 (95)
T 1ufw_A           82 VKGRAVKISGPS   93 (95)
T ss_dssp             ETTEEEEEECCC
T ss_pred             eCCeEEEEeccC
Confidence            999999999753

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=98.88  E-value=2.8e-09  Score=94.23  Aligned_cols=79  Identities=18%  Similarity=0.379  Sum_probs=65.6

Q ss_pred             CeEEEcCCC-----CCCCHHHHHHHHHhhCCccEEEEeccC----CCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEE
Q psy16184        102 KTLFIARVN-----YDTSESKLRREFEVYGPIKKIVMVHNK----VTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRR  172 (363)
Q Consensus       102 ~~l~V~nL~-----~~~t~~~L~~~F~~~G~i~~v~i~~d~----~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~  172 (363)
                      ..|.+.|+-     ..-.+++|.+.|++||.|..|.|+.+.    .++.++||+||+|.+.++|.+|+..|||..|+|+.
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            345555542     233568899999999999999998543    45589999999999999999999999999999999


Q ss_pred             EEEEeecc
Q psy16184        173 VLVDVERS  180 (363)
Q Consensus       173 i~V~~a~~  180 (363)
                      |.|.+...
T Consensus       205 i~~~~~~~  212 (222)
T 3dxb_A          205 VVAEVYDQ  212 (222)
T ss_dssp             CEEEECCH
T ss_pred             EEEEEcCH
Confidence            99999753

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.59  E-value=6e-07  Score=68.44  Aligned_cols=71  Identities=14%  Similarity=0.156  Sum_probs=66.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhh-----CCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEE
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVY-----GPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLV  175 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~-----G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V  175 (363)
                      .++|-|-|||..++...|+.++..+     |.|..|.+..|.      +-|+|+|.+...|.+|.-+|+|.+|.|++|.|
T Consensus        21 ~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH------~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~   94 (117)
T 2l9w_A           21 ETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF------NGAIIIFRDSKFAAKMLMILNGSQFQGKVIRS   94 (117)
T ss_dssp             TSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT------TEEEEECSCHHHHHHHHHHHSSEEETTEEEEE
T ss_pred             CcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC------CceEEEEccchhhHHHHhhcCCeeecCeEEEe
Confidence            5688899999999999999999999     999999998884      78999999999999999889999999999998


Q ss_pred             Ee
Q psy16184        176 DV  177 (363)
Q Consensus       176 ~~  177 (363)
                      --
T Consensus        95 gT   96 (117)
T 2l9w_A           95 GT   96 (117)
T ss_dssp             EC
T ss_pred             cC
Confidence            64

>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=97.87  E-value=4.3e-05  Score=58.00  Aligned_cols=76  Identities=13%  Similarity=0.112  Sum_probs=63.6

Q ss_pred             CCCeEEEcCCCCCC-C----HHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEE
Q psy16184        100 PFKTLFIARVNYDT-S----ESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVL  174 (363)
Q Consensus       100 ~~~~l~V~nL~~~~-t----~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~  174 (363)
                      ..++|+|+||+..+ +    ...++++|..|+++....+...      -.=..|.|.+.++|.+|-..|++..++|..|+
T Consensus         4 ~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkS------FRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r   77 (104)
T 1wey_A            4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVRINFSNPLSAADARLRLHKTEFLGKEMK   77 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT------TTEEEEECSSTTHHHHHHHTSTTSEETTEECE
T ss_pred             CCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCc------ceEEEEEeCChHHHHHHHHHhccceecCceeE
Confidence            35689999998765 2    2578999999999888777653      23578999999999999999999999999999


Q ss_pred             EEeeccc
Q psy16184        175 VDVERSR  181 (363)
Q Consensus       175 V~~a~~~  181 (363)
                      |-++.+.
T Consensus        78 ~YFgq~~   84 (104)
T 1wey_A           78 LYFAQTL   84 (104)
T ss_dssp             EECCCCS
T ss_pred             EEecCCC
Confidence            9999753

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.54  E-value=0.0013  Score=49.67  Aligned_cols=72  Identities=10%  Similarity=0.116  Sum_probs=60.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHh---h--CCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEE
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEV---Y--GPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVL  174 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~---~--G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~  174 (363)
                      ...+|.|.|||+.+.++.|.-+|+.   -  |.|..|....        +-|+|+|.+...|+..|.. ..+.|.+..|.
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k-~~H~L~~~~Ls   77 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQ-ADHELHGAQLS   77 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTC-SCCBSSSSBCE
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcC-CcceecCeEEE
Confidence            3579999999999999999999987   2  5888887743        5799999999999999883 47889999999


Q ss_pred             EEeecc
Q psy16184        175 VDVERS  180 (363)
Q Consensus       175 V~~a~~  180 (363)
                      |....+
T Consensus        78 V~P~~~   83 (104)
T 2dhx_A           78 LRPAPP   83 (104)
T ss_dssp             EEECCC
T ss_pred             EEcCCC
Confidence            876544

>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=0.00024  Score=52.94  Aligned_cols=78  Identities=13%  Similarity=0.161  Sum_probs=60.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCC--cceEEEEEecCHHHHHHHHHHhCCceeCC-----EEEE
Q psy16184        102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGK--PRGYAFIEYEHERDMHSAYKHADGKKIDG-----RRVL  174 (363)
Q Consensus       102 ~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~--~~g~afV~f~~~~~a~~Ai~~l~g~~i~g-----~~i~  174 (363)
                      ++|.|.+||+.+|++++.+.+..+..+.....+..+.+.+  .-.-|||.|.+.+++......++|+.+.+     ....
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            4899999999999999999999988777666655544333  34579999999999999999999987732     2345


Q ss_pred             EEeec
Q psy16184        175 VDVER  179 (363)
Q Consensus       175 V~~a~  179 (363)
                      |++|-
T Consensus        82 VE~AP   86 (91)
T 1uw4_A           82 VEFAP   86 (91)
T ss_dssp             EEECS
T ss_pred             EEEcC
Confidence            66653

>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=97.51  E-value=0.0004  Score=51.81  Aligned_cols=55  Identities=18%  Similarity=0.314  Sum_probs=46.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhC
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHAD  164 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~  164 (363)
                      ...++| ++|..+...+|.++|..||.| .|.++.|.       -|||.|.+.+.|..|+..++
T Consensus        16 ~HVf~l-~FP~ewKt~DI~~lFs~fggv-~I~WidDT-------sAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           16 DHVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CSEEEE-ECCTTCCHHHHHHHHTTTCSC-CCEEEETT-------EEEEECSCHHHHHHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHhhccCCE-EEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            445666 999999999999999999954 56676774       89999999999999999763

>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=97.20  E-value=0.0017  Score=50.57  Aligned_cols=70  Identities=20%  Similarity=0.214  Sum_probs=57.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC-EEEEEEee
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDG-RRVLVDVE  178 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g-~~i~V~~a  178 (363)
                      .+-|.|-+.|+.. ...|..+|++||.|.......      ...+-.|.|.+..+|++||. .||..|+| -.|-|...
T Consensus        24 ~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~~------~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p~   94 (119)
T 1wwh_A           24 DTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMSN------TGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPC   94 (119)
T ss_dssp             GGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECS------SSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEEC
T ss_pred             CCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCC------CCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEEC
Confidence            4578888999885 677888999999999887621      23599999999999999999 59999985 67777764

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=97.16  E-value=0.00037  Score=52.19  Aligned_cols=53  Identities=17%  Similarity=0.297  Sum_probs=45.5

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhC
Q psy16184        103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHAD  164 (363)
Q Consensus       103 ~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~  164 (363)
                      .++| ++|..+...+|..+|..|| -..|.++.|.       -|||.|.+++.|..|+..++
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            4556 9999999999999999999 4457777774       89999999999999999764

>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=97.11  E-value=2.1e-07  Score=73.30  Aligned_cols=92  Identities=13%  Similarity=0.171  Sum_probs=35.3

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccC--CCCCCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHH
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFE--DPKDTPPPTRVETREERLERRRRERAEQVAYKLEQE   84 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (363)
                      .+|..+|..+|+|..+. |+.+.  +.++|| |||.|.+...  .+...+....+.++.+.+...+...           
T Consensus        20 ~~L~~~F~~~G~v~~v~-i~~d~--~~~kg~-afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~~~-----------   84 (115)
T 4f25_A           20 KALYDTFSAFGNILSCK-VVCDE--NGSKGY-GFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK-----------   84 (115)
T ss_dssp             HHHHHHHGGGSCEEEEE-EEEET--TEEEEE-EEEEESCHHHHHHHHHHHTTCEETTEECEEEESSCCC-----------
T ss_pred             HHHHHHHhccCCEEEEE-EeecC--CCCCce-EEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCcc-----------
Confidence            46999999999998874 44443  458899 9999977443  1122234444444332221100000           


Q ss_pred             HhhcCCCCCCCCCCCCCCeEEEcCCCCCCCHHH
Q psy16184         85 IALWDPNSFPNATMDPFKTLFIARVNYDTSESK  117 (363)
Q Consensus        85 ~~~~~p~~~~~~~~~~~~~l~V~nL~~~~t~~~  117 (363)
                          .............++|||+|||+.+|++.
T Consensus        85 ----~~~~~~~~~~~~~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           85 ----EREAELGARAKEFTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             ----C----------------------------
T ss_pred             ----ccccccccccCCCCceEeCCCCCCccccc
Confidence                00000111122346899999999999764

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=96.81  E-value=0.0017  Score=48.65  Aligned_cols=78  Identities=12%  Similarity=0.120  Sum_probs=53.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCC--cceEEEEEecCHHHHHHHHHHhCCceeCC-----EEE
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGK--PRGYAFIEYEHERDMHSAYKHADGKKIDG-----RRV  173 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~--~~g~afV~f~~~~~a~~Ai~~l~g~~i~g-----~~i  173 (363)
                      +-+|.|..||+.+|++++.+.+..+=.+.....+....+.+  .-.-|||.|.+.+++..-...++|..+.+     -+.
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~~~a   88 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLEYPA   88 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCEEEE
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCEeee
Confidence            45899999999999999877776543332222222222222  23469999999999999999999987632     245


Q ss_pred             EEEee
Q psy16184        174 LVDVE  178 (363)
Q Consensus       174 ~V~~a  178 (363)
                      .|++|
T Consensus        89 ~VE~A   93 (97)
T 2l08_A           89 VVEFA   93 (97)
T ss_dssp             EEEEC
T ss_pred             EEEec
Confidence            66666

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.43  E-value=0.0052  Score=48.55  Aligned_cols=77  Identities=12%  Similarity=0.149  Sum_probs=55.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhhCCccEE-EEecc--------CCCC-----CcceEEEEEecCHHHHHHHHHHhCCce
Q psy16184        102 KTLFIARVNYDTSESKLRREFEVYGPIKKI-VMVHN--------KVTG-----KPRGYAFIEYEHERDMHSAYKHADGKK  167 (363)
Q Consensus       102 ~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v-~i~~d--------~~t~-----~~~g~afV~f~~~~~a~~Ai~~l~g~~  167 (363)
                      .-|.|-+.|+..+ ..|..+|++||.|.+- .+...        +...     ....+..|+|.+..+|.+||. .||..
T Consensus         8 ~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~i   85 (132)
T 3p3d_A            8 LAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGAV   85 (132)
T ss_dssp             CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTCE
T ss_pred             eEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCeE
Confidence            4677878877654 5677899999998762 11110        0001     123578999999999999999 59999


Q ss_pred             eCCEEEEEEeecc
Q psy16184        168 IDGRRVLVDVERS  180 (363)
Q Consensus       168 i~g~~i~V~~a~~  180 (363)
                      |+|..|-|.+...
T Consensus        86 i~G~mIGV~Py~~   98 (132)
T 3p3d_A           86 FNGVLLGVIPYTK   98 (132)
T ss_dssp             ETTEECEEEECCH
T ss_pred             eCcEEEEEEECCH
Confidence            9999888887653

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=95.88  E-value=0.0049  Score=59.58  Aligned_cols=55  Identities=22%  Similarity=0.347  Sum_probs=42.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHH
Q psy16184        102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH  162 (363)
Q Consensus       102 ~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~  162 (363)
                      ++|||. ++..+++.+|.++|++||.|..+.+..+.     .-||.|+|.+.++|..++..
T Consensus        54 rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~-----g~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           54 RTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF-----GLYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             TEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS-----SEEEEEECC---CCHHHHSS
T ss_pred             ceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC-----CeEEEEEeCCHHHHHHHHhc
Confidence            489997 79999999999999999999999887653     26999999999999977653

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=95.74  E-value=0.0034  Score=47.13  Aligned_cols=39  Identities=8%  Similarity=0.234  Sum_probs=31.6

Q ss_pred             hhhhhcCCCCCCCCCCC-CCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLP-PVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~-p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|+++|+|.... .+..++.|++++|| +||.|.+.
T Consensus        24 e~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~-aFV~f~~~   63 (95)
T 2lkz_A           24 DSIMTALSPYASLAVNNIRLIKDKQTQQNRGF-AFVQLSSA   63 (95)
T ss_dssp             HHHHHHSTTTCCCCGGGEECCCCSSSSSCSSE-EEEECSSS
T ss_pred             HHHHHHHHhhCCccEEEEEEEecCCCCCCceE-eEEEECCH
Confidence            46999999999876432 37789999999999 99999554

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=94.46  E-value=0.0024  Score=49.54  Aligned_cols=62  Identities=8%  Similarity=-0.025  Sum_probs=47.5

Q ss_pred             ChhhhhcCCCCCCCCC--------CCCCCCCCCCCCCCCCccccccccccC--CCCCCCCCCCcccHHHHHHHH
Q psy16184          6 PPNLLALFAPRDPVPY--------LPPVEKLPHEKKTHGYSGIAAFLNEFE--DPKDTPPPTRVETREERLERR   69 (363)
Q Consensus         6 p~~l~~~f~~~~pi~~--------~~p~~~~p~t~~s~g~~g~v~f~~~~~--~~~~~~~~~~~~~~~~~~~~~   69 (363)
                      ..+|..+|..+++|..        + -++.++.++.++|| +||.|.+...  .+...+....+.++.+.++..
T Consensus        21 ~~~l~~~F~~~G~i~~~~~~~~~~v-~i~~~~~~g~~~g~-afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   92 (116)
T 2lcw_A           21 IESVADYFKQIGIIKTNKKTGQPMI-NLYTDRETGKLKGE-ATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA   92 (116)
Confidence            3468999999999987        4 46677788999999 9999988655  333446778888887777653

>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=95.37  E-value=0.012  Score=48.01  Aligned_cols=35  Identities=11%  Similarity=0.135  Sum_probs=28.6

Q ss_pred             EEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCc
Q psy16184        130 KIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGK  166 (363)
Q Consensus       130 ~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~  166 (363)
                      .+.|+.+.  ..++|||||+|.+.++|++|+..+++.
T Consensus         2 ~~kl~ln~--~~~~G~~fV~f~~~~~A~~al~~~~~~   36 (158)
T 2kn4_A            2 QYKLILNG--KTLKGETTTEAVDAATAEKVFKQYAND   36 (158)
T ss_dssp             EEEEEEEC--SSCEEEEEEECSSHHHHHHHHHHHHHH
T ss_pred             cEEEEecC--ccccchhHHHHHHHHhHHHHHHhhccc
Confidence            45666664  368999999999999999999888764

>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=95.14  E-value=0.0071  Score=49.15  Aligned_cols=42  Identities=14%  Similarity=0.159  Sum_probs=37.9

Q ss_pred             CCCcceEEEEEecCHHHHHHHHHHh-CCceeCCEEEEEEeeccc
Q psy16184        139 TGKPRGYAFIEYEHERDMHSAYKHA-DGKKIDGRRVLVDVERSR  181 (363)
Q Consensus       139 t~~~~g~afV~f~~~~~a~~Ai~~l-~g~~i~g~~i~V~~a~~~  181 (363)
                      ....+|+++|+|.+.+.|++|+..| ||..|+| .|.|.++...
T Consensus         9 g~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~   51 (150)
T 2i2y_A            9 GKTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKT   51 (150)
T ss_dssp             CSSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTE
T ss_pred             cccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCc
Confidence            4567899999999999999999999 9999999 9999988653

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=94.93  E-value=0.0016  Score=51.59  Aligned_cols=37  Identities=5%  Similarity=0.028  Sum_probs=32.6

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCcccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLN   45 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~   45 (363)
                      ..|..+|+.+|+|..|. +..||.|+.|+|| |||.|.+
T Consensus        21 ~~Lk~~Fs~fGeV~~~~-li~Dp~Tg~slGf-gfVef~d   57 (136)
T 2j8a_A           21 ISIKNYFKKYGEISHFE-AFNDPNSALPLHV-YLIKYAS   57 (136)
T ss_dssp             HHHHHHHHTTSCCSEEE-EEECTTTCCEEEE-EEEECC-
T ss_pred             HHHHHHHHhcCCeEEEE-EEecCCCCceeeE-EEEEECC
Confidence            46899999999999994 6679999999999 9999985

>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=94.83  E-value=0.00048  Score=54.39  Aligned_cols=58  Identities=17%  Similarity=0.134  Sum_probs=40.8

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccC-CCCCCCCCCCcccHHHHH
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFE-DPKDTPPPTRVETREERL   66 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~-~~~~~~~~~~~~~~~~~~   66 (363)
                      .+|..+|.++++|..+ .++.+..+++++|| +||.|.+... ..+..+....+.++.+.+
T Consensus        40 ~~l~~~F~~~G~v~~~-~~~~~~~~g~~~G~-afV~F~~~~~a~~Al~~~g~~~~gr~i~V   98 (124)
T 1wel_A           40 KHVIDFFKKLDIVEDS-IYIAYGPNGKATGE-GFVEFRNEADYKAALCRHKQYMGNRFIQV   98 (124)
T ss_dssp             HHHHHHSCSSCBCTTT-CEEEECTTSSEEEE-EEEEBSSSHHHHHHHTSCSBCSTTSCBEE
T ss_pred             HHHHHHHHhcCCccce-EEEEECCCCCCCeE-EEEEECCHHHHHHHHHhCCCeECCcEEEE
Confidence            4689999999999886 34445668999999 9999988554 122225666666655443

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=94.70  E-value=0.0056  Score=45.37  Aligned_cols=38  Identities=5%  Similarity=0.170  Sum_probs=32.0

Q ss_pred             hhhhhcCCCCC-CCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRD-PVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~-pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|+++| +|..+ -++.++.|+.++|| +||.|.+.
T Consensus        16 ~~l~~~F~~~G~~v~~v-~i~~d~~t~~~rg~-aFV~F~~~   54 (91)
T 2lxi_A           16 DDIRGQLQSHGVQAREV-RLMRNKSSGQSRGF-AFVEFSHL   54 (91)
T ss_dssp             HHHHHHHHHHTCCCSBC-CSSSCSSSCCCSSE-EEEECSSH
T ss_pred             HHHHHHHHHhCCEeEEE-EEEecCCCCCcCce-EEEEecCH
Confidence            45999999999 78877 47779999999999 99999554

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=94.65  E-value=0.0027  Score=44.95  Aligned_cols=38  Identities=16%  Similarity=0.212  Sum_probs=32.4

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|.++|+|..+ .+..++.++.++|| +||.|.+.
T Consensus        14 ~~l~~~F~~~G~i~~v-~i~~~~~~~~~~g~-afV~f~~~   51 (75)
T 2mss_A           14 EDVKHYFEQFGKVDDA-MLMFDKTTNRHRGF-GFVTFESE   51 (75)
T ss_dssp             HHHHHHHHTTSCCSEE-CCCBCSSSTTSCBE-EEEECSCH
T ss_pred             HHHHHHHHhcCCEEEE-EEEecCCCCCcCcE-EEEEECCH
Confidence            4689999999999988 46678889999999 99998664

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=94.57  E-value=0.00038  Score=53.26  Aligned_cols=58  Identities=10%  Similarity=0.087  Sum_probs=41.7

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccC-CCCCCCCCCCcccHHHHHH
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFE-DPKDTPPPTRVETREERLE   67 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~-~~~~~~~~~~~~~~~~~~~   67 (363)
                      .+|..+|+++|+|..+ -++.++. +.++|| +||.|.+... ..+..+..+.+.++.+.++
T Consensus        26 ~~L~~~F~~~G~v~~v-~i~~d~~-g~~rG~-aFV~F~~~e~a~~Ai~~~~~~~~gr~l~V~   84 (103)
T 1s79_A           26 DDIKEWLEDKGQVLNI-QMRRTLH-KAFKGS-IFVVFDSIESAKKFVETPGQKYKETDLLIL   84 (103)
T ss_dssp             HHHHHHHHTSSCEEEE-EEECCCT-TSCCCE-EEEEESSHHHHHHHHTSSCCCCTTTTCEEE
T ss_pred             HHHHHHHhhcCCEEEE-EEEECCC-CCCccE-EEEEECCHHHHHHHHHcCCCEECCEEEEEE
Confidence            4689999999999887 4566776 999999 9999987544 2222355666777655444

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=94.33  E-value=0.0031  Score=47.61  Aligned_cols=37  Identities=19%  Similarity=0.144  Sum_probs=32.3

Q ss_pred             hhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          8 NLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         8 ~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      +|..+|+++|+|..+ -++.++.|++++|| +||.|.+.
T Consensus        28 ~L~~~F~~~G~i~~v-~i~~d~~tg~~kG~-afV~f~~~   64 (100)
T 3ns6_A           28 ALTSLFSKAGKVVNM-EFPIDEATGKTKGF-LFVECGSM   64 (100)
T ss_dssp             HHHHHHHTTSCEEEE-ECCEETTTTEECSE-EEEEESSH
T ss_pred             HHHHHHHhcCCEeEE-EEEEcCCCCccceE-EEEEECCH
Confidence            799999999999988 46778899999999 99999664

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=94.01  E-value=0.011  Score=46.86  Aligned_cols=39  Identities=15%  Similarity=0.207  Sum_probs=32.7

Q ss_pred             ChhhhhcCCCCCCCCC--CCCCCCCCCCCCCCCCccccccccc
Q psy16184          6 PPNLLALFAPRDPVPY--LPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         6 p~~l~~~f~~~~pi~~--~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      ..+|..+|.++|+|..  + -|+.++.|++++|| |||.|.+.
T Consensus        37 e~~L~~~F~~~G~v~~~~v-~i~~d~~tg~~rG~-aFV~f~~~   77 (131)
T 2m2b_A           37 MDSILGALAPYAVLSSSNV-RVIKDKQTQLNRGF-AFIQLSTI   77 (131)
T ss_dssp             SHHHHHHHGGGCCCCTTTE-ECCBCSSSSSBCSC-EEEECCHH
T ss_pred             HHHHHHHHHHhCCcceeeE-EEEEcCCCCCcceE-EEEEECCH
Confidence            3569999999999977  5 47778999999999 99999554

>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=93.96  E-value=0.00011  Score=57.26  Aligned_cols=35  Identities=14%  Similarity=0.329  Sum_probs=26.1

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|.++|+|..+. +..   ++.++|| +||.|.+.
T Consensus        23 ~~l~~~F~~~G~v~~v~-i~~---~~~~~g~-afV~f~~~   57 (115)
T 3lqv_A           23 EEMYDIFGKYGPIRQIR-VGN---TPETRGT-AYVVYEDI   57 (115)
T ss_dssp             HHHHHHHHTTSCEEEEE-EEC---STTTTTC-EEEEESSH
T ss_pred             HHHHHHHHhcCCeEEEE-Eee---CCCCCcE-EEEEECCH
Confidence            46899999999998763 322   4567999 89998553

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=93.95  E-value=0.015  Score=41.06  Aligned_cols=40  Identities=23%  Similarity=0.390  Sum_probs=33.2

Q ss_pred             ChhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccc
Q psy16184          6 PPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEF   47 (363)
Q Consensus         6 p~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~   47 (363)
                      ..+|..+|.++|+|..+ .+..++.++.++|| +||.|.+..
T Consensus        14 ~~~l~~~F~~~G~v~~v-~i~~~~~~~~~~g~-afV~f~~~~   53 (77)
T 1uaw_A           14 QEGLREYFGQFGEVKEC-LVMRDPLTKRSRGF-GFVTFMDQA   53 (77)
T ss_dssp             SHHHHHHHTTTSCCCCE-EEECCCCSSSCSSE-EEECCCCTT
T ss_pred             HHHHHHHHHhcCCEEEE-EEecCCCCCCcCce-EEEEEcCHH
Confidence            45789999999999887 46668889999999 999986643

>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=93.85  E-value=0.0039  Score=44.05  Aligned_cols=39  Identities=15%  Similarity=0.193  Sum_probs=32.8

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEF   47 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~   47 (363)
                      .+|..+|.++|+|..+ -+..++.++.++|| +||.|.+..
T Consensus        14 ~~l~~~F~~~G~i~~v-~i~~~~~~~~~~g~-afV~f~~~~   52 (75)
T 1iqt_A           14 EKIREYFGGFGEVESI-ELPMDNKTNKRRGF-CFITFKEEE   52 (75)
T ss_dssp             HHHHHHHHHHSCCSEE-CCCCSCCCSSSCCC-EEEECSSSH
T ss_pred             HHHHHHHHhcCCeEEE-EEEecCCCCCcCCE-EEEEECCHH
Confidence            4689999999999887 46678889999999 999997643

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=93.51  E-value=0.0046  Score=47.69  Aligned_cols=39  Identities=15%  Similarity=0.119  Sum_probs=33.4

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEF   47 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~   47 (363)
                      .+|..+|+++|+|..+ .|+.++.|++++|| +||.|.+..
T Consensus        21 ~~L~~~F~~~G~i~~v-~i~~d~~tg~~rG~-aFV~f~~~~   59 (110)
T 3s8s_A           21 TFLKDMCRKYGEVEEV-EILLHPRTRKHLGL-ARVLFTSTR   59 (110)
T ss_dssp             HHHHHHHTTTSCEEEE-EEEECTTTCCEEEE-EEEEESSHH
T ss_pred             HHHHHHHHhcCCeeEE-EEEECCCCCceeeE-EEEEECCHH
Confidence            4699999999999988 47779999999999 999996643

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=92.99  E-value=0.00025  Score=58.72  Aligned_cols=58  Identities=12%  Similarity=0.140  Sum_probs=41.0

Q ss_pred             hhhhhcCCCCC--CCCCCCCCCCCCCCCCCCCCccccccccccC--CCCCCCCCCCcccHHHHH
Q psy16184          7 PNLLALFAPRD--PVPYLPPVEKLPHEKKTHGYSGIAAFLNEFE--DPKDTPPPTRVETREERL   66 (363)
Q Consensus         7 ~~l~~~f~~~~--pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~--~~~~~~~~~~~~~~~~~~   66 (363)
                      .+|..+|..+|  +|..+ -++.++.|++++|| |||.|.+...  .+...+....+.++.+.+
T Consensus        70 ~~L~~~F~~~G~i~v~~v-~i~~d~~tg~skGf-aFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V  131 (156)
T 3n9u_C           70 QQLIQVIRSIGVYDVVEL-KFAENRANGQSKGY-AEVVVASENSVHKLLELLPGKVLNGEKVDV  131 (156)
T ss_dssp             HHHHHHHHHTTCCCEEEE-EEEECTTTCCEEEE-EEEEESCHHHHHHHHHHSTTCEETTEECEE
T ss_pred             HHHHHHHHHHCCccEEEE-EEEecCCCCccceE-EEEEECCHHHHHHHHHHcCCCEECCeEeEE
Confidence            46899999999  56656 36678889999999 9999987544  233345566666654433

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=92.78  E-value=0.017  Score=44.25  Aligned_cols=38  Identities=24%  Similarity=0.432  Sum_probs=32.1

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|..+|+|..+ .+..++.|+.++|| +||.|.+.
T Consensus        40 ~~L~~~F~~~G~i~~v-~i~~~~~tg~~kg~-afV~f~~~   77 (109)
T 2rs2_A           40 EGLREYFGQFGEVKEC-LVMRDPLTKRSRGF-GFVTFMDQ   77 (109)
T ss_dssp             HHHHHHHTTTSCEEEE-EECCCTTTCCCTTC-EEEEESSH
T ss_pred             HHHHHHHHccCCeEEE-EEEECCCCCCcCcE-EEEEECCH
Confidence            4589999999999887 46678889999999 99999554

>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=92.75  E-value=0.00095  Score=58.82  Aligned_cols=59  Identities=8%  Similarity=0.104  Sum_probs=43.7

Q ss_pred             hhhhhcCCCCC--CCCCCCCCCCCCCCCCCCCCccccccccccC--CCCCCCCCCCcccHHHHHH
Q psy16184          7 PNLLALFAPRD--PVPYLPPVEKLPHEKKTHGYSGIAAFLNEFE--DPKDTPPPTRVETREERLE   67 (363)
Q Consensus         7 ~~l~~~f~~~~--pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~--~~~~~~~~~~~~~~~~~~~   67 (363)
                      .+|..+|..++  .|..+ -|+.+..|++++|| +||.|.+...  .+...+....|.++.+.+.
T Consensus        83 ~~L~~~F~~~G~~~v~~v-~i~~d~~tg~skGf-aFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~  145 (229)
T 3q2s_C           83 EDLTEAVHSLGVNDILEI-KFFENRANGQSKGF-ALVGVGSEASSKKLMDLLPKRELHGQNPVVT  145 (229)
T ss_dssp             HHHHHHHHTTTCCCEEEE-EEEECTTTCCEEEE-EEEEESCTTHHHHHHTTSTTSCBTTBCCEEE
T ss_pred             HHHHHHHHHHCCcceEEE-EEEecCCCCccceE-EEEEECCHHHHHHHHHHcCCCeECCEEeEEE
Confidence            46899999999  77777 46678889999999 9999987554  3344466666666655444

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=92.65  E-value=0.037  Score=41.39  Aligned_cols=39  Identities=18%  Similarity=0.221  Sum_probs=32.5

Q ss_pred             ChhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          6 PPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         6 p~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      ..+|..+|..+++|..+ .++.++.++.++|| +||.|.+.
T Consensus        26 ~~~l~~~f~~~G~i~~v-~i~~~~~~~~~~g~-afV~f~~~   64 (102)
T 2cqb_A           26 DKVLHAAFIPFGDITDI-QIPLDYETEKHRGF-AFVEFELA   64 (102)
T ss_dssp             HHHHHHHHTTTSCCCCE-ECCCCSSSCCCSSE-EEECCSSH
T ss_pred             HHHHHHHhhccCCEEEE-EEEecCCCCCcceE-EEEEECCH
Confidence            35689999999999988 46678889999999 88888553

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=92.56  E-value=0.029  Score=41.48  Aligned_cols=39  Identities=18%  Similarity=0.294  Sum_probs=32.5

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|.++++|..+..++.++.++.++|| +||.|.+.
T Consensus        20 ~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~-afV~f~~~   58 (96)
T 1x5t_A           20 KLLYDTFSAFGVILQTPKIMRDPDTGNSKGY-AFINFASF   58 (96)
T ss_dssp             HHHHHHHHTTSCBSSCCEECCCTTTCSCCSE-EEEEBSSH
T ss_pred             HHHHHHHHhcCCeeEEEEEEEcCCCCCcCeE-EEEEECCH
Confidence            5689999999999888446678889999999 89998553

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=92.53  E-value=0.021  Score=41.28  Aligned_cols=38  Identities=21%  Similarity=0.289  Sum_probs=31.7

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|.++++|..+ .++.++.++.++|| +||.|.+.
T Consensus        20 ~~l~~~f~~~G~i~~~-~i~~~~~~~~~~g~-afV~f~~~   57 (85)
T 1x4e_A           20 QDLVKLCQPYGKIVST-KAILDKTTNKCKGY-GFVDFDSP   57 (85)
T ss_dssp             HHHHTTSTTTSCEEEE-EEECCSSSCSCCSE-EEEEESCH
T ss_pred             HHHHHHHHhcCCeEEE-EEEecCCCCCcCcE-EEEEECCH
Confidence            4689999999999887 46667889999999 89988553

>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=92.43  E-value=0.0035  Score=47.95  Aligned_cols=58  Identities=10%  Similarity=0.013  Sum_probs=38.2

Q ss_pred             ChhhhhcCCCCCC---CCCCCCCCCCCCCCCCCCCccccccccccC-CCCCCCCCCCcccHHHHH
Q psy16184          6 PPNLLALFAPRDP---VPYLPPVEKLPHEKKTHGYSGIAAFLNEFE-DPKDTPPPTRVETREERL   66 (363)
Q Consensus         6 p~~l~~~f~~~~p---i~~~~p~~~~p~t~~s~g~~g~v~f~~~~~-~~~~~~~~~~~~~~~~~~   66 (363)
                      ..+|..+|..+++   |..+ -+..++. ++++|| +||.|.+... ..+..+....+.++.+.+
T Consensus        25 e~~l~~~F~~~g~~~~v~~v-~i~~~~~-g~~~G~-afV~F~~~~~a~~Al~~~~~~~~gr~i~V   86 (107)
T 2lmi_A           25 MEDVLNFFSDCRIRNGENGI-HFLLNRD-GKRRGD-ALIEMESEQDVQKALEKHRMYMGQRYVEV   86 (107)
T ss_dssp             SHHHHHHTTTSCBTTTTTTE-ECCCCTT-STTCSE-EEEEBSSHHHHHHHHTTTTCCSSSSCCCC
T ss_pred             HHHHHHHHHhcCCcCCcceE-EEEECCC-CCEeeE-EEEEECCHHHHHHHHHhCcceeCCeEEEE
Confidence            4579999999888   6666 3555666 999999 9999987544 111224445555544433

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=92.40  E-value=0.0056  Score=44.06  Aligned_cols=37  Identities=14%  Similarity=0.145  Sum_probs=29.8

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEF   47 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~   47 (363)
                      .+|..+|+++|+|..+. ++  +.+++++|| +||.|.+..
T Consensus        22 ~~l~~~F~~~G~i~~v~-i~--~~~g~~~g~-afV~f~~~~   58 (81)
T 2krb_A           22 NVIHKIFSKFGKITNDF-YP--EEDGKTKGY-IFLEYASPA   58 (81)
T ss_dssp             HHHHHHHHTTCCEEEEE-CC--CBTTBCCCE-EEEEESSHH
T ss_pred             HHHHHHHhhcCCeEEEE-ec--CCCCcEeEE-EEEEECCHH
Confidence            56899999999998764 32  468999999 999997644

>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=92.29  E-value=0.045  Score=42.06  Aligned_cols=38  Identities=16%  Similarity=0.053  Sum_probs=30.3

Q ss_pred             hhhhhcCCCCCCC-CCCCCCCCCCCCCCCCCCcccccccccc
Q psy16184          7 PNLLALFAPRDPV-PYLPPVEKLPHEKKTHGYSGIAAFLNEF   47 (363)
Q Consensus         7 ~~l~~~f~~~~pi-~~~~p~~~~p~t~~s~g~~g~v~f~~~~   47 (363)
                      .+|..+|..+++| ..+ .|+.++ +++++|| +||.|.+..
T Consensus        30 ~~l~~~F~~~g~v~~~v-~i~~d~-~g~~~G~-afV~F~~~~   68 (114)
T 2cpy_A           30 MDVLQFLEGIPVDENAV-HVLVDN-NGQGLGQ-ALVQFKNED   68 (114)
T ss_dssp             HHHHHHTTTSCCCSTTE-EECCCT-TSSCSSC-EEEECSSHH
T ss_pred             HHHHHHHHhCCCcCCeE-EEEECC-CCCcceE-EEEEECCHH
Confidence            4699999999998 555 355677 8999999 999996643

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=92.20  E-value=0.028  Score=42.23  Aligned_cols=39  Identities=21%  Similarity=0.355  Sum_probs=32.6

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEF   47 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~   47 (363)
                      .+|..+|..+++|..+ .+..++.|+.++|| +||.|.+..
T Consensus        28 ~~l~~~f~~~G~i~~v-~i~~~~~~~~~~g~-afV~f~~~~   66 (103)
T 2dnm_A           28 DSLRRVFEKYGRVGDV-YIPREPHTKAPRGF-AFVRFHDRR   66 (103)
T ss_dssp             HHHHHHHTTTSCEEEE-ECCBCSSSCSBCSC-EEEEESSSS
T ss_pred             HHHHHHHHhcCCEEEE-EEEeCCCCCCCCeE-EEEEECCHH
Confidence            4689999999999887 46678889999999 999986643

>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=92.14  E-value=0.013  Score=43.03  Aligned_cols=38  Identities=8%  Similarity=0.110  Sum_probs=30.6

Q ss_pred             hhhhhcCCCCC--CCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRD--PVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~--pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|.++|  +|..+ -++.++.+++++|| +||.|.+.
T Consensus        16 ~~l~~~F~~~G~~~v~~v-~i~~~~~~g~~kG~-afV~f~~~   55 (90)
T 3p5t_L           16 EDLTEAVHSLGVNDILEI-KFFENRANGQSKGF-ALVGVGSE   55 (90)
T ss_dssp             HHHHHHHHTTTCCCCCCE-EEEECTTTCCEEEE-EEECC-CH
T ss_pred             HHHHHHHHHhCCCceEEE-EEEecCCCCccCcE-EEEEECCH
Confidence            46899999999  77766 36678889999999 99998554

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=92.07  E-value=0.028  Score=43.30  Aligned_cols=38  Identities=18%  Similarity=0.347  Sum_probs=32.2

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|.++++|..+ -++.++.++.++|| +||.|.+.
T Consensus        42 ~~l~~~F~~~G~i~~v-~i~~~~~~g~~~g~-afV~f~~~   79 (116)
T 1x4b_A           42 ESLRNYYEQWGKLTDC-VVMRDPASKRSRGF-GFVTFSSM   79 (116)
T ss_dssp             HHHHHHHTSSCCCSEE-EEECCTTTSSCCSE-EEEECSSH
T ss_pred             HHHHHHHHhcCCEEEE-EEEECCCCCCcCce-EEEEeCCH
Confidence            4689999999999888 46678889999999 99998554

>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=91.92  E-value=0.027  Score=43.28  Aligned_cols=39  Identities=13%  Similarity=0.191  Sum_probs=32.9

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEF   47 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~   47 (363)
                      .+|..+|..+++|..+ .+..++.++.++|| +||.|.+..
T Consensus        40 ~~l~~~F~~~G~i~~v-~i~~~~~~g~~~g~-afV~f~~~~   78 (114)
T 2cq4_A           40 RDLEDFFSAVGKVRDV-RIISDRNSRRSKGI-AYVEFCEIQ   78 (114)
T ss_dssp             HHHHHHHTTTSCEEEE-EECCSCCSSSCCCC-EEEEESCGG
T ss_pred             HHHHHHHHhCCCEeEE-EEEecCCCCccCcE-EEEEeCcHH
Confidence            4689999999999888 46668888999999 999997654

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=91.89  E-value=0.02  Score=45.78  Aligned_cols=39  Identities=15%  Similarity=0.232  Sum_probs=32.3

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEF   47 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~   47 (363)
                      .+|..+|+.+++|..+ .+..++.++.++|| +||.|.+..
T Consensus        62 ~~L~~~F~~~G~i~~v-~i~~~~~~g~~~G~-afV~F~~~~  100 (135)
T 2lea_A           62 DTLRRVFEKYGRVGDV-YIPRDRYTKESRGF-AFVRFHDKR  100 (135)
T ss_dssp             HHHHHHHGGGSCCSEE-ECCCCSSSSSCCSC-CEEECSCHH
T ss_pred             HHHHHHHHhcCCEEEE-EEEecCCCCccceE-EEEEECCHH
Confidence            4689999999999887 46667888999999 999996643

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=91.71  E-value=0.024  Score=42.28  Aligned_cols=38  Identities=18%  Similarity=0.294  Sum_probs=31.9

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|..+++|..+ .++.++.++.++|| +||.|.+.
T Consensus        25 ~~l~~~F~~~G~i~~v-~i~~~~~~~~~~g~-afV~f~~~   62 (99)
T 2dgs_A           25 TELREYFKKFGVVTEV-VMIYDAEKQRPRGF-GFITFEDE   62 (99)
T ss_dssp             HHHHHHHSSSSCEEEE-EECCCTTTCSCCSE-EEEEESSH
T ss_pred             HHHHHHHHhcCCeEEE-EEEeCCCCCCCCce-EEEEECCH
Confidence            5689999999999887 46678889999999 89998553

>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=91.68  E-value=0.0082  Score=45.26  Aligned_cols=38  Identities=18%  Similarity=0.313  Sum_probs=32.0

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|+++|+|..+ -+..++.|+.++|| +||.|.+.
T Consensus        34 ~~L~~~F~~~G~I~~v-~i~~d~~tg~~kG~-afV~f~~~   71 (99)
T 4fxv_A           34 DELRSLFSSIGEVESA-KLIRDKVAGHSLGY-GFVNYVTA   71 (99)
T ss_dssp             HHHHHHHHTTSCEEEE-EEEECSSSCCEEEE-EEEEESSH
T ss_pred             HHHHHHHHhcCCEEEe-EeeecCCCCccccc-EEEEECCH
Confidence            4689999999999987 46678889999999 99998553

>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=91.59  E-value=0.022  Score=43.38  Aligned_cols=38  Identities=18%  Similarity=0.347  Sum_probs=32.0

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|..+++|..+ .++.++.++.++|| +||.|.+.
T Consensus        30 ~~l~~~F~~~G~i~~v-~i~~~~~~g~~~g~-afV~f~~~   67 (111)
T 1x4h_A           30 EALGEVLQQFGDLKYV-RVVLHPDTEHSKGC-AFAQFMTQ   67 (111)
T ss_dssp             HHHHHHHHTTSCEEEE-ECCBCSSSCCBCSE-EEEEESSH
T ss_pred             HHHHHHHHhcCCeEEE-EEEecCCCCCCccE-EEEEECCH
Confidence            4689999999999888 46778889999999 99998554

>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=91.37  E-value=0.013  Score=42.68  Aligned_cols=38  Identities=18%  Similarity=0.350  Sum_probs=32.1

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|.++|+|..+ .+..++.+++++|| +||.|.+.
T Consensus        26 ~~l~~~F~~~G~i~~v-~i~~~~~~g~~~g~-afV~f~~~   63 (87)
T 3s7r_A           26 KDLKDYFTKFGEVVDC-TIKMDPNTGRSRGF-GFILFKDA   63 (87)
T ss_dssp             HHHHHHHTTTSCEEEE-EEEECTTTCCEEEE-EEEEESST
T ss_pred             HHHHHHHHhCCCEEEE-EEeecCCCCccccE-EEEEECCH
Confidence            4699999999999988 46667889999999 99998654

>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=91.19  E-value=0.0089  Score=45.31  Aligned_cols=38  Identities=18%  Similarity=0.391  Sum_probs=29.2

Q ss_pred             ChhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccc
Q psy16184          6 PPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEF   47 (363)
Q Consensus         6 p~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~   47 (363)
                      ..+|..+|.+++++ .+ .|+.++ +++++|| +||.|.+..
T Consensus        29 e~~l~~~F~~~G~~-~v-~i~~d~-~g~~~G~-afV~F~~~~   66 (102)
T 1wez_A           29 ENDIYNFFSPLNPM-RV-HIEIGP-DGRVTGE-ADVEFATHE   66 (102)
T ss_dssp             HHHHHHSSCSCCCS-EE-EEEESS-SSCEEEE-EEEECSSSH
T ss_pred             HHHHHHHHHHcCce-EE-EEEECC-CCCEeeE-EEEEECCHH
Confidence            35699999999965 44 355566 8999999 999996654

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=91.18  E-value=0.08  Score=40.63  Aligned_cols=37  Identities=19%  Similarity=0.268  Sum_probs=28.7

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCC---CCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHE---KKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t---~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|.++++|. + .++.+..+   ++++|| +||.|.+.
T Consensus        23 ~~L~~~F~~~G~i~-~-~~~~~~~~~~~g~~~G~-aFV~f~~~   62 (114)
T 2dnl_A           23 DEITASFRRFGPLV-V-DWPHKAESKSYFPPKGY-AFLLFQEE   62 (114)
T ss_dssp             HHHHHHTTTTCCCC-E-ECTTSSSSCCCSCTTSE-EEECCSSH
T ss_pred             HHHHHHHHhcCCEE-E-EEeecCCCCCCCCcccE-EEEEECCH
Confidence            46899999999998 4 34555566   799999 99998553

>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=90.96  E-value=0.66  Score=45.45  Aligned_cols=56  Identities=18%  Similarity=0.283  Sum_probs=46.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCC
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADG  165 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g  165 (363)
                      ...++|+ +|..+...+|.++|+.||.| .|.++.+       ..|||.|.+.+.|..++.+++.
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~widd-------t~a~V~~~~~~~a~~~l~~~~~  495 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWIDD-------TSAFVSLSQPEQVQIAVNTSKY  495 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEECSS-------SEEEEECSCHHHHHHHHHHHTT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEEcC-------CeEEEEECCHHHHHHHHHHHHh
Confidence            3466676 88888999999999999954 6666555       3899999999999999998853

>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=90.84  E-value=0.027  Score=42.55  Aligned_cols=38  Identities=18%  Similarity=0.181  Sum_probs=32.1

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|..+++|..+ .++.++.++.++|| +||.|.+.
T Consensus        28 ~~l~~~F~~~G~i~~v-~i~~~~~~g~~~g~-afV~f~~~   65 (106)
T 2dgp_A           28 KDLKPLFEEFGKIYEL-TVLKDRFTGMHKGC-AFLTYCER   65 (106)
T ss_dssp             HHHHHHHHHHSCCCEE-ECCCCSSSCSCCSE-EEEEESSH
T ss_pred             HHHHHHHHhcCCeeEE-EEEecCCCCCcceE-EEEEECCH
Confidence            4689999999999988 46778889999999 89998553

>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=90.76  E-value=0.033  Score=41.48  Aligned_cols=38  Identities=24%  Similarity=0.362  Sum_probs=31.7

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|.++++|..+ .+..++.++.++|| +||.|.+.
T Consensus        23 ~~l~~~F~~~G~i~~v-~i~~~~~~~~~~g~-afV~f~~~   60 (99)
T 1whw_A           23 EDLEKLFSAYGPLSEL-HYPIDSLTKKPKGF-AFVTFMFP   60 (99)
T ss_dssp             HHHHHHHHTTSCEEEE-ECCCCTTTCCCCSE-EEEEESSH
T ss_pred             HHHHHHHHhcCCEeEE-EEEecCCCCCcCeE-EEEEECCH
Confidence            4689999999999887 46667889999999 99998553

>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=90.66  E-value=0.043  Score=40.68  Aligned_cols=38  Identities=18%  Similarity=0.224  Sum_probs=31.1

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|.++++|..+ .++.++.+++++|| +||.|.+.
T Consensus        30 ~~l~~~F~~~G~v~~~-~~~~~~~~g~~~g~-afV~f~~~   67 (98)
T 2cqp_A           30 DEILDFFYGYQVIPGS-VCLKYNEKGMPTGE-AMVAFESR   67 (98)
T ss_dssp             HHHHHHTTTSCCCTTT-CEEEECSSSCEEEE-EEEEESCH
T ss_pred             HHHHHHHHHcCCccce-EEEEECCCCCeeeE-EEEEECCH
Confidence            4699999999999877 35567788999999 89998554

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=90.65  E-value=0.048  Score=40.06  Aligned_cols=38  Identities=21%  Similarity=0.365  Sum_probs=31.7

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|.++++|..+ .+..++.++.++|| +||.|.+.
T Consensus        31 ~~l~~~f~~~G~v~~v-~i~~~~~~~~~~g~-afV~f~~~   68 (94)
T 2e5h_A           31 NDLYRIFSKYGKVVKV-TIMKDKDTRKSKGV-AFILFLDK   68 (94)
T ss_dssp             HHHHHHTTTTSCEEEE-EECCCSSSCCCTTC-EEEEESCH
T ss_pred             HHHHHHHHhcCCeEEE-EEEeCCCCCCcccE-EEEEECCH
Confidence            4699999999999887 46667888999999 88988554

>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=90.62  E-value=0.022  Score=41.60  Aligned_cols=39  Identities=21%  Similarity=0.269  Sum_probs=32.5

Q ss_pred             ChhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          6 PPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         6 p~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      ..+|..+|+++|+|..+ .+..++.++.++|| +||.|.+.
T Consensus        15 ~~~l~~~F~~~G~i~~v-~i~~~~~~~~~~g~-afV~f~~~   53 (90)
T 2ki2_A           15 SEQVKELFSQFGKVFNV-KLIYDRETKKPKGF-GFVEMQEE   53 (90)
T ss_dssp             HHHHTTTHHHHTCCSEE-EECCCSSSCCCCEE-EEEEECTT
T ss_pred             HHHHHHHHHhcCCEEEE-EEEEcCCCCCcceE-EEEEECCH
Confidence            35689999999999887 46678888999999 99998654

>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=90.59  E-value=0.036  Score=41.75  Aligned_cols=38  Identities=34%  Similarity=0.515  Sum_probs=31.8

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|.++++|..+ .++.++.++.++|| +||.|.+.
T Consensus        30 ~~l~~~F~~~G~i~~v-~i~~~~~~~~~~g~-afV~f~~~   67 (105)
T 1x5u_A           30 PLLWELFLQAGPVVNT-HMPKDRVTGQHQGY-GFVEFLSE   67 (105)
T ss_dssp             HHHHHHHHTTSCEEEE-ECCBCSSSCSBCSC-EEEEESSH
T ss_pred             HHHHHHHHhcCCeEEE-EEEecCCCCcCCcE-EEEEECCH
Confidence            4689999999999887 46678889999999 99998554

>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=90.18  E-value=0.036  Score=41.04  Aligned_cols=38  Identities=24%  Similarity=0.375  Sum_probs=31.8

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|+.+|+|..+ -+..++.++.++|| +||.|.+.
T Consensus        17 ~~l~~~F~~~G~i~~v-~i~~~~~~g~~~g~-afV~f~~~   54 (96)
T 2x1f_A           17 EQILDLCSNVGPVINL-KMMFDPQTGRSKGY-AFIEFRDL   54 (96)
T ss_dssp             HHHHHHHHTTSCEEEE-ECCBCTTTCCBCSE-EEEEESSH
T ss_pred             HHHHHHHHhcCCEEEE-EEEeCCCCCccceE-EEEEECCH
Confidence            5689999999999887 46678889999999 89998543

>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=90.06  E-value=0.048  Score=40.12  Aligned_cols=38  Identities=18%  Similarity=0.224  Sum_probs=31.2

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|.++++|..+ .++.++.+++++|| +||.|.+.
T Consensus        30 ~~l~~~F~~~G~i~~~-~~~~~~~~g~~~g~-afV~f~~~   67 (95)
T 2ek1_A           30 DEILDFFYGYQVIPGS-VCLKYNEKGMPTGE-AMVAFESR   67 (95)
T ss_dssp             HHHHHHTTTSCBCTTC-CEEEECTTSCEEEE-EEEEESSH
T ss_pred             HHHHHHHHhcCCccce-EEEEeCCCCCEeeE-EEEEECCH
Confidence            5699999999999877 35567788999999 89998554

>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=89.96  E-value=0.045  Score=42.75  Aligned_cols=38  Identities=11%  Similarity=0.163  Sum_probs=31.8

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|..+++|..+ .++.++.++.++|| +||.|.+.
T Consensus        37 ~~l~~~F~~~G~i~~v-~i~~~~~~~~~~g~-afV~f~~~   74 (126)
T 3ex7_B           37 EDIHDKFAEYGEIKNI-HLNLDRRTGYLKGY-TLVEYETY   74 (126)
T ss_dssp             HHHHHHHHTTSCEEEE-ECCBCTTTSSBCSC-EEEEESSH
T ss_pred             HHHHHHHHhcCCeEEE-EEEecCCCCccceE-EEEEECCH
Confidence            4689999999999887 46678889999999 89998543

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=89.92  E-value=0.006  Score=45.64  Aligned_cols=38  Identities=13%  Similarity=0.106  Sum_probs=31.7

Q ss_pred             hhhhhcCCCCCCCC-CCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVP-YLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~-~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|.++++|. .+ .++.++.++.++|| +||.|.+.
T Consensus        24 ~~l~~~F~~~G~i~~~v-~i~~~~~~g~~~g~-afV~f~~~   62 (99)
T 2div_A           24 NFISRAFATMGETVMSV-KIIRNRLTGIPAGY-CFVEFADL   62 (99)
T ss_dssp             HHHHHHHHHTTCCCCEE-EEEECSSSCCEEEE-EEEECSCH
T ss_pred             HHHHHHHHHhCCcceEE-EEeecCCCCCcCCE-EEEEeCCH
Confidence            46899999999998 76 46678889999999 99998654

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=89.88  E-value=0.039  Score=40.63  Aligned_cols=39  Identities=21%  Similarity=0.404  Sum_probs=32.1

Q ss_pred             ChhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          6 PPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         6 p~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      ..+|..+|..+++|..+ .+..++.+++++|| +||.|.+.
T Consensus        19 ~~~l~~~f~~~G~v~~v-~i~~~~~~~~~~g~-afV~f~~~   57 (95)
T 2dnz_A           19 EDMLRGIFEPFGKIDNI-VLMKDSDTGRSKGY-GFITFSDS   57 (95)
T ss_dssp             HHHHHHHHTTTSCEEEE-EEECCSSSCCCCSE-EEEEESCH
T ss_pred             HHHHHHHHHhcCCEeEE-EEeecCCCCceeeE-EEEEECCH
Confidence            34689999999999887 46678889999999 88888543

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=89.85  E-value=0.046  Score=42.13  Aligned_cols=39  Identities=21%  Similarity=0.165  Sum_probs=32.3

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEF   47 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~   47 (363)
                      .+|..+|..+|+|..+ .+..++.++.++|| +||.|.+..
T Consensus        55 ~~l~~~F~~~G~i~~~-~i~~~~~~g~~~g~-afV~f~~~~   93 (118)
T 2khc_A           55 TDLASTFLPFGNVISA-KVFIDKQTSLSKCF-GFVSFDNPD   93 (118)
T ss_dssp             HHHHHHTTTSCEEEEE-EECCCSSSSCCCCE-EEEEEESSH
T ss_pred             HHHHHHHHhcCCEEEE-EEEeCCCCCCcCcE-EEEEECCHH
Confidence            4689999999999887 46667788999999 999996653

>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=89.77  E-value=0.037  Score=44.51  Aligned_cols=37  Identities=19%  Similarity=0.354  Sum_probs=28.0

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEF   47 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~   47 (363)
                      .+|..+|.++++ ..+ -|+.++. ++++|| +||.|.+..
T Consensus        61 ~dL~~~F~~~Gi-~~v-~i~~d~~-g~srGf-aFV~F~~~e   97 (139)
T 2hgn_A           61 NDIYNFFSPLNP-VRV-HIEIGPD-GRVTGE-ADVEFATHE   97 (139)
T ss_dssp             HHHHHHHCSCCC-SEE-ECCCSSS-SCSSCC-CEEECSHHH
T ss_pred             HHHHHHHHhcCC-eEE-EEEECCC-CCCceE-EEEEeCCHH
Confidence            469999999994 455 3555665 999999 999996643

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=89.71  E-value=0.096  Score=39.93  Aligned_cols=38  Identities=13%  Similarity=0.164  Sum_probs=30.8

Q ss_pred             hhhhhcCCCCCCCC--------CCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVP--------YLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~--------~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|..+++|.        .+ -+..++.+++++|| +||.|.+.
T Consensus        30 ~~l~~~F~~~G~i~~~~~~~~~~v-~i~~~~~~g~~~g~-afV~f~~~   75 (113)
T 2cpe_A           30 DDLADFFKQCGVVKMNKRTGQPMI-HIYLDKETGKPKGD-ATVSYEDP   75 (113)
T ss_dssp             HHHHHHHTTTSCBCBCSSSCCBSE-ECCBCTTTCSBCSE-EEEEBSSH
T ss_pred             HHHHHHHHhcCCEeEccccCccCE-EEEEeCCCCCeeeE-EEEEECCH
Confidence            46899999999998        34 36667789999999 89998554

>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=89.64  E-value=0.013  Score=45.38  Aligned_cols=39  Identities=23%  Similarity=0.336  Sum_probs=31.1

Q ss_pred             ChhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccc
Q psy16184          6 PPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEF   47 (363)
Q Consensus         6 p~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~   47 (363)
                      ..+|..+|+++++|..+ .+..++ ++.++|| +||.|.+..
T Consensus        21 ~~~l~~~F~~~G~i~~v-~i~~~~-~g~~~g~-afV~F~~~~   59 (116)
T 2fy1_A           21 EKMLKAVFGKHGPISEV-LLIKDR-TSKSRGF-AFITFENPA   59 (116)
T ss_dssp             HHHHHHHHHTSSCCSEE-EEECST-TTTCCCE-EEEECSSHH
T ss_pred             HHHHHHHHHhcCCEEEE-EEEECC-CCCcccE-EEEEECCHH
Confidence            35689999999999887 355566 8999999 999996643

>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=89.63  E-value=0.021  Score=40.94  Aligned_cols=38  Identities=18%  Similarity=0.152  Sum_probs=31.7

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|.++|+|..+ .++.++.++.++|| +||.|.+.
T Consensus        16 ~~l~~~f~~~G~i~~~-~i~~~~~~~~~~g~-afV~f~~~   53 (83)
T 3md1_A           16 ETLRNAFKDFPSYLSG-HVMWDMQTGSSRGY-GFVSFTSQ   53 (83)
T ss_dssp             HHHHHHHTTSTTEEEE-EEEECTTTCCEEEE-EEEEESCH
T ss_pred             HHHHHHHHhcCCeeEE-EEEEcCCCCCccce-EEEEECCH
Confidence            4689999999999887 46668889999999 99998543

>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=89.53  E-value=0.045  Score=41.33  Aligned_cols=37  Identities=14%  Similarity=0.338  Sum_probs=29.3

Q ss_pred             hhhhhcCCCCCCCCC-CCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPY-LPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~-~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|.++++|.. + -+..+ .+++++|| +||.|.+.
T Consensus        30 ~~l~~~F~~~G~v~~~v-~i~~~-~~g~~~G~-afV~F~~~   67 (104)
T 1wg5_A           30 EEIVQFFSGLEIVPNGM-TLPVD-FQGRSTGE-AFVQFASQ   67 (104)
T ss_dssp             HHHHHHTTTCCEEEEEE-ECCBC-SSSCBCSE-EEEEESSH
T ss_pred             HHHHHHHHhcCCcceeE-EEEEC-CCCCcceE-EEEEECCH
Confidence            469999999999875 3 34455 68999999 99999554

>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=89.48  E-value=0.042  Score=41.81  Aligned_cols=38  Identities=8%  Similarity=0.191  Sum_probs=31.6

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|.++|+|..+ .+..++.++.++|| +||.|.+.
T Consensus        41 ~~l~~~F~~~G~i~~v-~i~~~~~~~~~~g~-afV~f~~~   78 (110)
T 1oo0_B           41 DEIQEKFCDYGEIKNI-HLNLDRRTGFSKGY-ALVEYETH   78 (110)
T ss_dssp             HHHHHHHGGGSCEEEE-ECCBCTTTSSBCSE-EEEEESSH
T ss_pred             HHHHHHHHhcCCEEEE-EEEecCCCCCcceE-EEEEECCH
Confidence            4589999999999887 46667889999999 99998553

>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=89.47  E-value=0.075  Score=39.92  Aligned_cols=37  Identities=16%  Similarity=0.419  Sum_probs=30.0

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCC-CCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHE-KKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t-~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|..++ |..+ .++.++.| ++++|| +||.|.+.
T Consensus        30 ~~l~~~F~~~G-i~~v-~i~~~~~~~g~~~g~-afV~f~~~   67 (104)
T 1wi8_A           30 ESIKEFFRGLN-ISAV-RLPREPSNPERLKGF-GYAEFEDL   67 (104)
T ss_dssp             HHHHHHTTTSC-EEEE-ECCBCSSCTTSBCSC-EEEEESSH
T ss_pred             HHHHHHHHHCC-ceEE-EEecCCCCCCCcCeE-EEEEECCH
Confidence            46999999999 7777 46667877 999999 89998554

>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=89.41  E-value=0.045  Score=43.26  Aligned_cols=38  Identities=16%  Similarity=0.371  Sum_probs=31.8

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|.++++|..+ .+..++.++.++|| +||.|.+.
T Consensus        61 ~~L~~~F~~~G~I~~v-~i~~d~~tg~~~G~-afV~F~~~   98 (129)
T 2kxn_B           61 RDLREVFSKYGPIADV-SIVYDQQSRRSRGF-AFVYFENV   98 (129)
T ss_dssp             HHHHHHHTTTSCEEEE-EEECCSSSSCCCCE-EEEEESCH
T ss_pred             HHHHHHHHhcCCeEEE-EEEecCCCCccceE-EEEEECCH
Confidence            4689999999999887 46678889999999 89998554

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=89.38  E-value=0.033  Score=41.82  Aligned_cols=38  Identities=18%  Similarity=0.380  Sum_probs=31.7

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|.++++|..+ .+..++.++.++|| +||.|.+.
T Consensus        30 ~~l~~~f~~~G~i~~v-~i~~~~~~~~~~g~-afV~f~~~   67 (103)
T 2cq0_A           30 TDLQELFRPFGSISRI-YLAKDKTTGQSKGF-AFISFHRR   67 (103)
T ss_dssp             HHHHTTSTTTCCEEEE-EEEECSSSCSEEEE-EEEEESSH
T ss_pred             HHHHHHHHhCCCeEEE-EEeecCCCCceeeE-EEEEECCH
Confidence            4689999999999887 46667788999999 89998554

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=89.17  E-value=0.02  Score=43.26  Aligned_cols=39  Identities=18%  Similarity=0.261  Sum_probs=32.4

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEF   47 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~   47 (363)
                      .+|..+|..+++|..+ .++.++.++.++|| +||.|.+..
T Consensus        31 ~~l~~~F~~~G~v~~v-~i~~~~~~g~~~g~-afV~f~~~~   69 (105)
T 2dh8_A           31 ETLRSYFSQYGEVVDC-VIMKDKTTNQSRGF-GFVKFKDPN   69 (105)
T ss_dssp             HHHHHHHHTTSCEEEE-EEEECSSSCCEEEE-EEEEESSTT
T ss_pred             HHHHHHHHhcCCeEEE-EEeeCCCCCCcceE-EEEEECCHH
Confidence            4589999999999887 46678889999999 899986543

>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=89.04  E-value=0.018  Score=43.39  Aligned_cols=38  Identities=21%  Similarity=0.329  Sum_probs=31.8

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|.++++|..+ .++.++.++.++|| +||.|.+.
T Consensus        30 ~~l~~~F~~~G~i~~v-~i~~~~~~g~~~g~-afV~f~~~   67 (103)
T 2cqg_A           30 QDLKEYFSTFGEVLMV-QVKKDLKTGHSKGF-GFVRFTEY   67 (103)
T ss_dssp             HHHHHHHGGGSCEEEE-EEEECSSSCSEEEE-EEEEESSH
T ss_pred             HHHHHHHHhcCCeEEE-EEEecCCCCCccce-EEEEECCH
Confidence            4689999999999887 46678889999999 89998553

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=88.81  E-value=0.047  Score=41.98  Aligned_cols=38  Identities=18%  Similarity=0.247  Sum_probs=32.0

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|..+++|..+ -+..++.+++++|| +||.|.+.
T Consensus        32 ~~l~~~F~~~G~i~~v-~i~~~~~~~~~~g~-afV~f~~~   69 (116)
T 2cqd_A           32 ASLRKYFEGFGDIEEA-VVITDRQTGKSRGY-GFVTMADR   69 (116)
T ss_dssp             HHHHHHHHTTSCEEEE-EESCCSSSCCCCSE-EEEEESSH
T ss_pred             HHHHHHHHhCCCeeEE-EEEEcCCCCccceE-EEEEECCH
Confidence            4689999999999887 46678889999999 89998654

>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=88.74  E-value=0.034  Score=43.94  Aligned_cols=37  Identities=14%  Similarity=0.230  Sum_probs=28.2

Q ss_pred             hhhhhcCCCCCCCC--CCCCCCCCCCCCCCCCCcccccccccc
Q psy16184          7 PNLLALFAPRDPVP--YLPPVEKLPHEKKTHGYSGIAAFLNEF   47 (363)
Q Consensus         7 ~~l~~~f~~~~pi~--~~~p~~~~p~t~~s~g~~g~v~f~~~~   47 (363)
                      .+|..+|.++ .|.  .+ -|+.++. ++++|| +||.|.+..
T Consensus        57 ~dL~~~F~~~-~i~~~~v-~i~~d~~-GrsrGf-aFV~F~~~e   95 (126)
T 2hgm_A           57 EEIVQFFSGL-EIVPNGI-TLPVDPE-GKITGE-AFVQFASQE   95 (126)
T ss_dssp             HHHHHHTTTS-CEEEEEE-ECCCCSS-SSSCSE-EEEEESSTT
T ss_pred             HHHHHHHhcC-CceeeEE-EEEECCC-CCCceE-EEEEECCHH
Confidence            4699999999 454  44 3555666 999999 999997754

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=88.62  E-value=0.042  Score=41.10  Aligned_cols=38  Identities=21%  Similarity=0.366  Sum_probs=31.5

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|.++++|..+ .+..++.++.++|| +||.|.+.
T Consensus        27 ~~l~~~f~~~G~i~~v-~i~~~~~~~~~~g~-afV~f~~~   64 (102)
T 1x5s_A           27 QSLEQVFSKYGQISEV-VVVKDRETQRSRGF-GFVTFENI   64 (102)
T ss_dssp             HHHHHHHHHHSCCCEE-EECCCSSSCSCCSE-EEEECSSH
T ss_pred             HHHHHHHHhcCCeEEE-EEEeCCCCCCcccE-EEEEECCH
Confidence            4689999999999887 46667888999999 88888543

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=88.58  E-value=0.061  Score=40.52  Aligned_cols=38  Identities=16%  Similarity=0.350  Sum_probs=30.8

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCC-CCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKL-PHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~-p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|.++++|..+. ++.+ +.++.++|| +||.|.+.
T Consensus        30 ~~l~~~F~~~G~i~~v~-i~~~~~~~~~~~g~-afV~f~~~   68 (107)
T 2cph_A           30 REIRELFSTFGELKTVR-LPKKMTGTGAHRGF-GFVDFITK   68 (107)
T ss_dssp             HHHHHHHHTTSCEEEEE-CCCCCSSSCSSCSE-EEEEESSH
T ss_pred             HHHHHHHHccCCeEEEE-EecCCCCCCCcCce-EEEEECCH
Confidence            46899999999998874 5556 678999999 89988553

>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=88.57  E-value=0.029  Score=40.40  Aligned_cols=38  Identities=18%  Similarity=0.233  Sum_probs=31.5

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|.++|+|..+ .+..++.++.++|| +||.|.+.
T Consensus        22 ~~l~~~f~~~G~i~~v-~i~~~~~~~~~~g~-afV~f~~~   59 (85)
T 3mdf_A           22 KVLHAAFIPFGDITDI-QIPLDYETEKHRGF-AFVEFELA   59 (85)
T ss_dssp             HHHHHHHGGGSCEEEE-ECCEETTTTEECSE-EEEEESSH
T ss_pred             HHHHHHHhccCCEEEE-EEEECCCCCccccE-EEEEECCH
Confidence            4689999999999887 46667889999999 88988543

>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=88.42  E-value=0.03  Score=40.65  Aligned_cols=39  Identities=15%  Similarity=0.138  Sum_probs=32.1

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEF   47 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~   47 (363)
                      .+|..+|.++|+|..+ .+..++.++.++|| +||.|.+..
T Consensus        21 ~~l~~~F~~~G~i~~v-~i~~~~~~~~~~g~-afV~f~~~~   59 (89)
T 3ucg_A           21 EELEAHFHGCGSVNRV-TILCDKFSGHPKGF-AYIEFSDKE   59 (89)
T ss_dssp             HHHHHHHGGGCCEEEE-EEEESCSSSSCCEE-EEEEESSTH
T ss_pred             HHHHHHHHhCCCEEEE-EEEecCCCCCcceE-EEEEECCHH
Confidence            4689999999999887 46667789999999 999986643

>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=88.35  E-value=0.11  Score=38.73  Aligned_cols=37  Identities=16%  Similarity=0.419  Sum_probs=29.9

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCC-CCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLP-HEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p-~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|..+| |..+ -++.++ .+++++|| +||.|.+.
T Consensus        34 ~~l~~~F~~~G-i~~v-~i~~~~~~~g~~~g~-afV~f~~~   71 (100)
T 2j76_E           34 ESIKEFFRGLN-ISAV-RLPREPSNPERLKGF-GYAEFEDL   71 (100)
T ss_dssp             SHHHHHSCSSC-EEEE-ECSCCTTTTCCCCSC-EEEEECCH
T ss_pred             HHHHHHHHhcC-CeEE-EEEecCCcCCccCeE-EEEEECCH
Confidence            46899999999 8777 356666 68999999 99998654

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=87.71  E-value=0.068  Score=42.35  Aligned_cols=38  Identities=18%  Similarity=0.233  Sum_probs=32.0

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|.++++|..+ .+..++.++.++|| +||.|.+.
T Consensus        78 ~~l~~~f~~~G~i~~v-~i~~~~~~~~~~g~-afV~f~~~  115 (140)
T 2ku7_A           78 KVLHAAFIPFGDITDI-QIPLDYETEKHRGF-AFVEFELA  115 (140)
T ss_dssp             HHHHHHHGGGSCEEEE-ECCCCTTTCCCCSE-EEEEESCH
T ss_pred             HHHHHHHHhcCCEEEE-EEeecCCCCCcCcE-EEEEECCH
Confidence            4689999999999887 46678889999999 99998554

>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=87.54  E-value=0.038  Score=42.43  Aligned_cols=38  Identities=21%  Similarity=0.277  Sum_probs=31.7

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|..+++|..+ .+..++.++.++|| +||.|.+.
T Consensus        40 ~~l~~~F~~~G~i~~v-~i~~~~~~g~~~g~-afV~f~~~   77 (115)
T 2cpz_A           40 QDLLQMFMPFGNVVSA-KVFIDKQTNLSKCF-GFVSYDNP   77 (115)
T ss_dssp             HHHHHHHGGGSCCSEE-EEEECSSSCSEEEE-EEEECSSH
T ss_pred             HHHHHHHHhcCCeEEE-EEEECCCCCCcCcc-EEEEECCH
Confidence            4699999999999887 46667888999999 89998553

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=87.47  E-value=0.053  Score=40.37  Aligned_cols=38  Identities=11%  Similarity=0.093  Sum_probs=31.1

Q ss_pred             hhhhhcCCCCCCCCC--------CCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPY--------LPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~--------~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|..+|+|..        + .+..++.+++++|| +||.|.+.
T Consensus        28 ~~l~~~F~~~G~i~~~~~~~~~~v-~i~~~~~~g~~~G~-afV~f~~~   73 (99)
T 2la6_A           28 ESVADYFKQIGIIKTNKKTGQPMI-NLYTDRETGKLKGE-ATVSFDDP   73 (99)
T ss_dssp             HHHHHHHTTTSCBCEETTTTEESE-EEEECTTTCSEEEE-EEEEBSSH
T ss_pred             HHHHHHHHHhCCEeeccccccccE-EEEecCCCCCeeeE-EEEEECCH
Confidence            468999999999987        4 36667788999999 99998553

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=87.28  E-value=0.15  Score=39.01  Aligned_cols=36  Identities=19%  Similarity=0.274  Sum_probs=27.6

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|.++ .|..+ -|+.++. ++++|| +||.|.+.
T Consensus        31 ~dl~~~F~~~-~v~~v-~i~~d~~-g~~~G~-afV~F~~~   66 (109)
T 2dnn_A           31 NDVRDFFHGL-RVDAV-HLLKDHV-GRNNGN-GLVKFLSP   66 (109)
T ss_dssp             HHHHHHTTTS-CCCEE-EECCCTT-CCCCSE-EEEECSSH
T ss_pred             HHHHHHhccC-CeeEE-EEEECCC-CCCCeE-EEEEECCH
Confidence            4799999999 67665 3455664 999999 99999553

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=86.96  E-value=0.069  Score=40.34  Aligned_cols=37  Identities=14%  Similarity=0.145  Sum_probs=29.5

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEF   47 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~   47 (363)
                      .+|..+|+++|+|..+. +.  ..+++++|| +||.|.+..
T Consensus        36 ~~l~~~F~~~G~v~~v~-i~--~~~g~~~G~-afV~f~~~~   72 (105)
T 2nlw_A           36 NVIHKIFSKFGKITNDF-YP--EEDGKTKGY-IFLEYASPA   72 (105)
T ss_dssp             HHHHHHHGGGSCEEEEE-CC--CBTTBSCCE-EEEEECSSS
T ss_pred             HHHHHHHhcCCCEEEEE-ee--CCCCCeeeE-EEEEECCHH
Confidence            56899999999998874 32  468899999 999996654

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=86.61  E-value=0.031  Score=42.16  Aligned_cols=38  Identities=11%  Similarity=0.163  Sum_probs=31.8

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|..+|+|..+ .++.++.|+.++|| +||.|.+.
T Consensus        38 ~~l~~~f~~~G~i~~v-~i~~~~~~~~~~g~-afV~f~~~   75 (106)
T 1p27_B           38 EDIHDKFAEYGEIKNI-HLNLDRRTGYLKGY-TLVEYETY   75 (106)
T ss_dssp             HHHHHHHGGGSCEEEE-EEEECTTTSSEEEE-EEEEESCH
T ss_pred             HHHHHHHhccCCeEEE-EEEecCCCCceeeE-EEEEECCH
Confidence            4589999999999887 46678889999999 89998553

>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=86.58  E-value=0.036  Score=41.58  Aligned_cols=38  Identities=21%  Similarity=0.392  Sum_probs=31.6

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|..+|+|..+ .+..++.++.++|| +||.|.+.
T Consensus        23 ~~l~~~f~~~G~i~~~-~i~~~~~~g~~~g~-afV~f~~~   60 (104)
T 1p1t_A           23 EQLKDIFSEVGPVVSF-RLVYDRETGKPKGY-GFCEYQDQ   60 (104)
T ss_dssp             HHHHHHHHTTSCCSEE-EEEEETTTTEEEEE-EEEECSCH
T ss_pred             HHHHHHHHhcCCeeEE-EEEeCCCCCccceE-EEEEECCH
Confidence            4689999999999887 46667788999999 99998654

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=86.14  E-value=0.036  Score=40.82  Aligned_cols=38  Identities=16%  Similarity=0.371  Sum_probs=31.6

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|.++++|..+ .+..++.++.++|| +||.|.+.
T Consensus        30 ~~l~~~f~~~G~v~~v-~i~~~~~~~~~~g~-afV~f~~~   67 (95)
T 2cqc_A           30 RDLREVFSKYGPIADV-SIVYDQQSRRSRGF-AFVYFENV   67 (95)
T ss_dssp             HHHHHHHHTTSCEEEE-EEEECSSSSSEEEE-EEEEESSH
T ss_pred             HHHHHHHHhcCCeeEE-EEEEcCCCCCcccE-EEEEECCH
Confidence            4689999999999887 46678888999999 88888543

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=86.00  E-value=0.036  Score=41.50  Aligned_cols=39  Identities=21%  Similarity=0.407  Sum_probs=31.7

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccC
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFE   48 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~   48 (363)
                      .+|..+|..+|+|..+ .++.++ ++.++|| +||.|.+...
T Consensus        24 ~~l~~~F~~~G~i~~v-~i~~~~-~g~~~g~-afV~f~~~~~   62 (102)
T 2xs2_A           24 TEIRSFFARYGSVKEV-KIITDR-TGVSKGY-GFVSFYNDVD   62 (102)
T ss_dssp             HHHHHHHGGGSCEEEE-EEEECT-TSCEEEE-EEEEESSCCC
T ss_pred             HHHHHHHHhCCCeEEE-EEEECC-CCCccce-EEEEECCHHH
Confidence            4689999999999887 456666 8999999 9999976543

>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=85.84  E-value=0.034  Score=40.20  Aligned_cols=38  Identities=32%  Similarity=0.468  Sum_probs=31.4

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|+++++|..+ -+..++.++.++|| +||.|.+.
T Consensus        21 ~~l~~~F~~~G~i~~v-~i~~~~~~~~~~g~-afV~f~~~   58 (87)
T 3bs9_A           21 AAIAAAFAPFGRISDA-RVVKDMATGKSKGY-GFVSFFNK   58 (87)
T ss_dssp             HHHHHHHGGGSCEEEE-EEEECTTTCCEEEE-EEEEESSH
T ss_pred             HHHHHHHHhcCCEeEE-EEEecCCCCccceE-EEEEECCH
Confidence            4689999999999887 46667788999999 89998553

>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=85.83  E-value=0.065  Score=40.58  Aligned_cols=40  Identities=13%  Similarity=0.141  Sum_probs=32.0

Q ss_pred             hhhhhcCCCCCC-CCCCCCCCCCCCCCCCCCCcccccccccc
Q psy16184          7 PNLLALFAPRDP-VPYLPPVEKLPHEKKTHGYSGIAAFLNEF   47 (363)
Q Consensus         7 ~~l~~~f~~~~p-i~~~~p~~~~p~t~~s~g~~g~v~f~~~~   47 (363)
                      .+|..+|..+++ |..+..+..+..++.++|| +||.|.+..
T Consensus        23 ~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~-afV~f~~~~   63 (109)
T 2dis_A           23 EEILEEIAKVTEGVLDVIVYASAADKMKNRGF-AFVEYESHR   63 (109)
T ss_dssp             HHHHHHHHHHSTTEEEEECCSSSCTTTTTCCE-EEEEESSHH
T ss_pred             HHHHHHHHHhcCCceEEEEEccCCCCCCcCcE-EEEEecCHH
Confidence            468999999998 8877544477888999999 999986643

>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=85.46  E-value=0.12  Score=41.30  Aligned_cols=37  Identities=5%  Similarity=0.010  Sum_probs=29.3

Q ss_pred             hhhhhcCCCCCC---CCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDP---VPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~p---i~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|.++++   |..+ -|..++. ++++|| +||.|.+.
T Consensus        59 ~dL~~~F~~~G~v~~v~~v-~i~~d~~-g~srG~-aFV~F~~~   98 (136)
T 2hgl_A           59 EDVQNFLSDCTIHDGAAGV-HFIYTRE-GRQSGE-AFVELGSE   98 (136)
T ss_dssp             HHHHHHTTTCCCSSSSTTE-EEEECSS-SCEEEE-EEEECSSH
T ss_pred             HHHHHHHHHhCCcCceeEE-EEEECCC-CCCCeE-EEEEECCH
Confidence            469999999999   5666 3556666 999999 99999654

>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=85.43  E-value=0.043  Score=45.24  Aligned_cols=38  Identities=8%  Similarity=0.191  Sum_probs=31.9

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|.++|+|..| .|..++.|+.++|| +||.|.+.
T Consensus        87 ~~L~~~F~~~G~i~~v-~i~~~~~~g~~~g~-afV~f~~~  124 (165)
T 1rk8_A           87 DEIQEKFCDYGEIKNI-HLNLDRRTGFSKGY-ALVEYETH  124 (165)
T ss_dssp             HHHHHHHGGGSCEEEE-EEEECTTTSSEEEE-EEEEESSH
T ss_pred             HHHHHHhhcCCCEEEE-EEEecCCCCcEeeE-EEEEECCH
Confidence            4689999999999888 46667889999999 99998553

>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=85.36  E-value=0.04  Score=41.99  Aligned_cols=38  Identities=18%  Similarity=0.387  Sum_probs=31.3

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|.++|+|..+ .+..++.++.++|| +||.|.+.
T Consensus        41 ~~l~~~F~~~G~i~~v-~i~~~~~~g~~~g~-afV~F~~~   78 (108)
T 2jrs_A           41 DMLRGIFEPFGRIESI-QLMMDSETGRSKGY-GFITFSDS   78 (108)
T ss_dssp             HHHHHHHTTTSCEEEE-EEEEETTTTEEEEE-EEEEESCH
T ss_pred             HHHHHHHHhcCCeEEE-EEEEcCCCCccceE-EEEEECCH
Confidence            4689999999999887 46667788999999 89998554

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=84.97  E-value=0.046  Score=42.55  Aligned_cols=39  Identities=15%  Similarity=0.239  Sum_probs=32.2

Q ss_pred             ChhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          6 PPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         6 p~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      ..+|..+|..+|+|..+ .+..++.++.++|| +||.|.+.
T Consensus        50 ~~~l~~~F~~~G~i~~v-~i~~~~~~~~~~g~-afV~f~~~   88 (124)
T 2jwn_A           50 AQDLEAHFSSCGSINRI-TILCDKFSGHPKGY-AYIEFAER   88 (124)
T ss_dssp             HHHHHHHHHTTSCEEEE-EEEEECTTSSCEEE-EEEEESSH
T ss_pred             HHHHHHHHHhcCCEEEE-EEEecCCCCCcccE-EEEEECCH
Confidence            35689999999999887 46667789999999 99999654

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=84.93  E-value=0.13  Score=40.03  Aligned_cols=37  Identities=16%  Similarity=0.163  Sum_probs=30.1

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|..+|+|..+ .+..++ ++.++|| +||.|.+.
T Consensus        50 ~~l~~~F~~~G~v~~v-~i~~~~-~g~~~g~-afV~f~~~   86 (124)
T 2kt5_A           50 ADIQELFAEFGTLKKA-AVDYDR-SGRSLGT-ADVHFERR   86 (124)
T ss_dssp             HHHHHHHHTTSCCSEE-EEECCS-SSSCCSE-EEEEESSH
T ss_pred             HHHHHHHHhcCCeeEE-EEEECC-CCCEeeE-EEEEECCH
Confidence            4689999999999887 355566 8999999 89998553

>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=84.67  E-value=0.082  Score=40.38  Aligned_cols=37  Identities=16%  Similarity=0.202  Sum_probs=30.0

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|.++++|..+ -+..++ ++.++|| +||.|.+.
T Consensus        40 ~~l~~~F~~~G~i~~~-~i~~~~-~g~~~g~-afV~f~~~   76 (114)
T 1x5o_A           40 QELENMLKPFGQVIST-RILRDS-SGTSRGV-GFARMEST   76 (114)
T ss_dssp             HHHHHTTTTTSCEEEE-EEEECS-SSCEEEE-EEEEESCH
T ss_pred             HHHHHHHHhcCCEEEE-EEEECC-CCCcceE-EEEEECCH
Confidence            4689999999999887 355566 8999999 89998543

>2g0c_A ATP-dependent RNA helicase DBPA; RNA recognition motif, hydrolase; 1.70A {Bacillus subtilis} PDB: 3moj_B

Probab=84.36  E-value=1.8  Score=30.24  Aligned_cols=68  Identities=10%  Similarity=0.168  Sum_probs=43.1

Q ss_pred             eEEEc-CCCCCCCHHHHHHHHHhhCC-----ccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEE
Q psy16184        103 TLFIA-RVNYDTSESKLRREFEVYGP-----IKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD  176 (363)
Q Consensus       103 ~l~V~-nL~~~~t~~~L~~~F~~~G~-----i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~  176 (363)
                      +|||. +-...++..+|..++..-+.     |-.|.|..        .|.||+... ..|..++..|++..+.|+.+.|+
T Consensus         2 ~~~i~~Grk~~~~p~~ivg~i~~~~gi~~~~IG~I~i~d--------~~s~v~v~~-~~~~~~~~~l~~~~i~g~~~~v~   72 (76)
T 2g0c_A            2 KLYFNGGKKKKIRAVDFVGTIAKIDGVSADDIGIITIMD--------NASYVEILN-GKGPHVLKVMKNTTVKGKQLKVN   72 (76)
T ss_dssp             EEEESCCCC----CHHHHHHHHTSTTCCGGGEEEEEECS--------SCEEEEECT-TCHHHHHHHHTTCCC---CCCEE
T ss_pred             EEEEeCCCccCCCHHHHHHHHHHccCCChhhccEEEEeC--------CcEEEEECH-HHHHHHHHHhccccCcCceEEEE
Confidence            56664 22345677788888775543     44666633        389998865 45778888899999999999988


Q ss_pred             eec
Q psy16184        177 VER  179 (363)
Q Consensus       177 ~a~  179 (363)
                      .++
T Consensus        73 ~~~   75 (76)
T 2g0c_A           73 KAN   75 (76)
T ss_dssp             ECC
T ss_pred             ECC
Confidence            764

>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=84.16  E-value=0.066  Score=40.23  Aligned_cols=37  Identities=22%  Similarity=0.384  Sum_probs=29.5

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|..+++|..+. +..++ ++.++|| +||.|.+.
T Consensus        30 ~~l~~~F~~~G~i~~v~-i~~~~-~g~~~g~-afV~f~~~   66 (105)
T 2dnh_A           30 EDVLRLFQPFGVIDECT-VLRGP-DGSSKGC-AFVKFSSH   66 (105)
T ss_dssp             HHHHHHHTTTSCEEEEE-EEECS-SSCEEEE-EEEEESSH
T ss_pred             HHHHHHHHhcCCeEEEE-EEECC-CCCcCcE-EEEEeCCH
Confidence            46899999999998873 55566 7899999 88888553

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=83.88  E-value=0.05  Score=41.72  Aligned_cols=38  Identities=32%  Similarity=0.475  Sum_probs=31.6

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|..+++|..+ .+..++.++.++|| +||.|.+.
T Consensus        30 ~~l~~~F~~~G~i~~v-~i~~~~~~~~~~g~-afV~f~~~   67 (115)
T 2dgo_A           30 EDIKAAFAPFGRISDA-RVVKDMATGKSKGY-GFVSFFNK   67 (115)
T ss_dssp             HHHHHHHGGGSCEEEE-EEEECTTTCCEEEE-EEEEESSH
T ss_pred             HHHHHHHHhcCCeEEE-EEEEcCCCCCcceE-EEEEECCH
Confidence            4689999999999887 46667789999999 99998554

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=82.87  E-value=0.079  Score=39.41  Aligned_cols=37  Identities=19%  Similarity=0.205  Sum_probs=29.6

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|.++++|..+ -+..++ +++++|| +||.|.+.
T Consensus        32 ~~l~~~F~~~G~i~~v-~i~~~~-~g~~~g~-afV~f~~~   68 (100)
T 2do4_A           32 EELEEICKAHGTVKDL-RLVTNR-AGKPKGL-AYVEYENE   68 (100)
T ss_dssp             HHHHHHHTTTSCEEEE-EEEECT-TSCEEEE-EEEEESSH
T ss_pred             HHHHHHHHhCCCeEEE-EEEECC-CCCEEeE-EEEEECCH
Confidence            4699999999999887 355566 8999999 89988553

>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=82.67  E-value=0.19  Score=36.68  Aligned_cols=33  Identities=15%  Similarity=0.290  Sum_probs=25.6

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|+++|+|..+. ++.     .++|| |||.|.+.
T Consensus        26 ~~L~~~F~~~G~i~~v~-i~~-----~srGf-aFV~F~~~   58 (89)
T 3d2w_A           26 EELQQFFCQYGEVVDVF-IPK-----PFRAF-AFVTFADD   58 (89)
T ss_dssp             HHHHHHHTTTSCEEEEE-CCS-----SCCSE-EEEEESCH
T ss_pred             HHHHHHHhccCCEEEEE-Eee-----CCCCE-EEEEECCH
Confidence            45899999999998874 332     38999 99999654

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=82.25  E-value=0.19  Score=42.03  Aligned_cols=37  Identities=16%  Similarity=0.163  Sum_probs=30.1

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|..+++|..|. |..++ ++.++|| +||.|.+.
T Consensus       103 ~~L~~~F~~~G~I~~v~-i~~d~-~g~~kG~-afV~F~~~  139 (177)
T 2f3j_A          103 ADIQELFAEFGTLKKAA-VDYDR-SGRSLGT-ADVHFERR  139 (177)
T ss_dssp             HHHHHHHHHTSCCSEEE-ECCCT-TSSCSCC-EEEEESCH
T ss_pred             HHHHHHHHhcCCeEEEE-EEECC-CCCEeeE-EEEEeCCH
Confidence            46899999999998874 55566 8999999 89998553

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=82.03  E-value=0.11  Score=38.96  Aligned_cols=37  Identities=14%  Similarity=0.196  Sum_probs=29.8

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|..++ |..+ -++.++.|++++|| +||.|.+.
T Consensus        30 ~~l~~~F~~~g-i~~v-~i~~~~~~g~~~g~-afV~f~~~   66 (103)
T 2dng_A           30 GDIDAIFKDLS-IRSV-RLVRDKDTDKFKGF-CYVEFDEV   66 (103)
T ss_dssp             HHHHHHTTTSC-EEEE-EEEECSSSCSEEEE-EEEEESSH
T ss_pred             HHHHHHHHhCC-ceEE-EEeecCCCCccceE-EEEEECCH
Confidence            46899999995 7766 46678889999999 99998654

>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=81.92  E-value=0.068  Score=40.29  Aligned_cols=37  Identities=16%  Similarity=0.150  Sum_probs=29.6

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|.++++|..+ .+..++ ++.++|| +||.|.+.
T Consensus        44 ~~l~~~F~~~G~i~~v-~i~~~~-~g~~~g~-afV~f~~~   80 (107)
T 3ulh_A           44 ADIQELFAEFGTLKKA-AVHYDR-SGRSLGT-ADVHFERK   80 (107)
T ss_dssp             HHHHHHHHTTSCEEEE-EEEECT-TSCEEEE-EEEEESSH
T ss_pred             HHHHHHHHhcCCeEEE-EEEECC-CCCcceE-EEEEECCH
Confidence            4689999999999877 355566 8999999 89988543

>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=81.05  E-value=0.081  Score=43.02  Aligned_cols=38  Identities=11%  Similarity=0.248  Sum_probs=31.7

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|..+++|..| -|..++.|+.++|| +||.|.+.
T Consensus        54 ~~l~~~F~~~G~i~~v-~i~~~~~~~~~~g~-afV~f~~~   91 (156)
T 1h2v_Z           54 EQIYELFSKSGDIKKI-IMGLDKMKKTACGF-CFVEYYSR   91 (156)
T ss_dssp             HHHHHHHGGGSCEEEE-EEEECTTTCCEEEE-EEEEESSH
T ss_pred             HHHHHHHHhcCCeEEE-EEEecCCCCccceE-EEEEECCH
Confidence            4689999999999887 46668889999999 88988543

>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=80.59  E-value=0.094  Score=37.79  Aligned_cols=38  Identities=13%  Similarity=0.334  Sum_probs=29.3

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCC-CCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKK-THGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~-s~g~~g~v~f~~~   46 (363)
                      .+|..+|.++|+|..+ .+..++.++. ++|| +||.|.+.
T Consensus        19 ~~l~~~F~~~G~i~~~-~i~~~~~~~~~~~g~-afV~f~~~   57 (88)
T 4a8x_A           19 DHIMEIFSTYGKIKMI-DMPVERMHPHLSKGY-AYVEFENP   57 (88)
T ss_dssp             HHHHHHHHTTSCEEEE-ECCEETTEEEEECSE-EEEEESSH
T ss_pred             HHHHHHHHhCCCEEEE-EEEeCCCCCCCCCcE-EEEEEecH
Confidence            4689999999999877 3555666655 9999 89998543

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=80.49  E-value=0.11  Score=39.47  Aligned_cols=40  Identities=10%  Similarity=-0.069  Sum_probs=31.3

Q ss_pred             CChhhhhcCCCCCCCCCCCCCCCCCCC-CCCCCCccccccccc
Q psy16184          5 LPPNLLALFAPRDPVPYLPPVEKLPHE-KKTHGYSGIAAFLNE   46 (363)
Q Consensus         5 ~p~~l~~~f~~~~pi~~~~p~~~~p~t-~~s~g~~g~v~f~~~   46 (363)
                      +..+|..+|+++|+|..+ -|+.++.+ +.++|| +||.|.+.
T Consensus        26 ~~~dl~~~f~~~G~V~~v-~i~~~~~~~~~~~G~-~FV~f~~~   66 (105)
T 2pe8_A           26 LEVETKEECEKYGKVGKC-VIFEIPGAPDDEAVR-IFLEFERV   66 (105)
T ss_dssp             CHHHHHHHGGGGSCEEEE-EEEECSSCCTTTSEE-EEEEESSH
T ss_pred             HHHHHHHHHHhcCCEEEE-EEecCCCCCCCCcEE-EEEEECCH
Confidence            446789999999999987 35556654 689999 99999554

>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=80.19  E-value=0.61  Score=33.48  Aligned_cols=33  Identities=15%  Similarity=0.282  Sum_probs=25.4

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|.++++|..+. +..     .++|| +||.|.+.
T Consensus        20 ~~l~~~F~~~G~i~~v~-i~~-----~~~g~-afV~f~~~   52 (88)
T 1wf0_A           20 DELREFFSQYGDVMDVF-IPK-----PFRAF-AFVTFADD   52 (88)
T ss_dssp             HHHHHHSTTTSCCCEEE-CCS-----SCCSC-CEEECSCH
T ss_pred             HHHHHHHHHcCCeeEEE-Eec-----CCCCE-EEEEECCH
Confidence            46999999999998874 322     27899 99998554

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=80.13  E-value=0.13  Score=40.32  Aligned_cols=38  Identities=16%  Similarity=0.261  Sum_probs=28.5

Q ss_pred             hhhhhcCCCCCCCC----CCCCCCCCCCCCCCCCCcccccccccc
Q psy16184          7 PNLLALFAPRDPVP----YLPPVEKLPHEKKTHGYSGIAAFLNEF   47 (363)
Q Consensus         7 ~~l~~~f~~~~pi~----~~~p~~~~p~t~~s~g~~g~v~f~~~~   47 (363)
                      .+|..+|.++++|.    .+ -|..+ .+++++|| +||.|.+..
T Consensus        38 ~dl~~~F~~~g~v~g~v~~v-~i~~d-~~gr~~G~-aFV~F~~~~   79 (123)
T 2dha_A           38 EEVVAFFGQHCPITGGKEGI-LFVTY-PDGRPTGD-AFVLFACEE   79 (123)
T ss_dssp             HHHHHHHHTTSCCTTGGGGE-EEEEC-TTSCEEEE-EEECCSSHH
T ss_pred             HHHHHHHHhhCCccCCcceE-EEEEC-CCCCEeeE-EEEEECCHH
Confidence            46999999999873    33 24445 48999999 999996643

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=80.10  E-value=0.065  Score=40.20  Aligned_cols=37  Identities=22%  Similarity=0.221  Sum_probs=30.2

Q ss_pred             hhhhhcCCC-CCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAP-RDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~-~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|.+ +++|..+ .++.++ ++.++|| +||.|.+.
T Consensus        24 ~~l~~~F~~~~G~v~~v-~i~~~~-~g~~~g~-afV~f~~~   61 (104)
T 2dhg_A           24 GMLYEFFVKVYPSCRGG-KVVLDQ-TGVSKGY-GFVKFTDE   61 (104)
T ss_dssp             HHHHHHHHHHCTTEEEE-EEEECT-TCCEEEE-EEEEESCH
T ss_pred             HHHHHHHHHhCCCeEEE-EEEECC-CCCccce-EEEEECCH
Confidence            468999999 9999887 356677 8999999 99998654

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=80.04  E-value=0.16  Score=39.22  Aligned_cols=38  Identities=8%  Similarity=0.013  Sum_probs=28.4

Q ss_pred             hhhhhcCCCCCC---CCCCCCCCCCCCCCCCCCCcccccccccc
Q psy16184          7 PNLLALFAPRDP---VPYLPPVEKLPHEKKTHGYSGIAAFLNEF   47 (363)
Q Consensus         7 ~~l~~~f~~~~p---i~~~~p~~~~p~t~~s~g~~g~v~f~~~~   47 (363)
                      .+|..+|..+++   |..+ -+..++. ++++|| +||.|.+..
T Consensus        32 ~~l~~~F~~~G~~~~v~~v-~i~~~~~-g~~~G~-afV~F~~~~   72 (118)
T 2db1_A           32 EDVQNFLSDCTIHDGVAGV-HFIYTRE-GRQSGE-AFVELESED   72 (118)
T ss_dssp             HHHHHHTTTSCBTTGGGGE-EEEECSS-SCEEEE-EEEEBSSHH
T ss_pred             HHHHHHHHHcCCccCceeE-EEEECCC-CCCCeE-EEEEECCHH
Confidence            469999999998   4555 2444555 899999 999996643

---

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	363
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	1e-13
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	3e-13
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	5e-13
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	3e-12
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	3e-12
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	4e-12
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	9e-12
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	1e-11
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	2e-11
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	4e-11
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	5e-11
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	6e-11
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	7e-11
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	7e-11
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	1e-10
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	1e-10
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	1e-10
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	2e-10
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	2e-10
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	3e-10
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	3e-10
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 6e-10
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	9e-10
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	1e-09
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	1e-09
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-09
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	1e-09
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	2e-09
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	3e-09
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	5e-09
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	6e-09
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	7e-09
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	1e-08
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	1e-08
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	1e-08
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	1e-08
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	1e-08
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	2e-08
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	3e-08
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	3e-08
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	3e-08
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	4e-08
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	5e-08
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	5e-08
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	5e-08
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	5e-08
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	5e-08
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	8e-08
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	8e-08
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	1e-07
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-07
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-07
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	1e-07
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	2e-07
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	2e-07
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-07
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	2e-07
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	3e-07
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	5e-07
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	6e-07
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	1e-06
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	1e-06
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	2e-06
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	3e-06
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	5e-06
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	1e-05
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	2e-05
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	2e-05
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	5e-05
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	6e-05
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	6e-05
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	8e-05
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	1e-04
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	5e-04
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	0.002
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	0.002

>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 = 63.8 bits (155), Expect = 1e-13
 Identities = 18/74 (24%), Positives = 37/74 (50%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
           +L++  ++ D +E+ L  +F   GPI  I +  + +T +  GYA++ ++   D   A   
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 163 ADGKKIDGRRVLVD 176
            +   I G+ V + 
Sbjct: 62  MNFDVIKGKPVRIM 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 = 62.3 bits (151), Expect = 3e-13
 Identities = 14/74 (18%), Positives = 38/74 (51%), Gaps = 1/74 (1%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           +FI  +++ T++  LR  F  +G +K+ +++ + +T + RG+ F+ +  +  +       
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-Q 61

Query: 164 DGKKIDGRRVLVDV 177
              ++D + +   V
Sbjct: 62  SRHELDSKTIDPKV 75

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 61.9 bits (150), Expect = 5e-13
 Identities = 18/77 (23%), Positives = 35/77 (45%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
            L++  +    ++ +L   F  YG I +  ++ +K+TG+PRG AF+ Y    +   A   
Sbjct: 8   NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 67

Query: 163 ADGKKIDGRRVLVDVER 179
            +    +G    + V  
Sbjct: 68  LNNVIPEGGSQPLSVRL 84

>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 = 59.6 bits (144), Expect = 3e-12
 Identities = 21/77 (27%), Positives = 36/77 (46%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
            L +  +  D ++ +L   F   GPI    ++ +  TG   GYAF+++  E D   A K 
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 163 ADGKKIDGRRVLVDVER 179
            +G  +  +R+ V   R
Sbjct: 64  LNGITVRNKRLKVSYAR 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 = 60.0 bits (145), Expect = 3e-12
 Identities = 22/84 (26%), Positives = 44/84 (52%)

Query: 98  MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMH 157
           +    TL++  +++ T+E ++   F   G IKKI+M  +K+     G+ F+EY    D  
Sbjct: 4   LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAE 63

Query: 158 SAYKHADGKKIDGRRVLVDVERSR 181
           +A ++ +G ++D R +  D +   
Sbjct: 64  NAMRYINGTRLDDRIIRTDWDAGF 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 = 59.3 bits (143), Expect = 4e-12
 Identities = 27/77 (35%), Positives = 47/77 (61%)

Query: 99  DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHS 158
           DP   L +  ++  T+E  LR  F  YGPI  + +V+++ + + RG+AF+ +E+  D   
Sbjct: 7   DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 66

Query: 159 AYKHADGKKIDGRRVLV 175
           A + A+G ++DGRR+ V
Sbjct: 67  AKERANGMELDGRRIRV 83

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.5 bits (141), Expect = 9e-12
 Identities = 19/78 (24%), Positives = 39/78 (50%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
            L+++ +    ++ +L + F  YG I    ++ ++VTG  RG  FI ++   +   A K 
Sbjct: 8   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 67

Query: 163 ADGKKIDGRRVLVDVERS 180
            +G+K  G    + V+ +
Sbjct: 68  LNGQKPSGATEPITVKFA 85

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 57.6 bits (139), Expect = 1e-11
 Identities = 20/77 (25%), Positives = 41/77 (53%), Gaps = 1/77 (1%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           L ++ +++  S++ ++  F  +G +KK   VH   +G+  G A + +E + D   A K  
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKK-AAVHYDRSGRSLGTADVHFERKADALKAMKQY 61

Query: 164 DGKKIDGRRVLVDVERS 180
           +G  +DGR + + +  S
Sbjct: 62  NGVPLDGRPMNIQLVTS 78

>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 = 57.4 bits (138), Expect = 2e-11
 Identities = 20/83 (24%), Positives = 37/83 (44%), Gaps = 1/83 (1%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVH-NKVTGKPRGYAFIEYEHERDMHSAYKH 162
           +FI  ++ +  E  L   F  +G I +   +  +  TG  +GYAFI +       +A + 
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 163 ADGKKIDGRRVLVDVERSRTVKG 185
            +G+ +  R + V     +  KG
Sbjct: 61  MNGQYLCNRPITVSYAFKKDSKG 83

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.3 bits (135), Expect = 4e-11
 Identities = 18/77 (23%), Positives = 36/77 (46%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
            L +  +  + ++ + R  F   G I+   +V +K+TG+  GY F+ Y   +D   A   
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 163 ADGKKIDGRRVLVDVER 179
            +G ++  + + V   R
Sbjct: 64  LNGLRLQTKTIKVSYAR 80

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 56.6 bits (136), Expect = 5e-11
 Identities = 14/75 (18%), Positives = 30/75 (40%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
            + +  + +  S  ++   F  Y  I   V +     G P G A + +E   +  +A   
Sbjct: 11  IIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID 70

Query: 163 ADGKKIDGRRVLVDV 177
            + + I  R+V + +
Sbjct: 71  LNDRPIGSRKVKLVL 85

>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 = 56.1 bits (135), Expect = 6e-11
 Identities = 14/77 (18%), Positives = 38/77 (49%), Gaps = 2/77 (2%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKI-VMVHNKVTGKPRGYAFIEYEHERDMHSAY 160
             + +  + +  ++ ++R  F  +G +K + +      TG  RG+ F+++  ++D   A+
Sbjct: 9   SKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAF 68

Query: 161 KH-ADGKKIDGRRVLVD 176
                   + GRR++++
Sbjct: 69  NALCHSTHLYGRRLVLE 85

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.8 bits (134), Expect = 7e-11
 Identities = 19/73 (26%), Positives = 36/73 (49%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           LFI  +    ++ +++     +GP+K   +V +  TG  +GYAF EY        A    
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 164 DGKKIDGRRVLVD 176
           +G ++  +++LV 
Sbjct: 64  NGMQLGDKKLLVQ 76

>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 = 55.8 bits (134), Expect = 7e-11
 Identities = 20/83 (24%), Positives = 42/83 (50%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
           + L++  +  +  +  L   F  +G I  I +  +  T K RG+AF+E+E   D  +A  
Sbjct: 6   RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65

Query: 162 HADGKKIDGRRVLVDVERSRTVK 184
           + +  ++ GR + V++ +   +K
Sbjct: 66  NMNESELFGRTIRVNLAKPMRIK 88

>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 = 55.8 bits (134), Expect = 1e-10
 Identities = 24/88 (27%), Positives = 43/88 (48%)

Query: 94  PNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHE 153
           P +  +   T+++  ++   SE  L   F   GP+    M  ++VTG+ +GY F+E+  E
Sbjct: 2   PISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSE 61

Query: 154 RDMHSAYKHADGKKIDGRRVLVDVERSR 181
            D   A K  D  K+ G+ + V+   + 
Sbjct: 62  EDADYAIKIMDMIKLYGKPIRVNKASAH 89

>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 = 55.4 bits (133), Expect = 1e-10
 Identities = 23/82 (28%), Positives = 35/82 (42%), Gaps = 3/82 (3%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNK---VTGKPRGYAFIEYEHERDMHSAY 160
           LFI  +N+ T+E  L+  F   G IK   +   K         G+ F+EY+       A 
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 161 KHADGKKIDGRRVLVDVERSRT 182
           K   G  +DG ++ V +    T
Sbjct: 61  KQLQGHTVDGHKLEVRISERAT 82

>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 = 25/89 (28%), Positives = 42/89 (47%)

Query: 94  PNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHE 153
           PN   D   T+ +  ++ DT E+ L+  F  +G I +I +  +K TG+ +G+AFI +   
Sbjct: 1   PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRR 60

Query: 154 RDMHSAYKHADGKKIDGRRVLVDVERSRT 182
            D   A     G   D   + V+  +  T
Sbjct: 61  EDAARAIAGVSGFGYDHLILNVEWAKPST 89

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.6 bits (131), Expect = 2e-10
 Identities = 17/74 (22%), Positives = 35/74 (47%), Gaps = 1/74 (1%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           +F+  ++ DT E K+R  F  +G ++ I +  +  T K RG+ FI ++ E  +    +  
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-K 60

Query: 164 DGKKIDGRRVLVDV 177
               +   +  + V
Sbjct: 61  KYHNVGLSKCEIKV 74

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.3 bits (130), Expect = 2e-10
 Identities = 22/78 (28%), Positives = 42/78 (53%), Gaps = 1/78 (1%)

Query: 99  DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHS 158
           +  + LFI  ++++T++  LR  FE +G +   V++ +  T + RG+ F+ Y    ++ +
Sbjct: 4   EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 63

Query: 159 AYKHADGKKIDGRRVLVD 176
           A   A   K+DGR V   
Sbjct: 64  AMN-ARPHKVDGRVVEPK 80

>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 = 54.7 bits (131), Expect = 3e-10
 Identities = 24/96 (25%), Positives = 46/96 (47%), Gaps = 1/96 (1%)

Query: 90  PNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIE 149
           P        + F+ LFI  ++++T+E  LR  +E +G +   V++ +  + + RG+ F+ 
Sbjct: 9   PLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVT 68

Query: 150 YEHERDMHSAYKHADGKKIDGRRVLVDVERSRTVKG 185
           +    ++ +A   A    IDGR V      +R   G
Sbjct: 69  FSSMAEVDAAMA-ARPHSIDGRVVEPKRAVAREESG 103

>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 = 55.7 bits (133), Expect = 3e-10
 Identities = 30/117 (25%), Positives = 56/117 (47%)

Query: 80  KLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVT 139
           +L+Q+     P +  N   D  + L +  +     E +LR+ FE YGPI+ + +V ++ T
Sbjct: 21  QLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRET 80

Query: 140 GKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLG 196
            + RGY F++++       A    +G  I  +R+ V +  S   +  +   +G G G
Sbjct: 81  RQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIAGAVGDGNG 137

>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 = 53.9 bits (129), Expect = 6e-10
 Identities = 10/76 (13%), Positives = 28/76 (36%), Gaps = 1/76 (1%)

Query: 101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAY 160
              + +     +  E       E YG ++++ +  N       G  ++++  E D   A 
Sbjct: 27  VSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAV 85

Query: 161 KHADGKKIDGRRVLVD 176
              + +  +G+ +  +
Sbjct: 86  IDLNNRWFNGQPIHAE 101

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 52.5 bits (125), Expect = 9e-10
 Identities = 12/75 (16%), Positives = 31/75 (41%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
           TL++       ++  +R   +    +   + + +      R +A+I+   + D     + 
Sbjct: 3   TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEK 62

Query: 163 ADGKKIDGRRVLVDV 177
            +G KI+G  ++  V
Sbjct: 63  LNGLKIEGYTLVTKV 77

>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 = 53.5 bits (128), Expect = 1e-09
 Identities = 20/89 (22%), Positives = 40/89 (44%), Gaps = 3/89 (3%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
           + L+I  + Y  +  ++   F  YGPI++I + +     + RG A++ YE   D  +A  
Sbjct: 8   RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACD 64

Query: 162 HADGKKIDGRRVLVDVERSRTVKGWLPRR 190
           H  G  +  R ++V    +      +  +
Sbjct: 65  HLSGFNVCNRYLVVLYYNANRAFQKMDTK 93

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.8 bits (126), Expect = 1e-09
 Identities = 30/97 (30%), Positives = 48/97 (49%), Gaps = 5/97 (5%)

Query: 101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAY 160
           F  +F+  + Y T+++ LR+ FE +G I++ V++ ++ TGK RGY F+          A 
Sbjct: 10  FTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERAC 69

Query: 161 KHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGG 197
           K  +   IDGR+  V+        G  PR L  G   
Sbjct: 70  KDPNP-IIDGRKANVN----LAYLGAKPRSLQTGFAI 101

>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 = 52.6 bits (126), Expect = 1e-09
 Identities = 19/81 (23%), Positives = 36/81 (44%), Gaps = 9/81 (11%)

Query: 102 KTLFIARVN-YDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAY 160
             +FI  +N     +S +   F  YG I    +          G+AF++Y +ER+  +A 
Sbjct: 16  SRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHK--------GFAFVQYVNERNARAAV 67

Query: 161 KHADGKKIDGRRVLVDVERSR 181
              DG+ I G+ + +++    
Sbjct: 68  AGEDGRMIAGQVLDINLAAEP 88

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.3 bits (125), Expect = 1e-09
 Identities = 23/85 (27%), Positives = 37/85 (43%), Gaps = 6/85 (7%)

Query: 97  TMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDM 156
           TM   K L++  +   TSE  + +EF        I     +   K R YAF+ + +  D 
Sbjct: 4   TMSSVKILYVRNLMLSTSEEMIEKEFN------NIKPGAVERVKKIRDYAFVHFSNREDA 57

Query: 157 HSAYKHADGKKIDGRRVLVDVERSR 181
             A K  +GK +DG  + V + +  
Sbjct: 58  VEAMKALNGKVLDGSPIEVTLAKPV 82

>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 = 51.6 bits (123), Expect = 2e-09
 Identities = 23/79 (29%), Positives = 44/79 (55%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
            LF+  ++ +  E +++ +F  YG IK I +  ++ TG  +GYA +EYE  +   +A + 
Sbjct: 9   ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 68

Query: 163 ADGKKIDGRRVLVDVERSR 181
            +G +I G+ + VD    +
Sbjct: 69  LNGAEIMGQTIQVDWCFVK 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 = 51.5 bits (123), Expect = 3e-09
 Identities = 15/84 (17%), Positives = 32/84 (38%), Gaps = 2/84 (2%)

Query: 98  MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMH 157
           +     L +  + + T+E  L+  F  +G +  + +  +  TG  +G+ F+ +       
Sbjct: 5   VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQV 64

Query: 158 SAYKHADGKKIDGRRVLVDVERSR 181
                     IDGR     +  S+
Sbjct: 65  KVMS--QRHMIDGRWCDCKLPNSK 86

>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 = 50.9 bits (121), Expect = 5e-09
 Identities = 23/80 (28%), Positives = 40/80 (50%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
             LF+  ++Y +SE  L + F  YGP+ ++    + +T KP+G+AF+ +        AY 
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 162 HADGKKIDGRRVLVDVERSR 181
             DG+   GR + V     +
Sbjct: 69  EVDGQVFQGRMLHVLPSTIK 88

>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 = 50.0 bits (119), Expect = 6e-09
 Identities = 14/72 (19%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           +FI  +++DT++  L+  F  +G +    +  + +TG+ RG+ F+ ++    +       
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-Q 60

Query: 164 DGKKIDGRRVLV 175
              K++G+ +  
Sbjct: 61  KEHKLNGKVIDP 72

>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 = 50.0 bits (119), Expect = 7e-09
 Identities = 19/80 (23%), Positives = 35/80 (43%), Gaps = 8/80 (10%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
            TL++     D + + LR  F  +G I  + M        PR  AF+ YE       A  
Sbjct: 6   NTLYVY--GEDMTPTLLRGAFSPFGNIIDLSMDP------PRNCAFVTYEKMESADQAVA 57

Query: 162 HADGKKIDGRRVLVDVERSR 181
             +G +++  ++ V++ R +
Sbjct: 58  ELNGTQVESVQLKVNIARKQ 77

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.1 bits (119), Expect = 1e-08
 Identities = 17/83 (20%), Positives = 39/83 (46%)

Query: 100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSA 159
               LFI  +  +  +  L + F  +G +    +  +K T   + + F+ Y++     +A
Sbjct: 17  EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA 76

Query: 160 YKHADGKKIDGRRVLVDVERSRT 182
            +  +G +I  +R+ V ++RS+ 
Sbjct: 77  IQSMNGFQIGMKRLKVQLKRSKN 99

>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 = 50.0 bits (119), Expect = 1e-08
 Identities = 21/80 (26%), Positives = 39/80 (48%), Gaps = 5/80 (6%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
           +TL    ++++ +E +L+  FE    I+ +        GK +G A+IE++ E D     +
Sbjct: 17  RTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAYIEFKSEADAEKNLE 71

Query: 162 HADGKKIDGRRVLVDVERSR 181
              G +IDGR V +     +
Sbjct: 72  EKQGAEIDGRSVSLYYTGEK 91

>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 = 49.3 bits (117), Expect = 1e-08
 Identities = 21/76 (27%), Positives = 37/76 (48%), Gaps = 1/76 (1%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
           K +F+  +  DT E  LR  FE YG I+ I ++ ++ +GK RG+AF+ ++    +     
Sbjct: 3   KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 62

Query: 162 HADGKKIDGRRVLVDV 177
                 ++G    V  
Sbjct: 63  Q-KYHTVNGHNCEVRK 77

>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 = 1e-08
 Identities = 15/87 (17%), Positives = 33/87 (37%), Gaps = 6/87 (6%)

Query: 95  NATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHER 154
           N +     T++   +    ++  +R+ F  +G I +I +         +GY+F+ +    
Sbjct: 12  NQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF------PEKGYSFVRFSTHE 65

Query: 155 DMHSAYKHADGKKIDGRRVLVDVERSR 181
               A    +G  I+G  V     +  
Sbjct: 66  SAAHAIVSVNGTTIEGHVVKCYWGKES 92

>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 = 49.7 bits (118), Expect = 1e-08
 Identities = 22/83 (26%), Positives = 34/83 (40%), Gaps = 3/83 (3%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
            +++  +  D     +   F  YG I+    +  K       +AF+E+E  RD   A   
Sbjct: 16  RIYVGNLPPDIRTKDIEDVFYKYGAIR---DIDLKNRRGGPPFAFVEFEDPRDAEDAVYG 72

Query: 163 ADGKKIDGRRVLVDVERSRTVKG 185
            DG   DG R+ V+  RS    G
Sbjct: 73  RDGYDYDGYRLRVEFPRSGRGTG 95

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.6 bits (118), Expect = 2e-08
 Identities = 15/94 (15%), Positives = 32/94 (34%), Gaps = 4/94 (4%)

Query: 96  ATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERD 155
           A   P   + +  + Y  +   L + F  +G + KI+          +  A ++Y     
Sbjct: 2   AGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVS 57

Query: 156 MHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPR 189
              A    DG+ I      + ++ S+     +  
Sbjct: 58  AQHAKLSLDGQNIYNACCTLRIDFSKLTSLNVKY 91

>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 = 49.0 bits (116), Expect = 3e-08
 Identities = 18/91 (19%), Positives = 35/91 (38%), Gaps = 1/91 (1%)

Query: 99  DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHS 158
            P  T F+  + YD +E  ++  F         +        + +G+ + E+E    + S
Sbjct: 13  SPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLS 72

Query: 159 AYKHADGKKIDGRRVLVDVERSRTVKGWLPR 189
           A    + + +  +R+ VDV      K   P 
Sbjct: 73  ALS-LNEESLGNKRIRVDVADQAQDKDSGPS 102

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.6 bits (115), Expect = 3e-08
 Identities = 18/83 (21%), Positives = 41/83 (49%)

Query: 99  DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHS 158
           +P K L++  ++   +E  L   F  +   K   +    +TG+ RG AFI + ++     
Sbjct: 16  EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQ 75

Query: 159 AYKHADGKKIDGRRVLVDVERSR 181
           A    +G K+ G+ ++++  +++
Sbjct: 76  ALHLVNGYKLYGKILVIEFGKNK 98

>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 = 48.5 bits (115), Expect = 3e-08
 Identities = 18/78 (23%), Positives = 28/78 (35%), Gaps = 4/78 (5%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIV--MVHNKVTGKPRGYAFIEYEHERDMHSAY 160
            LFI  +       ++  E          V          K RG+AF+EYE  R    A 
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 161 KHADGK--KIDGRRVLVD 176
           +       ++ G ++ VD
Sbjct: 63  RKLMPGRIQLWGHQIAVD 80

>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 = 48.2 bits (114), Expect = 4e-08
 Identities = 26/80 (32%), Positives = 47/80 (58%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
            LF+  +++DT+E  L + F  YG I ++V+V ++ T + RG+ F+ +E+  D   A   
Sbjct: 7   KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 66

Query: 163 ADGKKIDGRRVLVDVERSRT 182
            +GK +DGR++ VD     +
Sbjct: 67  MNGKSVDGRQIRVDQAGKSS 86

>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 = 47.5 bits (112), Expect = 5e-08
 Identities = 13/74 (17%), Positives = 30/74 (40%), Gaps = 3/74 (4%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
           T+ +  +    +++K+ + F+  GPI  + +       K   +A IE+       +A   
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVA--DSLKKNFRFARIEFARYDGALAAITK 59

Query: 163 ADGKKIDGRRVLVD 176
              K +    ++V 
Sbjct: 60  -THKVVGQNEIIVS 72

>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 = 48.1 bits (114), Expect = 5e-08
 Identities = 13/84 (15%), Positives = 37/84 (44%), Gaps = 1/84 (1%)

Query: 100 PFKTLFIARVNYDTSESKLRRE-FEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHS 158
           P  T++I  +N    + +L++    ++    +I+ +    + K RG AF+ ++      +
Sbjct: 2   PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 61

Query: 159 AYKHADGKKIDGRRVLVDVERSRT 182
           A +   G     + + +   ++ +
Sbjct: 62  ALRSMQGFPFYDKPMRIQYAKTDS 85

>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 = 47.9 bits (113), Expect = 5e-08
 Identities = 14/77 (18%), Positives = 34/77 (44%), Gaps = 6/77 (7%)

Query: 103 TLFIARVNYDTSESKLRREFEV---YGPIKKIVMVHNKVTGK---PRGYAFIEYEHERDM 156
            +F+  ++   ++ ++ +  E    +G I K+V+ ++        P   A++ Y    D 
Sbjct: 10  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 69

Query: 157 HSAYKHADGKKIDGRRV 173
             A +  +   +DGR +
Sbjct: 70  LRAIQCVNNVVVDGRTL 86

>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 = 47.4 bits (112), Expect = 5e-08
 Identities = 14/73 (19%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           +F+  ++ +T+   ++  FE +G +   +++ +K T + RG+ F+ +E E  +    +  
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-I 60

Query: 164 DGKKIDGRRVLVD 176
              +I+ + V   
Sbjct: 61  HFHEINNKMVECK 73

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 47.7 bits (113), Expect = 5e-08
 Identities = 17/74 (22%), Positives = 32/74 (43%), Gaps = 6/74 (8%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
            LF+  +  D +E ++R+ FE YG   ++ +  +K       + FI  E       A   
Sbjct: 10  RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG------FGFIRLETRTLAEIAKVE 63

Query: 163 ADGKKIDGRRVLVD 176
            D   + G+++ V 
Sbjct: 64  LDNMPLRGKQLRVR 77

>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 = 47.4 bits (112), Expect = 8e-08
 Identities = 18/85 (21%), Positives = 42/85 (49%), Gaps = 2/85 (2%)

Query: 97  TMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDM 156
           +    K L ++ + +   +  LR+ F  +G I  + ++ N+     +G+ F+ +E+  D 
Sbjct: 7   SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADA 64

Query: 157 HSAYKHADGKKIDGRRVLVDVERSR 181
             A +   G  ++GR++ V+   +R
Sbjct: 65  DRAREKLHGTVVEGRKIEVNNATAR 89

>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 = 47.5 bits (112), Expect = 8e-08
 Identities = 23/101 (22%), Positives = 42/101 (41%), Gaps = 13/101 (12%)

Query: 89  DPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVH--------NKVTG 140
           DP+   + +      +++  +N   +   L   F+  G +K              +K TG
Sbjct: 1   DPDEDSDNS-----AIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETG 55

Query: 141 KPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERSR 181
           KP+G A + YE      +A +  DGK   G ++ V + R +
Sbjct: 56  KPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKK 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 = 47.2 bits (112), Expect = 1e-07
 Identities = 14/72 (19%), Positives = 27/72 (37%), Gaps = 4/72 (5%)

Query: 111 YDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDG 170
            +     LR E   +G I+K+++        P G A + +    +     +  DG+   G
Sbjct: 29  LNEIREDLRVECSKFGQIRKLLLFDRH----PDGVASVSFRDPEEADYCIQTLDGRWFGG 84

Query: 171 RRVLVDVERSRT 182
           R++        T
Sbjct: 85  RQITAQAWDGTT 96

>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 = 49.2 bits (116), Expect = 1e-07
 Identities = 16/63 (25%), Positives = 35/63 (55%)

Query: 99  DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHS 158
           +  + LFI  ++++T++  LR  FE +G +   V++ +  T + RG+ F+ Y    ++ +
Sbjct: 4   EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 63

Query: 159 AYK 161
           A  
Sbjct: 64  AMN 66

>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 = 1e-07
 Identities = 28/122 (22%), Positives = 50/122 (40%), Gaps = 1/122 (0%)

Query: 60  ETREERLERRRRERAEQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLR 119
            T EE          +     +E + A+   +S         K +F+  +  DT E  LR
Sbjct: 56  ATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLR 115

Query: 120 REFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 179
             FE YG I+ I ++ ++ +GK RG+AF+ ++    +           ++G    V    
Sbjct: 116 DYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKAL 174

Query: 180 SR 181
           S+
Sbjct: 175 SK 176

>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 = 46.7 bits (110), Expect = 1e-07
 Identities = 8/81 (9%), Positives = 28/81 (34%), Gaps = 7/81 (8%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
             + +  +  D++  ++    + Y      V        + +  AF+   +     +A +
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYDLKYCYVD-------RNKRTAFVTLLNGEQAQNAIQ 58

Query: 162 HADGKKIDGRRVLVDVERSRT 182
                   G+ ++V ++ +  
Sbjct: 59  MFHQYSFRGKDLIVQLQPTDA 79

>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 = 46.6 bits (110), Expect = 2e-07
 Identities = 21/75 (28%), Positives = 37/75 (49%), Gaps = 2/75 (2%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
           +TL++  ++ D +E  + + F   GP K   M+          Y F+E+   RD  +A  
Sbjct: 9   RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH--TSNDPYCFVEFYEHRDAAAALA 66

Query: 162 HADGKKIDGRRVLVD 176
             +G+KI G+ V V+
Sbjct: 67  AMNGRKILGKEVKVN 81

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.2 bits (109), Expect = 2e-07
 Identities = 16/80 (20%), Positives = 31/80 (38%), Gaps = 7/80 (8%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
             +F+ R   D +E +LR  F  YG +  + +         R +AF+ +  ++   S   
Sbjct: 6   SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCG 60

Query: 162 HADGKKIDGRRVLVDVERSR 181
             +   I G  V +     +
Sbjct: 61  --EDLIIKGISVHISNAEPK 78

>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 = 46.3 bits (109), Expect = 2e-07
 Identities = 11/79 (13%), Positives = 29/79 (36%), Gaps = 6/79 (7%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIV-----MVHNKVTGKPRGYAFIEYEHERDM 156
           + L++  + +  +E  +   F     +  +       V      + + +AF+E+    + 
Sbjct: 2   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 61

Query: 157 HSAYKHADGKKIDGRRVLV 175
             A    DG    G+ + +
Sbjct: 62  TQA-MAFDGIIFQGQSLKI 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 = 45.8 bits (108), Expect = 2e-07
 Identities = 17/80 (21%), Positives = 32/80 (40%), Gaps = 7/80 (8%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
            L+I  ++   +   LR+ F          +          GYAF++Y  +     A + 
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRK------LPLAGQVLLKSGYAFVDYPDQNWAIRAIET 56

Query: 163 ADGK-KIDGRRVLVDVERSR 181
             GK ++ G+ + VD   S+
Sbjct: 57  LSGKVELHGKIMEVDYSVSK 76

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.9 bits (108), Expect = 3e-07
 Identities = 28/92 (30%), Positives = 51/92 (55%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
           +++F+  + Y+ +E +L+  F   GP+    +V+++ TGKP+GY F EY+ +    SA +
Sbjct: 9   RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68

Query: 162 HADGKKIDGRRVLVDVERSRTVKGWLPRRLGG 193
           + +G++  GR + VD   S   K  L     G
Sbjct: 69  NLNGREFSGRALRVDNAASEKNKEELKSLGTG 100

>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 = 5e-07
 Identities = 20/86 (23%), Positives = 38/86 (44%), Gaps = 6/86 (6%)

Query: 100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSA 159
           P   L++  +  +TS + L REF+ +G I+ I  V          +A+I+YE      +A
Sbjct: 16  PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDS------FAYIQYESLDAAQAA 69

Query: 160 YKHADGKKIDGRRVLVDVERSRTVKG 185
                G  + G    + V+ +++   
Sbjct: 70  CAKMRGFPLGGPDRRLRVDFAKSGPS 95

>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 = 45.4 bits (107), Expect = 6e-07
 Identities = 11/80 (13%), Positives = 37/80 (46%), Gaps = 1/80 (1%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
           +T+F  ++        L   F   G ++ + ++ ++ + + +G A++E+   + +     
Sbjct: 19  RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVP-LAI 77

Query: 162 HADGKKIDGRRVLVDVERSR 181
              G+++ G  ++V   ++ 
Sbjct: 78  GLTGQRLLGVPIIVQASQAE 97

>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 = 43.6 bits (102), Expect = 1e-06
 Identities = 14/70 (20%), Positives = 29/70 (41%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           L+I  +   T++  L +  + YG I     + +K T K +GY F++++       A    
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 164 DGKKIDGRRV 173
               +  +  
Sbjct: 61  KASGVQAQMA 70

>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 = 43.9 bits (103), Expect = 1e-06
 Identities = 18/79 (22%), Positives = 35/79 (44%), Gaps = 2/79 (2%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
            +FI  ++       L   F  +G I    +V ++     +GY F+ +E +     A + 
Sbjct: 10  NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEK 67

Query: 163 ADGKKIDGRRVLVDVERSR 181
            +G  ++ R+V V   +SR
Sbjct: 68  MNGMLLNDRKVFVGRFKSR 86

>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 = 43.9 bits (103), Expect = 2e-06
 Identities = 18/93 (19%), Positives = 34/93 (36%), Gaps = 9/93 (9%)

Query: 95  NATMDPFKTLFIARVN--YDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEH 152
                  ++L +A        S ++L    E  G +  ++M  NK       Y+F  Y  
Sbjct: 12  ETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP------YSFARYRT 65

Query: 153 ERDMHSAYKHADGKKI-DGRRVLVDVERSRTVK 184
             +   AY   +GK++ D     + +  +   K
Sbjct: 66  TEESKRAYVTLNGKEVVDDLGQKITLYLNFVEK 98

>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 = 42.6 bits (99), Expect = 3e-06
 Identities = 17/80 (21%), Positives = 36/80 (45%), Gaps = 2/80 (2%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
             LFI  +N + S ++L+           + +V  + TG  R + ++++E   D+  A  
Sbjct: 14  FNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFESAEDLEKAL- 71

Query: 162 HADGKKIDGRRVLVDVERSR 181
              G K+ G  + ++  + R
Sbjct: 72  ELTGLKVFGNEIKLEKPKGR 91

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 42.5 bits (99), Expect = 5e-06
 Identities = 23/86 (26%), Positives = 43/86 (50%), Gaps = 6/86 (6%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
           KT+FI  +++D+ E  L    + +G +K + +V +  T   +G AF ++  +        
Sbjct: 9   KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 68

Query: 162 HA------DGKKIDGRRVLVDVERSR 181
            A       G K+DGR++ VD+  +R
Sbjct: 69  AASLEAEGGGLKLDGRQLKVDLAVTR 94

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.7 bits (97), Expect = 1e-05
 Identities = 14/82 (17%), Positives = 27/82 (32%), Gaps = 1/82 (1%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
            L+I+ +     E +L    + +G +    ++ +      RG  F   E      +   H
Sbjct: 20  NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSG-TSRGVGFARMESTEKCEAVIGH 78

Query: 163 ADGKKIDGRRVLVDVERSRTVK 184
            +GK I     +         K
Sbjct: 79  FNGKFIKTPPGVSAPTEPLLCK 100

>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 = 41.0 bits (95), Expect = 2e-05
 Identities = 19/96 (19%), Positives = 39/96 (40%), Gaps = 4/96 (4%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
               I  + +  ++  + +  E     +  V V     G+  G A +++++E D   + +
Sbjct: 9   VCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER 68

Query: 162 HADGKKIDGRRVLVDV---ERSRTVKGWLPRRLGGG 194
               KK++GR   V V   E  R ++   P +   G
Sbjct: 69  -LHRKKLNGREAFVHVVTLEDMREIEKNPPAQGKSG 103

>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 = 40.9 bits (95), Expect = 2e-05
 Identities = 9/87 (10%), Positives = 21/87 (24%), Gaps = 11/87 (12%)

Query: 103 TLFIARVNYD-----TSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMH 157
            L     N D      + +K    F  Y          +           I + +     
Sbjct: 7   GLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVRINFSNPLSAA 60

Query: 158 SAYKHADGKKIDGRRVLVDVERSRTVK 184
            A       +  G+ + +   ++  + 
Sbjct: 61  DARLRLHKTEFLGKEMKLYFAQTLHIG 87

>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 = 13/82 (15%), Positives = 30/82 (36%), Gaps = 3/82 (3%)

Query: 102 KTLFIARVNYD-TSESKLRREF-EVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSA 159
           + + I  ++ +   E+ LR  F       K  +    K        AF+ +E++     A
Sbjct: 5   REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA 64

Query: 160 YKHADGKKIDGRRVLVDVERSR 181
            +  +   +  R + V +   +
Sbjct: 65  LQ-MNRSLLGNREISVSLADKK 85

>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 = 39.7 bits (92), Expect = 6e-05
 Identities = 17/99 (17%), Positives = 36/99 (36%), Gaps = 8/99 (8%)

Query: 102 KTLFIARVN-YDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAY 160
             L ++ +N    +   L   F          +   K+    +  A ++         A 
Sbjct: 3   SVLLVSNLNPERVTPQSLFILF-----GVYGDVQRVKILFNKKENALVQMADGNQAQLAM 57

Query: 161 KHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGGTR 199
            H +G K+ G+ + + + + + V+  LPR      G T+
Sbjct: 58  SHLNGHKLHGKPIRITLSKHQNVQ--LPREGQEDQGLTK 94

>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 = 39.6 bits (92), Expect = 6e-05
 Identities = 17/68 (25%), Positives = 27/68 (39%), Gaps = 2/68 (2%)

Query: 111 YDTSESKLRREFEVYGPIK--KIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKI 168
           Y+     +R E   YG +K  +I    + V     G  F+E+    D   A +   G+K 
Sbjct: 24  YEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKF 83

Query: 169 DGRRVLVD 176
             R V+  
Sbjct: 84  ANRVVVTK 91

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.3 bits (91), Expect = 8e-05
 Identities = 15/87 (17%), Positives = 33/87 (37%), Gaps = 3/87 (3%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
            + +  + Y  +E+ +   F    P++  + +     G+  G A +E+    D  +A   
Sbjct: 17  CVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPD--GRVTGEADVEFATHEDAVAAMAK 74

Query: 163 ADGKKIDGRRVLVDVERSRTVKGWLPR 189
            D   +  R V + +  +    G  P 
Sbjct: 75  -DKANMQHRYVELFLNSTAGTSGSGPS 100

>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 = 37.6 bits (86), Expect = 1e-04
 Identities = 10/80 (12%), Positives = 26/80 (32%), Gaps = 7/80 (8%)

Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
           + I  +  D +  ++      Y               K +G AF+   +     +A    
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDYEL-------KYCFVDKYKGTAFVTLLNGEQAEAAINTF 53

Query: 164 DGKKIDGRRVLVDVERSRTV 183
              ++  R + V ++ +  +
Sbjct: 54  HQSRLRERELSVQLQPTDAL 73

>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 = 36.3 bits (83), Expect = 5e-04
 Identities = 11/74 (14%), Positives = 28/74 (37%), Gaps = 2/74 (2%)

Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
           ++++I     D +   ++   E  G +  I M    +    +G  F+ ++         +
Sbjct: 7   RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQM-RRTLHKAFKGSIFVVFDSIESAKKFVE 65

Query: 162 HADGKKIDGRRVLV 175
              G+K     +L+
Sbjct: 66  -TPGQKYKETDLLI 78

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 34.5 bits (79), Expect = 0.002
 Identities = 15/69 (21%), Positives = 26/69 (37%), Gaps = 8/69 (11%)

Query: 113 TSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRR 172
            S S +  +F  YG I K VM +         +  I Y+ +     A    DG+      
Sbjct: 15  ASASYILLQFAQYGNILKHVMSNTG------NWMHIRYQSKLQARKALSK-DGRIFGE-S 66

Query: 173 VLVDVERSR 181
           +++ V+   
Sbjct: 67  IMIGVKPCI 75

>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 = 35.1 bits (80), Expect = 0.002
 Identities = 12/88 (13%), Positives = 24/88 (27%), Gaps = 7/88 (7%)

Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
            + ++ +    S   L+      G +    +  +           +EY  + DM  A + 
Sbjct: 17  RVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKDG-------MGMVEYLRKEDMEYALRK 69

Query: 163 ADGKKIDGRRVLVDVERSRTVKGWLPRR 190
            D  K           R    +   P  
Sbjct: 70  LDDTKFRSHEGETSYIRVYPERSSGPSS 97

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	363
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.87
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.87
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.86
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.86
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.86
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.86
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.86
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.86
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.85
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.85
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.85
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.84
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.84
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.84
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.84
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.84
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.83
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.83
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.83
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.83
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.83
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.83
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.83
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.83
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.83
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.83
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.83
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.82
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.82
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.82
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.82
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.82
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.82
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.81
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.8
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.8
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.8
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.8
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.8
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.8
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.79
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.79
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.78
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.78
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.78
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.77
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.77
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.77
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.76
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.76
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.76
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.76
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.76
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.76
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.76
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.76
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.75
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.75
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.75
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.75
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.75
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.75
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.75
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.74
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.74
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.74
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.74
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.74
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.73
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.72
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.72
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.71
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.7
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.69
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.69
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.68
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.66
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.65
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.64
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.62
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	U2	99.57
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.54
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.48
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.48
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.46
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.4
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.38
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.98
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.56
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.53
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	96.65
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	96.22
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	95.99
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	95.43
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	95.42
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	95.33
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	95.21
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	94.69
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	94.54
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	94.52
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	94.15
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	93.91
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	93.85
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	93.83
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	93.15
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	93.08
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	93.0
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	92.84
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	92.68
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	92.15
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	92.07
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	92.0
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	91.86
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	91.78
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	91.65
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	91.02
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	91.0
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	90.89
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	90.65
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	90.6
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	90.33
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	89.88
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	89.66
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	89.15
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	88.74
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	88.66
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	88.5
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	87.34
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	86.33
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	85.65
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	85.11
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	84.54
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	83.98
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	83.94
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	80.52
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	80.06
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	80.02

>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=99.87  E-value=6.9e-22  Score=161.21  Aligned_cols=87  Identities=26%  Similarity=0.500  Sum_probs=81.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      ...++|||+|||+++|+++|.++|++||.|..|.|+.++.||.++|||||+|.+.++|..||..|||+.|+|+.|.|.+|
T Consensus        40 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a  119 (139)
T d1u6fa1          40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA  119 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            34578999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccCCCC
Q psy16184        179 RSRTVKG  185 (363)
Q Consensus       179 ~~~~~~~  185 (363)
                      .....+.
T Consensus       120 ~~~~~~p  126 (139)
T d1u6fa1         120 ASGHQRP  126 (139)
T ss_dssp             SCCCCCC
T ss_pred             CCCCCCC
Confidence            8765543

>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=99.87  E-value=3.3e-22  Score=150.68  Aligned_cols=86  Identities=27%  Similarity=0.447  Sum_probs=81.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEE
Q psy16184         97 TMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD  176 (363)
Q Consensus        97 ~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~  176 (363)
                      ..++.++|||+|||..+|+++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|+
T Consensus         4 ~~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~   83 (90)
T d2cq0a1           4 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVE   83 (90)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecccC
Q psy16184        177 VERSRT  182 (363)
Q Consensus       177 ~a~~~~  182 (363)
                      ||+++.
T Consensus        84 ~akp~~   89 (90)
T d2cq0a1          84 WAKPST   89 (90)
T ss_dssp             ESSCCC
T ss_pred             eeeCCC
Confidence            998753

>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=99.86  E-value=1.3e-21  Score=148.29  Aligned_cols=82  Identities=27%  Similarity=0.480  Sum_probs=78.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      ..+++|||+|||+++|+++|.++|++||.|..|.|+.++.++.++|||||+|.+.++|..||..|||..|+|+.|.|+|+
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a   84 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD   84 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cc
Q psy16184        179 RS  180 (363)
Q Consensus       179 ~~  180 (363)
                      .+
T Consensus        85 ~~   86 (93)
T d1h2vz_          85 AG   86 (93)
T ss_dssp             SC
T ss_pred             CC
Confidence            64

>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=99.86  E-value=4.9e-22  Score=147.04  Aligned_cols=80  Identities=26%  Similarity=0.458  Sum_probs=77.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeecc
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS  180 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~  180 (363)
                      .++|||+|||+.+|+++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++|+.||..|||..|.|+.|.|+||++
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999975

>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=99.86  E-value=6.6e-22  Score=148.66  Aligned_cols=83  Identities=23%  Similarity=0.435  Sum_probs=79.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      ..++|||+|||+++|+++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.+|+
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~   83 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   83 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            35799999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             ccC
Q psy16184        180 SRT  182 (363)
Q Consensus       180 ~~~  182 (363)
                      +..
T Consensus        84 p~~   86 (89)
T d2cqba1          84 PMR   86 (89)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            643

>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=99.86  E-value=7.3e-22  Score=149.61  Aligned_cols=85  Identities=27%  Similarity=0.420  Sum_probs=80.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184         98 MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      .++.++|||+|||+.+|+++|+++|++||.|..|.|+.++.||.++|||||+|.+.++|+.||..|||..|.|+.|.|.+
T Consensus         6 ~~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   85 (93)
T d1x5ua1           6 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNK   85 (93)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34567999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecccC
Q psy16184        178 ERSRT  182 (363)
Q Consensus       178 a~~~~  182 (363)
                      |.+..
T Consensus        86 A~~~~   90 (93)
T d1x5ua1          86 ASAHN   90 (93)
T ss_dssp             TTTTS
T ss_pred             cCCCC
Confidence            97653

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.86  E-value=1.4e-21  Score=146.45  Aligned_cols=82  Identities=28%  Similarity=0.473  Sum_probs=78.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      ..++|||+|||+.+|+++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++|+.||..|||..|.|+.|.|+||.
T Consensus         6 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a~   85 (88)
T d1rk8a_           6 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCF   85 (88)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEec
Confidence            46799999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             cc
Q psy16184        180 SR  181 (363)
Q Consensus       180 ~~  181 (363)
                      ++
T Consensus        86 ~k   87 (88)
T d1rk8a_          86 VK   87 (88)
T ss_dssp             EC
T ss_pred             CC
Confidence            64

>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=99.86  E-value=1.8e-21  Score=149.30  Aligned_cols=84  Identities=27%  Similarity=0.543  Sum_probs=79.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      ...++|||+|||+.+|+++|.++|.+||.|..|.|+.++.|+.++|||||+|.+.++|+.||..||+..|+|+.|.|.++
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            34678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccC
Q psy16184        179 RSRT  182 (363)
Q Consensus       179 ~~~~  182 (363)
                      ..+.
T Consensus        86 ~~~~   89 (99)
T d1whwa_          86 TIKK   89 (99)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            8754

>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=99.85  E-value=1.6e-21  Score=144.25  Aligned_cols=79  Identities=23%  Similarity=0.488  Sum_probs=76.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeecc
Q psy16184        102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS  180 (363)
Q Consensus       102 ~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~  180 (363)
                      ++|||+|||+.+|+++|.++|++||.|..|.|+.+..++.++|||||+|.+.++|+.|+..|||..|.|+.|.|.||+|
T Consensus         3 t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            5799999999999999999999999999999999989999999999999999999999999999999999999999975

>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=99.85  E-value=2.2e-21  Score=149.47  Aligned_cols=86  Identities=20%  Similarity=0.343  Sum_probs=81.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEE
Q psy16184         97 TMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD  176 (363)
Q Consensus        97 ~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~  176 (363)
                      ..++.++|||+|||+++|+++|.++|+.||.|..|.|+.++.+|.++|||||+|.+.++|+.||..|||..|.|+.|.|+
T Consensus        14 ~~p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~   93 (102)
T d2cpza1          14 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQ   93 (102)
T ss_dssp             CCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecccC
Q psy16184        177 VERSRT  182 (363)
Q Consensus       177 ~a~~~~  182 (363)
                      |+.++.
T Consensus        94 ~a~~k~   99 (102)
T d2cpza1          94 LKRSKN   99 (102)
T ss_dssp             CCCCSC
T ss_pred             EeCCCC
Confidence            998754

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=1.6e-21  Score=143.52  Aligned_cols=77  Identities=23%  Similarity=0.455  Sum_probs=75.3

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       103 ~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      +|||+|||+.+|+++|.++|.+||.|..|.|+.++.||.++|||||+|.+.++|..||..|||..|.|+.|.|.||+
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999985

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=3.8e-21  Score=142.50  Aligned_cols=77  Identities=35%  Similarity=0.616  Sum_probs=74.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEE
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLV  175 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V  175 (363)
                      .+.++|||+|||+.+|+++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|..||..|||..|+|+.|.|
T Consensus         7 ~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           7 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999987

>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=99.84  E-value=9.1e-21  Score=146.28  Aligned_cols=81  Identities=31%  Similarity=0.614  Sum_probs=76.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeecc
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS  180 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~  180 (363)
                      .++|||+|||+.+|+++|.++|++||.|..|.|+.++.||.++|||||+|.+.++|.+||+.||+ .|+|+.|.|.++..
T Consensus        10 ~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a~~   88 (103)
T d2cqda1          10 FTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAYL   88 (103)
T ss_dssp             SSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEESTT
T ss_pred             CcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEcCC
Confidence            46899999999999999999999999999999999999999999999999999999999998875 79999999999876


Q ss_pred             cC
Q psy16184        181 RT  182 (363)
Q Consensus       181 ~~  182 (363)
                      ..
T Consensus        89 ~~   90 (103)
T d2cqda1          89 GA   90 (103)
T ss_dssp             TC
T ss_pred             CC
Confidence            43

>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=99.84  E-value=3.8e-21  Score=141.83  Aligned_cols=79  Identities=15%  Similarity=0.273  Sum_probs=69.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeecc
Q psy16184        102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS  180 (363)
Q Consensus       102 ~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~  180 (363)
                      +||||+|||+++|+++|.++|+.||.|..+.++.+..+|.++|||||+|.+.++|..||..|||..|+|+.|.|++++|
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            6999999999999999999999999999998888888999999999999999999999999999999999999999975

>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=99.84  E-value=1.1e-21  Score=143.01  Aligned_cols=76  Identities=18%  Similarity=0.490  Sum_probs=73.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184        102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus       102 ~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      |+|||+|||+.+|+++|.++|++||.|..|.|+.|+.||.++|||||+|.+.++|++||. +|++.|+|+.|.|.+|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            689999999999999999999999999999999999999999999999999999999998 7999999999999986

>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=99.84  E-value=8.2e-21  Score=140.88  Aligned_cols=78  Identities=28%  Similarity=0.588  Sum_probs=74.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      .++|||+|||+++|+++|.++|++||.|..|.|+.++.||.++|||||+|.+.++|.+||. ++++.|+|+.|.|..|.
T Consensus         6 ~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            4689999999999999999999999999999999999999999999999999999999998 69999999999999874

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=2.1e-21  Score=144.51  Aligned_cols=80  Identities=24%  Similarity=0.465  Sum_probs=77.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeeccc
Q psy16184        102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERSR  181 (363)
Q Consensus       102 ~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~~  181 (363)
                      .+|||+|||+++|+++|.++|++||+|..|.|+.|+.||.++|||||+|.+.++|..|+..|||..|.|+.|.|.+|.+.
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            47999999999999999999999999999999999999999999999999999999999999999999999999999753

>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=99.83  E-value=1.1e-20  Score=142.00  Aligned_cols=81  Identities=19%  Similarity=0.398  Sum_probs=75.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      ..++|||+|||+++|+++|.++|++||.|..|.|+.|+.||.++|||||+|.+.++|.+||..  .+.|+|+.|.|.++.
T Consensus         7 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~i~v~~a~   84 (90)
T d2cqga1           7 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCKLPN   84 (90)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEECCC
T ss_pred             CCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccCCEEeEEEeCC
Confidence            467899999999999999999999999999999999999999999999999999999999985  458999999999997


Q ss_pred             ccC
Q psy16184        180 SRT  182 (363)
Q Consensus       180 ~~~  182 (363)
                      ++.
T Consensus        85 ~k~   87 (90)
T d2cqga1          85 SKQ   87 (90)
T ss_dssp             TTC
T ss_pred             CCC
Confidence            654

>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=99.83  E-value=6.7e-21  Score=141.15  Aligned_cols=80  Identities=23%  Similarity=0.426  Sum_probs=74.9

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhhCCccEE-EEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeecccC
Q psy16184        104 LFIARVNYDTSESKLRREFEVYGPIKKI-VMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERSRT  182 (363)
Q Consensus       104 l~V~nL~~~~t~~~L~~~F~~~G~i~~v-~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~~~  182 (363)
                      |||+|||+++|+++|.++|++||.|..+ .|+.++.+|+++|||||+|.+.++|..||..|||..|+|++|.|.||.++.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~   80 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   80 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCC
Confidence            8999999999999999999999999764 788898999999999999999999999999999999999999999998654


Q ss_pred             C
Q psy16184        183 V  183 (363)
Q Consensus       183 ~  183 (363)
                      .
T Consensus        81 ~   81 (83)
T d1x5ta1          81 S   81 (83)
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=99.83  E-value=7e-21  Score=146.67  Aligned_cols=82  Identities=27%  Similarity=0.555  Sum_probs=77.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeecc
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS  180 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~  180 (363)
                      .++|||+|||+++|+++|+++|.+||.|..+.|+.++.++.++|||||+|.+.++|.+||. |+++.|+|+.|.|.+|.+
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~~   98 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVA   98 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCSS
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECcc
Confidence            3589999999999999999999999999999999999999999999999999999999997 799999999999999887


Q ss_pred             cCC
Q psy16184        181 RTV  183 (363)
Q Consensus       181 ~~~  183 (363)
                      +..
T Consensus        99 ke~  101 (103)
T d1x4ba1          99 REE  101 (103)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            543

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=5.6e-21  Score=142.19  Aligned_cols=78  Identities=24%  Similarity=0.450  Sum_probs=74.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC--EEEEEEee
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDG--RRVLVDVE  178 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g--~~i~V~~a  178 (363)
                      .++|||+|||+.+|+++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|..|+..|||..|.|  .+|.|.||
T Consensus         6 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~A   85 (85)
T d1fxla2           6 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA   85 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEeC
Confidence            4689999999999999999999999999999999999999999999999999999999999999999998  45999886

>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=99.83  E-value=9.3e-21  Score=142.61  Aligned_cols=83  Identities=31%  Similarity=0.624  Sum_probs=78.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      ...+|||+|||+++|+++|+++|.+||.|..|.++.+..++.++|||||+|.+.++|+.||..|||..|+|+.|.|++|.
T Consensus         4 ~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~   83 (90)
T d1x5sa1           4 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAG   83 (90)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEE
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            35689999999999999999999999999999999998999999999999999999999999999999999999999997


Q ss_pred             ccC
Q psy16184        180 SRT  182 (363)
Q Consensus       180 ~~~  182 (363)
                      +..
T Consensus        84 ~~~   86 (90)
T d1x5sa1          84 KSS   86 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.83  E-value=1.5e-20  Score=137.48  Aligned_cols=76  Identities=22%  Similarity=0.502  Sum_probs=73.3

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       103 ~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      +|||+|||+.+|+++|.++|.+||.|..|.|+.++ +++++|||||+|.+.++|..||..|||..|+|+.|.|+++.
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            69999999999999999999999999999999885 89999999999999999999999999999999999999985

>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=99.83  E-value=3.2e-20  Score=139.58  Aligned_cols=82  Identities=26%  Similarity=0.463  Sum_probs=75.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      .+.++|||+|||..+|+++|.++|+.||.|..|.|+.+..++  +|||||+|.+.++|..|+..|||..|.|+.|.|.||
T Consensus         6 ~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~--~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a   83 (90)
T d2cqia1           6 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA   83 (90)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS--CCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc--ceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            456799999999999999999999999999999999886554  789999999999999999999999999999999999


Q ss_pred             cccC
Q psy16184        179 RSRT  182 (363)
Q Consensus       179 ~~~~  182 (363)
                      .+..
T Consensus        84 ~~~~   87 (90)
T d2cqia1          84 TTPS   87 (90)
T ss_dssp             CCTT
T ss_pred             CCCC
Confidence            7643

>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=99.83  E-value=3e-21  Score=148.31  Aligned_cols=79  Identities=15%  Similarity=0.380  Sum_probs=75.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeecc
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS  180 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~  180 (363)
                      .++|||+|||+.+|+++|.++|+.||.|..|.|+.+..+|+++|||||+|.+.++|.+||. |||..|.|+.|.|.++.+
T Consensus        18 ~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~~   96 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQA   96 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECCC
Confidence            4689999999999999999999999999999999999999999999999999999999996 999999999999999864

>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=99.83  E-value=9.9e-21  Score=143.55  Aligned_cols=83  Identities=18%  Similarity=0.502  Sum_probs=77.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccC-CCCCcceEEEEEecCHHHHHHHHHHh-CCceeCCEEEEEEe
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNK-VTGKPRGYAFIEYEHERDMHSAYKHA-DGKKIDGRRVLVDV  177 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~-~t~~~~g~afV~f~~~~~a~~Ai~~l-~g~~i~g~~i~V~~  177 (363)
                      ++++|||+|||+.+++++|..+|.+||.|..|.|+.+. .+|.++|||||+|.+.++|..||..| ||..|+|+.|.|+|
T Consensus         7 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~~   86 (94)
T d2cpha1           7 TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEW   86 (94)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEEE
Confidence            46789999999999999999999999999999998875 47999999999999999999999998 89999999999999


Q ss_pred             ecccC
Q psy16184        178 ERSRT  182 (363)
Q Consensus       178 a~~~~  182 (363)
                      |....
T Consensus        87 A~~~~   91 (94)
T d2cpha1          87 ADSEV   91 (94)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            97643

>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=99.83  E-value=9.4e-21  Score=140.98  Aligned_cols=79  Identities=23%  Similarity=0.471  Sum_probs=75.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC--EEEEEEe
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDG--RRVLVDV  177 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g--~~i~V~~  177 (363)
                      ..++|||+|||+.+|+++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..+.|  ++|.|+|
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            35689999999999999999999999999999999999999999999999999999999999999999977  8899998


Q ss_pred             e
Q psy16184        178 E  178 (363)
Q Consensus       178 a  178 (363)
                      |
T Consensus        85 A   85 (85)
T d1b7fa2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.82  E-value=1.8e-20  Score=139.43  Aligned_cols=78  Identities=28%  Similarity=0.555  Sum_probs=72.8

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCC---CcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeecc
Q psy16184        104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTG---KPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS  180 (363)
Q Consensus       104 l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~---~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~  180 (363)
                      |||+|||+++|+++|.++|++||.|..|.|+.++.++   .++|||||+|.+.++|..||..|||..|+|+.|.|+++..
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~   80 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISER   80 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            8999999999999999999999999999999887665   4689999999999999999999999999999999999865


Q ss_pred             c
Q psy16184        181 R  181 (363)
Q Consensus       181 ~  181 (363)
                      .
T Consensus        81 ~   81 (85)
T d2cpfa1          81 A   81 (85)
T ss_dssp             S
T ss_pred             C
Confidence            3

>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=99.82  E-value=9.6e-21  Score=137.42  Aligned_cols=75  Identities=19%  Similarity=0.507  Sum_probs=71.6

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184        103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus       103 ~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      +|||+|||+++|+++|.++|++||.|..|.|+.++.|++++|||||+|.+.++|++||. +++..|+|+.|.|..|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeEC
Confidence            49999999999999999999999999999999999999999999999999999999998 7999999999998754

>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=99.82  E-value=7.2e-20  Score=138.46  Aligned_cols=82  Identities=22%  Similarity=0.517  Sum_probs=75.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      ...++|||+|||+.+|+++|.++|.+||.|..|.|+.++  +.++|||||+|.+.++|..||..|||..|+|+.|.|++|
T Consensus         9 ~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~--~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A   86 (93)
T d2cq3a1           9 STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA   86 (93)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT--TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccc--cCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            346789999999999999999999999999999999875  336899999999999999999999999999999999999


Q ss_pred             cccC
Q psy16184        179 RSRT  182 (363)
Q Consensus       179 ~~~~  182 (363)
                      .++.
T Consensus        87 ~~r~   90 (93)
T d2cq3a1          87 TARV   90 (93)
T ss_dssp             CSSC
T ss_pred             CcCC
Confidence            8754

>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=99.82  E-value=1e-20  Score=146.31  Aligned_cols=81  Identities=31%  Similarity=0.677  Sum_probs=77.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeecc
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS  180 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~  180 (363)
                      .++|||+|||+++|+++|.++|++||.|..|.|+.++.||.++|||||+|.+.++|..||..|||..|.|+.|.|+++.+
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~   87 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            35899999999999999999999999999999999999999999999999999999999999999999999999999865


Q ss_pred             c
Q psy16184        181 R  181 (363)
Q Consensus       181 ~  181 (363)
                      .
T Consensus        88 ~   88 (104)
T d1p1ta_          88 E   88 (104)
T ss_dssp             T
T ss_pred             C
Confidence            3

>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=99.82  E-value=3.9e-20  Score=135.61  Aligned_cols=77  Identities=27%  Similarity=0.532  Sum_probs=73.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      .++|||+|||+++|+++|.++|++||.|..+.++.++.++.++|||||+|.+.++|.+|+. |||+.|+|+.|.|..|
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            4689999999999999999999999999999999999999999999999999999999997 8999999999999876

>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=99.82  E-value=7.2e-21  Score=137.88  Aligned_cols=75  Identities=23%  Similarity=0.454  Sum_probs=71.6

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184        103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus       103 ~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      +|||||||+++|+++|+++|++||.|..|.|+.++.|+.++|||||+|.+.++|++||+ ++++.|+|+.|.|..|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~-~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh-hCCCEECCEEeEEEEC
Confidence            59999999999999999999999999999999999999999999999999999999998 5888999999999875

>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=99.81  E-value=3.5e-20  Score=139.07  Aligned_cols=80  Identities=23%  Similarity=0.472  Sum_probs=74.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeecc
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS  180 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~  180 (363)
                      ..+|||+|||+.+|+++|.++|++||.|..|.|+.+.  +.++|||||+|.+.++|+.||..|||..|+|+.|.|.++++
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~   85 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   85 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT--TBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec--CCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            4589999999999999999999999999999999885  34679999999999999999999999999999999999976


Q ss_pred             cC
Q psy16184        181 RT  182 (363)
Q Consensus       181 ~~  182 (363)
                      +.
T Consensus        86 ~~   87 (89)
T d1cvja2          86 RK   87 (89)
T ss_dssp             TT
T ss_pred             CC
Confidence            43

>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=99.80  E-value=1e-19  Score=139.84  Aligned_cols=84  Identities=26%  Similarity=0.428  Sum_probs=76.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCcc--------EEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCE
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIK--------KIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGR  171 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~--------~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~  171 (363)
                      ..++|||+|||+.+|+++|.++|..||.|.        .+.+..+..+|.++|||||+|.+.++|..||..|||..|+|+
T Consensus         7 ~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr   86 (101)
T d2cpea1           7 DNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGS   86 (101)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEECCE
Confidence            467999999999999999999999999874        566777888899999999999999999999999999999999


Q ss_pred             EEEEEeecccCC
Q psy16184        172 RVLVDVERSRTV  183 (363)
Q Consensus       172 ~i~V~~a~~~~~  183 (363)
                      .|.|.+|+++..
T Consensus        87 ~i~V~~a~~~~p   98 (101)
T d2cpea1          87 KLKVSLARKKPP   98 (101)
T ss_dssp             ECEEECSSCCCC
T ss_pred             EEEEEEcCCCCC
Confidence            999999987543

>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=99.80  E-value=4.3e-20  Score=137.61  Aligned_cols=81  Identities=21%  Similarity=0.341  Sum_probs=71.0

Q ss_pred             CCCeEEEcCCCCCCC-HHHHHHHHHhhCCccEEEEecc-CCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184        100 PFKTLFIARVNYDTS-ESKLRREFEVYGPIKKIVMVHN-KVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t-~~~L~~~F~~~G~i~~v~i~~d-~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      ..++|||+|||+.+| +++|+++|++||.|..|.|+.+ ..++.++|||||+|.+.++|.+||+ |||+.|+|+.|.|.+
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            367999999999876 5679999999999999998764 5689999999999999999999996 999999999999999


Q ss_pred             eccc
Q psy16184        178 ERSR  181 (363)
Q Consensus       178 a~~~  181 (363)
                      +.++
T Consensus        82 a~~k   85 (86)
T d2ghpa3          82 ADKK   85 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9764

>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=99.80  E-value=1.9e-20  Score=144.31  Aligned_cols=86  Identities=21%  Similarity=0.373  Sum_probs=80.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEE
Q psy16184         97 TMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD  176 (363)
Q Consensus        97 ~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~  176 (363)
                      ...|+++|||+|||..+|+++|.++|.+||.|..+.|+.+..+|.++|||||+|.+.++|..||..|||..|.|+.|.|.
T Consensus        14 ~~~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   93 (102)
T d2cpxa1          14 PGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIE   93 (102)
T ss_dssp             CCSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34578899999999999999999999999999999998888899999999999999999999999999999999999999


Q ss_pred             eecccC
Q psy16184        177 VERSRT  182 (363)
Q Consensus       177 ~a~~~~  182 (363)
                      ||+++.
T Consensus        94 ~ak~k~   99 (102)
T d2cpxa1          94 FGKNKK   99 (102)
T ss_dssp             ECCCCS
T ss_pred             eCCCcc
Confidence            998754

>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=99.80  E-value=1.2e-19  Score=138.71  Aligned_cols=84  Identities=27%  Similarity=0.483  Sum_probs=77.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhC------CceeCCEE
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHAD------GKKIDGRR  172 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~------g~~i~g~~  172 (363)
                      ...++|||+|||+++|+++|+++|.+||.|..+.++.+..++.++|||||+|.+.++|..||..||      |..|.|+.
T Consensus         6 ~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~   85 (98)
T d1x4ha1           6 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQ   85 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCE
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEE
Confidence            346799999999999999999999999999999999998999999999999999999999999886      67899999


Q ss_pred             EEEEeecccC
Q psy16184        173 VLVDVERSRT  182 (363)
Q Consensus       173 i~V~~a~~~~  182 (363)
                      |.|.+|.++.
T Consensus        86 l~v~~a~~k~   95 (98)
T d1x4ha1          86 LKVDLAVTRD   95 (98)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEEECCCCC
Confidence            9999997653

>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=99.80  E-value=4.7e-20  Score=133.75  Aligned_cols=75  Identities=19%  Similarity=0.453  Sum_probs=72.3

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184        103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus       103 ~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      +|||+|||+++|+++|.++|++||.|..+.++.++.++.++|||||+|.+.++|.+||+ |||+.|+|+.|.|.+|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            49999999999999999999999999999999999999999999999999999999997 9999999999999876

>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=99.80  E-value=1.5e-19  Score=142.10  Aligned_cols=78  Identities=27%  Similarity=0.441  Sum_probs=72.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      .+++|||+|||+.+|+++|.++|++||.|..|.|+.   ++.++|||||+|.+.++|..||..|||+.|.|+.|.|.++.
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~---~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~   82 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYN   82 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEC---STTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccc---cCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            467999999999999999999999999999999975   46678999999999999999999999999999999999986


Q ss_pred             c
Q psy16184        180 S  180 (363)
Q Consensus       180 ~  180 (363)
                      .
T Consensus        83 ~   83 (114)
T d2f9da1          83 A   83 (114)
T ss_dssp             H
T ss_pred             C
Confidence            5

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=2.5e-19  Score=138.35  Aligned_cols=84  Identities=20%  Similarity=0.390  Sum_probs=74.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccC-CCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEE
Q psy16184         98 MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNK-VTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD  176 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~-~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~  176 (363)
                      ..|.++|||+|||+.+|+++|+++|+.|| |..+.|+.+. .++.++|||||+|.+.++|++|+. ||++.|+|+.|.|.
T Consensus        12 ~~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~-~~~~~~~gr~l~V~   89 (104)
T d1wi8a_          12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNKRIRVD   89 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHG-GGTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHH-cCCCEECCEEEEEE
Confidence            44678999999999999999999999999 7777777654 578899999999999999987775 99999999999999


Q ss_pred             eecccCC
Q psy16184        177 VERSRTV  183 (363)
Q Consensus       177 ~a~~~~~  183 (363)
                      +|.+...
T Consensus        90 ~a~~~~~   96 (104)
T d1wi8a_          90 VADQAQD   96 (104)
T ss_dssp             ECCCCCC
T ss_pred             ECCCCCC
Confidence            9977544

>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=99.79  E-value=4.7e-19  Score=134.46  Aligned_cols=79  Identities=27%  Similarity=0.433  Sum_probs=72.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      .+.++|||+|||+.+|+++|+++|..||.|..+.+..   ++..+|||||+|.+.++|+.||..|||+.|.|+.|.|+||
T Consensus        12 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~---~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a   88 (95)
T d1x4aa1          12 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN---RRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP   88 (95)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECC---SSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecc---cccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEec
Confidence            4567999999999999999999999999999988754   3557899999999999999999999999999999999998


Q ss_pred             cc
Q psy16184        179 RS  180 (363)
Q Consensus       179 ~~  180 (363)
                      +.
T Consensus        89 ~~   90 (95)
T d1x4aa1          89 RS   90 (95)
T ss_dssp             CC
T ss_pred             cC
Confidence            65

>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=99.78  E-value=5.2e-20  Score=138.57  Aligned_cols=79  Identities=20%  Similarity=0.368  Sum_probs=73.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      ...+|||+|||+.+|+++|+++|+.||.|..+.|+.+ .+|.++|||||+|.+.++|+.||+ |||..|+|+.|.|.+|+
T Consensus        12 ~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~ak   89 (91)
T d1fjeb1          12 TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPK   89 (91)
T ss_dssp             SSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECCC
T ss_pred             CCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEecC
Confidence            4568999999999999999999999999999888654 689999999999999999999997 99999999999999987


Q ss_pred             c
Q psy16184        180 S  180 (363)
Q Consensus       180 ~  180 (363)
                      .
T Consensus        90 ~   90 (91)
T d1fjeb1          90 G   90 (91)
T ss_dssp             C
T ss_pred             C
Confidence            5

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=4.7e-19  Score=134.64  Aligned_cols=76  Identities=18%  Similarity=0.389  Sum_probs=71.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      +.++|||+|||..+++++|.++|++||.|..|.|+.+      +|||||+|.+.++|..||..|||..|.|+.|.|.|++
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak   90 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGK   90 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            3578999999999999999999999999999999876      5899999999999999999999999999999999997


Q ss_pred             cc
Q psy16184        180 SR  181 (363)
Q Consensus       180 ~~  181 (363)
                      ..
T Consensus        91 ~~   92 (96)
T d1x4ga1          91 ES   92 (96)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=99.78  E-value=3.3e-21  Score=164.29  Aligned_cols=155  Identities=23%  Similarity=0.364  Sum_probs=111.6

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccCCC-CCCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHH
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFEDP-KDTPPPTRVETREERLERRRRERAEQVAYKLEQEI   85 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   85 (363)
                      .+|..+|..+|+|..+. +..++.++.++|| +||.|.+..... +.......+....+...                 .
T Consensus        21 ~~L~~~F~~~G~v~~~~-~~~~~~~~~~~g~-afv~f~~~~~a~~a~~~~~~~~~~~~~~~~-----------------~   81 (183)
T d1u1qa_          21 ESLRSHFEQWGTLTDCV-VMRDPNTKRSRGF-GFVTYATVEEVDAAMNARPHKVDGRVVEPK-----------------R   81 (183)
T ss_dssp             HHHHHHHGGGSCEEEEE-EEECTTTCCEEEE-EEEEESSHHHHHHHHHTCSCEETTEECEEE-----------------E
T ss_pred             HHHHHHHHHcCCEEEEE-eeecccCCCccCc-eecccCCHHHHHHHHHhcCCcccccchhhh-----------------h
Confidence            45999999999988773 5567889999999 888886543210 00000000000000000                 0


Q ss_pred             hhcCCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCC
Q psy16184         86 ALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADG  165 (363)
Q Consensus        86 ~~~~p~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g  165 (363)
                      ................++|||+|||+.+|+++|..+|..||.|..+.|+.+..++.++|||||+|.+.++|.+||. +++
T Consensus        82 ~~~~~~~~~~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~  160 (183)
T d1u1qa_          82 AVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKY  160 (183)
T ss_dssp             CCCTTGGGSTTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSC
T ss_pred             hhhcccccccccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCC
Confidence            0000000111233456799999999999999999999999999999999999999999999999999999999998 799


Q ss_pred             ceeCCEEEEEEeeccc
Q psy16184        166 KKIDGRRVLVDVERSR  181 (363)
Q Consensus       166 ~~i~g~~i~V~~a~~~  181 (363)
                      +.|+|+.|.|.+|.++
T Consensus       161 ~~~~G~~i~V~~A~~k  176 (183)
T d1u1qa_         161 HTVNGHNCEVRKALSK  176 (183)
T ss_dssp             EEETTEEEEEEECCCH
T ss_pred             CeECCEEEEEEecCCc
Confidence            9999999999998654

>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=99.77  E-value=6.1e-19  Score=130.91  Aligned_cols=77  Identities=14%  Similarity=0.242  Sum_probs=72.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      .++|||+|||+.+|+++|.++|+.||.|..|.|+.+. ++.++|||||+|.+.++|.+||+ +++..|.|+.|.|.++.
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            4699999999999999999999999999999998774 89999999999999999999997 79999999999999864

>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=99.77  E-value=5e-19  Score=130.86  Aligned_cols=78  Identities=23%  Similarity=0.360  Sum_probs=71.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCcee-CCEEEEE
Q psy16184         97 TMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKI-DGRRVLV  175 (363)
Q Consensus        97 ~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i-~g~~i~V  175 (363)
                      ..+|+++|||+|||.++|+++|..+|+.||.|..|.|+.+     .+|||||+|.+.++|..|+..|||..| +|+.|.|
T Consensus         4 ~~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v   78 (83)
T d2b0ga1           4 EQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN-----RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKI   78 (83)
T ss_dssp             CCSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT-----TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc-----cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEE
Confidence            3456889999999999999999999999999999999764     368999999999999999999999988 5689999


Q ss_pred             Eeec
Q psy16184        176 DVER  179 (363)
Q Consensus       176 ~~a~  179 (363)
                      .||+
T Consensus        79 ~~ak   82 (83)
T d2b0ga1          79 TFAK   82 (83)
T ss_dssp             EECC
T ss_pred             EEec
Confidence            9986

>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=99.77  E-value=3.1e-19  Score=133.71  Aligned_cols=78  Identities=17%  Similarity=0.319  Sum_probs=71.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHH---HHHHHhhCCccEEEEeccCCCCCc---ceEEEEEecCHHHHHHHHHHhCCceeCCEE
Q psy16184         99 DPFKTLFIARVNYDTSESKL---RREFEVYGPIKKIVMVHNKVTGKP---RGYAFIEYEHERDMHSAYKHADGKKIDGRR  172 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L---~~~F~~~G~i~~v~i~~d~~t~~~---~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~  172 (363)
                      .+.++|||+|||+.+++++|   .++|++||.|..|.|+.++.++..   .|||||+|.+.++|..||..|||..|+|+.
T Consensus         6 iq~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~   85 (89)
T d2cpia1           6 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRT   85 (89)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             EecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEE
Confidence            34678999999999999999   678999999999999998877654   499999999999999999999999999999


Q ss_pred             EEEE
Q psy16184        173 VLVD  176 (363)
Q Consensus       173 i~V~  176 (363)
                      |+|.
T Consensus        86 lkvS   89 (89)
T d2cpia1          86 LKAS   89 (89)
T ss_dssp             EEEE
T ss_pred             EEEC
Confidence            9984

>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=99.76  E-value=2.8e-19  Score=137.26  Aligned_cols=81  Identities=17%  Similarity=0.318  Sum_probs=75.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      ...++|||+|||+++|+++|.++|++||.|..+.++.+ .++.++|||||+|.+.++|.+||..|||..|.|++|.|.++
T Consensus        16 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~-~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~   94 (101)
T d1x5oa1          16 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT   94 (101)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEEC-SSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecc-cccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCC
Confidence            34679999999999999999999999999999999887 48899999999999999999999999999999999988877


Q ss_pred             cc
Q psy16184        179 RS  180 (363)
Q Consensus       179 ~~  180 (363)
                      .+
T Consensus        95 ~P   96 (101)
T d1x5oa1          95 EP   96 (101)
T ss_dssp             SC
T ss_pred             CC
Confidence            65

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=1.1e-18  Score=133.01  Aligned_cols=75  Identities=25%  Similarity=0.471  Sum_probs=68.2

Q ss_pred             CCCCeEEEcCCC-CCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184         99 DPFKTLFIARVN-YDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus        99 ~~~~~l~V~nL~-~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      ...++|||+||+ ..+++++|+++|.+||.|..|.|        ++|||||+|.+.++|++||..|||+.|.|+.|.|+|
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i--------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~   84 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINL   84 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE--------ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE--------eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            345689999997 57888999999999999999998        358999999999999999999999999999999999


Q ss_pred             eccc
Q psy16184        178 ERSR  181 (363)
Q Consensus       178 a~~~  181 (363)
                      +...
T Consensus        85 a~~~   88 (98)
T d1wf2a_          85 AAEP   88 (98)
T ss_dssp             TTSC
T ss_pred             CCCC
Confidence            9753

>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=99.76  E-value=8e-19  Score=133.44  Aligned_cols=79  Identities=27%  Similarity=0.474  Sum_probs=72.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      .+.++|||+|||+++|+++|.++|.+||.|..+..     ++.++|||||+|.+.++|..||..|||..|+|+.|.|.|+
T Consensus        14 ~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~-----~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a   88 (96)
T d1fjca_          14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT   88 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE-----TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee-----cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            45789999999999999999999999998876643     6788999999999999999999999999999999999999


Q ss_pred             cccC
Q psy16184        179 RSRT  182 (363)
Q Consensus       179 ~~~~  182 (363)
                      .++.
T Consensus        89 ~~k~   92 (96)
T d1fjca_          89 GEKG   92 (96)
T ss_dssp             SSSC
T ss_pred             CCCC
Confidence            7754

>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=99.76  E-value=9.9e-19  Score=130.72  Aligned_cols=78  Identities=21%  Similarity=0.261  Sum_probs=70.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCcee-CCEEEEEEe
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKI-DGRRVLVDV  177 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i-~g~~i~V~~  177 (363)
                      +|+++|||+|||+.+|+++|.++|..||.|..+.+..    ++.+|||||+|.+.++|..|+..|||..| +|+.|.|.|
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~----~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~   83 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF----QKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF   83 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEEC----SSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEee----ecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEe
Confidence            5688999999999999999999999999998887754    34678999999999999999999999988 589999999


Q ss_pred             ecc
Q psy16184        178 ERS  180 (363)
Q Consensus       178 a~~  180 (363)
                      +++
T Consensus        84 sk~   86 (88)
T d2adca2          84 SKS   86 (88)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            875

>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=99.76  E-value=3.5e-18  Score=127.13  Aligned_cols=77  Identities=26%  Similarity=0.426  Sum_probs=70.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      ..++|||+|||+++|+++|.++|++||.|..+.+..      ++|||||+|.+.++|..||..|||..|.|+.|.|.||+
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~------~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~ak   80 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK   80 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE------CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc------ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEecc
Confidence            457999999999999999999999999998887743      47899999999999999999999999999999999998


Q ss_pred             ccC
Q psy16184        180 SRT  182 (363)
Q Consensus       180 ~~~  182 (363)
                      +..
T Consensus        81 P~~   83 (86)
T d2cpda1          81 PVD   83 (86)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.76  E-value=6.1e-19  Score=132.72  Aligned_cols=80  Identities=20%  Similarity=0.401  Sum_probs=71.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHH----HHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEE
Q psy16184        100 PFKTLFIARVNYDTSESKLRR----EFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLV  175 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~----~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V  175 (363)
                      |+++|||+|||+.+|+++|++    +|++||+|..|.+..   ++.++|||||+|.+.++|..|+..|||..|.|+.|.|
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v   78 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   78 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            578999999999999998864    689999999988754   5678899999999999999999999999999999999


Q ss_pred             EeecccC
Q psy16184        176 DVERSRT  182 (363)
Q Consensus       176 ~~a~~~~  182 (363)
                      .||+...
T Consensus        79 ~~ak~~~   85 (91)
T d1nu4a_          79 QYAKTDS   85 (91)
T ss_dssp             EECSSCC
T ss_pred             EEeCCCc
Confidence            9997643

>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=99.76  E-value=2.3e-18  Score=134.02  Aligned_cols=77  Identities=19%  Similarity=0.435  Sum_probs=70.8

Q ss_pred             CCeEEEcCCCC-CCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        101 FKTLFIARVNY-DTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       101 ~~~l~V~nL~~-~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      +++|||+||++ .+|+++|.++|+.||.|..|.|+.++     +|||||+|.+.++|.+||..|||..|.|+.|.|.|++
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~-----kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~   76 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   76 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            56999999965 59999999999999999999998763     6999999999999999999999999999999999987


Q ss_pred             ccC
Q psy16184        180 SRT  182 (363)
Q Consensus       180 ~~~  182 (363)
                      ...
T Consensus        77 ~~~   79 (109)
T d2adca1          77 HQN   79 (109)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=1.1e-18  Score=129.81  Aligned_cols=76  Identities=22%  Similarity=0.412  Sum_probs=71.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      +.++|||+|||+.+++++|.++|++||.|..|.|+.+      +|||||+|.+.++|..|+..|||..|.|+.|.|+||.
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~   80 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFAC   80 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc------cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            3568999999999999999999999999999999865      5899999999999999999999999999999999997


Q ss_pred             cc
Q psy16184        180 SR  181 (363)
Q Consensus       180 ~~  181 (363)
                      ..
T Consensus        81 ~~   82 (86)
T d2cpja1          81 HS   82 (86)
T ss_dssp             CC
T ss_pred             Cc
Confidence            64

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.75  E-value=1.1e-18  Score=129.84  Aligned_cols=80  Identities=18%  Similarity=0.249  Sum_probs=71.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      +..++|||+|||+.+++++|.++|..||.|..+.++.+..++.++|||||+|.+.++|.+||..||+..|.|++|.|.++
T Consensus         7 p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           7 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            34567999999999999999999999999876433344468999999999999999999999999999999999999875

>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=99.75  E-value=8.6e-19  Score=131.03  Aligned_cols=78  Identities=21%  Similarity=0.369  Sum_probs=69.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      ..+++|||+|||+.+|+++|+++|++||.|..|.++.     .++|||||+|.+.++|+.||.  +++.|+|+.|.|.++
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~-----~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a   75 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNA   75 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCS-----SCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEee-----ccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeC
Confidence            3477999999999999999999999999999998754     367999999999999999985  789999999999999


Q ss_pred             cccCC
Q psy16184        179 RSRTV  183 (363)
Q Consensus       179 ~~~~~  183 (363)
                      .++..
T Consensus        76 ~~k~~   80 (88)
T d1wf0a_          76 EPKHN   80 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            76544

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=1.5e-18  Score=131.93  Aligned_cols=83  Identities=20%  Similarity=0.271  Sum_probs=73.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCC-ccEEEEeccC-CCCCcceEEEEEecCHHHHHHHHHHhCC--ceeCCEEEEEE
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGP-IKKIVMVHNK-VTGKPRGYAFIEYEHERDMHSAYKHADG--KKIDGRRVLVD  176 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~-i~~v~i~~d~-~t~~~~g~afV~f~~~~~a~~Ai~~l~g--~~i~g~~i~V~  176 (363)
                      +|+|||+|||..+|+++|.++|+.||. |..|.|+.+. .++.++|||||+|.+.++|..||..|++  ..+.|+.|.|.
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~   80 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVD   80 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEE
Confidence            368999999999999999999999996 8899998875 4688999999999999999999999864  45689999999


Q ss_pred             eecccCC
Q psy16184        177 VERSRTV  183 (363)
Q Consensus       177 ~a~~~~~  183 (363)
                      ||.+...
T Consensus        81 ~A~p~~~   87 (96)
T d2disa1          81 WAEPEID   87 (96)
T ss_dssp             ESCSSCS
T ss_pred             EcCCCCC
Confidence            9987544

>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=99.75  E-value=1.3e-18  Score=127.61  Aligned_cols=75  Identities=23%  Similarity=0.333  Sum_probs=68.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCc-eeCCEEEEEEeecc
Q psy16184        102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGK-KIDGRRVLVDVERS  180 (363)
Q Consensus       102 ~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~-~i~g~~i~V~~a~~  180 (363)
                      ++|||+|||+++|+++|.++|.+||.|..+.++.      .+|||||+|.+.++|..||+.|||. .|.|+.|.|+||.+
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~------~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~   75 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   75 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec------ccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCC
Confidence            4799999999999999999999999998777655      3699999999999999999999995 69999999999987


Q ss_pred             cC
Q psy16184        181 RT  182 (363)
Q Consensus       181 ~~  182 (363)
                      +.
T Consensus        76 k~   77 (80)
T d2cqha1          76 KK   77 (80)
T ss_dssp             CC
T ss_pred             cC
Confidence            54

>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=99.75  E-value=3.6e-19  Score=132.83  Aligned_cols=74  Identities=15%  Similarity=0.201  Sum_probs=68.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeeccc
Q psy16184        102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERSR  181 (363)
Q Consensus       102 ~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~~  181 (363)
                      ++|||+|||+.+|+++|+++|++||.|..|.|+.+       |||||+|.+.++|+.||..|||..|.|+.|.|.++...
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~   73 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   73 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhccccccccccc-------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecC
Confidence            37999999999999999999999999999999764       89999999999999999999999999999999988654


Q ss_pred             C
Q psy16184        182 T  182 (363)
Q Consensus       182 ~  182 (363)
                      .
T Consensus        74 ~   74 (87)
T d3begb1          74 V   74 (87)
T ss_dssp             E
T ss_pred             c
Confidence            3

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.75  E-value=2.7e-18  Score=124.18  Aligned_cols=74  Identities=18%  Similarity=0.254  Sum_probs=68.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184        102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus       102 ~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      ++|||+|||+++++++|+++|..||.|..|.|+.++.  ...+||||+|.+.++|.+||. ||++.|+|+.|.|..+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~--~~~~~afV~F~~~~~a~~Al~-~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK--KNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT--SSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecc--ccceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            4899999999999999999999999999999998764  345799999999999999996 8999999999999865

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=2e-18  Score=126.25  Aligned_cols=75  Identities=23%  Similarity=0.414  Sum_probs=69.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      .+++|||+||+  +|+++|.++|++||.|..|.+..+      +|||||+|.+.++|..|+..|||..|+|+.|.|.|++
T Consensus         4 ~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~   75 (79)
T d2bz2a1           4 KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIAR   75 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECC
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            46799999996  899999999999999999999754      5899999999999999999999999999999999997


Q ss_pred             ccC
Q psy16184        180 SRT  182 (363)
Q Consensus       180 ~~~  182 (363)
                      +++
T Consensus        76 ~~P   78 (79)
T d2bz2a1          76 KQP   78 (79)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            654

>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=99.74  E-value=1.8e-18  Score=132.93  Aligned_cols=85  Identities=14%  Similarity=0.181  Sum_probs=74.7

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEE
Q psy16184         96 ATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLV  175 (363)
Q Consensus        96 ~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V  175 (363)
                      .......+|||+|||+++|+++|+++|..|| |..|.++.+. ++..+|||||+|.+.++|++||+ ||++.|+|+.|.|
T Consensus        10 ~~~~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V   86 (102)
T d1weza_          10 FQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVEL   86 (102)
T ss_dssp             CCCSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEE
T ss_pred             CcCCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEec-CCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEE
Confidence            3445567999999999999999999999998 5577787774 68899999999999999999997 8999999999999


Q ss_pred             EeecccCC
Q psy16184        176 DVERSRTV  183 (363)
Q Consensus       176 ~~a~~~~~  183 (363)
                      .++.....
T Consensus        87 ~~s~~~~~   94 (102)
T d1weza_          87 FLNSTAGT   94 (102)
T ss_dssp             EEECCCCC
T ss_pred             EEcCCCCC
Confidence            99877543

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=2.9e-19  Score=128.44  Aligned_cols=71  Identities=20%  Similarity=0.384  Sum_probs=68.4

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEE
Q psy16184        104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVL  174 (363)
Q Consensus       104 l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~  174 (363)
                      |||+|||+++|+++|.++|.+||.|..+.++.++.++.++|||||+|.+.++|..||..|||..|+|+.|+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            89999999999999999999999999999999999999999999999999999999999999999998763

>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=4.7e-18  Score=126.86  Aligned_cols=77  Identities=10%  Similarity=0.236  Sum_probs=67.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      .+.+|||+|||+.+|+++|+++|.+|| |..+.+      +..+|||||+|.+.++|++||..||+..|.|+.|.|++++
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~   76 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeee------eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            357899999999999999999999999 334444      3357999999999999999999999999999999999997


Q ss_pred             ccCC
Q psy16184        180 SRTV  183 (363)
Q Consensus       180 ~~~~  183 (363)
                      ....
T Consensus        77 ~~~~   80 (88)
T d1wg1a_          77 TDAL   80 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6543

>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=99.74  E-value=5e-18  Score=130.90  Aligned_cols=83  Identities=13%  Similarity=0.177  Sum_probs=75.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      ...+|||+|||+++|+++|+++|..||.|..+.++.+..++.++|||||+|.+.++|++||. ||+..|.|+.|.|.++.
T Consensus        14 ~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~~~   92 (104)
T d1wg5a_          14 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKSS   92 (104)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEEEC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEECC
Confidence            45689999999999999999999999999887777777889999999999999999999997 89999999999999998


Q ss_pred             ccCC
Q psy16184        180 SRTV  183 (363)
Q Consensus       180 ~~~~  183 (363)
                      +...
T Consensus        93 ~~~~   96 (104)
T d1wg5a_          93 RAEV   96 (104)
T ss_dssp             TTTS
T ss_pred             HHHh
Confidence            7654

>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=99.74  E-value=1.7e-18  Score=135.23  Aligned_cols=75  Identities=11%  Similarity=0.223  Sum_probs=69.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeecc
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS  180 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~  180 (363)
                      .++|||+|||+.+++++|+++|+.||.|..|.|..      .+|||||+|.+.++|.+||..|||..|.|+.|.|+|+..
T Consensus        10 ~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~------~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~   83 (111)
T d1whxa_          10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPI   83 (111)
T ss_dssp             EEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEET
T ss_pred             CCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec------cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCC
Confidence            46899999999999999999999999999998843      469999999999999999999999999999999999865


Q ss_pred             c
Q psy16184        181 R  181 (363)
Q Consensus       181 ~  181 (363)
                      .
T Consensus        84 ~   84 (111)
T d1whxa_          84 G   84 (111)
T ss_dssp             T
T ss_pred             C
Confidence            4

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.73  E-value=6e-18  Score=128.86  Aligned_cols=77  Identities=16%  Similarity=0.158  Sum_probs=71.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       100 ~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      ...+|||+|||+.+++++|.++|.+||.|..|.|..       +|||||+|.+.++|+.||+.|||..|.|+.|.|.+++
T Consensus        14 ~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~   86 (98)
T d1wg4a_          14 SDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIR   86 (98)
T ss_dssp             CSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEe
Confidence            356899999999999999999999999999999864       4899999999999999999999999999999999997


Q ss_pred             ccCC
Q psy16184        180 SRTV  183 (363)
Q Consensus       180 ~~~~  183 (363)
                      ....
T Consensus        87 ~~~~   90 (98)
T d1wg4a_          87 VYPE   90 (98)
T ss_dssp             EECC
T ss_pred             cCCC
Confidence            7543

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.72  E-value=8.2e-18  Score=127.96  Aligned_cols=78  Identities=31%  Similarity=0.537  Sum_probs=71.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC--EEEEE
Q psy16184         98 MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDG--RRVLV  175 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g--~~i~V  175 (363)
                      ..|+++|||+|||+++|+++|+++|++||.|..|.|..+      ++||||+|.+.++|..|+..||+..|.|  ..|.|
T Consensus        14 ~~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v   87 (97)
T d1whya_          14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRV   87 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEE
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEE
Confidence            457899999999999999999999999999999999764      5899999999999999999999999987  58999


Q ss_pred             Eeeccc
Q psy16184        176 DVERSR  181 (363)
Q Consensus       176 ~~a~~~  181 (363)
                      +|+++.
T Consensus        88 ~~ak~~   93 (97)
T d1whya_          88 DFAKSG   93 (97)
T ss_dssp             EECCCC
T ss_pred             EeCCCC
Confidence            999763

>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=99.72  E-value=6.4e-18  Score=130.08  Aligned_cols=79  Identities=19%  Similarity=0.261  Sum_probs=71.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeecc
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS  180 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~  180 (363)
                      ..+|||+|||+.+|+++|.++|..||.|..+.++....+|.++|||||+|.+.++|+.||. ||+..|+|+.|.|.++..
T Consensus         8 ~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~~~   86 (103)
T d2cpya1           8 KVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVVTL   86 (103)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEECH
T ss_pred             ceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEECCH
Confidence            4579999999999999999999999999875455555789999999999999999999997 899999999999999754

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=2.3e-17  Score=123.08  Aligned_cols=80  Identities=14%  Similarity=0.241  Sum_probs=72.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHh--CCceeCCEEEE
Q psy16184         97 TMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA--DGKKIDGRRVL  174 (363)
Q Consensus        97 ~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l--~g~~i~g~~i~  174 (363)
                      ...|+++|||+|||+.+|+++|.++|++||.|..|.++.+      +|||||+|.+.++|..|+..|  ++..|.|+.|.
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 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIY   77 (88)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEE
Confidence            3568899999999999999999999999999999999765      489999999999999999865  67899999999


Q ss_pred             EEeecccC
Q psy16184        175 VDVERSRT  182 (363)
Q Consensus       175 V~~a~~~~  182 (363)
                      |.|++.+.
T Consensus        78 v~~sk~~~   85 (88)
T d2cq1a1          78 IQYSNHKE   85 (88)
T ss_dssp             EEECSCSS
T ss_pred             EEECCCCC
Confidence            99997654

>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=99.70  E-value=1.1e-17  Score=129.82  Aligned_cols=80  Identities=18%  Similarity=0.325  Sum_probs=71.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCcee--CCEEEEEE
Q psy16184         99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKI--DGRRVLVD  176 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i--~g~~i~V~  176 (363)
                      .+..+|||+|||+.+|+++|.++|++||.|..|.|+.++    .+|||||+|.+.++|+.||..|||..|  .|..|.|.
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            356789999999999999999999999999999998763    579999999999999999999999988  57889999


Q ss_pred             eecccC
Q psy16184        177 VERSRT  182 (363)
Q Consensus       177 ~a~~~~  182 (363)
                      +++...
T Consensus        81 ~s~~~~   86 (108)
T d2adba1          81 FSKLTS   86 (108)
T ss_dssp             ECSSCS
T ss_pred             ecCCcc
Confidence            987643

>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=99.69  E-value=4.4e-17  Score=117.66  Aligned_cols=71  Identities=15%  Similarity=0.279  Sum_probs=64.2

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeeccc
Q psy16184        104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERSR  181 (363)
Q Consensus       104 l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~~  181 (363)
                      |||+|||+++|+++|+++|++|| |..+.+      +.++|||||+|.+.++|.+|+..|||..|.|+.|.|+|+...
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~------~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee------cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            79999999999999999999999 555544      346799999999999999999999999999999999999654

>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=99.69  E-value=1.3e-16  Score=122.79  Aligned_cols=81  Identities=16%  Similarity=0.242  Sum_probs=72.1

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHh--CCceeCCEEE
Q psy16184         96 ATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA--DGKKIDGRRV  173 (363)
Q Consensus        96 ~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l--~g~~i~g~~i  173 (363)
                      ....++.+|||+|||+.+|+++|.++|..||.|..|.|..+      +|||||+|.+.++|+.||..|  ++..|.|+.|
T Consensus        10 ~~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l   83 (104)
T d1wexa_          10 HKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQA   83 (104)
T ss_dssp             CCCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBC
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEE
Confidence            34467889999999999999999999999999999999754      589999999999999999977  5677899999


Q ss_pred             EEEeecccC
Q psy16184        174 LVDVERSRT  182 (363)
Q Consensus       174 ~V~~a~~~~  182 (363)
                      .|.|++...
T Consensus        84 ~v~~s~~~~   92 (104)
T d1wexa_          84 FFNYSTSKR   92 (104)
T ss_dssp             EEEECSSSS
T ss_pred             EEEEcCCCc
Confidence            999997643

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=1.4e-17  Score=130.07  Aligned_cols=82  Identities=13%  Similarity=0.256  Sum_probs=73.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEe
Q psy16184         98 MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  177 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~  177 (363)
                      ..+.++|||+|||+.+|+++|.++|+.||.|..+.++.+..+|.++|||||+|.+.++|.+||. |||..|+|+.|.|..
T Consensus        15 ~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~   93 (112)
T d1wela1          15 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHP   93 (112)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEE
T ss_pred             CCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEE
Confidence            3457799999999999999999999999998876666666799999999999999999999997 899999999999998


Q ss_pred             ecc
Q psy16184        178 ERS  180 (363)
Q Consensus       178 a~~  180 (363)
                      +..
T Consensus        94 ~~~   96 (112)
T d1wela1          94 ITK   96 (112)
T ss_dssp             ECH
T ss_pred             cCh
Confidence            754

>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=99.66  E-value=1e-16  Score=122.23  Aligned_cols=79  Identities=23%  Similarity=0.309  Sum_probs=70.2

Q ss_pred             CCCCCCeEEEcCCCCC-CCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHH--HhCCceeCCEEE
Q psy16184         97 TMDPFKTLFIARVNYD-TSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK--HADGKKIDGRRV  173 (363)
Q Consensus        97 ~~~~~~~l~V~nL~~~-~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~--~l~g~~i~g~~i  173 (363)
                      ...++++|||+|||.. +|+++|.++|+.||.|..|.|+.+      +|||||+|.+.++|..||.  .+++..|.|+.|
T Consensus        14 ~~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l   87 (99)
T d1x4fa1          14 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCV   87 (99)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCC
T ss_pred             CCCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEEE
Confidence            3456789999999985 899999999999999999999765      5899999999999999997  478889999999


Q ss_pred             EEEeeccc
Q psy16184        174 LVDVERSR  181 (363)
Q Consensus       174 ~V~~a~~~  181 (363)
                      .|.+++..
T Consensus        88 ~V~~s~~~   95 (99)
T d1x4fa1          88 KVDLSEKY   95 (99)
T ss_dssp             EEEEECSC
T ss_pred             EEEEcCCc
Confidence            99999653

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.65  E-value=1.9e-16  Score=118.15  Aligned_cols=77  Identities=18%  Similarity=0.246  Sum_probs=69.4

Q ss_pred             CCCCCeEEEcCCCCC-CCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHh--CCceeCCEEEE
Q psy16184         98 MDPFKTLFIARVNYD-TSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA--DGKKIDGRRVL  174 (363)
Q Consensus        98 ~~~~~~l~V~nL~~~-~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l--~g~~i~g~~i~  174 (363)
                      ..++.+|||+|||.. +|+++|.++|++||.|..|.|+.+      ++||||+|.+.++|..|+..|  ++..|.|++|.
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~------k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~   78 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVR   78 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc------ceEEEEEEcchhhHHHHHHHHhhCCCccCCceEE
Confidence            456789999999986 789999999999999999999765      479999999999999999966  67899999999


Q ss_pred             EEeecc
Q psy16184        175 VDVERS  180 (363)
Q Consensus       175 V~~a~~  180 (363)
                      |.|++.
T Consensus        79 V~~s~~   84 (89)
T d1x4da1          79 VHLSQK   84 (89)
T ss_dssp             EEEECC
T ss_pred             EEECCC
Confidence            999964

>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=3.5e-16  Score=120.10  Aligned_cols=79  Identities=14%  Similarity=0.133  Sum_probs=69.9

Q ss_pred             CCCCeEEEcCCCCCC-CH----HHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEE
Q psy16184         99 DPFKTLFIARVNYDT-SE----SKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRV  173 (363)
Q Consensus        99 ~~~~~l~V~nL~~~~-t~----~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i  173 (363)
                      ..+++|||+||+..+ ++    ++|+.+|++||.|..|.++.      .++||||+|.+.++|..||..|||..|.|+.|
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k------~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l   76 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK------SFKRVRINFSNPLSAADARLRLHKTEFLGKEM   76 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET------TTTEEEEECSSTTHHHHHHHTSTTSEETTEEC
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec------CCCEEEEEECCHHHHHHHHHHhcccccCCCEe
Confidence            356799999999876 33    57999999999999999975      36899999999999999999999999999999


Q ss_pred             EEEeecccCC
Q psy16184        174 LVDVERSRTV  183 (363)
Q Consensus       174 ~V~~a~~~~~  183 (363)
                      .|.|+++...
T Consensus        77 ~v~~a~~~~~   86 (104)
T d1weya_          77 KLYFAQTLHI   86 (104)
T ss_dssp             EEECCCCSSC
T ss_pred             EEeecccCCC
Confidence            9999976543

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=6.4e-18  Score=126.78  Aligned_cols=77  Identities=13%  Similarity=0.304  Sum_probs=68.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEe-----ccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEE
Q psy16184        102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMV-----HNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD  176 (363)
Q Consensus       102 ~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~-----~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~  176 (363)
                      ++|||+|||+.+|+++|.++|+.||.|..+.+.     .+..++.++|||||+|.+.++|+.|+. |||..|.|+.|.|.
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            589999999999999999999999988876653     344678889999999999999999996 99999999999997


Q ss_pred             eec
Q psy16184        177 VER  179 (363)
Q Consensus       177 ~a~  179 (363)
                      .++
T Consensus        81 r~k   83 (90)
T d1u2fa_          81 RPH   83 (90)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            543

>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=99.57  E-value=2.2e-16  Score=121.21  Aligned_cols=75  Identities=13%  Similarity=0.272  Sum_probs=70.0

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEee
Q psy16184        103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  178 (363)
Q Consensus       103 ~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a  178 (363)
                      .++|.+++..+++++|.++|++||.|..|.|+.+ .+++++|||||+|.+.++|.+|+..|||..|+|+.|.|+++
T Consensus        29 ~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~-~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          29 DVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCS-SSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             hHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecC-CCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            4777888888899999999999999999999876 58999999999999999999999999999999999999985

>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=99.54  E-value=1e-14  Score=111.18  Aligned_cols=66  Identities=23%  Similarity=0.416  Sum_probs=59.5

Q ss_pred             CCCCCCeEEEcC--CCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCcee
Q psy16184         97 TMDPFKTLFIAR--VNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKI  168 (363)
Q Consensus        97 ~~~~~~~l~V~n--L~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i  168 (363)
                      ...|+.+|||+|  ||..+|+++|+.+|++||.|..|.++.+      ++||||+|.+.++|..|+..|||..|
T Consensus        14 ~~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            345678899955  9999999999999999999999988765      47999999999999999999999887

>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=99.48  E-value=1.3e-14  Score=112.95  Aligned_cols=74  Identities=20%  Similarity=0.179  Sum_probs=65.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCH-HHHHHHHHHhCCceeCCEEEEEEeec
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHE-RDMHSAYKHADGKKIDGRRVLVDVER  179 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~-~~a~~Ai~~l~g~~i~g~~i~V~~a~  179 (363)
                      ...+||||||+.+|+++|+++|++||+|..|.|+.+      +|||||.|.+. ++|..|+..||+..|.++.+.|.|+.
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~   84 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEV   84 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEE
T ss_pred             CeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEee
Confidence            346699999999999999999999999999999864      59999999985 78999999999999888888787764


Q ss_pred             c
Q psy16184        180 S  180 (363)
Q Consensus       180 ~  180 (363)
                      .
T Consensus        85 ~   85 (113)
T d1owxa_          85 L   85 (113)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=99.48  E-value=8.2e-14  Score=117.65  Aligned_cols=80  Identities=30%  Similarity=0.602  Sum_probs=73.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeecc
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS  180 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~  180 (363)
                      .++|||+|||+.+|+++|.++|++||.|..+.|+.+..++.++|||||+|.+.++|.+|+. +++..+.+..+.+.....
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~-~~~~~~~~~~~~~~~~~~   84 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAVS   84 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHH-hcCCcccccchhhhhhhh
Confidence            3699999999999999999999999999999999999999999999999999999999999 577888999888887654


Q ss_pred             c
Q psy16184        181 R  181 (363)
Q Consensus       181 ~  181 (363)
                      .
T Consensus        85 ~   85 (183)
T d1u1qa_          85 R   85 (183)
T ss_dssp             T
T ss_pred             c
Confidence            3

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.46  E-value=1.2e-13  Score=104.86  Aligned_cols=80  Identities=20%  Similarity=0.384  Sum_probs=68.2

Q ss_pred             CCCCeEEEcCC--CCCC---------CHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCce
Q psy16184         99 DPFKTLFIARV--NYDT---------SESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKK  167 (363)
Q Consensus        99 ~~~~~l~V~nL--~~~~---------t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~  167 (363)
                      ...++|+|.||  |..+         ..++|.+.|++||.|..|.+..+    .++|||||+|.+.++|..|+..|||..
T Consensus         6 ~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~lng~~   81 (99)
T d2dita1           6 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDGRW   81 (99)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhCCcE
Confidence            34679999998  4432         13678899999999999998654    467999999999999999999999999


Q ss_pred             eCCEEEEEEeecccC
Q psy16184        168 IDGRRVLVDVERSRT  182 (363)
Q Consensus       168 i~g~~i~V~~a~~~~  182 (363)
                      |+|+.|.|+++.++.
T Consensus        82 ~~gr~i~v~~~~g~~   96 (99)
T d2dita1          82 FGGRQITAQAWDGTT   96 (99)
T ss_dssp             ETTEECEEEECCSCC
T ss_pred             ECCEEEEEEEeCCcC
Confidence            999999999987653

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.40  E-value=1.9e-13  Score=99.47  Aligned_cols=72  Identities=19%  Similarity=0.209  Sum_probs=61.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEE-EEEEeec
Q psy16184        101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRR-VLVDVER  179 (363)
Q Consensus       101 ~~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~-i~V~~a~  179 (363)
                      .+.|+|+|||+.++++.| .+|++||+|..+.+..      .+|||||+|.+.++|++||. |||..|+|+. |.|..+.
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~------~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~   75 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSN------TGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCI   75 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECS------SSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECC
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEecC------CCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCC
Confidence            357999999999986655 5899999999998854      36899999999999999997 8999999974 5687664


Q ss_pred             c
Q psy16184        180 S  180 (363)
Q Consensus       180 ~  180 (363)
                      .
T Consensus        76 ~   76 (81)
T d1wwha1          76 D   76 (81)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.38  E-value=1.5e-13  Score=105.20  Aligned_cols=82  Identities=21%  Similarity=0.267  Sum_probs=69.6

Q ss_pred             CCCCeEEEcCC--CCCC--------CHHHHHHHHHhhCCccEEEEeccCCC--CCcceEEEEEecCHHHHHHHHHHhCCc
Q psy16184         99 DPFKTLFIARV--NYDT--------SESKLRREFEVYGPIKKIVMVHNKVT--GKPRGYAFIEYEHERDMHSAYKHADGK  166 (363)
Q Consensus        99 ~~~~~l~V~nL--~~~~--------t~~~L~~~F~~~G~i~~v~i~~d~~t--~~~~g~afV~f~~~~~a~~Ai~~l~g~  166 (363)
                      .|+++|.|.||  +..+        ..++|++.|++||.|..|.|+.+..+  ....|++||+|.+.++|.+|+..|||.
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            46889999999  4433        23578999999999999999876544  345689999999999999999999999


Q ss_pred             eeCCEEEEEEeecc
Q psy16184        167 KIDGRRVLVDVERS  180 (363)
Q Consensus       167 ~i~g~~i~V~~a~~  180 (363)
                      .|+|+.|.|.++..
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            99999999999854

>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=97.98  E-value=1.8e-05  Score=56.16  Aligned_cols=73  Identities=16%  Similarity=0.238  Sum_probs=58.5

Q ss_pred             CCCCCCeEEEcCCCCCCC---------HHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCce
Q psy16184         97 TMDPFKTLFIARVNYDTS---------ESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKK  167 (363)
Q Consensus        97 ~~~~~~~l~V~nL~~~~t---------~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~  167 (363)
                      ..+|--||.|.=+.+...         -.+|.+.|..||+|.-|+++.+        -..|+|.+-.+|.+|+. |+|..
T Consensus        11 qGPpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~-l~g~~   81 (95)
T d1ufwa_          11 QGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLD-VDGMK   81 (95)
T ss_dssp             CCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHH-GGGSE
T ss_pred             cCCCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhc-cCCeE
Confidence            345556888854443322         2467888999999999999875        78999999999999999 89999


Q ss_pred             eCCEEEEEEee
Q psy16184        168 IDGRRVLVDVE  178 (363)
Q Consensus       168 i~g~~i~V~~a  178 (363)
                      |.|+.|.|...
T Consensus        82 v~G~~l~It~~   92 (95)
T d1ufwa_          82 VKGRAVKISGP   92 (95)
T ss_dssp             ETTEEEEEECC
T ss_pred             EcceEEEEecC
Confidence            99999999854

>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=97.56  E-value=9.9e-05  Score=53.06  Aligned_cols=78  Identities=14%  Similarity=0.204  Sum_probs=62.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCc--ceEEEEEecCHHHHHHHHHHhCCceeCC-----EEEE
Q psy16184        102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKP--RGYAFIEYEHERDMHSAYKHADGKKIDG-----RRVL  174 (363)
Q Consensus       102 ~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~--~g~afV~f~~~~~a~~Ai~~l~g~~i~g-----~~i~  174 (363)
                      ++|.|..||+.+|++++.+.+...|.+........+.+.++  -.-|||.|.+.+++......++|+.+.+     ..-.
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            58999999999999999999999998887777665544333  3569999999999999999999987732     1346


Q ss_pred             EEeec
Q psy16184        175 VDVER  179 (363)
Q Consensus       175 V~~a~  179 (363)
                      |++|-
T Consensus        82 VE~AP   86 (91)
T d1uw4a_          82 VEFAP   86 (91)
T ss_dssp             EEECS
T ss_pred             EEEcC
Confidence            66653

>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=97.53  E-value=0.00039  Score=46.69  Aligned_cols=62  Identities=19%  Similarity=0.272  Sum_probs=52.3

Q ss_pred             HHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEEEEEEeecc
Q psy16184        116 SKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS  180 (363)
Q Consensus       116 ~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~g~~i~g~~i~V~~a~~  180 (363)
                      +.|...|.++|.|..+.|... ..+  .-.|-|...+..+|.-|+..|+-..|+++.|.|.++.+
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 QLLQEAFARHGKVKSVELSPH-TDY--QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATG   72 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSC-CST--TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             HHHHHHHHhheeEEEEEEEec-cCC--cEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEecC
Confidence            456778999999999998653 222  34799999999999999999999999999999999753

>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=96.65  E-value=7e-05  Score=52.46  Aligned_cols=40  Identities=23%  Similarity=0.390  Sum_probs=34.2

Q ss_pred             ChhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccc
Q psy16184          6 PPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEF   47 (363)
Q Consensus         6 p~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~   47 (363)
                      ..+|..+|.++|+|..+ .+..++.|++++|| |||.|.+..
T Consensus        14 e~~l~~~F~~~G~i~~v-~i~~d~~tg~~kG~-aFV~f~~~~   53 (77)
T d1uawa_          14 QEGLREYFGQFGEVKEC-LVMRDPLTKRSRGF-GFVTFMDQA   53 (77)
T ss_dssp             SHHHHHHHTTTSCCCCE-EEECCCCSSSCSSE-EEECCCCTT
T ss_pred             HHHHHHHHHHhCCccee-eeecccCCCCccce-EEEEECCHH
Confidence            45699999999999988 46679999999999 999997654

>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=96.22  E-value=8.7e-05  Score=51.69  Aligned_cols=53  Identities=13%  Similarity=0.088  Sum_probs=39.1

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccC-CCCCCCCCCCccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFE-DPKDTPPPTRVET   61 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~-~~~~~~~~~~~~~   61 (363)
                      .+|..+|+.+|+|..+ -++.++.|++++|| |||.|.+... ..+.+...+.+.+
T Consensus        14 ~~l~~~F~~~G~I~~v-~i~~d~~t~~~rG~-~FV~f~~~~~a~~al~~~~~~i~g   67 (75)
T d1x0fa1          14 EKIREYFGGFGEVESI-ELPMDNKTNKRRGF-CFITFKEEEPVKKIMEKKYHNVGL   67 (75)
T ss_dssp             HHHHHHHHHHSCEEEE-ECCCCTTTCCTTCC-EEEEESSSHHHHHHTTCSSCCBTT
T ss_pred             HHHHHHHHHhCCcccc-cccccccccccccE-EEEEECCHHHHHHHHhhCCCEECC
Confidence            4699999999999988 46778899999999 9999987543 2222334444444

>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=95.99  E-value=9.4e-05  Score=51.45  Aligned_cols=39  Identities=18%  Similarity=0.264  Sum_probs=33.5

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEF   47 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~   47 (363)
                      .+|..+|+.+|+|..+ .++.++.|++++|| +||.|.+..
T Consensus        14 ~~l~~~F~~~G~i~~~-~i~~d~~t~~~kg~-afV~f~~~~   52 (75)
T d1hd0a_          14 KDLKDYFSKFGEVVDC-TLKLDPITGRSRGF-GFVLFKESE   52 (75)
T ss_dssp             HHHHHHHHTTSCEEEE-ECCCBTTTTBCCSE-EEEEESSHH
T ss_pred             HHHHHHHHhhcccccc-ccccCCCCCCcCce-EEEEECCHH
Confidence            4699999999999988 46778999999999 999997654

>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=95.43  E-value=0.0021  Score=45.71  Aligned_cols=38  Identities=18%  Similarity=0.233  Sum_probs=32.5

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|+++|+|..+ .++.++.+++++|| +||.|.+.
T Consensus        20 ~~l~~~F~~~G~i~~v-~i~~d~~~~~~kg~-afV~f~~~   57 (89)
T d2cqba1          20 KVLHAAFIPFGDITDI-QIPLDYETEKHRGF-AFVEFELA   57 (89)
T ss_dssp             HHHHHHHTTTSCCCCE-ECCCCSSSCCCSSE-EEECCSSH
T ss_pred             HHHHHHHhhCCeEEec-ccccccccccccce-eEEEECCH
Confidence            4689999999999988 46778899999999 89998554

>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=95.42  E-value=0.0005  Score=48.45  Aligned_cols=40  Identities=18%  Similarity=0.249  Sum_probs=33.6

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEF   47 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~   47 (363)
                      .+|..+|+.+|+|..+.-++.++.|++++|| +||.|.+..
T Consensus        13 ~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~-afV~f~~~~   52 (83)
T d1x5ta1          13 KLLYDTFSAFGVILQTPKIMRDPDTGNSKGY-AFINFASFD   52 (83)
T ss_dssp             HHHHHHHHTTSCBSSCCEECCCTTTCSCCSE-EEEEBSSHH
T ss_pred             HHHHHHHHHhCceeeeEEEEeeccccccCce-EEEEECCHH
Confidence            4699999999999776557788899999999 999996654

>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=95.33  E-value=0.00029  Score=50.10  Aligned_cols=39  Identities=13%  Similarity=0.245  Sum_probs=33.7

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEF   47 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~   47 (363)
                      .+|..+|..+|+|..+ -++.++.|+.++|| +||.|.+..
T Consensus        16 ~~l~~~F~~~G~v~~v-~i~~d~~tg~~rg~-aFV~f~~~~   54 (85)
T d2u2fa_          16 DQVKELLTSFGPLKAF-NLVKDSATGLSKGY-AFCEYVDIN   54 (85)
T ss_dssp             HHHHHHHTSSSCEEEE-EEECCCSSSCCCCE-EEEEESSSH
T ss_pred             HHHHHHHHhcCccceE-Eeecccccccccee-EEEEECCHH
Confidence            4699999999999888 57778999999999 999996654

>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=95.21  E-value=0.00045  Score=51.05  Aligned_cols=39  Identities=18%  Similarity=0.319  Sum_probs=33.1

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEF   47 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~   47 (363)
                      .+|..+|.++|+|..+ .|..++.|+.++|| +||.|.+..
T Consensus        35 ~~L~~~F~~~G~i~~~-~i~~d~~~~~~kg~-aFV~f~~~~   73 (103)
T d1x4ba1          35 ESLRNYYEQWGKLTDC-VVMRDPASKRSRGF-GFVTFSSMA   73 (103)
T ss_dssp             HHHHHHHTSSCCCSEE-EEECCTTTSSCCSE-EEEECSSHH
T ss_pred             HHHHHHHHhhCcccce-eecccccCCCccCe-EEEEECCHH
Confidence            4699999999999987 46678889999999 999996643

>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=94.69  E-value=0.037  Score=39.40  Aligned_cols=55  Identities=15%  Similarity=0.252  Sum_probs=45.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhhCCccEEEEeccCCCCCcceEEEEEecCHHHHHHHHHHhC
Q psy16184        102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHAD  164 (363)
Q Consensus       102 ~~l~V~nL~~~~t~~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~f~~~~~a~~Ai~~l~  164 (363)
                      .-||.-..|..+...+|.++|+.||.|.-..| .+.       -|||...+.++|..++..++
T Consensus        16 dHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswI-ddT-------Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          16 DHVLHVTFPKEWKTSDLYQLFSAFGNIQISWI-DDT-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CSEEEEECCTTCCHHHHHHHHTTTCSCCCEEE-ETT-------EEEEECSCHHHHHHHHHHHH
T ss_pred             ceeEEEeCCcccchhHHHHHhcCCCceEEEEe-cCc-------eEEEEecCHHHHHHHHHHhc
Confidence            35888899999999999999999998864444 442       89999999999998887544

>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=94.54  E-value=0.00066  Score=48.77  Aligned_cols=38  Identities=21%  Similarity=0.329  Sum_probs=32.9

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|+++|+|..+ -|+.++.|+.++|| |||.|.+.
T Consensus        23 ~~l~~~F~~~G~i~~v-~i~~d~~tg~srG~-aFV~f~~~   60 (90)
T d2cqga1          23 QDLKEYFSTFGEVLMV-QVKKDLKTGHSKGF-GFVRFTEY   60 (90)
T ss_dssp             HHHHHHHGGGSCEEEE-EEEECSSSCSEEEE-EEEEESSH
T ss_pred             HHHHHHHHhhccccee-eeccCCCCcccCCE-EEEEECCH
Confidence            4689999999999988 57778999999999 99999554

>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=94.52  E-value=0.0027  Score=46.39  Aligned_cols=39  Identities=13%  Similarity=0.191  Sum_probs=33.1

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEF   47 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~   47 (363)
                      .+|..+|.++|+|..+ -+..+..|++++|| +||.|.+..
T Consensus        33 ~~l~~~F~~~G~V~~v-~i~~d~~tg~~kG~-afV~F~~~e   71 (101)
T d2cq4a1          33 RDLEDFFSAVGKVRDV-RIISDRNSRRSKGI-AYVEFCEIQ   71 (101)
T ss_dssp             HHHHHHHTTTSCEEEE-EECCSCCSSSCCCC-EEEEESCGG
T ss_pred             HHHHHHHcCCCeEEEE-EeeecCCCccccce-EEEEECCHH
Confidence            4689999999999887 46678889999999 999997654

>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=94.15  E-value=0.00021  Score=50.74  Aligned_cols=38  Identities=18%  Similarity=0.369  Sum_probs=32.7

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|+.+|+|..+. +..++.|++++|| +||.|.+.
T Consensus        21 ~~l~~~F~~~G~i~~v~-i~~d~~tg~~kG~-afV~f~~~   58 (84)
T d1l3ka1          21 ESLRSHFEQWGTLTDCV-VMRDPNTKRSRGF-GFVTYATV   58 (84)
T ss_dssp             HHHHHHHGGGSCEEEEE-EEECTTTCCEEEE-EEEEESSH
T ss_pred             HHHHHHHHhhcccccee-ecccccCCCcccE-EEEEEcCH
Confidence            46999999999999884 6678999999999 99999654

>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=93.91  E-value=0.00044  Score=48.45  Aligned_cols=39  Identities=21%  Similarity=0.346  Sum_probs=33.3

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEF   47 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~   47 (363)
                      .+|..+|..+|+|..+ -++.++.|++++|| +||.|.+..
T Consensus        15 ~~l~~~F~~~G~i~~v-~i~~d~~tg~~~g~-aFV~f~~~~   53 (80)
T d1cvja1          15 AMLYEKFSPAGPILSI-RVCRDMITRRSLGY-AYVNFQQPA   53 (80)
T ss_dssp             HHHHHHHGGGSCEEEE-EEEECTTTCCEEEE-EEEEESSHH
T ss_pred             HHHHHHHHHhCCEeEE-EEEecccccCCCCc-eEEEECCHH
Confidence            3589999999999887 47778999999999 999997654

>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=93.85  E-value=0.0037  Score=44.83  Aligned_cols=38  Identities=34%  Similarity=0.515  Sum_probs=32.8

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|+++|+|..+ .++.++.|+.++|| +||.|.+.
T Consensus        24 ~~l~~~F~~~G~v~~v-~~~~d~~tg~~kg~-afV~f~~~   61 (93)
T d1x5ua1          24 PLLWELFLQAGPVVNT-HMPKDRVTGQHQGY-GFVEFLSE   61 (93)
T ss_dssp             HHHHHHHHTTSCEEEE-ECCBCSSSCSBCSC-EEEEESSH
T ss_pred             HHHHHHHHHhCCcccc-ceeecccccccccc-eEEEECCH
Confidence            4699999999999887 47788999999999 99999654

>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=93.83  E-value=0.0014  Score=44.96  Aligned_cols=39  Identities=15%  Similarity=0.169  Sum_probs=32.3

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEF   47 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~   47 (363)
                      .+|..+|+.+|+|..+ .+..++.++.++|| +||.|.+..
T Consensus        14 ~~l~~~F~~~G~i~~~-~~~~~~~~~~~~~~-afV~F~~~~   52 (75)
T d2msta_          14 EDVKHYFEQFGKVDDA-MLMFDKTTNRHRGF-GFVTFESED   52 (75)
T ss_dssp             HHHHHHHHTTSCCSEE-CCBCCTTCTTSCCE-EEEECSCHH
T ss_pred             HHHHHHHHHhCCccee-eeeeeccccccCce-eEEEECCHH
Confidence            4699999999999988 46667888999999 999986643

>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=93.15  E-value=0.00059  Score=47.54  Aligned_cols=38  Identities=13%  Similarity=0.241  Sum_probs=32.4

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|+.+|+|..+ .+..++.++.++|| +||.|.+.
T Consensus        17 ~~l~~~F~~~G~i~~~-~~~~~~~~~~~~g~-afV~f~~~   54 (79)
T d1l3ka2          17 HHLRDYFEQYGKIEVI-EIMTDRGSGKKRGF-AFVTFDDH   54 (79)
T ss_dssp             HHHHHHHTTTSCEEEE-EEEECTTTCCEEEE-EEEEESSH
T ss_pred             HHHHHHHHHhcccccc-ccccCCCCcccccE-EEEEEcCH
Confidence            3599999999999988 46678889999999 99999664

>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=93.08  E-value=0.0056  Score=44.31  Aligned_cols=38  Identities=24%  Similarity=0.362  Sum_probs=32.1

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|..+++|..+ .++.++.|++++|| +||.|.+.
T Consensus        23 ~~l~~~F~~~g~v~~v-~i~~d~~tg~~~g~-afV~f~~~   60 (99)
T d1whwa_          23 EDLEKLFSAYGPLSEL-HYPIDSLTKKPKGF-AFVTFMFP   60 (99)
T ss_dssp             HHHHHHHHTTSCEEEE-ECCCCTTTCCCCSE-EEEEESSH
T ss_pred             HHHHHHHHhcCCceee-eecccccccccCcc-eEEEECCH
Confidence            4699999999999877 46678899999999 99998554

>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=93.00  E-value=0.00071  Score=50.66  Aligned_cols=57  Identities=18%  Similarity=0.126  Sum_probs=40.2

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccC-CCCCCCCCCCcccHHHH
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFE-DPKDTPPPTRVETREER   65 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~-~~~~~~~~~~~~~~~~~   65 (363)
                      .+|..||..++++..+. ++.+..++.+.|| +||.|.+... .++..+..+.|.++.+.
T Consensus        33 ~di~~~F~~~g~~~~~~-~~~~~~~g~~~G~-afVeF~~~e~a~~al~~~~~~i~gR~i~   90 (112)
T d1wela1          33 KHVIDFFKKLDIVEDSI-YIAYGPNGKATGE-GFVEFRNEADYKAALCRHKQYMGNRFIQ   90 (112)
T ss_dssp             HHHHHHSCSSCBCTTTC-EEEECTTSSEEEE-EEEEBSSSHHHHHHHTSCSBCSTTSCBE
T ss_pred             HHHhhHHhhccccccce-eeecCcccceeeE-EEEEECCHHHHHHHHHcCCCcCCCEEEE
Confidence            46999999999988763 4445668999999 9999988554 23334566666665443

>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=92.84  E-value=0.0052  Score=44.93  Aligned_cols=39  Identities=18%  Similarity=0.221  Sum_probs=32.7

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEF   47 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~   47 (363)
                      .+|..+|+.+|+|..+ .++.++.|++++|| +||.|.+..
T Consensus        25 ~~l~~~F~~~G~i~~v-~i~~d~~tg~~kg~-afV~f~~~~   63 (103)
T d2cqda1          25 ASLRKYFEGFGDIEEA-VVITDRQTGKSRGY-GFVTMADRA   63 (103)
T ss_dssp             HHHHHHHHTTSCEEEE-EESCCSSSCCCCSE-EEEEESSHH
T ss_pred             HHHHHHHhhcccccce-eccccccccccCCe-EEEEECCHH
Confidence            4699999999999887 46678889999999 999996543

>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=92.68  E-value=0.0032  Score=44.33  Aligned_cols=38  Identities=8%  Similarity=0.126  Sum_probs=32.3

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|+.+|+|..+ -+..++.+++++|| +||.|.+.
T Consensus        21 ~~l~~~F~~~G~i~~~-~~~~d~~~g~~~g~-afV~f~~~   58 (85)
T d1b7fa2          21 DQLDTIFGKYGSIVQK-NILRDKLTGRPRGV-AFVRYNKR   58 (85)
T ss_dssp             HHHHHHHTSSSCEEEE-EEEECTTTCCEEEE-EEEEESSH
T ss_pred             HHHHHHHHhhCCEeee-eeecccccccCcee-EEEEECCH
Confidence            4689999999999988 46678889999999 99999654

>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=92.15  E-value=0.0058  Score=43.40  Aligned_cols=38  Identities=18%  Similarity=0.380  Sum_probs=31.9

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|+.+|+|..+ -+..++.++.++|| +||.|.+.
T Consensus        23 ~~l~~~f~~~G~v~~v-~i~~d~~t~~~rg~-afV~f~~~   60 (90)
T d2cq0a1          23 TDLQELFRPFGSISRI-YLAKDKTTGQSKGF-AFISFHRR   60 (90)
T ss_dssp             HHHHTTSTTTCCEEEE-EEEECSSSCSEEEE-EEEEESSH
T ss_pred             HHHHHHHHHhcccccc-cccccccccccccc-eeEEECCH
Confidence            3699999999999887 46678889999999 99998554

>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=92.07  E-value=0.0027  Score=44.79  Aligned_cols=38  Identities=16%  Similarity=0.122  Sum_probs=32.1

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|+++|+|..+ .++.++.++.++|| +||.|.+.
T Consensus        21 ~~L~~~F~~~G~v~~v-~i~~d~~~g~~kg~-afV~f~~~   58 (85)
T d1fxla2          21 KELEQLFSQYGRIITS-RILVDQVTGVSRGV-GFIRFDKR   58 (85)
T ss_dssp             HHHHHHHGGGSCEEEE-EEEECTTTCCEEEE-EEEEESSH
T ss_pred             HHHHHHHHHhCCcccc-ccccccccccCCCe-eEEEEcCH
Confidence            4699999999999988 46668889999999 99998554

>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=92.00  E-value=0.01  Score=42.50  Aligned_cols=39  Identities=15%  Similarity=0.347  Sum_probs=29.9

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|.++|+|..+..+.....++.++|| |||.|.+.
T Consensus        23 ~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~-afV~f~~~   61 (94)
T d2cpha1          23 REIRELFSTFGELKTVRLPKKMTGTGAHRGF-GFVDFITK   61 (94)
T ss_dssp             HHHHHHHHTTSCEEEEECCCCCSSSCSSCSE-EEEEESSH
T ss_pred             HHHHHHHHHhCCceEEEEEeccccCCCcccE-EEEEECCH
Confidence            3589999999999887433323458999999 99999654

>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=91.86  E-value=0.0052  Score=42.72  Aligned_cols=38  Identities=24%  Similarity=0.348  Sum_probs=31.7

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|+++|+|..+ -+..++.+++++|| +||.|.+.
T Consensus        17 ~~l~~~F~~~G~v~~~-~i~~~~~~g~~~g~-afV~f~~~   54 (82)
T d1b7fa1          17 RELYALFRAIGPINTC-RIMRDYKTGYSYGY-AFVDFTSE   54 (82)
T ss_dssp             HHHHHHHHTTSCEEEE-ECCEETTTTEECSE-EEEEESSH
T ss_pred             HHHHHHHHHhCCccee-eeeeecccCCcccc-ceEEECCH
Confidence            4589999999999887 45667889999999 89998654

>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=91.78  E-value=0.001  Score=48.81  Aligned_cols=59  Identities=12%  Similarity=0.100  Sum_probs=41.3

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccC-CCCCCCCCCCcccHHHHHH
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFE-DPKDTPPPTRVETREERLE   67 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~-~~~~~~~~~~~~~~~~~~~   67 (363)
                      .+|..+|..++++..+ .+.....+++++|| +||.|.+... ..+..+....+.++.+.+.
T Consensus        23 ~~l~~~F~~~g~i~~~-~~~~~~~~g~~~G~-afV~F~s~~~a~~Al~~n~~~i~gr~i~V~   82 (103)
T d2cpya1          23 MDVLQFLEGIPVDENA-VHVLVDNNGQGLGQ-ALVQFKNEDDARKSERLHRKKLNGREAFVH   82 (103)
T ss_dssp             HHHHHHTTTSCCCSTT-EEECCCTTSSCSSC-EEEECSSHHHHHHHGGGCSEEETTEEEEEE
T ss_pred             HHHhhhhcccceEEEE-EEEEeCCCCCcCcc-EEEEECCHHHHHHHHhcCCCeECCcEEEEE
Confidence            5699999999998875 23344568999999 9999988655 2223456666666655443

>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=91.65  E-value=0.014  Score=39.26  Aligned_cols=38  Identities=21%  Similarity=0.289  Sum_probs=31.2

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|.++|+|..+. +..++.++.++|| +||.|.+.
T Consensus        13 ~~l~~~F~~~G~v~~~~-~~~~~~~~~~~g~-afV~f~~~   50 (72)
T d1x4ea1          13 QDLVKLCQPYGKIVSTK-AILDKTTNKCKGY-GFVDFDSP   50 (72)
T ss_dssp             HHHHTTSTTTSCEEEEE-EECCSSSCSCCSE-EEEEESCH
T ss_pred             HHHHHHHhhhccccccc-cccccccccccce-eEEEECCH
Confidence            46899999999998773 5557789999999 89998654

>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=91.02  E-value=0.0098  Score=41.75  Aligned_cols=37  Identities=11%  Similarity=0.038  Sum_probs=28.1

Q ss_pred             hhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          9 LLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         9 l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      |..+|+++|+|..+..+..+..+++++|| +||.|.+.
T Consensus        22 l~~~F~~~G~i~~v~i~~~~~~~~~~kg~-afV~f~~~   58 (86)
T d2ghpa3          22 LRESFEGFGSIEKINIPAGQKEHSFNNCC-AFMVFENK   58 (86)
T ss_dssp             HHHHHGGGSCEEEEECCSCCC---CCCEE-EEEEESSH
T ss_pred             HHHHHHhhhhccceeeecccCCcccccee-eeEEECCH
Confidence            88999999999888655556778999999 99999654

>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=91.00  E-value=0.0044  Score=43.88  Aligned_cols=38  Identities=8%  Similarity=0.191  Sum_probs=32.1

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|.++|+|..+ -+..++.|++++|| +||.|.+.
T Consensus        22 ~~l~~~F~~~G~i~~v-~i~~d~~tg~~~g~-afV~f~~~   59 (88)
T d1rk8a_          22 DEIQEKFCDYGEIKNI-HLNLDRRTGFSKGY-ALVEYETH   59 (88)
T ss_dssp             HHHHHHHGGGSCEEEE-EEEECTTTSSEEEE-EEEEESSH
T ss_pred             HHHHHHHHHcCCcccc-cccccccccccccc-eeEEECCH
Confidence            4699999999999887 46678899999999 89998554

>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=90.89  E-value=0.0093  Score=42.19  Aligned_cols=38  Identities=21%  Similarity=0.366  Sum_probs=30.9

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|.++|+|..+ .+..++.++.++|| +||.|.++
T Consensus        20 ~~l~~~F~~~G~i~~~-~~~~~~~~~~~~g~-afV~f~~~   57 (90)
T d1x5sa1          20 QSLEQVFSKYGQISEV-VVVKDRETQRSRGF-GFVTFENI   57 (90)
T ss_dssp             HHHHHHHHHHSCCCEE-EECCCSSSCSCCSE-EEEECSSH
T ss_pred             HHHHHhhhccccccce-eeccccccccccce-EEEEECCH
Confidence            3589999999999887 35557788999999 99998554

>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=90.65  E-value=0.0053  Score=42.83  Aligned_cols=38  Identities=16%  Similarity=0.371  Sum_probs=32.0

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|+++|+|..+ -+..++.+++++|| +||.|.+.
T Consensus        24 ~~l~~~F~~~G~i~~v-~i~~~~~~~~~~g~-afV~f~~~   61 (83)
T d2cqca1          24 RDLREVFSKYGPIADV-SIVYDQQSRRSRGF-AFVYFENV   61 (83)
T ss_dssp             HHHHHHHHTTSCEEEE-EEEECSSSSSEEEE-EEEEESSH
T ss_pred             HHHHHHHHHhCCCccc-cccccccccccccc-eEEEECCH
Confidence            4699999999999887 46678889999999 99998654

>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=90.60  E-value=0.0063  Score=44.43  Aligned_cols=38  Identities=21%  Similarity=0.392  Sum_probs=32.0

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|+++|+|..+ -++.++.|++++|| +||.|.+.
T Consensus        23 ~~l~~~f~~~G~i~~v-~i~~~~~tg~~~g~-afV~f~~~   60 (104)
T d1p1ta_          23 EQLKDIFSEVGPVVSF-RLVYDRETGKPKGY-GFCEYQDQ   60 (104)
T ss_dssp             HHHHHHHHTTSCCSEE-EEEEETTTTEEEEE-EEEECSCH
T ss_pred             HHHHHhhhcccccccc-ccccccceeccCCc-eEEEECCH
Confidence            4699999999999887 46678889999999 89998654

>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=90.33  E-value=0.0086  Score=43.58  Aligned_cols=38  Identities=21%  Similarity=0.277  Sum_probs=32.1

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|..+++|..+ .+..++.++.++|| +||.|.+.
T Consensus        33 ~~l~~~F~~~G~i~~~-~~~~~~~~g~~kG~-afV~f~~~   70 (102)
T d2cpza1          33 QDLLQMFMPFGNVVSA-KVFIDKQTNLSKCF-GFVSYDNP   70 (102)
T ss_dssp             HHHHHHHGGGSCCSEE-EEEECSSSCSEEEE-EEEECSSH
T ss_pred             HHHHHHHHhhcccccc-ceeeecccCCCccc-eEEEeCCH
Confidence            4699999999999987 46678899999999 99998554

>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=89.88  E-value=0.0029  Score=44.60  Aligned_cols=38  Identities=11%  Similarity=0.086  Sum_probs=30.0

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEF   47 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~   47 (363)
                      .+|..+|+.+|+|..+. +..+ .+++++|| +||.|.+..
T Consensus        21 ~~l~~~F~~~G~v~~v~-l~~~-~~~~~kG~-afV~f~~~e   58 (85)
T d1zh5a2          21 DDIKEWLEDKGQVLNIQ-MRRT-LHKAFKGS-IFVVFDSIE   58 (85)
T ss_dssp             HHHHHHHTTSCCEEEEE-EEEC-TTCCEEEE-EEEEESCHH
T ss_pred             HHHHHHHHHhcccccce-eeee-ccCCcceE-EEEEEcCHH
Confidence            46999999999998873 4433 47899999 999997643

>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=89.66  E-value=0.0068  Score=43.35  Aligned_cols=38  Identities=11%  Similarity=0.248  Sum_probs=31.9

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|+++|+|..+ .++.++.++.++|| +||.|.+.
T Consensus        22 ~~l~~~F~~~G~i~~v-~i~~~~~~~~~kg~-afV~f~~~   59 (93)
T d1h2vz_          22 EQIYELFSKSGDIKKI-IMGLDKMKKTACGF-CFVEYYSR   59 (93)
T ss_dssp             HHHHHHHGGGSCEEEE-EEEECTTTCCEEEE-EEEEESSH
T ss_pred             HHHHHHHHHHCCccee-ccccccccccccce-EEEEECCH
Confidence            4699999999999887 46678889999999 99998554

>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=89.15  E-value=0.02  Score=39.46  Aligned_cols=38  Identities=8%  Similarity=-0.007  Sum_probs=24.5

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|+++|+|..+ .+..+..++.++|| +||.|.+.
T Consensus        16 ~~l~~~f~~~G~v~~~-~~~~~~~~~~~~g~-afV~f~~~   53 (81)
T d2ghpa1          16 RNIRDLLQDINVVALS-IRLPSLRFNTSRRF-AYIDVTSK   53 (81)
T ss_dssp             HHHHHHHHHTTCCCCE-EECC-------CCE-EEEECSSH
T ss_pred             HHHHHHHHHhCcEEee-eeecccccccccce-eEEEECCH
Confidence            4689999999999876 34456678999999 89998554

>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=88.74  E-value=0.025  Score=40.37  Aligned_cols=38  Identities=18%  Similarity=0.347  Sum_probs=30.6

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|.++|+|..+ .+..++.++.++|| +||.|.+.
T Consensus        23 ~~l~~~f~~~G~v~~~-~~~~~~~~~~~~g~-afV~F~~~   60 (98)
T d1x4ha1          23 EALGEVLQQFGDLKYV-RVVLHPDTEHSKGC-AFAQFMTQ   60 (98)
T ss_dssp             HHHHHHHHTTSCEEEE-ECCBCSSSCCBCSE-EEEEESSH
T ss_pred             HHHHHHHhccccceee-eeccccccccccce-EEEEEcCH
Confidence            4589999999998766 35567778999999 99999554

>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=88.66  E-value=0.0095  Score=41.27  Aligned_cols=38  Identities=13%  Similarity=0.318  Sum_probs=31.4

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|+.+|+|..+. +..++.++.++|| +||.|.+.
T Consensus        17 ~~l~~~f~~~G~v~~v~-i~~~~~~~~~~g~-afv~f~~~   54 (82)
T d1fxla1          17 EEFRSLFGSIGEIESCK-LVRDKITGQSLGY-GFVNYIDP   54 (82)
T ss_dssp             HHHHHHHHTTSCEEEEE-EEECTTTCCEEEE-EEEEESSH
T ss_pred             HHHHHHHHHhCCccccc-ceeeccCCCceee-EEEEECCH
Confidence            46999999999998873 5567888999999 99998554

>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=88.50  E-value=0.009  Score=43.59  Aligned_cols=39  Identities=13%  Similarity=0.223  Sum_probs=29.3

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEF   47 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~   47 (363)
                      .+|.+||.+++++..+ .+..+..+++++|| +||.|.+..
T Consensus        30 ~dI~~~F~~~g~v~~~-v~~~~~~~~~~kG~-afV~F~~~e   68 (104)
T d1wg5a_          30 EEIVQFFSGLEIVPNG-MTLPVDFQGRSTGE-AFVQFASQE   68 (104)
T ss_dssp             HHHHHHTTTCCEEEEE-EECCBCSSSCBCSE-EEEEESSHH
T ss_pred             HHHHHHHHhcCCceEE-EEEEeCCCCCcceE-EEEEeCCHH
Confidence            4599999999988764 23335567899999 999996643

>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=87.34  E-value=0.0061  Score=47.04  Aligned_cols=39  Identities=21%  Similarity=0.368  Sum_probs=32.3

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEF   47 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~   47 (363)
                      .+|..+|+.+|+|..+ .|..++.|++++|| +||.|.+..
T Consensus        57 ~~l~~~F~~~G~i~~v-~i~~d~~t~~~rg~-afV~f~~~~   95 (139)
T d1u6fa1          57 VQLRQLFERYGPIESV-KIVCDRETRQSRGY-GFVKFQSGS   95 (139)
T ss_dssp             HHHHHHHHHHSCEEEE-EEEEETTTTEEEEE-EEEEESSHH
T ss_pred             HHHHHHHHhhcccccc-ccccccccccccce-eeEEECCHH
Confidence            3689999999999887 46668889999999 999996543

>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=86.33  E-value=0.018  Score=39.44  Aligned_cols=38  Identities=16%  Similarity=0.140  Sum_probs=29.7

Q ss_pred             ChhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          6 PPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         6 p~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      ..+|..+|.++|+|..+. +..++ +++++|| +||.|.+.
T Consensus        14 ~~~l~~~F~~~G~v~~~~-i~~~~-~g~~~g~-afV~f~~~   51 (78)
T d1no8a_          14 DADIQELFAEFGTLKKAA-VHYDR-SGRSLGT-ADVHFERK   51 (78)
T ss_dssp             HHHHHHHHHHHSCEEEEE-ESCSS-CCCSCCE-EEEEESCH
T ss_pred             HHHHHHHHHHhCCCeEEE-EEEee-cccccee-EEEEECCH
Confidence            346999999999998874 44444 7899999 99999654

>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=85.65  E-value=0.046  Score=38.34  Aligned_cols=60  Identities=7%  Similarity=0.041  Sum_probs=40.8

Q ss_pred             ChhhhhcCCCCCCCCCCCCC----CCCCCCCCCCCCccccccccccC-CCCCCCCCCCcccHHHHH
Q psy16184          6 PPNLLALFAPRDPVPYLPPV----EKLPHEKKTHGYSGIAAFLNEFE-DPKDTPPPTRVETREERL   66 (363)
Q Consensus         6 p~~l~~~f~~~~pi~~~~p~----~~~p~t~~s~g~~g~v~f~~~~~-~~~~~~~~~~~~~~~~~~   66 (363)
                      ..+|..+|..++++..+..+    ..+..+++++|| +||.|.+..+ ..+.++....+.++.+.+
T Consensus        15 e~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~-afV~f~~~e~a~~a~~l~g~~~~Gr~l~V   79 (90)
T d1u2fa_          15 EEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNF-AFLEFRSVDETTQAMAFDGIIFQGQSLKI   79 (90)
T ss_dssp             TTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTE-EEEEESSCTTTTTGGGGSSCCSSSSCCCC
T ss_pred             hHHHHHHHHhhCcEEEEEEeccceeeecccCCCceE-EEEEeCCHHHHHHHHhhCCcEECCEEEEE
Confidence            45688999998887765322    224567889999 9999988655 233356677776655443

>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=85.11  E-value=0.016  Score=40.79  Aligned_cols=38  Identities=18%  Similarity=0.199  Sum_probs=28.3

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccC
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFE   48 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~~~   48 (363)
                      .+|..+|+++|+|..+. +..+.  +.++|| +||.|.+...
T Consensus        23 ~~l~~~F~~~G~v~~~~-i~~~~--~~~kg~-afV~f~~~~~   60 (89)
T d1cvja2          23 KALYDTFSAFGNILSCK-VVCDE--NGSKGY-GFVHFETQEA   60 (89)
T ss_dssp             HHHHHHHHTTSCEEEEE-ECCBT--TBCCSC-EEEEESCHHH
T ss_pred             HHHHHHHHhcCCceEEE-EEeec--CCCcce-eEEEECCHHH
Confidence            46999999999998763 44343  457899 9999977543

>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=84.54  E-value=0.1  Score=37.43  Aligned_cols=38  Identities=13%  Similarity=0.216  Sum_probs=27.6

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|..++++... .+.....+++++|| +||.|.+.
T Consensus        30 ~~l~~~f~~~g~~~~~-~~~~~~~~g~~~g~-afV~f~~~   67 (104)
T d1wi8a_          30 ESIKEFFRGLNISAVR-LPREPSNPERLKGF-GYAEFEDL   67 (104)
T ss_dssp             HHHHHHTTTSCEEEEE-CCBCSSCTTSBCSC-EEEEESSH
T ss_pred             HHHHHHHHHhccccce-eeeeeccCCCccee-eeEEECCH
Confidence            4699999999855433 34445567899999 99998543

>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=83.98  E-value=0.12  Score=36.71  Aligned_cols=40  Identities=13%  Similarity=0.071  Sum_probs=29.6

Q ss_pred             hhhhhcCCCCCCCCCCC-------CCCCCCCCCCCCCCcccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLP-------PVEKLPHEKKTHGYSGIAAFLNEF   47 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~-------p~~~~p~t~~s~g~~g~v~f~~~~   47 (363)
                      .+|..+|..+|+|..+.       .+..++.+++++|| +||.|.+..
T Consensus        23 ~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~-afV~f~~~~   69 (101)
T d2cpea1          23 DDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGD-ATVSYEDPP   69 (101)
T ss_dssp             HHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSE-EEEEBSSHH
T ss_pred             HHHHHHHHHCceEEEeeecccceeEEeeccccccccce-eeEEecCHH
Confidence            46899999999985432       13456678899999 999996543

>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=83.94  E-value=0.014  Score=40.74  Aligned_cols=38  Identities=13%  Similarity=0.316  Sum_probs=28.3

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCC---CCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEK---KTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~---~s~g~~g~v~f~~~   46 (363)
                      .+|..+|+++|+|..+. +..++.++   .++|| +||.|.+.
T Consensus        13 ~~l~~~F~~~G~v~~v~-i~~~~~~~~~~~~kG~-afV~f~~~   53 (85)
T d2cpfa1          13 ETLKGVFSKVGAIKSCT-ISKKKNKAGVLLSMGF-GFVEYKKP   53 (85)
T ss_dssp             HHHHHHHHTTSCEEEEE-EEEEECTTCCEEEEEE-EEEEESSH
T ss_pred             HHHHHHHHHhCCccccc-eecccccccccccceE-EEEEECCH
Confidence            45899999999998873 44444443   57899 99999654

>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=80.52  E-value=0.047  Score=39.22  Aligned_cols=38  Identities=21%  Similarity=0.264  Sum_probs=30.9

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|+.+|+|..+ .+..+..+++++|| +||.|.+.
T Consensus        33 ~~l~~~f~~~G~v~~~-~~~~~~~~g~~~g~-~fV~f~~~   70 (102)
T d2cpxa1          33 RDLVSLFARFQEKKGP-PIQFRMMTGRMRGQ-AFITFPNK   70 (102)
T ss_dssp             HHHHHHTHHHHHSSSS-CCEEEEECSSSCSE-EEEECSSH
T ss_pred             HHHHHHHhhccceeeE-Eeeccccccccccc-ceEEeccH
Confidence            4589999999999887 46666778999999 89998553

>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=80.06  E-value=0.087  Score=36.71  Aligned_cols=34  Identities=15%  Similarity=0.269  Sum_probs=26.0

Q ss_pred             ChhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          6 PPNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         6 p~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      ..+|..+|.++++|..+. +     +..++|| +||.|.+.
T Consensus        19 e~~L~~~F~~~G~v~~v~-~-----~~~~~gf-afV~f~~~   52 (88)
T d1wf0a_          19 EDELREFFSQYGDVMDVF-I-----PKPFRAF-AFVTFADD   52 (88)
T ss_dssp             HHHHHHHSTTTSCCCEEE-C-----CSSCCSC-CEEECSCH
T ss_pred             HHHHHHHHHHcCCceEEE-E-----eeccCce-EEEEECCH
Confidence            357999999999988763 2     2457899 99999664

>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=80.02  E-value=0.087  Score=37.13  Aligned_cols=36  Identities=19%  Similarity=0.396  Sum_probs=27.4

Q ss_pred             hhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy16184          7 PNLLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNE   46 (363)
Q Consensus         7 ~~l~~~f~~~~pi~~~~p~~~~p~t~~s~g~~g~v~f~~~   46 (363)
                      .+|..+|.++|+|..+. +..++  +.++|| +||.|.+.
T Consensus        26 ~~L~~~F~~~G~v~~v~-~~~~~--~~~kg~-afV~f~~~   61 (93)
T d2cq3a1          26 PDLRQMFGQFGKILDVE-IIFNE--RGSKGF-GFVTFENS   61 (93)
T ss_dssp             HHHHHHGGGTSCEEEEE-EECCT--TTTCCE-EEEEESCH
T ss_pred             HHHHHHHhhcceeeecc-ccccc--cCCcce-eEEEECCH
Confidence            46999999999998873 44444  447899 89999554