Citrus Sinensis ID: 040243

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-------670-------680-------690-------700-------710-------720-------730-------740-------750-------760-------770-------780-------790-------
Protein Sequence
MESTVESNPQYQTLDFNQNPPLPQDTLDHDSQNPPKTLAPPDAQNPQPASENGHDKNNENSCNNNNDVAAADYIKQKPLLSENGLTNTHSGTDKDQSGGEEETTSRRRRRSRWDPPPSESGGTEGNGDSGSGTRKRRSRWADDEPKPVIQLPDFMKDFTGGIEFDPEIQALNSRLLEISRMLQSGLPLDDRPEGQRSPSPEPIYDNMGIRINTREYRARERLNKERQEIISQIIKRNPAFKPPADYRPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQPVDEVLNEHKRQQLRELAALNGTIRDEEYCRLCGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTIDCLVKGTTGKKMDDEYQNFLAELGGTLPESASKQSTTLALGPGSGSSGSNPPWANNSGSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGPPVPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATSSEAQQHSFPPGVQSESSSSAPAASANMYGSSMPPMPPNVQPAYATAPLGYSPYYNAVPPPPPPAPVSAADHSQNLGNVPWATNPPVQPPVSSAEKSNYGADAEYEKFMAEMK
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccEEEEEEcccccccccEEEEEEcccccHHHHHHHHHccEEEEEccccccccccccccccccccccccccEEEEEcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHccccccHHHcccccccccccccccccccccccHHHccccccccccEEEcccccccccccHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHccccEEEEEEEEcccccccccEEEEEcccHHHHHHHHHHHcccccccccEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
cccEEEccccccccccccccccccHHcccccccccccccccccccccccccccccccccccccccccccccHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccEcccHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccEcEEEEEcccccccEEEEEEEcccccHHHHHHHHcccEEEEEEcccEcccccccccccccccccccccEEEEEcccHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccEEEEEEccccccccccccccccccHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEcccccccHHHHHHHHHccccEEEEEEEEccccccEEEEEEEEEccHHHHHHHHHHHcccEEccEEcEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHcc
Coil and Loop (DISEMBL)
mestvesnpqyqtldfnqnpplpqdtldhdsqnppktlappdaqnpqpasenghdknnenscnnnndvaaadyikqkpllsengltnthsgtdkdqsggeeettsrrrrrsrwdpppsesggtegngdsgsgtrkrrsrwaddepkpviqlpdfmkdftggiefdpEIQALNSRLLEISRMLQsglplddrpegqrspspepiydnmgirinTREYRARERLNKERQEIISQIIkrnpafkppadyrppklqkklyipmkeypgynfigliigprgntqkrmERETGAKIVIrgkgsvkegrlqqkrdlkpdpsenedlhVLVEAETQESLEGAAAMVEKLLQPVDEVLNEHKRQQLRELAALNgtirdeeycrlcgepghrqyacpsrtstfksdvlckicgdgghptidclvkgttgkkmdDEYQNFLAElggtlpesaskqsttlalgpgsgssgsnppwannsgssgtpghpglgsngakpikelddtnlyigylpptldddgliRLFSTFGDIVMAKVIKDRVTgmskgygfVKYADIQMANNAIASMNGYRLEGRTIAVrvagkppqptvppgpptstmptypvsappvggypsqqyapggplpnppaasytgapvpwgppvpppyapyappppgstmyppvpgqpmppygvqypppvqtappgaltappgaptqtatsseaqqhsfppgvqsessssapaasanmygssmppmppnvqpayataplgyspyynavppppppapvsaadhsqnlgnvpwatnppvqppvssaeksnygadAEYEKFMAEMK
Flexible Loop (DISEMBL)
mestvesnpqyqTLDFNQNPPLPQDTLDHDSQNPPKTLAPPDAQNPQPASENGHDKNNENSCNNNNDVAAADYIKQKPLLSengltnthsgtdkdqsggeeettsrrrrrsrwdpppsesggtegngdsgsgtrkrrsrwaddepkpviqlPDFMKDFTGGIEFDPEIQALNSRLLEISRMLQSglplddrpegqrspspepiydnmgiriNTREYRARERLNKERQEIISqiikrnpafkppadyrppklQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGakivirgkgsvkegrlqqkrdlkpdpseneDLHVLVEAETQESLEGAAAMVEKLLQPVDEVLNEHKRQQLRELAALNGTIRDEEYCRLCGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTIDCLVKGTTGKKMDDEYQNFLAELGGTLPESASKQSTTLALGPGSGSSGSNPPWANNSGSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGPPVPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATSSEAQQHSFPPGVQSESSSSAPAASANMYGSSMPPMPPNVQPAYATAPLGYSPYYNAVPPPPPPAPVSAADHSQNLGNVPWatnppvqppvssaeksnygADAEYEKFMAEMK
Low Complexity Region (SEG)
MESTVESNPQYQTLDFNQNPPLPQDTLDHDSQNPPKTLAPPDAQNPQPASENGHDKnnenscnnnnDVAAADYIKQKPLLSENGLTNTHSGTDKDQsggeeettsrrrrrsrWDPPPsesggtegngdsgsgtRKRRSRWADDEPKPVIQLPDFMKDFTGGIEFDPEIQALNSRLLEISRMLQSGLPLDDRPEGQRSPSPEPIYDNMGIRINTREYRARERLNKERQEIISQIIKRNPAFKPPADYRPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQPVDEVLNEHKRQQLRELAALNGTIRDEEYCRLCGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTIDCLVKGTTGKKMDDEYQNFLAELGGTLPESASKQSTTLALgpgsgssgsnppwannsgssgTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKppqptvppgpptstmptypVSAPPVGGYPSQQYapggplpnppaaSYTGapvpwgppvpppyapyappppgstmyppvpgqpmppygvqypppvqtappgaltappgaptqtatSSEAQQHSFPPGVQsessssapaasaNMYGSSMPPMPPNVQPAYATAPLGyspyynavppppppapvsaaDHSQNLGNVPWATNPPVQPPVSSAEKSNYGADAEYEKFMAEMK
Disordered region (IsUnstruct)
****************************************************************************************************************************************************IQLPDFMKDFTGGIEFDPEIQALNSRLLEI******************************IRI******************ISQII****************LQKKLYIPMKEYPGYNFIGLIIGP******************************************************************LLQPVDEVL******QLRELAALNGTIRDEEYCRLCGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTIDCLVKGTTGKKMDDEYQNFLA*********************************************************LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV**************************************************************************************************************************************************************************************************************************************
Disordered Region (DISOPRED)
*************************************************************************************************************************************************KPVIQLPDFMKDFTGGIEFDPEIQALNSRLLEISRML*******************************REYRARERLNKERQEIISQIIKRNPAFKPPADYRPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRG************************LHVLVEAETQESLEGAAAMVEKLLQPVDEVLNEHKRQQLRELAALNGTIRDEEYCRLC**************STFKSDVLCKICGDGGHPTIDC***************NFLAEL***********************SGSNPPWANNSGSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV********************************************************************************************************************************************************************************************************************************FMA***
Disordered Region (DISEMBL)
**********YQTLDFNQNPPLPQDTLDHDSQNPPKT*****************DKNNENSCNNNNDVAAADYIKQKPLLSENGLTNT******************************************************DEPKPVIQLPDFMKDFTGGIEFDPEIQALNSRLLEISRMLQSGLPL*********PSPEPIYDNMGIRINTREYRARERLNKERQEIISQIIKRNPAFKPPADYRPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQPVDEVLNEHKRQQLRELAALNGTIRDEEYCRLCGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTIDCLVKGTTGKKMDDEYQNFLAELGGTLPE**********************PWANNSGSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGPPVPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGA****************************************MYGSSMPPMPPNVQPAYATAPLGYSPYYNAVPPPPPPAPVSAADHSQNLGNVPWATNPPV**********NYGADAEYEKFMAEMK
Disordered Region (DISPRO)
***TVES**QYQTLDFNQNPPLPQ***************************************************************************************************************************VIQLPDFMKDFTGGIEFDPEIQALNSRLLEISRMLQSGLPLDDRPEGQRSPSPEPIYDNMGIRINTREYRARERLNKERQEIISQIIKRNPAFKPPADYRPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVK****************NEDLHVLVEAETQESLEGAAAMVEKLLQPVDEVLNEHKRQQLRELAALNGTIRDEEYCRLCGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTIDCLVKGTTGKKMDDEYQNFLAELG******************************************************LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPP***VPPG****TMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGPPVPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATS****QHSFPPG****SSSSAPAASANMYGSSMPPMPPNVQPAYATAPLGYSPYYNAVPPPPP*******************************************KF*AEMK
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MESTVESNPQYQTLDFNQNPPLPQDTLDHDSQNPPKTLAPPDAQNPQPASENGHDKNNENSCNNNNDVAAADYIKQKPLLSENGLTNTHSGTDKDQSGGEEETTSRRRRRSRWDPPPSESGGTEGNGDSGSGTRKRRSRWADDEPKPVIQLPDFMKDFTGGIEFDPEIQALNSRLLEISRMLQSGLPLDDRPEGQRSPSPEPIYDNMGIRINTREYRARERLNKERQEIISQIIKRNPAFKPPADYRPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQPVDEVLNEHKRQQLRELAALNGTIRDEEYCRLCGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTIDCLVKGTTGKKMDDEYQNFLAELGGTLPESASKQSTTLALGPGSGSSGSNPPWANNSGSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGPPVPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATSSEAQQHSFPPGVQSESSSSAPAASANMYGSSMPPMPPNVQPAYATAPLGYSPYYNAVPPPPPPAPVSAADHSQNLGNVPWATNPPVQPPVSSAEKSNYGADAEYEKFMAEMK
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	797	2.2.26 [Sep-21-2011]
P0CO44	546	Branchpoint-bridging prot	yes	no	0.405	0.591	0.428	6e-68
P0CO45	546	Branchpoint-bridging prot	N/A	no	0.405	0.591	0.428	6e-68
Q8NIW7	607	Branchpoint-bridging prot	N/A	no	0.404	0.530	0.396	1e-65
Q4WXV6	566	Branchpoint-bridging prot	yes	no	0.406	0.572	0.408	2e-64
Q4P0H7	625	Branchpoint-bridging prot	N/A	no	0.377	0.481	0.404	3e-62
O74555	587	Branchpoint-bridging prot	yes	no	0.331	0.449	0.451	7e-61
Q54BM5	501	Branchpoint-bridging prot	yes	no	0.317	0.504	0.451	1e-56
Q6C187	605	Branchpoint-bridging prot	yes	no	0.459	0.604	0.375	5e-55
Q15637	639	Splicing factor 1 OS=Homo	no	no	0.407	0.508	0.370	3e-53
Q64213	653	Splicing factor 1 OS=Mus	no	no	0.407	0.497	0.370	3e-53

>sp|P0CO44|BBP_CRYNJ Branchpoint-bridging protein OS=Cryptococcus neoformans var. neoformans serotype D (strain JEC21 / ATCC MYA-565) GN=BBP PE=3 SV=1

 Score =  259 bits (662), Expect = 6e-68,   Method: Compositional matrix adjust.
 Identities = 151/352 (42%), Positives = 212/352 (60%), Gaps = 29/352 (8%)

Query: 104 TSRRRRRSRWDPPPSESG--GTEGNGDSGS----GTRKRRSRWADDEPKPVIQLPDFMKD 157
           + RR  RS+WD         G E + D G     G RKRRSRW D   K  + +P     
Sbjct: 93  SDRRDERSKWDEGDRREAPRGRERSRDRGDSNEDGPRKRRSRWGDASAK--VNVPGMPVA 150

Query: 158 FTGGI-EFDPEIQALNSRLLEISRMLQSGLPLDDRPEGQRSPSPEPIYDNMGIRINTREY 216
             G + + + +  A++ RL EI+R L++G  +   PEGQRSPSP P YD  G R NTRE 
Sbjct: 151 VMGNVSQTELDNYAIHVRLEEINRKLRTGDVVP--PEGQRSPSPTPQYDAYGRRTNTREL 208

Query: 217 RARERLNKERQEIISQIIKRNPAFKPPADY---RPPKLQKKLYIPMKEYPGYNFIGLIIG 273
           R R++L  ER  +I + +K +P F+PP D+   R  + Q K+YIP+KE+P  NF GL++G
Sbjct: 209 RYRKKLEDERTRLIDRAVKSDPNFRPPVDFQHKRGSRPQDKVYIPVKEFPEINFFGLLVG 268

Query: 274 PRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEG 333
           PRGN+ K+MERE+GAKI IRGKGSVKEG+    R       E ++LH L+ A+ +  ++ 
Sbjct: 269 PRGNSLKKMERESGAKISIRGKGSVKEGK---GRAGNFPQDEEDELHCLITADDESKVKT 325

Query: 334 AAAMVEKLLQPVD---EVLNEHKRQQLRELAALNGTIRDEE--YCRLCGEPGHRQYACPS 388
             A++ K+++      E  N+HKR QLRELA+LNGT+RD+E   C+ CGE GHR++ CP 
Sbjct: 326 CVALINKVIETAASTPEGENDHKRNQLRELASLNGTLRDDENQLCQNCGEKGHRRWECPQ 385

Query: 389 RTSTFKSDVLCKICGDGGHPTIDCLVKG----TTGKK--MDDEYQNFLAELG 434
           +   + ++V+C+ICG  GH   DC  +G    T  K+   D EY   +AELG
Sbjct: 386 Q-RVYSANVICRICGGAGHMARDCRGRGDPSLTQNKQTAFDSEYTALMAELG 436

Necessary for the splicing of pre-mRNA. Has a role in the recognition of the branch site (5'-UACUAAC-3'), the pyrimidine tract and the 3'-splice site at the 3'-end of introns.
Cryptococcus neoformans var. neoformans serotype D (strain JEC21 / ATCC MYA-565) (taxid: 214684)

>sp|P0CO45|BBP_CRYNB Branchpoint-bridging protein OS=Cryptococcus neoformans var. neoformans serotype D (strain B-3501A) GN=BBP PE=3 SV=1

 Score =  259 bits (662), Expect = 6e-68,   Method: Compositional matrix adjust.
 Identities = 151/352 (42%), Positives = 212/352 (60%), Gaps = 29/352 (8%)

Query: 104 TSRRRRRSRWDPPPSESG--GTEGNGDSGS----GTRKRRSRWADDEPKPVIQLPDFMKD 157
           + RR  RS+WD         G E + D G     G RKRRSRW D   K  + +P     
Sbjct: 93  SDRRDERSKWDEGDRREAPRGRERSRDRGDSNEDGPRKRRSRWGDASAK--VNVPGMPVA 150

Query: 158 FTGGI-EFDPEIQALNSRLLEISRMLQSGLPLDDRPEGQRSPSPEPIYDNMGIRINTREY 216
             G + + + +  A++ RL EI+R L++G  +   PEGQRSPSP P YD  G R NTRE 
Sbjct: 151 VMGNVSQTELDNYAIHVRLEEINRKLRTGDVVP--PEGQRSPSPTPQYDAYGRRTNTREL 208

Query: 217 RARERLNKERQEIISQIIKRNPAFKPPADY---RPPKLQKKLYIPMKEYPGYNFIGLIIG 273
           R R++L  ER  +I + +K +P F+PP D+   R  + Q K+YIP+KE+P  NF GL++G
Sbjct: 209 RYRKKLEDERTRLIDRAVKSDPNFRPPVDFQHKRGSRPQDKVYIPVKEFPEINFFGLLVG 268

Query: 274 PRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEG 333
           PRGN+ K+MERE+GAKI IRGKGSVKEG+    R       E ++LH L+ A+ +  ++ 
Sbjct: 269 PRGNSLKKMERESGAKISIRGKGSVKEGK---GRAGNFPQDEEDELHCLITADDESKVKT 325

Query: 334 AAAMVEKLLQPVD---EVLNEHKRQQLRELAALNGTIRDEE--YCRLCGEPGHRQYACPS 388
             A++ K+++      E  N+HKR QLRELA+LNGT+RD+E   C+ CGE GHR++ CP 
Sbjct: 326 CVALINKVIETAASTPEGENDHKRNQLRELASLNGTLRDDENQLCQNCGEKGHRRWECPQ 385

Query: 389 RTSTFKSDVLCKICGDGGHPTIDCLVKG----TTGKK--MDDEYQNFLAELG 434
           +   + ++V+C+ICG  GH   DC  +G    T  K+   D EY   +AELG
Sbjct: 386 Q-RVYSANVICRICGGAGHMARDCRGRGDPSLTQNKQTAFDSEYTALMAELG 436

Necessary for the splicing of pre-mRNA. Has a role in the recognition of the branch site (5'-UACUAAC-3'), the pyrimidine tract and the 3'-splice site at the 3'-end of introns.

Cryptococcus neoformans var. neoformans serotype D (strain B-3501A) (taxid: 283643)

>sp|Q8NIW7|BBP_NEUCR Branchpoint-bridging protein OS=Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) GN=bpb-1 PE=3 SV=1

 Score =  251 bits (642), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 144/363 (39%), Positives = 211/363 (58%), Gaps = 41/363 (11%)

Query: 134 RKRRSRWADDEPKPVIQLPDFMKDFTGGIEFDP-EIQALNSRLLEISRMLQSGLPLDDR- 191
           RK+R+RW +        L          +  +  E   L+ R+ EI++ L+    +DD  
Sbjct: 79  RKKRNRWGEATENKAAGLMGLPTAIVANMTSEQLEAYTLHLRIEEITQKLK----IDDVV 134

Query: 192 -PEGQRSPSPEPIYDNMGIRINTREYRARERLNKERQEIISQIIKRNPAFKPPADYR-PP 249
             +G RSPSP P YDN G R+NTREYR R++L  ER ++I + +K  P + PP+DYR P 
Sbjct: 135 PADGDRSPSPAPQYDNHGRRVNTREYRYRKKLEDERHKLIEKAMKTIPNYHPPSDYRRPT 194

Query: 250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDL 309
           K Q+K+Y+P+ +YP  NFIGL+IGPRGNT K+ME E+GAKI IRGKGSVKEG+   + D 
Sbjct: 195 KTQEKVYVPVNDYPEINFIGLLIGPRGNTLKKMETESGAKIAIRGKGSVKEGK--GRSDA 252

Query: 310 KPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQ---PVDEVLNEHKRQQLRELAALNGT 366
               ++ EDLH L+ A+T+E +  A  ++  +++    + E  NE KR QLRELAALNGT
Sbjct: 253 AHSSNQEEDLHCLIMADTEEKVNKAKKLIHNIIETAASIPEGQNELKRNQLRELAALNGT 312

Query: 367 IRDEE--YCRLCGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTIDC------------ 412
           +RD+E   C+ CG+ GHR+Y CP + + + ++++C++CG+ GH   DC            
Sbjct: 313 LRDDENQACQNCGQIGHRKYDCPEKQN-YTANIICRVCGNAGHMARDCPDRQRGASWRND 371

Query: 413 ----------LVKGTTGKKMDDEYQNFLAELGGTLPESASKQS--TTLALGPGSGSSGSN 460
                     +     G  +D EY+  + ELGGT    A  ++   + + GP SG +G  
Sbjct: 372 GPGAGRTAGRIGSSGGGDAVDREYEQLMQELGGTGAAPARIEAGPGSFSNGP-SGGNGDA 430

Query: 461 PPW 463
            PW
Sbjct: 431 KPW 433

Necessary for the splicing of pre-mRNA. Has a role in the recognition of the branch site (5'-UACUAAC-3'), the pyrimidine tract and the 3'-splice site at the 3'-end of introns.

Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (taxid: 367110)

>sp|Q4WXV6|BBP_ASPFU Branchpoint-bridging protein OS=Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) GN=bbp PE=3 SV=1

 Score =  248 bits (632), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 149/365 (40%), Positives = 213/365 (58%), Gaps = 41/365 (11%)

Query: 130 GSGTRKRRSRWAD---DEPKPVIQLPD-FMKDFTGGIEFDPEIQALNSRLLEISRMLQSG 185
           G   RK+R+RW D   ++   ++ LP   M +FT       E   L+ R+ EIS+ L+  
Sbjct: 60  GVKRRKKRNRWGDAQENKAAGLMGLPTMIMANFT---NEQLEAYTLHLRIEEISQKLRIN 116

Query: 186 --LPLDDRPEGQRSPSPEPIYDNMGIRINTREYRARERLNKERQEIISQIIKRNPAFKPP 243
             +P D    G RSPSP P YDN G R+NTREYR R+RL  ER +++ + +K  P + PP
Sbjct: 117 DVVPAD----GDRSPSPPPQYDNFGRRVNTREYRYRKRLEDERHKLVEKAMKTIPNYHPP 172

Query: 244 ADYR-PPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGR 302
           +DYR P K Q+K+Y+P+ +YP  NFIGL+IGPRGNT K+ME E+GAKI IRGKGSVKEG+
Sbjct: 173 SDYRRPTKTQEKVYVPVNDYPEINFIGLLIGPRGNTLKKMEAESGAKIAIRGKGSVKEGK 232

Query: 303 LQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQ---PVDEVLNEHKRQQLRE 359
              + D     ++ EDLH L+ A+T+E +  A  +V  +++    + E  NE KR QLRE
Sbjct: 233 --GRSDAAHASNQEEDLHCLIMADTEEKVNKAKKLVHNVIETAASIPEGQNELKRNQLRE 290

Query: 360 LAALNGTIRDEE--YCRLCGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTIDC--LVK 415
           LAALNGT+RD+E   C+ CG+ GHR+Y CP + + F ++++C++CG+ GH   DC    +
Sbjct: 291 LAALNGTLRDDENQACQNCGQIGHRKYDCPEQRN-FTANIICRVCGNAGHMARDCPDRQR 349

Query: 416 GT----------------TGKKMDDEYQNFLAELGGTLPESASKQSTTLALGPGSGSSGS 459
           G+                 G  +D E +  + EL G  P    +    +  GP  G    
Sbjct: 350 GSDWRNGGGYGGGRRAIGQGDAVDREMEQLMQELSGGAPGPDGQPPRRIEAGPDHGYDDR 409

Query: 460 N-PPW 463
           +  PW
Sbjct: 410 DVKPW 414

Necessary for the splicing of pre-mRNA. Has a role in the recognition of the branch site (5'-UACUAAC-3'), the pyrimidine tract and the 3'-splice site at the 3'-end of introns.

Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (taxid: 330879)

>sp|Q4P0H7|BBP_USTMA Branchpoint-bridging protein OS=Ustilago maydis (strain 521 / FGSC 9021) GN=BBP PE=3 SV=1

 Score =  240 bits (613), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 137/339 (40%), Positives = 195/339 (57%), Gaps = 38/339 (11%)

Query: 120 SGGTEGNGDSGSGTRKRRSRWADDEPKPVIQLPDFMKDFTGGIEFDPEIQALNSRLLEIS 179
           S  T     + +G RKR+SRW D   K  I +P  +       E D    A+  RL EIS
Sbjct: 119 SASTADGSGADAGPRKRKSRWGDANDK--ITIPTAIGANVSAQELDK--YAIQVRLDEIS 174

Query: 180 RMLQSG--LPLDDRPEGQRSPSPEPIYDNMGIRINTREYRARERLNKERQEIISQIIKRN 237
           R L+SG  +P    P+ +RSPSP P YDN G R NTRE R R++L  ER  ++ + +K +
Sbjct: 175 RKLRSGDFVP----PDRERSPSPPPTYDNQGRRTNTREVRYRKKLEDERVALVDRQLKLD 230

Query: 238 PAFKPPADYRPPKLQK----KLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIR 293
           P F+PP+DY   K  +    K+Y+P+KE+P   F GL++GPRGNT K MER++GAKI IR
Sbjct: 231 PNFRPPSDYHAIKRNQRPTEKVYLPIKEFPEIKFFGLLVGPRGNTLKTMERQSGAKISIR 290

Query: 294 GKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQPVD---EVLN 350
           GKGSVK G+ +   D      + E++H +V A+ + S++    ++ ++++      E  N
Sbjct: 291 GKGSVKTGKGKMDAD-----EDEEEMHCVVTADDEASVKKCIKLINQVIETAASTPEGEN 345

Query: 351 EHKRQQLRELAALNGTIRDEE--YCRLCGEPGHRQYACPSRTSTFKSDVLCKICGDGGHP 408
           +HKR QLRELAALNGT+RD+E   C+ CG  GHR + CP + + + + ++C  CG  GH 
Sbjct: 346 DHKRNQLRELAALNGTLRDDENQLCKNCGNKGHRAFECPEQRN-WTAHIICHRCGGQGHL 404

Query: 409 TIDCL-------------VKGTTGKKMDDEYQNFLAELG 434
             DC                GT  ++ D EY N +AELG
Sbjct: 405 ARDCTQGRAGAFNGAPPGAAGTGNRQFDSEYANLMAELG 443

Necessary for the splicing of pre-mRNA. Has a role in the recognition of the branch site (5'-UACUAAC-3'), the pyrimidine tract and the 3'-splice site at the 3'-end of introns.

Ustilago maydis (strain 521 / FGSC 9021) (taxid: 237631)

>sp|O74555|BBP_SCHPO Branchpoint-bridging protein OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=bpb1 PE=1 SV=1

 Score =  236 bits (601), Expect = 7e-61,   Method: Compositional matrix adjust.
 Identities = 126/279 (45%), Positives = 180/279 (64%), Gaps = 15/279 (5%)

Query: 167 EIQALNSRLLEISRMLQSGLPLDDRPEGQRSPSPEPIYDNMGIRINTREYRARERLNKER 226
           E+ +LN RL EI++ L++G  +    E  RSPSP P YDN G R+NTRE R +++L  ER
Sbjct: 103 ELYSLNVRLEEITQKLRTGDVVPHHRE--RSPSPPPQYDNHGRRLNTREIRYKKKLEDER 160

Query: 227 QEIISQIIKRNPAFKPPADYR-PPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERE 285
             II + +K  P F+ P+DYR P K Q+K+Y+P+K+YP  NFIGL+IGPRG+T K ME +
Sbjct: 161 HRIIERAMKMVPGFRAPSDYRRPAKTQEKVYVPVKDYPEINFIGLLIGPRGHTLKDMEAK 220

Query: 286 TGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQ-- 343
           +GAKI IRGKGSVKEG+ +    ++ +    EDLH LV A++++ +  A  +++ ++Q  
Sbjct: 221 SGAKIAIRGKGSVKEGKGRSDPSVRGN--MEEDLHCLVTADSEDKINHAIKLIDNVIQTA 278

Query: 344 -PVDEVLNEHKRQQLRELAALNGTIRDEE--YCRLCGEPGHRQYACPSRTSTFKSDVLCK 400
             V E  N+ KR QLR+LA LNGT+RD+E   C+ CG  GHR++ CP R +    +++C+
Sbjct: 279 ASVPEGQNDLKRNQLRQLATLNGTLRDDENQVCQNCGNVGHRRFDCPERIN-HTMNIVCR 337

Query: 401 ICGDGGHPTIDCLVKG----TTGKKMDDEYQNFLAELGG 435
            CG  GH   DC V+           D EYQ+ + ELGG
Sbjct: 338 HCGSIGHIARDCPVRDQQPPMADSTADREYQSLMQELGG 376

Necessary for the splicing of pre-mRNA. The BPB1(SF1)-u2af59-u2af23 complex has a role in the recognition of the branch site (5'-UACUAAC-3'), the pyrimidine tract and the 3'-splice site at the 3'-end of introns.

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

>sp|Q54BM5|BBP_DICDI Branchpoint-bridging protein OS=Dictyostelium discoideum GN=sf1 PE=3 SV=1

 Score =  222 bits (565), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 127/281 (45%), Positives = 178/281 (63%), Gaps = 28/281 (9%)

Query: 165 DPEIQALNSRLL--EISRMLQSG-LPLDDRPEGQRSPSPEPIYDNMGIRINTREYRARER 221
           D +I AL  RL   EI++ +  G +   +R + +RSPSP P YDN G R NTRE R +E+
Sbjct: 89  DEQIAALILRLRVDEITKKITIGPIEFTER-DRERSPSPPPTYDNNGKRSNTREQRIKEK 147

Query: 222 LNKERQEIISQIIKRNPAFKPPADYRPP--KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQ 279
           L KER +++    + NP +KPP+DY+PP  K  +K+YIP+K +P YNFIGLIIGPRGNTQ
Sbjct: 148 LQKERHQLVVTAQQINPTYKPPSDYQPPNEKKTRKIYIPIKNHPEYNFIGLIIGPRGNTQ 207

Query: 280 KRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVE 339
           KRME+E+GAKI IRGKGS ++G     +  K    EN++LHVL+ A+T + L+ A  +V 
Sbjct: 208 KRMEKESGAKIAIRGKGSSRDG-----KPTKLQFQENDELHVLLTADTVDQLDKAEVLVR 262

Query: 340 KLLQPVDEVLNEHKRQQLRELAALNGTIRDE-EYCRLCGEPGHRQYACPSRTSTFKSDVL 398
           + L PV+E  NEHKRQQLRELA +NGT+R+   Y       G+R +           D+ 
Sbjct: 263 EFLIPVEEGKNEHKRQQLRELAEMNGTLRERPAYM------GNRSWT--------PVDIK 308

Query: 399 CKICGDGGHPTIDCLVKGTTGKK--MDDEYQNFLAELGGTL 437
           C  CG+  HP+ DC ++     +  ++ EYQ F+ E+  +L
Sbjct: 309 CVQCGETSHPSSDCPLRSNESNQQYIESEYQKFIDEMSKSL 349

Necessary for the splicing of pre-mRNA.

Dictyostelium discoideum (taxid: 44689)

>sp|Q6C187|BBP_YARLI Branchpoint-bridging protein OS=Yarrowia lipolytica (strain CLIB 122 / E 150) GN=BBP PE=3 SV=1

 Score =  216 bits (551), Expect = 5e-55,   Method: Compositional matrix adjust.
 Identities = 153/407 (37%), Positives = 220/407 (54%), Gaps = 41/407 (10%)

Query: 94  KDQSGGEEETTSRRRRRSRWDPPPSESGGTEG---------NGDSGSGTR--KRRSRWAD 142
           KD S     TT   RRR R+D  P++ G               D G+  +  +R+ RW+ 
Sbjct: 13  KDTSSSGSNTTPLARRR-RFDEGPADPGSAPHLDSFVVPPTRHDDGTKRQPGRRKQRWSH 71

Query: 143 DEPK--PVIQLPDFMKDFTGGIE-FDPEIQALNSRLLEISRMLQSG--LPLDDRPEGQRS 197
            E K   ++Q+P  +   TG +     E  A+  R+ EIS+ L+ G  +P    PE +RS
Sbjct: 72  GENKVADLLQMPTAL---TGHLTPEQAEAYAIYYRIEEISQQLRLGDIVP----PEDERS 124

Query: 198 PSPEPIYDNMGIRINTREYRARERLNKERQEIISQIIKRNPAFKPPADY-RPPKLQKKLY 256
           PSP P YD+MG R NTR+ R   +L +ER  +I +  +  P ++PP DY +P K Q+ +Y
Sbjct: 125 PSPPPQYDSMGKRTNTRDARYTRQLEEERHRLIERAQRLIPNYRPPVDYHKPAKTQEVVY 184

Query: 257 IPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSEN 316
           IP+ EYP  NFIG ++G RG T K+ME+E+GAKI IRG+GSVK+G+   + D+    +  
Sbjct: 185 IPVNEYPDINFIGQLLGARGKTLKKMEQESGAKICIRGRGSVKQGK--GRTDIPFQSTAE 242

Query: 317 EDLHVLVEAETQESLEGAAAMVEKLLQ---PVDEVLNEHKRQQLRELAALNGTIRDEEYC 373
           +DLH L+ +E +E +  A  +V++++     V E  NE KR QLRELAALNGT+RD+E  
Sbjct: 243 DDLHCLIISEDEEKIARAVQLVQQVIDTAASVPEGQNELKRSQLRELAALNGTLRDDE-- 300

Query: 374 RLCGEP----GHRQYACPSRTSTFKSDVLCKICGDGGHPTIDCLVKGT---TGKKMDDEY 426
              G P    G        R + F S ++C ICG  GH   DCL KGT   T +  D EY
Sbjct: 301 NYGGAPQSSSGDEMDDRNKRRNNFMSSIVCHICGSKGHFARDCLEKGTNAGTSENADREY 360

Query: 427 QNFLAELGGTLPESASKQSTTLALGPGSGSSGSNPPWANNSGSSGTP 473
              + EL G      + Q  ++A  P + +    PP    +GS+  P
Sbjct: 361 DALMRELQGEGVIDTASQQQSIAQNPNTNNVSKLPPAV--TGSNAAP 405

Necessary for the splicing of pre-mRNA. Has a role in the recognition of the branch site (5'-UACUAAC-3'), the pyrimidine tract and the 3'-splice site at the 3'-end of introns.

Yarrowia lipolytica (strain CLIB 122 / E 150) (taxid: 284591)

>sp|Q15637|SF01_HUMAN Splicing factor 1 OS=Homo sapiens GN=SF1 PE=1 SV=4

 Score =  210 bits (535), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 140/378 (37%), Positives = 209/378 (55%), Gaps = 53/378 (14%)

Query: 134 RKRRSRWADDEPKPVIQLPDFMKDFTGGIEFDPE-IQALNSRLLEISRMLQSG-LPLDDR 191
           +++RSRW  D  +    +P        G+  + E    +  ++ +++R L++G L +   
Sbjct: 16  KRKRSRWNQDTMEQKTVIPGMPTVIPPGLTREQERAYIVQLQIEDLTRKLRTGDLGIPPN 75

Query: 192 PEGQRSPSPEPIYDNMGIRINTREYRARERLNKERQEIISQIIKRNPAFKPPADYRPP-- 249
           PE  RSPSPEPIY++ G R+NTRE+R R++L +ER  +I++++  NP FKPPADY+PP  
Sbjct: 76  PE-DRSPSPEPIYNSEGKRLNTREFRTRKKLEEERHNLITEMVALNPDFKPPADYKPPAT 134

Query: 250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDL 309
           ++  K+ IP  EYP  NF+GL+IGPRGNT K +E+E  AKI+IRGKGSVKEG++ +K D 
Sbjct: 135 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRK-DG 193

Query: 310 KPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQ-----PVDEVLNEHKRQQLRELAALN 364
           +  P E+E LH LV A T E+++ A   +  +L+     P D+  N+ ++ QLRELA LN
Sbjct: 194 QMLPGEDEPLHALVTANTMENVKKAVEQIRNILKQGIETPEDQ--NDLRKMQLRELARLN 251

Query: 365 GTIRDEEYCRLCGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTIDCLVK-------GT 417
           GT+R+++   L      R +   S T +  +  +C  CG  GH   DC  +         
Sbjct: 252 GTLREDDNRIL------RPWQS-SETRSITNTTVCTKCGGAGHIASDCKFQRPGDPQSAQ 304

Query: 418 TGKKMDDEYQNFLAELGGTLPESASKQSTTLALGPGS----------------------G 455
              +MD EY + +AELG   P  AS  ST+   GP +                       
Sbjct: 305 DKARMDKEYLSLMAELG-EAPVPASVGSTS---GPATTPLASAPRPAAPANNPPPPSLMS 360

Query: 456 SSGSNPPWANNSGSSGTP 473
           ++ S PPW N+  S   P
Sbjct: 361 TTQSRPPWMNSGPSESRP 378

Necessary for the ATP-dependent first step of spliceosome assembly. Binds to the intron branch point sequence (BPS) 5'-UACUAAC-3' of the pre-mRNA. May act as transcription repressor.

Homo sapiens (taxid: 9606)

>sp|Q64213|SF01_MOUSE Splicing factor 1 OS=Mus musculus GN=Sf1 PE=1 SV=6

 Score =  210 bits (535), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 140/378 (37%), Positives = 209/378 (55%), Gaps = 53/378 (14%)

Query: 134 RKRRSRWADDEPKPVIQLPDFMKDFTGGIEFDPE-IQALNSRLLEISRMLQSG-LPLDDR 191
           +++RSRW  D  +    +P        G+  + E    +  ++ +++R L++G L +   
Sbjct: 16  KRKRSRWNQDTMEQKTVIPGMPTVIPPGLTREQERAYIVQLQIEDLTRKLRTGDLGIPPN 75

Query: 192 PEGQRSPSPEPIYDNMGIRINTREYRARERLNKERQEIISQIIKRNPAFKPPADYRPP-- 249
           PE  RSPSPEPIY++ G R+NTRE+R R++L +ER  +I++++  NP FKPPADY+PP  
Sbjct: 76  PE-DRSPSPEPIYNSEGKRLNTREFRTRKKLEEERHTLITEMVALNPDFKPPADYKPPAT 134

Query: 250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDL 309
           ++  K+ IP  EYP  NF+GL+IGPRGNT K +E+E  AKI+IRGKGSVKEG++ +K D 
Sbjct: 135 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRK-DG 193

Query: 310 KPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQ-----PVDEVLNEHKRQQLRELAALN 364
           +  P E+E LH LV A T E+++ A   +  +L+     P D+  N+ ++ QLRELA LN
Sbjct: 194 QMLPGEDEPLHALVTANTMENVKKAVEQIRNILKQGIETPEDQ--NDLRKMQLRELARLN 251

Query: 365 GTIRDEEYCRLCGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTIDCLVK-------GT 417
           GT+R+++   L      R +   S T +  +  +C  CG  GH   DC  +         
Sbjct: 252 GTLREDDNRIL------RPWQS-SETRSITNTTVCTKCGGAGHIASDCKFQRPGDPQSAQ 304

Query: 418 TGKKMDDEYQNFLAELGGTLPESASKQSTTLALGPGS----------------------G 455
              +MD EY + +AELG   P  AS  ST+   GP +                       
Sbjct: 305 DKARMDKEYLSLMAELGEA-PVPASVGSTS---GPATTPLASAPRPAAPASNPPPPSLMS 360

Query: 456 SSGSNPPWANNSGSSGTP 473
           ++ S PPW N+  S   P
Sbjct: 361 TTQSRPPWMNSGPSENRP 378

Necessary for the ATP-dependent first step of spliceosome assembly. Binds to the intron branch point sequence (BPS) 5'-UACUAAC-3' of the pre-mRNA. May act as transcription repressor.

Mus musculus (taxid: 10090)

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	797
449458337	777	PREDICTED: uncharacterized protein LOC10	0.937	0.961	0.757	0.0
449525351	778	PREDICTED: uncharacterized LOC101205455	0.937	0.960	0.755	0.0
224071499	794	predicted protein [Populus trichocarpa]	0.908	0.911	0.759	0.0
15241418	804	splicing factor 1 [Arabidopsis thaliana]	0.949	0.941	0.681	0.0
255539831	798	zinc finger protein, putative [Ricinus c	0.963	0.962	0.731	0.0
224138468	704	predicted protein [Populus trichocarpa]	0.851	0.964	0.789	0.0
13877739	804	unknown protein [Arabidopsis thaliana]	0.949	0.941	0.680	0.0
225461650	794	PREDICTED: uncharacterized protein LOC10	0.961	0.964	0.745	0.0
297795935	798	hypothetical protein ARALYDRAFT_495202 [	0.908	0.907	0.707	0.0
387169546	806	hypothetical protein 34G24.3 [Capsella r	0.947	0.936	0.675	0.0

>gi|449458337|ref|XP_004146904.1| PREDICTED: uncharacterized protein LOC101205455 [Cucumis sativus]

 Score = 1041 bits (2693), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 585/772 (75%), Positives = 640/772 (82%), Gaps = 25/772 (3%)

Query: 28  DHDSQNPPKTLAPPDAQNPQPASENGHDKNNENSCNNNNDVAAADYIKQKPLLSENGLTN 87
           DHD ++P   L     +N   +S NGH +N     +  N V   + I QKPL+SENG TN
Sbjct: 29  DHD-RDPNSLLKEIKGENSGFSSGNGHAENQ--PADGVNYVPKVEII-QKPLVSENGFTN 84

Query: 88  THSGTDKDQSGGEEETTSRRRRRSRWDPPPSESGGTEGNGDSGSGTRKRRSRWADDEPKP 147
           THSGTDKD SGGEEETTSRRRRRSRWDP P  +   +  G+SGSG RKR+SRWADD+PKP
Sbjct: 85  THSGTDKDFSGGEEETTSRRRRRSRWDPQPESN--EQSGGESGSGARKRKSRWADDDPKP 142

Query: 148 VIQLPDFMKDFTGGIEFDPEIQALNSRLLEISRMLQSGLPLDDRPEGQRSPSPEPIYDNM 207
           VIQLPDFM    GGIEFDPEIQALNSRLLEISRMLQSG+PLDDRPEG RSPSPEPIYDNM
Sbjct: 143 VIQLPDFM----GGIEFDPEIQALNSRLLEISRMLQSGMPLDDRPEGARSPSPEPIYDNM 198

Query: 208 GIRINTREYRARERLNKERQEIISQIIKRNPAFKPPADYRPPKLQKKLYIPMKEYPGYNF 267
           GIRINTREYRARE+LN ERQEIISQIIK+NPAFKPPADYRPPKLQKKLYIPMKEYPGYNF
Sbjct: 199 GIRINTREYRAREKLNTERQEIISQIIKKNPAFKPPADYRPPKLQKKLYIPMKEYPGYNF 258

Query: 268 IGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAET 327
           IGLIIGPRGNTQKRME++TGAKIVIRGKGSVKEGRLQQKRDLK DP+ENEDLHVLVEAET
Sbjct: 259 IGLIIGPRGNTQKRMEKQTGAKIVIRGKGSVKEGRLQQKRDLKHDPAENEDLHVLVEAET 318

Query: 328 QESLEGAAAMVEKLLQPVDEVLNEHKRQQLRELAALNGTIRDEEYCRLCGEPGHRQYACP 387
           QESLE AA MVEKLLQPVDEVLNEHKRQQLRELAALNGTIRDEE+CRLCGE GHRQYACP
Sbjct: 319 QESLEAAAEMVEKLLQPVDEVLNEHKRQQLRELAALNGTIRDEEFCRLCGEAGHRQYACP 378

Query: 388 SRTSTFKSDVLCKICGDGGHPTIDCLVKGTTGKKMDDEYQNFLAELGGTLPESASKQSTT 447
           SRTSTFKSDVLCKICGDGGHPTIDC VKGTTGKKMDDEYQNFLAELGGT+PESA+KQ+ T
Sbjct: 379 SRTSTFKSDVLCKICGDGGHPTIDCPVKGTTGKKMDDEYQNFLAELGGTIPESATKQTPT 438

Query: 448 LALGPGSGSSGSNPPWANNSGSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDG 507
           LA+  GSG+SG+NPPWANN+ S+       +G+NG KP KE DDTNLYIGYLPPT DDDG
Sbjct: 439 LAI--GSGTSGTNPPWANNTTSASNTPQASVGANGVKPAKEYDDTNLYIGYLPPTFDDDG 496

Query: 508 LIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV 567
           LIRLFSTFGDIVMAKVIKDRV+G+SKGYGFVKY+DIQMANNAIASMNGYRLEGRTIAVRV
Sbjct: 497 LIRLFSTFGDIVMAKVIKDRVSGLSKGYGFVKYSDIQMANNAIASMNGYRLEGRTIAVRV 556

Query: 568 AGKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPN-PPAASYTGAPVPWGP 626
           AGKPPQPTVPP PP ST+PTYPVS+ PVG YPSQQ+ PGGPL N PP  SY+  PVPWGP
Sbjct: 557 AGKPPQPTVPPCPPASTVPTYPVSSQPVGVYPSQQFMPGGPLGNVPPPTSYSATPVPWGP 616

Query: 627 PVPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATSS 686
           PVP PYA Y PPPPGS +YP V GQ MPPYGVQY   VQ       TAPPGAP+Q  TS 
Sbjct: 617 PVPSPYASYPPPPPGSNVYPAVQGQAMPPYGVQY-SQVQ-------TAPPGAPSQPVTSG 668

Query: 687 EAQQHSFPPGVQSESSSSAPAASANMYGSSMPPMPPNVQPAYATAPLGYSPYYNAVPPPP 746
           EAQQ SFPPG+ SE+ +S P  +   YG+++  MPP+ QP+Y  +  GYS YY+AV   P
Sbjct: 669 EAQQ-SFPPGLPSENPTSQPLQTT-AYGNTLYSMPPSAQPSYPPS-YGYSAYYSAVSTHP 725

Query: 747 PPAPVSAADHSQ-NLGNVPWATNPPVQPPVSSAEKSNYGADAEYEKFMAEMK 797
            P      D  Q   G  PWATNPP+ PP+ SAEK++ GADAEYEKFMA+MK
Sbjct: 726 LPMSAPTTDQPQPPSGAAPWATNPPMPPPMPSAEKTSSGADAEYEKFMADMK 777

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449525351|ref|XP_004169681.1| PREDICTED: uncharacterized LOC101205455 [Cucumis sativus]

 Score = 1036 bits (2680), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 584/773 (75%), Positives = 639/773 (82%), Gaps = 26/773 (3%)

Query: 28  DHDSQNPPKTLAPPDAQNPQPASENGHDKNNENSCNNNNDVAAADYIKQKPLLSENGLTN 87
           DHD ++P   L     +N   +S NGH +N     +  N V   + I QKPL+SENG TN
Sbjct: 29  DHD-RDPNSLLKEIKGENSGFSSGNGHAENQ--PADGVNYVPKVEII-QKPLVSENGFTN 84

Query: 88  THSGTDKDQSGGEEETTSRRRRRSRWDPPPSESGGTEGNGDSGSGTRKRRSRWADDEPKP 147
           THSGTDKD SGGEEETTSRRRRRSRWDP P  +   +  G+SGSG RKR+SRWADD+PKP
Sbjct: 85  THSGTDKDFSGGEEETTSRRRRRSRWDPQPESN--EQSGGESGSGARKRKSRWADDDPKP 142

Query: 148 VIQLPDFMKDFTGGIEFDPEIQALNSRLLEISRMLQSGLPLDDRPEGQRSPSPEPIYDNM 207
           VIQLPDFM    GGIEFDPEIQALNSRLLEISRMLQSG+PLDDRPEG RSPSPEPIYDNM
Sbjct: 143 VIQLPDFM----GGIEFDPEIQALNSRLLEISRMLQSGMPLDDRPEGARSPSPEPIYDNM 198

Query: 208 GIRINTREYRARERLNKERQEIISQIIKRNPAFKPPADYRPPKLQKKLYIPMKEYPGYNF 267
           GIRINTREYRARE+LN ERQEIISQIIK+NPAFKPPADYRPPKLQKKLYIPMKEYPGYNF
Sbjct: 199 GIRINTREYRAREKLNTERQEIISQIIKKNPAFKPPADYRPPKLQKKLYIPMKEYPGYNF 258

Query: 268 IGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAET 327
           IGLIIGPRGNTQKRME++TGAKIVIRGKGSVKEGRLQQKRDLK DP+ENEDLHVLVEAET
Sbjct: 259 IGLIIGPRGNTQKRMEKQTGAKIVIRGKGSVKEGRLQQKRDLKHDPAENEDLHVLVEAET 318

Query: 328 QESLEGAAAMVEKLLQPVDEVLNEHKRQQLRELAALNGTIRDEEYCRLCGEPGHRQYACP 387
           QESLE AA MVEKLLQPVDEVLNEHKRQQLRELAALNGTIRDEE+CRLCGE GHRQYACP
Sbjct: 319 QESLEAAAEMVEKLLQPVDEVLNEHKRQQLRELAALNGTIRDEEFCRLCGEAGHRQYACP 378

Query: 388 SRTSTFKSDVLCKICGDGGHPTIDCLVKGTTGKKMDDEYQNFLAELGGTLPESASKQSTT 447
           SRTSTFKSDVLCKICGDGGHPTIDC VKGTTGKKMDDEYQNFLAELGGT+PESA+KQ+ T
Sbjct: 379 SRTSTFKSDVLCKICGDGGHPTIDCPVKGTTGKKMDDEYQNFLAELGGTIPESATKQTPT 438

Query: 448 LALGPGSGSSGSNPPWANNSGSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDG 507
           LA+  GSG+SG+NPPWANN+ S+       +G+NG KP KE DDTNLYIGYLPPT DDDG
Sbjct: 439 LAI--GSGTSGTNPPWANNTTSASNTPQASVGANGVKPAKEYDDTNLYIGYLPPTFDDDG 496

Query: 508 LIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV 567
           LIRLFSTFGDIVMAKVIKDRV+G+SKGYGFVKY+DIQMANNAIASMNGYRLEGRTIAVRV
Sbjct: 497 LIRLFSTFGDIVMAKVIKDRVSGLSKGYGFVKYSDIQMANNAIASMNGYRLEGRTIAVRV 556

Query: 568 AGKPPQPTVPPGPPTSTMPTYPVSA-PPVGGYPSQQYAPGGPLPN-PPAASYTGAPVPWG 625
           AGKPPQPTVPP P  ST+PTYPVS+  PVG YPSQQ+ PGGPL N PP  SY+  PVPWG
Sbjct: 557 AGKPPQPTVPPCPSASTVPTYPVSSQQPVGVYPSQQFMPGGPLGNVPPPTSYSATPVPWG 616

Query: 626 PPVPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATS 685
           PPVP PYA Y PPPPGS +YP V GQ MPPYGVQY   VQ       TAPPGAP+Q  TS
Sbjct: 617 PPVPSPYASYPPPPPGSNVYPAVQGQAMPPYGVQY-SQVQ-------TAPPGAPSQPVTS 668

Query: 686 SEAQQHSFPPGVQSESSSSAPAASANMYGSSMPPMPPNVQPAYATAPLGYSPYYNAVPPP 745
            EAQQ SFPPG+ SE+ +S P  +   YG+++  MPP+ QP+Y  +  GYS YY+AV   
Sbjct: 669 GEAQQ-SFPPGLPSENPTSQPLQTT-AYGNTLYSMPPSAQPSYPPS-YGYSAYYSAVSTH 725

Query: 746 PPPAPVSAADHSQ-NLGNVPWATNPPVQPPVSSAEKSNYGADAEYEKFMAEMK 797
           P P      D  Q   G  PWATNPP+ PP+ SAEK++ GADAEYEKFMA+MK
Sbjct: 726 PLPMSAPTTDQPQPPSGAAPWATNPPMPPPMPSAEKTSSGADAEYEKFMADMK 778

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224071499|ref|XP_002303489.1| predicted protein [Populus trichocarpa] gi|222840921|gb|EEE78468.1| predicted protein [Populus trichocarpa]

 Score =  999 bits (2582), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 594/782 (75%), Positives = 637/782 (81%), Gaps = 58/782 (7%)

Query: 30  DSQNPPKTLAPPDAQNPQPASENGHDKNNENSCNNNNDVAAADYIKQKPLLSENGLTNTH 89
           D QNP KTL    +  PQ A ENGH   N  +     ++        K LLSENG+ NT+
Sbjct: 57  DPQNPHKTLI---SNPPQIAPENGH---NPQTTTPKPEIP-------KSLLSENGVANTN 103

Query: 90  SGTDKDQSGGEEETTSRRRRRSRWDPPPSESGGTEGNGDSGSGTRKRRSRWADDEPKPVI 149
           SG D+D SGGEEETTSRRRRRSRWDPP         N DSGSGTRKR+SRWADDEPKPVI
Sbjct: 104 SG-DRDCSGGEEETTSRRRRRSRWDPPADAGADGSNNNDSGSGTRKRKSRWADDEPKPVI 162

Query: 150 QLPDFMKDFTGGIEFDPEIQALNSRLLEISRMLQSGLPLDDRPEGQRSPSPEPIYDNMGI 209
           QLPDFMKDFTGGIEFDPEIQALN+RLLEISRMLQSGLPLDDRPEG RSPSPEPIYDNMGI
Sbjct: 163 QLPDFMKDFTGGIEFDPEIQALNARLLEISRMLQSGLPLDDRPEGARSPSPEPIYDNMGI 222

Query: 210 RINTREYRARERLNKERQEIISQIIKRNPAFKPPADYRPPKLQKKLYIPMKEYPGYNFIG 269
           RINTREYRARERLNKERQEIISQIIKRNPAFKPPADYRPPKLQKKLYIPMKEYPGYNFIG
Sbjct: 223 RINTREYRARERLNKERQEIISQIIKRNPAFKPPADYRPPKLQKKLYIPMKEYPGYNFIG 282

Query: 270 LIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQE 329
           LIIGPRGNTQKRMERETG KIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQE
Sbjct: 283 LIIGPRGNTQKRMERETGGKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQE 342

Query: 330 SLEGAAAMVEKLLQPVDEVLNEHKRQQLRELAALNGTIRDEEYCRLCGEPGHRQYACPSR 389
           +L+ AA MVEKLLQPVDEVLNEHKRQQLRELAALNGTIRDEEYCRLCGEPGHRQYACPSR
Sbjct: 343 ALDAAAGMVEKLLQPVDEVLNEHKRQQLRELAALNGTIRDEEYCRLCGEPGHRQYACPSR 402

Query: 390 TSTFKSDVLCKICGDGGHPTIDCLVKGTTGKKMDDEYQNFLAELGGTLPESASKQSTTLA 449
           TSTFKSDVLCKICGDGGHPTIDC +KGT GKKMDDEYQNFLAELGGT+PESA+KQ+ TLA
Sbjct: 403 TSTFKSDVLCKICGDGGHPTIDCPMKGTAGKKMDDEYQNFLAELGGTMPESATKQTATLA 462

Query: 450 LGPGSGSSGSNPPWA-NNSGSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGL 508
           L   S  SG+NPPWA +N+G  G+    GLG+NG KP KE DDTNLYIGYLPP LDDDGL
Sbjct: 463 L--ESSGSGNNPPWAGSNTGGLGSANQAGLGANGLKP-KEYDDTNLYIGYLPPNLDDDGL 519

Query: 509 IRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA 568
           I LFS+FG+IVMAKVIKDR+TG+SKGYGFVKY D+QMANNAIASMNGYR++GRTIAVRVA
Sbjct: 520 IGLFSSFGEIVMAKVIKDRITGLSKGYGFVKYCDVQMANNAIASMNGYRIDGRTIAVRVA 579

Query: 569 GKPPQPTVPPGPPTSTMPTYPVSAPPVGG-YPSQQYAPGGPLPNPP-------AASYTGA 620
           GKPPQPTVPPGPPTSTMP YP+   P+GG YPSQQ+  GGPLPN P        ASY G 
Sbjct: 580 GKPPQPTVPPGPPTSTMPAYPIPTQPLGGAYPSQQFTAGGPLPNGPPTSYVGAHASYRGT 639

Query: 621 PVPWGPPV----PPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPP 676
           PVPWGPPV     P   P  PPPPGSTMYPP+PGQP+PPYGVQYPPPVQ  P G L    
Sbjct: 640 PVPWGPPVPSPYGPYAPPPPPPPPGSTMYPPIPGQPIPPYGVQYPPPVQPVPSGTL---- 695

Query: 677 GAPTQTATSSEAQQHSFPPGVQSESSSSAPAASANMYGSSMPPMPPNVQPAYATAPLGYS 736
              TQT  SSEAQQ S+PPGV SE+S SAP A++N+YG S                +GYS
Sbjct: 696 ---TQTVASSEAQQ-SYPPGVPSENSLSAPLAASNVYGHS----------------IGYS 735

Query: 737 PYYNAVPPPPPPAPVSAADHSQNLGNVPWATNPPVQPP-VSSAEKSNYGADAEYEKFMAE 795
            YY+AV   PPP P  A DHSQ +GNVPWA+N  + PP  SSAEK+ YGADAEY KFMAE
Sbjct: 736 SYYSAV---PPPPPPPATDHSQGMGNVPWASNSTMPPPHSSSAEKARYGADAEYAKFMAE 792

Query: 796 MK 797
           MK
Sbjct: 793 MK 794

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15241418|ref|NP_199943.1| splicing factor 1 [Arabidopsis thaliana] gi|30696034|ref|NP_851169.1| splicing factor 1 [Arabidopsis thaliana] gi|79330558|ref|NP_001032055.1| splicing factor 1 [Arabidopsis thaliana] gi|8843867|dbj|BAA97393.1| unnamed protein product [Arabidopsis thaliana] gi|23297082|gb|AAN13087.1| unknown protein [Arabidopsis thaliana] gi|222423074|dbj|BAH19518.1| AT5G51300 [Arabidopsis thaliana] gi|222423561|dbj|BAH19750.1| AT5G51300 [Arabidopsis thaliana] gi|332008680|gb|AED96063.1| splicing factor 1 [Arabidopsis thaliana] gi|332008681|gb|AED96064.1| splicing factor 1 [Arabidopsis thaliana] gi|332008682|gb|AED96065.1| splicing factor 1 [Arabidopsis thaliana]

 Score =  997 bits (2577), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 575/844 (68%), Positives = 635/844 (75%), Gaps = 87/844 (10%)

Query: 1   MESTVESNPQYQTLDFNQNPPLPQDTLDHDSQNPPKTLAPPDAQNPQPASENGHDKNNEN 60
           MES   +NP  QTLD  Q PP        +    P  L   D  NPQ +     + ++  
Sbjct: 1   MESVEMNNPNSQTLD--QPPP------SSNGDTAPLAL---DHMNPQNSESVALNGSSTP 49

Query: 61  SCNNNNDVAAADYIKQKPLLSENGLTNTHSGTDKDQSGGEEETTSRRRRRSRWDPPPSES 120
             + N   A  + ++  PLLSENG++ T SG DKDQSGGEEETTSRR+RRSRWDPPPSES
Sbjct: 50  IPDTNGSSAKPELLR--PLLSENGVSKTLSGNDKDQSGGEEETTSRRKRRSRWDPPPSES 107

Query: 121 G---GTEGNGDSGSGTRKRRSRWADDEPKPVIQLPDFMKDFTGGIEFDPEIQALNSRLLE 177
                 EG  DSG+GTRKR+SRWADDEP+  IQLPDFMKDFTGGIEFDPEIQALNSRLLE
Sbjct: 108 INNPSAEGGTDSGTGTRKRKSRWADDEPRTQIQLPDFMKDFTGGIEFDPEIQALNSRLLE 167

Query: 178 ISRMLQSGLPLDDRPEGQRSPSPEPIYDNMGIRINTREYRARERLNKERQEIISQIIKRN 237
           ISRMLQSG+PLDDRPEGQRSPSPEP+YDNMGIRINTREYRARERLN+ERQEII+QIIK+N
Sbjct: 168 ISRMLQSGMPLDDRPEGQRSPSPEPVYDNMGIRINTREYRARERLNRERQEIIAQIIKKN 227

Query: 238 PAFKPPADYRPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGS 297
           PAFKPPADYRPPKL KKL+IPMKE+PGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGS
Sbjct: 228 PAFKPPADYRPPKLHKKLFIPMKEFPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGS 287

Query: 298 VKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQPVDEVLNEHKRQQL 357
           VKEGR QQK+DLK DPSENEDLHVLVEAETQE+LE AA MVEKLLQPVDEVLNEHKRQQL
Sbjct: 288 VKEGRHQQKKDLKYDPSENEDLHVLVEAETQEALEAAAGMVEKLLQPVDEVLNEHKRQQL 347

Query: 358 RELAALNGTIRDEEYCRLCGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTIDCLVKGT 417
           RELA LNGTIRDEE+CRLCGEPGHRQYACPSRT+TFKSDVLCKICGDGGHPTIDC VKGT
Sbjct: 348 RELATLNGTIRDEEFCRLCGEPGHRQYACPSRTNTFKSDVLCKICGDGGHPTIDCPVKGT 407

Query: 418 TGKKMDDEYQNFLAELGGTLPESASKQSTTLALGPGSGSSGSNPPWANNSGSSGTPGHPG 477
           TGKKMDDEYQNFLAELGGT+PES+ KQS TLALGP  GSSGSNPPWANN+G +G   HPG
Sbjct: 408 TGKKMDDEYQNFLAELGGTVPESSLKQSATLALGP--GSSGSNPPWANNAG-NGASAHPG 464

Query: 478 LGSNGAK-PIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYG 536
           LGS   K P KE D+TNLYIG+LPP L+DDGLI LFS+FG+IVMAKVIKDRVTG+SKGYG
Sbjct: 465 LGSTPTKPPSKEYDETNLYIGFLPPMLEDDGLINLFSSFGEIVMAKVIKDRVTGLSKGYG 524

Query: 537 FVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPGPPTSTMPT--YPVSAPP 594
           FVKYAD+QMAN A+ +MNGYR EGRT+AVR+AGK P P  PPGPP    PT  YP S  P
Sbjct: 525 FVKYADVQMANTAVQAMNGYRFEGRTLAVRIAGKSPPPIAPPGPPAPQPPTQGYPPSNQP 584

Query: 595 VGGYPSQQYAPGGPLPNPPAASYTGAPVPWGPPVPPPYAPYAPPPPGSTMYPPVPGQPMP 654
            G YPSQQYA GG         Y+ APVPWGPPV P Y+PYA PPP    Y PV GQ MP
Sbjct: 585 PGAYPSQQYATGG---------YSTAPVPWGPPV-PSYSPYALPPPPPGSYHPVHGQHMP 634

Query: 655 PYGVQYPPPVQTAPPGALTAPPGAPTQTATSSEAQQHSFPPGVQSESSSSAPAASANMYG 714
           PYG+QYPPP    PP    APP   TQ  +SSE QQ SFPPGVQ++S ++  +   N+YG
Sbjct: 635 PYGMQYPPP----PPHVTQAPPPGTTQNPSSSEPQQ-SFPPGVQADSGAATSSIPPNVYG 689

Query: 715 SSMPPMPPNVQPAYATAPLGYSPYYNAVPPPPPPAPVSAADHSQNLGNVPWATN------ 768
           SS+  MP   QP Y    + Y  YYNAVPPP PPAP S+ DHSQN+GN+PWA N      
Sbjct: 690 SSVTAMP--GQPPY----MSYPSYYNAVPPPTPPAPASSTDHSQNMGNMPWANNPSVSTP 743

Query: 769 -----------------------------------PPVQPPVSSAEKSNYGADAEYEKFM 793
                                              PPVQPP   AE  +   ++EYEKFM
Sbjct: 744 DHSQGLVNAPWAPNPPMPPTVGYSQSMGNVPWAPKPPVQPP---AENPSSVGESEYEKFM 800

Query: 794 AEMK 797
           AEMK
Sbjct: 801 AEMK 804

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255539831|ref|XP_002510980.1| zinc finger protein, putative [Ricinus communis] gi|223550095|gb|EEF51582.1| zinc finger protein, putative [Ricinus communis]

 Score =  997 bits (2577), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 597/816 (73%), Positives = 652/816 (79%), Gaps = 48/816 (5%)

Query: 8   NPQYQTLDFNQNPPLPQDTLDHDSQNPPKTLAPPDAQNPQPASENGHDK----NNENSCN 63
           N Q+Q+ D +Q PP   +TLD   +N P    P D    Q       D+    N +   N
Sbjct: 5   NHQFQSFDPSQPPP--PETLDSHFENHPPPPPPQDES--QILDSQNLDRTLNGNAQTILN 60

Query: 64  NNNDVAAADYIKQKPLLSENGLTNTHSGTDKDQSGGEEETTSRRRRRSRWDPPPSESGGT 123
           N ND A       KPLLSENGLTNT+SG D+D SGGEEETTSRRRRRSRWDPP   +  +
Sbjct: 61  NGNDTALK---IPKPLLSENGLTNTNSG-DRDFSGGEEETTSRRRRRSRWDPPADSTANS 116

Query: 124 E----------GNGDSGSG--TRKRRSRWADDEPKPVIQLPDFMKDFTGGIEFDPEIQAL 171
                       N DSG+G  TRKR+SRWADDEPKP IQLPDFMKDFTGGIEFDPEIQAL
Sbjct: 117 NSNNNSQSTDANNSDSGTGGTTRKRKSRWADDEPKPTIQLPDFMKDFTGGIEFDPEIQAL 176

Query: 172 NSRLLEISRMLQSGLPLDDRPEGQRSPSPEPIYDNMGIRINTREYRARERLNKERQEIIS 231
           N+RLLEI+R+ QSG+PLDDRPEG RSPSPEPIYDNMGIRINTRE+RARERL KERQ+I++
Sbjct: 177 NARLLEITRLFQSGMPLDDRPEGARSPSPEPIYDNMGIRINTREFRARERLTKERQDILT 236

Query: 232 QIIKRNPAFKPPADYRPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIV 291
           Q+IKRNPAFKPPADYRPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIV
Sbjct: 237 QMIKRNPAFKPPADYRPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIV 296

Query: 292 IRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQPVDEVLNE 351
           IRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQE+L+ AA MVEKLLQPVDEVLNE
Sbjct: 297 IRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQEALDAAAGMVEKLLQPVDEVLNE 356

Query: 352 HKRQQLRELAALNGTIRDEEYCRLCGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTID 411
           HKRQQLRELAALNGTIRDEEYCRLCGE GHRQYACPSRT+TFKSDVLCKICGDGGHPTID
Sbjct: 357 HKRQQLRELAALNGTIRDEEYCRLCGEQGHRQYACPSRTTTFKSDVLCKICGDGGHPTID 416

Query: 412 CLVKGTTGKKMDDEYQNFLAELGGTLPESASKQSTTLALGPGSGSSGSNPPW-ANNSGSS 470
           C VKGTTGKKMDDEYQNFLAELGGT+PES++KQ+ TLALGP  GSSGSNPPW ++N+G  
Sbjct: 417 CPVKGTTGKKMDDEYQNFLAELGGTMPESSTKQTATLALGP--GSSGSNPPWSSSNTGGL 474

Query: 471 GTPGHP-GLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVT 529
           G+     GLG+NG KPIKE DDTNLYIGYLPP LDDDGLI LFS FGDIVMAKVIKDRVT
Sbjct: 475 GSANQAGGLGANGVKPIKEYDDTNLYIGYLPPNLDDDGLIGLFSAFGDIVMAKVIKDRVT 534

Query: 530 GMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPGPPTSTMPTYP 589
           G+SKGYGFVKY DIQMANNAIASMNGYR++GRTIAVRVAGKPPQPTVPPGPP STMP YP
Sbjct: 535 GVSKGYGFVKYRDIQMANNAIASMNGYRIDGRTIAVRVAGKPPQPTVPPGPPASTMPAYP 594

Query: 590 VSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWG-------PPVPPPYAPYAPPPPGS 642
           +++ PVG YPSQQ+ PGGPLPN P A Y G P  +G       PPVPPPYAPYAPPPPGS
Sbjct: 595 IASQPVGAYPSQQFTPGGPLPNAPPAGYAGPPASYGGAPVPWGPPVPPPYAPYAPPPPGS 654

Query: 643 TMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATSSEAQQHSFPPGVQSESS 702
           TMYPPV            P P    PP    AP GAPT T TSSEAQQ S+PPGVQSE+S
Sbjct: 655 TMYPPV---------PGQPMPPYGYPPPVQPAPSGAPTPTVTSSEAQQ-SYPPGVQSENS 704

Query: 703 SSAPAASANMYGSSMPPMPPNVQPAYATAPLGYSPYYNAVPPPPPPAPVSAADHSQNLGN 762
           +SAP +S+N+Y SS+  +P   QPAY TA LGYS YYNAV P PPPAP S  DH+Q + N
Sbjct: 705 TSAPPSSSNIYCSSV-AVPSGAQPAYVTASLGYSSYYNAV-PTPPPAPASTGDHTQGISN 762

Query: 763 V-PWATNPPVQPPVSSAEKSNYGADAEYEKFMAEMK 797
           V      P   P  SS+EK+ YGAD+EYEKFMAEMK
Sbjct: 763 VPWAPNPPLPPPVSSSSEKTAYGADSEYEKFMAEMK 798

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224138468|ref|XP_002326610.1| predicted protein [Populus trichocarpa] gi|222833932|gb|EEE72409.1| predicted protein [Populus trichocarpa]

 Score =  996 bits (2576), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 569/721 (78%), Positives = 608/721 (84%), Gaps = 42/721 (5%)

Query: 77  KPLLSENGLTNTHSGTDKDQSGGEEETTSRRRRRSRWDPPPSESGGTEGNGDSGS----- 131
           KPLLSENG+ NT+SG D+D SGGEEETTSRRRRRSRWDPP        G G S +     
Sbjct: 6   KPLLSENGVANTNSG-DRDYSGGEEETTSRRRRRSRWDPPADSGTDGGGGGSSSNTNNND 64

Query: 132 ---GTRKRRSRWADDEPKPVIQLPDFMKDFTGGIEFDPEIQALNSRLLEISRMLQSGLPL 188
              GTRKR+SRWADDEPKPVIQLPDFMKDFTGGIEFDPEIQALN+RLLEISRMLQSGLPL
Sbjct: 65  SGSGTRKRKSRWADDEPKPVIQLPDFMKDFTGGIEFDPEIQALNARLLEISRMLQSGLPL 124

Query: 189 DDRPEGQRSPSPEPIYDNMGIRINTREYRARERLNKERQEIISQIIKRNPAFKPPADYRP 248
           DDRPEG RSPSPEPIYDNMGIRINTREYRARERLNKERQEIISQIIKRNPAFKPPADYRP
Sbjct: 125 DDRPEGARSPSPEPIYDNMGIRINTREYRARERLNKERQEIISQIIKRNPAFKPPADYRP 184

Query: 249 PKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRD 308
           PKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRD
Sbjct: 185 PKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRD 244

Query: 309 LKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQPVDEVLNEHKRQQLRELAALNGTIR 368
           LKPDPSENEDLHVLVEA+TQE+L+ AA MVEKLLQPVDEVLNEHKRQQLRELA LNGTIR
Sbjct: 245 LKPDPSENEDLHVLVEADTQEALDAAAGMVEKLLQPVDEVLNEHKRQQLRELATLNGTIR 304

Query: 369 DEEYCRLCGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTIDCLVKGTTGKKMDDEYQN 428
           DEEYCRLCGEPGHRQYACPSRT+TFKSDVLCKICGDGGHPTIDC +KGTTGKKMDDEYQN
Sbjct: 305 DEEYCRLCGEPGHRQYACPSRTTTFKSDVLCKICGDGGHPTIDCPMKGTTGKKMDDEYQN 364

Query: 429 FLAELGGTLPESASKQSTTLALGPGSGSSGSNPPWA-NNSGSSGTPGHPGLGSNGAKPIK 487
           FLAELGGT+PESA+KQ+ TLAL  GS  SGSNPPWA +N+G  G+    GLG+NG K +K
Sbjct: 365 FLAELGGTMPESATKQTATLAL--GSSGSGSNPPWASSNTGGLGSANQAGLGANGLK-LK 421

Query: 488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMAN 547
           E DDTNLYIGYLPP LDDDGLI LFS+FG+IVMAKVIKDR+TG+SKGYGFVKY D+QMAN
Sbjct: 422 EYDDTNLYIGYLPPNLDDDGLIGLFSSFGEIVMAKVIKDRITGLSKGYGFVKYRDVQMAN 481

Query: 548 NAIASMNGYRLEGRTIAVRVAGKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGG 607
           NAIASMNGYR++GRTIAVRVAGKPPQPTVPPGPP STMP YPVS  P+G Y SQQ+  GG
Sbjct: 482 NAIASMNGYRIDGRTIAVRVAGKPPQPTVPPGPPASTMPAYPVSTQPLGAYQSQQFTAGG 541

Query: 608 PLPNPPAASYTGA-------PVPWGPPV----PPPYAPYAPPPPGSTMYPPVPGQPMPPY 656
           PLPN P  SYTGA       PVPWG PV     P  AP  PPPPGSTMYPP+PGQPMPPY
Sbjct: 542 PLPNGPPTSYTGAPANYTGTPVPWGSPVPPPYAPYAAPPPPPPPGSTMYPPIPGQPMPPY 601

Query: 657 GVQYPPPVQTAPPGALTAPPGAPTQTATSSEAQQHSFPPGVQSESSSSAPAASANMYGSS 716
           GVQYPP VQ         PPGAPTQT T SEAQQ S+PPGV SE+S+SAP A++N+YG S
Sbjct: 602 GVQYPPLVQ-------PVPPGAPTQTVTPSEAQQ-SYPPGVPSENSTSAPPATSNVYGQS 653

Query: 717 MPPMPPNVQPAYATAPLGYSPYYNAVPPPPPPAPVSAADHSQNLGNVPWATNPPVQPPVS 776
                   QPAY T+ LGYS YY+AV   PPPAP     HSQ +GNVPWA+N  V PP S
Sbjct: 654 ------GAQPAYTTS-LGYSSYYSAV---PPPAPQPTTGHSQGMGNVPWASNLTVPPPHS 703

Query: 777 S 777
           S
Sbjct: 704 S 704

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|13877739|gb|AAK43947.1|AF370132_1 unknown protein [Arabidopsis thaliana]

 Score =  995 bits (2572), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 574/844 (68%), Positives = 634/844 (75%), Gaps = 87/844 (10%)

Query: 1   MESTVESNPQYQTLDFNQNPPLPQDTLDHDSQNPPKTLAPPDAQNPQPASENGHDKNNEN 60
           MES   +NP  QTLD  Q PP        +    P  L   D  NPQ +     + ++  
Sbjct: 1   MESVEMNNPNSQTLD--QPPP------SSNGDTAPLAL---DHMNPQNSESVALNGSSTP 49

Query: 61  SCNNNNDVAAADYIKQKPLLSENGLTNTHSGTDKDQSGGEEETTSRRRRRSRWDPPPSES 120
             + N   A  + ++  PLLSENG++ T SG DKDQSGGEEETTSRR+RRSRWDPPPSES
Sbjct: 50  IPDTNGSSAKPELLR--PLLSENGVSKTLSGNDKDQSGGEEETTSRRKRRSRWDPPPSES 107

Query: 121 G---GTEGNGDSGSGTRKRRSRWADDEPKPVIQLPDFMKDFTGGIEFDPEIQALNSRLLE 177
                 EG  DSG+ TRKR+SRWADDEP+  IQLPDFMKDFTGGIEFDPEIQALNSRLLE
Sbjct: 108 INNPSAEGGTDSGTETRKRKSRWADDEPRTQIQLPDFMKDFTGGIEFDPEIQALNSRLLE 167

Query: 178 ISRMLQSGLPLDDRPEGQRSPSPEPIYDNMGIRINTREYRARERLNKERQEIISQIIKRN 237
           ISRMLQSG+PLDDRPEGQRSPSPEP+YDNMGIRINTREYRARERLN+ERQEII+QIIK+N
Sbjct: 168 ISRMLQSGMPLDDRPEGQRSPSPEPVYDNMGIRINTREYRARERLNRERQEIIAQIIKKN 227

Query: 238 PAFKPPADYRPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGS 297
           PAFKPPADYRPPKL KKL+IPMKE+PGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGS
Sbjct: 228 PAFKPPADYRPPKLHKKLFIPMKEFPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGS 287

Query: 298 VKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQPVDEVLNEHKRQQL 357
           VKEGR QQK+DLK DPSENEDLHVLVEAETQE+LE AA MVEKLLQPVDEVLNEHKRQQL
Sbjct: 288 VKEGRHQQKKDLKYDPSENEDLHVLVEAETQEALEAAAGMVEKLLQPVDEVLNEHKRQQL 347

Query: 358 RELAALNGTIRDEEYCRLCGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTIDCLVKGT 417
           RELA LNGTIRDEE+CRLCGEPGHRQYACPSRT+TFKSDVLCKICGDGGHPTIDC VKGT
Sbjct: 348 RELATLNGTIRDEEFCRLCGEPGHRQYACPSRTNTFKSDVLCKICGDGGHPTIDCPVKGT 407

Query: 418 TGKKMDDEYQNFLAELGGTLPESASKQSTTLALGPGSGSSGSNPPWANNSGSSGTPGHPG 477
           TGKKMDDEYQNFLAELGGT+PES+ KQS TLALGP  GSSGSNPPWANN+G +G   HPG
Sbjct: 408 TGKKMDDEYQNFLAELGGTVPESSLKQSATLALGP--GSSGSNPPWANNAG-NGASAHPG 464

Query: 478 LGSNGAK-PIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYG 536
           LGS   K P KE D+TNLYIG+LPP L+DDGLI LFS+FG+IVMAKVIKDRVTG+SKGYG
Sbjct: 465 LGSTPTKPPSKEYDETNLYIGFLPPMLEDDGLINLFSSFGEIVMAKVIKDRVTGLSKGYG 524

Query: 537 FVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPGPPTSTMPT--YPVSAPP 594
           FVKYAD+QMAN A+ +MNGYR EGRT+AVR+AGK P P  PPGPP    PT  YP S  P
Sbjct: 525 FVKYADVQMANTAVQAMNGYRFEGRTLAVRIAGKSPPPIAPPGPPAPQPPTQGYPPSNQP 584

Query: 595 VGGYPSQQYAPGGPLPNPPAASYTGAPVPWGPPVPPPYAPYAPPPPGSTMYPPVPGQPMP 654
            G YPSQQYA GG         Y+ APVPWGPPV P Y+PYA PPP    Y PV GQ MP
Sbjct: 585 PGAYPSQQYATGG---------YSTAPVPWGPPV-PSYSPYALPPPPPGSYHPVHGQHMP 634

Query: 655 PYGVQYPPPVQTAPPGALTAPPGAPTQTATSSEAQQHSFPPGVQSESSSSAPAASANMYG 714
           PYG+QYPPP    PP    APP   TQ  +SSE QQ SFPPGVQ++S ++  +   N+YG
Sbjct: 635 PYGMQYPPP----PPHVTQAPPPGTTQNPSSSEPQQ-SFPPGVQADSGAATSSIPPNVYG 689

Query: 715 SSMPPMPPNVQPAYATAPLGYSPYYNAVPPPPPPAPVSAADHSQNLGNVPWATN------ 768
           SS+  MP   QP Y    + Y  YYNAVPPP PPAP S+ DHSQN+GN+PWA N      
Sbjct: 690 SSVTAMP--GQPPY----MSYPSYYNAVPPPTPPAPASSTDHSQNMGNMPWANNPSVSTP 743

Query: 769 -----------------------------------PPVQPPVSSAEKSNYGADAEYEKFM 793
                                              PPVQPP   AE  +   ++EYEKFM
Sbjct: 744 DHSQGLVNAPWAPNPPMPPTVGYSQSMGNVPWAPKPPVQPP---AENPSSVGESEYEKFM 800

Query: 794 AEMK 797
           AEMK
Sbjct: 801 AEMK 804

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225461650|ref|XP_002283115.1| PREDICTED: uncharacterized protein LOC100267539 [Vitis vinifera]

 Score =  992 bits (2565), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 583/782 (74%), Positives = 629/782 (80%), Gaps = 16/782 (2%)

Query: 18  QNPPLPQDTLDHDSQNPPKTLAP--PDAQNPQPASENGHDKNNENSCNNNNDVAAADYIK 75
           Q P  P  +LD   QNP KTLA   PD+ +P   S+N    +N    N         +  
Sbjct: 27  QYPSPPSQSLDSSFQNPSKTLASDHPDSISPNSDSQNLASFSN----NGQTHFEGPKFDL 82

Query: 76  QKPLLSENGLTNTHSGTDKDQSGGEEETTSRRRRRSRWDPPPSESGGTEGNGDSGSGTRK 135
           QKPL+SENG+TNT SGTDKD SGGEEETTSRRRRRSRWDPP      T G    G+G RK
Sbjct: 83  QKPLVSENGVTNTQSGTDKDYSGGEEETTSRRRRRSRWDPPSDSGNQTAGEAAEGTGARK 142

Query: 136 RRSRWADDEPKPVIQLPDFMKDFTGGIEFDPEIQALNSRLLEISRMLQSGLPLDDRPEGQ 195
           R+SRWADDEPKP+IQLPDFMKDFTGGIEFDPEIQALNSRLLEISRMLQSGLPLDDRPEG 
Sbjct: 143 RKSRWADDEPKPLIQLPDFMKDFTGGIEFDPEIQALNSRLLEISRMLQSGLPLDDRPEGA 202

Query: 196 RSPSPEPIYDNMGIRINTREYRARERLNKERQEIISQIIKRNPAFKPPADYRPPKLQKKL 255
           RSPSPEPIYDNMGIRINTREYRARERLN+ERQEIISQI+KRNPAFKPPADYRPPKLQKKL
Sbjct: 203 RSPSPEPIYDNMGIRINTREYRARERLNRERQEIISQILKRNPAFKPPADYRPPKLQKKL 262

Query: 256 YIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSE 315
           YIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSE
Sbjct: 263 YIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSE 322

Query: 316 NEDLHVLVEAETQESLEGAAAMVEKLLQPVDEVLNEHKRQQLRELAALNGTIRDEEYCRL 375
           NEDLHVLVEA+TQE+L+ AA MVEKLLQPVDEVLNEHKRQQLRELAALNGTIRDEEYCRL
Sbjct: 323 NEDLHVLVEADTQEALDAAAGMVEKLLQPVDEVLNEHKRQQLRELAALNGTIRDEEYCRL 382

Query: 376 CGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTIDCLVKGTTGKKMDDEYQNFLAELGG 435
           CGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTIDC VKGTTGKKMDDEYQNFLAELGG
Sbjct: 383 CGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTIDCPVKGTTGKKMDDEYQNFLAELGG 442

Query: 436 TLPESASKQSTTLALGPGSGSSGSNPPWANNSGSSGTPGHPGLGSNGAKPIKELDDTNLY 495
           T+P+S  K +  L +  GS  SGSNPPW+NN+G +      GLG+NGAKPIKE DDTNLY
Sbjct: 443 TVPDSLIKPNNALPI-TGSSGSGSNPPWSNNAGGT---AQAGLGANGAKPIKEYDDTNLY 498

Query: 496 IGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNG 555
           IGYLPPTL+DD LIRLFS FGDIVMAKVIKDRVTG+SKGYGFVKY+D+Q AN+AIASMNG
Sbjct: 499 IGYLPPTLEDDALIRLFSPFGDIVMAKVIKDRVTGLSKGYGFVKYSDVQQANSAIASMNG 558

Query: 556 YRLEGRTIAVRVAGKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAA 615
           YRLEGRTIAVRVAGKPPQP VPPGPP   MPTYP S   VG YPSQQ+  GGPL N P  
Sbjct: 559 YRLEGRTIAVRVAGKPPQPAVPPGPPPPAMPTYPSSNQAVGAYPSQQFTAGGPLGNTPPP 618

Query: 616 SYTGAPVPWGPPVPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAP 675
           SY         PVPPPYAPY PPPPGS++Y PVPGQP+      Y       PP   +  
Sbjct: 619 SYAPGAPVPWGPVPPPYAPYPPPPPGSSLYTPVPGQPV----PPYGVQYPPPPPPTQSVS 674

Query: 676 PGAPTQTATSSEAQQHSFPPGVQSESSSSAPAASANMYGSSMPPMPPNVQPAYATAPLGY 735
            GAP QT  SSEAQQ+ FPPGVQSES SS  +   ++YGSS+  +PPN QPAY+T+  GY
Sbjct: 675 AGAPAQTVVSSEAQQN-FPPGVQSESGSSVQSVPTSVYGSSLSAIPPNPQPAYSTSSYGY 733

Query: 736 SPYYNAVPPPPPPAPVSAADHSQNLGNVPWATNPPVQPPVSSAEKSNYGADAEYEKFMAE 795
           S Y  A  PPP P P   AD SQN+GN PW++ PPV PPV  AEK  +G DAEYEKFMAE
Sbjct: 734 SYYGVAP-PPPLPVPYPMADQSQNMGNAPWSSAPPVPPPVPPAEKKTHGTDAEYEKFMAE 792

Query: 796 MK 797
           MK
Sbjct: 793 MK 794

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297795935|ref|XP_002865852.1| hypothetical protein ARALYDRAFT_495202 [Arabidopsis lyrata subsp. lyrata] gi|297311687|gb|EFH42111.1| hypothetical protein ARALYDRAFT_495202 [Arabidopsis lyrata subsp. lyrata]

 Score =  981 bits (2537), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 561/793 (70%), Positives = 618/793 (77%), Gaps = 69/793 (8%)

Query: 49  ASENGHDKNNENSCNNNNDVAAADYIKQKPLLSENGLTNTHSGTDKDQSGGEEETTSRRR 108
           AS++ + +N+E+   N  + ++A     +PLLSENG++ T SG DKDQSGGEEETTSRR+
Sbjct: 31  ASDHMNPQNSESVTLNGTNGSSAKPEFLRPLLSENGVSKTLSGNDKDQSGGEEETTSRRK 90

Query: 109 RRSRWDPPPSESG---GTEGNGDSGSGTRKRRSRWADDEPKPVIQLPDFMKDFTGGIEFD 165
           RRSRWDPPPSESG     EG+ DSG+GTRKR+SRWADDEPKP IQLPDFMKDFTGGIEFD
Sbjct: 91  RRSRWDPPPSESGNNPSAEGSTDSGTGTRKRKSRWADDEPKPHIQLPDFMKDFTGGIEFD 150

Query: 166 PEIQALNSRLLEISRMLQSGLPLDDRPEGQRSPSPEPIYDNMGIRINTREYRARERLNKE 225
           PEIQALNSRLLEISRMLQSG+PLDDRPEGQRSPSPEP+YDNMGIRINTREYRARERLN+E
Sbjct: 151 PEIQALNSRLLEISRMLQSGMPLDDRPEGQRSPSPEPVYDNMGIRINTREYRARERLNRE 210

Query: 226 RQEIISQIIKRNPAFKPPADYRPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERE 285
           RQEII+QIIK+NPAFKPPADYRPPKL KKL+IPMKE+PGYNFIGLIIGPRGNTQKRMERE
Sbjct: 211 RQEIIAQIIKKNPAFKPPADYRPPKLHKKLFIPMKEFPGYNFIGLIIGPRGNTQKRMERE 270

Query: 286 TGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQPV 345
           TGAKIVIRGKGSVKEGR QQK+DLK DPSENEDLHVLVEAETQ++LE AA MVEKLLQPV
Sbjct: 271 TGAKIVIRGKGSVKEGRHQQKKDLKYDPSENEDLHVLVEAETQDALEAAAGMVEKLLQPV 330

Query: 346 DEVLNEHKRQQLRELAALNGTIRDEEYCRLCGEPGHRQYACPSRTSTFKSDVLCKICGDG 405
           DEVLNEHKRQQLRELA LNGTIRDEE+CRLCGEPGHRQYACPSRT+TFKSDVLCKICGDG
Sbjct: 331 DEVLNEHKRQQLRELATLNGTIRDEEFCRLCGEPGHRQYACPSRTNTFKSDVLCKICGDG 390

Query: 406 GHPTIDCLVKGTTGKKMDDEYQNFLAELGGTLPESASKQSTTLALGPGSGSSGSNPPWAN 465
           GHPTIDC VKGTTGKKMDDEYQNFLAELGGT+PES+ KQS TLALGP  GSSGSNPPWAN
Sbjct: 391 GHPTIDCPVKGTTGKKMDDEYQNFLAELGGTVPESSLKQSATLALGP--GSSGSNPPWAN 448

Query: 466 NSGSSGTPGHPGLGSNGAK-PIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVI 524
           N+G +G   HPGLGS   K P KE D+TNLYIG+LPP L+DDGLI LFS+FG+IVMAKVI
Sbjct: 449 NAG-NGASAHPGLGSTPTKPPSKEYDETNLYIGFLPPMLEDDGLINLFSSFGEIVMAKVI 507

Query: 525 KDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGK--PPQPTVPPGPPT 582
           KDRVTG+SKGYGFVKYAD+QMAN A+ +MNGYR EGRT+AVR+AGK  PP     P  P 
Sbjct: 508 KDRVTGLSKGYGFVKYADVQMANTAVQAMNGYRFEGRTLAVRIAGKVPPPTAPPGPPAPQ 567

Query: 583 STMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGPPVPPPYAPYAPPPPGS 642
                YP S  P G YPSQQYA GG         Y+ APVPWGPPV P Y+PYAPPPP  
Sbjct: 568 PPTQGYPPSNQPPGAYPSQQYATGG---------YSTAPVPWGPPV-PSYSPYAPPPPPP 617

Query: 643 TMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATSSEAQQHSFPPGVQSESS 702
             Y PV GQ M PYG+QYPPP    PP    APP   TQ   SSE QQ SFPPGVQ++ S
Sbjct: 618 GSYHPVHGQHMSPYGMQYPPP----PPHVTQAPPPGTTQNPASSEPQQ-SFPPGVQAD-S 671

Query: 703 SSAPAASANMYGSSMPPMPPNVQPAYATAPLGYSPYYNAVPPPPPPAPVSAADHSQNLGN 762
            SA +   N+YGSS+  MP   QP Y    + Y  YYNAVPPPPPPAP S+ DHSQN+GN
Sbjct: 672 GSATSVPPNVYGSSVTAMP--GQPPY----MSYQSYYNAVPPPPPPAPASSTDHSQNMGN 725

Query: 763 VPWATNPPVQPPVSS--------------------------------------AEKSNYG 784
           +PWA NPPV  P  S                                      AE  +  
Sbjct: 726 MPWANNPPVSTPDHSQGPGNAHWAPTPPMPPTVGYSQSMGNVPWAPKPPVQPPAENPSAV 785

Query: 785 ADAEYEKFMAEMK 797
            D+EYEKFMAEMK
Sbjct: 786 GDSEYEKFMAEMK 798

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|387169546|gb|AFJ66205.1| hypothetical protein 34G24.3 [Capsella rubella]

 Score =  949 bits (2452), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 565/836 (67%), Positives = 622/836 (74%), Gaps = 81/836 (9%)

Query: 6   ESNPQYQTLDFNQNPPLPQDTLDHDSQNPPKTLAPPDAQNPQPASENGHDKNNENSCNNN 65
           +SNP   TL  NQ PP         S N        D  NP   ++NG    N ++   N
Sbjct: 8   DSNPNSHTL--NQPPP---------SSNGDTAPLASDHLNPDSLAQNGSSAPNPDT---N 53

Query: 66  NDVAAADYIKQKPLLSENGLTNTHSGTDKDQSGGEEETTSRRRRRSRWDPPPSESGG--- 122
             VA  ++++  PL+SENG++ T SG DKDQSGGEEETTSRR+RRSRWDPPPSES     
Sbjct: 54  GSVAKPEFLR--PLISENGVSKTLSGNDKDQSGGEEETTSRRKRRSRWDPPPSESINNPS 111

Query: 123 TEGNGDSGSGTRKRRSRWADDEPKPVIQLPDFMKDFTGGIEFDPEIQALNSRLLEISRML 182
            EG  DSG+GTRKR+SRWADDEPKP IQLPDFMKDFTGGIEFDPEIQALNSRLLEISRML
Sbjct: 112 AEGGNDSGTGTRKRKSRWADDEPKPQIQLPDFMKDFTGGIEFDPEIQALNSRLLEISRML 171

Query: 183 QSGLPLDDRPEGQRSPSPEPIYDNMGIRINTREYRARERLNKERQEIISQIIKRNPAFKP 242
           QSG+PLDDRPEGQRSPSPEP+YDNMGIRINTREYRARERLN+ERQEII+QIIK+NPAFKP
Sbjct: 172 QSGMPLDDRPEGQRSPSPEPVYDNMGIRINTREYRARERLNRERQEIIAQIIKKNPAFKP 231

Query: 243 PADYRPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGR 302
           PADYRPPKLQKKL+IPMKE+PGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGR
Sbjct: 232 PADYRPPKLQKKLFIPMKEFPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGR 291

Query: 303 LQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQPVDEVLNEHKRQQLRELAA 362
            QQK+DLK DPSENEDLHVLVEAETQ++LE AA MVEKLLQPVDEVLNEHKRQQLRELA 
Sbjct: 292 HQQKKDLKYDPSENEDLHVLVEAETQDALEAAAGMVEKLLQPVDEVLNEHKRQQLRELAT 351

Query: 363 LNGTIRDEEYCRLCGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTIDCLVKGTTGKKM 422
           LNGTIRDEE+CR CGEPGHRQYACPSRT+TFKSDVLCKICGDGGHPTIDC VKGTTGKKM
Sbjct: 352 LNGTIRDEEFCRQCGEPGHRQYACPSRTNTFKSDVLCKICGDGGHPTIDCPVKGTTGKKM 411

Query: 423 DDEYQNFLAELGGTLPESASKQSTTLALGPGSGSSGSNPPWANNSGSSGTPGHPGLGSNG 482
           DDEYQNFLAELGGT+PES+ KQS TLALGPGS  SGSNPPWANN+G+ G   HPGLGS  
Sbjct: 412 DDEYQNFLAELGGTVPESSLKQSATLALGPGS--SGSNPPWANNAGN-GASAHPGLGSTP 468

Query: 483 AKP-IKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYA 541
           +KP  KE D+TNLYIG+LPP LDDDGLI LFS+FG+IVMAKVIKDRVTG+SK YGFVKYA
Sbjct: 469 SKPPSKEYDETNLYIGFLPPMLDDDGLINLFSSFGEIVMAKVIKDRVTGLSKTYGFVKYA 528

Query: 542 DIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPGPPTSTMPT--YPVSAPPVGGYP 599
           D+QMAN A+ +MNGYR EGRT+AVR+AGK P P  PPGPP    PT  YP S  P G YP
Sbjct: 529 DVQMANTAVQAMNGYRFEGRTLAVRIAGKMPPPAAPPGPPAPQAPTQGYPPSNQPPGAYP 588

Query: 600 SQQYAPGGPLPNPPAASYTGAPVPWGPPVPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQ 659
           SQQYA GG LPNPP   Y+ APVPWGPPVP       PPPP  + +P V GQ MPPYG+Q
Sbjct: 589 SQQYATGGQLPNPPVG-YSTAPVPWGPPVPSYSPYAPPPPPPGSYHP-VHGQHMPPYGMQ 646

Query: 660 YPPPVQTAPPGALTAPPGAPTQTATSSEAQQHSFPPGVQSESSSSAPAASANMYGSS-MP 718
           YPPP       A        TQ  +SSE QQ SFPPGVQ++  ++  +   N+YGS+ MP
Sbjct: 647 YPPPPPPHVAQAPPP---GTTQNPSSSEPQQ-SFPPGVQADGGAATSSVPPNVYGSTAMP 702

Query: 719 PMPPNVQPAYATAPLGYSPYYNAVP-------------------PPPPPAPVSAADHSQN 759
             PP          + Y  YYNAVP                   P     PVS  DHSQ 
Sbjct: 703 GQPPY---------MSYPSYYNAVPPPPPAPASSTDHSQNMGNMPWANNPPVSTPDHSQG 753

Query: 760 L------------------GNVPWATNPPVQPPVSSAEKSNYGADAEYEKFMAEMK 797
           L                   N PWA  PPVQPP   AE  +   D+EYEKFMAEMK
Sbjct: 754 LVNAPWAPNPPMPPSVGYSQNAPWAPKPPVQPP---AENPSSVGDSEYEKFMAEMK 806

Source: Capsella rubella

Species: Capsella rubella

Genus: Capsella

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	797
TAIR|locus:2176222	804	AT5G51300 [Arabidopsis thalian	0.736	0.730	0.678	7.8e-225
ASPGD|ASPL0000074583	554	AN10615 [Emericella nidulans (	0.338	0.487	0.479	9.8e-66
FB|FBgn0025571	787	SF1 "Splicing factor 1" [Droso	0.385	0.390	0.423	5.4e-63
UNIPROTKB|A2VDM7	639	SF1 "Uncharacterized protein"	0.381	0.475	0.402	2.6e-61
UNIPROTKB|Q15637	639	SF1 "Splicing factor 1" [Homo	0.381	0.475	0.402	2.6e-61
UNIPROTKB|F1RQR0	639	SF1 "Uncharacterized protein"	0.381	0.475	0.402	2.6e-61
UNIPROTKB|E2RRT4	638	SF1 "Uncharacterized protein"	0.381	0.476	0.402	2.6e-61
ZFIN|ZDB-GENE-030131-2492	663	sf1 "splicing factor 1" [Danio	0.373	0.449	0.408	9.6e-60
POMBASE|SPCC962.06c	587	bpb1 "zinc finger splicing fac	0.331	0.449	0.455	1.3e-59
MGI|MGI:1095403	653	Sf1 "splicing factor 1" [Mus m	0.381	0.465	0.402	1.4e-58

TAIR|locus:2176222 AT5G51300 [Arabidopsis thaliana (taxid:3702)]

 Score = 2032 (720.4 bits), Expect = 7.8e-225, Sum P(3) = 7.8e-225
 Identities = 413/609 (67%), Positives = 449/609 (73%)

Query:     1 MESTVESNPQYQTLDFNQNPPLPQDTLDHDSQNPPKTLAPPDAQNPQPASENGHDKXXXX 60
             MES   +NP  QTLD  Q PP        +    P  L   + QN +  + NG       
Sbjct:     1 MESVEMNNPNSQTLD--QPPP------SSNGDTAPLALDHMNPQNSESVALNGSSTPIPD 52

Query:    61 XXXXXXDVAAADYIKQKPLLSENGLTNTHSGTDKDQXXXXXXXXXXXXXXXXWDPPPXXX 120
                     A  + ++  PLLSENG++ T SG DKDQ                WDPPP   
Sbjct:    53 TNGSS---AKPELLR--PLLSENGVSKTLSGNDKDQSGGEEETTSRRKRRSRWDPPPSES 107

Query:   121 X---XXXXXXXXXXXXRKRRSRWADDEPKPVIQLPDFMKDFTGGIEFDPEIQALNSRLLE 177
                             RKR+SRWADDEP+  IQLPDFMKDFTGGIEFDPEIQALNSRLLE
Sbjct:   108 INNPSAEGGTDSGTGTRKRKSRWADDEPRTQIQLPDFMKDFTGGIEFDPEIQALNSRLLE 167

Query:   178 ISRMLQSGLPLDDRPEGQRSPSPEPIYDNMGIRINTREYRARERLNKERQEIISQIIKRN 237
             ISRMLQSG+PLDDRPEGQRSPSPEP+YDNMGIRINTREYRARERLN+ERQEII+QIIK+N
Sbjct:   168 ISRMLQSGMPLDDRPEGQRSPSPEPVYDNMGIRINTREYRARERLNRERQEIIAQIIKKN 227

Query:   238 PAFKPPADYRPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGS 297
             PAFKPPADYRPPKL KKL+IPMKE+PGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGS
Sbjct:   228 PAFKPPADYRPPKLHKKLFIPMKEFPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGS 287

Query:   298 VKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQPVDEVLNEHKRQQL 357
             VKEGR QQK+DLK DPSENEDLHVLVEAETQE+LE AA MVEKLLQPVDEVLNEHKRQQL
Sbjct:   288 VKEGRHQQKKDLKYDPSENEDLHVLVEAETQEALEAAAGMVEKLLQPVDEVLNEHKRQQL 347

Query:   358 RELAALNGTIRDEEYCRLCGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTIDCLVKGT 417
             RELA LNGTIRDEE+CRLCGEPGHRQYACPSRT+TFKSDVLCKICGDGGHPTIDC VKGT
Sbjct:   348 RELATLNGTIRDEEFCRLCGEPGHRQYACPSRTNTFKSDVLCKICGDGGHPTIDCPVKGT 407

Query:   418 TGKKMDDEYQNFLAELGGTLPESASKQSTTLALXXXXXXXXXXXXXXXXXXXXXTPGHPG 477
             TGKKMDDEYQNFLAELGGT+PES+ KQS TLAL                        HPG
Sbjct:   408 TGKKMDDEYQNFLAELGGTVPESSLKQSATLALGPGSSGSNPPWANNAGNGASA---HPG 464

Query:   478 LGSNGAKP-IKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYG 536
             LGS   KP  KE D+TNLYIG+LPP L+DDGLI LFS+FG+IVMAKVIKDRVTG+SKGYG
Sbjct:   465 LGSTPTKPPSKEYDETNLYIGFLPPMLEDDGLINLFSSFGEIVMAKVIKDRVTGLSKGYG 524

Query:   537 FVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKXXXXXXXXXXXXXXXXXXXV--SAPP 594
             FVKYAD+QMAN A+ +MNGYR EGRT+AVR+AGK                      S  P
Sbjct:   525 FVKYADVQMANTAVQAMNGYRFEGRTLAVRIAGKSPPPIAPPGPPAPQPPTQGYPPSNQP 584

Query:   595 VGGYPSQQY 603
              G YPSQQY
Sbjct:   585 PGAYPSQQY 593

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0008380 "RNA splicing" evidence=NAS

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

ASPGD|ASPL0000074583 AN10615 [Emericella nidulans (taxid:162425)]

 Score = 644 (231.8 bits), Expect = 9.8e-66, Sum P(2) = 9.8e-66
 Identities = 139/290 (47%), Positives = 192/290 (66%)

Query:   134 RKRRSRWAD-DEPKP--VIQLPDF-MKDFTGGIEFDPEIQALNSRLLEISRMLQSGLPLD 189
             RK+R+RW D  E K   ++ LP   M +FT   E   E   L+ R+ EIS+ L+     D
Sbjct:    59 RKKRNRWGDAQENKAAGLMGLPTMIMANFT--TE-QLEAYTLHLRIEEISQKLRIN---D 112

Query:   190 DRP-EGQRSPSPEPIYDNMGIRINTREYRARERLNKERQEIISQIIKRNPAFKPPADYR- 247
               P +G RSPSP P YDN G R+NTREYR R+RL  ER +++ + IK  P + PP+DYR 
Sbjct:   113 VVPADGDRSPSPPPQYDNFGRRVNTREYRYRKRLEDERHKLVEKAIKTIPNYHPPSDYRR 172

Query:   248 PPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKR 307
             P K Q+K+Y+P+ +YP  NFIGL+IGPRGNT K+ME E+GAKI IRGKGSVKEG+   + 
Sbjct:   173 PTKTQEKVYVPVNDYPEINFIGLLIGPRGNTLKKMETESGAKIAIRGKGSVKEGK--GRS 230

Query:   308 DLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQP---VDEVLNEHKRQQLRELAALN 364
             D     ++ EDLH L+ A+T+E +  A  +V  +++    + E  NE KR QLRELAALN
Sbjct:   231 DAAHASNQEEDLHCLIMADTEEKVNKAKKLVHNVIETAASIPEGQNELKRNQLRELAALN 290

Query:   365 GTIRDEEY--CRLCGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTIDC 412
             GT+RD+E   C+ CG+ GHR+Y CP + + F ++++C++CG+ GH   DC
Sbjct:   291 GTLRDDENQACQNCGQIGHRKYDCPEQRN-FTANIICRVCGNAGHMARDC 339

GO:0000349 "generation of catalytic spliceosome for first transesterification step" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005829 "cytosol" evidence=IEA

GO:0000243 "commitment complex" evidence=IEA

FB|FBgn0025571 SF1 "Splicing factor 1" [Drosophila melanogaster (taxid:7227)]

 Score = 617 (222.3 bits), Expect = 5.4e-63, Sum P(2) = 5.4e-63
 Identities = 141/333 (42%), Positives = 204/333 (61%)

Query:   134 RKRRSRWADDE-PKPVIQ-LPDFMKDFTGGIEFDPEIQALNSRLLEISRMLQSG-LPLDD 190
             RKR+SRW   E  K  I  +P  +       +   E   +  ++ EISR L++G L +  
Sbjct:   272 RKRKSRWGGSENDKTFIPGMPTILPSTLDPAQ--QEAYLVQFQIEEISRKLRTGDLGITQ 329

Query:   191 RPEGQRSPSPEPIYDNMGIRINTREYRARERLNKERQEIISQIIKRNPAFKPPADYRPP- 249
              PE +RSPSPEPIY + G R+NTRE+R R+RL ++R ++I ++   NP FKPPADY+PP 
Sbjct:   330 NPE-ERSPSPEPIYSSDGKRLNTREFRYRKRLEEQRHQLIVKMQTVNPEFKPPADYKPPV 388

Query:   250 -KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRD 308
              ++  K+ IP +++P  NF+GL+IGPRGNT K ME++TGAKI+IRGKGSVKEG++ +K D
Sbjct:   389 TRVSDKVLIPQEQHPDINFVGLLIGPRGNTLKAMEKDTGAKIIIRGKGSVKEGKVGRK-D 447

Query:   309 LKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQP---VDEVLNEHKRQQLRELAALNG 365
              +P P E+E LH  + A   E++  A   ++ +++    V E  N+ +R QLRELA LNG
Sbjct:   448 GQPLPGEDEPLHAFITAPNPEAVRKAVDKIKDVIRQGIEVPEGHNDLRRMQLRELAQLNG 507

Query:   366 TIRDEEYCRL-CGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTIDCLVK----GTTGK 420
             T+R+ +  R  CG   H+ + CP +     + ++C  CG  GH T DC  K    G  G 
Sbjct:   508 TLRENDIQRCTCGSTDHKSWQCPDKP-IITNTIVCTSCGGTGHLTKDCRNKRPGSGVPGM 566

Query:   421 -------KMDDEYQNFLAELG-GTLPESASKQS 445
                    K+D+EY + +AELG G  P SAS ++
Sbjct:   567 ACEDSQAKIDEEYMSLMAELGEGPPPPSASAKT 599

GO:0005634 "nucleus" evidence=IDA

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

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0071011 "precatalytic spliceosome" evidence=IDA

GO:0002121 "inter-male aggressive behavior" evidence=IMP

GO:0007476 "imaginal disc-derived wing morphogenesis" evidence=IMP

GO:0022008 "neurogenesis" evidence=IMP

UNIPROTKB|A2VDM7 SF1 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 562 (202.9 bits), Expect = 2.6e-61, Sum P(3) = 2.6e-61
 Identities = 132/328 (40%), Positives = 198/328 (60%)

Query:   134 RKRRSRWADDEPKPVIQLPDFMKDFTGGIEFDPE-IQALNSRLLEISRMLQSG-LPLDDR 191
             +++RSRW  D  +    +P        G+  + E    +  ++ +++R L++G L +   
Sbjct:    16 KRKRSRWNQDTMEQKTVIPGMPTVIPPGLTREQERAYIVQLQIEDLTRKLRTGDLGIPPN 75

Query:   192 PEGQRSPSPEPIYDNMGIRINTREYRARERLNKERQEIISQIIKRNPAFKPPADYRPP-- 249
             PE  RSPSPEPIY++ G R+NTRE+R R++L +ER  +I++++  NP FKPPADY+PP  
Sbjct:    76 PE-DRSPSPEPIYNSEGKRLNTREFRTRKKLEEERHNLITEMVALNPDFKPPADYKPPAT 134

Query:   250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDL 309
             ++  K+ IP  EYP  NF+GL+IGPRGNT K +E+E  AKI+IRGKGSVKEG++ +K D 
Sbjct:   135 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRK-DG 193

Query:   310 KPDPSENEDLHVLVEAETQESLEGAAAMVEKLL-QPVD--EVLNEHKRQQLRELAALNGT 366
             +  P E+E LH LV A T E+++ A   +  +L Q ++  E  N+ ++ QLRELA LNGT
Sbjct:   194 QMLPGEDEPLHALVTANTMENVKKAVEQIRNILKQGIETPEDQNDLRKMQLRELARLNGT 253

Query:   367 IRDEEYCRLCGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTIDCLVK------GTTGK 420
             +R+++  R+      R +   S T +  +  +C  CG  GH   DC  +          K
Sbjct:   254 LREDDN-RIL-----RPWQS-SETRSITNTTVCTKCGGAGHIASDCKFQRPGDPQSAQDK 306

Query:   421 -KMDDEYQNFLAELGGTLPESASKQSTT 447
              +MD EY + +AELG   P  AS  ST+
Sbjct:   307 ARMDKEYLSLMAELGEA-PVPASVGSTS 333

GO:0050810 "regulation of steroid biosynthetic process" evidence=IEA

GO:0033327 "Leydig cell differentiation" evidence=IEA

GO:0030238 "male sex determination" evidence=IEA

GO:0022402 "cell cycle process" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|Q15637 SF1 "Splicing factor 1" [Homo sapiens (taxid:9606)]

 Score = 562 (202.9 bits), Expect = 2.6e-61, Sum P(3) = 2.6e-61
 Identities = 132/328 (40%), Positives = 198/328 (60%)

Query:   134 RKRRSRWADDEPKPVIQLPDFMKDFTGGIEFDPE-IQALNSRLLEISRMLQSG-LPLDDR 191
             +++RSRW  D  +    +P        G+  + E    +  ++ +++R L++G L +   
Sbjct:    16 KRKRSRWNQDTMEQKTVIPGMPTVIPPGLTREQERAYIVQLQIEDLTRKLRTGDLGIPPN 75

Query:   192 PEGQRSPSPEPIYDNMGIRINTREYRARERLNKERQEIISQIIKRNPAFKPPADYRPP-- 249
             PE  RSPSPEPIY++ G R+NTRE+R R++L +ER  +I++++  NP FKPPADY+PP  
Sbjct:    76 PE-DRSPSPEPIYNSEGKRLNTREFRTRKKLEEERHNLITEMVALNPDFKPPADYKPPAT 134

Query:   250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDL 309
             ++  K+ IP  EYP  NF+GL+IGPRGNT K +E+E  AKI+IRGKGSVKEG++ +K D 
Sbjct:   135 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRK-DG 193

Query:   310 KPDPSENEDLHVLVEAETQESLEGAAAMVEKLL-QPVD--EVLNEHKRQQLRELAALNGT 366
             +  P E+E LH LV A T E+++ A   +  +L Q ++  E  N+ ++ QLRELA LNGT
Sbjct:   194 QMLPGEDEPLHALVTANTMENVKKAVEQIRNILKQGIETPEDQNDLRKMQLRELARLNGT 253

Query:   367 IRDEEYCRLCGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTIDCLVK------GTTGK 420
             +R+++  R+      R +   S T +  +  +C  CG  GH   DC  +          K
Sbjct:   254 LREDDN-RIL-----RPWQS-SETRSITNTTVCTKCGGAGHIASDCKFQRPGDPQSAQDK 306

Query:   421 -KMDDEYQNFLAELGGTLPESASKQSTT 447
              +MD EY + +AELG   P  AS  ST+
Sbjct:   307 ARMDKEYLSLMAELGEA-PVPASVGSTS 333

GO:0008270 "zinc ion binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0022402 "cell cycle process" evidence=IEA

GO:0030238 "male sex determination" evidence=IEA

GO:0033327 "Leydig cell differentiation" evidence=IEA

GO:0050810 "regulation of steroid biosynthetic process" evidence=IEA

GO:0003723 "RNA binding" evidence=TAS

GO:0000245 "spliceosomal complex assembly" evidence=NAS

GO:0005840 "ribosome" evidence=NAS

GO:0003676 "nucleic acid binding" evidence=NAS

GO:0005634 "nucleus" evidence=IDA;NAS

GO:0003714 "transcription corepressor activity" evidence=TAS

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

GO:0005681 "spliceosomal complex" evidence=IDA

GO:0000389 "mRNA 3'-splice site recognition" evidence=TAS

GO:0005730 "nucleolus" evidence=IDA

UNIPROTKB|F1RQR0 SF1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 562 (202.9 bits), Expect = 2.6e-61, Sum P(3) = 2.6e-61
 Identities = 132/328 (40%), Positives = 198/328 (60%)

Query:   134 RKRRSRWADDEPKPVIQLPDFMKDFTGGIEFDPE-IQALNSRLLEISRMLQSG-LPLDDR 191
             +++RSRW  D  +    +P        G+  + E    +  ++ +++R L++G L +   
Sbjct:    16 KRKRSRWNQDTMEQKTVIPGMPTVIPPGLTREQERAYIVQLQIEDLTRKLRTGDLGIPPN 75

Query:   192 PEGQRSPSPEPIYDNMGIRINTREYRARERLNKERQEIISQIIKRNPAFKPPADYRPP-- 249
             PE  RSPSPEPIY++ G R+NTRE+R R++L +ER  +I++++  NP FKPPADY+PP  
Sbjct:    76 PE-DRSPSPEPIYNSEGKRLNTREFRTRKKLEEERHNLITEMVALNPDFKPPADYKPPAT 134

Query:   250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDL 309
             ++  K+ IP  EYP  NF+GL+IGPRGNT K +E+E  AKI+IRGKGSVKEG++ +K D 
Sbjct:   135 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRK-DG 193

Query:   310 KPDPSENEDLHVLVEAETQESLEGAAAMVEKLL-QPVD--EVLNEHKRQQLRELAALNGT 366
             +  P E+E LH LV A T E+++ A   +  +L Q ++  E  N+ ++ QLRELA LNGT
Sbjct:   194 QMLPGEDEPLHALVTANTMENVKKAVEQIRNILKQGIETPEDQNDLRKMQLRELARLNGT 253

Query:   367 IRDEEYCRLCGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTIDCLVK------GTTGK 420
             +R+++  R+      R +   S T +  +  +C  CG  GH   DC  +          K
Sbjct:   254 LREDDN-RIL-----RPWQS-SETRSITNTTVCTKCGGAGHIASDCKFQRPGDPQSAQDK 306

Query:   421 -KMDDEYQNFLAELGGTLPESASKQSTT 447
              +MD EY + +AELG   P  AS  ST+
Sbjct:   307 ARMDKEYLSLMAELGEA-PVPASVGSTS 333

GO:0050810 "regulation of steroid biosynthetic process" evidence=IEA

GO:0033327 "Leydig cell differentiation" evidence=IEA

GO:0030238 "male sex determination" evidence=IEA

GO:0022402 "cell cycle process" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|E2RRT4 SF1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 562 (202.9 bits), Expect = 2.6e-61, Sum P(3) = 2.6e-61
 Identities = 132/328 (40%), Positives = 198/328 (60%)

Query:   134 RKRRSRWADDEPKPVIQLPDFMKDFTGGIEFDPE-IQALNSRLLEISRMLQSG-LPLDDR 191
             +++RSRW  D  +    +P        G+  + E    +  ++ +++R L++G L +   
Sbjct:    16 KRKRSRWNQDTMEQKTVIPGMPTVIPPGLTREQERAYIVQLQIEDLTRKLRTGDLGIPPN 75

Query:   192 PEGQRSPSPEPIYDNMGIRINTREYRARERLNKERQEIISQIIKRNPAFKPPADYRPP-- 249
             PE  RSPSPEPIY++ G R+NTRE+R R++L +ER  +I++++  NP FKPPADY+PP  
Sbjct:    76 PE-DRSPSPEPIYNSEGKRLNTREFRTRKKLEEERHNLITEMVALNPDFKPPADYKPPAT 134

Query:   250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDL 309
             ++  K+ IP  EYP  NF+GL+IGPRGNT K +E+E  AKI+IRGKGSVKEG++ +K D 
Sbjct:   135 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRK-DG 193

Query:   310 KPDPSENEDLHVLVEAETQESLEGAAAMVEKLL-QPVD--EVLNEHKRQQLRELAALNGT 366
             +  P E+E LH LV A T E+++ A   +  +L Q ++  E  N+ ++ QLRELA LNGT
Sbjct:   194 QMLPGEDEPLHALVTANTMENVKKAVEQIRNILKQGIETPEDQNDLRKMQLRELARLNGT 253

Query:   367 IRDEEYCRLCGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTIDCLVK------GTTGK 420
             +R+++  R+      R +   S T +  +  +C  CG  GH   DC  +          K
Sbjct:   254 LREDDN-RIL-----RPWQS-SETRSITNTTVCTKCGGAGHIASDCKFQRPGDPQSAQDK 306

Query:   421 -KMDDEYQNFLAELGGTLPESASKQSTT 447
              +MD EY + +AELG   P  AS  ST+
Sbjct:   307 ARMDKEYLSLMAELGEA-PVPASVGSTS 333

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

ZFIN|ZDB-GENE-030131-2492 sf1 "splicing factor 1" [Danio rerio (taxid:7955)]

 Score = 554 (200.1 bits), Expect = 9.6e-60, Sum P(3) = 9.6e-60
 Identities = 134/328 (40%), Positives = 199/328 (60%)

Query:   134 RKRRSRWADDEPKPVIQLPDFMKDFTGGIEFDPE-IQALNSRLLEISRMLQSG-LPLDDR 191
             +++RSRW+ + P     +P        G+  D E    +  ++ +++R L++G L +   
Sbjct:    88 KRKRSRWSSETPDQKTVIPGMPTVIPPGLTRDQERAYIVQLQIEDLTRKLRTGDLGIPVN 147

Query:   192 PEGQRSPSPEPIYDNMGIRINTREYRARERLNKERQEIISQIIKRNPAFKPPADYRPP-- 249
             PE  RSPSPEPIY++ G R+NTREYR R++L +ER  +I++++  NP FKPPADY+PP  
Sbjct:   148 PE-DRSPSPEPIYNSEGKRLNTREYRTRKKLEEERHSLITEMVGLNPEFKPPADYKPPAT 206

Query:   250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDL 309
             ++  K+ IP  EYP  NF+GL+IGPRGNT K +E+E  AKI+IRGKGSVKEG++ +K D 
Sbjct:   207 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECCAKIMIRGKGSVKEGKVGRK-DG 265

Query:   310 KPDPSENEDLHVLVEAETQESLEGAAAMVEKLL-QPVD--EVLNEHKRQQLRELAALNGT 366
             +  P E+E LH LV A T E+++ A   +  +L Q ++  E  N+ ++ QLRELA LNGT
Sbjct:   266 QMLPGEDEPLHALVTANTMENVKKAVEQIRNILKQGIETPEDQNDLRKMQLRELARLNGT 325

Query:   367 IRDEEYCRLCGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTIDCLVKGT----TGK-- 420
             +R+++  R+   P   Q   P R+ T  +  LC  CG  GH + DC    +     G+  
Sbjct:   326 LREDDN-RIL-RPW--QSTEP-RSIT--NTTLCTKCGGAGHISSDCKFTSSFAPRPGEPP 378

Query:   421 -------KMDDEYQNFLAELG-GTLPES 440
                    +MD EY + +AELG   +P S
Sbjct:   379 QSAQDKARMDKEYLSLMAELGEAPVPSS 406

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0060041 "retina development in camera-type eye" evidence=IMP

POMBASE|SPCC962.06c bpb1 "zinc finger splicing factor Bpb1" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 592 (213.5 bits), Expect = 1.3e-59, Sum P(2) = 1.3e-59
 Identities = 127/279 (45%), Positives = 179/279 (64%)

Query:   167 EIQALNSRLLEISRMLQSGLPLDDRPEGQRSPSPEPIYDNMGIRINTREYRARERLNKER 226
             E+ +LN RL EI++ L++G  +    E  RSPSP P YDN G R+NTRE R +++L  ER
Sbjct:   103 ELYSLNVRLEEITQKLRTGDVVPHHRE--RSPSPPPQYDNHGRRLNTREIRYKKKLEDER 160

Query:   227 QEIISQIIKRNPAFKPPADYR-PPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERE 285
               II + +K  P F+ P+DYR P K Q+K+Y+P+K+YP  NFIGL+IGPRG+T K ME +
Sbjct:   161 HRIIERAMKMVPGFRAPSDYRRPAKTQEKVYVPVKDYPEINFIGLLIGPRGHTLKDMEAK 220

Query:   286 TGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQP- 344
             +GAKI IRGKGSVKEG+   + D     +  EDLH LV A++++ +  A  +++ ++Q  
Sbjct:   221 SGAKIAIRGKGSVKEGK--GRSDPSVRGNMEEDLHCLVTADSEDKINHAIKLIDNVIQTA 278

Query:   345 --VDEVLNEHKRQQLRELAALNGTIRDEE--YCRLCGEPGHRQYACPSRTSTFKSDVLCK 400
               V E  N+ KR QLR+LA LNGT+RD+E   C+ CG  GHR++ CP R +    +++C+
Sbjct:   279 ASVPEGQNDLKRNQLRQLATLNGTLRDDENQVCQNCGNVGHRRFDCPERIN-HTMNIVCR 337

Query:   401 ICGDGGHPTIDCLVKGT----TGKKMDDEYQNFLAELGG 435
              CG  GH   DC V+           D EYQ+ + ELGG
Sbjct:   338 HCGSIGHIARDCPVRDQQPPMADSTADREYQSLMQELGG 376

GO:0000243 "commitment complex" evidence=IDA

GO:0000349 "generation of catalytic spliceosome for first transesterification step" evidence=IDA

GO:0003723 "RNA binding" evidence=ISM

GO:0005634 "nucleus" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0008270 "zinc ion binding" evidence=IEA

MGI|MGI:1095403 Sf1 "splicing factor 1" [Mus musculus (taxid:10090)]

 Score = 561 (202.5 bits), Expect = 1.4e-58, Sum P(2) = 1.4e-58
 Identities = 132/328 (40%), Positives = 198/328 (60%)

Query:   134 RKRRSRWADDEPKPVIQLPDFMKDFTGGIEFDPE-IQALNSRLLEISRMLQSG-LPLDDR 191
             +++RSRW  D  +    +P        G+  + E    +  ++ +++R L++G L +   
Sbjct:    16 KRKRSRWNQDTMEQKTVIPGMPTVIPPGLTREQERAYIVQLQIEDLTRKLRTGDLGIPPN 75

Query:   192 PEGQRSPSPEPIYDNMGIRINTREYRARERLNKERQEIISQIIKRNPAFKPPADYRPP-- 249
             PE  RSPSPEPIY++ G R+NTRE+R R++L +ER  +I++++  NP FKPPADY+PP  
Sbjct:    76 PE-DRSPSPEPIYNSEGKRLNTREFRTRKKLEEERHTLITEMVALNPDFKPPADYKPPAT 134

Query:   250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDL 309
             ++  K+ IP  EYP  NF+GL+IGPRGNT K +E+E  AKI+IRGKGSVKEG++ +K D 
Sbjct:   135 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRK-DG 193

Query:   310 KPDPSENEDLHVLVEAETQESLEGAAAMVEKLL-QPVD--EVLNEHKRQQLRELAALNGT 366
             +  P E+E LH LV A T E+++ A   +  +L Q ++  E  N+ ++ QLRELA LNGT
Sbjct:   194 QMLPGEDEPLHALVTANTMENVKKAVEQIRNILKQGIETPEDQNDLRKMQLRELARLNGT 253

Query:   367 IRDEEYCRLCGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTIDCLVK------GTTGK 420
             +R+++  R+      R +   S T +  +  +C  CG  GH   DC  +          K
Sbjct:   254 LREDDN-RIL-----RPWQS-SETRSITNTTVCTKCGGAGHIASDCKFQRPGDPQSAQDK 306

Query:   421 -KMDDEYQNFLAELGGTLPESASKQSTT 447
              +MD EY + +AELG   P  AS  ST+
Sbjct:   307 ARMDKEYLSLMAELGEA-PVPASVGSTS 333

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISS

GO:0005681 "spliceosomal complex" evidence=ISO

GO:0005737 "cytoplasm" evidence=ISS

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0022402 "cell cycle process" evidence=IGI

GO:0030238 "male sex determination" evidence=IGI

GO:0033327 "Leydig cell differentiation" evidence=IGI

GO:0046872 "metal ion binding" evidence=IEA

GO:0048662 "negative regulation of smooth muscle cell proliferation" evidence=ISO

GO:0050810 "regulation of steroid biosynthetic process" evidence=IGI

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: gw1.29.285.1 hypothetical protein (704 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	797
cd02395	120	cd02395, SF1_like-KH, Splicing factor 1 (SF1) K ho	2e-54
COG5176	269	COG5176, MSL5, Splicing factor (branch point bindi	4e-42
smart00360	73	smart00360, RRM, RNA recognition motif	9e-25
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	1e-24
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	2e-22
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	6e-21
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	6e-21
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	2e-20
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	7e-20
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	1e-19
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	2e-19
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	3e-18
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	5e-18
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	1e-17
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	2e-17
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	9e-17
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	2e-16
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	2e-16
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	2e-16
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	3e-16
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	4e-16
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	7e-16
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	8e-16
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	1e-15
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	2e-15
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	2e-15
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	2e-15
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	4e-15
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	4e-15
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	4e-15
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	4e-15
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	5e-15
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	6e-15
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	1e-14
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	1e-14
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	3e-14
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	3e-14
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	3e-14
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	6e-14
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	9e-14
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	9e-14
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	2e-13
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	2e-13
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	2e-13
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	2e-13
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	3e-13
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	4e-13
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	5e-13
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	6e-13
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	8e-13
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	9e-13
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	4e-12
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	4e-12
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	5e-12
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	8e-12
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	1e-11
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	1e-11
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	1e-11
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	2e-11
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	2e-11
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	2e-11
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	2e-11
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	2e-11
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	3e-11
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	3e-11
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	3e-11
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	3e-11
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	3e-11
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	4e-11
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	4e-11
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	7e-11
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	7e-11
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	7e-11
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	8e-11
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	9e-11
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	1e-10
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	1e-10
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	1e-10
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	1e-10
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	2e-10
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	2e-10
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	2e-10
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	2e-10
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-10
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	3e-10
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	3e-10
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	3e-10
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	4e-10
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	4e-10
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	5e-10
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	5e-10
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	5e-10
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	6e-10
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	7e-10
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	8e-10
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	8e-10
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	9e-10
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	9e-10
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	1e-09
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	1e-09
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	1e-09
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	1e-09
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	2e-09
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	2e-09
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	3e-09
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	4e-09
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	4e-09
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	7e-09
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	7e-09
cd12612	82	cd12612, RRM2_SECp43, RNA recognition motif 2 in t	7e-09
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	8e-09
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-08
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	1e-08
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	1e-08
pfam09770	804	pfam09770, PAT1, Topoisomerase II-associated prote	1e-08
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	1e-08
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	1e-08
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	2e-08
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	2e-08
PRK12323	700	PRK12323, PRK12323, DNA polymerase III subunits ga	2e-08
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	2e-08
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	2e-08
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	2e-08
cd12610	84	cd12610, RRM1_SECp43, RNA recognition motif 1 in t	2e-08
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	2e-08
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	2e-08
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	3e-08
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	3e-08
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	3e-08
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	3e-08
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	4e-08
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	4e-08
cd12622	74	cd12622, RRM3_PUB1, RNA recognition motif 3 in yea	5e-08
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	5e-08
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	6e-08
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	7e-08
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	7e-08
PRK07003	830	PRK07003, PRK07003, DNA polymerase III subunits ga	8e-08
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	9e-08
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	9e-08
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	9e-08
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	1e-07
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	1e-07
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	2e-07
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	2e-07
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	2e-07
cd12487	78	cd12487, RRM1_DND1, RNA recognition motif 1 found	2e-07
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-07
cd12486	78	cd12486, RRM1_ACF, RNA recognition motif 1 found i	3e-07
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	3e-07
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	3e-07
smart00322	68	smart00322, KH, K homology RNA-binding domain	3e-07
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	4e-07
cd12635	81	cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2	4e-07
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	4e-07
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	4e-07
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	4e-07
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	5e-07
PRK07003	830	PRK07003, PRK07003, DNA polymerase III subunits ga	6e-07
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	6e-07
pfam09770	804	pfam09770, PAT1, Topoisomerase II-associated prote	7e-07
PRK14951	618	PRK14951, PRK14951, DNA polymerase III subunits ga	7e-07
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	7e-07
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	7e-07
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	8e-07
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	1e-06
PRK14086	617	PRK14086, dnaA, chromosomal replication initiation	1e-06
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	1e-06
PRK07994	647	PRK07994, PRK07994, DNA polymerase III subunits ga	1e-06
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	1e-06
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	2e-06
pfam09770	804	pfam09770, PAT1, Topoisomerase II-associated prote	2e-06
PHA03307	1352	PHA03307, PHA03307, transcriptional regulator ICP4	2e-06
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	2e-06
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	2e-06
pfam00013	59	pfam00013, KH_1, KH domain	2e-06
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	2e-06
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	2e-06
PRK14951	618	PRK14951, PRK14951, DNA polymerase III subunits ga	3e-06
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	3e-06
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	3e-06
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	4e-06
cd12453	86	cd12453, RRM1_RIM4_like, RNA recognition motif 1 i	4e-06
cd12369	68	cd12369, RRM4_RBM45, RNA recognition motif 4 in RN	4e-06
PHA03378	991	PHA03378, PHA03378, EBNA-3B; Provisional	5e-06
cd12358	73	cd12358, RRM1_VICKZ, RNA recognition motif 1 in th	5e-06
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	5e-06
cd12679	76	cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in	6e-06
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	7e-06
PRK10263	1355	PRK10263, PRK10263, DNA translocase FtsK; Provisio	7e-06
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	8e-06
pfam04652	315	pfam04652, DUF605, Vta1 like	9e-06
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	1e-05
PRK14951	618	PRK14951, PRK14951, DNA polymerase III subunits ga	1e-05
PRK14086	617	PRK14086, dnaA, chromosomal replication initiation	1e-05
pfam04652	315	pfam04652, DUF605, Vta1 like	1e-05
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	1e-05
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	1e-05
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	1e-05
pfam13014	42	pfam13014, KH_3, KH domain	1e-05
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	1e-05
pfam04652	315	pfam04652, DUF605, Vta1 like	2e-05
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	2e-05
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	2e-05
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	2e-05
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	2e-05
cd12661	77	cd12661, RRM3_hnRNPM, RNA recognition motif 3 in v	3e-05
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	3e-05
PRK14965	576	PRK14965, PRK14965, DNA polymerase III subunits ga	3e-05
cd12611	81	cd12611, RRM1_NGR1_NAM8_like, RNA recognition moti	3e-05
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	3e-05
cd12621	74	cd12621, RRM3_TIA1, RNA recognition motif 3 in nuc	3e-05
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	4e-05
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	4e-05
cd12665	77	cd12665, RRM2_RAVER1, RNA recognition motif 2 foun	4e-05
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	4e-05
cd12534	83	cd12534, RRM_SARFH, RNA recognition motif in Droso	4e-05
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	4e-05
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	5e-05
cd12620	73	cd12620, RRM3_TIAR, RNA recognition motif 3 in nuc	5e-05
PHA03307	1352	PHA03307, PHA03307, transcriptional regulator ICP4	6e-05
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	6e-05
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	6e-05
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	6e-05
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	8e-05
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	8e-05
pfam03154	979	pfam03154, Atrophin-1, Atrophin-1 family	8e-05
cd12473	85	cd12473, RRM2_MSSP1, RNA recognition motif 2 found	8e-05
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	8e-05
PRK14950	585	PRK14950, PRK14950, DNA polymerase III subunits ga	8e-05
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	9e-05
PRK07994	647	PRK07994, PRK07994, DNA polymerase III subunits ga	9e-05
PRK14950	585	PRK14950, PRK14950, DNA polymerase III subunits ga	9e-05
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	9e-05
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	1e-04
PRK12323	700	PRK12323, PRK12323, DNA polymerase III subunits ga	1e-04
PRK14951	618	PRK14951, PRK14951, DNA polymerase III subunits ga	1e-04
cd12634	81	cd12634, RRM2_CELF1_2, RNA recognition motif 2 in	1e-04
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	1e-04
cd12666	77	cd12666, RRM2_RAVER2, RNA recognition motif 2 in v	1e-04
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	2e-04
PRK07003	830	PRK07003, PRK07003, DNA polymerase III subunits ga	2e-04
PRK07994	647	PRK07994, PRK07994, DNA polymerase III subunits ga	2e-04
cd12596	70	cd12596, RRM1_SRSF6, RNA recognition motif 1 in ve	2e-04
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	2e-04
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	2e-04
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	2e-04
pfam07223	357	pfam07223, DUF1421, Protein of unknown function (D	2e-04
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	2e-04
cd12482	79	cd12482, RRM1_hnRNPR, RNA recognition motif 1 in v	2e-04
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	2e-04
pfam07777	189	pfam07777, MFMR, G-box binding protein MFMR	2e-04
cd12604	76	cd12604, RRM_RALY, RNA recognition motif in verteb	2e-04
pfam03276	582	pfam03276, Gag_spuma, Spumavirus gag protein	2e-04
PRK10263	1355	PRK10263, PRK10263, DNA translocase FtsK; Provisio	3e-04
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	3e-04
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	3e-04
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	3e-04
cd12485	78	cd12485, RRM1_RBM47, RNA recognition motif 1 found	3e-04
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	3e-04
cd12474	86	cd12474, RRM2_MSSP2, RNA recognition motif 2 found	3e-04
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	3e-04
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	4e-04
PHA03307	1352	PHA03307, PHA03307, transcriptional regulator ICP4	4e-04
pfam07223	357	pfam07223, DUF1421, Protein of unknown function (D	4e-04
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	4e-04
PLN03209	576	PLN03209, PLN03209, translocon at the inner envelo	4e-04
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	5e-04
pfam09770	804	pfam09770, PAT1, Topoisomerase II-associated prote	5e-04
pfam03154	979	pfam03154, Atrophin-1, Atrophin-1 family	5e-04
pfam03153	332	pfam03153, TFIIA, Transcription factor IIA, alpha/	5e-04
pfam05518	753	pfam05518, Totivirus_coat, Totivirus coat protein	5e-04
cd12475	88	cd12475, RRM2_RBMS3, RNA recognition motif 2 found	5e-04
cd12484	78	cd12484, RRM1_RBM46, RNA recognition motif 1 found	5e-04
cd12555	87	cd12555, RRM2_RBM15, RNA recognition motif 2 in ve	5e-04
PHA03378	991	PHA03378, PHA03378, EBNA-3B; Provisional	6e-04
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	6e-04
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	6e-04
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	6e-04
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	7e-04
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	7e-04
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	7e-04
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	7e-04
cd12615	74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	7e-04
PRK14971	614	PRK14971, PRK14971, DNA polymerase III subunits ga	7e-04
cd12348	75	cd12348, RRM1_SHARP, RNA recognition motif 1 in SM	8e-04
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	8e-04
PRK14959	624	PRK14959, PRK14959, DNA polymerase III subunits ga	9e-04
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	0.001
cd12616	81	cd12616, RRM1_TIAR, RNA recognition motif 1 in nuc	0.001
cd12368	75	cd12368, RRM3_RBM45, RNA recognition motif 3 in RN	0.001
cd12556	85	cd12556, RRM2_RBM15B, RNA recognition motif 2 in p	0.001
cd12424	71	cd12424, RRM3_hnRNPL_like, RNA recognition motif 1	0.001
cd12238	73	cd12238, RRM1_RBM40_like, RNA recognition motif 1	0.001
cd12232	89	cd12232, RRM3_U2AF65, RNA recognition motif 3 foun	0.001
PHA03369	663	PHA03369, PHA03369, capsid maturational protease;	0.001
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	0.002
PRK12323	700	PRK12323, PRK12323, DNA polymerase III subunits ga	0.002
PRK10263	1355	PRK10263, PRK10263, DNA translocase FtsK; Provisio	0.002
pfam03154	979	pfam03154, Atrophin-1, Atrophin-1 family	0.002
pfam05518	753	pfam05518, Totivirus_coat, Totivirus coat protein	0.002
PHA03369	663	PHA03369, PHA03369, capsid maturational protease;	0.002
cd12342	71	cd12342, RRM_Nab3p, RNA recognition motif in yeast	0.002
cd12423	74	cd12423, RRM3_PTBP1_like, RNA recognition motif 3	0.002
PRK03427	333	PRK03427, PRK03427, cell division protein ZipA; Pr	0.002
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	0.002
cd12476	78	cd12476, RRM1_SNF, RNA recognition motif 1 found i	0.002
cd12587	71	cd12587, RRM1_PSF, RNA recognition motif 1 in vert	0.002
pfam06409	350	pfam06409, NPIP, Nuclear pore complex interacting	0.002
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	0.002
cd12529	71	cd12529, RRM2_MEI2_like, RNA recognition motif 2 i	0.002
cd12662	77	cd12662, RRM3_MYEF2, RNA recognition motif 3 in ve	0.003
PRK14954	620	PRK14954, PRK14954, DNA polymerase III subunits ga	0.003
cd12285	85	cd12285, RRM3_RBM39_like, RNA recognition motif 3	0.003
cd12385	76	cd12385, RRM1_hnRNPM_like, RNA recognition motif 1	0.003
cd02393	61	cd02393, PNPase_KH, Polynucleotide phosphorylase (	0.003
cd12697	76	cd12697, RRM3_ROD1, RNA recognition motif 3 in ver	0.003
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	0.003
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	0.003
cd12523	78	cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA	0.003
cd12333	80	cd12333, RRM2_p54nrb_like, RNA recognition motif 2	0.003
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	0.003
cd12364	81	cd12364, RRM_RDM1, RNA recognition motif of RAD52	0.003
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	0.003
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	0.004
cd12594	74	cd12594, RRM1_SRSF4, RNA recognition motif 1 in ve	0.004
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	0.004
cd12280	81	cd12280, RRM_FET, RNA recognition motif in the FET	0.004
pfam07174	297	pfam07174, FAP, Fibronectin-attachment protein (FA	0.004

>gnl|CDD|239088 cd02395, SF1_like-KH, Splicing factor 1 (SF1) K homology RNA-binding domain (KH)

 Score =  183 bits (466), Expect = 2e-54
 Identities = 66/120 (55%), Positives = 89/120 (74%), Gaps = 3/120 (2%)

Query: 252 QKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKP 311
            +K+YIP+K+YP YNF+GLI+GPRGNT K++E+ETGAKI IRGKGS+K+G+ +++     
Sbjct: 1   TEKVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPK 60

Query: 312 DPSENEDLHVLVEAET--QESLEGAAAMVEKLLQPVDEVL-NEHKRQQLRELAALNGTIR 368
               NE LHVL+ AET  +E+L  A   +E+LL+P  E   +E KR+QLRELA LNGT R
Sbjct: 61  YAHLNEPLHVLITAETPPEEALAKAVEAIEELLKPAIEGGNDELKREQLRELALLNGTYR 120

Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. Length = 120

>gnl|CDD|227503 COG5176, MSL5, Splicing factor (branch point binding protein) [RNA processing and modification]

 Score =  154 bits (390), Expect = 4e-42
 Identities = 85/209 (40%), Positives = 119/209 (56%), Gaps = 8/209 (3%)

Query: 167 EIQALNSRLLEISRMLQSGLPLDDRPEGQRSPSPEPIYDNMGIRINTREYRARERLNKER 226
               +  R  EI+  L++   +  + E  RSPSP P YD +G R+NTRE R  ++L  ER
Sbjct: 64  YSYQVMMRPFEITEKLRTPDGVPSKRE-LRSPSPPPRYDEIGRRLNTREARYNKKLEDER 122

Query: 227 QEIISQIIKRNPAFKPPADY-RPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERE 285
             +  +  K  P F  P DY RP K Q K+YIP++EYP  NF+GL+IGPRG+T K++ER 
Sbjct: 123 LWLKERAQKILPRFVLPNDYIRPSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERI 182

Query: 286 TGAKIVIRGKGSVKEGRLQQKRDLKPDPSE-NEDLHVLVEAETQESLEGAAAMVEKLLQP 344
           + AKI IRG GSVKEG++    D           LH L+EA++++ +          ++ 
Sbjct: 183 SRAKIAIRGSGSVKEGKISS--DTPESLKNAEAVLHCLIEADSEDKICRLIKSQLNAIRE 240

Query: 345 ---VDEVLNEHKRQQLRELAALNGTIRDE 370
                E  N+ KR QLR LA LNGT+R +
Sbjct: 241 ARRNPEGQNDLKRFQLRWLAHLNGTLRAD 269

Length = 269

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

 Score = 97.7 bits (244), Expect = 9e-25
 Identities = 27/73 (36%), Positives = 46/73 (63%)

Query: 493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
            L++G LPP   ++ L  LFS FG +   ++++D+ TG SKG+ FV++   + A  A+ +
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 553 MNGYRLEGRTIAV 565
           +NG  L+GR + V
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score = 97.5 bits (243), Expect = 1e-24
 Identities = 37/77 (48%), Positives = 50/77 (64%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           TNL + YLP  +  D +  LFS+ G+I   K+I+D+VTG S GYGFV Y D + A  AI 
Sbjct: 2   TNLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAIN 61

Query: 552 SMNGYRLEGRTIAVRVA 568
           ++NG RL+ +TI V  A
Sbjct: 62  TLNGLRLQNKTIKVSYA 78

This subfamily corresponds to the RRM1 of the Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 78

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

 Score = 91.6 bits (228), Expect = 2e-22
 Identities = 31/77 (40%), Positives = 44/77 (57%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           TNL + YLP  +  + L  LF   G I   K+++DR+TG S GYGFV Y D   A  AI 
Sbjct: 1   TNLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAIN 60

Query: 552 SMNGYRLEGRTIAVRVA 568
           ++NG+ +  + + V  A
Sbjct: 61  TLNGFEIRNKRLKVSYA 77

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

 Score = 97.2 bits (242), Expect = 6e-21
 Identities = 70/253 (27%), Positives = 105/253 (41%), Gaps = 30/253 (11%)

Query: 493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
           NLY+  L  T+ D+ L  LFS  G+I  AKV+ D   G+S+G+GFV +++ + AN A+  
Sbjct: 287 NLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDE-KGVSRGFGFVCFSNPEEANRAVTE 345

Query: 553 MNGYRLEGRTIAVRVAGK----------------PPQPTVPPGPPTSTMPTYPVSAPPVG 596
           M+G  L G+ + V +A +                P    +P G P        +  PP  
Sbjct: 346 MHGRMLGGKPLYVALAQRKEQRRAHLQDQFMQLQPRMRQLPMGSPMGGA----MGQPPYY 401

Query: 597 GYPSQQYAPGGPLPNPPAASYTGAPVPWGPPVPPPYAPYAPPPPGSTMYPPVPGQPMPPY 656
           G   QQ   G PL  P  +       P GP  P   AP       S        +P P  
Sbjct: 402 GQGPQQQFNGQPLGWPRMSMMPTPMGPGGPLRPNGLAPMNAVRAPSRNAQNAAQKP-PMQ 460

Query: 657 GVQYPPPVQTAPPGALTAPPGAPTQTATSSEAQQHSFPPGVQSESSSSAPAASANMYGSS 716
            V YPP  Q+ P          P   +T+S+  Q+     +    +S+ P     + G  
Sbjct: 461 PVMYPPNYQSLP-----LSQDLPQPQSTASQGGQN---KKLAQVLASATPQMQKQVLGER 512

Query: 717 MPPMPPNVQPAYA 729
           + P+   ++PA A
Sbjct: 513 LFPLVEAIEPALA 525

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

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

 Score = 86.9 bits (216), Expect = 6e-21
 Identities = 28/70 (40%), Positives = 44/70 (62%), Gaps = 1/70 (1%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L++G LPP   ++ L  LFS FG I   ++++D  TG SKG+ FV++ D + A  A+ ++
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDE-TGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 554 NGYRLEGRTI 563
           NG  L 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|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins

 Score = 85.7 bits (213), Expect = 2e-20
 Identities = 34/76 (44%), Positives = 47/76 (61%)

Query: 493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
           NLY+G LP  + ++ L  LF  FG++  A+VI DR TG S+G+GFV+    + AN AI  
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 553 MNGYRLEGRTIAVRVA 568
           +NG    GRT+ V  A
Sbjct: 61  LNGTDFGGRTLTVNEA 76

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

>gnl|CDD|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 = 84.2 bits (209), Expect = 7e-20
 Identities = 29/79 (36%), Positives = 43/79 (54%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
             L++  L     +  L  LFS FG +    ++KD  TG S+G+GFV +  ++ A+ AI 
Sbjct: 2   NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61

Query: 552 SMNGYRLEGRTIAVRVAGK 570
            +NG  LEGR I V  A +
Sbjct: 62  DLNGKELEGRVIKVEKAKR 80

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

 Score = 83.1 bits (206), Expect = 1e-19
 Identities = 27/73 (36%), Positives = 46/73 (63%), Gaps = 1/73 (1%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L++G LPP   ++ L  LFS FG+I   ++++D+  G SKG+ FV++   + A  A+ ++
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDK-DGKSKGFAFVEFESPEDAEKALEAL 59

Query: 554 NGYRLEGRTIAVR 566
           NG  L+GR + 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|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 = 83.1 bits (206), Expect = 2e-19
 Identities = 30/72 (41%), Positives = 47/72 (65%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L+I +LP    D  L +LF+ FG+++ AKV  D+ TG SK +GFV Y + + A  AI +M
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 554 NGYRLEGRTIAV 565
           NG+++ G+ + V
Sbjct: 61  NGFQVGGKRLKV 72

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

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

 Score = 79.7 bits (197), Expect = 3e-18
 Identities = 34/74 (45%), Positives = 46/74 (62%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
             +++  LPP  D+  L +LFS FG +   KVI+D  T   KGYGFV   + + A +AIA
Sbjct: 2   WCIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIA 61

Query: 552 SMNGYRLEGRTIAV 565
           S+NGYRL GR + V
Sbjct: 62  SLNGYRLGGRVLQV 75

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

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

 Score = 78.6 bits (194), Expect = 5e-18
 Identities = 31/76 (40%), Positives = 47/76 (61%)

Query: 493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
            L++G L  ++DD+ L   F  FG +V A+VI DR TG S+G+G+V +   + A  AI +
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 553 MNGYRLEGRTIAVRVA 568
           M+G  L+GR I V  +
Sbjct: 61  MDGKELDGRPINVDFS 76

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

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

 Score = 77.6 bits (192), Expect = 1e-17
 Identities = 31/79 (39%), Positives = 46/79 (58%), Gaps = 1/79 (1%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           TN+Y+  L   +DD+ L  LF  +G I  AKV+KD   G SKG+GFV + + + A  A+ 
Sbjct: 2   TNVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDD-EGKSKGFGFVNFENHEAAQKAVE 60

Query: 552 SMNGYRLEGRTIAVRVAGK 570
            +NG  + G+ + V  A K
Sbjct: 61  ELNGKEVNGKKLYVGRAQK 79

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

 Score = 76.5 bits (189), Expect = 2e-17
 Identities = 30/72 (41%), Positives = 45/72 (62%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           LY+G L   + +D L  +F  FG+I   ++ +D  TG SKGYGF+++AD + A  A+  +
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 554 NGYRLEGRTIAV 565
           NG+ L GR I V
Sbjct: 61  NGFELAGRPIKV 72

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

>gnl|CDD|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 = 75.3 bits (186), Expect = 9e-17
 Identities = 28/75 (37%), Positives = 45/75 (60%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           ++IG LP  L +D +  L  +FG +    ++KD  TG+SKGY F +Y D  + + AIA +
Sbjct: 3   IFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAGL 62

Query: 554 NGYRLEGRTIAVRVA 568
           NG +L  + + V+ A
Sbjct: 63  NGMQLGDKKLTVQRA 77

This subfamily corresponds to the RRM2 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Length = 77

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

 Score = 74.6 bits (184), Expect = 2e-16
 Identities = 33/77 (42%), Positives = 44/77 (57%), Gaps = 1/77 (1%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           T +++G LP    DD L + FS FG+I  A VI DR TG S+GYGFV + D + A  A  
Sbjct: 1   TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60

Query: 552 SMNGYRLEGRTIAVRVA 568
             N   ++GR   V +A
Sbjct: 61  DPNP-IIDGRKANVNLA 76

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

 Score = 74.2 bits (183), Expect = 2e-16
 Identities = 28/69 (40%), Positives = 38/69 (55%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           TN+YI  LPP   D+ L +L   FG I+  K I D+ T   KGYGFV +   + A  AI 
Sbjct: 1   TNVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIE 60

Query: 552 SMNGYRLEG 560
            +NG  ++ 
Sbjct: 61  GLNGRGVQA 69

This subfamily corresponds to the RRM1 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus, they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. Moreover, the family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot. . Length = 71

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

 Score = 74.3 bits (183), Expect = 2e-16
 Identities = 34/71 (47%), Positives = 46/71 (64%)

Query: 493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
           ++++G L P +D + L   F+ FG+I  A+V+KD  TG SKGYGFV +   + A NAI S
Sbjct: 1   HIFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQS 60

Query: 553 MNGYRLEGRTI 563
           MNG  L GR I
Sbjct: 61  MNGQWLGGRAI 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|241213 cd12769, RRM1_HuR, RNA recognition motif 1 in vertebrate Hu-antigen R (HuR)

 Score = 74.0 bits (181), Expect = 3e-16
 Identities = 36/77 (46%), Positives = 50/77 (64%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           TNL + YLP  +  D L  LFS+ G++  AK+I+D+V G S GYGFV Y + + A  AI 
Sbjct: 2   TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAIN 61

Query: 552 SMNGYRLEGRTIAVRVA 568
           ++NG RL+ +TI V  A
Sbjct: 62  TLNGLRLQSKTIKVSYA 78

This subgroup corresponds to the RRM1 of HuR, also termed ELAV-like protein 1 (ELAV-1), a ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response; it binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. Meanwhile, HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

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

 Score = 75.5 bits (185), Expect = 4e-16
 Identities = 44/102 (43%), Positives = 54/102 (52%), Gaps = 6/102 (5%)

Query: 477 GLGSNGAKPIK------ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTG 530
            + SNG  P+        L  T L+IG L    DD  L   F+ FGD+V AKVI DR TG
Sbjct: 14  NISSNGNVPVTSMLGSLRLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETG 73

Query: 531 MSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPP 572
            S+G+GFV + D   A  AI+ M+G  L GR I V  A   P
Sbjct: 74  RSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPANDRP 115

Length = 144

>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 = 72.6 bits (179), Expect = 7e-16
 Identities = 25/75 (33%), Positives = 45/75 (60%), Gaps = 1/75 (1%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L++G LP T  ++ +  LF  +G+I    +I+D+ TG SKG  FVK++  + A  AI ++
Sbjct: 2   LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEAL 61

Query: 554 NG-YRLEGRTIAVRV 567
           +G   + G +  ++V
Sbjct: 62  HGKVTMPGASRPLQV 76

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

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

 Score = 72.7 bits (179), Expect = 8e-16
 Identities = 33/80 (41%), Positives = 46/80 (57%), Gaps = 1/80 (1%)

Query: 493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMA-KVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           NL+IG L P +D+  L   FS FG I+   K+++D  TG SKG+ F+ Y   + ++ AI 
Sbjct: 3   NLFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIE 62

Query: 552 SMNGYRLEGRTIAVRVAGKP 571
           +MNG  L  R I V  A K 
Sbjct: 63  AMNGQYLCNRPITVSYAFKK 82

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

>gnl|CDD|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 = 72.2 bits (177), Expect = 1e-15
 Identities = 31/77 (40%), Positives = 47/77 (61%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L+IG L    ++  L ++FS +G I    V+KDR T  S+G+GFV + +   A +A+ +M
Sbjct: 3   LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62

Query: 554 NGYRLEGRTIAVRVAGK 570
           NG  ++GR I V  AGK
Sbjct: 63  NGKSVDGRQIRVDQAGK 79

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

 Score = 71.8 bits (177), Expect = 2e-15
 Identities = 28/73 (38%), Positives = 40/73 (54%), Gaps = 1/73 (1%)

Query: 493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
           N++I  L  ++D+  L   FS FG+I+  KV  D   G SKGYGFV +   + A  AI  
Sbjct: 4   NIFIKNLDKSIDNKALYDTFSAFGNILSCKVATDE-NGGSKGYGFVHFETEEAAVRAIEK 62

Query: 553 MNGYRLEGRTIAV 565
           +NG  L  + + V
Sbjct: 63  VNGMLLNDKKVFV 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|241093 cd12649, RRM1_SXL, RNA recognition motif 1 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 71.7 bits (176), Expect = 2e-15
 Identities = 32/77 (41%), Positives = 45/77 (58%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           TNL I YLP TL D+    LF   G +   K+++D+ TG S G+GFV Y   + A  AI 
Sbjct: 1   TNLIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIR 60

Query: 552 SMNGYRLEGRTIAVRVA 568
           ++NG +L+ + I V  A
Sbjct: 61  TLNGLQLQNKRIKVAYA 77

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

 Score = 78.1 bits (192), Expect = 2e-15
 Identities = 34/77 (44%), Positives = 50/77 (64%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           TNL + YLP T+  + +  LF++ G+I   K+++D+VTG S GYGFV Y   + A  A+ 
Sbjct: 4   TNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVN 63

Query: 552 SMNGYRLEGRTIAVRVA 568
           S+NG RL+ +TI V  A
Sbjct: 64  SLNGLRLQNKTIKVSYA 80

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

 Score = 70.9 bits (173), Expect = 4e-15
 Identities = 35/81 (43%), Positives = 50/81 (61%)

Query: 488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMAN 547
           E   TNL + YLP  +  + L  LF + G+I   K+++D++TG S GYGFV Y D + A 
Sbjct: 1   EDSKTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAE 60

Query: 548 NAIASMNGYRLEGRTIAVRVA 568
            AI ++NG RL+ +TI V  A
Sbjct: 61  KAINTLNGLRLQTKTIKVSYA 81

This subgroup corresponds to the RRM1 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads and is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 83

>gnl|CDD|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate Hu-antigen C (HuC)

 Score = 70.9 bits (173), Expect = 4e-15
 Identities = 32/77 (41%), Positives = 48/77 (62%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           TNL + YLP  +  +    LF + G+I   K+++D++TG S GYGFV Y D   A+ AI 
Sbjct: 4   TNLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAIN 63

Query: 552 SMNGYRLEGRTIAVRVA 568
           ++NG +L+ +TI V  A
Sbjct: 64  TLNGLKLQTKTIKVSYA 80

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

 Score = 70.4 bits (173), Expect = 4e-15
 Identities = 24/78 (30%), Positives = 46/78 (58%)

Query: 491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAI 550
            + +Y+  LP +L ++ L ++FS +G +V   ++KD+ T  SKG  F+ + D + A+  +
Sbjct: 1   KSTVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCV 60

Query: 551 ASMNGYRLEGRTIAVRVA 568
            ++N   L GRT+   +A
Sbjct: 61  KALNNKELFGRTLKCSIA 78

This subfamily corresponds to the RRM of ZCRB1, also termed MADP-1, or U11/U12 small nuclear ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or U11/U12-31K), a novel multi-functional nuclear factor, which may be involved in morphine dependence, cold/heat stress, and hepatocarcinoma. It is located in the nucleoplasm, but outside the nucleolus. ZCRB1 is one of the components of U11/U12 snRNPs that bind to U12-type pre-mRNAs and form a di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence. ZCRB1 is characterized by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCHC-type Zinc finger motif. In addition, it contains core nucleocapsid motifs, and Lys- and Glu-rich domains. . Length = 78

>gnl|CDD|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 = 70.3 bits (173), Expect = 4e-15
 Identities = 28/71 (39%), Positives = 45/71 (63%)

Query: 495 YIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMN 554
           ++G +P    ++ LI +FS  G +V  +++ DR TG  KGYGF ++ DI+ A +AI ++N
Sbjct: 2   FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61

Query: 555 GYRLEGRTIAV 565
           GY   GR + V
Sbjct: 62  GYEFNGRALRV 72

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

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

 Score = 70.7 bits (174), Expect = 5e-15
 Identities = 29/72 (40%), Positives = 47/72 (65%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           +YIG LP  L +  ++ +FS +G+IV   +++D+ TG SKG+ F+ Y D +    A+ ++
Sbjct: 12  IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71

Query: 554 NGYRLEGRTIAV 565
           NG +L GRTI V
Sbjct: 72  NGIKLLGRTIRV 83

This subfamily corresponds to the RRM of the ist3 family that includes fungal U2 small nuclear ribonucleoprotein (snRNP) component increased sodium tolerance protein 3 (ist3), X-linked 2 RNA-binding motif proteins (RBMX2) found in Metazoa and plants, and similar proteins. Gene IST3 encoding ist3, also termed U2 snRNP protein SNU17 (Snu17p), is a novel yeast Saccharomyces cerevisiae protein required for the first catalytic step of splicing and for progression of spliceosome assembly. It binds specifically to the U2 snRNP and is an intrinsic component of prespliceosomes and spliceosomes. Yeast ist3 contains an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In the yeast pre-mRNA retention and splicing complex, the atypical RRM of ist3 functions as a scaffold that organizes the other two constituents, Bud13p (bud site selection 13) and Pml1p (pre-mRNA leakage 1). Fission yeast Schizosaccharomyces pombe gene cwf29 encoding ist3, also termed cell cycle control protein cwf29, is an RNA-binding protein complexed with cdc5 protein 29. It also contains one RRM. The biological function of RBMX2 remains unclear. It shows high sequence similarity to yeast ist3 protein and harbors one RRM as well. . Length = 89

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

 Score = 70.0 bits (172), Expect = 6e-15
 Identities = 29/75 (38%), Positives = 43/75 (57%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           +Y+  + P L +D +  +F  FG I    +  D  TG  KGYGF++Y + Q A +AIASM
Sbjct: 3   IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASM 62

Query: 554 NGYRLEGRTIAVRVA 568
           N + L G+ + V  A
Sbjct: 63  NLFDLGGQQLRVGKA 77

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

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

 Score = 69.2 bits (170), Expect = 1e-14
 Identities = 31/76 (40%), Positives = 45/76 (59%), Gaps = 1/76 (1%)

Query: 493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
           NLY+  L  ++DD+ L   FS FG I  AKV+ D   G SKG+GFV ++  + A  A+  
Sbjct: 3   NLYVKNLDDSIDDERLREEFSPFGTITSAKVMTDE-KGRSKGFGFVCFSSPEEATKAVTE 61

Query: 553 MNGYRLEGRTIAVRVA 568
           MNG  + G+ + V +A
Sbjct: 62  MNGRIIGGKPLYVALA 77

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

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

 Score = 69.1 bits (169), Expect = 1e-14
 Identities = 30/71 (42%), Positives = 39/71 (54%)

Query: 493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
           N+++G L P + D  L   FS F     A+V+ D  +G S+GYGFV +   Q A NAI  
Sbjct: 1   NIFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINE 60

Query: 553 MNGYRLEGRTI 563
           MNG  L  R I
Sbjct: 61  MNGKWLGSRPI 71

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

>gnl|CDD|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 = 68.0 bits (167), Expect = 3e-14
 Identities = 28/72 (38%), Positives = 41/72 (56%), Gaps = 6/72 (8%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           T +Y+G LP  L ++ L R FS FG I   +V KD      KGY FV++   + A  AI 
Sbjct: 1   TTVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD------KGYAFVRFDTHEAAATAIV 54

Query: 552 SMNGYRLEGRTI 563
           ++NG  + G+T+
Sbjct: 55  AVNGTSINGQTV 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|240791 cd12345, RRM2_SECp43_like, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 68.1 bits (167), Expect = 3e-14
 Identities = 29/79 (36%), Positives = 42/79 (53%), Gaps = 1/79 (1%)

Query: 491 DTNLYIGYLPPTLDDDGLIRLFST-FGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNA 549
           D ++++G L P + D  L   F   +  +  AKV+ D VTG SKGYGFV++ D    + A
Sbjct: 1   DHSIFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRA 60

Query: 550 IASMNGYRLEGRTIAVRVA 568
           +  MNG     R + V  A
Sbjct: 61  LTEMNGVYCSSRPMRVSPA 79

This subfamily corresponds to the RRM2 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs. . Length = 80

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

 Score = 68.2 bits (166), Expect = 3e-14
 Identities = 33/77 (42%), Positives = 48/77 (62%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           TNL + YLP  +  +    LF + G+I   K+++D++TG S GYGFV Y D + A  AI 
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

Query: 552 SMNGYRLEGRTIAVRVA 568
           ++NG RL+ +TI V  A
Sbjct: 63  TLNGLRLQTKTIKVSYA 79

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

 Score = 67.2 bits (165), Expect = 6e-14
 Identities = 23/71 (32%), Positives = 43/71 (60%), Gaps = 1/71 (1%)

Query: 495 YIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMN 554
           ++G LP  ++++ L + F   GD+   ++++DR TG+ KG+G+V +        A+  +N
Sbjct: 3   FVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALK-LN 61

Query: 555 GYRLEGRTIAV 565
           G +L+GR I V
Sbjct: 62  GIKLKGRKIRV 72

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

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

 Score = 72.7 bits (177), Expect = 9e-14
 Identities = 31/102 (30%), Positives = 54/102 (52%)

Query: 473 PGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMS 532
                  S  ++   + ++  L++G LP  + ++ L  LF  FG +   ++++DR TG S
Sbjct: 97  ELFRSSESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKS 156

Query: 533 KGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQP 574
           +G+ FV++   + A  AI  +NG  LEGR + V+ A    QP
Sbjct: 157 RGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQP 198

Length = 306

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

 Score = 66.8 bits (163), Expect = 9e-14
 Identities = 31/79 (39%), Positives = 49/79 (62%), Gaps = 2/79 (2%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           TNLY+  LP  L +D L ++F  +G+IV   +++D+ TG+ +G  FV+Y   + A  AI+
Sbjct: 1   TNLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAIS 60

Query: 552 SMNGYRLEGRT--IAVRVA 568
           S+NG    G T  ++VR A
Sbjct: 61  SLNGTIPPGSTMPLSVRYA 79

This subfamily corresponds to the RRM2 of the sex-lethal protein (SXL) which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 79

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

 Score = 65.7 bits (161), Expect = 2e-13
 Identities = 27/72 (37%), Positives = 39/72 (54%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           LY+G L   +D+  L   F  FGDI   ++  D  T   +G+ FV++ + + A  AI +M
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 554 NGYRLEGRTIAV 565
           N   L GRTI V
Sbjct: 61  NESELFGRTIRV 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|240753 cd12307, RRM_NIFK_like, RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) and similar proteins

 Score = 65.7 bits (161), Expect = 2e-13
 Identities = 24/73 (32%), Positives = 40/73 (54%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           +YIG+LP    +  L + FS FG +   ++ + + TG SKGY FV++   ++A     +M
Sbjct: 2   VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETM 61

Query: 554 NGYRLEGRTIAVR 566
           N Y L  R +  +
Sbjct: 62  NNYLLFERLLKCK 74

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

>gnl|CDD|241096 cd12652, RRM2_Hu, RNA recognition motif 2 in the Hu proteins family

 Score = 65.8 bits (161), Expect = 2e-13
 Identities = 30/78 (38%), Positives = 46/78 (58%), Gaps = 2/78 (2%)

Query: 493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
           NLY+  LP T+    L  LFS +G I+ ++++ D VTG+S+G GF+++     A  AI +
Sbjct: 2   NLYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKA 61

Query: 553 MNGYRLEGRT--IAVRVA 568
           +NG    G T  I V+ A
Sbjct: 62  LNGTIPPGATEPITVKFA 79

This subfamily corresponds to the RRM2 of Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Moreover, HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 79

>gnl|CDD|241083 cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 65.6 bits (160), Expect = 2e-13
 Identities = 27/69 (39%), Positives = 43/69 (62%)

Query: 490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNA 549
           +  NL+I +LP    D  L+++F  FG+++ AKV  DR T  SK +GFV + +   A  A
Sbjct: 3   EGCNLFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAA 62

Query: 550 IASMNGYRL 558
           I +MNG+++
Sbjct: 63  IQAMNGFQI 71

This subgroup corresponds to the RRM3 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contains three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. Both, RRM1 and RRM2 of CELF-4, can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 79

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

 Score = 65.3 bits (160), Expect = 3e-13
 Identities = 28/80 (35%), Positives = 46/80 (57%), Gaps = 5/80 (6%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAI--- 550
           ++I  LP    ++ L  LFS FG++  A+++KD++TG SKG  FVK+   + A   +   
Sbjct: 3   VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAA 62

Query: 551 --ASMNGYRLEGRTIAVRVA 568
             A  +G  L+GR + V +A
Sbjct: 63  DNAEDSGLSLDGRRLIVTLA 82

This subfamily corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 82

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

 Score = 65.0 bits (159), Expect = 4e-13
 Identities = 24/73 (32%), Positives = 42/73 (57%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L++G L P +D+  +   F+  G++   K+I+++ TG S GYGFV++A  + A  A+ S+
Sbjct: 2   LWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSL 61

Query: 554 NGYRLEGRTIAVR 566
           NG  +       R
Sbjct: 62  NGKPIPNTQQRFR 74

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

 Score = 64.3 bits (157), Expect = 5e-13
 Identities = 25/70 (35%), Positives = 41/70 (58%), Gaps = 2/70 (2%)

Query: 499 LPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRL 558
           LP    +  L   FSTFG+++M +V KD  TG SKG+GFV++AD +     ++    + +
Sbjct: 7   LPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLS--QRHMI 64

Query: 559 EGRTIAVRVA 568
           +GR   V++ 
Sbjct: 65  DGRWCDVKIP 74

This subfamily corresponds to the RRM1 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. . Length = 77

>gnl|CDD|240822 cd12376, RRM2_Hu_like, RNA recognition motif 2 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 64.6 bits (157), Expect = 6e-13
 Identities = 29/79 (36%), Positives = 50/79 (63%), Gaps = 2/79 (2%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
            NLY+  LP T+    L +LFS +G I+ +++++D++TG+S+G GF+++     A  AI 
Sbjct: 1   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIK 60

Query: 552 SMNGYRLEGRT--IAVRVA 568
            +NG + EG +  I V+ A
Sbjct: 61  GLNGQKPEGASEPITVKFA 79

This subfamily corresponds to the RRM2 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. Also included in this subfamily is the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 79

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

 Score = 63.8 bits (156), Expect = 8e-13
 Identities = 26/72 (36%), Positives = 37/72 (51%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L +G LP    D+    L S FG +    ++    TG SKGYGFV+YA    A  A   +
Sbjct: 2   LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQL 61

Query: 554 NGYRLEGRTIAV 565
           +G ++ GR + V
Sbjct: 62  DGKQIGGRKLQV 73

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

 Score = 71.3 bits (174), Expect = 9e-13
 Identities = 57/210 (27%), Positives = 85/210 (40%), Gaps = 19/210 (9%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           +Y+  + P L +  +  +F  FG+IV  ++ +       KGYGF++Y ++Q  + AIASM
Sbjct: 207 IYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASM 266

Query: 554 NGYRLEGRTIAVRVAGKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGG-----P 608
           N + L G+ + V     PP   + P   ++      V+A           A  G     P
Sbjct: 267 NLFDLGGQYLRVGKCVTPPDALLQPATVSAIPAAAAVAAAAATAKIMAAEAVAGAAVLGP 326

Query: 609 LPNPPAASYTGAPVPWGPP--VPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQT 666
               PA   +  P   G    V          PP     P      + P  ++ P PV  
Sbjct: 327 RAQSPATPSSSLPTDIGNKAVVSSAKKEAEEVPP----LPQAAPAVVKPGPMEIPTPV-- 380

Query: 667 APPG----ALTAPPG--APTQTATSSEAQQ 690
            PPG    +L APPG  APT+   S  A  
Sbjct: 381 PPPGLAIPSLVAPPGLVAPTEINPSFLASP 410

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

 Score = 62.0 bits (150), Expect = 4e-12
 Identities = 31/71 (43%), Positives = 42/71 (59%)

Query: 493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
           ++++G L P +  D +   F+ FG I  A+V+KD  TG SKGYGFV + +   A NAI  
Sbjct: 3   HVFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 62

Query: 553 MNGYRLEGRTI 563
           M G  L GR I
Sbjct: 63  MGGQWLGGRQI 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|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 = 4e-12
 Identities = 20/73 (27%), Positives = 40/73 (54%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L++G L   ++ D L  +FS +G +    +  DR   + +GY +V++   + A  AI  M
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 554 NGYRLEGRTIAVR 566
           +G +++G+ + V 
Sbjct: 61  DGGQIDGQEVTVE 73

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

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

 Score = 61.5 bits (150), Expect = 5e-12
 Identities = 28/72 (38%), Positives = 40/72 (55%), Gaps = 3/72 (4%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           LY+G L  T+ +D L  LFS  G I   K+I++   G    Y FV+Y D + A  A+ +M
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIRE--HGNDP-YAFVEYYDHRSAAAALQTM 57

Query: 554 NGYRLEGRTIAV 565
           NG  + G+ I V
Sbjct: 58  NGRLILGQEIKV 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|240996 cd12552, RRM_Nop15p, RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins

 Score = 61.4 bits (149), Expect = 8e-12
 Identities = 28/74 (37%), Positives = 44/74 (59%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           +YIG+LP    +  L + FS FG +   +V + + TG SK YGF+++ + ++A  A  SM
Sbjct: 2   IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61

Query: 554 NGYRLEGRTIAVRV 567
           N Y L G+ + V V
Sbjct: 62  NNYLLMGKVLQVHV 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|241061 cd12617, RRM2_TIAR, RNA recognition motif 2 in nucleolysin TIAR and similar proteins

 Score = 60.9 bits (147), Expect = 1e-11
 Identities = 30/71 (42%), Positives = 42/71 (59%)

Query: 493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
           ++++G L P +  + +   F+ FG I  A+V+KD  TG SKGYGFV + +   A NAI  
Sbjct: 3   HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 62

Query: 553 MNGYRLEGRTI 563
           M G  L GR I
Sbjct: 63  MGGQWLGGRQI 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|240683 cd12237, RRM_snRNP35, RNA recognition motif found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K) and similar proteins

 Score = 61.1 bits (149), Expect = 1e-11
 Identities = 25/72 (34%), Positives = 40/72 (55%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L++G L     ++ L  +FS +GDI   ++++D VTG SKGY FV+Y   + A  A    
Sbjct: 6   LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDA 65

Query: 554 NGYRLEGRTIAV 565
           +   ++G  I V
Sbjct: 66  HKLVIDGSEIFV 77

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

 Score = 60.3 bits (147), Expect = 1e-11
 Identities = 27/73 (36%), Positives = 41/73 (56%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           +Y+G L   + ++ L  LF   G +V   + KDRVT   +GYGFV++   + A+ AI  M
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 554 NGYRLEGRTIAVR 566
           N  +L G+ I V 
Sbjct: 61  NMIKLYGKPIRVN 73

This subfamily corresponds to the RRM1 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145. . Length = 74

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

 Score = 60.2 bits (146), Expect = 2e-11
 Identities = 25/75 (33%), Positives = 41/75 (54%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L++  L  ++  + L   FS    I  A V+ D  TG S+GYGFV +A ++ A  A+A +
Sbjct: 2   LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 554 NGYRLEGRTIAVRVA 568
              +L GR + + +A
Sbjct: 62  KNKKLHGRILRLDIA 76

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

 Score = 60.5 bits (146), Expect = 2e-11
 Identities = 30/72 (41%), Positives = 41/72 (56%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           +++  L P  D+  L +LF  FG +   KVI+D  T   KG+GFV   +   A  AIAS+
Sbjct: 4   IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63

Query: 554 NGYRLEGRTIAV 565
           NGYRL  R + V
Sbjct: 64  NGYRLGDRVLQV 75

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

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

 Score = 59.7 bits (145), Expect = 2e-11
 Identities = 24/75 (32%), Positives = 43/75 (57%), Gaps = 1/75 (1%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           +++G LPP + ++     FS FG +V A++++D  TG S+G+GFV +   + A   + S 
Sbjct: 2   IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDS-ESAVERVFSA 60

Query: 554 NGYRLEGRTIAVRVA 568
               L G+ + V+ A
Sbjct: 61  GMLELGGKQVEVKRA 75

This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway; it binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y. . Length = 75

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 67.3 bits (165), Expect = 2e-11
 Identities = 45/226 (19%), Positives = 57/226 (25%), Gaps = 8/226 (3%)

Query: 560 GRTIAVRV----AGKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAA 615
           G    V      A        PP  P S+ P    + P     P+   AP         A
Sbjct: 579 GGDWQVEAVVGPAPGAAGGEGPP-APASSGPPEEAARPAAPAAPAAPAAPAPAGAAAAPA 637

Query: 616 SYTGAPVPWGPPVPPPYAPYAPPPPGSTMY--PPVPGQPMPPYGVQYPPPVQTAPPGALT 673
             + AP P            A P         P   G   P      P P   A P    
Sbjct: 638 EASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKAGGAAPAAPPPAPAPAAPAAPAGAA 697

Query: 674 APPGAPTQTATSSEAQQHSFPPGVQSESSSSAPAASANMYGSSMPPMPPNVQPAYATAPL 733
               AP   AT    Q           +  ++  + A      +PP P +  P  A AP 
Sbjct: 698 PAQPAPAPAATPPAGQADDPAAQPPQAAQGASAPSPAADDPVPLPPEPDD-PPDPAGAPA 756

Query: 734 GYSPYYNAVPPPPPPAPVSAADHSQNLGNVPWATNPPVQPPVSSAE 779
              P     P   P A    +  S+                   AE
Sbjct: 757 QPPPPPAPAPAAAPAAAPPPSPPSEEEEMAEDDAPSMDDEDRRDAE 802

Length = 824

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

 Score = 66.5 bits (162), Expect = 2e-11
 Identities = 30/84 (35%), Positives = 44/84 (52%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           +YIG LP  L +D +  L  +FGD+    +IKD  TG+SKGY F +Y D  + + AIA++
Sbjct: 298 IYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAAL 357

Query: 554 NGYRLEGRTIAVRVAGKPPQPTVP 577
           NG       + V+ A         
Sbjct: 358 NGKDTGDNKLHVQRACVGANQATI 381

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|241219 cd12775, RRM2_HuB, RNA recognition motif 2 in vertebrate Hu-antigen B (HuB)

 Score = 60.2 bits (145), Expect = 3e-11
 Identities = 33/85 (38%), Positives = 51/85 (60%), Gaps = 2/85 (2%)

Query: 491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAI 550
           D NLY+  LP T+    L +LFS +G I+ ++++ D+VTG+S+G GF+++     A  AI
Sbjct: 5   DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 64

Query: 551 ASMNGYRLEGRT--IAVRVAGKPPQ 573
             +NG +  G T  I V+ A  P Q
Sbjct: 65  KGLNGQKPPGATEPITVKFANNPSQ 89

This subgroup corresponds to the RRM2 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 90

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

 Score = 59.5 bits (145), Expect = 3e-11
 Identities = 29/77 (37%), Positives = 44/77 (57%)

Query: 490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNA 549
           +D  +++G L   + D+ L R FS +     AKV++D+ TG SKGYGFV ++D      A
Sbjct: 5   NDFRIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKA 64

Query: 550 IASMNGYRLEGRTIAVR 566
           +  MNG  +  R I +R
Sbjct: 65  MKEMNGKYVGNRPIKLR 81

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

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

 Score = 59.6 bits (144), Expect = 3e-11
 Identities = 28/75 (37%), Positives = 45/75 (60%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
            NL+I +LP    D  L + F  FG+++ AKV  D+ T +SK +GFV Y +   A  AI 
Sbjct: 5   CNLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAIQ 64

Query: 552 SMNGYRLEGRTIAVR 566
           +MNG+++  + + V+
Sbjct: 65  AMNGFQIGTKRLKVQ 79

This subgroup corresponds to the RRM3 of Bruno protein, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 79

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

 Score = 59.6 bits (145), Expect = 3e-11
 Identities = 23/75 (30%), Positives = 38/75 (50%)

Query: 491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAI 550
           +  L++  L P   D+ L  +FS FG I   +VI+D+ TG S  Y F+++   +    A 
Sbjct: 3   ENVLFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAY 62

Query: 551 ASMNGYRLEGRTIAV 565
             M+   ++ R I V
Sbjct: 63  FKMDNVLIDDRRIHV 77

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

>gnl|CDD|241218 cd12774, RRM2_HuD, RNA recognition motif 2 in vertebrate Hu-antigen D (HuD)

 Score = 59.7 bits (144), Expect = 3e-11
 Identities = 28/77 (36%), Positives = 46/77 (59%)

Query: 491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAI 550
           D NLY+  LP T+    L +LFS +G I+ ++++ D+VTG+S+G GF+++     A  AI
Sbjct: 2   DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 61

Query: 551 ASMNGYRLEGRTIAVRV 567
             +NG +  G    + V
Sbjct: 62  KGLNGQKPSGAAEPITV 78

This subgroup corresponds to the RRM2 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells and also regulates the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

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

 Score = 59.5 bits (145), Expect = 4e-11
 Identities = 21/70 (30%), Positives = 39/70 (55%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           LY+G L P + +  L  +FS  G ++  +V +D +T  S GY +V + +   A  A+ ++
Sbjct: 2   LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTL 61

Query: 554 NGYRLEGRTI 563
           N   ++G+ I
Sbjct: 62  NFDVIKGKPI 71

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

 Score = 59.2 bits (144), Expect = 4e-11
 Identities = 26/81 (32%), Positives = 40/81 (49%), Gaps = 7/81 (8%)

Query: 493 NLYIGYLPPTLDDDGLIRLFSTFG-----DIVMAKVIKDRVTGMSKGYGFVKYADIQMAN 547
            L+IG L   L +  L++LFS +G     D +  K    +  G  +GY FV +   + A 
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLK--GQPRGYCFVTFETKEEAE 58

Query: 548 NAIASMNGYRLEGRTIAVRVA 568
            A+ S+NG    G+ + VR A
Sbjct: 59  KALKSLNGKTALGKKLVVRWA 79

This subfamily corresponds to the RRM of RBM18, a putative RNA-binding protein containing a well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of RBM18 remains unclear. . Length = 80

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

 Score = 64.2 bits (156), Expect = 7e-11
 Identities = 45/172 (26%), Positives = 70/172 (40%), Gaps = 14/172 (8%)

Query: 483 AKPIKE-LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYA 541
           A+P  + +   NLY+  LP T+    L  +FS FG I+ ++++ D VTG+SKG GF+++ 
Sbjct: 80  ARPSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFD 139

Query: 542 DIQMANNAIASMNGYRLEGRT--IAVRVAGKPPQPTVPPGPPTSTMPTYPVSAPP-VGGY 598
               A+ AI ++NG    G T  I V+ A  P           S +          V   
Sbjct: 140 KRDEADRAIKTLNGTTPSGCTEPITVKFANNPSSSN--SKGLLSQLEAVQNPQTTRVPLS 197

Query: 599 PSQQYAPGGPL--------PNPPAASYTGAPVPWGPPVPPPYAPYAPPPPGS 642
                A  GP+        P+    +   A       V   +A     PP +
Sbjct: 198 TILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAAQRASPPAT 249

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|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 = 58.7 bits (142), Expect = 7e-11
 Identities = 28/75 (37%), Positives = 46/75 (61%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           +++G +P    ++ L  +FS  G +V  +++ DR TG  KGYGF +Y D + A +A+ ++
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 554 NGYRLEGRTIAVRVA 568
           NGY L GR + V  A
Sbjct: 61  NGYELNGRQLRVDNA 75

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

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

 Score = 58.5 bits (142), Expect = 7e-11
 Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 1/75 (1%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L+IG L     DD L   FS +G+I    V+KD  T  S+G+GFV +A     + A+ + 
Sbjct: 2   LFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNA- 60

Query: 554 NGYRLEGRTIAVRVA 568
             ++++GR +  + A
Sbjct: 61  RPHKVDGREVEPKRA 75

This subfamily corresponds to the RRM1 in hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 78

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

 Score = 58.4 bits (142), Expect = 8e-11
 Identities = 23/60 (38%), Positives = 34/60 (56%), Gaps = 1/60 (1%)

Query: 495 YIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMN 554
           ++G +PP   ++ L   FS FG +   K+I DR  G+SKGYGFV +   + A   +A  N
Sbjct: 6   FVGGIPPDTTEEELRDFFSRFGSVKDVKIITDR-AGVSKGYGFVTFETQEDAEKILAMGN 64

This subfamily corresponds to the RRM domain of two Deleted in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE. BOULE is the founder member of the family and DAZL arose from BOULE in an ancestor of vertebrates. The DAZ gene subsequently originated from a duplication transposition of the DAZL gene. Invertebrates contain a single DAZ homolog, BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. The family members encode closely related RNA-binding proteins that are required for fertility in numerous organisms. These proteins contain an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a varying number of copies of a DAZ motif, believed to mediate protein-protein interactions. DAZL and BOULE contain a single copy of the DAZ motif, while DAZ proteins can contain 8-24 copies of this repeat. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 80

>gnl|CDD|241082 cd12638, RRM3_CELF1_2, RNA recognition motif 3 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 58.5 bits (141), Expect = 9e-11
 Identities = 29/75 (38%), Positives = 48/75 (64%)

Query: 493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
           NL+I +LP    D  L+++F  FG++V AKV  D+ T +SK +GFV Y +   A  AI +
Sbjct: 9   NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQA 68

Query: 553 MNGYRLEGRTIAVRV 567
           MNG+++  + + V++
Sbjct: 69  MNGFQIGMKRLKVQL 83

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

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

 Score = 63.8 bits (155), Expect = 1e-10
 Identities = 31/114 (27%), Positives = 50/114 (43%), Gaps = 6/114 (5%)

Query: 452 PGSGSSGSNPPWANNSGSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRL 511
               ++    P A +  ++G      + ++            +++  L P  D+  L +L
Sbjct: 236 AQQHAAQRASPPATDGQTAGLAAGAQIAASDGA------GYCIFVYNLSPDTDETVLWQL 289

Query: 512 FSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAV 565
           F  FG +   K+I+D  T   KGYGFV   +   A  AI S+NGY L  R + V
Sbjct: 290 FGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQV 343

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

>gnl|CDD|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate Hu-antigen B (HuB)

 Score = 58.2 bits (140), Expect = 1e-10
 Identities = 29/72 (40%), Positives = 41/72 (56%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           +++  L P  D+  L ++F  FG +   KVI+D  T   KG+GFV   +   A  AIAS+
Sbjct: 6   IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 554 NGYRLEGRTIAV 565
           NGYRL  R + V
Sbjct: 66  NGYRLGDRVLQV 77

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

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

 Score = 57.9 bits (141), Expect = 1e-10
 Identities = 22/60 (36%), Positives = 31/60 (51%)

Query: 499 LPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRL 558
           L    D+D L  LF  FG I    + KD+ TG S+G+ FV +   + A  AI  +NG+  
Sbjct: 7   LSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNGFGY 66

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|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 65.0 bits (158), Expect = 1e-10
 Identities = 50/227 (22%), Positives = 64/227 (28%), Gaps = 22/227 (9%)

Query: 568  AGKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQ----QYAPGGPLPNPPAASYTGAPVP 623
            A  PPQ         +      ++ PP      +          PLP  PAA+   +P  
Sbjct: 2676 ASSPPQRPRRRAARPTVGSLTSLADPPPPPPTPEPAPHALVSATPLPPGPAAARQASPAL 2735

Query: 624  WGPPVPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTA 683
               P PP   P  P  PG    P  P     P     P      PP  LT P  A    +
Sbjct: 2736 PAAPAPPA-VPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSES 2794

Query: 684  TSSEAQQHSFPPGVQSESSSSAPAASANMYGSSMPPMPPNVQPAYATAPLGYSPYYNAV- 742
              S       P    +   + A A       +   P P + QP     P G  P    + 
Sbjct: 2795 RES-LPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLG 2853

Query: 743  ------------PPPPPPAPVSAADHSQNLGNVPWATNPPVQPPVSS 777
                        PP   PA   AA     +  +     P V     S
Sbjct: 2854 GSVAPGGDVRRRPPSRSPAAKPAAPARPPVRRLA---RPAVSRSTES 2897

Length = 3151

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

 Score = 57.3 bits (139), Expect = 2e-10
 Identities = 27/73 (36%), Positives = 39/73 (53%), Gaps = 1/73 (1%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           +++  LP ++    L  LF   G+++ A V  D   G SKG+G V +   + A  AI   
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDN-DGRSKGFGTVLFESPEDAQRAIEMF 59

Query: 554 NGYRLEGRTIAVR 566
           NGY LEGR + VR
Sbjct: 60  NGYDLEGRELEVR 72

This subfamily corresponds to the RRM3 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 72

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

 Score = 57.7 bits (140), Expect = 2e-10
 Identities = 26/83 (31%), Positives = 41/83 (49%), Gaps = 4/83 (4%)

Query: 494 LYIGYLPPTLDDDGLIR-LFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
           L++  LP T  D  ++R LFS  G     ++      G  +G+ FV+YA  + A  A  +
Sbjct: 5   LFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAP-NGQPRGFAFVEYATAEDAEEAQQA 63

Query: 553 MNGYRLEGRTIAVRVAGKPPQPT 575
           +NG+ L+G  I  RV+   P   
Sbjct: 64  LNGHSLQGSPI--RVSFGNPGRP 84

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|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate Hu-antigen D (HuD)

 Score = 57.4 bits (138), Expect = 2e-10
 Identities = 30/72 (41%), Positives = 41/72 (56%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           +++  L P  D+  L +LF  FG +   KVI+D  T   KG+GFV   +   A  AIAS+
Sbjct: 6   IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 554 NGYRLEGRTIAV 565
           NGYRL  R + V
Sbjct: 66  NGYRLGDRVLQV 77

This subgroup corresponds to the RRM3 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells. And it also regulates the neurite elongation and morphological differentiation. HuD specifically bound poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 86

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

 Score = 56.8 bits (138), Expect = 2e-10
 Identities = 25/70 (35%), Positives = 42/70 (60%), Gaps = 1/70 (1%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L+IG L     ++ L   FS +G++V   ++KD +TG S+G+GFV +AD    +  +A+ 
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAK 60

Query: 554 NGYRLEGRTI 563
             + L+GR I
Sbjct: 61  P-HVLDGREI 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|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 63.3 bits (154), Expect = 3e-10
 Identities = 30/78 (38%), Positives = 48/78 (61%), Gaps = 3/78 (3%)

Query: 483 AKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYAD 542
           A P+K+   TNLY+  L P++++D L  LF+ FG+I  A V+KD  +G S+G+ FV +  
Sbjct: 172 AAPLKKF--TNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDG-SGRSRGFAFVNFEK 228

Query: 543 IQMANNAIASMNGYRLEG 560
            + A  A+  MNG ++  
Sbjct: 229 HEDAAKAVEEMNGKKIGL 246

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

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 63.8 bits (155), Expect = 3e-10
 Identities = 58/231 (25%), Positives = 69/231 (29%), Gaps = 25/231 (10%)

Query: 568  AGKPPQPTVPPGPPTSTMP--------TYPVSAPPVGGYPSQQYAPGGPL-----PNPPA 614
               P +P   P P   + P            S+PP            G L     P PP 
Sbjct: 2646 VPPPERPRDDPAPGRVSRPRRARRLGRAAQASSPPQRPRRRAARPTVGSLTSLADPPPPP 2705

Query: 615  ASYTGAPVPWGPPVPPPYAPYA-----PPPPGSTMYPPVPGQPMPPYGVQYP--PPVQTA 667
             +   AP       P P  P A     P  P +   P VP  P  P G   P  PP    
Sbjct: 2706 PTPEPAPHALVSATPLPPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAG 2765

Query: 668  P--PGALTAPPGAPTQTATSSEAQQHSFPPGVQSESSSSAPAASANMYGSSMPPMPPNVQ 725
            P  P    AP   P +  T       S     +S  S   PA       +    +PP   
Sbjct: 2766 PPAPAPPAAPAAGPPRRLTRPAVA--SLSESRESLPSPWDPADPPAAVLAPAAALPPAAS 2823

Query: 726  PAYATAPLGYSPYYNAVPPPPPPAPVSAADHSQNLGNVPWATNPPVQPPVS 776
            PA    P   S    A PPPP P P S                PP + P +
Sbjct: 2824 PA-GPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSPAA 2873

Length = 3151

>gnl|CDD|241220 cd12776, RRM2_HuC, RNA recognition motif 2 in vertebrate Hu-antigen C (HuC)

 Score = 56.9 bits (137), Expect = 3e-10
 Identities = 29/80 (36%), Positives = 48/80 (60%), Gaps = 2/80 (2%)

Query: 491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAI 550
           D NLY+  LP T+    + +LFS +G I+ ++++ D+VTG+S+G GF+++     A  AI
Sbjct: 1   DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAI 60

Query: 551 ASMNGYRLEGRT--IAVRVA 568
             +NG +  G    I V+ A
Sbjct: 61  KGLNGQKPLGAAEPITVKFA 80

This subgroup corresponds to the RRM2 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

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

 Score = 56.9 bits (138), Expect = 3e-10
 Identities = 24/77 (31%), Positives = 37/77 (48%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L++  LP    D+ L   FS  G I    V+KD+ +   +G+G+V +A  + A  A+   
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 554 NGYRLEGRTIAVRVAGK 570
              +  GR I V  A K
Sbjct: 62  KKTKFGGRKIHVEFAKK 78

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|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 63.4 bits (154), Expect = 4e-10
 Identities = 51/243 (20%), Positives = 70/243 (28%), Gaps = 32/243 (13%)

Query: 568  AGKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAAS---------YT 618
            A  PP P  P   P + +   P+   P     +    P  P P    A            
Sbjct: 2699 ADPPPPPPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPA 2758

Query: 619  GAPVPWGPPVP-PPYAPYAPPPP------GSTMYPPVPGQPMPPYGVQYPPPV------- 664
              P   GPP P PP AP A PP        +++       P P      P  V       
Sbjct: 2759 RPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAAL 2818

Query: 665  -QTAPPGALTAPPGAPTQTATS--------SEAQQHSFPPGVQSESSSSAPAASANMYGS 715
               A P     PP +   TA          S     S  PG        + + +A     
Sbjct: 2819 PPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSPAAKPAAP 2878

Query: 716  SMPPMPPNVQPAYATAPLGYSPYYNAVPPPPPPAPVSAADHSQNLGNVPWATNPPVQPPV 775
            + PP+    +PA + +   ++   +    PP P               P    PP  PP 
Sbjct: 2879 ARPPVRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPR 2938

Query: 776  SSA 778
               
Sbjct: 2939 PQP 2941

Length = 3151

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

 Score = 56.4 bits (136), Expect = 4e-10
 Identities = 27/76 (35%), Positives = 44/76 (57%), Gaps = 1/76 (1%)

Query: 494 LYIGYLPPTLDDDGLIRLF-STFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
           +++G L P +++  L+ LF S F     AK++ D VTG+S+GYGFV+++D      A+  
Sbjct: 4   IFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALIE 63

Query: 553 MNGYRLEGRTIAVRVA 568
           M G    GR + +  A
Sbjct: 64  MQGVYCGGRPMRISTA 79

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

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

 Score = 56.1 bits (136), Expect = 5e-10
 Identities = 22/67 (32%), Positives = 35/67 (52%), Gaps = 1/67 (1%)

Query: 499 LPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRL 558
           LP    +  L +LFS FG +    + +    G  KG+ FV++     A  AI  +NG ++
Sbjct: 7   LPFKCTEADLKKLFSPFGFVWEVTIPRKP-DGKKKGFAFVQFTSKADAEKAIKGVNGKKI 65

Query: 559 EGRTIAV 565
           +GR +AV
Sbjct: 66  KGRPVAV 72

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|241217 cd12773, RRM2_HuR, RNA recognition motif 2 in vertebrate Hu-antigen R (HuR)

 Score = 56.2 bits (135), Expect = 5e-10
 Identities = 31/83 (37%), Positives = 48/83 (57%), Gaps = 2/83 (2%)

Query: 493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
           NLYI  LP T+    +  +FS FG I+ ++V+ D+ TG+S+G  F+++     A  AI S
Sbjct: 2   NLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITS 61

Query: 553 MNGYRLEGRT--IAVRVAGKPPQ 573
            NG++  G +  I V+ A  P Q
Sbjct: 62  FNGHKPPGSSEPITVKFAANPNQ 84

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

>gnl|CDD|240789 cd12343, RRM1_2_CoAA_like, RNA recognition motif 1 and 2 in RRM-containing coactivator activator/modulator (CoAA) and similar proteins

 Score = 55.7 bits (135), Expect = 5e-10
 Identities = 23/72 (31%), Positives = 36/72 (50%), Gaps = 8/72 (11%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L++G LP     + L  LF  +G +    V+K+        YGFV   + + A +AI ++
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGTVTECDVVKN--------YGFVHMEEEEDAEDAIKAL 53

Query: 554 NGYRLEGRTIAV 565
           NGY   G+ I 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|240770 cd12324, RRM_RBM8, RNA recognition motif in RNA-binding protein RBM8A, RBM8B nd similar proteins

 Score = 56.1 bits (136), Expect = 6e-10
 Identities = 22/61 (36%), Positives = 34/61 (55%)

Query: 505 DDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIA 564
           ++ +   F+ FG+I    +  DR TG  KGY  ++Y   + A  AI  +NG  L G+TI+
Sbjct: 20  EEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGLNGKELLGQTIS 79

Query: 565 V 565
           V
Sbjct: 80  V 80

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

 Score = 55.4 bits (134), Expect = 7e-10
 Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 6/73 (8%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L++G LP  + ++    LFS +G++    + K+      KG+GF++      A  A A +
Sbjct: 4   LFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE------KGFGFIRLDTRTNAEKAKAEL 57

Query: 554 NGYRLEGRTIAVR 566
           +G   +GR + VR
Sbjct: 58  DGIMRKGRQLRVR 70

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

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

 Score = 55.3 bits (134), Expect = 8e-10
 Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 1/77 (1%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           + + +  LP  + +D L   F + G++   KV++ R  G S+ +GFV +   + A  A+ 
Sbjct: 1   SRIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTR-DGKSRRFGFVGFKSEEDAQQAVK 59

Query: 552 SMNGYRLEGRTIAVRVA 568
             N   ++   I+V +A
Sbjct: 60  YFNKTFIDTSKISVELA 76

This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

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

 Score = 55.3 bits (134), Expect = 8e-10
 Identities = 29/78 (37%), Positives = 40/78 (51%), Gaps = 9/78 (11%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           LY+  LP +  ++ L  LFS +G++   K IKD        Y FV + +   A  A+  M
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD--------YAFVHFEERDDAVKAMEEM 55

Query: 554 NGYRLEGRTIAVRVAGKP 571
           NG  LEG  I V +A KP
Sbjct: 56  NGKELEGSPIEVSLA-KP 72

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

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

 Score = 55.1 bits (133), Expect = 9e-10
 Identities = 20/70 (28%), Positives = 39/70 (55%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L++G L    D+D +   F  +G+I   ++  D  +G  KG+G+V+++  + A  A+ ++
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 554 NGYRLEGRTI 563
            G  L GR +
Sbjct: 61  GGTDLLGRPV 70

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

 Score = 61.5 bits (149), Expect = 9e-10
 Identities = 29/75 (38%), Positives = 44/75 (58%)

Query: 491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAI 550
              LY+G L   + +  L ++F  FGDI   ++ +D  TG SKG+GF+++ D + A  A+
Sbjct: 186 FLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEAL 245

Query: 551 ASMNGYRLEGRTIAV 565
             MNG+ L GR I V
Sbjct: 246 EVMNGFELAGRPIKV 260

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 61.9 bits (150), Expect = 1e-09
 Identities = 52/235 (22%), Positives = 63/235 (26%), Gaps = 19/235 (8%)

Query: 560  GRTIAVRVAGKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPL--PNPPAASY 617
                A      PP    PP  P        VS P       +      P   P   AA  
Sbjct: 2631 PSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAAQASSPPQRPRRRAARP 2690

Query: 618  TGAPVPWGPPVPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAP-- 675
            T   +      PPP     P P       P+P  P          P   APP     P  
Sbjct: 2691 TVGSLTSLADPPPPPPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAPPAVPAGPAT 2750

Query: 676  PGAPTQTATSSEAQQHSFPPGVQSESSSSAPAASANMYGSSMPPMPPNVQPAYATAPLGY 735
            PG P + A          PP      + + PAA A        P     +PA A+     
Sbjct: 2751 PGGPARPAR---------PPTTAGPPAPAPPAAPAA------GPPRRLTRPAVASLSESR 2795

Query: 736  SPYYNAVPPPPPPAPVSAADHSQNLGNVPWATNPPVQPPVSSAEKSNYGADAEYE 790
                +   P  PPA V A   +      P    PP      +A     G      
Sbjct: 2796 ESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSL 2850

Length = 3151

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

 Score = 55.3 bits (134), Expect = 1e-09
 Identities = 24/64 (37%), Positives = 38/64 (59%), Gaps = 1/64 (1%)

Query: 502 TLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGR 561
           T + D L  +FS +G I   +V+ D+ TG S+G+GFV +  ++ A  A   +NG  ++GR
Sbjct: 11  TTERD-LREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEIDGR 69

Query: 562 TIAV 565
            I V
Sbjct: 70  RIRV 73

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

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

 Score = 54.9 bits (133), Expect = 1e-09
 Identities = 21/70 (30%), Positives = 42/70 (60%), Gaps = 2/70 (2%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           LY+  LPP++ ++ L   FS +G +   +++++      +G+ FV++A  + A  A+  +
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRN--KDRPRGFAFVEFASPEDAEAALKKL 58

Query: 554 NGYRLEGRTI 563
           NG  L+GRT+
Sbjct: 59  NGLVLDGRTL 68

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

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

 Score = 55.1 bits (132), Expect = 1e-09
 Identities = 26/62 (41%), Positives = 39/62 (62%), Gaps = 1/62 (1%)

Query: 505 DDGLI-RLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTI 563
           D+G++ ++F  FG +   KVI+D  T   KG+GFV   + + A  AIAS+NGYRL  + +
Sbjct: 14  DEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASLNGYRLGDKIL 73

Query: 564 AV 565
            V
Sbjct: 74  QV 75

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

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 61.5 bits (149), Expect = 2e-09
 Identities = 41/211 (19%), Positives = 62/211 (29%), Gaps = 12/211 (5%)

Query: 571  PPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGPPVPP 630
            PP+P   P  P  T       APP     ++  AP       P      +P+P     P 
Sbjct: 2570 PPRPAPRPSEPAVTSRARRPDAPP---QSARPRAPVDD-RGDPRGPAPPSPLPPDTHAPD 2625

Query: 631  PYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATSSEAQQ 690
            P  P   P        P P  P P      P P + + P        A   ++     ++
Sbjct: 2626 PPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAAQASSPPQRPRR 2685

Query: 691  HSFPPGVQSESSSSAPAASANMYGSSMPPMPPNVQPAYATAPLGYSPYYNAVPPPPPPAP 750
             +  P V S +S + P         +   +          A    +       P PP  P
Sbjct: 2686 RAARPTVGSLTSLADPPPPPPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAPPAVP 2745

Query: 751  VSAADHSQNLGNVPWATNPPVQPPVSSAEKS 781
               A         P     P +PP ++   +
Sbjct: 2746 AGPA--------TPGGPARPARPPTTAGPPA 2768

Length = 3151

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

 Score = 54.2 bits (131), Expect = 2e-09
 Identities = 21/60 (35%), Positives = 38/60 (63%)

Query: 506 DGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAV 565
           D L R+F  +G++    + +DR T  S+G+ FV++ D + A +A+ +M+G  L+GR + V
Sbjct: 13  DDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDGKELDGRELRV 72

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

>gnl|CDD|240863 cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold attachment factor (SAFB) family

 Score = 53.9 bits (130), Expect = 3e-09
 Identities = 23/73 (31%), Positives = 40/73 (54%)

Query: 493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
           NL++  L  T     L +LFS +G +V AK++ +  +  ++ +GFV  A ++ A   I  
Sbjct: 1   NLWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQH 60

Query: 553 MNGYRLEGRTIAV 565
           ++   L GR I+V
Sbjct: 61  LHRTELHGRVISV 73

This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM. . Length = 74

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 60.3 bits (146), Expect = 4e-09
 Identities = 56/233 (24%), Positives = 72/233 (30%), Gaps = 16/233 (6%)

Query: 548  NAIASMNGYRLEGRTIAVRVAGKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGG 607
               A+  G     R         P  P  P   P   +    V++       S++  P  
Sbjct: 2746 AGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLS----ESRESLPSP 2801

Query: 608  PLPNPPAASYTGAPVPWGPPVPPPYAPYAPPPPGSTMYPPVPGQPMPPY----GVQYP-- 661
              P  P A+   AP    PP   P  P  PP       PP P  P PP     G   P  
Sbjct: 2802 WDPADPPAAVL-APAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGG 2860

Query: 662  PPVQTAPPGALTAPPGAPTQTATSSEAQQHSFPPGVQSESSSSAPAASANMYGSSMPPMP 721
               +  P  +  A P AP +      A+    P   +S  S + P            P P
Sbjct: 2861 DVRRRPPSRSPAAKPAAPARPPVRRLAR----PAVSRSTESFALPPDQPERPPQPQAPPP 2916

Query: 722  PNVQPAYATAPLGYSPYYNAVPPPPPPAPVS-AADHSQNLGNVPWATNPPVQP 773
            P  QP     P    P      P PP AP +  A   +  G VP      + P
Sbjct: 2917 PQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVP 2969

Length = 3151

>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 = 53.9 bits (130), Expect = 4e-09
 Identities = 24/63 (38%), Positives = 34/63 (53%)

Query: 487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMA 546
           K+ D   L++G +P  L++  L  LF  FG I    V+KD+ TGM KG  F+ Y   + A
Sbjct: 1   KDDDAIKLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESA 60

Query: 547 NNA 549
             A
Sbjct: 61  LKA 63

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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 52.1 bits (126), Expect = 7e-09
 Identities = 18/61 (29%), Positives = 30/61 (49%), Gaps = 5/61 (8%)

Query: 508 LIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV 567
           L +LFS FG      V K ++     G+ FV+++  + A  A+  +NG    GR + V  
Sbjct: 1   LYKLFSPFG-----NVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDY 55

Query: 568 A 568
           +
Sbjct: 56  S 56

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. Length = 56

>gnl|CDD|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 52.9 bits (126), Expect = 7e-09
 Identities = 30/66 (45%), Positives = 37/66 (56%)

Query: 488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMAN 547
           +L  TNLYI  LPP   D  LI+L   +G IV  K I D+ T   KGYGFV +     A 
Sbjct: 1   QLSKTNLYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQ 60

Query: 548 NAIASM 553
            A+AS+
Sbjct: 61  KAVASL 66

This subgroup corresponds to the RRM1 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. RBMS3 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines. . Length = 80

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

 Score = 52.7 bits (127), Expect = 7e-09
 Identities = 29/77 (37%), Positives = 42/77 (54%), Gaps = 3/77 (3%)

Query: 494 LYIGYLPPTLDDDGLIRLFST-FGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
           L++G L P +DD  L   FS  +     AKV+ D+  G S+GYGFV+++D      A+  
Sbjct: 4   LFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLDQ-NGNSRGYGFVRFSDESEQKRALTE 62

Query: 553 MNGYR-LEGRTIAVRVA 568
           M G   L G+ I V +A
Sbjct: 63  MQGASGLGGKPIRVSLA 79

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

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

 Score = 52.7 bits (127), Expect = 8e-09
 Identities = 23/56 (41%), Positives = 32/56 (57%)

Query: 512 FSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV 567
           F+ FG+I    V+KD+ T  SKG  +VK+A    A  A+  MNG  L G T  ++V
Sbjct: 23  FAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCLGGDTKPLKV 78

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

 Score = 57.9 bits (140), Expect = 1e-08
 Identities = 26/74 (35%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
            N+++  L  ++D+  L   FS FG+I+  KV  D   G S+GYGFV +   + A  AI 
Sbjct: 89  GNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATD-ENGKSRGYGFVHFEKEESAKAAIQ 147

Query: 552 SMNGYRLEGRTIAV 565
            +NG  L  + + V
Sbjct: 148 KVNGMLLNDKEVYV 161

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

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

 Score = 52.5 bits (126), Expect = 1e-08
 Identities = 29/86 (33%), Positives = 45/86 (52%), Gaps = 8/86 (9%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L++G L      + L R FS +G++V   ++KD+ T  S+G+GFVK+ D       +A  
Sbjct: 2   LFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAG- 60

Query: 554 NGYRLEGRTIAVRVAGKPPQPTVPPG 579
             + L+GRTI        P+P  P G
Sbjct: 61  GPHTLDGRTI-------DPKPCTPRG 79

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

 Score = 51.8 bits (125), Expect = 1e-08
 Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 13/75 (17%)

Query: 494 LYIGYLPPT-LDDDGLIRLFSTFGDIVMAKVIKDRVTGMS--KGYGFVKYADIQMANNAI 550
           +++G L    +  + L  +FS +G          ++ G+S  KGYGFV++ + + A  A+
Sbjct: 3   VFVGNLNTDKVSKEDLEEIFSKYG----------KILGISLHKGYGFVQFDNEEDARAAV 52

Query: 551 ASMNGYRLEGRTIAV 565
           A  NG  + G+ + +
Sbjct: 53  AGENGREIAGQKLDI 67

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|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1

 Score = 58.2 bits (141), Expect = 1e-08
 Identities = 35/157 (22%), Positives = 42/157 (26%), Gaps = 17/157 (10%)

Query: 571 PPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGPPVPP 630
             Q    P PP   +P      P    +P Q        P  P   Y   P      V P
Sbjct: 166 RQQAPQLPQPPQQVLP--QGMPPRQAAFPQQGP------PEQPPG-YPQPPQGHPEQVQP 216

Query: 631 PYAPYAPPPPGSTM-YPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATSSEAQ 689
                AP    +    PP   Q  PP      P +    P     PP  P Q     + Q
Sbjct: 217 QQFLPAPSQAPAQPPLPPQLPQQPPPLQQPQFPGLSQQMPP---PPPQPPQQQQQPPQPQ 273

Query: 690 QHSFPPGVQSESSSSAPAASANMYGSSMPPMPPNVQP 726
               PP     +         N      PP  P + P
Sbjct: 274 AQ--PPPQNQPTPHPGLPQGQN--APLPPPQQPQLLP 306

Members of this family are necessary for accurate chromosome transmission during cell division. Length = 804

>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 = 51.9 bits (125), Expect = 1e-08
 Identities = 23/72 (31%), Positives = 38/72 (52%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L++  LP T  ++ L  LF  FG+I    +  D+ T  SKG+ FV +   + A  A + +
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 554 NGYRLEGRTIAV 565
           +G   +GR + V
Sbjct: 62  DGSIFQGRLLHV 73

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

 Score = 52.2 bits (126), Expect = 1e-08
 Identities = 24/76 (31%), Positives = 43/76 (56%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           T +++G +P  + DD + +L    G ++  K +KD  TG  K +GF ++ D + A  A+ 
Sbjct: 1   TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALR 60

Query: 552 SMNGYRLEGRTIAVRV 567
            +NG  L G+ + V+V
Sbjct: 61  LLNGLELGGKKLLVKV 76

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|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 58.1 bits (141), Expect = 2e-08
 Identities = 30/126 (23%), Positives = 40/126 (31%), Gaps = 6/126 (4%)

Query: 585 MPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGPPVPPPYAPYAPPPPGSTM 644
           +     +  P    PS   A     P P AA    AP     P P      AP P  +  
Sbjct: 385 LGVAGGAGAPAAAAPSAAAAAPAAAPAPAAA----APAAAAAPAPAAAPQPAPAPAPAP- 439

Query: 645 YPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATSSEAQQHSFPPGVQSESSSS 704
             P       P G    PP   AP       P A  +   +      + P    + ++ +
Sbjct: 440 -APPSPAGNAPAGGAPSPPPAAAPSAQPAPAPAAAPEPTAAPAPAPPAAPAPAAAPAAPA 498

Query: 705 APAASA 710
           APAA A
Sbjct: 499 APAAPA 504

Length = 824

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 58.0 bits (140), Expect = 2e-08
 Identities = 56/236 (23%), Positives = 67/236 (28%), Gaps = 29/236 (12%)

Query: 564  AVRVAGKPPQPTVP------------PGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPN 611
            A   AG P + T P            P P     P   V AP     P+   +P GPLP 
Sbjct: 2773 AAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAA--SPAGPLPP 2830

Query: 612  PPAASYTGAPVPWGPPVP--PPYAPYAP-------PPPGSTMYPPVPGQPMPPYGVQYPP 662
            P +A  T  P P GPP P  P     AP       PP  S      P  P  P   +   
Sbjct: 2831 PTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSP--AAKPAAPARPPVRRLAR 2888

Query: 663  PVQTAPPGALTAPPGAPTQTATSSEAQQHSFPPGVQSESSSSAPAASANMYGSSMPPMPP 722
            P  +    +   PP  P +             P          P           PP+ P
Sbjct: 2889 PAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQ---PQPPPPPPPRPQPPLAP 2945

Query: 723  NVQPAYATAPLGYSPYYNAVPPPPPPAPVSAADHSQNLGNVPWATNPPVQPPVSSA 778
               PA A  P G  P        P    V      Q   +   A      P    +
Sbjct: 2946 TTDPAGAGEPSGAVPQPWLGALVPGRVAVPRFRVPQPAPSRE-APASSTPPLTGHS 3000

Length = 3151

>gnl|CDD|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau; Provisional

 Score = 58.0 bits (140), Expect = 2e-08
 Identities = 40/228 (17%), Positives = 57/228 (25%), Gaps = 15/228 (6%)

Query: 571 PPQPTVPP--GPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGPPV 628
           P      P   P  +       +  P     +   AP         A+      P   P 
Sbjct: 374 PATAAAAPVAQPAPAAAAPAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPARRSP--APE 431

Query: 629 PPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATSSEA 688
               A  A          P P     P     P      P  A  A   A    A +   
Sbjct: 432 ALAAARQASARGPGGAPAPAPAPAAAPAAAARPAAAGPRPVAAAAAAAPARAAPAAAPAP 491

Query: 689 QQHSFPPGVQSESSSSAPAASANMYGSSMPPMPPNVQPAYATAPLGYSPYYNAVPPPPPP 748
                PP  +     ++PA +      +         PA A     +     A  P   P
Sbjct: 492 ADDDPPPWEELPPEFASPAPAQPDAAPAGWVAESIPDPATADPDDAFET--LAPAPAAAP 549

Query: 749 APVSAADHSQNLGNVPWATNPPVQPPVSSAEKSNYGADAEYEKFMAEM 796
           AP +AA                 +PP +SA       D ++    A +
Sbjct: 550 APRAAA---------ATEPVVAPRPPRASASGLPDMFDGDWPALAARL 588

Length = 700

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

 Score = 57.0 bits (137), Expect = 2e-08
 Identities = 37/122 (30%), Positives = 54/122 (44%), Gaps = 13/122 (10%)

Query: 451 GPGSGSSGSNPPWAN----NSGSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDD 506
             G GS G+    A+    NS  SG        ++G         TNL + YLP  + D 
Sbjct: 72  ACGLGSMGNMANMASTNSLNSLGSGGSDDNDTNNSG---------TNLIVNYLPQDMTDR 122

Query: 507 GLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR 566
            L  LF T G I   ++++D  TG S GY FV +     +  AI ++NG  +  + + V 
Sbjct: 123 ELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVS 182

Query: 567 VA 568
            A
Sbjct: 183 YA 184

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

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

 Score = 56.6 bits (136), Expect = 2e-08
 Identities = 33/89 (37%), Positives = 54/89 (60%), Gaps = 3/89 (3%)

Query: 483 AKPIKE-LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYA 541
           A+P  E + DTNLY+  LP T+ DD L  +F  +G IV   +++D++TG  +G  FV++ 
Sbjct: 184 ARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFN 243

Query: 542 DIQMANNAIASMNGYRLEGRT--IAVRVA 568
             + A  AI+++N    EG +  + VR+A
Sbjct: 244 KREEAQEAISALNNVIPEGGSQPLTVRLA 272

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

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

 Score = 51.9 bits (125), Expect = 2e-08
 Identities = 19/74 (25%), Positives = 38/74 (51%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L++  L     +  L R F  +G I   ++++D+ TG  +GY F+++   +    A    
Sbjct: 4   LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYA 63

Query: 554 NGYRLEGRTIAVRV 567
           +G +++GR + V V
Sbjct: 64  DGKKIDGRRVLVDV 77

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

 Score = 51.6 bits (124), Expect = 2e-08
 Identities = 24/74 (32%), Positives = 45/74 (60%), Gaps = 1/74 (1%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMA-KVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
           L++G L P +D++ + R F++ G+ V++ K+I++++TG   GY FV++AD   A   +  
Sbjct: 2   LWMGDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLHK 61

Query: 553 MNGYRLEGRTIAVR 566
           +NG  + G     R
Sbjct: 62  LNGKPIPGSNPPKR 75

This subgroup corresponds to the RRM1 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. . Length = 84

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

 Score = 51.4 bits (123), Expect = 2e-08
 Identities = 24/70 (34%), Positives = 39/70 (55%), Gaps = 4/70 (5%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA-- 551
           L++G L   + +  L   FS FG +  A+VI D+ TG  +G+GFV + +   A+ A    
Sbjct: 2   LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVVK 61

Query: 552 --SMNGYRLE 559
              +NG+R+E
Sbjct: 62  FHPINGHRVE 71

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

 Score = 52.2 bits (125), Expect = 2e-08
 Identities = 23/90 (25%), Positives = 35/90 (38%), Gaps = 3/90 (3%)

Query: 491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAI 550
           D  L++  LP    ++ L   FS FG +  A  + D+ TG +KG GFV + D    N  +
Sbjct: 1   DFTLFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACL 60

Query: 551 ASMNGYRLEGRTIAVRVAGKPPQPTVPPGP 580
                    G T  +  +           P
Sbjct: 61  K---NAPAAGSTSLLSGSSLTADIGDDVMP 87

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|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 56.9 bits (138), Expect = 3e-08
 Identities = 39/210 (18%), Positives = 53/210 (25%), Gaps = 23/210 (10%)

Query: 561 RTIAVRVAGKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGA 620
            T      G   Q     GP        P +A   G        P      P A +   A
Sbjct: 571 VTALAEELGGDWQVEAVVGPA-------PGAAGGEGPPAPASSGPPEEAARPAAPAAPAA 623

Query: 621 PV------------PWGPPVPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAP 668
           P                    P  A     P    +     G    P       P    P
Sbjct: 624 PAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKAGGAAPAAPPP 683

Query: 669 PGALTAPPGAPTQTATSSEAQQHSFPPGVQSESSSSAPAASANMYG----SSMPPMPPNV 724
             A  AP                + PP  Q++  ++ P  +A        ++  P+P   
Sbjct: 684 APAPAAPAAPAGAAPAQPAPAPAATPPAGQADDPAAQPPQAAQGASAPSPAADDPVPLPP 743

Query: 725 QPAYATAPLGYSPYYNAVPPPPPPAPVSAA 754
           +P     P G        P P P A  +AA
Sbjct: 744 EPDDPPDPAGAPAQPPPPPAPAPAAAPAAA 773

Length = 824

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 57.6 bits (139), Expect = 3e-08
 Identities = 43/193 (22%), Positives = 59/193 (30%), Gaps = 22/193 (11%)

Query: 597  GYPSQQYAPGGPLPNPPAASYTGAPVPWGPPVPPPYAPYAPPPPGSTMYPPVP-GQPMPP 655
            G P  +       P         AP P G   P P AP AP      + P  P G+P+ P
Sbjct: 2476 GAPVYRRPAEARFPFAA----GAAPDPGGGGPPDPDAPPAPSRLAPAILPDEPVGEPVHP 2531

Query: 656  YGVQYPPPVQT---------APPGALTAPPGAPTQTATSSEAQQHSFPPGVQS-ESSSSA 705
              + +   ++           PP    APP AP ++            P V S      A
Sbjct: 2532 RMLTWIRGLEELASDDAGDPPPPLPPAAPPAAPDRSVPPPRPAPRPSEPAVTSRARRPDA 2591

Query: 706  PAASANMYGSSMPPMPPNVQPAYATAPLGYSPYYNAVPPPPPPAPVSAADHSQNLGNVPW 765
            P  SA           P      +  P            P PP P  +   ++   + P 
Sbjct: 2592 PPQSARPRAPVDDRGDPRGPAPPSPLP-------PDTHAPDPPPPSPSPAANEPDPHPPP 2644

Query: 766  ATNPPVQPPVSSA 778
               PP +P    A
Sbjct: 2645 TVPPPERPRDDPA 2657

Length = 3151

>gnl|CDD|238053 cd00105, KH-I, K homology RNA-binding domain, type I

 Score = 50.6 bits (122), Expect = 3e-08
 Identities = 22/86 (25%), Positives = 35/86 (40%), Gaps = 24/86 (27%)

Query: 254 KLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDP 313
           ++ +P         +G IIG  G+T K +  ETGAKI I                     
Sbjct: 3   RVLVPSS------LVGRIIGKGGSTIKEIREETGAKIKIP-----------------DSG 39

Query: 314 SENEDLHVLVEAETQESLEGAAAMVE 339
           S +E+  V +   T E++E A  ++ 
Sbjct: 40  SGSEERIVTITG-TPEAVEKAKELIL 64

KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension. Length = 64

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

 Score = 50.9 bits (122), Expect = 3e-08
 Identities = 26/76 (34%), Positives = 42/76 (55%), Gaps = 4/76 (5%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVI-KDRVTGMSKGYGFVKYADIQMANNAIAS 552
           L++  +P    D  L ++F  FG I+  ++I  +R    SKG+GFV +A+   A+ A   
Sbjct: 3   LHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNER---GSKGFGFVTFANSADADRAREK 59

Query: 553 MNGYRLEGRTIAVRVA 568
           ++G  +EGR I V  A
Sbjct: 60  LHGTVVEGRKIEVNNA 75

This subfamily corresponds to the RRM of several tissue-specific alternative splicing isoforms of vertebrate RNA binding protein Fox-1 homologs, which show high sequence similarity to the Caenorhabditis elegans feminizing locus on X (Fox-1) gene encoding Fox-1 protein. RNA binding protein Fox-1 homolog 1 (RBFOX1), also termed ataxin-2-binding protein 1 (A2BP1), or Fox-1 homolog A, or hexaribonucleotide-binding protein 1 (HRNBP1), is predominantly expressed in neurons, skeletal muscle and heart. It regulates alternative splicing of tissue-specific exons by binding to UGCAUG elements. Moreover, RBFOX1 binds to the C-terminus of ataxin-2 and forms an ataxin-2/A2BP1 complex involved in RNA processing. RNA binding protein fox-1 homolog 2 (RBFOX2), also termed Fox-1 homolog B, or hexaribonucleotide-binding protein 2 (HRNBP2), or RNA-binding motif protein 9 (RBM9), or repressor of tamoxifen transcriptional activity, is expressed in ovary, whole embryo, and human embryonic cell lines in addition to neurons and muscle. RBFOX2 activates splicing of neuron-specific exons through binding to downstream UGCAUG elements. RBFOX2 also functions as a repressor of tamoxifen activation of the estrogen receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3 or NeuN or HRNBP3), also termed Fox-1 homolog C, is a nuclear RNA-binding protein that regulates alternative splicing of the RBFOX2 pre-mRNA, producing a message encoding a dominant negative form of the RBFOX2 protein. Its message is detected exclusively in post-mitotic regions of embryonic brain. Like RBFOX1, both RBFOX2 and RBFOX3 bind to the hexanucleotide UGCAUG elements and modulate brain and muscle-specific splicing of exon EIIIB of fibronectin, exon N1 of c-src, and calcitonin/CGRP. Members in this family also harbor one RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 76

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

 Score = 50.8 bits (122), Expect = 4e-08
 Identities = 23/77 (29%), Positives = 41/77 (53%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           T+LY+  +      D L RLF  +G IV   +  D  T   +G+ +V++ D++ A +A+ 
Sbjct: 1   TSLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALY 60

Query: 552 SMNGYRLEGRTIAVRVA 568
            ++  R  GR I ++ A
Sbjct: 61  YLDRTRFLGREIEIQFA 77

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

 Score = 50.6 bits (122), Expect = 4e-08
 Identities = 27/74 (36%), Positives = 40/74 (54%), Gaps = 4/74 (5%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIK--DRVTGMSKGYGFVKYADIQMANNAIA 551
           LY+G L     ++ +  LFS  GDI   ++I   DR T    G+ FV+Y   + A NA+ 
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDI--KRIIMGLDRFTKTPCGFCFVEYYTREDAENAVK 58

Query: 552 SMNGYRLEGRTIAV 565
            +NG +L+ R I V
Sbjct: 59  YLNGTKLDDRIIRV 72

This subfamily corresponds to the RRM of CBP20, also termed nuclear cap-binding protein subunit 2 (NCBP2), or cell proliferation-inducing gene 55 protein, or NCBP-interacting protein 1 (NIP1). CBP20 is the small subunit of the nuclear cap binding complex (CBC), which is a conserved eukaryotic heterodimeric protein complex binding to 5'-capped polymerase II transcripts and plays a central role in the maturation of pre-mRNA and uracil-rich small nuclear RNA (U snRNA). CBP20 is most likely responsible for the binding of capped RNA. It contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and interacts with the second and third domains of CBP80, the large subunit of CBC. . Length = 78

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

 Score = 50.2 bits (120), Expect = 5e-08
 Identities = 24/72 (33%), Positives = 35/72 (48%), Gaps = 6/72 (8%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           T +Y+G +PP      LI LF  FG I+  +   DR      G+ FVK    + A  AI 
Sbjct: 1   TTVYVGNIPPYTTQADLIPLFQNFGYILEFRHQPDR------GFAFVKLDTHEQAAMAIV 54

Query: 552 SMNGYRLEGRTI 563
            + G+ + GR +
Sbjct: 55  QLQGFPVHGRPL 66

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

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

 Score = 50.0 bits (120), Expect = 5e-08
 Identities = 24/73 (32%), Positives = 36/73 (49%), Gaps = 6/73 (8%)

Query: 491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAI 550
           +T +++G L P + +D L  LF  FG+IV  K+         KG GFV++     A  AI
Sbjct: 1   NTTVFVGGLDPAVTEDELRSLFGPFGEIVYVKI------PPGKGCGFVQFVHRAAAEAAI 54

Query: 551 ASMNGYRLEGRTI 563
             + G  + G  I
Sbjct: 55  QQLQGTIIGGSRI 67

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

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

 Score = 50.0 bits (120), Expect = 6e-08
 Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 2/75 (2%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L++G L  + + D L   F   G++V  ++ +D   G SKG+G V++A  + A  A+   
Sbjct: 2   LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDD-DGRSKGFGHVEFATEEGAQKALE-K 59

Query: 554 NGYRLEGRTIAVRVA 568
           +G  L GR I V +A
Sbjct: 60  SGEELLGREIRVDLA 74

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|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 50.6 bits (120), Expect = 7e-08
 Identities = 27/66 (40%), Positives = 37/66 (56%)

Query: 488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMAN 547
           +L  TNLYI  LPP   D  L++L   +G IV  K I D+ T   KGYGFV +     A 
Sbjct: 4   QLSKTNLYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQ 63

Query: 548 NAIASM 553
            A++++
Sbjct: 64  KAVSAL 69

This subgroup corresponds to the RRM1 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 86

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

 Score = 50.1 bits (120), Expect = 7e-08
 Identities = 24/72 (33%), Positives = 41/72 (56%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L++  LP +  +D L +LFS FG++    V  D+ +G SKG+ +V + D + A  A   +
Sbjct: 5   LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKEL 64

Query: 554 NGYRLEGRTIAV 565
           +G   +GR I +
Sbjct: 65  DGKVFQGRLIHI 76

This subgroup corresponds to the RRM2 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 79

>gnl|CDD|235906 PRK07003, PRK07003, DNA polymerase III subunits gamma and tau; Validated

 Score = 55.6 bits (134), Expect = 8e-08
 Identities = 40/196 (20%), Positives = 51/196 (26%), Gaps = 13/196 (6%)

Query: 568 AGKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGPP 627
            G  P   VP     +       +A  VG                  A    A       
Sbjct: 364 GGGAPGGGVPARVAGAVPAPGARAAAAVGASAVPAVTAVTGAAGAALAPKAAAAAAATRA 423

Query: 628 VPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATSSE 687
             PP AP APP           G    P          +        PP      +  + 
Sbjct: 424 EAPPAAP-APPATADRGDDAADGDAPVPAKANARASADSRCDERDAQPPADSGSASAPAS 482

Query: 688 AQQHSFPPGVQSESSSSAPAASANMYGSSMPPMPPNVQPAYATAPLGYSPYYNAVPPP-- 745
                 PP    E +  A A SA    +      P      A A    +P   A P P  
Sbjct: 483 DA----PPDAAFEPAPRAAAPSAATPAAVPDARAP------AAASREDAPAAAAPPAPEA 532

Query: 746 PPPAPVSAADHSQNLG 761
            PP P +AA  ++  G
Sbjct: 533 RPPTPAAAAPAARAGG 548

Length = 830

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

 Score = 49.3 bits (118), Expect = 9e-08
 Identities = 18/72 (25%), Positives = 34/72 (47%), Gaps = 4/72 (5%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           +Y G  P +     + RLF T G +    ++   V      + F+ + +++ A  AI ++
Sbjct: 2   VYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTVQP----HAFITFENLEAAQLAIETL 57

Query: 554 NGYRLEGRTIAV 565
           NG  ++G  I V
Sbjct: 58  NGASVDGNCIKV 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|240816 cd12370, RRM1_PUF60, RNA recognition motif 1 in (U)-binding-splicing factor PUF60 and similar proteins

 Score = 49.7 bits (119), Expect = 9e-08
 Identities = 27/72 (37%), Positives = 38/72 (52%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           +Y+G +   L +D + + FS FG I    +  D VT   KG+ FV+Y   + A  A+  M
Sbjct: 3   VYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQM 62

Query: 554 NGYRLEGRTIAV 565
           NG  L GR I 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|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split end) protein family

 Score = 49.7 bits (119), Expect = 9e-08
 Identities = 21/63 (33%), Positives = 34/63 (53%), Gaps = 1/63 (1%)

Query: 493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
            L++G L  T+ ++ L R F  +G +V    IK    G    Y FVK+ ++ MA+ A  +
Sbjct: 4   TLFVGNLEITITEEELRRAFERYG-VVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRAKVA 62

Query: 553 MNG 555
           M+G
Sbjct: 63  MSG 65

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

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

 Score = 49.1 bits (117), Expect = 1e-07
 Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 1/75 (1%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           LY+G L P + +D L ++F   G +   K+I D+       YGFV+Y     A  A+ ++
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDK-NNKGVNYGFVEYHQSHDAEIALQTL 59

Query: 554 NGYRLEGRTIAVRVA 568
           NG ++E   I V  A
Sbjct: 60  NGRQIENNEIRVNWA 74

This subgroup corresponds to the RRM1 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 74

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

 Score = 48.8 bits (117), Expect = 1e-07
 Identities = 27/73 (36%), Positives = 39/73 (53%), Gaps = 1/73 (1%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L++G LP T+    L   FS FG +    V  D+ TG+SKGYGFV ++      NA+   
Sbjct: 2   LFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENAL-QK 60

Query: 554 NGYRLEGRTIAVR 566
             + LEG  + V+
Sbjct: 61  QKHILEGNKLQVQ 73

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

 Score = 48.8 bits (117), Expect = 2e-07
 Identities = 26/75 (34%), Positives = 41/75 (54%), Gaps = 4/75 (5%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGD---IVMAKVIKDRVTGMSKGYGFVKYADIQMANNAI 550
           +Y+  L   LD+D L  +FS FG+   I + K   ++   ++ G+ FV + D   A NA+
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62

Query: 551 ASMNGYRLEGRTIAV 565
             +NG  L GR I+V
Sbjct: 63  -QLNGTELGGRKISV 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|240838 cd12392, RRM2_SART3, RNA recognition motif 2 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 48.9 bits (117), Expect = 2e-07
 Identities = 21/78 (26%), Positives = 45/78 (57%), Gaps = 1/78 (1%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L++  LP ++  + L +LF   G +   +++ +R +G  KG  +V+Y +   A+ A+  M
Sbjct: 5   LFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNR-SGKPKGLAYVEYENESSASQAVLKM 63

Query: 554 NGYRLEGRTIAVRVAGKP 571
           +G  ++ +TI+V ++  P
Sbjct: 64  DGTEIKEKTISVAISNPP 81

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|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins

 Score = 48.8 bits (117), Expect = 2e-07
 Identities = 20/68 (29%), Positives = 35/68 (51%), Gaps = 1/68 (1%)

Query: 499 LPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRL 558
           L   + +  L   FS  G +   ++I+DR +  SKG  +V++ D +    A+  + G RL
Sbjct: 7   LSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALG-LTGQRL 65

Query: 559 EGRTIAVR 566
            G+ I V+
Sbjct: 66  LGQPIMVQ 73

This subfamily corresponds to the RRM1 of RNA-binding protein 39 (RBM39), RNA-binding protein 23 (RBM23) and similar proteins. RBM39 (also termed HCC1) is a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor. . Length = 73

>gnl|CDD|240931 cd12487, RRM1_DND1, RNA recognition motif 1 found in vertebrate dead end protein homolog 1 (DND1)

 Score = 48.6 bits (116), Expect = 2e-07
 Identities = 23/74 (31%), Positives = 46/74 (62%), Gaps = 2/74 (2%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           ++IG +P  + +D LI LF + G +   +++    +G+++G+ + KY+D + A+ AIA++
Sbjct: 4   VFIGKIPQDVYEDRLIPLFQSVGTLYEFRLMMT-FSGLNRGFAYAKYSDRRGASAAIATL 62

Query: 554 NGYRL-EGRTIAVR 566
           + Y L EG  + V 
Sbjct: 63  HNYELPEGCCLLVC 76

This subgroup corresponds to the RRM1 of DND1, also termed RNA-binding motif, single-stranded-interacting protein 4, an RNA-binding protein that is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. For instance, DND1 binds cell cycle inhibitor, P27 (p27Kip1, CDKN1B), and cell cycle regulator and tumor suppressor, LATS2 (large tumor suppressor, homolog 2 of Drosophila). It helps maintain their protein expression through blocking the inhibitory function of microRNAs (miRNA) from these transcripts. DND1 may also impose another level of translational regulation to modulate expression of critical factors in embryonic stem (ES) cells. DND1 interacts specifically with apolipoprotein B editing complex 3 (APOBEC3), a multi-functional protein inhibiting retroviral replication. The DND1-APOBEC3 interaction may play a role in maintaining viability of germ cells and for preventing germ cell tumor development. DND1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

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

 Score = 53.3 bits (128), Expect = 3e-07
 Identities = 27/72 (37%), Positives = 41/72 (56%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           LY+G L P + +  L  LF  FG ++  +V +D VT  S GYG+V + +   A  A+ +M
Sbjct: 3   LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETM 62

Query: 554 NGYRLEGRTIAV 565
           N  RL G+ I +
Sbjct: 63  NFKRLGGKPIRI 74

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

>gnl|CDD|240930 cd12486, RRM1_ACF, RNA recognition motif 1 found in vertebrate APOBEC-1 complementation factor (ACF)

 Score = 48.4 bits (115), Expect = 3e-07
 Identities = 27/73 (36%), Positives = 41/73 (56%), Gaps = 2/73 (2%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           ++IG LP  L +D LI L    G I   +++ D   G ++GY FV +++ Q A NAI  +
Sbjct: 4   IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMD-FNGNNRGYAFVTFSNKQEAKNAIKQL 62

Query: 554 NGYRLE-GRTIAV 565
           N Y +  GR + V
Sbjct: 63  NNYEIRNGRLLGV 75

This subgroup corresponds to the RRM1 of ACF, also termed APOBEC-1-stimulating protein, 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. ACF shuttles between the cytoplasm and nucleus. It contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1. . Length = 78

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

 Score = 48.4 bits (115), Expect = 3e-07
 Identities = 26/76 (34%), Positives = 38/76 (50%), Gaps = 1/76 (1%)

Query: 491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAI 550
           D  L++G L   + ++ L  LF   G +    + KD+  G  K +GFV +   +    AI
Sbjct: 1   DRTLFVGNLECRVREEILYELFLQAGPLTKVTICKDK-EGKPKSFGFVCFKHSESVPYAI 59

Query: 551 ASMNGYRLEGRTIAVR 566
           A +NG RL GR I V 
Sbjct: 60  ALLNGIRLYGRPIKVH 75

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

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

 Score = 48.5 bits (116), Expect = 3e-07
 Identities = 22/76 (28%), Positives = 38/76 (50%), Gaps = 2/76 (2%)

Query: 490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNA 549
           D  ++++G L P +  + L   FS  G I+   +IK R    +  + F+K+   Q A  A
Sbjct: 2   DKYSIFVGQLSPDVTKEELNERFSRHGKILEVNLIK-RANHTN-AFAFIKFEREQAAARA 59

Query: 550 IASMNGYRLEGRTIAV 565
           + S N   L+ +T+ V
Sbjct: 60  VESENHSMLKNKTMHV 75

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

>gnl|CDD|197652 smart00322, KH, K homology RNA-binding domain

 Score = 48.1 bits (115), Expect = 3e-07
 Identities = 25/77 (32%), Positives = 38/77 (49%), Gaps = 20/77 (25%)

Query: 266 NFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEA 325
           + +GLIIG  G+T K++E ETG KI I G GS                   E+  V +  
Sbjct: 12  DKVGLIIGKGGSTIKKIEEETGVKIDIPGPGS-------------------EERVVEITG 52

Query: 326 ETQESLEGAAAMVEKLL 342
              E++E AA ++ ++L
Sbjct: 53  PP-ENVEKAAELILEIL 68

Length = 68

>gnl|CDD|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 48.1 bits (114), Expect = 4e-07
 Identities = 23/75 (30%), Positives = 42/75 (56%), Gaps = 1/75 (1%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           ++IG L      +GL   F  FG++    V++D +T  S+G+GFV + D Q   + + + 
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMD-QAGVDKVLAQ 61

Query: 554 NGYRLEGRTIAVRVA 568
           + + L+ +TI  +VA
Sbjct: 62  SRHELDSKTIDPKVA 76

This subgroup corresponds to the RRM1 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). Musashi-1 has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, it represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 77

>gnl|CDD|241079 cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 48.2 bits (115), Expect = 4e-07
 Identities = 22/67 (32%), Positives = 35/67 (52%), Gaps = 1/67 (1%)

Query: 491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAI 550
           D  L++G L     +D + RLF  FG I    +++    G SKG  FVK++    A  AI
Sbjct: 1   DRKLFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGP-DGNSKGCAFVKFSSHAEAQAAI 59

Query: 551 ASMNGYR 557
            +++G +
Sbjct: 60  NALHGSQ 66

This subgroup corresponds to the RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, being highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, being strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in a muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 81

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

 Score = 47.6 bits (114), Expect = 4e-07
 Identities = 18/70 (25%), Positives = 38/70 (54%), Gaps = 4/70 (5%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS- 552
           L++G L   + ++ L   FS +G++   +++ D+ TG  +G+ FV + D    +  +   
Sbjct: 2   LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQK 61

Query: 553 ---MNGYRLE 559
              +NG+R+E
Sbjct: 62  YHTINGHRVE 71

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|240690 cd12244, RRM2_MSSP, RNA recognition motif 2 in the c-myc gene single-strand binding proteins (MSSP) family

 Score = 47.7 bits (114), Expect = 4e-07
 Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 1/71 (1%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           TNLYI  LP  +D+  L  +   +G ++  ++++D   G S+G GF +    +   + I+
Sbjct: 1   TNLYISNLPLHMDEQDLETMLKPYGQVISTRILRDS-KGQSRGVGFARMESREKCEDIIS 59

Query: 552 SMNGYRLEGRT 562
             NG  L+G  
Sbjct: 60  KFNGKYLKGEG 70

This subfamily corresponds to the RRM2 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. Moreover, they family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot. . Length = 79

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

 Score = 48.0 bits (115), Expect = 4e-07
 Identities = 20/55 (36%), Positives = 33/55 (60%), Gaps = 7/55 (12%)

Query: 508 LIRLFSTFGDIVMAKVIKDRV----TGMSKGYGFVKYADIQMANNAIASMNGYRL 558
           L ++FS FG     K++   +    TG +KGY FV++A  + A  A+ ++NGY+L
Sbjct: 24  LRKIFSKFGVG---KIVGIYMPVDETGKTKGYAFVEFATPEEAKEAVKALNGYKL 75

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

 Score = 47.4 bits (113), Expect = 5e-07
 Identities = 19/51 (37%), Positives = 29/51 (56%)

Query: 500 PPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAI 550
           P +  ++ L   F  FGDI    ++KD+ TG SKG+G+VK+     A  A+
Sbjct: 9   PKSYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVAL 59

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|235906 PRK07003, PRK07003, DNA polymerase III subunits gamma and tau; Validated

 Score = 52.9 bits (127), Expect = 6e-07
 Identities = 29/175 (16%), Positives = 45/175 (25%), Gaps = 20/175 (11%)

Query: 613 PAASYTGAPVPWGPPVPPPYAP----YAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAP 668
           PA +  GAP    P       P     A    G++  P V            P     A 
Sbjct: 360 PAVTGGGAPGGGVPARVAGAVPAPGARAAAAVGASAVPAVTAVTGAAGAALAPKAAAAAA 419

Query: 669 PGALTAPPGAPTQTATSSEAQQHSF-PPGVQSESSSSAPAASANMYGSSMPPMPPNVQPA 727
                APP AP   AT+      +     V +++++ A A S             + QP 
Sbjct: 420 ATRAEAPPAAPAPPATADRGDDAADGDAPVPAKANARASADSR--------CDERDAQPP 471

Query: 728 YATAPLGYSPYYNAVPPPPPPAPVSAADHSQNLGNVPWATNPPVQPPVSSAEKSN 782
             +          + P    P   +     +                  +A    
Sbjct: 472 ADSGS-------ASAPASDAPPDAAFEPAPRAAAPSAATPAAVPDARAPAAASRE 519

Length = 830

>gnl|CDD|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 47.5 bits (113), Expect = 6e-07
 Identities = 21/82 (25%), Positives = 39/82 (47%), Gaps = 5/82 (6%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVI-----KDRVTGMSKGYGFVKYADIQMANN 548
           L++  L  +  +  L   F      V A+V      K     +S G+GFV +   + A  
Sbjct: 3   LFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQA 62

Query: 549 AIASMNGYRLEGRTIAVRVAGK 570
           A+ +M+G+ L+G T+ V+ + +
Sbjct: 63  ALKAMDGFVLDGHTLVVKFSHR 84

This subfamily corresponds to the RRM4 of MRD1which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 84

>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1

 Score = 52.5 bits (126), Expect = 7e-07
 Identities = 32/219 (14%), Positives = 39/219 (17%), Gaps = 20/219 (9%)

Query: 569 GKPPQPTVPPGPPTSTMPTYPVSAPPV-GGYPSQQYAPGGPLPNPPAASYTGAPVPWGPP 627
              P       P   T     +S   V      +Q AP  P P          P     P
Sbjct: 133 EPQPPQAPESQPQPQTPAQKMLSLEEVEAQLQQRQQAPQLPQPPQQVLPQGMPPRQAAFP 192

Query: 628 ---VPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTAT 684
               P     Y  PP G             P      PP+    P               
Sbjct: 193 QQGPPEQPPGYPQPPQGHPEQVQPQQFLPAPSQAPAQPPLPPQLPQQPPPLQQPQ----- 247

Query: 685 SSEAQQHSFPPGVQSESSSSAPAASANMYGSSMPPMPPNVQPAYATAPLGYSPYYNAVPP 744
                    PP                          P+                   P 
Sbjct: 248 -FPGLSQQMPPPPPQPPQQQQQPPQPQAQPPPQNQPTPHPGLPQGQNA----------PL 296

Query: 745 PPPPAPVSAADHSQNLGNVPWATNPPVQPPVSSAEKSNY 783
           PPP  P       Q  G             +S  ++   
Sbjct: 297 PPPQQPQLLPLVQQPQGQQRGPQFREQLVQLSQQQREAL 335

Members of this family are necessary for accurate chromosome transmission during cell division. Length = 804

>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau; Provisional

 Score = 52.4 bits (126), Expect = 7e-07
 Identities = 38/167 (22%), Positives = 46/167 (27%), Gaps = 35/167 (20%)

Query: 568 AGKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGPP 627
           A KP        P     P  P +A P     +Q  A   P   P AA    A  P  PP
Sbjct: 363 AFKPAAAAEAAAPAEKKTPARPEAAAPAAAPVAQAAAAPAPAAAPAAA----ASAPAAPP 418

Query: 628 VPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATSSE 687
              P AP A P   +                  P     A P A+   P  P Q A  + 
Sbjct: 419 AAAPPAPVAAPAAAA------------------PAAAPAAAPAAVALAPAPPAQAAPETV 460

Query: 688 AQQHSFPPGVQSESSSSAPAASANMYGSSMPPMPPNVQPAYATAPLG 734
           A     P  V  E + ++ A           P              G
Sbjct: 461 A----IPVRVAPEPAVASAAP---------APAAAPAAARLTPTEEG 494

Length = 618

>gnl|CDD|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering time control protein FCA and similar proteins

 Score = 47.3 bits (112), Expect = 7e-07
 Identities = 24/75 (32%), Positives = 43/75 (57%), Gaps = 1/75 (1%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L++G +P T+ +  +  +F   G+++   +IKD+ TG  +G  FVKY+    A+ AI ++
Sbjct: 2   LFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRAL 61

Query: 554 NGYR-LEGRTIAVRV 567
           +  R L G    V+V
Sbjct: 62  HNQRTLPGGASPVQV 76

This subgroup corresponds to the RRM1 of FCA, a gene controlling flowering time in Arabidopsis, encoding a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain. . Length = 80

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

 Score = 47.0 bits (112), Expect = 7e-07
 Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 1/75 (1%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           ++IG L      +GL   FS FG+I    V++D  T  S+G+GFV ++D    +  +A  
Sbjct: 1   MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQ- 59

Query: 554 NGYRLEGRTIAVRVA 568
             + L+G+ I  +VA
Sbjct: 60  GPHELDGKKIDPKVA 74

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|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins

 Score = 46.8 bits (112), Expect = 8e-07
 Identities = 23/72 (31%), Positives = 35/72 (48%), Gaps = 3/72 (4%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           LY+  LP  +  + L  LF  +G I     I+   T  ++G  FV Y DI  A NA   +
Sbjct: 5   LYVRNLPFKISSEELYDLFGKYGAIRQ---IRIGNTKETRGTAFVVYEDIYDAKNACDHL 61

Query: 554 NGYRLEGRTIAV 565
           +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|240764 cd12318, RRM5_RBM19_like, RNA recognition motif 5 in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins

 Score = 46.8 bits (112), Expect = 1e-06
 Identities = 15/68 (22%), Positives = 32/68 (47%), Gaps = 5/68 (7%)

Query: 505 DDGLIRLFSTFGDIVMAKVIKDRV-----TGMSKGYGFVKYADIQMANNAIASMNGYRLE 559
           ++ L + F   G +    + K +        +S GYGFV++   + A  A+  + G  L+
Sbjct: 14  EETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQKALKRLQGTVLD 73

Query: 560 GRTIAVRV 567
           G  + +++
Sbjct: 74  GHALELKL 81

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|237605 PRK14086, dnaA, chromosomal replication initiation protein; Provisional

 Score = 51.7 bits (124), Expect = 1e-06
 Identities = 32/185 (17%), Positives = 41/185 (22%), Gaps = 26/185 (14%)

Query: 567 VAGKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPS-QQYAPGGPLPNPPAASYTGAPVPWG 625
             G          P        P + P    YP+ QQ    G  P   A  Y       G
Sbjct: 118 YEGYGGPRADDRPPGLPRQDQLPTARP---AYPAYQQRPEPGAWP-RAADDYGWQQQRLG 173

Query: 626 PPVPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATS 685
            P   PYA  A   P             P Y  +        P                 
Sbjct: 174 FPPRAPYASPASYAPEQERDREPYDAGRPEYDQRRRDYDHPRP----------------- 216

Query: 686 SEAQQHSFPPGVQSESSSSAPAASANMYGSSMPPMPPNVQPAYATAPLGYSPYYNAVPPP 745
            +  +   P   +++     P A     G   PP   +                   P P
Sbjct: 217 -DWDR---PRRDRTDRPEPPPGAGHVHRGGPGPPERDDAPVVPIRPSAPGPLAAQPAPAP 272

Query: 746 PPPAP 750
            P  P
Sbjct: 273 GPGEP 277

Length = 617

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

 Score = 46.3 bits (110), Expect = 1e-06
 Identities = 21/75 (28%), Positives = 40/75 (53%), Gaps = 1/75 (1%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L++G L     D GL R F+ +G +    V+ D  T  S+G+GF+ ++    A+ A+ + 
Sbjct: 5   LFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAMEAQ 64

Query: 554 NGYRLEGRTIAVRVA 568
             + ++G  I ++ A
Sbjct: 65  -PHSIDGNQIELKRA 78

This subfamily corresponds to the RRM1 of hnRNP A0 which is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 79

>gnl|CDD|236138 PRK07994, PRK07994, DNA polymerase III subunits gamma and tau; Validated

 Score = 51.8 bits (125), Expect = 1e-06
 Identities = 32/167 (19%), Positives = 41/167 (24%), Gaps = 24/167 (14%)

Query: 627 PVPPPYAPYAP-PPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATS 685
           P+P P  P     P  S      P   + P      PP   + P      P  P    TS
Sbjct: 364 PLPEPEVPPQSAAPAASAQATAAPTAAVAPPQAPAVPPPPASAP---QQAPAVPLPETTS 420

Query: 686 SEAQQHSFPPGVQSESSSSAPAASANMYGSSMPPMPPNVQPAYATAPLGYSPYYNAVPPP 745
                      +Q    ++    S        P      +P    + L         P  
Sbjct: 421 QLLAA---RQQLQRAQGATKAKKSE-------PAAASRARP--VNSALERLASVRPAPSA 468

Query: 746 PPPAPVSAADHSQNLGNVPW-ATNPPVQPPVSSAEKSNYGADAEYEK 791
              AP              W ATNP        A         E+EK
Sbjct: 469 LEKAPAKKEA-------YRWKATNPVEVKKEPVATPKALKKALEHEK 508

Length = 647

>gnl|CDD|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the U1A/U2B"/SNF protein family

 Score = 46.4 bits (111), Expect = 1e-06
 Identities = 27/82 (32%), Positives = 41/82 (50%), Gaps = 13/82 (15%)

Query: 494 LYIGYLPPTLDDDGLIR----LFSTFG---DIVMAKVIKDRVTGMSKGYGFVKYADIQMA 546
           LYI  L   +  D L R    LFS FG   DIV +K +K R      G  FV + D++ A
Sbjct: 2   LYINNLNEKIKKDELKRSLYALFSQFGPVLDIVASKTLKMR------GQAFVVFKDVESA 55

Query: 547 NNAIASMNGYRLEGRTIAVRVA 568
            NA+ ++ G+    + + ++ A
Sbjct: 56  TNALRALQGFPFYDKPMRIQYA 77

This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding. . Length = 78

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 51.5 bits (123), Expect = 2e-06
 Identities = 51/220 (23%), Positives = 63/220 (28%), Gaps = 29/220 (13%)

Query: 568  AGKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGPP 627
            AG PP P  P  PP +   + P   P              P P+ PA +         P 
Sbjct: 2548 AGDPPPPLPPAAPPAAPDRSVPPPRP-------------APRPSEPAVTSRARR----PD 2590

Query: 628  VPP-PYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATSS 686
             PP    P AP         P P  P+PP      PP  +  P A    P  P       
Sbjct: 2591 APPQSARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPE 2650

Query: 687  EAQQHSFPPGV----QSESSSSAPAASANMYGSSMPPMPPNVQPAYATAPLGYSPYYNAV 742
              +    P  V    ++     A  AS+           P V        L   P     
Sbjct: 2651 RPRDDPAPGRVSRPRRARRLGRAAQASSPPQRPRRRAARPTVGS---LTSLADPPPPPPT 2707

Query: 743  PPPPPPAPVSAAD----HSQNLGNVPWATNPPVQPPVSSA 778
            P P P A VSA       +      P     P  P V + 
Sbjct: 2708 PEPAPHALVSATPLPPGPAAARQASPALPAAPAPPAVPAG 2747

Length = 3151

>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1

 Score = 50.9 bits (122), Expect = 2e-06
 Identities = 44/209 (21%), Positives = 54/209 (25%), Gaps = 15/209 (7%)

Query: 576 VPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAAS-YTGAPVPWGPPVPPPYAP 634
            P   P S +     +  P          P       P  S +  AP P   P   P + 
Sbjct: 84  APSVGPDSDLSQKTSTFSPCQSGYEASTDPEYIPDLQPDPSLWGTAPKPEPQPPQAPESQ 143

Query: 635 YAPPPPGSTM---------YPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATS 685
             P  P   M                P  P   Q   P    P  A     G P Q    
Sbjct: 144 PQPQTPAQKMLSLEEVEAQLQQRQQAPQLPQPPQQVLPQGMPPRQAAFPQQGPPEQPPGY 203

Query: 686 SEAQQHSFPPGVQSESSSSAPAASANMYGSSMPPMPPNVQPAYATAPLGYSPYYNAVPPP 745
            +  Q   P  VQ +    AP+ +       +PP  P   P               +PPP
Sbjct: 204 PQPPQG-HPEQVQPQQFLPAPSQAPAQP--PLPPQLPQQPPPLQQPQFPGLS--QQMPPP 258

Query: 746 PPPAPVSAADHSQNLGNVPWATNPPVQPP 774
           PP  P       Q     P    P   P 
Sbjct: 259 PPQPPQQQQQPPQPQAQPPPQNQPTPHPG 287

Members of this family are necessary for accurate chromosome transmission during cell division. Length = 804

>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional

 Score = 51.7 bits (124), Expect = 2e-06
 Identities = 42/219 (19%), Positives = 67/219 (30%), Gaps = 3/219 (1%)

Query: 568 AGKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGPP 627
           +  PP P+ P  PP +  P  P  +P        +       P   +    GA       
Sbjct: 105 SPTPPGPSSPDPPPPTPPPASPPPSPAPDLSEMLRPVGSPGPPPAASPPAAGASPAAVAS 164

Query: 628 VPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATSSE 687
                   A P          P  P        PP   +  P   ++P  A   +   + 
Sbjct: 165 DAASSRQAALPLSSPEETARAPSSPPAEPPPSTPPAAASPRPPRRSSPISASASSPAPAP 224

Query: 688 AQQHSFPPGVQSESSSSAPAASANMYGSSMPPMPPNVQPAYATAPLGYSPYYNAVPPPPP 747
            +  +   G  S  SSS+ ++       +  P+P    PA  T P           P   
Sbjct: 225 GRSAADDAGASSSDSSSSESSGCGWGPENECPLPR---PAPITLPTRIWEASGWNGPSSR 281

Query: 748 PAPVSAADHSQNLGNVPWATNPPVQPPVSSAEKSNYGAD 786
           P P S++   +     P  ++P   P  SS   S+  + 
Sbjct: 282 PGPASSSSSPRERSPSPSPSSPGSGPAPSSPRASSSSSS 320

Length = 1352

>gnl|CDD|240915 cd12471, RRM1_MSSP2, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 45.9 bits (108), Expect = 2e-06
 Identities = 25/62 (40%), Positives = 33/62 (53%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           TNLYI  L P   D  L++L   +G IV  K I D+ T   KGYGFV +     A  A+ 
Sbjct: 2   TNLYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 61

Query: 552 SM 553
           ++
Sbjct: 62  AL 63

This subgroup corresponds to the RRM1 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 75

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

 Score = 46.1 bits (110), Expect = 2e-06
 Identities = 19/77 (24%), Positives = 38/77 (49%), Gaps = 3/77 (3%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVI---KDRVTGMSKGYGFVKYADIQMANN 548
           TNLY+G L P + ++ L + F  FG +   K++    +     ++  GFV + +   A  
Sbjct: 2   TNLYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAER 61

Query: 549 AIASMNGYRLEGRTIAV 565
           A+  ++G  + G  + +
Sbjct: 62  ALDELDGKDVMGYELKL 78

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

>gnl|CDD|215657 pfam00013, KH_1, KH domain

 Score = 45.2 bits (108), Expect = 2e-06
 Identities = 12/32 (37%), Positives = 16/32 (50%)

Query: 266 NFIGLIIGPRGNTQKRMERETGAKIVIRGKGS 297
           + +G IIG  G+  K +  ETG KI I     
Sbjct: 9   DKVGRIIGKGGSNIKEIREETGVKIRIPDDRD 40

KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia. Length = 59

>gnl|CDD|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 45.2 bits (107), Expect = 2e-06
 Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 8/72 (11%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L++G LPP   +  +  LF  +G ++   +IK+        YGFV   D   A+ AI ++
Sbjct: 3   LFVGNLPPEATEQEIRSLFEQYGKVLECDIIKN--------YGFVHMDDKTAADEAIRNL 54

Query: 554 NGYRLEGRTIAV 565
           + Y+L G  I V
Sbjct: 55  HHYKLHGVAINV 66

This subgroup corresponds to the RRM1 of RBM4, a ubiquitously expressed splicing factor that has two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may function as a translational regulator of stress-associated mRNAs and also plays a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. The C-terminal region may be crucial for nuclear localization and protein-protein interaction. The RRMs, in combination with the C-terminal region, are responsible for the splicing function of RBM4. . Length = 67

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

 Score = 45.6 bits (109), Expect = 2e-06
 Identities = 15/72 (20%), Positives = 42/72 (58%), Gaps = 5/72 (6%)

Query: 499 LPPTLDDDGLIRLFSTFGDIVMA--KVIKDRVTGMSKGYGFVKYADIQMA---NNAIASM 553
           L     ++ +++  S    + +   ++I+D++TG S+G+ FV++  ++ A    +A+ ++
Sbjct: 10  LDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMDALNNL 69

Query: 554 NGYRLEGRTIAV 565
           + + ++GR + V
Sbjct: 70  DPFVIDGRVVRV 81

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

>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau; Provisional

 Score = 50.5 bits (121), Expect = 3e-06
 Identities = 34/143 (23%), Positives = 40/143 (27%), Gaps = 17/143 (11%)

Query: 612 PPAASYTGAPVPWGPPVPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGA 671
           P AA+   AP     P  P  A  A  P       P P    P      P     A P A
Sbjct: 366 PAAAAEAAAPAEKKTPARPEAAAPAAAPVAQAAAAPAP-AAAPAAAASAPAAPPAAAPPA 424

Query: 672 LTAPPGAPTQTATSSEAQQHSFPPGVQSESSSSAPAASANMYGSSMPPMPPNVQPAYATA 731
             A P A    A        + P  V    +  A AA           +P  V P  A A
Sbjct: 425 PVAAPAAAAPAAA-----PAAAPAAVALAPAPPAQAAP------ETVAIPVRVAPEPAVA 473

Query: 732 PLGYSPYYNAVPPPPPPAPVSAA 754
                    A    P  A ++  
Sbjct: 474 SAA-----PAPAAAPAAARLTPT 491

Length = 618

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

 Score = 45.4 bits (108), Expect = 3e-06
 Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 8/75 (10%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           +YIG LP    +  + R F  +G I        R   +  G+GFV++ D + A++A+  +
Sbjct: 2   VYIGRLPYRARERDVERFFKGYGRI--------REINLKNGFGFVEFEDPRDADDAVYEL 53

Query: 554 NGYRLEGRTIAVRVA 568
           NG  L G  + V  A
Sbjct: 54  NGKELCGERVIVEHA 68

This subfamily corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an important role in both, constitutive and alternative, splicing of many pre-mRNAs. It can shuttle between the nucleus and cytoplasm. SRSF5 regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and essential for enhancer activation. SRSF6 preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. Members in this family contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 70

>gnl|CDD|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end) protein family

 Score = 44.9 bits (107), Expect = 3e-06
 Identities = 21/74 (28%), Positives = 34/74 (45%), Gaps = 6/74 (8%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L++G L P      L R F  FG I   ++  D      + Y +++Y  I+ A  A  ++
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGAI--RRIDYDP----GRNYAYIEYESIEAAQAAKEAL 54

Query: 554 NGYRLEGRTIAVRV 567
            G+ L G    +RV
Sbjct: 55  RGFPLGGPGRRLRV 68

This subfamily corresponds to the RRM3 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B) and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and is a novel component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 72

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

 Score = 45.0 bits (107), Expect = 4e-06
 Identities = 20/82 (24%), Positives = 36/82 (43%), Gaps = 4/82 (4%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           +Y+  LP     + L  +FS +G +V   + + + TG  KG+ F+++   + A  A   +
Sbjct: 2   VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61

Query: 554 NGYRLEGRTIAVRVAGKPPQPT 575
           N         A    GK P+  
Sbjct: 62  N----NPPETATDKPGKFPKTV 79

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|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic activator RIM4 and similar proteins

 Score = 45.1 bits (107), Expect = 4e-06
 Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 7/74 (9%)

Query: 494 LYIGYLPPTLDDDGL----IRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNA 549
           +++  LP +  DD L       FS +G +V  KV++D      + Y FV++ +   A NA
Sbjct: 5   VFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRDW---RQRPYAFVQFTNDDDAKNA 61

Query: 550 IASMNGYRLEGRTI 563
           +A   G  L+GR I
Sbjct: 62  LAKGQGTILDGRHI 75

This subfamily corresponds to the RRM1 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. . Length = 86

>gnl|CDD|240815 cd12369, RRM4_RBM45, RNA recognition motif 4 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 44.6 bits (106), Expect = 4e-06
 Identities = 21/73 (28%), Positives = 34/73 (46%), Gaps = 6/73 (8%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L+I   P    D  L  +F  FG ++   ++        K YG+ KYAD + A  AI ++
Sbjct: 2   LFIVCNPSPPPDYILEDVFCRFGGLIDVYLVPG------KNYGYAKYADRESAERAITTL 55

Query: 554 NGYRLEGRTIAVR 566
           +G  + G  + V 
Sbjct: 56  HGKEVNGVKLKVM 68

This subfamily corresponds to the RRM4 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 68

>gnl|CDD|223065 PHA03378, PHA03378, EBNA-3B; Provisional

 Score = 50.1 bits (119), Expect = 5e-06
 Identities = 60/236 (25%), Positives = 77/236 (32%), Gaps = 35/236 (14%)

Query: 561 RTIAVRVAGKP---PQPTVPPGPPTS-------------TMPTYPVSAPPVGGYPSQQYA 604
            + A   A  P   P P+  P PPT+              MP  P+   P+   P     
Sbjct: 586 ASSAPSYAQTPWPVPHPSQTPEPPTTQSHIPETSAPRQWPMPLRPIPMRPLRMQPITFNV 645

Query: 605 PGGPLPN-PPAASYTGAPVPWGPPVPPPYAPYAPPPPG-STMYPP--VPGQPMPPYGVQY 660
              P P+ PP    T     W       + PY P P G +TM P    PG   PP     
Sbjct: 646 LVFPTPHQPPQVEITPYKPTW---TQIGHIPYQPSPTGANTMLPIQWAPGTMQPPPRAPT 702

Query: 661 PPPVQTAPPGALTAPPGAPTQTATSSEAQQHSFPPGVQSESSSSAPAASANMYGSSMPPM 720
           P     APPG    P  A  +    + A   + PP       ++AP  +     +     
Sbjct: 703 PMRPPAAPPGRAQRPAAATGRARPPAAAPGRARPP-------AAAPGRARPPAAAPGRAR 755

Query: 721 PPNVQPAYATAPLGYSPYYNAVPPPPPPAPVSAADHSQNLGNVPWATNPPVQPPVS 776
           PP   P  A  P          P PPP AP +     +     P    PP   P S
Sbjct: 756 PPAAAPGRARPPAAAPG--APTPQPPPQAPPAPQQRPRG---APTPQPPPQAGPTS 806

Length = 991

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

 Score = 44.7 bits (106), Expect = 5e-06
 Identities = 26/79 (32%), Positives = 37/79 (46%), Gaps = 8/79 (10%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           LYIG L   +++  L +LF      V + ++K        GY FV   D   A+ AI  +
Sbjct: 1   LYIGNLSSDVNESDLRQLFEEHKIPVSSVLVKKG------GYAFVDCPDQSWADKAIEKL 54

Query: 554 NGYRLEGRTIAV--RVAGK 570
           NG  L+G+ I V   V  K
Sbjct: 55  NGKILQGKVIEVEHSVPKK 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|241080 cd12636, RRM2_Bruno_like, RNA recognition motif 2 in Drosophila melanogaster Bruno protein and similar proteins

 Score = 44.8 bits (106), Expect = 5e-06
 Identities = 21/61 (34%), Positives = 36/61 (59%), Gaps = 1/61 (1%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L++G L    +++ +  +F+ FG I    V++D+  G S+G  FV +A  Q A NAI +M
Sbjct: 4   LFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQ-NGQSRGCAFVTFASRQCALNAIKAM 62

Query: 554 N 554
           +
Sbjct: 63  H 63

This subgroup corresponds to the RRM2 of Bruno, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 81

>gnl|CDD|241123 cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), and similar proteins

 Score = 44.7 bits (105), Expect = 6e-06
 Identities = 24/73 (32%), Positives = 38/73 (52%)

Query: 493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
           NL++  L  T     L  LFS +G +V AKV+ +  +  ++ YGFV  +  + A   I  
Sbjct: 3   NLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCINH 62

Query: 553 MNGYRLEGRTIAV 565
           ++   L GR I+V
Sbjct: 63  LHRTELHGRMISV 75

This subgroup corresponds to RRM of SAFB1, also termed scaffold attachment factor B (SAF-B), heat-shock protein 27 estrogen response element ERE and TATA-box-binding protein (HET), or heterogeneous nuclear ribonucleoprotein hnRNP A1- associated protein (HAP), a large multi-domain protein with well-described functions in transcriptional repression, RNA splicing and metabolism, and a proposed role in chromatin organization. Based on the numerous functions, SAFB1 has been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. SAFB1 specifically binds to AT-rich scaffold or matrix attachment region DNA elements (S/MAR DNA) by using its N-terminal scaffold attachment factor-box (SAF-box, also known as SAP domain), a homeodomain-like DNA binding motif. The central region of SAFB1 is composed of an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a nuclear localization signal (NLS). The C-terminus of SAFB1 contains Glu/Arg- and Gly-rich regions that might be involved in protein-protein interaction. Additional studies indicate that the C-terminal region contains a potent and transferable transcriptional repression domain. Another family member is SAFB2, a homolog of SAFB1. Both SAFB1 and SAFB2 are ubiquitously coexpressed and share very high sequence similarity, suggesting that they might function in a similar manner. However, unlike SAFB1, exclusively existing in the nucleus, SAFB2 is also present in the cytoplasm. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1. Length = 76

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

 Score = 44.2 bits (105), Expect = 7e-06
 Identities = 23/76 (30%), Positives = 36/76 (47%), Gaps = 1/76 (1%)

Query: 491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAI 550
           D  L++G L   + ++ L  LF   G +   K+ KD   G  K + FV +        AI
Sbjct: 1   DRTLFVGNLDARVTEEILYELFLQAGPLEGVKIPKDP-NGKPKSFAFVTFKHEVSVPYAI 59

Query: 551 ASMNGYRLEGRTIAVR 566
             +NG RL GR + ++
Sbjct: 60  QLLNGIRLFGRELRIK 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|236669 PRK10263, PRK10263, DNA translocase FtsK; Provisional

 Score = 49.3 bits (117), Expect = 7e-06
 Identities = 49/221 (22%), Positives = 67/221 (30%), Gaps = 13/221 (5%)

Query: 571 PPQPTVP----PGP--PTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNP-PAASYTGAPVP 623
           P QPTV     PGP      +   P   P    Y         PL  P        AP  
Sbjct: 353 PAQPTVAWQPVPGPQTGEPVIAPAPEGYPQQSQYAQPAVQYNEPLQQPVQPQQPYYAPAA 412

Query: 624 WGPPVPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTA 683
             P   P YAP    P     Y P P QP+     Q      T  P +         Q A
Sbjct: 413 EQPAQQPYYAPAPEQPAQQPYYAPAPEQPVAGNAWQAEEQQSTFAPQSTYQTEQTYQQPA 472

Query: 684 TSSEAQQHSFPPGVQSESSSSAPAASANMYGSSMPPMP--PNVQPAYATAPLGYSPYYNA 741
                 Q    P    +     P         + PP+     V+   A      + +Y  
Sbjct: 473 AQEPLYQ---QPQPVEQQPVVEPEPVVEETKPARPPLYYFEEVEEKRAREREQLAAWYQP 529

Query: 742 VPPP-PPPAPVSAADHSQNLGNVPWATNPPVQPPVSSAEKS 781
           +P P   P P+ ++  + ++  VP         P++S  K 
Sbjct: 530 IPEPVKEPEPIKSSLKAPSVAAVPPVEAAAAVSPLASGVKK 570

Length = 1355

>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 = 44.1 bits (105), Expect = 8e-06
 Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 1/61 (1%)

Query: 508 LIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV 567
           L  LFS FG +   ++ K +  G  +G+ FV++   Q A NA+ ++    L GR + +  
Sbjct: 17  LRELFSPFGQVKSVRLPK-KFDGSHRGFAFVEFVTKQEAQNAMEALKSTHLYGRHLVLEY 75

Query: 568 A 568
           A
Sbjct: 76  A 76

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|218191 pfam04652, DUF605, Vta1 like

 Score = 48.1 bits (115), Expect = 9e-06
 Identities = 20/120 (16%), Positives = 29/120 (24%), Gaps = 4/120 (3%)

Query: 572 PQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGPPVPPP 631
               V      ++ P                 +PG P  + P+     +         PP
Sbjct: 159 EDADVATTNSDNSFPGEDADPASASPSDPPSSSPGVP--SFPSPPEDPSSPS--DSSLPP 214

Query: 632 YAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATSSEAQQH 691
                                 PP     PPP     P   TA P  P+ +AT +     
Sbjct: 215 APSSFQSDTPPPSPESPTNPSPPPGPAAPPPPPVQQVPPLSTAKPTPPSASATPAPIGGI 274

Vta1 (VPS20-associated protein 1) is a positive regulator of Vps4. Vps4 is an ATPase that is required in the multivesicular body (MVB) sorting pathway to dissociate the endosomal sorting complex required for transport (ESCRT). Vta1 promotes correct assembly of Vps4 and stimulates its ATPase activity through its conserved Vta1/SBP1/LIP5 region. Length = 315

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 48.8 bits (116), Expect = 1e-05
 Identities = 47/219 (21%), Positives = 64/219 (29%), Gaps = 16/219 (7%)

Query: 571  PPQPTVPPGPPTSTMP-------TYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVP 623
              +P  P  PP   +        T   + PP       Q     P    P       P P
Sbjct: 2872 AAKPAAPARPPVRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQP 2931

Query: 624  WGPPVPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTA 683
              PP P P  P AP    +    P    P P  G   P  V  A P      P    +  
Sbjct: 2932 PPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRV--AVPRFRVPQPAPSREAP 2989

Query: 684  TSSEAQQHSFP-PGVQSESSSSAPAASANMYGSSMPPMPPNVQPAYATAPLGYSPYYNAV 742
             SS           V S +SS A      ++  + PP     Q  +       S   +  
Sbjct: 2990 ASSTPPLTGHSLSRVSSWASSLA------LHEETDPPPVSLKQTLWPPDDTEDSDADSLF 3043

Query: 743  PPPPPPAPVSAADHSQNLGNVPWATNPPVQPPVSSAEKS 781
                  + + A D      + P+A  P    P + A +S
Sbjct: 3044 DSDSERSDLEALDPLPPEPHDPFAHEPDPATPEAGARES 3082

Length = 3151

>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau; Provisional

 Score = 48.6 bits (116), Expect = 1e-05
 Identities = 34/143 (23%), Positives = 43/143 (30%), Gaps = 7/143 (4%)

Query: 629 PPPYAPYAPPPPGSTMYPPVPGQPMP-PYGVQYPPPVQTAPPGALTAPPGAPTQTATSSE 687
           P   A  A P    T   P    P   P       P   A P A  + P AP   A  + 
Sbjct: 366 PAAAAEAAAPAEKKTPARPEAAAPAAAPVAQAAAAPAPAAAPAAAASAPAAPPAAAPPAP 425

Query: 688 AQQHSFPPGVQSESSSSAPAASANMYGSSMPPMPPNVQPAYATAPLGYSPYYNAVPPPPP 747
                      + + ++APAA A          P  V      AP    P   +  P P 
Sbjct: 426 VAAP--AAAAPAAAPAAAPAAVALAPAPPAQAAPETVAIPVRVAP---EPAVASAAPAPA 480

Query: 748 PAPVSAADHSQNLGNVPWATNPP 770
            AP +A       G+V W     
Sbjct: 481 AAPAAARLTPTEEGDV-WHATVQ 502

Length = 618

>gnl|CDD|237605 PRK14086, dnaA, chromosomal replication initiation protein; Provisional

 Score = 48.7 bits (116), Expect = 1e-05
 Identities = 33/197 (16%), Positives = 48/197 (24%), Gaps = 12/197 (6%)

Query: 565 VRVAGKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPW 624
           +R+A         P PP            P    P ++   G   P              
Sbjct: 82  IRIAITVDPSAGEPAPPPPHARRTS---EPELPRPGRRPYEGYGGPRADDRPPGLPRQDQ 138

Query: 625 GPPVPPPYAPYAPPP-PGSTMYPPVPGQPMPPYGVQYPP--PVQTAPPGALTAPPGAPTQ 681
            P   P Y  Y   P PG+  +P         YG Q         AP  +  +      +
Sbjct: 139 LPTARPAYPAYQQRPEPGA--WPRAAD----DYGWQQQRLGFPPRAPYASPASYAPEQER 192

Query: 682 TATSSEAQQHSFPPGVQSESSSSAPAASANMYGSSMPPMPPNVQPAYATAPLGYSPYYNA 741
                +A +  +    +                +  P  PP     +   P         
Sbjct: 193 DREPYDAGRPEYDQRRRDYDHPRPDWDRPRRDRTDRPEPPPGAGHVHRGGPGPPERDDAP 252

Query: 742 VPPPPPPAPVSAADHSQ 758
           V P  P AP   A    
Sbjct: 253 VVPIRPSAPGPLAAQPA 269

Length = 617

>gnl|CDD|218191 pfam04652, DUF605, Vta1 like

 Score = 47.8 bits (114), Expect = 1e-05
 Identities = 28/132 (21%), Positives = 35/132 (26%), Gaps = 8/132 (6%)

Query: 580 PPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGPPVPPPYAPYAPPP 639
           P              V    S    PG    +P +AS +  P         P  P  P  
Sbjct: 148 PNPGPPLDEEDEDADVATTNSDNSFPGED-ADPASASPSDPPSSSPGVPSFPSPPEDPSS 206

Query: 640 PGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPG--APTQTATSSEAQQHSFPPGV 697
           P           P P       PP     P   + PPG  AP            +  P  
Sbjct: 207 P-----SDSSLPPAPSSFQSDTPPPSPESPTNPSPPPGPAAPPPPPVQQVPPLSTAKPTP 261

Query: 698 QSESSSSAPAAS 709
            S S++ AP   
Sbjct: 262 PSASATPAPIGG 273

Vta1 (VPS20-associated protein 1) is a positive regulator of Vps4. Vps4 is an ATPase that is required in the multivesicular body (MVB) sorting pathway to dissociate the endosomal sorting complex required for transport (ESCRT). Vta1 promotes correct assembly of Vps4 and stimulates its ATPase activity through its conserved Vta1/SBP1/LIP5 region. Length = 315

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

 Score = 43.7 bits (103), Expect = 1e-05
 Identities = 21/70 (30%), Positives = 36/70 (51%), Gaps = 2/70 (2%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           ++IG L     DD L   F  FG++    V++D  TG S+G+GF+ +   +  N  +   
Sbjct: 1   MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKE 60

Query: 554 NGYRLEGRTI 563
             + L+G+ I
Sbjct: 61  --HILDGKII 68

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

 Score = 43.8 bits (103), Expect = 1e-05
 Identities = 20/55 (36%), Positives = 31/55 (56%)

Query: 511 LFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAV 565
           +FS +G +    V+ D+ TG S+G+ FV +  I  +  A+   NG  L+GR I V
Sbjct: 19  VFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGMELDGRRIRV 73

This subgroup corresponds to the RRM of TRA2-alpha or TRA-2-alpha, also termed transformer-2 protein homolog A, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein (SRp40) that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-alpha contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. . Length = 79

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

 Score = 43.3 bits (102), Expect = 1e-05
 Identities = 23/74 (31%), Positives = 34/74 (45%), Gaps = 8/74 (10%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
             +++G +  T   D L  LF  FG +V    +KD        Y FV     + A  AI 
Sbjct: 1   WKIFVGNVSATCTSDELRGLFEEFGRVVECDKVKD--------YAFVHMEREEEALAAIE 52

Query: 552 SMNGYRLEGRTIAV 565
           ++NG  ++GR I V
Sbjct: 53  ALNGKEVKGRRINV 66

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|221895 pfam13014, KH_3, KH domain

 Score = 42.2 bits (100), Expect = 1e-05
 Identities = 14/26 (53%), Positives = 16/26 (61%)

Query: 267 FIGLIIGPRGNTQKRMERETGAKIVI 292
            +G IIG  G T K +  ETGAKI I
Sbjct: 1   LVGAIIGKGGETIKEIREETGAKIQI 26

KH motifs bind RNA in vitro. This RNA-binding domain is required for the efficient anchoring of ASH1-mRNA to the distal tip of the daughter cell. ASH1 is a specific repressor of transcription that localizes asymmetrically to the daughter cell nucleus. RNA localisation is a widespread mechanism for achieving localised protein synthesis. Length = 42

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

 Score = 43.7 bits (103), Expect = 1e-05
 Identities = 21/69 (30%), Positives = 40/69 (57%), Gaps = 4/69 (5%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKY---ADIQMANNAI 550
           +++G +   +D+  +   F+ +G +   K+I DR TG+SKGYGFV +    D+Q    + 
Sbjct: 8   VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDR-TGVSKGYGFVSFYDDVDVQKIVESQ 66

Query: 551 ASMNGYRLE 559
            + +G +L+
Sbjct: 67  INFHGKKLK 75

This subgroup corresponds to the RRM of DAZL, also termed SPGY-like-autosomal, encoded by the autosomal homolog of DAZ gene, DAZL. It is ancestral to the deleted in azoospermia (DAZ) protein. DAZL is germ-cell-specific RNA-binding protein that contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a DAZ motif, a protein-protein interaction domain. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 82

>gnl|CDD|218191 pfam04652, DUF605, Vta1 like

 Score = 47.0 bits (112), Expect = 2e-05
 Identities = 27/133 (20%), Positives = 39/133 (29%), Gaps = 12/133 (9%)

Query: 646 PPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATSSEAQQHSFPPGVQSESSSSA 705
            P PG P+             +            + + +   +     P      S  S 
Sbjct: 147 DPNPGPPLDEEDEDADVATTNSDNSFPGEDADPASASPSDPPSSSPGVP------SFPSP 200

Query: 706 PAASANMYGSSMPPMPPNVQPAYATAPLGYSPYYNAVPPPPPPAPVSAADHSQNLGNVPW 765
           P   ++   SS+PP P +      T P       N  PPP P AP             P 
Sbjct: 201 PEDPSSPSDSSLPPAPSS--FQSDTPPPSPESPTNPSPPPGPAAPPPPPVQQVP----PL 254

Query: 766 ATNPPVQPPVSSA 778
           +T  P  P  S+ 
Sbjct: 255 STAKPTPPSASAT 267

Vta1 (VPS20-associated protein 1) is a positive regulator of Vps4. Vps4 is an ATPase that is required in the multivesicular body (MVB) sorting pathway to dissociate the endosomal sorting complex required for transport (ESCRT). Vta1 promotes correct assembly of Vps4 and stimulates its ATPase activity through its conserved Vta1/SBP1/LIP5 region. Length = 315

>gnl|CDD|240722 cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in Mei2-like proteins and terminal EAR1-like proteins

 Score = 43.0 bits (102), Expect = 2e-05
 Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 5/73 (6%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L +  L   + D  L  LFS FG++   K I++     S+   FV++ DI+ A  A+ ++
Sbjct: 4   LLVFNLDSPISDQELRSLFSQFGEV---KDIRETPLRPSQ--KFVEFYDIRAAEAALDAL 58

Query: 554 NGYRLEGRTIAVR 566
           NG    G  + V+
Sbjct: 59  NGRPFLGGRLKVK 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|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 43.3 bits (103), Expect = 2e-05
 Identities = 21/76 (27%), Positives = 42/76 (55%), Gaps = 2/76 (2%)

Query: 491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAI 550
              +++G +P  L +D L+ LF   G I   +++ D  +G+++GY FV Y + + A  A+
Sbjct: 1   GCEVFVGKIPRDLFEDELVPLFEKAGPIYELRLMMD-FSGLNRGYAFVTYTNKEAAQRAV 59

Query: 551 ASMNGYRLE-GRTIAV 565
             ++ Y +  G+ + V
Sbjct: 60  KQLHNYEIRPGKRLGV 75

This subfamily corresponds to the RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs); DND1 harbors only two RRMs. . Length = 78

>gnl|CDD|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 43.3 bits (103), Expect = 2e-05
 Identities = 19/76 (25%), Positives = 36/76 (47%), Gaps = 4/76 (5%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTF--GDIVMAKVIKDRV--TGMSKGYGFVKYADIQMANNA 549
           LY+  L   + ++ L+ +F  F         +   R+   G  KG  FV +   ++A  A
Sbjct: 4   LYVKNLSKRVTEEDLVYIFGRFVDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEIATKA 63

Query: 550 IASMNGYRLEGRTIAV 565
           +  +NGY L+G+ + +
Sbjct: 64  LNLVNGYVLKGKPMVI 79

This subfamily corresponds to the RRM2 of RBM40 and the RRM of RBM41. RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein). It serves as a bridging factor between the U11 and U12 snRNPs. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. RBM41 contains only one RRM. Its biological function remains unclear. . Length = 82

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

 Score = 43.0 bits (102), Expect = 2e-05
 Identities = 22/74 (29%), Positives = 35/74 (47%), Gaps = 7/74 (9%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDI-VMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
           L++  +   ++D+ L  LF  FGDI  +    K R      G+  V Y DI+ A  A  +
Sbjct: 4   LFVRNINSNVEDEELRALFEQFGDIRTLYTACKHR------GFIMVSYYDIRAARRAKRA 57

Query: 553 MNGYRLEGRTIAVR 566
           + G  L GR + + 
Sbjct: 58  LQGTELGGRKLDIH 71

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

 Score = 42.6 bits (100), Expect = 3e-05
 Identities = 21/56 (37%), Positives = 32/56 (57%), Gaps = 2/56 (3%)

Query: 512 FSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV 567
           F+  G ++ A +  +   G SKG G V++   ++A  A   MNGY+L GR I VR+
Sbjct: 20  FNECGHVLYADIKME--NGKSKGCGVVRFESPEVAERACRMMNGYKLNGREIDVRI 73

This subgroup corresponds to the RRM3 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 77

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

 Score = 42.4 bits (100), Expect = 3e-05
 Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 3/72 (4%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L++G L     +D L   F   G I   +++    +G  KG+ FV + +I+ A NA   +
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNA---L 57

Query: 554 NGYRLEGRTIAV 565
            G  L GR + V
Sbjct: 58  KGKHLNGRALRV 69

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|237871 PRK14965, PRK14965, DNA polymerase III subunits gamma and tau; Provisional

 Score = 47.0 bits (112), Expect = 3e-05
 Identities = 29/83 (34%), Positives = 32/83 (38%), Gaps = 10/83 (12%)

Query: 606 GGPLPNPPAASYTGAPVPWGPPVPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQ 665
           G P P   A    GAP P  P  PPP A  APP P +    P   +P P      P P  
Sbjct: 380 GAPAPPSAAW---GAPTPAAPAAPPPAA--APPVPPAAPARPAAARPAPA-----PAPPA 429

Query: 666 TAPPGALTAPPGAPTQTATSSEA 688
            A P A +A P A         A
Sbjct: 430 AAAPPARSADPAAAASAGDRWRA 452

Length = 576

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

 Score = 42.8 bits (101), Expect = 3e-05
 Identities = 22/63 (34%), Positives = 42/63 (66%), Gaps = 2/63 (3%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFG-DIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
           L++G L P +D++ + +++++ G + V  KVI+ R +G++ GY FV++     A NA+ S
Sbjct: 2   LWMGDLEPWMDENFIKQVWASLGLEPVNVKVIRSRNSGLNAGYCFVEFPSPHAAQNAL-S 60

Query: 553 MNG 555
           +NG
Sbjct: 61  LNG 63

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

>gnl|CDD|240927 cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 42.7 bits (100), Expect = 3e-05
 Identities = 23/78 (29%), Positives = 44/78 (56%), Gaps = 1/78 (1%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           T +++G +P  L +D L+ LF   G I   +++ D +TG+++GY FV +   + A  A+ 
Sbjct: 2   TEIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAVK 61

Query: 552 SMNGYRLE-GRTIAVRVA 568
             N + +  G+ I V ++
Sbjct: 62  LYNNHEIRPGKHIGVCIS 79

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|241065 cd12621, RRM3_TIA1, RNA recognition motif 3 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 42.4 bits (99), Expect = 3e-05
 Identities = 23/70 (32%), Positives = 37/70 (52%), Gaps = 6/70 (8%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           +Y G +   L +  + + FS FG I+  +V  D      KGY FV++   + A +AI S+
Sbjct: 3   VYCGGVTSGLTEQLMRQTFSPFGQIMEVRVFPD------KGYSFVRFNSHESAAHAIVSV 56

Query: 554 NGYRLEGRTI 563
           NG  +EG  +
Sbjct: 57  NGTTIEGHVV 66

This subgroup corresponds to the RRM3 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1) and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 74

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 46.9 bits (112), Expect = 4e-05
 Identities = 33/133 (24%), Positives = 41/133 (30%), Gaps = 13/133 (9%)

Query: 602 QYAPGGPLPNPPAASYTGAPVPWGPPVPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYP 661
             A G   P   A S   A     P  P   AP A   P     P    QP P      P
Sbjct: 386 GVAGGAGAPAAAAPSAAAAAPAAAPA-PAAAAPAAAAAPA----PAAAPQPAPA-----P 435

Query: 662 PPVQTAPPGALTAPPGAPTQTATSSEAQQHSFPPGVQSESSSSAPAASANMYGSSMPPMP 721
            P    P  A  AP G       ++       P    +   ++APA +     ++  P  
Sbjct: 436 APAPAPPSPAGNAPAGGAPSPPPAAAPSAQPAPAPAAAPEPTAAPAPAPP---AAPAPAA 492

Query: 722 PNVQPAYATAPLG 734
               PA   AP G
Sbjct: 493 APAAPAAPAAPAG 505

Length = 824

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 46.9 bits (112), Expect = 4e-05
 Identities = 29/123 (23%), Positives = 32/123 (26%), Gaps = 2/123 (1%)

Query: 559 EGRTIAVRVAGKPPQPTVPPGP--PTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAAS 616
                       PP    P  P  P    P  P  AP       Q   P    P     +
Sbjct: 669 WPAKAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPAGQADDPAAQPPQAAQGA 728

Query: 617 YTGAPVPWGPPVPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPP 676
              +P    P   PP     P P G+   PP P  P P       PP          A  
Sbjct: 729 SAPSPAADDPVPLPPEPDDPPDPAGAPAQPPPPPAPAPAAAPAAAPPPSPPSEEEEMAED 788

Query: 677 GAP 679
            AP
Sbjct: 789 DAP 791

Length = 824

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

 Score = 42.2 bits (99), Expect = 4e-05
 Identities = 26/72 (36%), Positives = 35/72 (48%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L I  LPPT        L   FG++    ++    TG SKGYGFV+Y     A  A + +
Sbjct: 2   LCIANLPPTYTQQQFEELVRPFGNLERCFLVYSETTGHSKGYGFVEYMKKDSAARAKSDL 61

Query: 554 NGYRLEGRTIAV 565
            G +L  RT+ V
Sbjct: 62  LGKQLGSRTLYV 73

This subgroup corresponds to the RRM2 of raver-1, a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-1 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two PTB-binding [SG][IL]LGxxP motifs. Raver1 binds to PTB through the PTB-binding motifs at its C-terminal half, and binds to other partners, such as RNA having the sequence UCAUGCAGUCUG, through its N-terminal RRMs. Interestingly, the 12-nucleotide RNA having the sequence UCAUGCAGUCUG with micromolar affinity is found in vinculin mRNA. Additional research indicates that the RRM1 of raver-1 directs its interaction with the tail domain of activated vinculin. Then the raver1/vinculin tail (Vt) complex binds to vinculin mRNA, which is permissive for vinculin binding to F-actin. . Length = 77

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

 Score = 42.4 bits (100), Expect = 4e-05
 Identities = 18/76 (23%), Positives = 33/76 (43%)

Query: 490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNA 549
           D   L++G LP  + +D L   F  FG+++  ++      G    +GFV + D +     
Sbjct: 2   DSHQLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKI 61

Query: 550 IASMNGYRLEGRTIAV 565
           +A+   Y      + V
Sbjct: 62  LANKPIYFRGDHRLNV 77

This subfamily corresponds to the RRM domain in the G3BP family of RNA-binding and SH3 domain-binding proteins. G3BP acts at the level of RNA metabolism in response to cell signaling, possibly as RNA transcript stabilizing factors or an RNase. Members include G3BP1, G3BP2 and similar proteins. These proteins associate directly with the SH3 domain of GTPase-activating protein (GAP), which functions as an inhibitor of Ras. They all contain an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing PXXP motif(s), an RNA recognition motif (RRM), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). Length = 81

>gnl|CDD|240978 cd12534, RRM_SARFH, RNA recognition motif in Drosophila melanogaster RNA-binding protein cabeza and similar proteins

 Score = 42.4 bits (100), Expect = 4e-05
 Identities = 26/83 (31%), Positives = 36/83 (43%), Gaps = 8/83 (9%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAK--------VIKDRVTGMSKGYGFVKYADIQM 545
           +++  LPP   +  L   F + G I + K        + KD+ TG  KG   V Y D   
Sbjct: 1   VFVSNLPPNTTEQDLAEHFGSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYDDPHA 60

Query: 546 ANNAIASMNGYRLEGRTIAVRVA 568
           A+ AI   N     G TI V +A
Sbjct: 61  ASAAIEWFNNKDFMGNTIKVSLA 83

This subgroup corresponds to the RRM in cabeza, also termed P19, or sarcoma-associated RNA-binding fly homolog (SARFH). It is a putative homolog of human RNA-binding proteins FUS (also termed TLS or Pigpen or hnRNP P2), EWS (also termed EWSR1), TAF15 (also termed hTAFII68 or TAF2N or RPB56), and belongs to the of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a nuclear RNA binding protein that may play an important role in the regulation of RNA metabolism during fly development. Cabeza contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 83

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

 Score = 42.4 bits (100), Expect = 4e-05
 Identities = 17/75 (22%), Positives = 37/75 (49%), Gaps = 1/75 (1%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           +++G LPP + +  L + FS FG +    V+ D      +G+GF+ +      +  +   
Sbjct: 5   IFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVVN-E 63

Query: 554 NGYRLEGRTIAVRVA 568
           + + + G+ + V+ A
Sbjct: 64  HFHDINGKKVEVKRA 78

This subfamily corresponds to the RRM2 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated is predominantly nuclear and the nonacetylated form is in cytoplasm. DAZAP1 also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain. . Length = 80

>gnl|CDD|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast nucleolar protein 12 (Nop12p) and similar proteins

 Score = 42.2 bits (99), Expect = 5e-05
 Identities = 18/75 (24%), Positives = 38/75 (50%), Gaps = 4/75 (5%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           +++G L     ++GL R+F   G I   ++++D  T + KG+ +V++ D      A+  +
Sbjct: 2   VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKALL-L 60

Query: 554 NGYR---LEGRTIAV 565
           N  +   +  R + V
Sbjct: 61  NEKKFPPMLPRELRV 75

This subgroup corresponds to the RRM2 of Nop12p, which is encoded by YOL041C from Saccharomyces cerevisiae. It is a novel nucleolar protein required for pre-25S rRNA processing and normal rates of cell growth at low temperatures. Nop12p shares high sequence similarity with nucleolar protein 13 (Nop13p). Both, Nop12p and Nop13p, are not essential for growth. However, unlike Nop13p that localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent, Nop12p is localized to the nucleolus. Nop12p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|241064 cd12620, RRM3_TIAR, RNA recognition motif 3 in nucleolysin TIAR and similar proteins

 Score = 41.5 bits (97), Expect = 5e-05
 Identities = 21/70 (30%), Positives = 38/70 (54%), Gaps = 6/70 (8%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           +Y G +   L +  + + FS FG I+  +V  +      KGY F++++  + A +AI S+
Sbjct: 3   VYCGGIASGLTEQLMRQTFSPFGQIMEIRVFPE------KGYSFIRFSTHESAAHAIVSV 56

Query: 554 NGYRLEGRTI 563
           NG  +EG  +
Sbjct: 57  NGTTIEGHVV 66

This subgroup corresponds to the RRM3 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 73

>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional

 Score = 46.3 bits (110), Expect = 6e-05
 Identities = 42/216 (19%), Positives = 63/216 (29%), Gaps = 7/216 (3%)

Query: 563 IAVRVAGKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPV 622
                  +   PT PP  P +  P     + P     +   A      +P     +    
Sbjct: 57  AGAAACDRFEPPTGPPPGPGTEAPANESRSTPTWSLSTLAPASPAREGSPTPPGPSSPDP 116

Query: 623 PWGPPVPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQT 682
           P  P  PP   P +P P  S M  PV     PP           A   +  A        
Sbjct: 117 P-PPTPPPASPPPSPAPDLSEMLRPVGSPGPPPAASPPAAGASPAAVASDAASSRQAALP 175

Query: 683 ATSSEAQQHSFPPGVQSESSSSAPAASANMYGSSMPPMPPNVQPAYATAPLGYSPYYNAV 742
            +S E    +          S+ PAA++           P    A + AP   +P  +A 
Sbjct: 176 LSSPEETARAPSSPPAEPPPSTPPAAAS---PRPPRRSSPISASASSPAP---APGRSAA 229

Query: 743 PPPPPPAPVSAADHSQNLGNVPWATNPPVQPPVSSA 778
                 +  S++  S   G  P    P  +P   + 
Sbjct: 230 DDAGASSSDSSSSESSGCGWGPENECPLPRPAPITL 265

Length = 1352

>gnl|CDD|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 41.8 bits (98), Expect = 6e-05
 Identities = 17/61 (27%), Positives = 31/61 (50%), Gaps = 1/61 (1%)

Query: 508 LIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV 567
           L ++F  +G +  A + + R   +  G+ FV     + A  A+ + NG  ++GR +AV  
Sbjct: 18  LKKIFGRYGKVREATIPRKRGGKLC-GFAFVTMKKRKNAEIALENTNGLEIDGRPVAVDW 76

Query: 568 A 568
           A
Sbjct: 77  A 77

This subgroup corresponds to the RRM2 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 83

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

 Score = 41.8 bits (99), Expect = 6e-05
 Identities = 18/79 (22%), Positives = 41/79 (51%), Gaps = 7/79 (8%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMA----NNA 549
           L++G L P++ +  L   FS FG +   ++IK +  G  +G+ ++   D++ +       
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYI---DLRTSEAQLKKC 58

Query: 550 IASMNGYRLEGRTIAVRVA 568
            +++NG + +G  + +  A
Sbjct: 59  KSTLNGTKWKGSVLKIEEA 77

This model corresponds to the RRM of NOL8 (also termed Nop132) encoded by a novel NOL8 gene that is up-regulated in the majority of diffuse-type, but not intestinal-type, gastric cancers. Thus, NOL8 may be a good molecular target for treatment of diffuse-type gastric cancer. Also, NOL8 is a phosphorylated protein that contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), suggesting NOL8 is likely to function as a novel RNA-binding protein. It may be involved in regulation of gene expression at the post-transcriptional level or in ribosome biogenesis in cancer cells. Length = 78

>gnl|CDD|240938 cd12494, RRM3_hnRNPR, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 41.6 bits (97), Expect = 6e-05
 Identities = 25/78 (32%), Positives = 38/78 (48%), Gaps = 9/78 (11%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L++  L  T+ ++ L + FS FG +   K +KD        Y FV + +   A  A+  M
Sbjct: 4   LFVRNLATTVTEEILEKSFSEFGKLERVKKLKD--------YAFVHFEERDAAVRAMDEM 55

Query: 554 NGYRLEGRTIAVRVAGKP 571
           NG  +EG  I + V  KP
Sbjct: 56  NGKEIEGEEIEI-VLAKP 72

This subgroup corresponds to the RRM3 of hnRNP R. a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP R is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, as well as in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP R binds RNA through its RRM domains. . Length = 72

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 46.1 bits (110), Expect = 8e-05
 Identities = 23/114 (20%), Positives = 27/114 (23%), Gaps = 5/114 (4%)

Query: 564 AVRVAGKPPQPTVPPGPPTSTM---PTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGA 620
           A   A   P     P          P    +  P          P      P   + +  
Sbjct: 398 APSAAAAAPAAAPAPAAAAPAAAAAPAPAAAPQPAPAPAPAPAPPSPAGNAPAGGAPSPP 457

Query: 621 PVPWGPPVPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTA 674
           P       P P    AP P  +    P P     P      P    AP GA  A
Sbjct: 458 PAAAPSAQPAPAPAAAPEPTAAP--APAPPAAPAPAAAPAAPAAPAAPAGADDA 509

Length = 824

>gnl|CDD|240939 cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 41.1 bits (96), Expect = 8e-05
 Identities = 24/78 (30%), Positives = 37/78 (47%), Gaps = 9/78 (11%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L++  L  T+ ++ L + F  FG +   K +KD        Y F+ + +   A  A+  M
Sbjct: 4   LFVRNLANTVTEEILEKAFGQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEEM 55

Query: 554 NGYRLEGRTIAVRVAGKP 571
           NG  LEG  I + V  KP
Sbjct: 56  NGKELEGENIEI-VFAKP 72

This subgroup corresponds to the RRM3 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP that is a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. . Length = 72

>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family

 Score = 46.2 bits (109), Expect = 8e-05
 Identities = 48/204 (23%), Positives = 63/204 (30%), Gaps = 9/204 (4%)

Query: 571 PPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGPPVPP 630
           PP P++P   P  T P  P        +P     P  P P  P+       +     +P 
Sbjct: 338 PPAPSMPHIKPPPTTPI-PQLPNQSHKHPPHLQGPS-PFPQMPSNLPPPPALKPLSSLPT 395

Query: 631 PYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATSSEAQQ 690
            + P A PPP   M    P Q   P         Q+ PP A T P          S   Q
Sbjct: 396 HHPPSAHPPPLQLMPQSQPLQS-VPAQPPVLTQSQSLPPKASTHPHSGLHSGPPQSPFAQ 454

Query: 691 HSFPPGVQSESSSSAPAASANMYGSSMPPMPPNVQPAYATAPLGYSPYYNAVPPPPPPAP 750
           H F  G      +  P  S     +S P  PP                     P PP  P
Sbjct: 455 HPFTSGGLP---AIGPPPSLP---TSTPAAPPRASSGSQPPGSALPSSGGCAGPGPPLPP 508

Query: 751 VSAADHSQNLGNVPWATNPPVQPP 774
           +   +   +    P +  PP + P
Sbjct: 509 IQIKEEPLDEAEEPESPPPPPRSP 532

Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. Length = 979

>gnl|CDD|240917 cd12473, RRM2_MSSP1, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 41.6 bits (97), Expect = 8e-05
 Identities = 20/64 (31%), Positives = 35/64 (54%), Gaps = 1/64 (1%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           TNLYI  LP ++D+  L  +   FG ++  ++++D  +G S+G GF +    +     I+
Sbjct: 1   TNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIS 59

Query: 552 SMNG 555
             NG
Sbjct: 60  HFNG 63

This subgroup corresponds to the RRM2 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2). MSSP-1 is a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 85

>gnl|CDD|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 = 40.9 bits (96), Expect = 8e-05
 Identities = 19/73 (26%), Positives = 38/73 (52%), Gaps = 8/73 (10%)

Query: 496 IGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNG 555
           +G+ P T  ++ + +LF  FG +V       R   + K + FV++ D + A  A+ +++G
Sbjct: 5   VGFDPGTTREEDIEKLFEPFGPLV-------RCD-IRKTFAFVEFEDSEDATKALEALHG 56

Query: 556 YRLEGRTIAVRVA 568
            R++G  + V   
Sbjct: 57  SRIDGSVLTVEFV 69

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|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau; Provisional

 Score = 45.6 bits (108), Expect = 8e-05
 Identities = 30/117 (25%), Positives = 36/117 (30%), Gaps = 16/117 (13%)

Query: 572 PQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGPPVPPP 631
           P P   P  PT+  P+ PV   P         AP    P   AA    A +P   PV   
Sbjct: 362 PVPAPQPAKPTAAAPS-PVRPTP---------APSTR-PKAAAA----ANIPPKEPVRET 406

Query: 632 YAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATSSEA 688
            A   P PP     P        P   +   PV   P     APP    +   +   
Sbjct: 407 -ATPPPVPPRPVAPPVPHTPESAPKLTRAAIPVDEKPKYTPPAPPKEEEKALIADGD 462

Length = 585

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 45.7 bits (109), Expect = 9e-05
 Identities = 26/129 (20%), Positives = 30/129 (23%), Gaps = 3/129 (2%)

Query: 564 AVRVAGKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVP 623
           A   A  P      P  P    P  P  AP       Q   P    P     +   +P  
Sbjct: 676 AAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPAGQADDPAAQPPQAAQGASAPSPAA 735

Query: 624 WG---PPVPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPT 680
                 P  P   P     P     PP P     P     P P       A    P    
Sbjct: 736 DDPVPLPPEPDDPPDPAGAPAQPPPPPAPAPAAAPAAAPPPSPPSEEEEMAEDDAPSMDD 795

Query: 681 QTATSSEAQ 689
           +    +E  
Sbjct: 796 EDRRDAEEV 804

Length = 824

>gnl|CDD|236138 PRK07994, PRK07994, DNA polymerase III subunits gamma and tau; Validated

 Score = 45.6 bits (109), Expect = 9e-05
 Identities = 30/149 (20%), Positives = 37/149 (24%), Gaps = 14/149 (9%)

Query: 608 PLPNPPAASYTGAPVPWGPPVPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTA 667
           P    PAAS      P     PP      PPP  +    P    P     +         
Sbjct: 372 PQSAAPAASAQATAAPTAAVAPPQAPAVPPPPASAPQQAPAVPLPETTSQLLAARQQLQR 431

Query: 668 PPGALTAPPGAPTQTATSSEAQQHSFPPGVQSESSSSAPAASANMYGSSMPPMPPNVQPA 727
             GA  A    P   + +                +S  PA SA           P  + A
Sbjct: 432 AQGATKAKKSEPAAASRARPV------NSALERLASVRPAPSA-------LEKAPAKKEA 478

Query: 728 YATAPLGYSPYYNAVPPPPPPAPVSAADH 756
           Y              P   P A   A +H
Sbjct: 479 YRWKAT-NPVEVKKEPVATPKALKKALEH 506

Length = 647

>gnl|CDD|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau; Provisional

 Score = 45.6 bits (108), Expect = 9e-05
 Identities = 26/96 (27%), Positives = 31/96 (32%), Gaps = 9/96 (9%)

Query: 561 RTIAVRVAGKPPQPT-VPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTG 619
                        P+ V P P  ST P    +A      P ++ A   P+P  P A    
Sbjct: 363 VPAPQPAKPTAAAPSPVRPTPAPSTRPKAAAAANIPPKEPVRETATPPPVPPRPVAP--- 419

Query: 620 APVPWGPPVPPPYAPYAPPPPGSTMYPPVPGQPMPP 655
            PVP  P   P     A P      Y P    P PP
Sbjct: 420 -PVPHTPESAPKLTRAAIPVDEKPKYTP----PAPP 450

Length = 585

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

 Score = 41.1 bits (97), Expect = 9e-05
 Identities = 16/54 (29%), Positives = 27/54 (50%), Gaps = 1/54 (1%)

Query: 512 FSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAV 565
           F + G I    ++ D+ TG  KG+ ++++ D     NA+  +N     GR I V
Sbjct: 20  FKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALL-LNESEFRGRQIKV 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|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 44.9 bits (106), Expect = 1e-04
 Identities = 26/92 (28%), Positives = 43/92 (46%), Gaps = 6/92 (6%)

Query: 480 SNGAKPIKEL-----DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKG 534
            +G    + L     DD  +++  L     +  L   FS  G +   + IKDR +  SKG
Sbjct: 73  RSGRNTKEPLTEAERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKG 132

Query: 535 YGFVKYADIQMANNAIASMNGYRLEGRTIAVR 566
             +V++ D++    A+A + G  L GR I V+
Sbjct: 133 VAYVEFYDVESVIKALA-LTGQMLLGRPIIVQ 163

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|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau; Provisional

 Score = 45.6 bits (108), Expect = 1e-04
 Identities = 27/135 (20%), Positives = 30/135 (22%), Gaps = 8/135 (5%)

Query: 566 RVAGKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPW- 624
                 P P     P  +  P      P      +   AP    P    A     P PW 
Sbjct: 444 PGGAPAPAPAPAAAPAAAARPAAAGPRPVA---AAAAAAPARAAPAAAPAPADDDPPPWE 500

Query: 625 ----GPPVPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPT 680
                   P P  P A P        P P    P    +   P   A P    A    P 
Sbjct: 501 ELPPEFASPAPAQPDAAPAGWVAESIPDPATADPDDAFETLAPAPAAAPAPRAAAATEPV 560

Query: 681 QTATSSEAQQHSFPP 695
                  A     P 
Sbjct: 561 VAPRPPRASASGLPD 575

Length = 700

>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau; Provisional

 Score = 45.5 bits (108), Expect = 1e-04
 Identities = 27/112 (24%), Positives = 32/112 (28%), Gaps = 2/112 (1%)

Query: 564 AVRVAGKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVP 623
             R     P          +  P    +A           AP  P+  P AA+   AP  
Sbjct: 381 PARPEAAAPAAAPVAQAAAAPAPAAAPAAAASAPAAPPAAAPPAPVAAPAAAAPAAAPAA 440

Query: 624 WGPPVPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAP 675
               V    AP A   P  T+  PV   P P       P    AP  A   P
Sbjct: 441 APAAVALAPAPPAQAAP-ETVAIPVRVAPEPA-VASAAPAPAAAPAAARLTP 490

Length = 618

>gnl|CDD|241078 cd12634, RRM2_CELF1_2, RNA recognition motif 2 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 41.2 bits (96), Expect = 1e-04
 Identities = 19/64 (29%), Positives = 35/64 (54%), Gaps = 1/64 (1%)

Query: 491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAI 550
           D  L+IG +    +++ +  +FS FG I   ++++    G+S+G  FV +    MA  AI
Sbjct: 1   DRKLFIGMVSKKCNENDIRVMFSPFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAI 59

Query: 551 ASMN 554
            +M+
Sbjct: 60  KAMH 63

This subgroup corresponds to the RRM2 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. Human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it preferentially binds to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. . Length = 81

>gnl|CDD|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding protein 19 (RBM19), yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 40.7 bits (96), Expect = 1e-04
 Identities = 18/68 (26%), Positives = 29/68 (42%), Gaps = 2/68 (2%)

Query: 499 LPPTLDDDGLIRLFSTF-GDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYR 557
           LP +L +  L   FS   G+I   K+++    G S+   F+ Y   + A  A    N   
Sbjct: 8   LPASLTEAELKEHFSKHGGEITDVKLLRTE-DGKSRRIAFIGYKTEEEAQKAKDYFNNTY 66

Query: 558 LEGRTIAV 565
           +    I+V
Sbjct: 67  INTSKISV 74

This subfamily corresponds to the RRM1 of RBM19 and MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 77

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

 Score = 40.7 bits (95), Expect = 1e-04
 Identities = 22/73 (30%), Positives = 35/73 (47%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L +  LP +   +    L   +G+I    ++   VTG SKGYGFV+Y     A+ A   +
Sbjct: 2   LCVTNLPISFTLEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKARLEL 61

Query: 554 NGYRLEGRTIAVR 566
            G +L   T+  +
Sbjct: 62  LGKQLGESTLFAQ 74

This subgroup corresponds to the RRM2 of raver-2, a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It is present in vertebrates and shows high sequence homology to raver-1, a ubiquitously expressed co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. In contrast, raver-2 exerts a distinct spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Raver-2 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. Raver-2 binds to PTB through the SLLGEPP motif only, and binds to RNA through its RRMs. . Length = 77

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 44.6 bits (106), Expect = 2e-04
 Identities = 27/130 (20%), Positives = 32/130 (24%), Gaps = 12/130 (9%)

Query: 625 GPPVPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTAT 684
              V       A   P +    P               P   A P    AP  AP     
Sbjct: 384 RLGVAGGAGAPAAAAPSAAAAAPAAAPAPAA-----AAPAAAAAPAPAAAPQPAPAPAPA 438

Query: 685 SSEAQQHSFPPGVQSESSSSAPAASANMYGSSMPPMPPNVQPAYATAPLGYSPYYNAVPP 744
            +        P   + S   A A SA        P P        TA    +P     P 
Sbjct: 439 PAPPSPAGNAPAGGAPSPPPAAAPSA-------QPAPAPAAAPEPTAAPAPAPPAAPAPA 491

Query: 745 PPPPAPVSAA 754
             P AP + A
Sbjct: 492 AAPAAPAAPA 501

Length = 824

>gnl|CDD|235906 PRK07003, PRK07003, DNA polymerase III subunits gamma and tau; Validated

 Score = 44.5 bits (105), Expect = 2e-04
 Identities = 40/205 (19%), Positives = 56/205 (27%), Gaps = 22/205 (10%)

Query: 572 PQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGPPVP-- 629
           P+         +  P  P +  P         A  G  P P  A+   +           
Sbjct: 412 PKAAAAAAATRAEAP--PAAPAPPATADRGDDAADGDAPVPAKANARASADSRCDERDAQ 469

Query: 630 PPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATSSEAQ 689
           PP    +   P S   P    +P P             P     A        A ++   
Sbjct: 470 PPADSGSASAPASDAPPDAAFEPAPRAAAPSAATPAAVPDARAPAAASREDAPAAAAPPA 529

Query: 690 QHSFPPGVQSESSSS----APAA-----SANMYGSS------MPPMPPNVQPAYATAPLG 734
             + PP   + + ++    A AA     +A M  SS           P   PA A  P  
Sbjct: 530 PEARPPTPAAAAPAARAGGAAAALDVLRNAGMRVSSDRGARAAAAAKPAAAPAAAPKPAA 589

Query: 735 YSPYYNAVPPPPPPAPVSAADHSQN 759
                 AV  P P A  +  D   N
Sbjct: 590 PRV---AVQVPTPRARAATGDAPPN 611

Length = 830

>gnl|CDD|236138 PRK07994, PRK07994, DNA polymerase III subunits gamma and tau; Validated

 Score = 44.5 bits (106), Expect = 2e-04
 Identities = 19/118 (16%), Positives = 30/118 (25%), Gaps = 8/118 (6%)

Query: 669 PGALTAPPGAPTQTATSSEAQQHSFPPGVQSESSSSAPAASANMYGSSMPPMPPNVQPAY 728
           P A    P  P Q+A  + + Q +  P        +          +S P   P V    
Sbjct: 361 PAAPLPEPEVPPQSAAPAASAQATAAPTAAVAPPQAPAVPPP---PASAPQQAPAVPLPE 417

Query: 729 ATAPL-----GYSPYYNAVPPPPPPAPVSAADHSQNLGNVPWATNPPVQPPVSSAEKS 781
            T+ L            A          ++     N      A+  P    +  A   
Sbjct: 418 TTSQLLAARQQLQRAQGATKAKKSEPAAASRARPVNSALERLASVRPAPSALEKAPAK 475

Length = 647

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

 Score = 40.3 bits (94), Expect = 2e-04
 Identities = 21/75 (28%), Positives = 37/75 (49%), Gaps = 8/75 (10%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           +YIG L   + +  + R F  +G ++           +  GYGFV++ D + A++A+  +
Sbjct: 2   VYIGRLSYHVREKDIQRFFGGYGKLLEID--------LKNGYGFVEFEDSRDADDAVYEL 53

Query: 554 NGYRLEGRTIAVRVA 568
           NG  L G  + V  A
Sbjct: 54  NGKDLCGERVIVEHA 68

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

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

 Score = 40.3 bits (95), Expect = 2e-04
 Identities = 18/75 (24%), Positives = 37/75 (49%), Gaps = 5/75 (6%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           +Y+G L P      L   F  +G +    V ++       G+ FV++ D + A +A+ ++
Sbjct: 2   VYVGNLGPRATKRELEDEFEKYGPLRSVWVARN-----PPGFAFVEFEDPRDAEDAVRAL 56

Query: 554 NGYRLEGRTIAVRVA 568
           +G R+ G  + V ++
Sbjct: 57  DGRRICGNRVRVELS 71

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

 Score = 40.3 bits (94), Expect = 2e-04
 Identities = 19/73 (26%), Positives = 38/73 (52%), Gaps = 6/73 (8%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L++G LP  + ++   +LF  +G+     + +DR      G+GF++     +A  A A +
Sbjct: 4   LFVGNLPTDITEEDFKKLFEKYGEPSEVFINRDR------GFGFIRLESRTLAEIAKAEL 57

Query: 554 NGYRLEGRTIAVR 566
           +G  L+ R + +R
Sbjct: 58  DGTILKNRPLRIR 70

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

>gnl|CDD|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 39.9 bits (93), Expect = 2e-04
 Identities = 21/75 (28%), Positives = 39/75 (52%), Gaps = 6/75 (8%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           + L++G LPP + ++ + +LF  +G      + KD      KG+GF++     +A  A A
Sbjct: 2   SRLFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKD------KGFGFIRLETRTLAEIAKA 55

Query: 552 SMNGYRLEGRTIAVR 566
            ++   L G+ + VR
Sbjct: 56  ELDNMPLRGKQLRVR 70

This subgroup corresponds to the RRM1 of p54nrb, also termed non-POU domain-containing octamer-binding protein (NonO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. It is ubiquitously expressed and highly conserved in vertebrates. p54nrb binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. It forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manneras well as with polypyrimidine tract-binding protein-associated-splicing factor (PSF). p54nrb contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

>gnl|CDD|219339 pfam07223, DUF1421, Protein of unknown function (DUF1421)

 Score = 44.2 bits (104), Expect = 2e-04
 Identities = 43/198 (21%), Positives = 53/198 (26%), Gaps = 6/198 (3%)

Query: 582 TSTMPTYPVSAPPVGGYPSQQYAPGGPLPN--PPAASYTGAPVPWGPPVPPPYAPYAPPP 639
                T    AP          AP   +    PPA +              P +   P  
Sbjct: 42  FHVDSTKQPPAPEQVAKHELADAPLQQVNAALPPAPAPQSPQPDQQQQSQAPPSHQYPSQ 101

Query: 640 PGSTMYPPVPGQPMPPYGVQYPPPVQ-TAPPGALTAPPGAPTQTATSSEAQQHSFPPGVQ 698
                   VP QP P     YPPP Q   PP                 + Q  S P   Q
Sbjct: 102 LPPQQVQSVPQQPTPQQEPYYPPPSQPQPPPAQQPQAQQPQPPPQVPQQQQYQSPPQQPQ 161

Query: 699 SESSSSAPAASANMYGSSMPPMPPNVQPAYATAPLGYSPYYNAVPPPPPPAPVSAADHSQ 758
            + +    A SA       P   P    +Y       S    A+ PP   AP S   +  
Sbjct: 162 YQQNPPPQAQSAPQVSGLYPEESPYQPQSYPPNEPLPSSM--AMQPPYSGAPPSQQFYGP 219

Query: 759 NLGNVPWATNPPVQPPVS 776
                P+    P   P S
Sbjct: 220 PQ-PSPYMYGGPGGRPNS 236

This family represents a conserved region approximately 350 residues long within a number of plant proteins of unknown function. Length = 357

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

 Score = 39.9 bits (94), Expect = 2e-04
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 1/69 (1%)

Query: 499 LPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRL 558
           L   + ++ L  LF   G++   K+  DR +G S+G   V +   + A  AI   NG  L
Sbjct: 8   LHYDVTEEDLEELFGRVGEVKKVKINYDR-SGRSEGTADVVFEKREDAERAIKQFNGVLL 66

Query: 559 EGRTIAVRV 567
           +G+ + V +
Sbjct: 67  DGQPMQVEL 75

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|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 40.3 bits (94), Expect = 2e-04
 Identities = 20/78 (25%), Positives = 43/78 (55%), Gaps = 1/78 (1%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           T +++G +P  L +D L+ LF   G I   +++ D ++G ++GY F+ +   + A  A+ 
Sbjct: 2   TEVFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAVK 61

Query: 552 SMNGYRLE-GRTIAVRVA 568
             + Y +  G+ + V ++
Sbjct: 62  LCDNYEIRPGKHLGVCIS 79

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|240784 cd12338, RRM1_SRSF1_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 40.1 bits (94), Expect = 2e-04
 Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 3/72 (4%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           +Y+G LP  + +  +  LF  +G I  A  +K+R  G    + FV++ D + A +A+   
Sbjct: 2   IYVGNLPGDIRERDIEDLFYKYGPIK-AIDLKNRRRG--PPFAFVEFEDPRDAEDAVRGR 58

Query: 554 NGYRLEGRTIAV 565
           +GY  +G  + V
Sbjct: 59  DGYDFDGYRLRV 70

This subgroup corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C), and plant pre-mRNA-splicing factor SF2 (SR1). SRSF1 is a shuttling SR protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF9 has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. It can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. Both, SRSF1 and SRSF9, contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RS domains rich in serine-arginine dipeptides. In contrast, SF2 contains two N-terminal RRMs and a C-terminal PSK domain rich in proline, serine and lysine residues. . Length = 72

>gnl|CDD|219569 pfam07777, MFMR, G-box binding protein MFMR

 Score = 42.5 bits (100), Expect = 2e-04
 Identities = 32/126 (25%), Positives = 41/126 (32%), Gaps = 5/126 (3%)

Query: 570 KPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGPPVP 629
               P       T T   YP  +     Y  +   P     +  A+S    P  WGP   
Sbjct: 10  SKSSPKTSVQEDTPTPTVYPDWSAMQAYYGPR--PPPPYFNSSVASSPQPHPYMWGPQ-Q 66

Query: 630 PPYAPYAPPPPGSTMYPP--VPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATSSE 687
           P   PY  PPP + MYPP  V   P  P G     P          + P +    A SS+
Sbjct: 67  PMMPPYGTPPPYAAMYPPGGVYAHPSMPPGSHPFSPYAMPSAEVPGSTPLSMETDAKSSD 126

Query: 688 AQQHSF 693
            +    
Sbjct: 127 NKDKGS 132

This region is found to the N-terminus of the pfam00170 transcription factor domain. It is between 150 and 200 amino acids in length. The N-terminal half is rather rich in proline residues and has been termed the PRD (proline rich domain), whereas the C-terminal half is more polar and has been called the MFMR (multifunctional mosaic region). It has been suggested that this family is composed of three sub-families called A, B and C, classified according to motif composition. It has been suggested that some of these motifs may be involved in mediating protein-protein interactions. The MFMR region contains a nuclear localisation signal in bZIP opaque and GBF-2. The MFMR also contains a transregulatory activity in TAF-1. The MFMR in CPRF-2 contains cytoplasmic retention signals. Length = 189

>gnl|CDD|241048 cd12604, RRM_RALY, RNA recognition motif in vertebrate RNA-binding protein Raly

 Score = 40.0 bits (93), Expect = 2e-04
 Identities = 20/47 (42%), Positives = 30/47 (63%), Gaps = 2/47 (4%)

Query: 527 RVTGMS--KGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKP 571
           RV G S  KGY FV+Y++ + A  A+   NG  L G+T+ + +AG+P
Sbjct: 28  RVVGCSVHKGYAFVQYSNERHARGAVIGENGRVLAGQTLDINMAGEP 74

This subgroup corresponds to the RRM of Raly, also termed autoantigen p542, or heterogeneous nuclear ribonucleoprotein C-like 2, or hnRNP core protein C-like 2, or hnRNP associated with lethal yellow protein homolog, an RNA-binding protein that may play a critical role in embryonic development. It is encoded by Raly, a ubiquitously expressed gene of unknown function. Raly shows a high degree of identity with the 5' sequences of p542 gene encoding autoantigen, which can cross-react with EBNA-1 of the Epstein Barr virus. Raly contains two distinct domains, an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain that includes a unique glycine/serine-rich stretch. . Length = 76

>gnl|CDD|217469 pfam03276, Gag_spuma, Spumavirus gag protein

 Score = 44.1 bits (104), Expect = 2e-04
 Identities = 31/96 (32%), Positives = 41/96 (42%), Gaps = 8/96 (8%)

Query: 560 GRTIAVRVAGKPPQPTVPPGPPTSTMPTYPV-SAPPVGGYPSQQYAPGGPLPNPPAASYT 618
           GR   +  A +PP P+  PG P  +    P  S+ P    P   + P  P P+P   S  
Sbjct: 177 GRGGNIPGAIQPPPPSSLPGLPPGSSSLAPSASSTPGNRLPRVSFNPFLPGPSPAQPSAP 236

Query: 619 GAPVPWGPPVPPPYAPYAPPPPGSTMYPPVPGQPMP 654
            A +P  PP+PP     APPP       P P   +P
Sbjct: 237 PASIP-APPIPPVIQYVAPPP------VPPPQPIIP 265

Length = 582

>gnl|CDD|236669 PRK10263, PRK10263, DNA translocase FtsK; Provisional

 Score = 44.3 bits (104), Expect = 3e-04
 Identities = 38/183 (20%), Positives = 50/183 (27%), Gaps = 4/183 (2%)

Query: 610 PNPPAASYTGAPVPWGPPVPPPY-APYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAP 668
           P   AA+ T A   W  PV P    P           P V  QP+P  G Q   PV    
Sbjct: 319 PVAVAAAATTATQSWAAPVEPVTQTPPVASVDVPPAQPTVAWQPVP--GPQTGEPVIAPA 376

Query: 669 PGALTAPPGAPTQTATSSEAQQHSFPPGVQSESSSSAPAASANMYGSSMPPMPPNVQPAY 728
           P                +E  Q    P     + ++   A    Y  +          A 
Sbjct: 377 PEGYPQQSQYAQPAVQYNEPLQQPVQPQQPYYAPAAEQPAQQPYYAPAPEQPAQQPYYAP 436

Query: 729 ATAPLGYSPYYNAVPPPPPPAPVSAADHSQNLGNVPWATNPPVQPPVSSAEKSNYGADAE 788
           A         + A       AP S     Q     P A  P  Q P    ++     +  
Sbjct: 437 APEQPVAGNAWQAEEQQSTFAPQSTYQTEQTYQQ-PAAQEPLYQQPQPVEQQPVVEPEPV 495

Query: 789 YEK 791
            E+
Sbjct: 496 VEE 498

Length = 1355

>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 = 40.0 bits (94), Expect = 3e-04
 Identities = 21/74 (28%), Positives = 35/74 (47%), Gaps = 6/74 (8%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           T L+IG+L   + ++ L  LF  +G+I    +I  R      G  +V     Q A+ A+ 
Sbjct: 3   TTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIPPR------GCAYVCMETRQDAHRALQ 56

Query: 552 SMNGYRLEGRTIAV 565
            +   +L G+ I V
Sbjct: 57  KLRNVKLAGKKIKV 70

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

 Score = 39.9 bits (93), Expect = 3e-04
 Identities = 22/70 (31%), Positives = 35/70 (50%), Gaps = 1/70 (1%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           +++G L        L   FS FG++V   +  D VTG S+G+GFV + D       +   
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVL-DQ 59

Query: 554 NGYRLEGRTI 563
             ++L+GR I
Sbjct: 60  KEHKLDGRVI 69

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

>gnl|CDD|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding protein Musashi homolog 2 (Musashi-2 ) and similar proteins

 Score = 39.7 bits (92), Expect = 3e-04
 Identities = 26/75 (34%), Positives = 41/75 (54%), Gaps = 1/75 (1%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           ++IG L      D L   FS FG+I    V++D  T  S+G+GFV +AD    +  +A  
Sbjct: 2   MFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLAQP 61

Query: 554 NGYRLEGRTIAVRVA 568
           + + L+ +TI  +VA
Sbjct: 62  H-HELDSKTIDPKVA 75

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 76

>gnl|CDD|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate RNA-binding protein 47 (RBM47)

 Score = 39.6 bits (92), Expect = 3e-04
 Identities = 21/73 (28%), Positives = 39/73 (53%), Gaps = 2/73 (2%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           +++G +P  + +D L+ +F + G I   +++ D   G ++GY FV Y     A  A+  +
Sbjct: 4   VFVGKIPRDVYEDELVPVFESVGRIYEMRLMMD-FDGKNRGYAFVMYTQKHEAKRAVREL 62

Query: 554 NGYRLE-GRTIAV 565
           N Y +  GR + V
Sbjct: 63  NNYEIRPGRLLGV 75

This subgroup corresponds to the RRM1 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

>gnl|CDD|240751 cd12305, RRM_NELFE, RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins

 Score = 39.6 bits (93), Expect = 3e-04
 Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 6/59 (10%)

Query: 512 FSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGK 570
           FS FG+I+   + K+      K  GFV +  ++ A+ AIA +NG  ++G  + V +A K
Sbjct: 23  FSPFGNIINISMEKE------KNCGFVTFEKMESADRAIAELNGTTVQGVQLKVSLARK 75

This subfamily corresponds to the RRM of NELF-E, also termed RNA-binding protein RD. NELF-E is the RNA-binding subunit of cellular negative transcription elongation factor NELF (negative elongation factor) involved in transcriptional regulation of HIV-1 by binding to the stem of the viral transactivation-response element (TAR) RNA which is synthesized by cellular RNA polymerase II at the viral long terminal repeat. NELF is a heterotetrameric protein consisting of NELF A, B, C or the splice variant D, and E. NELF-E contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It plays a role in the control of HIV transcription by binding to TAR RNA. In addition, NELF-E is associated with the NELF-B subunit, probably via a leucine zipper motif. . Length = 75

>gnl|CDD|240918 cd12474, RRM2_MSSP2, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 40.0 bits (93), Expect = 3e-04
 Identities = 24/89 (26%), Positives = 40/89 (44%), Gaps = 11/89 (12%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           TNLYI  LP ++D+  L  +   FG ++  ++++D  +G S+G GF +    +     I 
Sbjct: 1   TNLYISNLPLSMDEQELESMLKPFGQVISTRILRD-ASGTSRGVGFARMESTEKCEAIIT 59

Query: 552 SMNGYRLEGRTIAVRVAGKPPQPTVPPGP 580
             NG  ++           PP    P  P
Sbjct: 60  HFNGKYIK----------TPPGVPAPTEP 78

This subgroup corresponds to the RRM2 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3). MSSP-2 is a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 86

>gnl|CDD|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP DL) and similar proteins

 Score = 39.6 bits (92), Expect = 3e-04
 Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 1/70 (1%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           ++IG L        L    S FG+++   +  D VTG S+G+GFV + D    +  +  +
Sbjct: 2   MFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVL-EL 60

Query: 554 NGYRLEGRTI 563
             ++L+G+ I
Sbjct: 61  KEHKLDGKLI 70

This subgroup corresponds to the RRM1 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), which is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 76

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 43.4 bits (103), Expect = 4e-04
 Identities = 33/142 (23%), Positives = 41/142 (28%), Gaps = 18/142 (12%)

Query: 615 ASYTGAPVPWGPPVPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTA 674
               G         P   A      P              P     P P     P    A
Sbjct: 385 LGVAGGAGAPAAAAPSAAAAAPAAAP--------APAAAAPAAAAAPAPAAAPQPAPAPA 436

Query: 675 PPGAPTQTATSSEAQQHSFPPGVQSESSSSAPAASANMYGSSMPPMPPNVQPAYATAPLG 734
           P  AP   A ++ A     PP   + S+  APA +A    ++ P   P   PA A AP  
Sbjct: 437 PAPAPPSPAGNAPAGGAPSPPPAAAPSAQPAPAPAAAPEPTAAPAPAPPAAPAPAAAP-- 494

Query: 735 YSPYYNAVPPPPPPAPVSAADH 756
                     P  PA  + AD 
Sbjct: 495 --------AAPAAPAAPAGADD 508

Length = 824

>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional

 Score = 43.6 bits (103), Expect = 4e-04
 Identities = 42/210 (20%), Positives = 57/210 (27%), Gaps = 17/210 (8%)

Query: 564 AVRVAGKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVP 623
              VAG        P       P     A      P+   +   P       S T     
Sbjct: 53  VTVVAGAAACDRFEPPTGPPPGPGTEAPANESRSTPTWSLSTLAPASPAREGSPTPPGPS 112

Query: 624 WGPPVPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTA 683
              P PP   P +PPP      P      M        PP   +PP A  +P    +  A
Sbjct: 113 SPDPPPPTPPPASPPPS-----PAPDLSEMLRPVGSPGPPPAASPPAAGASPAAVASDAA 167

Query: 684 TSSEAQQHSFPPGVQSESSSSAPAASANMYGSSMPPMPPNVQPAYATAPLGYSPYYNAVP 743
           +S +A          +   SS    +     SS P  PP   P  A +P           
Sbjct: 168 SSRQA----------ALPLSSPEETARA--PSSPPAEPPPSTPPAAASPRPPRRSSPISA 215

Query: 744 PPPPPAPVSAADHSQNLGNVPWATNPPVQP 773
               PAP      + + G     ++     
Sbjct: 216 SASSPAPAPGRSAADDAGASSSDSSSSESS 245

Length = 1352

>gnl|CDD|219339 pfam07223, DUF1421, Protein of unknown function (DUF1421)

 Score = 43.0 bits (101), Expect = 4e-04
 Identities = 32/151 (21%), Positives = 38/151 (25%), Gaps = 1/151 (0%)

Query: 573 QPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPV-PWGPPVPPP 631
            P   P PP +  P      PP      QQY      P         A   P    + P 
Sbjct: 123 PPPSQPQPPPAQQPQAQQPQPPPQVPQQQQYQSPPQQPQYQQNPPPQAQSAPQVSGLYPE 182

Query: 632 YAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATSSEAQQH 691
            +PY P         P      PPY    P      PP       G P     S      
Sbjct: 183 ESPYQPQSYPPNEPLPSSMAMQPPYSGAPPSQQFYGPPQPSPYMYGGPGGRPNSGFPSGQ 242

Query: 692 SFPPGVQSESSSSAPAASANMYGSSMPPMPP 722
             PP    E    +    +     S+    P
Sbjct: 243 QPPPSQGQEGYGYSGPPPSKGNHGSVASYAP 273

This family represents a conserved region approximately 350 residues long within a number of plant proteins of unknown function. Length = 357

>gnl|CDD|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering time control protein FCA and similar proteins

 Score = 39.4 bits (92), Expect = 4e-04
 Identities = 24/78 (30%), Positives = 43/78 (55%), Gaps = 4/78 (5%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L++G L     +  +  +FS +G +    +++D +   S+G  FVKY+  +MA  AI ++
Sbjct: 2   LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMK-QSRGCAFVKYSSKEMAQAAIKAL 60

Query: 554 NG-YRLEG--RTIAVRVA 568
           NG Y + G  + + VR A
Sbjct: 61  NGVYTMRGCDQPLIVRFA 78

This subgroup corresponds to the RRM2 of FCA, a gene controlling flowering time in Arabidopsis, which encodes a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. The flowering time control protein FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain. . Length = 80

>gnl|CDD|178748 PLN03209, PLN03209, translocon at the inner envelope of chloroplast subunit 62; Provisional

 Score = 43.4 bits (102), Expect = 4e-04
 Identities = 43/184 (23%), Positives = 59/184 (32%), Gaps = 21/184 (11%)

Query: 580 PPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGPPVPP----PYAPY 635
           PPTS +PT P S+P           P  P   P   S +  P      V      P +PY
Sbjct: 382 PPTSPIPTPPSSSPASSKSVDAVAKPAEPDVVPSPGSASNVPEVEPAQVEAKKTRPLSPY 441

Query: 636 APPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATSSEAQQHSFPP 695
           A       + PP    P  P GV        +   ++ A P     TA +  A       
Sbjct: 442 ARYE---DLKPPTSPSPTAPTGVSPS----VSSTSSVPAVPDTAPATAATDAAAP----- 489

Query: 696 GVQSESSSSAPAASANMYGSSMPPMPPN-VQPAYATAPLGYSPYYNAVPPPPPPAPVSAA 754
                 ++  P +   +Y    PP  P+   P    AP   +         PP A     
Sbjct: 490 ----PPANMRPLSPYAVYDDLKPPTSPSPAAPVGKVAPSSTNEVVKVGNSAPPTALADEQ 545

Query: 755 DHSQ 758
            H+Q
Sbjct: 546 HHAQ 549

Length = 576

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

 Score = 43.1 bits (101), Expect = 5e-04
 Identities = 29/80 (36%), Positives = 39/80 (48%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           +Y+G +   L +D + R F  FG I    +  D  TG  KG+ FV+Y   + A  A+  M
Sbjct: 110 VYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQM 169

Query: 554 NGYRLEGRTIAVRVAGKPPQ 573
           NG  L GR I V      PQ
Sbjct: 170 NGQMLGGRNIKVGRPSNMPQ 189

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|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1

 Score = 43.2 bits (102), Expect = 5e-04
 Identities = 35/142 (24%), Positives = 41/142 (28%), Gaps = 10/142 (7%)

Query: 569 GKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGPPV 628
            +PPQ       P   +P  P  AP     P Q      P   PP        +    P 
Sbjct: 204 PQPPQGHPEQVQPQQFLP-APSQAPAQPPLPPQL-----PQQPPPLQQPQFPGLSQQMPP 257

Query: 629 PPPYAP-YAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATSSE 687
           PPP  P     PP     PP   QP P       P  Q AP      P   P       +
Sbjct: 258 PPPQPPQQQQQPPQPQAQPPPQNQPTPH---PGLPQGQNAPLPPPQQPQLLPLVQQPQGQ 314

Query: 688 AQQHSFPPGVQSESSSSAPAAS 709
            +   F   +   S     A S
Sbjct: 315 QRGPQFREQLVQLSQQQREALS 336

Members of this family are necessary for accurate chromosome transmission during cell division. Length = 804

>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family

 Score = 43.5 bits (102), Expect = 5e-04
 Identities = 53/231 (22%), Positives = 65/231 (28%), Gaps = 28/231 (12%)

Query: 571 PPQPTVPPGPPTSTMPTYPVSAP-------PVGGYPSQQYAPGGPLPNPPAASYTGAPVP 623
            P    P   P    P   +SAP       P    P Q        P PPA S       
Sbjct: 208 SPIAAQPAPQPQQPSPLSLISAPSLHPQRLPSPHPPLQPQTASQQSPQPPAPSSRHPQSS 267

Query: 624 W---GPPVPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPT 680
               GPP+P             +  PP P           P P Q  P         A  
Sbjct: 268 HHGPGPPMPHALQQGPVFLQHPSSNPPQPFGLAQSQVPPLPLPSQAQPHSHTPPSQSALQ 327

Query: 681 QTATSSEAQQHSFPPGVQSESSSSAPAASANMYGSSMPP----------MPPNVQPAYAT 730
                 E      P     +   + P           PP          MP N+ P  A 
Sbjct: 328 PQQPPREQPLPPAPSMPHIKPPPTTPIPQLPNQSHKHPPHLQGPSPFPQMPSNLPPPPAL 387

Query: 731 APLGYSPYYNAVPPPPPPAPVSAADHSQNLGNVPWATNPPVQPPVSSAEKS 781
            PL   P ++  PP   P P+     SQ L       + P QPPV +  +S
Sbjct: 388 KPLSSLPTHH--PPSAHPPPLQLMPQSQPL------QSVPAQPPVLTQSQS 430

Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. Length = 979

>gnl|CDD|217392 pfam03153, TFIIA, Transcription factor IIA, alpha/beta subunit

 Score = 42.8 bits (101), Expect = 5e-04
 Identities = 35/163 (21%), Positives = 46/163 (28%), Gaps = 12/163 (7%)

Query: 571 PPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGPPVPP 630
           PP     P P     PT  + A P G           P  +P A       +P GP  P 
Sbjct: 56  PPPVAQLPQPLPQPPPTQALQALPAGDQQQHN----TPTGSPAANPPATFALPAGPAGPT 111

Query: 631 PYAPYAPPPPGSTMYPPVP-GQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATSSEAQ 689
                    PG      VP      P       P Q      L    GAP      S+ Q
Sbjct: 112 -----IQTEPGQLYPVQVPVMVTQNPANSPLDQPAQQRALQQLQQRYGAPASGQLPSQQQ 166

Query: 690 --QHSFPPGVQSESSSSAPAASANMYGSSMPPMPPNVQPAYAT 730
             Q +    +Q + +   P    +  G         ++ A  T
Sbjct: 167 SAQKNDESQLQQQPNGETPPQQTDGAGDDESEALVRLREADGT 209

Transcription initiation factor IIA (TFIIA) is a heterotrimer, the three subunits being known as alpha, beta, and gamma, in order of molecular weight. The N and C-terminal domains of the gamma subunit are represented in pfam02268 and pfam02751, respectively. This family represents the precursor that yields both the alpha and beta subunits. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II. Together with TFIID, TFIIA binds to the promoter region; this is the first step in the formation of a pre-initiation complex (PIC). Binding of the rest of the transcription machinery follows this step. After initiation, the PIC does not completely dissociate from the promoter. Some components, including TFIIA, remain attached and re-initiate a subsequent round of transcription. Length = 332

>gnl|CDD|218621 pfam05518, Totivirus_coat, Totivirus coat protein

 Score = 43.2 bits (102), Expect = 5e-04
 Identities = 32/149 (21%), Positives = 41/149 (27%), Gaps = 16/149 (10%)

Query: 544 QMANNAIASMNGYRLEGR--TIAVRVAGKPPQP-TVPPGP---PTSTMPTYPVSAP---- 593
                A+A     R  GR     + ++G PP   T  P P            V  P    
Sbjct: 610 TRGARALAQA---RTFGRATVGEMIISGFPPVFKTALPRPDYNRGGEAGGPGVPGPVPVG 666

Query: 594 -PVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGPPVPPPYAPYAPPPPGSTMYPPVPGQP 652
            P       + A G P+      +   AP    P  PP      PPPP   +       P
Sbjct: 667 MPAHTARPSRVARGDPVRPTAHHAALRAPQAPRPGGPPGGGGGLPPPP--DLPAAAGPAP 724

Query: 653 MPPYGVQYPPPVQTAPPGALTAPPGAPTQ 681
                +  P       P       GA  Q
Sbjct: 725 CGSSLIASPTAPPEPEPPGAEQADGAENQ 753

Length = 753

>gnl|CDD|240919 cd12475, RRM2_RBMS3, RNA recognition motif 2 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 39.3 bits (91), Expect = 5e-04
 Identities = 27/95 (28%), Positives = 42/95 (44%), Gaps = 17/95 (17%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           TNLYI  LP ++D+  L  +   FG ++  ++++D   G+S+G GF +    +     I 
Sbjct: 2   TNLYISNLPVSMDEQELENMLKPFGHVISTRILRD-ANGVSRGVGFARMESTEKCEVVIQ 60

Query: 552 SMNGYRLEGRTIAVRVAGKPPQPTVPPGPPTSTMP 586
             NG  L+                 PPG P  T P
Sbjct: 61  HFNGKYLK----------------TPPGVPAPTEP 79

This subgroup corresponds to the RRM2 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. RBMS3 contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines. . Length = 88

>gnl|CDD|240928 cd12484, RRM1_RBM46, RNA recognition motif 1 found in vertebrate RNA-binding protein 46 (RBM46)

 Score = 39.1 bits (91), Expect = 5e-04
 Identities = 23/76 (30%), Positives = 42/76 (55%), Gaps = 2/76 (2%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           +++G +P  + +D L+ LF   G I   +++ +  +G ++GY FV Y   + A  AI  +
Sbjct: 4   VFVGKIPRDMYEDELVPLFERAGKIYEFRLMME-FSGENRGYAFVMYTTKEEAQLAIRIL 62

Query: 554 NGYRL-EGRTIAVRVA 568
           N Y +  G+ I V V+
Sbjct: 63  NNYEIRPGKFIGVCVS 78

This subgroup corresponds to the RRM1 of RBM46, also termed cancer/testis antigen 68 (CT68), a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM46 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

>gnl|CDD|240999 cd12555, RRM2_RBM15, RNA recognition motif 2 in vertebrate RNA binding motif protein 15 (RBM15)

 Score = 39.5 bits (92), Expect = 5e-04
 Identities = 22/62 (35%), Positives = 34/62 (54%), Gaps = 1/62 (1%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L++G L  T+ +  L R F  FG I     IK    G +  YGF+K+ ++ MA+ A  +M
Sbjct: 10  LFLGNLDITVTETDLRRAFDRFGVITEVD-IKRPGRGQTSTYGFLKFENLDMAHRAKLAM 68

Query: 554 NG 555
           +G
Sbjct: 69  SG 70

This subgroup corresponds to the RRM2 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contain three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties. . Length = 87

>gnl|CDD|223065 PHA03378, PHA03378, EBNA-3B; Provisional

 Score = 43.1 bits (101), Expect = 6e-04
 Identities = 47/179 (26%), Positives = 56/179 (31%), Gaps = 9/179 (5%)

Query: 566 RVAGKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAP-GGPLPNPPAASYTGAPVP- 623
           R       P  PPG            A P    P +   P   P    P A+  G   P 
Sbjct: 699 RAPTPMRPPAAPPGRAQRPAAA-TGRARPPAAAPGRARPPAAAPGRARPPAAAPGRARPP 757

Query: 624 ---WGPPVPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPT 680
               G   PP  AP AP P      PP P Q  P       PP Q  P      P  AP 
Sbjct: 758 AAAPGRARPPAAAPGAPTPQPPPQAPPAPQQ-RPRGAPTPQPPPQAGPTSMQLMPRAAPG 816

Query: 681 QTATSSEAQQHSFPPGVQS-ESSSSAPAASANMYGSSMPPMPPNVQPAYAT-APLGYSP 737
           Q   + +  +     GV+    S   PAA      +   P P +        AP+ Y P
Sbjct: 817 QQGPTKQILRQLLTGGVKRGRPSLKKPAALERQAAAGPTPSPGSGTSDKIVQAPVFYPP 875

Length = 991

>gnl|CDD|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding protein 7 (RBM7)

 Score = 38.7 bits (90), Expect = 6e-04
 Identities = 21/76 (27%), Positives = 39/76 (51%), Gaps = 1/76 (1%)

Query: 491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAI 550
           D  L++G L P + ++ +  LF   G ++  K+ KD+  G  K + FV +        A+
Sbjct: 1   DRTLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDK-DGKPKQFAFVNFKHEVSVPYAM 59

Query: 551 ASMNGYRLEGRTIAVR 566
             +NG +L GR + ++
Sbjct: 60  NLLNGIKLYGRPLNIQ 75

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

 Score = 38.9 bits (91), Expect = 6e-04
 Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 1/63 (1%)

Query: 504 DDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTI 563
               L  +F   G +V A + +D+  G S+G G V++     A  AI+  NG  L  R +
Sbjct: 11  GWKKLKEVFKLAGKVVRADIKEDK-EGKSRGMGVVQFEHPIEAVQAISMFNGQMLFDRPM 69

Query: 564 AVR 566
            V+
Sbjct: 70  RVK 72

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

>gnl|CDD|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 38.4 bits (90), Expect = 6e-04
 Identities = 19/72 (26%), Positives = 42/72 (58%), Gaps = 2/72 (2%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           +++  L  ++ +D L +LFS  G+I   +++K+   G SKGY +V++ + +    A+  +
Sbjct: 2   VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYK-GKSKGYAYVEFENEESVQEAL-KL 59

Query: 554 NGYRLEGRTIAV 565
           +   ++GR + V
Sbjct: 60  DRELIKGRPMFV 71

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|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 42.7 bits (101), Expect = 7e-04
 Identities = 35/137 (25%), Positives = 43/137 (31%), Gaps = 15/137 (10%)

Query: 619 GAPVPWGPPVPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGA 678
              V  G   P   AP A     +            P     P P     P    AP  A
Sbjct: 384 RLGVAGGAGAPAAAAPSAAAAAPA---AAPAPAAAAPAAAAAPAPAAAPQPAPAPAPAPA 440

Query: 679 PTQTATSSEAQQHSFPPGVQSESSSSAPAASANMYGSSMPPMPPNVQPAYATAPLGYSPY 738
           P   A ++ A     PP   + S+  APA +A    +  P   P   P  A AP      
Sbjct: 441 PPSPAGNAPAGGAPSPPPAAAPSAQPAPAPAA----APEPTAAPAPAPPAAPAP------ 490

Query: 739 YNAVPPPPPPAPVSAAD 755
             A  P  P AP + A 
Sbjct: 491 --AAAPAAPAAPAAPAG 505

Length = 824

>gnl|CDD|239089 cd02396, PCBP_like_KH, K homology RNA-binding domain, PCBP_like

 Score = 38.2 bits (90), Expect = 7e-04
 Identities = 15/39 (38%), Positives = 21/39 (53%), Gaps = 6/39 (15%)

Query: 254 KLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVI 292
           +L +P  +       G IIG  G+T K +  ETGAKI +
Sbjct: 3   RLLVPSSQ------AGSIIGKGGSTIKEIREETGAKIRV 35

Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. Length = 65

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

 Score = 38.5 bits (90), Expect = 7e-04
 Identities = 23/65 (35%), Positives = 31/65 (47%), Gaps = 3/65 (4%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L+IG L  T     L   F  FG+I+    IK +  G    Y F++YADI     A+  M
Sbjct: 5   LFIGNLEKTTTYSDLREAFERFGEIIDID-IK-KQGGNPA-YAFIQYADIASVVKAMRKM 61

Query: 554 NGYRL 558
           +G  L
Sbjct: 62  DGEYL 66

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|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 38.9 bits (90), Expect = 7e-04
 Identities = 22/75 (29%), Positives = 42/75 (56%), Gaps = 1/75 (1%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L+IG L     DD L   F  +G +    V++D  T  S+G+GFV Y+ ++  + A+++ 
Sbjct: 5   LFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMSA- 63

Query: 554 NGYRLEGRTIAVRVA 568
             ++++GR +  + A
Sbjct: 64  RPHKVDGRVVEPKRA 78

This subgroup corresponds to the RRM1 of hnRNP A3 which is a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

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

 Score = 38.5 bits (89), Expect = 7e-04
 Identities = 23/75 (30%), Positives = 42/75 (56%), Gaps = 2/75 (2%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           LY+G L   + +  +++LFS  G     K+I D  T  +  Y FV++ + + A  ++A+M
Sbjct: 2   LYVGNLSRDVTEALILQLFSQIGPCKSCKMIMD--TAGNDPYCFVEFFEHRHAAASLAAM 59

Query: 554 NGYRLEGRTIAVRVA 568
           NG ++ G+ + V  A
Sbjct: 60  NGRKIMGKEVKVNWA 74

This subgroup corresponds to the RRM1 of TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1) and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and functions as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 74

>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau; Provisional

 Score = 42.8 bits (101), Expect = 7e-04
 Identities = 21/128 (16%), Positives = 30/128 (23%), Gaps = 4/128 (3%)

Query: 564 AVRVAGKPPQPTVPPGPPTSTMPTYPVSA--PPVGGYPSQQYAPGGPLPNPPAASYTGAP 621
            +   G        P      + T P +A  P      S   +       P A      P
Sbjct: 361 QLTQKGDDASGGRGPKQHIKPVFTQPAAAPQPSAAAAASPSPSQSSAAAQPSAPQSATQP 420

Query: 622 VPWGPPVPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQ 681
               P V        P  P ST    V          +  P  + +  G  T  P     
Sbjct: 421 AGTPPTVSVDPPAAVPVNPPSTAPQAVRPAQFKE--EKKIPVSKVSSLGPSTLRPIQEKA 478

Query: 682 TATSSEAQ 689
              +   +
Sbjct: 479 EQATGNIK 486

Length = 614

>gnl|CDD|240794 cd12348, RRM1_SHARP, RNA recognition motif 1 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 38.6 bits (90), Expect = 8e-04
 Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 4/69 (5%)

Query: 493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADI---QMANNA 549
           +L++G LP  + ++ +   F  +G +   K++  R +       FV + DI   Q A+NA
Sbjct: 1   HLWVGNLPENVREERISEHFKRYGRVESVKILPKRGSDGGVA-AFVDFVDIKSAQKAHNA 59

Query: 550 IASMNGYRL 558
           +  M    L
Sbjct: 60  VNKMGDRDL 68

This subfamily corresponds to the RRM1 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 = 75

>gnl|CDD|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 38.6 bits (90), Expect = 8e-04
 Identities = 16/47 (34%), Positives = 30/47 (63%), Gaps = 1/47 (2%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKY 540
           +++G +    +++ L + FS +G +   K++ DR  G+SKGYGFV +
Sbjct: 5   IFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDR-AGVSKGYGFVTF 50

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|184923 PRK14959, PRK14959, DNA polymerase III subunits gamma and tau; Provisional

 Score = 42.4 bits (99), Expect = 9e-04
 Identities = 35/117 (29%), Positives = 42/117 (35%), Gaps = 7/117 (5%)

Query: 569 GKPPQPTVPPGPPT---STMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAP-VPW 624
              P  +   GP +   +T+PT P +  P G  P+    P    P  PA S   +P VPW
Sbjct: 378 ASAPSGSAAEGPASGGAATIPT-PGTQGPQGTAPAAGMTPSSAAPATPAPSAAPSPRVPW 436

Query: 625 --GPPVPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAP 679
              PP PP       P P      PVPG P         PP    P       P  P
Sbjct: 437 DDAPPAPPRSGIPPRPAPRMPEASPVPGAPDSVASASDAPPTLGDPSDTAEHTPSGP 493

Length = 624

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 42.2 bits (99), Expect = 0.001
 Identities = 28/117 (23%), Positives = 39/117 (33%), Gaps = 4/117 (3%)

Query: 580 PPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGPPVPPPYAPYAPPP 639
           P  +++PT    +      P  +   G     P A      P P   PVP      APPP
Sbjct: 375 PKRASLPTRKRRSARHAATPFARGPGGDDQTRPAAPVPASVPTPAPTPVPAS----APPP 430

Query: 640 PGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATSSEAQQHSFPPG 696
           P + +    PG    P       P   A   A   P  A  +   +   ++   PPG
Sbjct: 431 PATPLPSAEPGSDDGPAPPPERQPPAPATEPAPDDPDDATRKALDALRERRPPEPPG 487

Length = 3151

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

 Score = 38.6 bits (89), Expect = 0.001
 Identities = 23/78 (29%), Positives = 43/78 (55%), Gaps = 2/78 (2%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           LY+G L   + +  +++LFS  G     K+I +  +  +  Y FV++ + + A  A+A+M
Sbjct: 2   LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAM 59

Query: 554 NGYRLEGRTIAVRVAGKP 571
           NG ++ G+ + V  A  P
Sbjct: 60  NGRKILGKEVKVNWATTP 77

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|240814 cd12368, RRM3_RBM45, RNA recognition motif 3 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 38.1 bits (89), Expect = 0.001
 Identities = 18/67 (26%), Positives = 32/67 (47%), Gaps = 1/67 (1%)

Query: 501 PTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRL-E 559
            ++  + L RLF     +    + +D  TG SKG+ +V Y++   A  A   +NG+    
Sbjct: 9   KSVTQEQLHRLFDIIPGLEYCDLKRDPYTGKSKGFAYVTYSNPASAIYAKEKLNGFEYPP 68

Query: 560 GRTIAVR 566
           G  + V+
Sbjct: 69  GNRLKVK 75

This subfamily corresponds to the RRM3 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 75

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

 Score = 38.4 bits (89), Expect = 0.001
 Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
           NL+IG L   + +  L R F  +G I+   VIK    G    Y F+K+ ++ MA+ A  +
Sbjct: 10  NLFIGNLDHNVSEVELRRAFDKYG-IIEEVVIKRPARGQGGAYAFLKFQNLDMAHRAKVA 68

Query: 553 MNGYRLEGRTIAV 565
           M+G  +    I +
Sbjct: 69  MSGRVIGRNPIKI 81

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|240870 cd12424, RRM3_hnRNPL_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and similar proteins

 Score = 37.6 bits (88), Expect = 0.001
 Identities = 19/66 (28%), Positives = 31/66 (46%), Gaps = 5/66 (7%)

Query: 500 PPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLE 559
              ++ D L  LF  +G+++  K +K +      G   V+  D Q A  AI  +NG  L 
Sbjct: 9   KDKMNCDKLFNLFCLYGNVLRIKFLKSK-----PGTAMVQMGDPQAAERAIEYLNGVVLF 63

Query: 560 GRTIAV 565
           G+ + V
Sbjct: 64  GQKLEV 69

This subfamily corresponds to the RRM3 of heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), and similar proteins. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. It is closely related in domain structure and sequence to hnRNP-L, which contains three RNA-recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. Like PTB, PTBPH3 contains four RRMs. Length = 71

>gnl|CDD|240684 cd12238, RRM1_RBM40_like, RNA recognition motif 1 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 38.0 bits (89), Expect = 0.001
 Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 3/72 (4%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L + +LPP L +D    L   FG     +V+  R  G  K   F  + + Q A+ A++ +
Sbjct: 2   LLVRHLPPELSEDDKEDLLKHFG-ASSVRVMSRR--GKLKNTAFATFDNEQAASQALSRL 58

Query: 554 NGYRLEGRTIAV 565
           +  ++ G+ + V
Sbjct: 59  HQLKILGKRLVV 70

This subfamily corresponds to the RRM1 of RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein), It serves as a bridging factor between the U11 and U12 snRNPs. It contains two repeats of RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. . Length = 73

>gnl|CDD|240678 cd12232, RRM3_U2AF65, RNA recognition motif 3 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 38.3 bits (90), Expect = 0.001
 Identities = 14/57 (24%), Positives = 29/57 (50%), Gaps = 3/57 (5%)

Query: 512 FSTFGDIVMAKVIKDRVTGMSK-GYG--FVKYADIQMANNAIASMNGYRLEGRTIAV 565
              +G ++   + +    G+   G G  FV++AD++ A  A  ++ G + +GRT+  
Sbjct: 32  CGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVEDAQKAQLALAGRKFDGRTVVA 88

This subfamily corresponds to the RRM3 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Length = 89

>gnl|CDD|223061 PHA03369, PHA03369, capsid maturational protease; Provisional

 Score = 41.9 bits (98), Expect = 0.001
 Identities = 25/106 (23%), Positives = 28/106 (26%), Gaps = 1/106 (0%)

Query: 547 NNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPG 606
           N   A     +    T   RV     +  V   P T T P          G P    A  
Sbjct: 339 NGLKAHNEILKTASLTAPSRVLAAAAKVAVIAAPQTHTGPADRQRPQRPDGIPYSVPARS 398

Query: 607 GPLPNPPAASYTGAPVPWGPPVPPPYAPYAPPPPGSTMYPPVPGQP 652
                PP   + G P    P  P        P P     PP P  P
Sbjct: 399 PMTAYPPVPQFCGDPGLVSPYNPQSPGTSYGPEPV-GPVPPQPTNP 443

Length = 663

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 41.5 bits (98), Expect = 0.002
 Identities = 25/94 (26%), Positives = 28/94 (29%), Gaps = 4/94 (4%)

Query: 549 AIASMNGYRLEGRTIAVRVAGKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGP 608
           A A+                   P P  P G      P     +PP    PS Q AP   
Sbjct: 416 APAAAAAPAPAAAPQPAPAPAPAPAPPSPAGNA----PAGGAPSPPPAAAPSAQPAPAPA 471

Query: 609 LPNPPAASYTGAPVPWGPPVPPPYAPYAPPPPGS 642
               P A+   AP     P   P AP AP  P  
Sbjct: 472 AAPEPTAAPAPAPPAAPAPAAAPAAPAAPAAPAG 505

Length = 824

>gnl|CDD|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau; Provisional

 Score = 41.4 bits (97), Expect = 0.002
 Identities = 39/174 (22%), Positives = 48/174 (27%), Gaps = 14/174 (8%)

Query: 559 EGRTIAVRVAGKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYT 618
             R      A    +     GP  +  P    +A P     + + A  GP P   AA   
Sbjct: 423 PARRSPAPEALAAARQASARGPGGAPAPAPAPAAAPA---AAARPAAAGPRPVAAAA--A 477

Query: 619 GAPVPWGPPVPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAP---PGALTAP 675
            AP    P   P  A   PPP      PP    P P      P          P      
Sbjct: 478 AAPARAAPAAAPAPADDDPPPWEEL--PPEFASPAPAQPDAAPAGWVAESIPDPATADPD 535

Query: 676 PGAPTQTATSSEAQQHSFPPGVQSESSSSAPAASANMYGSSMPPMPPNVQPAYA 729
               T     + A         +   +   P ASA    S +P M     PA A
Sbjct: 536 DAFETLAPAPAAAPAPRAAAATEPVVAPRPPRASA----SGLPDMFDGDWPALA 585

Length = 700

>gnl|CDD|236669 PRK10263, PRK10263, DNA translocase FtsK; Provisional

 Score = 42.0 bits (98), Expect = 0.002
 Identities = 37/213 (17%), Positives = 47/213 (22%), Gaps = 7/213 (3%)

Query: 572 PQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGPPVPPP 631
           P P   P       P    + P       QQ         P    Y           P  
Sbjct: 375 PAPEGYPQQSQYAQPAVQYNEPLQQPVQPQQPYYAPAAEQPAQQPYYAPAPEQPAQQPYY 434

Query: 632 YAPYAPPPPGSTMYPPVPG---QPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATSS-- 686
                 P  G+            P   Y  +       A       P     Q       
Sbjct: 435 APAPEQPVAGNAWQAEEQQSTFAPQSTYQTEQTYQQPAAQEPLYQQPQPVEQQPVVEPEP 494

Query: 687 --EAQQHSFPPGVQSESSSSAPAASANMYGSSMPPMPPNVQPAYATAPLGYSPYYNAVPP 744
             E  + + PP    E      A       +   P+P  V+          +P   AVPP
Sbjct: 495 VVEETKPARPPLYYFEEVEEKRAREREQLAAWYQPIPEPVKEPEPIKSSLKAPSVAAVPP 554

Query: 745 PPPPAPVSAADHSQNLGNVPWATNPPVQPPVSS 777
               A VS          +       V  PV S
Sbjct: 555 VEAAAAVSPLASGVKKATLATGAAATVAAPVFS 587

Length = 1355

>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family

 Score = 41.2 bits (96), Expect = 0.002
 Identities = 36/178 (20%), Positives = 56/178 (31%), Gaps = 12/178 (6%)

Query: 602 QYAPGGPLPNPPAASYTGAPVPWGPPVPPPYAPYAPPP-PGSTMYPPVPGQPMPPYGVQY 660
           Q      +  PP A+   +  P     P P A   PP        P    Q   P  +  
Sbjct: 174 QPQGPPSIQVPPGAALAPSAPP-----PTPSAQAVPPQGSPIAAQPAPQPQQPSPLSLIS 228

Query: 661 PPPVQTAPPGALTAPPGAPTQTATSSEAQQHSFPPGVQSESSSSAPAASANMYGSSMPPM 720
            P   +  P  L +P         S ++ Q   P     +SS   P         ++   
Sbjct: 229 AP---SLHPQRLPSPHPPLQPQTASQQSPQPPAPSSRHPQSSHHGPGPPMP---HALQQG 282

Query: 721 PPNVQPAYATAPLGYSPYYNAVPPPPPPAPVSAADHSQNLGNVPWATNPPVQPPVSSA 778
           P  +Q   +  P  +    + VPP P P+      H+    +      PP + P+  A
Sbjct: 283 PVFLQHPSSNPPQPFGLAQSQVPPLPLPSQAQPHSHTPPSQSALQPQQPPREQPLPPA 340

Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. Length = 979

>gnl|CDD|218621 pfam05518, Totivirus_coat, Totivirus coat protein

 Score = 41.3 bits (97), Expect = 0.002
 Identities = 27/123 (21%), Positives = 30/123 (24%), Gaps = 13/123 (10%)

Query: 581 PTSTMPTYPVSAPPVGGY--PSQQYAPGGPLPNPPAASYTGAPVPW---GPPVPPP---Y 632
             S  P    +A P   Y    +   PG P P P       A       G PV P     
Sbjct: 631 IISGFPPVFKTALPRPDYNRGGEAGGPGVPGPVPVGMPAHTARPSRVARGDPVRPTAHHA 690

Query: 633 APYAPPPPGSTMYPP----VPGQPMPPYGVQYPP-PVQTAPPGALTAPPGAPTQTATSSE 687
           A  AP  P     P     +P  P  P      P              P  P        
Sbjct: 691 ALRAPQAPRPGGPPGGGGGLPPPPDLPAAAGPAPCGSSLIASPTAPPEPEPPGAEQADGA 750

Query: 688 AQQ 690
             Q
Sbjct: 751 ENQ 753

Length = 753

>gnl|CDD|223061 PHA03369, PHA03369, capsid maturational protease; Provisional

 Score = 41.1 bits (96), Expect = 0.002
 Identities = 19/104 (18%), Positives = 25/104 (24%), Gaps = 6/104 (5%)

Query: 604 APGGPLPNPPAASYTGAPVPWGPPVPPPYAPYAPPPPGSTMYPP----VPGQPMPPYGVQ 659
           A    +   P      A      P  P   PY+ P        P      G P       
Sbjct: 363 AAKVAVIAAPQTHTGPADRQ--RPQRPDGIPYSVPARSPMTAYPPVPQFCGDPGLVSPYN 420

Query: 660 YPPPVQTAPPGALTAPPGAPTQTATSSEAQQHSFPPGVQSESSS 703
              P  +  P  +   P  PT       +  +   PG   E   
Sbjct: 421 PQSPGTSYGPEPVGPVPPQPTNPYVMPISMANMVYPGHPQEHGH 464

Length = 663

>gnl|CDD|240788 cd12342, RRM_Nab3p, RNA recognition motif in yeast nuclear polyadenylated RNA-binding protein 3 (Nab3p) and similar proteins

 Score = 37.4 bits (87), Expect = 0.002
 Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 9/76 (11%)

Query: 494 LYIGYLP-PTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
           L+IG LP   +  + L R+FST+G++    V+K         YGFV++   +   NAI  
Sbjct: 2   LFIGNLPTKRVSKEDLFRIFSTYGEL-AQIVLK-------NAYGFVQFDSPESCANAINC 53

Query: 553 MNGYRLEGRTIAVRVA 568
             G  + GR + + V+
Sbjct: 54  EQGKMIRGRKLHLEVS 69

This subfamily corresponds to the RRM of Nab3p, an acidic nuclear polyadenylated RNA-binding protein encoded by Saccharomyces cerevisiae NAB3 gene that is essential for cell viability. Nab3p is predominantly localized within the nucleoplasm and essential for growth in yeast. It may play an important role in packaging pre-mRNAs into ribonucleoprotein structures amenable to efficient nuclear RNA processing. Nab3p contains an N-terminal aspartic/glutamic acid-rich region, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal region rich in glutamine and proline residues. . Length = 71

>gnl|CDD|240869 cd12423, RRM3_PTBP1_like, RNA recognition motif 3 in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins

 Score = 37.6 bits (88), Expect = 0.002
 Identities = 21/63 (33%), Positives = 31/63 (49%), Gaps = 11/63 (17%)

Query: 506 DGLIRLFSTFGDIVMAKVI---KDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRT 562
           D L  LF  +GD+V  K++   KD           ++ AD Q A  A+  +NG RL G+ 
Sbjct: 15  DALFTLFGVYGDVVRVKILFNKKDT--------ALIQMADPQQAQTALTHLNGIRLHGKK 66

Query: 563 IAV 565
           + V
Sbjct: 67  LRV 69

This subfamily corresponds to the RRM3 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), and similar proteins found in Metazoa. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 also contains four RRMs. ROD1 coding protein Rod1 is a mammalian PTB homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It may play a role controlling differentiation in mammals. All members in this family contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 74

>gnl|CDD|235124 PRK03427, PRK03427, cell division protein ZipA; Provisional

 Score = 41.2 bits (97), Expect = 0.002
 Identities = 19/120 (15%), Positives = 26/120 (21%), Gaps = 1/120 (0%)

Query: 591 SAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGPPVPPPYAPYAPPPPGSTMYPPVPG 650
                     +  A   P P         +  P  P   PP A   P        P    
Sbjct: 70  RVNHAPANAQEHEAAR-PSPQHQYQPPYASAQPRQPVQQPPEAQVPPQHAPRPAQPAPQP 128

Query: 651 QPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATSSEAQQHSFPPGVQSESSSSAPAASA 710
              P Y  Q   P+Q      +   P         ++       P    +    A  A  
Sbjct: 129 VQQPAYQPQPEQPLQQPVSPQVAPAPQPVHSAPQPAQQAFQPAEPVAAPQPEPVAEPAPV 188

Length = 333

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

 Score = 37.6 bits (87), Expect = 0.002
 Identities = 20/61 (32%), Positives = 34/61 (55%), Gaps = 1/61 (1%)

Query: 511 LFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGK 570
           L  +F   + A+++ DR TG SKG+GFV ++  + A  A  +M    ++G  + +  A K
Sbjct: 17  LKESFDGSIAARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAMEDGEIDGNKVTLDFA-K 75

Query: 571 P 571
           P
Sbjct: 76  P 76

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|240920 cd12476, RRM1_SNF, RNA recognition motif 1 found in Drosophila melanogaster sex determination protein SNF and similar proteins

 Score = 37.6 bits (87), Expect = 0.002
 Identities = 22/52 (42%), Positives = 27/52 (51%), Gaps = 9/52 (17%)

Query: 508 LIRLFSTFG---DIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGY 556
           L  +FS FG   DIV  K +K R      G  FV + DI  A NA+ SM G+
Sbjct: 20  LYAIFSQFGQILDIVALKTLKMR------GQAFVVFKDISSATNALRSMQGF 65

This subgroup corresponds to the RRM1 of SNF (Sans fille), also termed U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A), an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila. It is essential in Drosophila sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). SNF contains two RNA recognition motifs (RRMs); it can self-associate through RRM1, and each RRM can recognize poly(U) RNA binding independently. . Length = 78

>gnl|CDD|241031 cd12587, RRM1_PSF, RNA recognition motif 1 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

 Score = 37.2 bits (86), Expect = 0.002
 Identities = 21/73 (28%), Positives = 37/73 (50%), Gaps = 6/73 (8%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L++G LP  + +D   +LF+ +G+     + K       KG+GF+K     +A  A A +
Sbjct: 4   LFVGNLPADITEDEFKKLFAKYGEPGEVFINK------GKGFGFIKLESRALAEIAKAEL 57

Query: 554 NGYRLEGRTIAVR 566
           +   + GR + VR
Sbjct: 58  DDTPMRGRQLRVR 70

This subgroup corresponds to the RRM1 of PSF, also termed proline- and glutamine-rich splicing factor, or 100 kDa DNA-pairing protein (POMp100), or 100 kDa subunit of DNA-binding p52/p100 complex, a multifunctional protein that mediates diverse activities in the cell. It is ubiquitously expressed and highly conserved in vertebrates. PSF binds not only RNA but also both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and facilitates the renaturation of complementary ssDNAs. Besides, it promotes the formation of D-loops in superhelical duplex DNA, and is involved in cell proliferation. PSF can also interact with multiple factors. It is an RNA-binding component of spliceosomes and binds to insulin-like growth factor response element (IGFRE). PSF functions as a transcriptional repressor interacting with Sin3A and mediating silencing through the recruitment of histone deacetylases (HDACs) to the DNA binding domain (DBD) of nuclear hormone receptors. Additionally, PSF is an essential pre-mRNA splicing factor and is dissociated from PTB and binds to U1-70K and serine-arginine (SR) proteins during apoptosis. PSF forms a heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO). The PSF/p54nrb complex displays a variety of functions, such as DNA recombination and RNA synthesis, processing, and transport. PSF contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for interactions with RNA and for the localization of the protein in speckles. It also contains an N-terminal region rich in proline, glycine, and glutamine residues, which may play a role in interactions recruiting other molecules. . Length = 71

>gnl|CDD|191511 pfam06409, NPIP, Nuclear pore complex interacting protein (NPIP)

 Score = 40.9 bits (95), Expect = 0.002
 Identities = 27/108 (25%), Positives = 36/108 (33%), Gaps = 10/108 (9%)

Query: 558 LEGRTIAVRVAGKPPQPTVPPG----------PPTSTMPTYPVSAPPVGGYPSQQYAPGG 607
           L   T+  R+  +PP PT              PP   +   P SA P      +  A   
Sbjct: 234 LTAETLKNRMGHQPPPPTQQHSIIDNSLSLKTPPECLLTPLPPSALPSADDNLKTPAECL 293

Query: 608 PLPNPPAASYTGAPVPWGPPVPPPYAPYAPPPPGSTMYPPVPGQPMPP 655
             P PP+A       P     PPP  P         +  P+P   +PP
Sbjct: 294 LRPLPPSADDNIKECPLALKPPPPLPPSVDDNLKECLLAPLPPSALPP 341

This family consists of a series of primate specific nuclear pore complex interacting protein (NPIP) sequences. The function of this family is unknown but is well conserved from African apes to humans. Length = 350

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

 Score = 37.4 bits (87), Expect = 0.002
 Identities = 22/72 (30%), Positives = 38/72 (52%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L+I  L  T  ++ L +LFS +G +    +  D++T   KG+ FV Y   + A  A A +
Sbjct: 5   LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAEL 64

Query: 554 NGYRLEGRTIAV 565
           +G   +GR + +
Sbjct: 65  DGTVFQGRLLHL 76

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|240973 cd12529, RRM2_MEI2_like, RNA recognition motif 2 in plant Mei2-like proteins

 Score = 37.1 bits (86), Expect = 0.002
 Identities = 18/67 (26%), Positives = 38/67 (56%), Gaps = 5/67 (7%)

Query: 499 LPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRL 558
           L P++ +D L ++F  +G+I   K I  R T   + + F+++ D++ A  A+ ++N   +
Sbjct: 9   LDPSVSNDDLHQIFGAYGEI---KEI--RETPNKRHHKFIEFYDVRSAEAALKALNRSEI 63

Query: 559 EGRTIAV 565
            G+ I +
Sbjct: 64  AGKRIKL 70

This subgroup corresponds to the RRM2 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and is highly conserved between plants and fungi. To date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 71

>gnl|CDD|241106 cd12662, RRM3_MYEF2, RNA recognition motif 3 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 36.9 bits (85), Expect = 0.003
 Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 2/74 (2%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           +++  LP  L    L   FS  G ++ A++  +   G SKG G V++   + A  A   M
Sbjct: 2   IFVRNLPFDLTWQKLKEKFSQCGHVMFAEIKME--NGKSKGCGTVRFDSPESAEKACRLM 59

Query: 554 NGYRLEGRTIAVRV 567
           NG ++ GR I VR+
Sbjct: 60  NGIKINGREIDVRL 73

This subgroup corresponds to the RRM3 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 77

>gnl|CDD|184918 PRK14954, PRK14954, DNA polymerase III subunits gamma and tau; Provisional

 Score = 41.1 bits (96), Expect = 0.003
 Identities = 28/133 (21%), Positives = 38/133 (28%), Gaps = 23/133 (17%)

Query: 586 PTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGPPVPPPYAPYAPPPPGSTM- 644
               V+  P G    ++ AP   LP P        P P  P  P       P P  +   
Sbjct: 376 NDGGVAPSPAGSPDVKKKAPEPDLPQPDRH-----PGPAKPEAPGARPAELPSPASAPTP 430

Query: 645 --YPPVP-GQPMPPYGVQYPPPVQTAPPGAL--------------TAPPGAPTQTATSSE 687
              PPV    P+PP      P    +    +                    P Q ++S  
Sbjct: 431 EQQPPVARSAPLPPSPQASAPRNVASGKPGVDLGSWQGKFMNFTRNGSRKQPVQASSSDA 490

Query: 688 AQQHSFPPGVQSE 700
           AQ   F    + E
Sbjct: 491 AQTGVFEGVAELE 503

Length = 620

>gnl|CDD|240731 cd12285, RRM3_RBM39_like, RNA recognition motif 3 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins

 Score = 37.1 bits (87), Expect = 0.003
 Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 4/53 (7%)

Query: 513 STFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAV 565
           S FG +   KV K+      +G  +VK+  ++ A   I ++NG   +GR I  
Sbjct: 33  SKFGPVEHIKVDKNS----PEGVVYVKFKTVEAAQKCIQALNGRWFDGRQITA 81

This subfamily corresponds to the RRM3 of RBM39, also termed hepatocellular carcinoma protein 1, or RNA-binding region-containing protein 2, or splicing factor HCC1, ia nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Based on the specific domain composition, RBM39 has been classified into a family of non-snRNP (small nuclear ribonucleoprotein) splicing factors that are usually not complexed to snRNAs. . Length = 85

>gnl|CDD|240831 cd12385, RRM1_hnRNPM_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 37.0 bits (86), Expect = 0.003
 Identities = 19/57 (33%), Positives = 32/57 (56%), Gaps = 2/57 (3%)

Query: 511 LF-STFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR 566
           LF    G++   ++ KD   G S+G G V++ D +    A+ +MN Y L+GR + V+
Sbjct: 19  LFREKVGEVTYVELFKDE-EGKSRGCGVVEFKDKESVQKALETMNRYELKGRKLVVK 74

This subfamily corresponds to the RRM1 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 76

>gnl|CDD|239086 cd02393, PNPase_KH, Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH)

 Score = 36.4 bits (85), Expect = 0.003
 Identities = 21/72 (29%), Positives = 29/72 (40%), Gaps = 23/72 (31%)

Query: 268 IGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAET 327
           I  +IGP G T K++  ETG KI I   G+V                        + A  
Sbjct: 13  IRDVIGPGGKTIKKIIEETGVKIDIEDDGTVY-----------------------IAASD 49

Query: 328 QESLEGAAAMVE 339
           +E+ E A  M+E
Sbjct: 50  KEAAEKAKKMIE 61

PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. Length = 61

>gnl|CDD|241141 cd12697, RRM3_ROD1, RNA recognition motif 3 in vertebrate regulator of differentiation 1 (Rod1)

 Score = 36.8 bits (85), Expect = 0.003
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 5/69 (7%)

Query: 500 PPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLE 559
           P  +   GL  LF  +GD+   K++ ++     K    V+ AD   A  A++ +NG RL 
Sbjct: 10  PDAITPHGLFILFGVYGDVHRVKIMFNK-----KENALVQMADATQAQLAMSHLNGQRLY 64

Query: 560 GRTIAVRVA 568
           G+ I   ++
Sbjct: 65  GKVIRATLS 73

This subgroup corresponds to the RRM3 of ROD1 coding protein Rod1, a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. Rod1 contains four repeats of RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain) and does have RNA binding activities. . Length = 76

>gnl|CDD|241124 cd12680, RRM_THOC4, RNA recognition motif in THO complex subunit 4 (THOC4) and similar proteins

 Score = 36.8 bits (86), Expect = 0.003
 Identities = 24/70 (34%), Positives = 33/70 (47%), Gaps = 1/70 (1%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           T L +  L   + DD +  LF+ FG +  A V  DR +G S G   V +     A  A+ 
Sbjct: 1   TKLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDR-SGRSLGTADVVFERRADALKAMK 59

Query: 552 SMNGYRLEGR 561
             NG  L+GR
Sbjct: 60  QYNGVPLDGR 69

This subgroup corresponds to the RRM of THOC4, also termed transcriptional coactivator Aly/REF, or ally of AML-1 and LEF-1, or bZIP-enhancing factor BEF, an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus. THOC4 was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid. It might be a novel transcription cofactor for erythroid-specific genes. . Length = 75

>gnl|CDD|240775 cd12329, RRM2_hnRNPD_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 37.0 bits (86), Expect = 0.003
 Identities = 12/47 (25%), Positives = 26/47 (55%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKY 540
           +++G L P   ++ +   F  FG+IV  ++  D+ T   +G+ F+ +
Sbjct: 2   IFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITF 48

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

 Score = 37.0 bits (86), Expect = 0.003
 Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 6/61 (9%)

Query: 493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
           N+YIG LP +  ++ L      FG I   K++K+      K   FV +  I  A   + +
Sbjct: 5   NVYIGNLPESYSEEELREDLEKFGPIDQIKIVKE------KNIAFVHFLSIANAIKVVTT 58

Query: 553 M 553
           +
Sbjct: 59  L 59

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

>gnl|CDD|240779 cd12333, RRM2_p54nrb_like, RNA recognition motif 2 in the p54nrb/PSF/PSP1 family

 Score = 36.9 bits (86), Expect = 0.003
 Identities = 19/53 (35%), Positives = 28/53 (52%), Gaps = 1/53 (1%)

Query: 499 LPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           L P + ++ L + FS FG++  A VI D   G S G G V+++    A  AI 
Sbjct: 7   LSPFVSNELLEQAFSQFGEVERAVVIVD-DRGRSTGEGIVEFSRKPGAQAAIK 58

This subfamily corresponds to the RRM2 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. The family also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contains a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members. . Length = 80

>gnl|CDD|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed

 Score = 40.6 bits (96), Expect = 0.003
 Identities = 20/89 (22%), Positives = 21/89 (23%), Gaps = 4/89 (4%)

Query: 601 QQYAPGGPLPNPPAASYTGAPVPWGPPVPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQY 660
             Y PG       AA+   A        P   AP AP P      P       PP     
Sbjct: 34  ADYGPGSTAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAP----PAAAAPAAPPKPAAA 89

Query: 661 PPPVQTAPPGALTAPPGAPTQTATSSEAQ 689
                        A   AP   A   E  
Sbjct: 90  AAAAAAPAAPPAAAAAAAPAAAAVEDEVT 118

Length = 1228

>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 = 0.003
 Identities = 23/80 (28%), Positives = 35/80 (43%), Gaps = 5/80 (6%)

Query: 493 NLYIGYLPPTLDDD----GLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANN 548
            LY+  + P L ++     L   FS FG +   KV  +        Y FVK+   + A+ 
Sbjct: 2   TLYVWGISPKLTEEEIYESLCSAFSQFGLLYSVKVFPNAAVATPGFYAFVKFYSARAASR 61

Query: 549 AIASMNGYRL-EGRTIAVRV 567
           A  + NG  L +G  + VR 
Sbjct: 62  AQKACNGKWLFQGSPLKVRF 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|240846 cd12400, RRM_Nop6, RNA recognition motif in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and similar proteins

 Score = 36.6 bits (85), Expect = 0.003
 Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 1/72 (1%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L++G LP     + L+  F   G     +++ D+ TG SKG  FV++ D   A      +
Sbjct: 3   LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEF-DTAEAMTKALKL 61

Query: 554 NGYRLEGRTIAV 565
           +   L+GR I V
Sbjct: 62  HHTLLKGRKINV 73

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|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed

 Score = 40.6 bits (96), Expect = 0.004
 Identities = 13/74 (17%), Positives = 15/74 (20%)

Query: 568 AGKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGPP 627
            G    PT       +       +             P    P  P      A     P 
Sbjct: 38  PGSTAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAAAAAAAAAPA 97

Query: 628 VPPPYAPYAPPPPG 641
            PP  A  A P   
Sbjct: 98  APPAAAAAAAPAAA 111

Length = 1228

>gnl|CDD|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 4 (SRSF4)

 Score = 36.5 bits (84), Expect = 0.004
 Identities = 23/78 (29%), Positives = 38/78 (48%), Gaps = 8/78 (10%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           +YIG L     +  + R F  +G I+           +  GYGFV++ D++ A++A+  +
Sbjct: 2   VYIGRLSYQARERDVERFFKGYGKILEVD--------LKNGYGFVEFDDLRDADDAVYEL 53

Query: 554 NGYRLEGRTIAVRVAGKP 571
           NG  L G  + V  A  P
Sbjct: 54  NGKDLCGERVIVEHARGP 71

This subgroup corresponds to the RRM1 of SRSF4, also termed pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing factor, arginine/serine-rich 4 (SFRS4). SRSF4 is a splicing regulatory serine/arginine (SR) protein that plays an important role in both constitutive splicing and alternative splicing of many pre-mRNAs. For instance, it interacts with heterogeneous nuclear ribonucleoproteins, hnRNP G and hnRNP E2, and further regulates the 5' splice site of tau exon 10, whose misregulation causes frontotemporal dementia. SFSF4 also induces production of HIV-1 vpr mRNA through the inhibition of the 5'-splice site of exon 3. In addition, it activates splicing of the cardiac troponin T (cTNT) alternative exon by direct interactions with the cTNT exon 5 enhancer RNA. SRSF4 can shuttle between the nucleus and cytoplasm. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine-rich region, an internal region homologous to the RRM, and a very long, highly phosphorylated C-terminal SR domains rich in serine-arginine dipeptides. . Length = 74

>gnl|CDD|240847 cd12401, RRM_eIF4H, RNA recognition motif in eukaryotic translation initiation factor 4H (eIF-4H) and similar proteins

 Score = 36.5 bits (85), Expect = 0.004
 Identities = 16/74 (21%), Positives = 37/74 (50%), Gaps = 2/74 (2%)

Query: 495 YIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMN 554
           ++G LP       L  +F     +   ++++D+ T   KG+ +V++ D++    A+   +
Sbjct: 5   FVGNLPFNTVQGDLDAIFKDL-SVKSVRLVRDKETDKFKGFCYVEFEDVESLKEALE-YD 62

Query: 555 GYRLEGRTIAVRVA 568
           G   + R++ V +A
Sbjct: 63  GALFDDRSLRVDIA 76

This subfamily corresponds to the RRM of eIF-4H, also termed Williams-Beuren syndrome chromosomal region 1 protein, which, together with elf-4B/eIF-4G, serves as the accessory protein of RNA helicase eIF-4A. eIF-4H contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It stimulates protein synthesis by enhancing the helicase activity of eIF-4A in the initiation step of mRNA translation. . Length = 76

>gnl|CDD|240726 cd12280, RRM_FET, RNA recognition motif in the FET family of RNA-binding proteins

 Score = 36.5 bits (85), Expect = 0.004
 Identities = 28/80 (35%), Positives = 33/80 (41%), Gaps = 9/80 (11%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIV--------MAKVIKDRVTGMSKGYGFVKYADIQM 545
           +YI  LP  + +D L  LF   G I         M K+  D+ T   KG   V Y D   
Sbjct: 1   IYISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKETE-PKGEATVTYDDPSA 59

Query: 546 ANNAIASMNGYRLEGRTIAV 565
           A  AI   NGY   G  I V
Sbjct: 60  AQAAIEWFNGYEFRGNKIKV 79

This subfamily corresponds to the RRM of FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA-binding proteins. This ubiquitously expressed family of similarly structured proteins predominantly localizing to the nuclear, includes FUS (also known as TLS or Pigpen or hnRNP P2), EWS (also known as EWSR1), TAF15 (also known as hTAFII68 or TAF2N or RPB56), and Drosophila Cabeza (also known as SARFH). The corresponding coding genes of these proteins are involved in deleterious genomic rearrangements with transcription factor genes in a variety of human sarcomas and acute leukemias. All FET proteins interact with each other and are therefore likely to be part of the very same protein complexes, which suggests a general bridging role for FET proteins coupling RNA transcription, processing, transport, and DNA repair. The FET proteins contain multiple copies of a degenerate hexapeptide repeat motif at the N-terminus. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a putative zinc-finger domain, and a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is flanked by 3 arginine-glycine-glycine (RGG) boxes. FUS and EWS might have similar sequence specificity; both bind preferentially to GGUG-containing RNAs. FUS has also been shown to bind strongly to human telomeric RNA and to small low-copy-number RNAs tethered to the promoter of cyclin D1. To date, nothing is known about the RNA binding specificity of TAF15. . Length = 81

>gnl|CDD|219321 pfam07174, FAP, Fibronectin-attachment protein (FAP)

 Score = 39.9 bits (93), Expect = 0.004
 Identities = 28/74 (37%), Positives = 32/74 (43%), Gaps = 5/74 (6%)

Query: 567 VAGKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGP 626
            A   P P  PP P T+     P + PP    P    AP  P P+ P A+    P     
Sbjct: 36  TANADPAPP-PPPPSTAAAAPAPAAPPP----PPPPAAPPAPQPDDPNAAPPPPPADPNA 90

Query: 627 PVPPPYAPYAPPPP 640
           P PPP  P APPPP
Sbjct: 91  PPPPPVDPNAPPPP 104

This family contains bacterial fibronectin-attachment proteins (FAP). Family members are rich in alanine and proline, are approximately 300 long, and seem to be restricted to mycobacteria. These proteins contain a fibronectin-binding motif that allows mycobacteria to bind to fibronectin in the extracellular matrix. Length = 297

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	797
KOG0119	554	consensus Splicing factor 1/branch point binding p	100.0
COG5176	269	MSL5 Splicing factor (branch point binding protein	100.0
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	100.0
KOG1588	259	consensus RNA-binding protein Sam68 and related KH	100.0
KOG0122	270	consensus Translation initiation factor 3, subunit	99.92
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.68
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.67
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.59
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.57
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.55
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.53
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.52
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.49
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.47
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.43
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.43
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.43
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.42
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	99.4
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.39
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.38
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.37
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.35
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.35
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.35
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.34
PLN03120	260	nucleic acid binding protein; Provisional	99.33
PLN03213	759	repressor of silencing 3; Provisional	99.33
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.32
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.32
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.31
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.3
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.29
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.29
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.28
smart00362	72	RRM_2 RNA recognition motif.	99.28
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.27
smart00360	71	RRM RNA recognition motif.	99.26
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.25
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.23
PLN03121	243	nucleic acid binding protein; Provisional	99.23
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.23
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.2
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.2
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.19
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.17
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.16
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.15
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.14
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.12
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.12
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.1
smart00361	70	RRM_1 RNA recognition motif.	99.08
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.07
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.06
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.04
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.04
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.03
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.02
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.02
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.0
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.0
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	98.99
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	98.97
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	98.95
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.86
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.86
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	98.85
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	98.85
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	98.82
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	98.81
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.8
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	98.79
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.79
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.78
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.78
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	98.73
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	98.72
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	98.69
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	98.66
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	98.61
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	98.58
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.55
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	98.53
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	98.53
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	98.52
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.5
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	98.48
KOG0226	290	consensus RNA-binding proteins [General function p	98.45
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	98.45
smart00322	69	KH K homology RNA-binding domain.	98.42
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.41
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	98.39
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.39
KOG1960	531	consensus Predicted RNA-binding protein, contains	98.39
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.37
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	98.35
KOG0151	877	consensus Predicted splicing regulator, contains R	98.27
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.25
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.22
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.21
PRK13763	180	putative RNA-processing protein; Provisional	98.2
KOG1995	351	consensus Conserved Zn-finger protein [General fun	98.15
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	98.12
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.11
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.09
PF13014	43	KH_3: KH domain	97.91
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	97.91
KOG1676	600	consensus K-homology type RNA binding proteins [RN	97.9
KOG1924	1102	consensus RhoA GTPase effector DIA/Diaphanous [Sig	97.85
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	97.84
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	97.84
KOG1676	600	consensus K-homology type RNA binding proteins [RN	97.84
PRK13763	180	putative RNA-processing protein; Provisional	97.81
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	97.8
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	97.72
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	97.66
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	97.51
COG1094	194	Predicted RNA-binding protein (contains KH domains	97.46
PHA03247	3151	large tegument protein UL36; Provisional	97.45
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.4
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	97.35
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	97.34
KOG4210	285	consensus Nuclear localization sequence binding pr	97.3
PHA03247	3151	large tegument protein UL36; Provisional	97.25
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.25
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	97.18
KOG1457	284	consensus RNA binding protein (contains RRM repeat	97.16
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	97.1
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	97.1
KOG2191	402	consensus RNA-binding protein NOVA1/PASILLA and re	97.04
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	97.02
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	96.97
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	96.9
KOG2191	402	consensus RNA-binding protein NOVA1/PASILLA and re	96.84
PF12353	128	eIF3g: Eukaryotic translation initiation factor 3	96.75
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	96.69
KOG2190	485	consensus PolyC-binding proteins alphaCP-1 and rel	96.66
PTZ00368	148	universal minicircle sequence binding protein (UMS	96.66
KOG2314	698	consensus Translation initiation factor 3, subunit	96.56
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	96.51
KOG3152	278	consensus TBP-binding protein, activator of basal	96.45
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	96.45
KOG1548	382	consensus Transcription elongation factor TAT-SF1	96.42
PRK00106	535	hypothetical protein; Provisional	96.41
KOG3671	569	consensus Actin regulatory protein (Wiskott-Aldric	96.35
PRK12704	520	phosphodiesterase; Provisional	96.35
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	96.29
KOG2814	345	consensus Transcription coactivator complex, P50 c	96.28
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	96.2
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	96.18
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	96.05
KOG1855	484	consensus Predicted RNA-binding protein [General f	95.95
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	95.71
PF00098	18	zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi	95.7
PTZ00368	148	universal minicircle sequence binding protein (UMS	95.6
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	95.5
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	95.21
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	95.16
PF13696	32	zf-CCHC_2: Zinc knuckle	95.12
KOG3671	569	consensus Actin regulatory protein (Wiskott-Aldric	95.07
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	95.02
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	94.98
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	94.94
KOG2874	356	consensus rRNA processing protein [Translation, ri	94.73
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	94.73
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	94.54
PRK12705	508	hypothetical protein; Provisional	94.51
KOG0307	1049	consensus Vesicle coat complex COPII, subunit SEC3	94.3
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	94.27
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	94.21
KOG1996	378	consensus mRNA splicing factor [RNA processing and	94.03
KOG2068	327	consensus MOT2 transcription factor [Transcription	93.98
KOG1960	531	consensus Predicted RNA-binding protein, contains	93.88
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	93.53
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	93.41
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	93.27
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	93.11
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	92.44
KOG4400	261	consensus E3 ubiquitin ligase interacting with arg	92.28
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	92.06
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	91.69
COG1094	194	Predicted RNA-binding protein (contains KH domains	91.57
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	91.2
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	90.91
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	90.65
PF08920	144	SF3b1: Splicing factor 3B subunit 1; InterPro: IPR	90.47
PF13917	42	zf-CCHC_3: Zinc knuckle	90.01
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	89.83
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	89.81
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	89.45
PF15288	40	zf-CCHC_6: Zinc knuckle	89.42
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	89.19
KOG2135	526	consensus Proteins containing the RNA recognition	88.93
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	88.03
KOG2893	341	consensus Zn finger protein [General function pred	87.96
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	87.77
KOG4210	285	consensus Nuclear localization sequence binding pr	87.69
KOG0119	554	consensus Splicing factor 1/branch point binding p	87.35
PF00098	18	zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi	86.98
KOG4400	261	consensus E3 ubiquitin ligase interacting with arg	86.94
KOG2192	390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	86.4
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	85.95
KOG4660	549	consensus Protein Mei2, essential for commitment t	85.45
KOG2192	390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	84.8
KOG1984	1007	consensus Vesicle coat complex COPII, subunit SFB3	84.72
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	84.28
KOG2591	684	consensus c-Mpl binding protein, contains La domai	83.66
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	83.59
PF13917	42	zf-CCHC_3: Zinc knuckle	83.42
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	82.84
KOG2190	485	consensus PolyC-binding proteins alphaCP-1 and rel	82.66
PF14787	36	zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB:	81.95

>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]

Probab=100.00  E-value=1.3e-82  Score=689.84  Aligned_cols=308  Identities=54%  Similarity=0.872  Sum_probs=272.6

Q ss_pred             cchhhhhcccCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCcccCCccccccCCCCcCCHHHHHHHHHHHHHHHH
Q 040243          102 ETTSRRRRRSRWDPPPSESGGTEGNGDSGSGTRKRRSRWADDEPKPVIQLPDFMKDFTGGIEFDPEIQALNSRLLEISRM  181 (797)
Q Consensus       102 ~~~~~~~r~s~w~~~~~~~~~~~~~~~~~~~~~~r~srw~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~r~~ei~~~  181 (797)
                      ++-+ |||||||+++.-++..                   .++...++.||++|....  +..+.+.|.|++||+||+++
T Consensus        10 ~~~p-~~~rS~w~~~~~es~~-------------------~~s~~~~~~lp~~m~~~l--t~eq~~~y~l~~~iee~t~k   67 (554)
T KOG0119|consen   10 ASVP-RRNRSRWDRDTVESDV-------------------VNSMTSTSALPSSMPGGL--TEEQKESYSLNLRIEEITRK   67 (554)
T ss_pred             cccc-chhhccCCCCcccccc-------------------ccCccccccccccccccc--chhhhhhhhHHHHHHHhhhh
Confidence            3344 4459999888655432                   111223567888887433  66778889999999999999


Q ss_pred             HhcCCCCCCCCCCCCCCCCCcccCCCCcccChHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCCCC-ceEEEEEecCC
Q 040243          182 LQSGLPLDDRPEGQRSPSPEPIYDNMGIRINTREYRARERLNKERQEIISQIIKRNPAFKPPADYRPP-KLQKKLYIPMK  260 (797)
Q Consensus       182 l~~~~~~~~~~~~~rspsp~p~yd~~g~r~ntre~r~~~~le~er~~li~~~~~~~p~~~pp~dy~p~-~~~~Ki~IP~~  260 (797)
                      |+++++....+...||||++|+||+.|+||||||+|+|++||.|||+||++|+|+||.|++|.|||+. ++++|||||||
T Consensus        68 Lrt~d~~~p~~~e~rSPsp~p~yda~g~R~ntRe~R~r~~Le~er~e~I~~~lk~nP~fkpP~DYk~p~~~~~Kv~IPvk  147 (554)
T KOG0119|consen   68 LRTGDVGVPPPRELRSPSPEPVYDAKGKRLNTREQRARKKLEDERHEIIEEILKLNPGFKPPADYKPPAKLHDKVYIPVK  147 (554)
T ss_pred             hccccCCCCCCccccCCCcchhhhhhccchhhHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCcccCcccccccceecchh
Confidence            99999866666778999999999999999999999999999999999999999999999999999988 99999999999


Q ss_pred             CCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHH
Q 040243          261 EYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEK  340 (797)
Q Consensus       261 ~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v~~A~~~I~~  340 (797)
                      +||+||||||||||||+|||+||+||||||.||||||+|||| ..+.|......++|+|||+|+|+|+|+|++|+++|++
T Consensus       148 e~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk-~~~~d~~~~~~~~epLH~~Isadt~eki~~Ai~vien  226 (554)
T KOG0119|consen  148 EFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGK-GRSDDLSYIPKENEPLHCLISADTQEKIKKAIAVIEN  226 (554)
T ss_pred             hcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccc-cCCcccccccccccceeEEEecchHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999 4445567777899999999999999999999999999


Q ss_pred             hcC---CChHHHHHHHHHHHHHHHhhcCCcCccc--hhcccCCCCCccccCCCCCCCccccccceecCCCCCCcccCCCC
Q 040243          341 LLQ---PVDEVLNEHKRQQLRELAALNGTIRDEE--YCRLCGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTIDCLVK  415 (797)
Q Consensus       341 ll~---~~~e~~n~~k~~Ql~ela~lnGt~r~~~--~c~~cg~~gh~~~~cp~~~~~~~~~v~Cr~CG~~gH~t~dCp~k  415 (797)
                      ||+   .+.|++|++||.||||||.||||+|+++  +|++||.+||++|+||++.+++++  +|++||..|||++||+++
T Consensus       227 li~~av~~~e~~n~l~~~Qlrela~lNgt~r~~d~~~c~~cg~~~H~q~~cp~r~~~~~n--~c~~cg~~gH~~~dc~~~  304 (554)
T KOG0119|consen  227 LIQSAVSVPEGQNDLKRLQLRELARLNGTLRDDDNRACRNCGSTGHKQYDCPGRIPNTTN--VCKICGPLGHISIDCKVN  304 (554)
T ss_pred             HHHhhccCccccccccHHHHHHHHHhCCCCCccccccccccCCCccccccCCcccccccc--cccccCCcccccccCCCc
Confidence            998   5789999999999999999999999987  999999999999999999666666  999999999999999998


Q ss_pred             Cc----CCCCcchHHHHHHhhhc
Q 040243          416 GT----TGKKMDDEYQNFLAELG  434 (797)
Q Consensus       416 ~~----~g~~ld~eY~~~m~Elg  434 (797)
                      +.    ....||.||..+|.||+
T Consensus       305 ~q~~~~~~~~~d~ey~~lm~e~~  327 (554)
T KOG0119|consen  305 DQQMPMSSANFDREYASLMLELG  327 (554)
T ss_pred             ccccchhhhccCHHHHhhhcccc
Confidence            42    22348999999999888

>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]

Probab=100.00  E-value=5.1e-50  Score=394.48  Aligned_cols=217  Identities=39%  Similarity=0.594  Sum_probs=190.5

Q ss_pred             cccCCccccccCCCCcCCH-HHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCcccCCCCcccChHHHHHHHHHHHHH
Q 040243          148 VIQLPDFMKDFTGGIEFDP-EIQALNSRLLEISRMLQSGLPLDDRPEGQRSPSPEPIYDNMGIRINTREYRARERLNKER  226 (797)
Q Consensus       148 ~~~~p~~~~~~~~~~~~~~-~~~~~~~r~~ei~~~l~~~~~~~~~~~~~rspsp~p~yd~~g~r~ntre~r~~~~le~er  226 (797)
                      +..||..++.   +++..+ +.|+++.|+.||+.||++++.+... ...|||||+|.||+.|+|+||||.|++++||+||
T Consensus        47 ~~~l~s~i~~---~lt~eqi~~y~~~~r~~eit~Klrt~d~Vp~~-re~Rspsppp~yd~~GrRlntre~ry~kkLeder  122 (269)
T COG5176          47 FNSLPSKISG---ALTREQIYSYQVMMRPFEITEKLRTPDGVPSK-RELRSPSPPPRYDEIGRRLNTREARYNKKLEDER  122 (269)
T ss_pred             hhcchhHhhh---hhhHHHHHHHHHhccHhhhhhhhcCCCCCCch-hhccCCCCCcchhHHhhhhhHHHHHHhhhhhHHH
Confidence            4467766643   334322 3446789999999999999977432 3479999999999999999999999999999999


Q ss_pred             HHHHHHHHHhCCCCCCCCCCC-CCceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEecccccccccccc
Q 040243          227 QEIISQIIKRNPAFKPPADYR-PPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQ  305 (797)
Q Consensus       227 ~~li~~~~~~~p~~~pp~dy~-p~~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~  305 (797)
                      +.|++.+++++|.|+.|.||+ |.+++.||||||++||++|||||||||||.|+|+||+.|+|||.|||+||+|+|+...
T Consensus       123 ~~l~era~k~lp~fv~p~dy~rpsk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKegk~ss  202 (269)
T COG5176         123 LWLKERAQKILPRFVLPNDYIRPSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISS  202 (269)
T ss_pred             HHHHHHHHHhcCcccCCccccCcccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecccccccCcccc
Confidence            999999999999999999995 8899999999999999999999999999999999999999999999999999998752


Q ss_pred             ccCCCCC-CCCCCCceEEEEecCHHHHHHHHHHHHHhcC---CChHHHHHHHHHHHHHHHhhcCCcCcc
Q 040243          306 KRDLKPD-PSENEDLHVLVEAETQESLEGAAAMVEKLLQ---PVDEVLNEHKRQQLRELAALNGTIRDE  370 (797)
Q Consensus       306 ~~~~~~~-~~~~e~LHv~I~a~~~e~v~~A~~~I~~ll~---~~~e~~n~~k~~Ql~ela~lnGt~r~~  370 (797)
                        |.... -...++|||+|++++++++.+++..+.++|.   .+.+|+|++||.||++||.||||+|+|
T Consensus       203 --d~p~~~~N~e~~lhcLI~adsedki~~~ik~~~n~I~~a~~~PeGqnDlkR~qlr~la~lngtlr~d  269 (269)
T COG5176         203 --DTPESLKNAEAVLHCLIEADSEDKICRLIKSQLNAIREARRNPEGQNDLKRFQLRWLAHLNGTLRAD  269 (269)
T ss_pred             --cCchhhhhhHHhHHHHhhcchhhhHHHHHHHHHHHHHHHhcCCcccchHHHHHHHHHHHhcceecCC
Confidence              33322 3678899999999999999999999988886   467999999999999999999999875

>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH)

Probab=100.00  E-value=5.1e-35  Score=274.99  Aligned_cols=117  Identities=56%  Similarity=0.865  Sum_probs=108.1

Q ss_pred             EEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecC--HH
Q 040243          252 QKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAET--QE  329 (797)
Q Consensus       252 ~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~--~e  329 (797)
                      ++|||||+++||+|||||+||||||+|+|+||++|||||.|||+||+|+++.+.........+.+|+|||+|+|++  .+
T Consensus         1 ~~ki~iP~~~~P~~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e   80 (120)
T cd02395           1 TEKVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEE   80 (120)
T ss_pred             CCEEEcCcccCCCCCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHH
Confidence            4799999999999999999999999999999999999999999999999887654433455689999999999999  99


Q ss_pred             HHHHHHHHHHHhcCCChHH-HHHHHHHHHHHHHhhcCCcC
Q 040243          330 SLEGAAAMVEKLLQPVDEV-LNEHKRQQLRELAALNGTIR  368 (797)
Q Consensus       330 ~v~~A~~~I~~ll~~~~e~-~n~~k~~Ql~ela~lnGt~r  368 (797)
                      ++++|+++|+.||..+.+. .|++||.||+|||.+|||||
T Consensus        81 ~~~~A~~~I~~ll~~~~~~~~~~~k~~ql~~la~~nGt~~  120 (120)
T cd02395          81 ALAKAVEAIEELLKPAIEGGNDELKREQLRELALLNGTYR  120 (120)
T ss_pred             HHHHHHHHHHHHhccCCCccchHHHHHHHHHHHHhcccCC
Confidence            9999999999999988776 89999999999999999986

Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]

Probab=100.00  E-value=6e-35  Score=300.99  Aligned_cols=152  Identities=41%  Similarity=0.621  Sum_probs=129.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHh---CCCCC---CCCCCCCCceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEE
Q 040243          217 RARERLNKERQEIISQIIKR---NPAFK---PPADYRPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKI  290 (797)
Q Consensus       217 r~~~~le~er~~li~~~~~~---~p~~~---pp~dy~p~~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI  290 (797)
                      .+.++|.+|+.++...+.+.   .+.-.   .-.+-+++|+++||+||+++||+|||||+||||||+|+|+||+||||||
T Consensus        52 ~~~rLL~~Ei~rv~~~~~~~~~~~~~~~~~~~~~~~~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki  131 (259)
T KOG1588|consen   52 HAERLLDEEIERVQTSGRQHGSKEPEELPYADVYSGKPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKI  131 (259)
T ss_pred             HHHHHHHHHHHHHHhhhhhccCCCchhcccccCccCCceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeE
Confidence            57789999999988777653   23221   2334478999999999999999999999999999999999999999999


Q ss_pred             EEeccccccccccccccCCCCCC-CCCCCceEEEEecCHH-----HHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHhhc
Q 040243          291 VIRGKGSVKEGRLQQKRDLKPDP-SENEDLHVLVEAETQE-----SLEGAAAMVEKLLQPVDEVLNEHKRQQLRELAALN  364 (797)
Q Consensus       291 ~IrGkGS~k~g~~~~~~~~~~~~-~~~e~LHv~I~a~~~e-----~v~~A~~~I~~ll~~~~e~~n~~k~~Ql~ela~ln  364 (797)
                      .||||||+|+..++++...++.+ |++|||||+|++....     +|.+|++.|++||++..++.+  ||+||+|||.||
T Consensus       132 ~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~~p~~ea~~rl~~AleeI~klL~P~~e~~d--k~~QL~ELa~ln  209 (259)
T KOG1588|consen  132 MIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIETEAPPAEAYARLAYALEEIKKLLVPDHEDED--KREQLRELAILN  209 (259)
T ss_pred             EEecCCcccchHHHHHhhcCcchHHhCCCcEEEEEEeCCHHHHHHHHHHHHHHHHHhcCCCCCCch--HHHHHHHHhhcC
Confidence            99999999997776665555554 8999999999998764     578999999999999988776  999999999999


Q ss_pred             CCcCcc
Q 040243          365 GTIRDE  370 (797)
Q Consensus       365 Gt~r~~  370 (797)
                      ||+..+
T Consensus       210 gt~~~~  215 (259)
T KOG1588|consen  210 GTYLRS  215 (259)
T ss_pred             Cccccc
Confidence            996544

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

Probab=99.92  E-value=6.3e-25  Score=222.99  Aligned_cols=152  Identities=30%  Similarity=0.485  Sum_probs=119.7

Q ss_pred             ccccceecCCCCCCcccCCCCCcCCCCcchHHHHHHhhhcCCCCcccccccccccCCCCCCCCCCCCCCCCCCCCCCCCC
Q 040243          395 SDVLCKICGDGGHPTIDCLVKGTTGKKMDDEYQNFLAELGGTLPESASKQSTTLALGPGSGSSGSNPPWANNSGSSGTPG  474 (797)
Q Consensus       395 ~~v~Cr~CG~~gH~t~dCp~k~~~g~~ld~eY~~~m~Elg~~~pe~a~ka~~~~a~g~g~gg~G~~~p~~~~~g~~g~~g  474 (797)
                      +.+.||+|+ +.||+.+||||++.+.        +|++     +..+..+.+..+-   ++..|.|+|.+.+.|+.+..+
T Consensus       118 ~~~~CR~C~-gdHwt~~CPyK~~~~~--------~lde-----~~~~e~~~~~~ap---~~~~g~yvpP~mR~ga~~~~g  180 (270)
T KOG0122|consen  118 SIVACRICK-GDHWTTNCPYKDTLSP--------ALDE-----PATAESPAESAAP---GTKKGKYVPPSMRAGADRASG  180 (270)
T ss_pred             ceeeeeecC-CCeeeecCCchhhccc--------cccC-----CcccccchhhcCc---CCcCccccCccccCCcccccc
Confidence            678999995 9999999999998753        2222     1111111111111   346778888888776532211


Q ss_pred             CCCCCCCCCCCCCCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcC
Q 040243          475 HPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMN  554 (797)
Q Consensus       475 ~~g~g~~~~~~~~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~Ln  554 (797)
                              .......+.++|.|.||+.+++|++|++||..||.|.+|+|.+|+.||.+||||||+|.++++|.+||+.||
T Consensus       181 --------~~~R~R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~Ln  252 (270)
T KOG0122|consen  181 --------SDMRERDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLN  252 (270)
T ss_pred             --------cccccCCccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHcc
Confidence                    111134588999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ceeeccceEEEEecCCC
Q 040243          555 GYRLEGRTIAVRVAGKP  571 (797)
Q Consensus       555 G~~l~Gr~L~V~~A~~~  571 (797)
                      |+.+++..|+|+|+++.
T Consensus       253 G~gyd~LILrvEwskP~  269 (270)
T KOG0122|consen  253 GYGYDNLILRVEWSKPS  269 (270)
T ss_pred             CcccceEEEEEEecCCC
Confidence            99999999999999864

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

Probab=99.68  E-value=6.9e-16  Score=150.44  Aligned_cols=85  Identities=47%  Similarity=0.688  Sum_probs=80.3

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ...++|||+||+++++|++|+++|++||.|.+|+|+.|+.|+++||||||+|.+.++|++||+.||+..|+|+.|+|+|+
T Consensus        32 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a  111 (144)
T PLN03134         32 LMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPA  111 (144)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeC
Confidence            35679999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCC
Q 040243          569 GKPPQ  573 (797)
Q Consensus       569 ~~~~~  573 (797)
                      ..+..
T Consensus       112 ~~~~~  116 (144)
T PLN03134        112 NDRPS  116 (144)
T ss_pred             CcCCC
Confidence            76543

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

Probab=99.67  E-value=7.5e-16  Score=180.44  Aligned_cols=83  Identities=37%  Similarity=0.621  Sum_probs=78.9

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ...++|||+||++++++++|+++|++||.|.+|+|+.| .+|++||||||+|.+.++|++||+.|||+.|+|+.|+|.||
T Consensus       283 ~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d-~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a  361 (562)
T TIGR01628       283 AQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALA  361 (562)
T ss_pred             cCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEEC-CCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEec
Confidence            45678999999999999999999999999999999999 58999999999999999999999999999999999999999


Q ss_pred             CCCC
Q 040243          569 GKPP  572 (797)
Q Consensus       569 ~~~~  572 (797)
                      ..+.
T Consensus       362 ~~k~  365 (562)
T TIGR01628       362 QRKE  365 (562)
T ss_pred             cCcH
Confidence            8764

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

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.59  E-value=1.1e-14  Score=160.82  Aligned_cols=85  Identities=32%  Similarity=0.542  Sum_probs=80.8

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      .....++|||+||+++++|++|+++|+.||.|++|+|++|+.|+++||||||+|.++++|++||+.|++..|.+++|+|.
T Consensus       103 ~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~  182 (346)
T TIGR01659       103 TNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVS  182 (346)
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeee
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCC
Q 040243          567 VAGKP  571 (797)
Q Consensus       567 ~A~~~  571 (797)
                      |++..
T Consensus       183 ~a~p~  187 (346)
T TIGR01659       183 YARPG  187 (346)
T ss_pred             ccccc
Confidence            98653

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

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.57  E-value=8.4e-15  Score=161.10  Aligned_cols=84  Identities=33%  Similarity=0.534  Sum_probs=79.9

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ..+.+|||+||++.+++++|+++|++||.|.+|+|++|+.||++||||||+|.+.++|.+||+.|||+.|+||.|+|.|+
T Consensus       267 ~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~  346 (352)
T TIGR01661       267 GAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFK  346 (352)
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEc
Confidence            34568999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 040243          569 GKPP  572 (797)
Q Consensus       569 ~~~~  572 (797)
                      ..+.
T Consensus       347 ~~~~  350 (352)
T TIGR01661       347 TNKA  350 (352)
T ss_pred             cCCC
Confidence            7664

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

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

Probab=99.55  E-value=2.1e-14  Score=146.43  Aligned_cols=86  Identities=34%  Similarity=0.508  Sum_probs=77.9

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      .+..-++||||+|+|.+..++|+++|++||+|++..|+.|+.||+||||+||+|.+.++|++|++. ..-.|+||+..|.
T Consensus         8 ~DT~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcn   86 (247)
T KOG0149|consen    8 GDTTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCN   86 (247)
T ss_pred             CCceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccc
Confidence            345678999999999999999999999999999999999999999999999999999999999975 4567999999999


Q ss_pred             ecCCCCC
Q 040243          567 VAGKPPQ  573 (797)
Q Consensus       567 ~A~~~~~  573 (797)
                      +|.-...
T Consensus        87 lA~lg~~   93 (247)
T KOG0149|consen   87 LASLGGK   93 (247)
T ss_pred             hhhhcCc
Confidence            9876433

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.53  E-value=2.9e-14  Score=156.83  Aligned_cols=83  Identities=41%  Similarity=0.726  Sum_probs=79.0

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      ..++|||+||+..++|++|+++|++||.|.+|+|++|+.+|++||||||+|.+.++|++||+.|||..|.|+.|+|+|++
T Consensus         2 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~   81 (352)
T TIGR01661         2 SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYAR   81 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeec
Confidence            35799999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CCC
Q 040243          570 KPP  572 (797)
Q Consensus       570 ~~~  572 (797)
                      ...
T Consensus        82 ~~~   84 (352)
T TIGR01661        82 PSS   84 (352)
T ss_pred             ccc
Confidence            543

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

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

Probab=99.52  E-value=2e-12  Score=148.76  Aligned_cols=76  Identities=25%  Similarity=0.454  Sum_probs=71.0

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      .++|||||.|+.+++|+||..+|+.||+|.+|.++..      ||||||++..+++|++|+.+|+.+.+.++.|+|.||.
T Consensus       420 ~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~------R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~  493 (894)
T KOG0132|consen  420 CSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP------RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAV  493 (894)
T ss_pred             eeeeeeeccccchhhHHHHHHHHHhcccceeEeeccC------CceeEEEEeehhHHHHHHHHHhcccccceeeEEeeec
Confidence            3689999999999999999999999999999998775      4899999999999999999999999999999999986


Q ss_pred             CC
Q 040243          570 KP  571 (797)
Q Consensus       570 ~~  571 (797)
                      .+
T Consensus       494 g~  495 (894)
T KOG0132|consen  494 GK  495 (894)
T ss_pred             cC
Confidence            53

>PF00076 RRM_1: RNA recognition motif

Probab=99.49  E-value=1.2e-13  Score=115.58  Aligned_cols=70  Identities=40%  Similarity=0.796  Sum_probs=67.6

Q ss_pred             EEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEE
Q 040243          494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIA  564 (797)
Q Consensus       494 LfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~  564 (797)
                      |||+||+.++++++|+++|++||.|..+++..+ .+++.+|||||+|.+.++|++|++.|+|+.++|+.|+
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            799999999999999999999999999999998 6899999999999999999999999999999999986

(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=99.47  E-value=4e-13  Score=148.49  Aligned_cols=84  Identities=36%  Similarity=0.673  Sum_probs=78.1

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeecc--ceEEEEe
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEG--RTIAVRV  567 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~G--r~L~V~~  567 (797)
                      ..++|||+||+++++|++|+++|++||+|.+|+|++|+.|+++||||||+|.+.++|++||+.||+..|.+  +.|+|+|
T Consensus       192 ~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~  271 (346)
T TIGR01659       192 KDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRL  271 (346)
T ss_pred             ccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEE
Confidence            35689999999999999999999999999999999999999999999999999999999999999999876  6899999


Q ss_pred             cCCCCC
Q 040243          568 AGKPPQ  573 (797)
Q Consensus       568 A~~~~~  573 (797)
                      |+....
T Consensus       272 a~~~~~  277 (346)
T TIGR01659       272 AEEHGK  277 (346)
T ss_pred             CCcccc
Confidence            886543

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).

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.43  E-value=6.8e-13  Score=137.34  Aligned_cols=141  Identities=25%  Similarity=0.364  Sum_probs=98.8

Q ss_pred             CCcchHHHHHHhhhcCCCCcccccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcEEEEecC
Q 040243          420 KKMDDEYQNFLAELGGTLPESASKQSTTLALGPGSGSSGSNPPWANNSGSSGTPGHPGLGSNGAKPIKELDDTNLYIGYL  499 (797)
Q Consensus       420 ~~ld~eY~~~m~Elg~~~pe~a~ka~~~~a~g~g~gg~G~~~p~~~~~g~~g~~g~~g~g~~~~~~~~~~~~~tLfVgNL  499 (797)
                      +...+.|++|-....   .|-|+..|+...+|    ++..+.-|+.|......  +....-.-.-.+...++++||||||
T Consensus       102 KsKGYgFVSf~~k~d---AEnAI~~MnGqWlG----~R~IRTNWATRKp~e~n--~~~ltfdeV~NQssp~NtsVY~G~I  172 (321)
T KOG0148|consen  102 KSKGYGFVSFPNKED---AENAIQQMNGQWLG----RRTIRTNWATRKPSEMN--GKPLTFDEVYNQSSPDNTSVYVGNI  172 (321)
T ss_pred             cccceeEEeccchHH---HHHHHHHhCCeeec----cceeeccccccCccccC--CCCccHHHHhccCCCCCceEEeCCc
Confidence            344555555554322   22233334444443    34456667776552111  1111000000224568899999999


Q ss_pred             CCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecCCCCCCC
Q 040243          500 PPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPT  575 (797)
Q Consensus       500 p~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~~~~~~~  575 (797)
                      ...++|++|++.|+.||.|.+|+|++|+      ||+||.|++.|+|..||..+|+.+|+|..+++.|.+......
T Consensus       173 ~~~lte~~mr~~Fs~fG~I~EVRvFk~q------GYaFVrF~tkEaAahAIv~mNntei~G~~VkCsWGKe~~~~~  242 (321)
T KOG0148|consen  173 ASGLTEDLMRQTFSPFGPIQEVRVFKDQ------GYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGKEGDDGI  242 (321)
T ss_pred             CccccHHHHHHhcccCCcceEEEEeccc------ceEEEEecchhhHHHHHHHhcCceeCceEEEEeccccCCCCC
Confidence            9999999999999999999999999996      899999999999999999999999999999999988655433

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

Probab=99.43  E-value=1.8e-13  Score=127.80  Aligned_cols=81  Identities=27%  Similarity=0.421  Sum_probs=77.9

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ..++|||||||++.++|+.|.++|+++|.|.+|.+-.|+.+....|||||+|.+.++|+.|++.++|..|+.+.|+|.|.
T Consensus        34 r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D  113 (153)
T KOG0121|consen   34 RKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWD  113 (153)
T ss_pred             hhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeecc
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999999986


Q ss_pred             C
Q 040243          569 G  569 (797)
Q Consensus       569 ~  569 (797)
                      -
T Consensus       114 ~  114 (153)
T KOG0121|consen  114 A  114 (153)
T ss_pred             c
Confidence            3

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

Probab=99.43  E-value=5.8e-13  Score=155.25  Aligned_cols=84  Identities=31%  Similarity=0.603  Sum_probs=79.5

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      ..++|||+||+.++++++|+++|+.||.|.+|+|.+|+.++++||||||+|.+.++|.+||+.||++.|+|+.|+|.++.
T Consensus       203 ~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi  282 (612)
T TIGR01645       203 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  282 (612)
T ss_pred             ccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecC
Confidence            35689999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             CCCC
Q 040243          570 KPPQ  573 (797)
Q Consensus       570 ~~~~  573 (797)
                      .++.
T Consensus       283 ~pP~  286 (612)
T TIGR01645       283 TPPD  286 (612)
T ss_pred             CCcc
Confidence            6543

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

Probab=99.42  E-value=2e-13  Score=136.46  Aligned_cols=87  Identities=29%  Similarity=0.449  Sum_probs=81.7

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      +-..-++|-|-||.+.++.++|+.+|++||.|.+|+|.+|+.|++++|||||-|.+..+|+.|++.|+|.+|+|+.|+|+
T Consensus         9 dv~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq   88 (256)
T KOG4207|consen    9 DVEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQ   88 (256)
T ss_pred             CcccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeeh
Confidence            44556789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 040243          567 VAGKPPQ  573 (797)
Q Consensus       567 ~A~~~~~  573 (797)
                      +|+....
T Consensus        89 ~arygr~   95 (256)
T KOG4207|consen   89 MARYGRP   95 (256)
T ss_pred             hhhcCCC
Confidence            9976544

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=99.40  E-value=6.7e-11  Score=125.83  Aligned_cols=77  Identities=19%  Similarity=0.320  Sum_probs=70.7

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCC--CEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFG--DIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG--~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      ....+|||||-||+|++||.+.+...|  .+.+++++.++.+|++||||+|...+..+.++.++.|-.++|+|+.-.|-
T Consensus        79 rk~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~  157 (498)
T KOG4849|consen   79 RKYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVL  157 (498)
T ss_pred             ceEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeee
Confidence            345799999999999999999998876  78889999999999999999999999999999999999999999887664

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.39  E-value=1.6e-12  Score=110.02  Aligned_cols=70  Identities=33%  Similarity=0.720  Sum_probs=65.5

Q ss_pred             EEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEE
Q 040243          494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIA  564 (797)
Q Consensus       494 LfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~  564 (797)
                      |||+||++++++++|+++|+.||.|..+++..++. ++++|+|||+|.+.++|.+|++.+++..|+|+.|+
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            79999999999999999999999999999999987 99999999999999999999999999999999885

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 ....

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

Probab=99.38  E-value=1.1e-12  Score=153.04  Aligned_cols=79  Identities=34%  Similarity=0.521  Sum_probs=76.0

Q ss_pred             CcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       491 ~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      .++||||||++.+++++|+++|.+||.|.+|+|++|+.||++||||||+|.+.++|++||+.|||..|+|+.|+|.+..
T Consensus       107 ~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~  185 (612)
T TIGR01645       107 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  185 (612)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecccc
Confidence            4589999999999999999999999999999999999999999999999999999999999999999999999998654

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.37  E-value=1e-12  Score=135.99  Aligned_cols=83  Identities=42%  Similarity=0.697  Sum_probs=80.1

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      ...-||||.|...++.++|++.|.+||+|.+++|++|..|+++|||+||.|-+.++|++||+.|||..|++|.|+-.||.
T Consensus        61 ~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWAT  140 (321)
T KOG0148|consen   61 QHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWAT  140 (321)
T ss_pred             cceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeeccccc
Confidence            35679999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCC
Q 040243          570 KPP  572 (797)
Q Consensus       570 ~~~  572 (797)
                      .+.
T Consensus       141 RKp  143 (321)
T KOG0148|consen  141 RKP  143 (321)
T ss_pred             cCc
Confidence            776

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

Probab=99.35  E-value=3.3e-12  Score=135.36  Aligned_cols=81  Identities=30%  Similarity=0.450  Sum_probs=75.0

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      +..++|+|+||++...|-||+.+|++||.|++|.|+.+.  .-|||||||+|++.++|++|-++|+|..|.||+|+|..|
T Consensus        94 ~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE--RGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~A  171 (376)
T KOG0125|consen   94 DTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE--RGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNA  171 (376)
T ss_pred             CCCceeEeecCCccccCccHHHHHHhhCceeeEEEEecc--CCCCccceEEecChhhHHHHHHHhhcceeeceEEEEecc
Confidence            456789999999999999999999999999999998873  459999999999999999999999999999999999998


Q ss_pred             CCC
Q 040243          569 GKP  571 (797)
Q Consensus       569 ~~~  571 (797)
                      ...
T Consensus       172 Tar  174 (376)
T KOG0125|consen  172 TAR  174 (376)
T ss_pred             chh
Confidence            754

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

Probab=99.35  E-value=1.5e-13  Score=135.14  Aligned_cols=81  Identities=37%  Similarity=0.655  Sum_probs=77.2

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      .++.-||||||++..||.||..+|++||+|+.|.+++|+.||+|+||||+.|++..+..-|+..|||..|.||.|+|...
T Consensus        33 kdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv  112 (219)
T KOG0126|consen   33 KDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHV  112 (219)
T ss_pred             ccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeec
Confidence            46678999999999999999999999999999999999999999999999999999999999999999999999999854


Q ss_pred             C
Q 040243          569 G  569 (797)
Q Consensus       569 ~  569 (797)
                      .
T Consensus       113 ~  113 (219)
T KOG0126|consen  113 S  113 (219)
T ss_pred             c
Confidence            3

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

Probab=99.35  E-value=3e-12  Score=134.28  Aligned_cols=84  Identities=29%  Similarity=0.501  Sum_probs=79.2

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      +.-+||||+-|+.+++|..|+..|++||.|..|+|++|+.||++||||||+|.++.+...|.+..+|..|+|+.|.|.+-
T Consensus        99 DPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDvE  178 (335)
T KOG0113|consen   99 DPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDVE  178 (335)
T ss_pred             CccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEec
Confidence            45679999999999999999999999999999999999999999999999999999999999999999999999999986


Q ss_pred             CCCC
Q 040243          569 GKPP  572 (797)
Q Consensus       569 ~~~~  572 (797)
                      ....
T Consensus       179 RgRT  182 (335)
T KOG0113|consen  179 RGRT  182 (335)
T ss_pred             cccc
Confidence            5443

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

Probab=99.34  E-value=1.9e-12  Score=126.84  Aligned_cols=80  Identities=26%  Similarity=0.491  Sum_probs=74.2

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ...++||||||...+++.+|+.+|..||.|.+|.|..++     -|||||+|++..+|+.|+..|+|..|.|..|+|+++
T Consensus         8 ~~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnP-----PGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S   82 (195)
T KOG0107|consen    8 NGNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNP-----PGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELS   82 (195)
T ss_pred             CCCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecC-----CCceEEeccCcccHHHHHhhcCCccccCceEEEEee
Confidence            457899999999999999999999999999999998864     599999999999999999999999999999999998


Q ss_pred             CCCCC
Q 040243          569 GKPPQ  573 (797)
Q Consensus       569 ~~~~~  573 (797)
                      .....
T Consensus        83 ~G~~r   87 (195)
T KOG0107|consen   83 TGRPR   87 (195)
T ss_pred             cCCcc
Confidence            76554

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.33  E-value=4e-12  Score=133.59  Aligned_cols=77  Identities=16%  Similarity=0.257  Sum_probs=71.5

Q ss_pred             CcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecCC
Q 040243          491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGK  570 (797)
Q Consensus       491 ~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~~  570 (797)
                      .++|||+||++.+++++|+++|+.||.|.+|.|++|+.   .+|||||+|.+.++|+.|| .|+|..|.|+.|+|.++..
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~Al-lLnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETAL-LLSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHH-HhcCCeeCCceEEEEeccC
Confidence            56999999999999999999999999999999999864   5799999999999999999 4999999999999999764


Q ss_pred             C
Q 040243          571 P  571 (797)
Q Consensus       571 ~  571 (797)
                      -
T Consensus        80 ~   80 (260)
T PLN03120         80 Y   80 (260)
T ss_pred             C
Confidence            3

>PLN03213 repressor of silencing 3; Provisional

Probab=99.33  E-value=2.9e-12  Score=140.86  Aligned_cols=77  Identities=18%  Similarity=0.454  Sum_probs=71.5

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCH--HHHHHHHHhcCceeeccceEEEEe
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADI--QMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~--e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      ...+||||||.+.+++++|+.+|..||.|.+|.|+  +.||  ||||||+|.+.  .++.+||..|||..++|+.|+|..
T Consensus         9 ~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIp--RETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNK   84 (759)
T PLN03213          9 GGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFV--RTKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEK   84 (759)
T ss_pred             cceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEe--cccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEee
Confidence            34689999999999999999999999999999999  5577  99999999977  789999999999999999999998


Q ss_pred             cCC
Q 040243          568 AGK  570 (797)
Q Consensus       568 A~~  570 (797)
                      |+.
T Consensus        85 AKP   87 (759)
T PLN03213         85 AKE   87 (759)
T ss_pred             ccH
Confidence            865

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

Probab=99.32  E-value=3.8e-12  Score=149.36  Aligned_cols=78  Identities=35%  Similarity=0.619  Sum_probs=75.8

Q ss_pred             EEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecCC
Q 040243          493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGK  570 (797)
Q Consensus       493 tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~~  570 (797)
                      +||||||+.+++|++|+++|++||.|.+|+|.+|+.|++++|||||+|.+.++|++||+.|++..|.|+.|+|.|+..
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~   79 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQR   79 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeecccc
Confidence            799999999999999999999999999999999999999999999999999999999999999999999999999754

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

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

Probab=99.32  E-value=3.5e-12  Score=131.17  Aligned_cols=85  Identities=40%  Similarity=0.708  Sum_probs=81.3

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      +...++|.|..||.++|+++|+.+|...|+|.+|++++|+.||++.||+||.|.+.++|++||..|||..|..+.|+|+|
T Consensus        38 ~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSy  117 (360)
T KOG0145|consen   38 DESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSY  117 (360)
T ss_pred             CcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEe
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 040243          568 AGKPP  572 (797)
Q Consensus       568 A~~~~  572 (797)
                      |++..
T Consensus       118 ARPSs  122 (360)
T KOG0145|consen  118 ARPSS  122 (360)
T ss_pred             ccCCh
Confidence            98654

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

Probab=99.31  E-value=7.9e-12  Score=144.50  Aligned_cols=83  Identities=36%  Similarity=0.603  Sum_probs=78.9

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      ..++|||+||++.+++++|+++|+.||.|..+.|+++..+|+++|||||+|.+.++|..||+.|+|..|+|+.|+|.+|.
T Consensus       294 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~  373 (509)
T TIGR01642       294 SKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRAC  373 (509)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECc
Confidence            45799999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CCC
Q 040243          570 KPP  572 (797)
Q Consensus       570 ~~~  572 (797)
                      ...
T Consensus       374 ~~~  376 (509)
T TIGR01642       374 VGA  376 (509)
T ss_pred             cCC
Confidence            543

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

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

Probab=99.30  E-value=1.3e-12  Score=131.61  Aligned_cols=84  Identities=32%  Similarity=0.472  Sum_probs=80.6

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ...++||||+|...++|.-|...|-.||.|.+|.+..|.+++++||||||+|...++|.+||+.||+.+|.||.|+|.+|
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~A   87 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLA   87 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeec
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCC
Q 040243          569 GKPP  572 (797)
Q Consensus       569 ~~~~  572 (797)
                      ++..
T Consensus        88 kP~k   91 (298)
T KOG0111|consen   88 KPEK   91 (298)
T ss_pred             CCcc
Confidence            8754

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

Probab=99.29  E-value=8.4e-12  Score=142.47  Aligned_cols=80  Identities=38%  Similarity=0.659  Sum_probs=77.4

Q ss_pred             CcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecCC
Q 040243          491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGK  570 (797)
Q Consensus       491 ~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~~  570 (797)
                      .++|||+||+..+++++|+++|+.||.|..|.|+.+..+|+++|||||+|.+.++|.+||+.|||+.|.|+.|+|.|+..
T Consensus       186 ~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~  265 (457)
T TIGR01622       186 FLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQD  265 (457)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccC
Confidence            56899999999999999999999999999999999999999999999999999999999999999999999999999873

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.

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

Probab=99.29  E-value=1e-11  Score=127.37  Aligned_cols=80  Identities=35%  Similarity=0.696  Sum_probs=77.5

Q ss_pred             CcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecCC
Q 040243          491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGK  570 (797)
Q Consensus       491 ~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~~  570 (797)
                      .++|||+||++.+++++|+++|.+||.|..+.+..|+.+++++|||||+|.+.++|..|++.|++..|.|+.|+|.++..
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~~  194 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQP  194 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeecccc
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999763

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

Probab=99.28  E-value=4.6e-12  Score=119.35  Aligned_cols=89  Identities=24%  Similarity=0.420  Sum_probs=83.3

Q ss_pred             CCCCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEE
Q 040243          485 PIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIA  564 (797)
Q Consensus       485 ~~~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~  564 (797)
                      +++...+..|||.++...++|++|.+.|..||+|+.|++-.|+.||..||||+|+|++.+.|++||+.|||..|.|+.|.
T Consensus        66 PqrSVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~  145 (170)
T KOG0130|consen   66 PQRSVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVS  145 (170)
T ss_pred             CccceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCcee
Confidence            34667889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEecCCCCC
Q 040243          565 VRVAGKPPQ  573 (797)
Q Consensus       565 V~~A~~~~~  573 (797)
                      |.|+..+..
T Consensus       146 VDw~Fv~gp  154 (170)
T KOG0130|consen  146 VDWCFVKGP  154 (170)
T ss_pred             EEEEEecCC
Confidence            999865443

>smart00362 RRM_2 RNA recognition motif

Probab=99.28  E-value=1.4e-11  Score=101.57  Aligned_cols=72  Identities=42%  Similarity=0.774  Sum_probs=68.0

Q ss_pred             EEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       493 tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      +|||+||+.++++++|+++|.+||.|..+++..++  +.++|+|||+|.+.++|++|++.|++..+.|+.|+|+
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            58999999999999999999999999999999886  7889999999999999999999999999999998874

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

Probab=99.27  E-value=8.1e-12  Score=145.44  Aligned_cols=78  Identities=28%  Similarity=0.628  Sum_probs=72.3

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeec-cceEEEEec
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLE-GRTIAVRVA  568 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~-Gr~L~V~~A  568 (797)
                      ..++|||+||+++++|++|+++|++||.|.+|+|++| .+|++||||||+|.+.++|++||+.||++.|. |+.|.|.++
T Consensus        57 ~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S  135 (578)
T TIGR01648        57 RGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCIS  135 (578)
T ss_pred             CCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCcccccccc
Confidence            5689999999999999999999999999999999999 79999999999999999999999999999885 777766654

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.

>smart00360 RRM RNA recognition motif

Probab=99.26  E-value=2e-11  Score=100.20  Aligned_cols=71  Identities=38%  Similarity=0.779  Sum_probs=67.7

Q ss_pred             EecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          496 IGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       496 VgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      |+||+..+++++|+++|.+||.|..+.+..++.+++++|||||+|.+.++|.+|++.|++..++|+.|+|+
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            67999999999999999999999999999998889999999999999999999999999999999999874

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

Probab=99.25  E-value=1.9e-11  Score=139.55  Aligned_cols=83  Identities=30%  Similarity=0.468  Sum_probs=77.7

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      +...++|||+||+..+++++|+++|++||.|.+|+|++|+.+++++|||||+|.+.++|.+||. |+|..|.|+.|.|.+
T Consensus        86 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~  164 (457)
T TIGR01622        86 ERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQS  164 (457)
T ss_pred             ccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEee
Confidence            4457899999999999999999999999999999999999999999999999999999999996 899999999999998


Q ss_pred             cCCC
Q 040243          568 AGKP  571 (797)
Q Consensus       568 A~~~  571 (797)
                      +...
T Consensus       165 ~~~~  168 (457)
T TIGR01622       165 SQAE  168 (457)
T ss_pred             cchh
Confidence            6543

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

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

Probab=99.23  E-value=8.4e-12  Score=123.10  Aligned_cols=82  Identities=35%  Similarity=0.534  Sum_probs=78.9

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      .....|||||||+..++++-|.++|.+.|.|+++++.+|+.|...+|||||+|.++++|+-||+.||...|.||.|+|..
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            35678999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cC
Q 040243          568 AG  569 (797)
Q Consensus       568 A~  569 (797)
                      +.
T Consensus        86 as   87 (203)
T KOG0131|consen   86 AS   87 (203)
T ss_pred             cc
Confidence            87

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.23  E-value=3.1e-11  Score=125.17  Aligned_cols=77  Identities=16%  Similarity=0.297  Sum_probs=70.6

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      .+++|||+||++.+|+++|+++|+.||.|.+|+|++|.   +.+|||||+|.+.++|+.|| .|+|..|.++.|.|..+.
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAl-lLnGa~l~d~~I~It~~~   79 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAV-LLSGATIVDQRVCITRWG   79 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHH-hcCCCeeCCceEEEEeCc
Confidence            46799999999999999999999999999999999984   45689999999999999999 699999999999998755


Q ss_pred             C
Q 040243          570 K  570 (797)
Q Consensus       570 ~  570 (797)
                      .
T Consensus        80 ~   80 (243)
T PLN03121         80 Q   80 (243)
T ss_pred             c
Confidence            3

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

Probab=99.23  E-value=1.7e-11  Score=134.34  Aligned_cols=80  Identities=28%  Similarity=0.598  Sum_probs=75.6

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeec-cceEEEEe
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLE-GRTIAVRV  567 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~-Gr~L~V~~  567 (797)
                      ..++.||||.||.++.|++|.-+|++.|+|-+++|++|+.+|.+||||||+|.+.+.|++||+.||+++|. |+.|.|++
T Consensus        81 ~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~  160 (506)
T KOG0117|consen   81 PRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCV  160 (506)
T ss_pred             CCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEE
Confidence            45778999999999999999999999999999999999999999999999999999999999999999885 88898876


Q ss_pred             c
Q 040243          568 A  568 (797)
Q Consensus       568 A  568 (797)
                      +
T Consensus       161 S  161 (506)
T KOG0117|consen  161 S  161 (506)
T ss_pred             e
Confidence            5

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

Probab=99.20  E-value=2.5e-11  Score=136.73  Aligned_cols=81  Identities=30%  Similarity=0.628  Sum_probs=78.6

Q ss_pred             cEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecCCC
Q 040243          492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKP  571 (797)
Q Consensus       492 ~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~~~  571 (797)
                      +.||||||++.++|++|.++|+..|.|.+++++.|+.||+.|||||++|.+.++|++|++.|||.++.|++|+|.|+...
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            78999999999999999999999999999999999999999999999999999999999999999999999999998765


Q ss_pred             C
Q 040243          572 P  572 (797)
Q Consensus       572 ~  572 (797)
                      .
T Consensus        99 ~   99 (435)
T KOG0108|consen   99 K   99 (435)
T ss_pred             c
Confidence            4

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

Probab=99.20  E-value=6.5e-11  Score=122.00  Aligned_cols=82  Identities=37%  Similarity=0.580  Sum_probs=78.0

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      .++.|||-||..+++|.-|..+|..||.|..|+|++|..|.++|||+||++.+.++|..||..|||+.+++|.|.|.|..
T Consensus       277 ~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFKt  356 (360)
T KOG0145|consen  277 GGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKT  356 (360)
T ss_pred             CeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEec
Confidence            35689999999999999999999999999999999999999999999999999999999999999999999999999865


Q ss_pred             CC
Q 040243          570 KP  571 (797)
Q Consensus       570 ~~  571 (797)
                      .+
T Consensus       357 nk  358 (360)
T KOG0145|consen  357 NK  358 (360)
T ss_pred             CC
Confidence            43

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

Probab=99.19  E-value=1.8e-11  Score=126.46  Aligned_cols=87  Identities=36%  Similarity=0.581  Sum_probs=82.2

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      +..++|+|||-.|+.+..+.+|..+|..||.|++.+|+.|+.|++||+|+||.|++..+|+.||..|||+.|+-++|+|.
T Consensus       281 eGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQ  360 (371)
T KOG0146|consen  281 EGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQ  360 (371)
T ss_pred             cCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhh
Confidence            34578999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 040243          567 VAGKPPQ  573 (797)
Q Consensus       567 ~A~~~~~  573 (797)
                      +.+++..
T Consensus       361 LKRPkda  367 (371)
T KOG0146|consen  361 LKRPKDA  367 (371)
T ss_pred             hcCcccc
Confidence            9776654

>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=99.17  E-value=1.5e-10  Score=95.93  Aligned_cols=74  Identities=36%  Similarity=0.759  Sum_probs=69.5

Q ss_pred             EEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       493 tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      +|||+||+.++++++|+++|..||.|..+.+..+..+ ..+|+|||+|.+.++|..|++.+++..+.|+.|.|.+
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            4899999999999999999999999999999988754 7899999999999999999999999999999999875

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).

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

Probab=99.16  E-value=2.3e-11  Score=132.70  Aligned_cols=83  Identities=30%  Similarity=0.632  Sum_probs=76.2

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCcee-ecc--ceEEEE
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYR-LEG--RTIAVR  566 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~-l~G--r~L~V~  566 (797)
                      +.++||||-|+..++|++++++|++||.|.+|+|++|. .+.|||||||+|.+++.|..||+.|||.. +.|  ..|.|+
T Consensus       123 ~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~-~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVk  201 (510)
T KOG0144|consen  123 EERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDP-DGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVK  201 (510)
T ss_pred             cchhhhhhhccccccHHHHHHHHHhhCccchhhheecc-cccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEE
Confidence            57899999999999999999999999999999999996 79999999999999999999999999964 544  679999


Q ss_pred             ecCCCCC
Q 040243          567 VAGKPPQ  573 (797)
Q Consensus       567 ~A~~~~~  573 (797)
                      ||..+..
T Consensus       202 FADtqkd  208 (510)
T KOG0144|consen  202 FADTQKD  208 (510)
T ss_pred             ecccCCC
Confidence            9987654

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

Probab=99.15  E-value=6.3e-10  Score=122.19  Aligned_cols=78  Identities=29%  Similarity=0.466  Sum_probs=72.3

Q ss_pred             CcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecCC
Q 040243          491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGK  570 (797)
Q Consensus       491 ~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~~  570 (797)
                      -.-|||.||..++||+.|+++|.+||.|.+|+.++|        ||||+|.++++|.+|++.+||++|+|..|.|.+|++
T Consensus       259 VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD--------YaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP  330 (506)
T KOG0117|consen  259 VKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD--------YAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKP  330 (506)
T ss_pred             eeeeeeeccchhhhHHHHHHHHHhccceEEeecccc--------eeEEeecchHHHHHHHHHhcCceecCceEEEEecCC
Confidence            457999999999999999999999999999998876        999999999999999999999999999999999998


Q ss_pred             CCCCCC
Q 040243          571 PPQPTV  576 (797)
Q Consensus       571 ~~~~~~  576 (797)
                      ......
T Consensus       331 ~~k~k~  336 (506)
T KOG0117|consen  331 VDKKKK  336 (506)
T ss_pred             hhhhcc
Confidence            765443

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

Probab=99.14  E-value=7.7e-11  Score=128.66  Aligned_cols=86  Identities=31%  Similarity=0.546  Sum_probs=76.4

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCce-eecc--ceE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGY-RLEG--RTI  563 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~-~l~G--r~L  563 (797)
                      .+.+.-+||||.|+..++|.||+++|++||.|.+|.|++||.|+.++|||||.|.++++|.+||..|+.. +|-|  ..|
T Consensus        30 ~d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pv  109 (510)
T KOG0144|consen   30 PDGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPV  109 (510)
T ss_pred             CCchhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcce
Confidence            4466789999999999999999999999999999999999999999999999999999999999999765 4543  668


Q ss_pred             EEEecCCCC
Q 040243          564 AVRVAGKPP  572 (797)
Q Consensus       564 ~V~~A~~~~  572 (797)
                      .|++|....
T Consensus       110 qvk~Ad~E~  118 (510)
T KOG0144|consen  110 QVKYADGER  118 (510)
T ss_pred             eecccchhh
Confidence            888886543

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

Probab=99.12  E-value=4.4e-11  Score=133.31  Aligned_cols=122  Identities=30%  Similarity=0.501  Sum_probs=102.0

Q ss_pred             CcchHHHHHHhhhcCCCCcccccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcEEEEecCC
Q 040243          421 KMDDEYQNFLAELGGTLPESASKQSTTLALGPGSGSSGSNPPWANNSGSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLP  500 (797)
Q Consensus       421 ~ld~eY~~~m~Elg~~~pe~a~ka~~~~a~g~g~gg~G~~~p~~~~~g~~g~~g~~g~g~~~~~~~~~~~~~tLfVgNLp  500 (797)
                      .+.+.|++|..      +++|++|+.+++..... +.-...+|+.+...                       .|||.||+
T Consensus        36 slgy~yvnf~~------~~da~~A~~~~n~~~~~-~~~~rim~s~rd~~-----------------------~~~i~nl~   85 (369)
T KOG0123|consen   36 SLGYAYVNFQQ------PADAERALDTMNFDVLK-GKPIRIMWSQRDPS-----------------------LVFIKNLD   85 (369)
T ss_pred             ccceEEEecCC------HHHHHHHHHHcCCcccC-CcEEEeehhccCCc-----------------------eeeecCCC
Confidence            46777888775      66788888888876554 23346677776543                       19999999


Q ss_pred             CCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecCCCCCCC
Q 040243          501 PTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPT  575 (797)
Q Consensus       501 ~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~~~~~~~  575 (797)
                      ..++..+|.++|+.||.|++|+|..|. +| +||| ||+|+++++|.+||+.|||..+.+++|.|.....+....
T Consensus        86 ~~~~~~~~~d~f~~~g~ilS~kv~~~~-~g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~er~  157 (369)
T KOG0123|consen   86 ESIDNKSLYDTFSEFGNILSCKVATDE-NG-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKEERE  157 (369)
T ss_pred             cccCcHHHHHHHHhhcCeeEEEEEEcC-CC-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchhhhc
Confidence            999999999999999999999999997 56 9999 999999999999999999999999999998877655433

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

Probab=99.12  E-value=1.9e-10  Score=132.81  Aligned_cols=79  Identities=24%  Similarity=0.379  Sum_probs=72.9

Q ss_pred             CCCcEEEEecCCC-CCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          489 LDDTNLYIGYLPP-TLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       489 ~~~~tLfVgNLp~-~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      ...++|||+||++ .+++++|+++|+.||.|.+|+|++++     +|||||+|.+.++|++||+.|||..|.|+.|+|.+
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            3568999999998 69999999999999999999999874     69999999999999999999999999999999999


Q ss_pred             cCCCC
Q 040243          568 AGKPP  572 (797)
Q Consensus       568 A~~~~  572 (797)
                      ++...
T Consensus       348 s~~~~  352 (481)
T TIGR01649       348 SKQQN  352 (481)
T ss_pred             ccccc
Confidence            86543

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).

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

Probab=99.10  E-value=2.3e-10  Score=133.48  Aligned_cols=76  Identities=32%  Similarity=0.476  Sum_probs=69.8

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcC--CCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTF--GDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~f--G~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      ..++|||+||++++++++|+++|++|  |.|.+|++++        +||||+|.+.++|++||+.||+..|+|+.|+|+|
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            34689999999999999999999999  9999998754        5999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 040243          568 AGKPPQ  573 (797)
Q Consensus       568 A~~~~~  573 (797)
                      |+....
T Consensus       304 Akp~~~  309 (578)
T TIGR01648       304 AKPVDK  309 (578)
T ss_pred             ccCCCc
Confidence            986543

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.

>smart00361 RRM_1 RNA recognition motif

Probab=99.08  E-value=3e-10  Score=97.18  Aligned_cols=62  Identities=27%  Similarity=0.500  Sum_probs=57.1

Q ss_pred             HHHHHHHhh----cCCCEEEEE-EEecCCC--CcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          505 DDGLIRLFS----TFGDIVMAK-VIKDRVT--GMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       505 e~dL~~~Fs----~fG~I~~v~-v~~dk~T--GksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      +++|+++|+    +||.|.+|. |+.++.+  +.+||||||+|.+.++|.+|++.|||..++|+.|+++
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~~   70 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKAE   70 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEeC
Confidence            578889998    999999995 8888777  9999999999999999999999999999999999873

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

Probab=99.07  E-value=1.6e-10  Score=120.95  Aligned_cols=76  Identities=32%  Similarity=0.653  Sum_probs=71.5

Q ss_pred             cEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecCCC
Q 040243          492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKP  571 (797)
Q Consensus       492 ~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~~~  571 (797)
                      .+||||||+..+++.+|+.+|++||.|++|.|+++        ||||+.++...|+.||..|+|+.|+|..|+|+-++.+
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            37999999999999999999999999999999987        9999999999999999999999999999999999887


Q ss_pred             CCCC
Q 040243          572 PQPT  575 (797)
Q Consensus       572 ~~~~  575 (797)
                      ....
T Consensus        75 sk~s   78 (346)
T KOG0109|consen   75 SKAS   78 (346)
T ss_pred             CCCc
Confidence            5444

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

Probab=99.06  E-value=3.3e-10  Score=126.66  Aligned_cols=81  Identities=28%  Similarity=0.460  Sum_probs=75.4

Q ss_pred             CcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecCC
Q 040243          491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGK  570 (797)
Q Consensus       491 ~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~~  570 (797)
                      ..+|.|+||||.+.+.+|+.+|+.||.|.+|.|.+.+. |+-+|||||.|....+|..||+.+|+..|+||.|-|.||-.
T Consensus       117 k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~d-gklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~  195 (678)
T KOG0127|consen  117 KWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKD-GKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVD  195 (678)
T ss_pred             cceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCC-CCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeecc
Confidence            78999999999999999999999999999999998775 55559999999999999999999999999999999999976


Q ss_pred             CC
Q 040243          571 PP  572 (797)
Q Consensus       571 ~~  572 (797)
                      +.
T Consensus       196 Kd  197 (678)
T KOG0127|consen  196 KD  197 (678)
T ss_pred             cc
Confidence            54

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

Probab=99.04  E-value=3.1e-10  Score=112.11  Aligned_cols=80  Identities=23%  Similarity=0.450  Sum_probs=70.7

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      ..++|||||||.++.+.+|+++|.+||.|.+|.|-.-+   ..-.||||+|++..+|+.||..-+|+.++|.+|+|+|+.
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~---g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfpr   81 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRP---GPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPR   81 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCC---CCCCeeEEEecCccchhhhhhcccccccCcceEEEEecc
Confidence            56799999999999999999999999999999863322   235799999999999999999999999999999999987


Q ss_pred             CCC
Q 040243          570 KPP  572 (797)
Q Consensus       570 ~~~  572 (797)
                      ...
T Consensus        82 ggr   84 (241)
T KOG0105|consen   82 GGR   84 (241)
T ss_pred             CCC
Confidence            543

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

Probab=99.04  E-value=6.8e-10  Score=100.64  Aligned_cols=78  Identities=27%  Similarity=0.462  Sum_probs=71.2

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ...+-|||.|||+++|.++..++|.+||.|..|+|-..+.   .||-|||+|++..+|.+|++.|+|+.++++-|.|-+-
T Consensus        16 evnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~---TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyy   92 (124)
T KOG0114|consen   16 EVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKE---TRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYY   92 (124)
T ss_pred             hhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccC---cCceEEEEehHhhhHHHHHHHhcccccCCceEEEEec
Confidence            3467899999999999999999999999999999977654   5899999999999999999999999999999999765


Q ss_pred             C
Q 040243          569 G  569 (797)
Q Consensus       569 ~  569 (797)
                      .
T Consensus        93 q   93 (124)
T KOG0114|consen   93 Q   93 (124)
T ss_pred             C
Confidence            4

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

Probab=99.03  E-value=1.7e-10  Score=123.37  Aligned_cols=77  Identities=35%  Similarity=0.546  Sum_probs=74.5

Q ss_pred             cEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       492 ~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      |+||||.|.+.+.|+.|+..|..||.|++|.+..|..|+++||||||+|+-.+.|+.|++.|||.+++||.|+|..-
T Consensus       114 cRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrP  190 (544)
T KOG0124|consen  114 CRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  190 (544)
T ss_pred             HheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCC
Confidence            57999999999999999999999999999999999999999999999999999999999999999999999999743

>PF13893 RRM_5: RNA recognition motif

Probab=99.02  E-value=8.1e-10  Score=90.01  Aligned_cols=56  Identities=38%  Similarity=0.770  Sum_probs=51.4

Q ss_pred             HHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          508 LIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       508 L~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      |+++|++||.|.++.+..++     +++|||+|.+.++|++|++.|||..++|+.|+|+||
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            78999999999999997764     689999999999999999999999999999999986

(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 ....

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

Probab=99.02  E-value=7.4e-10  Score=127.99  Aligned_cols=75  Identities=13%  Similarity=0.240  Sum_probs=68.7

Q ss_pred             CcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHh--cCceeeccceEEEEec
Q 040243          491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS--MNGYRLEGRTIAVRVA  568 (797)
Q Consensus       491 ~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~--LnG~~l~Gr~L~V~~A  568 (797)
                      .++|||+||++.+++++|+++|++||.|.+|+|+++      ||||||+|.+.++|++||+.  +++..|+|+.|+|.|+
T Consensus         2 s~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~------k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s   75 (481)
T TIGR01649         2 SPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPG------KRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYS   75 (481)
T ss_pred             ccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECC------CCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEec
Confidence            468999999999999999999999999999999864      48999999999999999986  4788999999999999


Q ss_pred             CCC
Q 040243          569 GKP  571 (797)
Q Consensus       569 ~~~  571 (797)
                      ..+
T Consensus        76 ~~~   78 (481)
T TIGR01649        76 TSQ   78 (481)
T ss_pred             CCc
Confidence            754

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).

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

Probab=99.00  E-value=4.1e-10  Score=111.33  Aligned_cols=86  Identities=38%  Similarity=0.622  Sum_probs=80.2

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEE-EEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMA-KVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v-~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      .+.+|||+||.+.++|..|.++|+.||.|.+. ++++|..||.++|||||.|++.+.+.+||+.|||..+..+++.|.++
T Consensus        95 vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~ya  174 (203)
T KOG0131|consen   95 VGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVSYA  174 (203)
T ss_pred             ccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEEEE
Confidence            34789999999999999999999999988875 89999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCC
Q 040243          569 GKPPQPT  575 (797)
Q Consensus       569 ~~~~~~~  575 (797)
                      .++....
T Consensus       175 ~k~~~kg  181 (203)
T KOG0131|consen  175 FKKDTKG  181 (203)
T ss_pred             EecCCCc
Confidence            8876655

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

Probab=99.00  E-value=3.5e-10  Score=127.07  Aligned_cols=78  Identities=37%  Similarity=0.667  Sum_probs=74.7

Q ss_pred             EEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecCCC
Q 040243          494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKP  571 (797)
Q Consensus       494 LfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~~~  571 (797)
                      ||||||.+++++++|+.+|+.||.|..|.+.+|..||++|||+||+|.+.++|.+|++.|||++|.|+.|+|......
T Consensus       281 l~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r  358 (549)
T KOG0147|consen  281 LYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTER  358 (549)
T ss_pred             hhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeee
Confidence            999999999999999999999999999999999999999999999999999999999999999999999999875543

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

Probab=98.99  E-value=5.4e-10  Score=124.97  Aligned_cols=86  Identities=27%  Similarity=0.448  Sum_probs=81.1

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      ++.||||++|++.++.++|.++|+.+|.|..+.++.++.++.+|||+||+|.-.+++++|+..+++..|+|+.|+|.+|.
T Consensus         4 ~g~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~   83 (678)
T KOG0127|consen    4 SGATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAK   83 (678)
T ss_pred             CCceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceeccccccc
Confidence            44799999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCCCC
Q 040243          570 KPPQPT  575 (797)
Q Consensus       570 ~~~~~~  575 (797)
                      ...+..
T Consensus        84 ~R~r~e   89 (678)
T KOG0127|consen   84 KRARSE   89 (678)
T ss_pred             ccccch
Confidence            766543

>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH)

Probab=98.97  E-value=1.8e-09  Score=90.39  Aligned_cols=59  Identities=39%  Similarity=0.561  Sum_probs=52.5

Q ss_pred             EEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHHHH
Q 040243          252 QKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESL  331 (797)
Q Consensus       252 ~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v  331 (797)
                      .+.|.||.      +++|+|||++|.|+|+||++|||+|.|...|                       .|.|+|.+.+++
T Consensus         3 ~~~i~Ip~------~~ig~iIGkgG~~ik~I~~~tg~~I~i~~~g-----------------------~v~I~G~~~~~v   53 (61)
T cd02393           3 IETMKIPP------DKIRDVIGPGGKTIKKIIEETGVKIDIEDDG-----------------------TVYIAASDKEAA   53 (61)
T ss_pred             EEEEEeCh------hheeeeECCCchHHHHHHHHHCCEEEeCCCC-----------------------EEEEEeCCHHHH
Confidence            45677998      9999999999999999999999999987422                       699999999999


Q ss_pred             HHHHHHHH
Q 040243          332 EGAAAMVE  339 (797)
Q Consensus       332 ~~A~~~I~  339 (797)
                      ++|.++|+
T Consensus        54 ~~A~~~I~   61 (61)
T cd02393          54 EKAKKMIE   61 (61)
T ss_pred             HHHHHHhC
Confidence            99999884

PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=98.95  E-value=2.7e-09  Score=126.20  Aligned_cols=97  Identities=30%  Similarity=0.483  Sum_probs=88.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCCCCCCCCCCceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccc
Q 040243          217 RARERLNKERQEIISQIIKRNPAFKPPADYRPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKG  296 (797)
Q Consensus       217 r~~~~le~er~~li~~~~~~~p~~~pp~dy~p~~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkG  296 (797)
                      ++.++-.+-|.+|++.|.+.+......++|.|+..+.+  |+.      +.||.||||+|+|+|.|+++|||+|.|...|
T Consensus       546 ~aL~~A~~g~~~Il~~m~~al~~p~~~s~~aP~~~~~~--I~~------~ki~~vIG~gGk~I~~i~~~tg~~Idi~d~G  617 (719)
T TIGR02696       546 SALKQARDARLAILDVMAEAIDTPDEMSPYAPRIITVK--IPV------DKIGEVIGPKGKMINQIQDETGAEISIEDDG  617 (719)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCccccccCCCeeEEEE--eCh------HHhhheeCCCcHhHHHHHHHHCCEEEEecCc
Confidence            56677788899999999998887766899999988877  887      8999999999999999999999999999877


Q ss_pred             cccccccccccCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHhcCC
Q 040243          297 SVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQP  344 (797)
Q Consensus       297 S~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v~~A~~~I~~ll~~  344 (797)
                                             +|.|+|.+.+++++|+++|+.|+..
T Consensus       618 -----------------------~V~I~a~d~~~~~~A~~~I~~i~~~  642 (719)
T TIGR02696       618 -----------------------TVYIGAADGPSAEAARAMINAIANP  642 (719)
T ss_pred             -----------------------EEEEEeCCHHHHHHHHHHHHHhhCc
Confidence                                   8999999999999999999999984

Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.

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

Probab=98.86  E-value=4.3e-09  Score=106.16  Aligned_cols=82  Identities=24%  Similarity=0.455  Sum_probs=75.2

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcC-CCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTF-GDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~f-G~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      ....-+||..++..+.+..|..+|.+| |.|.++++.+++.||.|||||||+|++.+.|+-|.+.||++.|.++.|.|.+
T Consensus        47 ~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~v  126 (214)
T KOG4208|consen   47 EIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHV  126 (214)
T ss_pred             CCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEE
Confidence            344569999999999999999999998 7888889999999999999999999999999999999999999999999987


Q ss_pred             cCC
Q 040243          568 AGK  570 (797)
Q Consensus       568 A~~  570 (797)
                      --+
T Consensus       127 mpp  129 (214)
T KOG4208|consen  127 MPP  129 (214)
T ss_pred             eCc
Confidence            543

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

Probab=98.86  E-value=5.1e-09  Score=107.10  Aligned_cols=80  Identities=29%  Similarity=0.538  Sum_probs=73.8

Q ss_pred             CcEEEEecCCCCCcHHHHHH----HhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          491 DTNLYIGYLPPTLDDDGLIR----LFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       491 ~~tLfVgNLp~~vte~dL~~----~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      ..||||.||++.+..++|+.    +|++||.|++|...+   |.+.||-|||+|.+.+.|-.|++.|+|+.+.|+.++|.
T Consensus         9 n~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k---t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriq   85 (221)
T KOG4206|consen    9 NGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK---TPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQ   85 (221)
T ss_pred             CceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC---CCCccCceEEEecChhHHHHHHHHhcCCcccCchhhee
Confidence            34999999999999998887    999999999998765   67899999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 040243          567 VAGKPPQ  573 (797)
Q Consensus       567 ~A~~~~~  573 (797)
                      ||+.+..
T Consensus        86 yA~s~sd   92 (221)
T KOG4206|consen   86 YAKSDSD   92 (221)
T ss_pred             cccCccc
Confidence            9988764

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

Probab=98.85  E-value=9.4e-09  Score=112.48  Aligned_cols=77  Identities=22%  Similarity=0.475  Sum_probs=71.9

Q ss_pred             CcEEEEecCCCCCcHHHHHHHhhc-CCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          491 DTNLYIGYLPPTLDDDGLIRLFST-FGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       491 ~~tLfVgNLp~~vte~dL~~~Fs~-fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      .+.+||.||++++.|.+|+++|.. .|+|..|.++.|. +|++||||.|+|++++.+++|++.||.+.+.||.|+|+-.
T Consensus        44 ~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~-~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd  121 (608)
T KOG4212|consen   44 DRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDE-SGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKED  121 (608)
T ss_pred             cceEEEecCcchhhhHhHHHHHHHhcCceEeeeeeccc-CCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEecc
Confidence            345999999999999999999975 7999999999996 8999999999999999999999999999999999999743

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

Probab=98.85  E-value=8.1e-09  Score=112.99  Aligned_cols=77  Identities=31%  Similarity=0.433  Sum_probs=70.9

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      ..+..++|||.|||+++||+.|++-|..||.|..+.|+.   +|++||  .|.|.+.++|++|+..|+|..|+||.|+|.
T Consensus       532 aarKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadime---~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I~V~  606 (608)
T KOG4212|consen  532 AARKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIME---NGKSKG--VVRFFSPEDAERACALMNGSRLDGRNIKVT  606 (608)
T ss_pred             ccccccEEEEecCCccccHHHHHHHHHhccceehhhhhc---cCCccc--eEEecCHHHHHHHHHHhccCcccCceeeee
Confidence            456789999999999999999999999999999998843   688888  899999999999999999999999999998


Q ss_pred             ec
Q 040243          567 VA  568 (797)
Q Consensus       567 ~A  568 (797)
                      |+
T Consensus       607 y~  608 (608)
T KOG4212|consen  607 YF  608 (608)
T ss_pred             eC
Confidence            74

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

Probab=98.82  E-value=4.6e-09  Score=110.30  Aligned_cols=80  Identities=23%  Similarity=0.474  Sum_probs=73.9

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ...++|+||||.+.++..+|++.|.+||.|.+|+|++|        |+||+|+-.++|..||+.|++.+|.|++|+|.++
T Consensus        76 k~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd--------y~fvh~d~~eda~~air~l~~~~~~gk~m~vq~s  147 (346)
T KOG0109|consen   76 KASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD--------YAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLS  147 (346)
T ss_pred             CCccccccCCCCccccCHHHhhhhcccCCceeeeeecc--------eeEEEEeeccchHHHHhcccccccccceeeeeee
Confidence            45679999999999999999999999999999999886        9999999999999999999999999999999998


Q ss_pred             CCCCCCCC
Q 040243          569 GKPPQPTV  576 (797)
Q Consensus       569 ~~~~~~~~  576 (797)
                      ...-+..+
T Consensus       148 tsrlrtap  155 (346)
T KOG0109|consen  148 TSRLRTAP  155 (346)
T ss_pred             ccccccCC
Confidence            87655443

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=98.81  E-value=9.1e-09  Score=123.28  Aligned_cols=96  Identities=30%  Similarity=0.377  Sum_probs=87.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHhCCCC-CCCCCCCCCceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEecc
Q 040243          217 RARERLNKERQEIISQIIKRNPAF-KPPADYRPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGK  295 (797)
Q Consensus       217 r~~~~le~er~~li~~~~~~~p~~-~pp~dy~p~~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGk  295 (797)
                      ++.++-.+.|.+|++.|.+.+..+ ...++|.|+..+.+  ||.      ++||.||||+|+|+|.|+++|||+|.|...
T Consensus       518 ~al~~a~~~~~~I~~~m~~~l~~~~~~~~~~~p~~~~~~--I~~------~kI~~vIG~gGk~Ik~I~~~tg~~I~i~dd  589 (684)
T TIGR03591       518 QALEQAKEGRLHILGEMNKVISEPRAELSPYAPRIETIK--INP------DKIRDVIGPGGKVIREITEETGAKIDIEDD  589 (684)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhhccccccCCeEEEEe--cCH------HHHHhhcCCCcHHHHHHHHHHCCEEEEecC
Confidence            566677788999999999999999 56999999998888  887      899999999999999999999999999987


Q ss_pred             ccccccccccccCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHhcC
Q 040243          296 GSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQ  343 (797)
Q Consensus       296 GS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v~~A~~~I~~ll~  343 (797)
                      |                       +|.|.+.+.+.+++|.++|+.+..
T Consensus       590 G-----------------------~V~i~~~~~~~~~~a~~~I~~~~~  614 (684)
T TIGR03591       590 G-----------------------TVKIAASDGEAAEAAIKMIEGITA  614 (684)
T ss_pred             e-----------------------EEEEEECcHHHHHHHHHHHHhhhc
Confidence            7                       899999999999999999999865

Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).

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

Probab=98.80  E-value=1.4e-08  Score=109.09  Aligned_cols=82  Identities=21%  Similarity=0.400  Sum_probs=73.3

Q ss_pred             CCCCCCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHH-hcCceeeccc
Q 040243          483 AKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA-SMNGYRLEGR  561 (797)
Q Consensus       483 ~~~~~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~-~LnG~~l~Gr  561 (797)
                      ..+.++....+|||++|...++|.+|+++|.+||+|.++.++..+      ++|||+|.++++|+.|.+ .++...|+|+
T Consensus       220 lepPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~~------~CAFv~ftTR~aAE~Aae~~~n~lvI~G~  293 (377)
T KOG0153|consen  220 LEPPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPRK------GCAFVTFTTREAAEKAAEKSFNKLVINGF  293 (377)
T ss_pred             cCCCcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeeccc------ccceeeehhhHHHHHHHHhhcceeeecce
Confidence            445678889999999999999999999999999999999987764      699999999999999887 4566679999


Q ss_pred             eEEEEecCC
Q 040243          562 TIAVRVAGK  570 (797)
Q Consensus       562 ~L~V~~A~~  570 (797)
                      +|+|.|+..
T Consensus       294 Rl~i~Wg~~  302 (377)
T KOG0153|consen  294 RLKIKWGRP  302 (377)
T ss_pred             EEEEEeCCC
Confidence            999999987

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=98.79  E-value=6.1e-09  Score=125.63  Aligned_cols=99  Identities=26%  Similarity=0.355  Sum_probs=89.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCC-CCCCCCCCceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcE-EEEec
Q 040243          217 RARERLNKERQEIISQIIKRNPAFK-PPADYRPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAK-IVIRG  294 (797)
Q Consensus       217 r~~~~le~er~~li~~~~~~~p~~~-pp~dy~p~~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgak-I~IrG  294 (797)
                      .+.++-.+.|.+|++.|.+.++..+ ..++|.|+..+.+  |+.      +.||.||||+|+|||.|++|||++ |.|+.
T Consensus       652 eAL~~A~~g~~~Il~~M~~~i~~pr~~~s~~aP~i~~~~--i~~------~ki~~vIG~GGktIk~I~eetg~~~Idi~d  723 (891)
T PLN00207        652 RALLQAKDGRKHILAEMSKCSPPPSKRLSKYAPLIHIMK--VKP------EKVNMIIGSGGKKVKSIIEETGVEAIDTQD  723 (891)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhhhhhcccCCeeEEEE--cCH------HHHHHHhcCCchhHHHHHHHHCCCccCcCC
Confidence            4666777889999999999999995 5999999999888  787      999999999999999999999999 99997


Q ss_pred             cccccccccccccCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHhcCCCh
Q 040243          295 KGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQPVD  346 (797)
Q Consensus       295 kGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v~~A~~~I~~ll~~~~  346 (797)
                      .|                       +|.|.+.+.+++++|+++|+.|+....
T Consensus       724 dg-----------------------~V~I~a~d~~~i~~A~~~I~~l~~~~~  752 (891)
T PLN00207        724 DG-----------------------TVKITAKDLSSLEKSKAIISSLTMVPT  752 (891)
T ss_pred             Ce-----------------------eEEEEeCCHHHHHHHHHHHHHHhcCcC
Confidence            76                       899999999999999999999987543

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

Probab=98.79  E-value=2.2e-08  Score=112.17  Aligned_cols=83  Identities=30%  Similarity=0.435  Sum_probs=77.8

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      ...+++|||.+|...+...||+.+|++||.|+-.+|+.+..+--.|+|+||++.+.++|.+||+.|+..+|+|+.|.|+.
T Consensus       402 s~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEk  481 (940)
T KOG4661|consen  402 STLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEK  481 (940)
T ss_pred             cccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeee
Confidence            44678999999999999999999999999999999999988888899999999999999999999999999999999988


Q ss_pred             cCC
Q 040243          568 AGK  570 (797)
Q Consensus       568 A~~  570 (797)
                      ++.
T Consensus       482 aKN  484 (940)
T KOG4661|consen  482 AKN  484 (940)
T ss_pred             ccc
Confidence            765

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

Probab=98.78  E-value=8e-09  Score=110.63  Aligned_cols=83  Identities=30%  Similarity=0.508  Sum_probs=78.4

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      ..+-|||--|++-++++||.-+|+.||.|.+|.|++|+.||.+..||||+|++.+++++|.-+|+...|+.++|.|.|+.
T Consensus       238 PeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDFSQ  317 (479)
T KOG0415|consen  238 PENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDFSQ  317 (479)
T ss_pred             CcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeehhh
Confidence            45689999999999999999999999999999999999999999999999999999999999999999999999999876


Q ss_pred             CCC
Q 040243          570 KPP  572 (797)
Q Consensus       570 ~~~  572 (797)
                      .-.
T Consensus       318 SVs  320 (479)
T KOG0415|consen  318 SVS  320 (479)
T ss_pred             hhh
Confidence            433

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

Probab=98.78  E-value=4.7e-09  Score=113.98  Aligned_cols=82  Identities=28%  Similarity=0.518  Sum_probs=75.0

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      +.++||||+|+|.++++.|++.|.+||+|.+|.+++|+.|+++|||+||+|++.+...++|. ..-+.|+|+.|.++.|.
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            67899999999999999999999999999999999999999999999999999999998885 45677999999988876


Q ss_pred             CCC
Q 040243          570 KPP  572 (797)
Q Consensus       570 ~~~  572 (797)
                      +..
T Consensus        84 ~r~   86 (311)
T KOG4205|consen   84 SRE   86 (311)
T ss_pred             Ccc
Confidence            654

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

Probab=98.73  E-value=2.6e-08  Score=115.33  Aligned_cols=76  Identities=14%  Similarity=0.423  Sum_probs=63.0

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcC------------CCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcC
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTF------------GDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMN  554 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~f------------G~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~Ln  554 (797)
                      .....++||||||++.+++++|+++|..|            +.|..+.+      ++.+|||||+|.+.++|..|| .|+
T Consensus       171 ~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~------~~~kg~afVeF~~~e~A~~Al-~l~  243 (509)
T TIGR01642       171 ATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI------NKEKNFAFLEFRTVEEATFAM-ALD  243 (509)
T ss_pred             CCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEE------CCCCCEEEEEeCCHHHHhhhh-cCC
Confidence            34567899999999999999999999975            23333433      456799999999999999999 599


Q ss_pred             ceeeccceEEEEecC
Q 040243          555 GYRLEGRTIAVRVAG  569 (797)
Q Consensus       555 G~~l~Gr~L~V~~A~  569 (797)
                      |..|.|+.|+|....
T Consensus       244 g~~~~g~~l~v~r~~  258 (509)
T TIGR01642       244 SIIYSNVFLKIRRPH  258 (509)
T ss_pred             CeEeeCceeEecCcc
Confidence            999999999997543

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

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

Probab=98.72  E-value=2.8e-08  Score=106.72  Aligned_cols=84  Identities=31%  Similarity=0.603  Sum_probs=78.7

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      .-++|||..+..+.+|+||+.+|+.||+|++|.+.++..++.+|||+|++|.+..+...||..||-+.|+|+-|+|..+.
T Consensus       209 ~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~v  288 (544)
T KOG0124|consen  209 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  288 (544)
T ss_pred             hhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEeccccc
Confidence            45799999999999999999999999999999999999999999999999999999999999999999999999998776


Q ss_pred             CCCC
Q 040243          570 KPPQ  573 (797)
Q Consensus       570 ~~~~  573 (797)
                      .++.
T Consensus       289 TPP~  292 (544)
T KOG0124|consen  289 TPPD  292 (544)
T ss_pred             CCCc
Confidence            5543

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

Probab=98.69  E-value=1.7e-08  Score=104.80  Aligned_cols=83  Identities=31%  Similarity=0.571  Sum_probs=74.8

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceee-c--cceEEEE
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRL-E--GRTIAVR  566 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l-~--Gr~L~V~  566 (797)
                      +.++||||-|...-.|+|++.+|..||.|.+|.+++.. .|.+||||||.|.+..+|+.||..|+|..- -  ...|.|+
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            46789999999999999999999999999999999986 799999999999999999999999999753 3  3669999


Q ss_pred             ecCCCCC
Q 040243          567 VAGKPPQ  573 (797)
Q Consensus       567 ~A~~~~~  573 (797)
                      ||.....
T Consensus        97 ~ADTdkE  103 (371)
T KOG0146|consen   97 FADTDKE  103 (371)
T ss_pred             eccchHH
Confidence            9987653

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=98.66  E-value=2.9e-08  Score=82.19  Aligned_cols=60  Identities=33%  Similarity=0.558  Sum_probs=52.4

Q ss_pred             EEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHHHH
Q 040243          252 QKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESL  331 (797)
Q Consensus       252 ~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v  331 (797)
                      +.+|.||.      +++|+|||.+|.++|+||++|||+|.|..++                    +.-.|.|+| +.++|
T Consensus         1 T~~i~vp~------~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~~--------------------~~~~v~I~G-~~~~v   53 (60)
T PF00013_consen    1 TERIEVPS------SLVGRIIGKKGSNIKEIEEETGVKIQIPDDD--------------------ERDIVTISG-SPEQV   53 (60)
T ss_dssp             EEEEEEEH------HHHHHHHTGGGHHHHHHHHHHTSEEEEESTT--------------------EEEEEEEEE-SHHHH
T ss_pred             CEEEEECH------HHcCEEECCCCCcHHHhhhhcCeEEEEcCCC--------------------CcEEEEEEe-CHHHH
Confidence            56888998      9999999999999999999999999997541                    122899999 99999


Q ss_pred             HHHHHHH
Q 040243          332 EGAAAMV  338 (797)
Q Consensus       332 ~~A~~~I  338 (797)
                      ++|.++|
T Consensus        54 ~~A~~~I   60 (60)
T PF00013_consen   54 EKAKKMI   60 (60)
T ss_dssp             HHHHHHH
T ss_pred             HHHHhhC
Confidence            9999887

; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....

>cd00105 KH-I K homology RNA-binding domain, type I

Probab=98.61  E-value=1.2e-07  Score=78.90  Aligned_cols=63  Identities=35%  Similarity=0.569  Sum_probs=52.3

Q ss_pred             EEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHHHHH
Q 040243          253 KKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLE  332 (797)
Q Consensus       253 ~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v~  332 (797)
                      .+|.||.      +++|+|||++|+++++|+++|||+|.|...++                 ...+-.|.|.|. .+.+.
T Consensus         2 ~~i~ip~------~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~-----------------~~~~~~v~i~G~-~~~v~   57 (64)
T cd00105           2 ERVLVPS------SLVGRIIGKGGSTIKEIREETGAKIKIPDSGS-----------------GSEERIVTITGT-PEAVE   57 (64)
T ss_pred             EEEEEch------hhcceeECCCCHHHHHHHHHHCCEEEEcCCCC-----------------CCCceEEEEEcC-HHHHH
Confidence            5788998      99999999999999999999999999996542                 223347889988 68888


Q ss_pred             HHHHHHH
Q 040243          333 GAAAMVE  339 (797)
Q Consensus       333 ~A~~~I~  339 (797)
                      +|..+|+
T Consensus        58 ~a~~~i~   64 (64)
T cd00105          58 KAKELIL   64 (64)
T ss_pred             HHHHHhC
Confidence            8888763

KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.

>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]

Probab=98.58  E-value=8.8e-08  Score=111.40  Aligned_cols=100  Identities=29%  Similarity=0.324  Sum_probs=90.2

Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCCC-CCCCCCCCceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccc
Q 040243          218 ARERLNKERQEIISQIIKRNPAFK-PPADYRPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKG  296 (797)
Q Consensus       218 ~~~~le~er~~li~~~~~~~p~~~-pp~dy~p~~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkG  296 (797)
                      +-.+....|.+|++.|.+.+...+ +.+.|+|...+.|  |++      +.|+.+|||+|+|+|.|.++|||||.|..+|
T Consensus       520 AL~QAk~aRlhIL~~M~~ai~~pr~els~~aPri~t~~--i~~------dKI~dvIG~gGk~I~~I~eetg~~IdieddG  591 (692)
T COG1185         520 ALEQAKGARLHILIVMNEAISEPRKELSPYAPRIETIK--IDP------DKIRDVIGPGGKTIKAITEETGVKIDIEDDG  591 (692)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhhhhhccCCceEEEc--cCH------HHHhhccCCcccchhhhhhhhCcEEEecCCC
Confidence            556667889999999999999995 8999999999999  777      7889999999999999999999999999888


Q ss_pred             cccccccccccCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHhcCCChHH
Q 040243          297 SVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQPVDEV  348 (797)
Q Consensus       297 S~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v~~A~~~I~~ll~~~~e~  348 (797)
                                             .|.|++.+.+++.+|.+.|+.++..+..+
T Consensus       592 -----------------------tv~i~~s~~~~~~~ak~~I~~i~~e~evg  620 (692)
T COG1185         592 -----------------------TVKIAASDGESAKKAKERIEAITREVEVG  620 (692)
T ss_pred             -----------------------cEEEEecchHHHHHHHHHHHHHHhhcccc
Confidence                                   68899999999999999999999665544

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

Probab=98.55  E-value=1.9e-07  Score=98.16  Aligned_cols=86  Identities=30%  Similarity=0.470  Sum_probs=78.8

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      +...++|+|.||+..|+++||+++|..||.+..+.|.+|+ +|.+.|.|-|.|...++|.+|++.|+|..|+|+.|++.+
T Consensus        80 ~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~  158 (243)
T KOG0533|consen   80 ETRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEI  158 (243)
T ss_pred             CCCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEE
Confidence            3445899999999999999999999999999999999997 899999999999999999999999999999999999998


Q ss_pred             cCCCCCC
Q 040243          568 AGKPPQP  574 (797)
Q Consensus       568 A~~~~~~  574 (797)
                      .......
T Consensus       159 i~~~~~~  165 (243)
T KOG0533|consen  159 ISSPSQS  165 (243)
T ss_pred             ecCcccc
Confidence            7765543

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

Probab=98.53  E-value=1.5e-07  Score=108.89  Aligned_cols=79  Identities=25%  Similarity=0.503  Sum_probs=71.1

Q ss_pred             CcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCC---cccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTG---MSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       491 ~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TG---ksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      .++|||.||++.++.++|..+|...|.|.++.|.+.+...   .|.|||||+|.+.++|++|++.|+|+.|+|+.|.|++
T Consensus       515 ~t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~  594 (725)
T KOG0110|consen  515 ETKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKI  594 (725)
T ss_pred             chhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEe
Confidence            3449999999999999999999999999999887665321   3569999999999999999999999999999999999


Q ss_pred             cC
Q 040243          568 AG  569 (797)
Q Consensus       568 A~  569 (797)
                      +.
T Consensus       595 S~  596 (725)
T KOG0110|consen  595 SE  596 (725)
T ss_pred             cc
Confidence            98

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

Probab=98.53  E-value=1.7e-07  Score=104.89  Aligned_cols=75  Identities=31%  Similarity=0.546  Sum_probs=70.9

Q ss_pred             cEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecCCC
Q 040243          492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKP  571 (797)
Q Consensus       492 ~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~~~  571 (797)
                      ..||||   .++||.+|.++|+.+|.|++++|.+|- |  +-|||||.|.+.++|++||+.||...|.|+.|++.|+...
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t--slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd   75 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T--SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRD   75 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecC-C--ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccC
Confidence            369999   899999999999999999999999998 6  9999999999999999999999999999999999998765


Q ss_pred             C
Q 040243          572 P  572 (797)
Q Consensus       572 ~  572 (797)
                      .
T Consensus        76 ~   76 (369)
T KOG0123|consen   76 P   76 (369)
T ss_pred             C
Confidence            4

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

Probab=98.52  E-value=6.7e-08  Score=111.65  Aligned_cols=83  Identities=23%  Similarity=0.436  Sum_probs=77.1

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      ..++|+|.||++..+-.+++.+|..||.|.+|+|..-...+.+||||||+|-+..+|.+|++.|..+-|.||+|.++||+
T Consensus       612 ~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~  691 (725)
T KOG0110|consen  612 KGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAK  691 (725)
T ss_pred             ccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehhc
Confidence            46799999999999999999999999999999998876677789999999999999999999999999999999999997


Q ss_pred             CCC
Q 040243          570 KPP  572 (797)
Q Consensus       570 ~~~  572 (797)
                      ...
T Consensus       692 ~d~  694 (725)
T KOG0110|consen  692 SDN  694 (725)
T ss_pred             cch
Confidence            643

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

Probab=98.50  E-value=1.3e-07  Score=103.03  Aligned_cols=85  Identities=19%  Similarity=0.427  Sum_probs=78.5

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      ...+||||+|+.++++++|++.|.+||.|.++.++.|..+.++|||+||+|.+++++.+++. ..-+.|.++.+.|+.|.
T Consensus        96 ~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~~~gk~vevkrA~  174 (311)
T KOG4205|consen   96 RTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHDFNGKKVEVKRAI  174 (311)
T ss_pred             ceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-cceeeecCceeeEeecc
Confidence            45689999999999999999999999999999999999999999999999999999999985 57889999999999998


Q ss_pred             CCCCCC
Q 040243          570 KPPQPT  575 (797)
Q Consensus       570 ~~~~~~  575 (797)
                      ++....
T Consensus       175 pk~~~~  180 (311)
T KOG4205|consen  175 PKEVMQ  180 (311)
T ss_pred             chhhcc
Confidence            876544

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=98.48  E-value=1.7e-07  Score=112.77  Aligned_cols=97  Identities=30%  Similarity=0.394  Sum_probs=87.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCC-CCCCCCCCceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEecc
Q 040243          217 RARERLNKERQEIISQIIKRNPAFK-PPADYRPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGK  295 (797)
Q Consensus       217 r~~~~le~er~~li~~~~~~~p~~~-pp~dy~p~~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGk  295 (797)
                      ++.++-.+.|.+|++.|.+.+...+ ..++|.|+..+.+  |+.      +.|+.|||++|.|||.|+++||++|.|+..
T Consensus       521 ~al~~a~~g~~~I~~~M~~aI~~~r~~~~~~ap~~~~~~--I~~------~kI~~vIG~gg~~ik~I~~~~~~~idi~d~  592 (693)
T PRK11824        521 EALEQAKEGRLHILGKMNEAISEPRAELSPYAPRIETIK--IPP------DKIRDVIGPGGKTIREITEETGAKIDIEDD  592 (693)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCChhhhcccCchheeec--CCH------HHHHHHhcCCchhHHHHHHHHCCccccCCC
Confidence            5667777889999999999999884 5889999888888  565      889999999999999999999999999977


Q ss_pred             ccccccccccccCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHhcCC
Q 040243          296 GSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQP  344 (797)
Q Consensus       296 GS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v~~A~~~I~~ll~~  344 (797)
                      |                       +|.|++.+.+++++|.++|+.++..
T Consensus       593 G-----------------------~v~i~~~~~~~~~~a~~~I~~~~~~  618 (693)
T PRK11824        593 G-----------------------TVKIAATDGEAAEAAKERIEGITAE  618 (693)
T ss_pred             c-----------------------eEEEEcccHHHHHHHHHHHHHhccc
Confidence            7                       8999999999999999999998854

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

Probab=98.45  E-value=1.3e-07  Score=98.14  Aligned_cols=84  Identities=38%  Similarity=0.550  Sum_probs=77.9

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      +.+..+||+|.|...++++.|...|.+|-.....++++|+.||+++||+||.|.+..++.+|+..|+|..++.+.|+++-
T Consensus       187 ~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRk  266 (290)
T KOG0226|consen  187 DEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRK  266 (290)
T ss_pred             ccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhh
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999998875


Q ss_pred             cCCC
Q 040243          568 AGKP  571 (797)
Q Consensus       568 A~~~  571 (797)
                      +..+
T Consensus       267 S~wk  270 (290)
T KOG0226|consen  267 SEWK  270 (290)
T ss_pred             hhHH
Confidence            5443

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=98.45  E-value=2.3e-07  Score=77.28  Aligned_cols=60  Identities=25%  Similarity=0.463  Sum_probs=50.6

Q ss_pred             EEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHHHHH
Q 040243          253 KKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLE  332 (797)
Q Consensus       253 ~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v~  332 (797)
                      ++|.||.      .++|.|||++|+++|+|+++|||+|.|-...                   +..=.|.|+|. .++|.
T Consensus         2 ~~i~Vp~------~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~-------------------~~~~~v~I~G~-~~~v~   55 (62)
T cd02394           2 EEVEIPK------KLHRFIIGKKGSNIRKIMEETGVKIRFPDPG-------------------SKSDTITITGP-KENVE   55 (62)
T ss_pred             eEEEeCH------HHhhhccCCCCCcHHHHHHHhCCEEEcCCCC-------------------CCCCEEEEEcC-HHHHH
Confidence            5678888      8899999999999999999999999998644                   11127999999 78999


Q ss_pred             HHHHHH
Q 040243          333 GAAAMV  338 (797)
Q Consensus       333 ~A~~~I  338 (797)
                      +|+++|
T Consensus        56 ~A~~~i   61 (62)
T cd02394          56 KAKEEI   61 (62)
T ss_pred             HHHHHh
Confidence            998876

The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>smart00322 KH K homology RNA-binding domain

Probab=98.42  E-value=1.1e-06  Score=72.65  Aligned_cols=66  Identities=39%  Similarity=0.600  Sum_probs=56.5

Q ss_pred             eEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHHH
Q 040243          251 LQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQES  330 (797)
Q Consensus       251 ~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~  330 (797)
                      .+.+|.||.      +++|+|||.+|+++|+|+++|||+|.|....+                   ..-+|.|.+. .+.
T Consensus         3 ~~~~i~i~~------~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~-------------------~~~~v~i~g~-~~~   56 (69)
T smart00322        3 VTIEVLIPA------DKVGLIIGKGGSTIKKIEEETGVKIDIPEDGS-------------------EERVVEITGP-PEN   56 (69)
T ss_pred             eEEEEEEcc------hhcceeECCCchHHHHHHHHHCCEEEECCCCC-------------------CccEEEEEcC-HHH
Confidence            567888988      89999999999999999999999999986542                   2237899998 789


Q ss_pred             HHHHHHHHHHhc
Q 040243          331 LEGAAAMVEKLL  342 (797)
Q Consensus       331 v~~A~~~I~~ll  342 (797)
                      +..|..+|.+++
T Consensus        57 v~~a~~~i~~~~   68 (69)
T smart00322       57 VEKAAELILEIL   68 (69)
T ss_pred             HHHHHHHHHHHh
Confidence            999999998876

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

Probab=98.41  E-value=1.4e-06  Score=88.92  Aligned_cols=87  Identities=20%  Similarity=0.341  Sum_probs=70.7

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEE-EecCCCCcccceEEEEecCHHHHHHHHHhcCceeec---cceEEE
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKV-IKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLE---GRTIAV  565 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v-~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~---Gr~L~V  565 (797)
                      ..+||||.+||.++.-.+|..+|..|---..+.| +.++....++-+|||+|.+.+.|..|+..|||..|+   +..|++
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            4679999999999999999999999843333333 344444456789999999999999999999999997   788999


Q ss_pred             EecCCCCCCCC
Q 040243          566 RVAGKPPQPTV  576 (797)
Q Consensus       566 ~~A~~~~~~~~  576 (797)
                      ++|+...+...
T Consensus       113 ElAKSNtK~kr  123 (284)
T KOG1457|consen  113 ELAKSNTKRKR  123 (284)
T ss_pred             eehhcCccccc
Confidence            99987655443

>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]

Probab=98.39  E-value=7.2e-08  Score=96.85  Aligned_cols=87  Identities=25%  Similarity=0.442  Sum_probs=60.8

Q ss_pred             CCceEEEEecCHHHHHHHHHHHHHhcCCC---hHHHHHHHHHHHHHHHhhcCCcCc-cchhcccCCCCCccccCC-----
Q 040243          317 EDLHVLVEAETQESLEGAAAMVEKLLQPV---DEVLNEHKRQQLRELAALNGTIRD-EEYCRLCGEPGHRQYACP-----  387 (797)
Q Consensus       317 e~LHv~I~a~~~e~v~~A~~~I~~ll~~~---~e~~n~~k~~Ql~ela~lnGt~r~-~~~c~~cg~~gh~~~~cp-----  387 (797)
                      +++|.+|+..++|.......++-.-++.-   ...++..             ++++ ...|-+||+.||++++||     
T Consensus        16 ~~~~~~~~~s~ee~~~~~~~~~~~~~~~~~~~~~~~d~~-------------~~~~~~~~C~nCg~~GH~~~DCP~~iC~   82 (190)
T COG5082          16 LPIDKLSANSIEESSSNPNELRSLRSSGRYEDRSVEDVS-------------AIREENPVCFNCGQNGHLRRDCPHSICY   82 (190)
T ss_pred             cChhhhcccchhhhhcCccceeeccceeeeecccccccc-------------cccccccccchhcccCcccccCChhHhh
Confidence            89999999999998877766655544321   1111111             4444 359999999999999999     


Q ss_pred             ------CCCCCccccccceecCCCCCCcccC-CCCC
Q 040243          388 ------SRTSTFKSDVLCKICGDGGHPTIDC-LVKG  416 (797)
Q Consensus       388 ------~~~~~~~~~v~Cr~CG~~gH~t~dC-p~k~  416 (797)
                            ...+-....++|.+||..||+.+|| |.+.
T Consensus        83 ~C~~~~H~s~~C~~~~~C~~Cg~~GH~~~dC~P~~~  118 (190)
T COG5082          83 NCSWDGHRSNHCPKPKKCYNCGETGHLSRDCNPSKD  118 (190)
T ss_pred             hcCCCCcccccCCcccccccccccCccccccCcccc
Confidence                  1111123458999999999999999 5543

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.39  E-value=3.7e-07  Score=95.88  Aligned_cols=84  Identities=23%  Similarity=0.450  Sum_probs=78.9

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      .+.+...+||+|+.++++.+++...|+.||.|..+.|..|+.++.+|||+||+|.+.+.++.|+. |++..|.|+.+.|.
T Consensus        97 ~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt  175 (231)
T KOG4209|consen   97 KEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVT  175 (231)
T ss_pred             hccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceee
Confidence            45678899999999999999999999999999999999999999999999999999999999997 99999999999999


Q ss_pred             ecCCC
Q 040243          567 VAGKP  571 (797)
Q Consensus       567 ~A~~~  571 (797)
                      +....
T Consensus       176 ~~r~~  180 (231)
T KOG4209|consen  176 LKRTN  180 (231)
T ss_pred             eeeee
Confidence            87654

>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]

Probab=98.39  E-value=3.5e-07  Score=99.60  Aligned_cols=93  Identities=18%  Similarity=0.092  Sum_probs=80.9

Q ss_pred             ceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHH
Q 040243          250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQE  329 (797)
Q Consensus       250 ~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e  329 (797)
                      ++..|++|++| .|.||.-+..=|++..+|..+|.||++++.||||+|+.       ++.-.+.+.+|+++|+|++.+.+
T Consensus       209 ~Y~~k~~v~~~-~P~~~~K~~~~~r~d~~La~~~ie~~i~~l~~Gr~SG~-------iEP~~G~EsnEPMYI~i~h~~~~  280 (531)
T KOG1960|consen  209 YYPNKALATDK-DPPLYLKIVSHNRKDLTLALQEIESWINPLIDGRRSGR-------REPNEGNESNEPMYIFSTHGNGN  280 (531)
T ss_pred             cchhheecccC-CcchhhhhhccCccchhhhhhhhhhhhhhhhccccccc-------cCcccccccCCceeEEeecCCch
Confidence            45558999987 79999999999999999999999999999999999975       23334558899999999999999


Q ss_pred             HHHHHHHHHHHhcCCChHHHH
Q 040243          330 SLEGAAAMVEKLLQPVDEVLN  350 (797)
Q Consensus       330 ~v~~A~~~I~~ll~~~~e~~n  350 (797)
                      .+.+|+.+|++|++.|.-.+.
T Consensus       281 g~~~A~r~~~nl~~~v~~~~s  301 (531)
T KOG1960|consen  281 GENGAPRRKWNLEEKVYINLS  301 (531)
T ss_pred             hhccchhHHHhHHHHHHHHhh
Confidence            999999999999988765443

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

Probab=98.37  E-value=8.5e-07  Score=95.47  Aligned_cols=81  Identities=25%  Similarity=0.343  Sum_probs=74.8

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEE--------EEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeecc
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVM--------AKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEG  560 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~--------v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~G  560 (797)
                      ..++.|||.|||.++|.+++.++|++||.|.+        |+|.++. .|+.||=|++.|..+++++.||..|++..|.|
T Consensus       132 ~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~-~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg  210 (382)
T KOG1548|consen  132 KVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDN-QGKLKGDALCCYIKRESVELAIKILDEDELRG  210 (382)
T ss_pred             ccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecC-CCCccCceEEEeecccHHHHHHHHhCcccccC
Confidence            45677999999999999999999999998865        8999997 59999999999999999999999999999999


Q ss_pred             ceEEEEecCC
Q 040243          561 RTIAVRVAGK  570 (797)
Q Consensus       561 r~L~V~~A~~  570 (797)
                      +.|+|+.|+-
T Consensus       211 ~~~rVerAkf  220 (382)
T KOG1548|consen  211 KKLRVERAKF  220 (382)
T ss_pred             cEEEEehhhh
Confidence            9999998853

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=98.35  E-value=1.3e-06  Score=73.80  Aligned_cols=63  Identities=30%  Similarity=0.452  Sum_probs=50.3

Q ss_pred             EEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHHHHH
Q 040243          253 KKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLE  332 (797)
Q Consensus       253 ~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v~  332 (797)
                      .||+||.      +.+|+|||.+|.++|+|+++|||+|.|.....               ...++ --|.|+|+ .+.++
T Consensus         2 ~r~~ip~------~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~---------------~~~~~-r~v~I~G~-~~~v~   58 (65)
T cd02396           2 LRLLVPS------SQAGSIIGKGGSTIKEIREETGAKIRVSKSVL---------------PGSTE-RVVTISGK-PSAVQ   58 (65)
T ss_pred             EEEEECH------HHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC---------------CCCCc-eEEEEEeC-HHHHH
Confidence            5889998      99999999999999999999999999964321               01122 25778876 78999


Q ss_pred             HHHHHH
Q 040243          333 GAAAMV  338 (797)
Q Consensus       333 ~A~~~I  338 (797)
                      +|.++|
T Consensus        59 ~A~~~I   64 (65)
T cd02396          59 KALLLI   64 (65)
T ss_pred             HHHHhh
Confidence            998887

Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.27  E-value=3.3e-06  Score=97.64  Aligned_cols=85  Identities=26%  Similarity=0.483  Sum_probs=75.4

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCC---CCcccceEEEEecCHHHHHHHHHhcCceeeccceEE
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRV---TGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIA  564 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~---TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~  564 (797)
                      +...++|||+||+..++++.|...|..||.|..|+|+.-+.   ..+-+-|+||.|.+..+|++|++.|+|..+.++.++
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            34568999999999999999999999999999999987662   234567999999999999999999999999999999


Q ss_pred             EEecCCCC
Q 040243          565 VRVAGKPP  572 (797)
Q Consensus       565 V~~A~~~~  572 (797)
                      +.|++.-.
T Consensus       251 ~gWgk~V~  258 (877)
T KOG0151|consen  251 LGWGKAVP  258 (877)
T ss_pred             eccccccc
Confidence            99987543

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

Probab=98.25  E-value=3.2e-07  Score=93.36  Aligned_cols=79  Identities=16%  Similarity=0.169  Sum_probs=72.8

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      ..+||||+||...++|+-|.++|.+-|.|.+|.|..++ .++.| ||||.|.++.++.-|++.|||..+.++.|.|.+-.
T Consensus         8 ~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~-d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r~   85 (267)
T KOG4454|consen    8 MDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQ-DQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLRC   85 (267)
T ss_pred             hhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCc-cCCCc-eeeeecccccchhhhhhhcccchhccchhhccccc
Confidence            46799999999999999999999999999999998887 56777 99999999999999999999999999999998755


Q ss_pred             C
Q 040243          570 K  570 (797)
Q Consensus       570 ~  570 (797)
                      .
T Consensus        86 G   86 (267)
T KOG4454|consen   86 G   86 (267)
T ss_pred             C
Confidence            4

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=98.22  E-value=1.8e-06  Score=97.35  Aligned_cols=83  Identities=23%  Similarity=0.408  Sum_probs=69.6

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ....+|||+|||.+++.++|+++|.+||.|+...|..-.-.++..+||||+|.+.++++.||+. +-..|++++|.|+-.
T Consensus       286 ~~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek  364 (419)
T KOG0116|consen  286 ADGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEK  364 (419)
T ss_pred             ecccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEec
Confidence            3455699999999999999999999999999988765443455559999999999999999975 577899999999875


Q ss_pred             CCCC
Q 040243          569 GKPP  572 (797)
Q Consensus       569 ~~~~  572 (797)
                      +...
T Consensus       365 ~~~~  368 (419)
T KOG0116|consen  365 RPGF  368 (419)
T ss_pred             cccc
Confidence            5433

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

Probab=98.21  E-value=8.8e-07  Score=91.47  Aligned_cols=73  Identities=30%  Similarity=0.564  Sum_probs=66.5

Q ss_pred             cEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecCCC
Q 040243          492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKP  571 (797)
Q Consensus       492 ~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~~~  571 (797)
                      ..||||+|++.+.+.+|..||..||.|.+|.+..        ||+||+|.+..+|..||..||+.+|.|.++.|+|+...
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            3699999999999999999999999999987633        69999999999999999999999999999999998754


Q ss_pred             C
Q 040243          572 P  572 (797)
Q Consensus       572 ~  572 (797)
                      .
T Consensus        74 ~   74 (216)
T KOG0106|consen   74 R   74 (216)
T ss_pred             c
Confidence            3

>PRK13763 putative RNA-processing protein; Provisional

Probab=98.20  E-value=2.2e-06  Score=86.91  Aligned_cols=66  Identities=30%  Similarity=0.531  Sum_probs=58.8

Q ss_pred             eEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEecc-ccccccccccccCCCCCCCCCCCceEEEE---ec
Q 040243          251 LQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGK-GSVKEGRLQQKRDLKPDPSENEDLHVLVE---AE  326 (797)
Q Consensus       251 ~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGk-GS~k~g~~~~~~~~~~~~~~~e~LHv~I~---a~  326 (797)
                      ....|.||.      +.||+|||++|+|+|.|+++|||+|.|..+ |                       .|.|.   +.
T Consensus         3 ~~~~i~IP~------~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~~g-----------------------~V~I~~~~~~   53 (180)
T PRK13763          3 MMEYVKIPK------DRIGVLIGKKGETKKEIEERTGVKLEIDSETG-----------------------EVIIEPTDGE   53 (180)
T ss_pred             ceEEEEcCH------HHhhhHhccchhHHHHHHHHHCcEEEEECCCC-----------------------eEEEEeCCCC
Confidence            345777888      899999999999999999999999999965 3                       78898   88


Q ss_pred             CHHHHHHHHHHHHHhcCCC
Q 040243          327 TQESLEGAAAMVEKLLQPV  345 (797)
Q Consensus       327 ~~e~v~~A~~~I~~ll~~~  345 (797)
                      +.+++++|.++|+.|+..+
T Consensus        54 d~~~i~kA~~~I~ai~~gf   72 (180)
T PRK13763         54 DPLAVLKARDIVKAIGRGF   72 (180)
T ss_pred             CHHHHHHHHHHHHHHhcCC
Confidence            9999999999999998853

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=98.15  E-value=4.6e-06  Score=90.63  Aligned_cols=87  Identities=26%  Similarity=0.364  Sum_probs=80.0

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEE--------EEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceee
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVM--------AKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRL  558 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~--------v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l  558 (797)
                      ......+|||-+|+..+++++|.++|.++|.|..        |+|.+|+.|++.||-|.|+|++...|+.||+.+++..|
T Consensus        62 ~~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf  141 (351)
T KOG1995|consen   62 DKSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDF  141 (351)
T ss_pred             cccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccc
Confidence            3566789999999999999999999999998854        78999999999999999999999999999999999999


Q ss_pred             ccceEEEEecCCCCC
Q 040243          559 EGRTIAVRVAGKPPQ  573 (797)
Q Consensus       559 ~Gr~L~V~~A~~~~~  573 (797)
                      .+..|+|.+|.....
T Consensus       142 ~gn~ikvs~a~~r~~  156 (351)
T KOG1995|consen  142 CGNTIKVSLAERRTG  156 (351)
T ss_pred             cCCCchhhhhhhccC
Confidence            999999999876653

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=98.12  E-value=2.5e-06  Score=85.95  Aligned_cols=62  Identities=32%  Similarity=0.505  Sum_probs=54.5

Q ss_pred             EEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEecc-ccccccccccccCCCCCCCCCCCceEEE--EecCHHHH
Q 040243          255 LYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGK-GSVKEGRLQQKRDLKPDPSENEDLHVLV--EAETQESL  331 (797)
Q Consensus       255 i~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGk-GS~k~g~~~~~~~~~~~~~~~e~LHv~I--~a~~~e~v  331 (797)
                      |.||.      +.||+|||++|+|+|+||++|||+|.|..+ |                       .|.|  .+.+.+++
T Consensus         2 i~Ip~------~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~~g-----------------------~V~I~~~t~d~~~i   52 (172)
T TIGR03665         2 VKIPK------DRIGVLIGKGGETKKEIEERTGVKLDIDSETG-----------------------EVKIEEEDEDPLAV   52 (172)
T ss_pred             ccCCH------HHhhhHhCCchhHHHHHHHHhCcEEEEEcCCc-----------------------eEEEecCCCCHHHH
Confidence            45666      899999999999999999999999999954 3                       6788  68889999


Q ss_pred             HHHHHHHHHhcCCC
Q 040243          332 EGAAAMVEKLLQPV  345 (797)
Q Consensus       332 ~~A~~~I~~ll~~~  345 (797)
                      .+|.++|+.|+..+
T Consensus        53 ~kA~~~I~~i~~gf   66 (172)
T TIGR03665        53 MKAREVVKAIGRGF   66 (172)
T ss_pred             HHHHHHHHHHHcCC
Confidence            99999999998853

This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.11  E-value=1.3e-05  Score=73.23  Aligned_cols=81  Identities=20%  Similarity=0.265  Sum_probs=71.4

Q ss_pred             CcEEEEecCCCCCcHHHHHHHhhc--CCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeec----cceEE
Q 040243          491 DTNLYIGYLPPTLDDDGLIRLFST--FGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLE----GRTIA  564 (797)
Q Consensus       491 ~~tLfVgNLp~~vte~dL~~~Fs~--fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~----Gr~L~  564 (797)
                      .+||.|.|||...+.++|.+++..  .|....+++..|-.++.+.|||||.|.+.+.|.+-.+.++|+.+.    .+.+.
T Consensus         1 RTTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~   80 (97)
T PF04059_consen    1 RTTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCE   80 (97)
T ss_pred             CeeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEE
Confidence            369999999999999999988876  377788999999999999999999999999999999999998775    56788


Q ss_pred             EEecCCC
Q 040243          565 VRVAGKP  571 (797)
Q Consensus       565 V~~A~~~  571 (797)
                      |.||+-+
T Consensus        81 i~yAriQ   87 (97)
T PF04059_consen   81 ISYARIQ   87 (97)
T ss_pred             EehhHhh
Confidence            8888643

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

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

Probab=98.09  E-value=2e-06  Score=97.56  Aligned_cols=73  Identities=26%  Similarity=0.547  Sum_probs=66.3

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIA  564 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~  564 (797)
                      .+....+|+|-||+..|++++|+.+|+.||+|+.|+...     ..+|..||+|.|..+|++|++.|++..+.|+.|+
T Consensus        71 ~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~-----~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   71 KDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETP-----NKRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             ccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhccc-----ccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            355678999999999999999999999999999976544     4579999999999999999999999999999988

>PF13014 KH_3: KH domain

Probab=97.91  E-value=8.4e-06  Score=63.28  Aligned_cols=28  Identities=54%  Similarity=0.771  Sum_probs=26.9

Q ss_pred             eeeeeeCCCchhHHHHHHHhCcEEEEec
Q 040243          267 FIGLIIGPRGNTQKRMERETGAKIVIRG  294 (797)
Q Consensus       267 fiG~iiGPrG~t~K~le~eTgakI~IrG  294 (797)
                      |+|+|||++|.|+|+|+++|||+|.|--
T Consensus         1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~   28 (43)
T PF13014_consen    1 FVGRIIGKGGSTIKEIREETGAKIQIPP   28 (43)
T ss_pred             CcCeEECCCChHHHHHHHHhCcEEEECC
Confidence            6899999999999999999999999985

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

Probab=97.91  E-value=1.1e-05  Score=92.42  Aligned_cols=88  Identities=30%  Similarity=0.536  Sum_probs=81.6

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      -...+++||++|+..+++..++++...||.+....++.|..+|.++||||.+|.+......||..|||..++++.|.|..
T Consensus       286 ~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~  365 (500)
T KOG0120|consen  286 PDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQR  365 (500)
T ss_pred             ccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeeh
Confidence            35678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCCC
Q 040243          568 AGKPPQPT  575 (797)
Q Consensus       568 A~~~~~~~  575 (797)
                      |.......
T Consensus       366 A~~g~~~~  373 (500)
T KOG0120|consen  366 AIVGASNA  373 (500)
T ss_pred             hhccchhc
Confidence            87655433

>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]

Probab=97.90  E-value=1.8e-05  Score=90.81  Aligned_cols=73  Identities=25%  Similarity=0.429  Sum_probs=56.3

Q ss_pred             EEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHHHH
Q 040243          252 QKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESL  331 (797)
Q Consensus       252 ~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v  331 (797)
                      +..|-||-      +.||.|||-+|.|||+|+.|||+||.++=             |+    +..-++.+++.=-+.++|
T Consensus       231 ~~~V~VPr------~~VG~IIGkgGE~IKklq~etG~KIQfkp-------------Dd----~p~speR~~~IiG~~d~i  287 (600)
T KOG1676|consen  231 TREVKVPR------SKVGIIIGKGGEMIKKLQNETGAKIQFKP-------------DD----DPSSPERPAQIIGTVDQI  287 (600)
T ss_pred             eeEEeccc------cceeeEEecCchHHHHHhhccCceeEeec-------------CC----CCCCccceeeeecCHHHH
Confidence            55566887      89999999999999999999999999983             21    113334444444467999


Q ss_pred             HHHHHHHHHhcCCChH
Q 040243          332 EGAAAMVEKLLQPVDE  347 (797)
Q Consensus       332 ~~A~~~I~~ll~~~~e  347 (797)
                      .+|.+||.+||..+.+
T Consensus       288 e~Aa~lI~eii~~~~~  303 (600)
T KOG1676|consen  288 EHAAELINEIIAEAEA  303 (600)
T ss_pred             HHHHHHHHHHHHHHhc
Confidence            9999999999986443

>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]

Probab=97.85  E-value=9.2e-05  Score=86.75  Aligned_cols=8  Identities=13%  Similarity=0.343  Sum_probs=3.0

Q ss_pred             HHHHHHHh
Q 040243          334 AAAMVEKL  341 (797)
Q Consensus       334 A~~~I~~l  341 (797)
                      |++++-.|
T Consensus       254 vvkllsal  261 (1102)
T KOG1924|consen  254 VVKLLSAL  261 (1102)
T ss_pred             HHHHHHHH
Confidence            33333333

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

Probab=97.84  E-value=5.1e-06  Score=94.23  Aligned_cols=82  Identities=28%  Similarity=0.419  Sum_probs=77.4

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      ++.+.+|||+-.|.-.++..+|.++|+.+|.|.+|.++.|+.++.+||.|||+|.+.+++..|| .|.|..+.|..|.|.
T Consensus       175 eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~ai-aLsGqrllg~pv~vq  253 (549)
T KOG0147|consen  175 EERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAI-ALSGQRLLGVPVIVQ  253 (549)
T ss_pred             hHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHh-hhcCCcccCceeEec
Confidence            5677899999999999999999999999999999999999999999999999999999999999 699999999999998


Q ss_pred             ecC
Q 040243          567 VAG  569 (797)
Q Consensus       567 ~A~  569 (797)
                      ...
T Consensus       254 ~sE  256 (549)
T KOG0147|consen  254 LSE  256 (549)
T ss_pred             ccH
Confidence            754

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=97.84  E-value=2.2e-05  Score=79.14  Aligned_cols=53  Identities=32%  Similarity=0.446  Sum_probs=48.7

Q ss_pred             eeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHhcCC
Q 040243          267 FIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQP  344 (797)
Q Consensus       267 fiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v~~A~~~I~~ll~~  344 (797)
                      .+|+|||++|.|+|.||..|||+|.|-|+                        .|.|.| +.+.++.|.++|+.||..
T Consensus        99 ~~griIG~~G~t~~~ie~~t~~~i~i~~~------------------------~v~i~G-~~~~~~~A~~~i~~li~~  151 (172)
T TIGR03665        99 IKGRIIGEGGKTRRIIEELTGVSISVYGK------------------------TVGIIG-DPEQVQIAREAIEMLIEG  151 (172)
T ss_pred             HHhhhcCCCcHHHHHHHHHHCCeEEEcCC------------------------EEEEEC-CHHHHHHHHHHHHHHHcC
Confidence            68999999999999999999999999741                        799999 899999999999999964

This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.

>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]

Probab=97.84  E-value=5.8e-05  Score=86.78  Aligned_cols=75  Identities=27%  Similarity=0.552  Sum_probs=62.1

Q ss_pred             CCceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecC
Q 040243          248 PPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAET  327 (797)
Q Consensus       248 p~~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~  327 (797)
                      ..+.+.+|.||.      |.+|+|||-+|.|+|+|+++||||+.+--.|+.-.+             .+.  -+.|+++ 
T Consensus       136 ~~~ttqeI~IPa------~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~-------------~~K--plritGd-  193 (600)
T KOG1676|consen  136 SVETTQEILIPA------NKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATG-------------ADK--PLRITGD-  193 (600)
T ss_pred             ccceeeeeccCc------cceeeEeccCccHHHHHHhhcCCceEEEecCCcCCC-------------CCC--ceeecCC-
Confidence            577899999998      999999999999999999999999998877754332             122  3456665 


Q ss_pred             HHHHHHHHHHHHHhcCC
Q 040243          328 QESLEGAAAMVEKLLQP  344 (797)
Q Consensus       328 ~e~v~~A~~~I~~ll~~  344 (797)
                      .++|+.|.+||.++|..
T Consensus       194 p~~ve~a~~lV~dil~e  210 (600)
T KOG1676|consen  194 PDKVEQAKQLVADILRE  210 (600)
T ss_pred             HHHHHHHHHHHHHHHHh
Confidence            68999999999999985

>PRK13763 putative RNA-processing protein; Provisional

Probab=97.81  E-value=7e-05  Score=76.08  Aligned_cols=53  Identities=34%  Similarity=0.480  Sum_probs=47.6

Q ss_pred             eeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHhcCC
Q 040243          267 FIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQP  344 (797)
Q Consensus       267 fiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v~~A~~~I~~ll~~  344 (797)
                      .+|+|||++|+|+|.||+.|||+|.|-++                        .|.|.| +.+.++.|.+.|+.|+..
T Consensus       105 ~~griIG~~G~~~k~ie~~t~~~i~i~~~------------------------~v~i~G-~~~~~~~A~~~I~~li~g  157 (180)
T PRK13763        105 IKGRIIGEGGKTRRIIEELTGVDISVYGK------------------------TVAIIG-DPEQVEIAREAIEMLIEG  157 (180)
T ss_pred             HhhheeCCCcHHHHHHHHHHCcEEEEcCC------------------------EEEEEe-CHHHHHHHHHHHHHHHcC
Confidence            68999999999999999999999999741                        477887 789999999999999974

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

Probab=97.80  E-value=5.5e-05  Score=83.26  Aligned_cols=79  Identities=22%  Similarity=0.401  Sum_probs=71.4

Q ss_pred             CcEEEEecCCC-CCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          491 DTNLYIGYLPP-TLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       491 ~~tLfVgNLp~-~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      ...|.|.||.. .+|.+.|..+|+-||.|.+|+|+.++.     --|+|.|.+...|+-|++.|+|+.|.|++|+|.+++
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkk-----d~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SK  371 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKK-----DNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSK  371 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCC-----cceeeeecchhHHHHHHHHhhcceecCceEEEeecc
Confidence            67899999985 489999999999999999999999863     589999999999999999999999999999999988


Q ss_pred             CCCCC
Q 040243          570 KPPQP  574 (797)
Q Consensus       570 ~~~~~  574 (797)
                      -..-.
T Consensus       372 H~~vq  376 (492)
T KOG1190|consen  372 HTNVQ  376 (492)
T ss_pred             Ccccc
Confidence            65543

>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]

Probab=97.72  E-value=5.9e-05  Score=85.84  Aligned_cols=95  Identities=24%  Similarity=0.346  Sum_probs=80.2

Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCC-CCCCCCCCCceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccc
Q 040243          218 ARERLNKERQEIISQIIKRNPAF-KPPADYRPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKG  296 (797)
Q Consensus       218 ~~~~le~er~~li~~~~~~~p~~-~pp~dy~p~~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkG  296 (797)
                      ..++....|.+|++.|.+.++.. .-...|.|+..+.|  ++.      ..+-.||||+|..+|+||.|||+.-+|. .|
T Consensus       565 al~~a~~ar~~Il~~m~k~i~~Pr~~~~~y~P~~~tlk--v~~------sk~~~lIGp~G~~~kki~~EtGai~~vD-e~  635 (760)
T KOG1067|consen  565 ALQKAREARLQILDIMEKNINSPRGSDKEYSPVLETLK--VSP------SKRATLIGPGGVLKKKIEVETGAISQVD-EG  635 (760)
T ss_pred             HHHhhhHHHHHHHHHHHhhcCCcccCccccCceeeEEe--ecc------hhhheeecCccceeeeEeeeccceeeec-Cc
Confidence            44566778999999999999988 66788999999988  444      5567999999999999999999544443 22


Q ss_pred             cccccccccccCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHhcCC
Q 040243          297 SVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQP  344 (797)
Q Consensus       297 S~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v~~A~~~I~~ll~~  344 (797)
                                             |+.|.|.++..+++|.+.|..|+..
T Consensus       636 -----------------------t~~i~A~~~~am~~Ak~~I~~i~~~  660 (760)
T KOG1067|consen  636 -----------------------TFSIFAPTQAAMEEAKEFIDGIIKD  660 (760)
T ss_pred             -----------------------eEEEEecCHHHHHHHHHHHHHHhcC
Confidence                                   9999999999999999999999875

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

Probab=97.66  E-value=0.0001  Score=83.09  Aligned_cols=75  Identities=20%  Similarity=0.300  Sum_probs=63.4

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ...-|.+.+|||++|++||.++|+.++ |.++.+.  +.+|+..|-|||+|.+++++++|++ ++...+..|-|.|--+
T Consensus         9 ~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~--r~~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~   83 (510)
T KOG4211|consen    9 TAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIP--RRNGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTA   83 (510)
T ss_pred             cceEEEecCCCccccHHHHHHHHhcCc-eeEEEEe--ccCCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEcc
Confidence            456788999999999999999999995 6665444  4589999999999999999999997 4777788888888544

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

Probab=97.51  E-value=0.00055  Score=68.64  Aligned_cols=66  Identities=21%  Similarity=0.360  Sum_probs=60.2

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeec
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLE  559 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~  559 (797)
                      ......+|.|.+|+...+++||+++..+-|.|....+.+|       |++.|+|...++.+-||.+|+...+.
T Consensus       111 srrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD-------g~GvV~~~r~eDMkYAvr~ld~~~~~  176 (241)
T KOG0105|consen  111 SRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD-------GVGVVEYLRKEDMKYAVRKLDDQKFR  176 (241)
T ss_pred             ccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc-------cceeeeeeehhhHHHHHHhhcccccc
Confidence            5567889999999999999999999999999999999888       59999999999999999999876654

>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]

Probab=97.46  E-value=0.00037  Score=70.80  Aligned_cols=55  Identities=35%  Similarity=0.437  Sum_probs=49.3

Q ss_pred             eeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHhcCCCh
Q 040243          267 FIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQPVD  346 (797)
Q Consensus       267 fiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v~~A~~~I~~ll~~~~  346 (797)
                      ..|||||..|+|.+.||+-|||.|+|.|+                        +|.|-|+ ++.|+.|.+.|++||...+
T Consensus       112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~g~------------------------tVaiiG~-~~~v~iAr~AVemli~G~~  166 (194)
T COG1094         112 IKGRIIGREGKTRRAIEELTGVYISVYGK------------------------TVAIIGG-FEQVEIAREAVEMLINGAP  166 (194)
T ss_pred             hhceeeCCCchHHHHHHHHhCCeEEEeCc------------------------EEEEecC-hhhhHHHHHHHHHHHcCCC
Confidence            46999999999999999999999999975                        7888886 7899999999999998543

>PHA03247 large tegument protein UL36; Provisional

Probab=97.45  E-value=0.024  Score=74.55  Aligned_cols=41  Identities=20%  Similarity=0.184  Sum_probs=22.5

Q ss_pred             HHHHHHHHHHHHHhhcC--CcCccchhcccCCCC----CccccCCCC
Q 040243          349 LNEHKRQQLRELAALNG--TIRDEEYCRLCGEPG----HRQYACPSR  389 (797)
Q Consensus       349 ~n~~k~~Ql~ela~lnG--t~r~~~~c~~cg~~g----h~~~~cp~~  389 (797)
                      +|----.||.+|..|=-  -|.....|-+-=..+    +--|+-++-
T Consensus      2371 ENACL~~QLe~LSaLiAsKPLa~aPPCLvlvD~~m~p~~VLWe~~~~ 2417 (3151)
T PHA03247       2371 ENACLAAQLPALSALIAARPLARSPPCLVLVDISMAPLFVLWEQPDP 2417 (3151)
T ss_pred             HHHHHHHHHHHHHHHHhcCcccCCCCeEEEEcCCCceeEEeccCCCC
Confidence            34444678888876642  344555675544333    335665443

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=97.40  E-value=0.00051  Score=60.89  Aligned_cols=70  Identities=24%  Similarity=0.423  Sum_probs=48.7

Q ss_pred             cEEEEecCCCCCcHHH----HHHHhhcCC-CEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          492 TNLYIGYLPPTLDDDG----LIRLFSTFG-DIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       492 ~tLfVgNLp~~vte~d----L~~~Fs~fG-~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      +.|||.|||.+.+-..    |+.++.-|| .|.+|.          .+-|+|.|.+.+.|++|.+.|+|..+.|.+|.|+
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            4799999999988765    567777775 766652          3699999999999999999999999999999999


Q ss_pred             ecCCC
Q 040243          567 VAGKP  571 (797)
Q Consensus       567 ~A~~~  571 (797)
                      +....
T Consensus        73 ~~~~~   77 (90)
T PF11608_consen   73 FSPKN   77 (90)
T ss_dssp             SS--S
T ss_pred             EcCCc
Confidence            97543

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

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

Probab=97.35  E-value=0.00018  Score=74.55  Aligned_cols=74  Identities=20%  Similarity=0.397  Sum_probs=65.1

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      ....+.|+|.+|..++.+.+|.+.|..+|.+....+        .++++||+|.+.++|.+||+.|++..+.++.|.|..
T Consensus        96 ~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--------~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~  167 (216)
T KOG0106|consen   96 SRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--------RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVEK  167 (216)
T ss_pred             ccccceeeeccchhhhhHHHHhhhhcccCCCchhhh--------hccccceeehhhhhhhhcchhccchhhcCceeeecc
Confidence            457789999999999999999999999999844333        357999999999999999999999999999999965


Q ss_pred             cC
Q 040243          568 AG  569 (797)
Q Consensus       568 A~  569 (797)
                      ..
T Consensus       168 ~~  169 (216)
T KOG0106|consen  168 NS  169 (216)
T ss_pred             cC
Confidence            43

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=97.34  E-value=0.00029  Score=74.55  Aligned_cols=63  Identities=21%  Similarity=0.342  Sum_probs=56.4

Q ss_pred             EEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHHHHHH
Q 040243          254 KLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEG  333 (797)
Q Consensus       254 Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v~~  333 (797)
                      .+-||.      ++|++|||++|.++|.|.++|+|+|.|--.|                       .|+|+|.+.+.+++
T Consensus       148 ~~~V~~------~~i~~lig~~g~~i~~l~~~~~~~I~ig~NG-----------------------~VwI~~~~~~~~~~  198 (235)
T PRK04163        148 IVEIKP------VKVPRVIGKKGSMINMLKEETGCDIIVGQNG-----------------------RIWIKGPDEEDEEI  198 (235)
T ss_pred             EEEECH------HHHHhhcCCCChhHhhhhhhhCcEEEEcCCc-----------------------EEEEeeCCHHHHHH
Confidence            344777      8999999999999999999999999997655                       89999999999999


Q ss_pred             HHHHHHHhcCCC
Q 040243          334 AAAMVEKLLQPV  345 (797)
Q Consensus       334 A~~~I~~ll~~~  345 (797)
                      |+++|+++-...
T Consensus       199 a~~~I~~~e~~~  210 (235)
T PRK04163        199 AIEAIKKIEREA  210 (235)
T ss_pred             HHHHHHHHHhhh
Confidence            999999987653

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=97.30  E-value=0.00014  Score=78.86  Aligned_cols=81  Identities=22%  Similarity=0.418  Sum_probs=73.8

Q ss_pred             CcEEE-EecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          491 DTNLY-IGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       491 ~~tLf-VgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      ..++| |++|++.+++++|+.+|..+|.|..+++..+..++.++|||||.|.+...+..++.. +...+.++.++|....
T Consensus       184 s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~  262 (285)
T KOG4210|consen  184 SDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEEDE  262 (285)
T ss_pred             cccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccCC
Confidence            34555 999999999999999999999999999999999999999999999999999999976 7888999999999876


Q ss_pred             CCC
Q 040243          570 KPP  572 (797)
Q Consensus       570 ~~~  572 (797)
                      ...
T Consensus       263 ~~~  265 (285)
T KOG4210|consen  263 PRP  265 (285)
T ss_pred             CCc
Confidence            554

>PHA03247 large tegument protein UL36; Provisional

Probab=97.25  E-value=0.052  Score=71.68  Aligned_cols=8  Identities=0%  Similarity=-0.205  Sum_probs=3.4

Q ss_pred             CccccCCC
Q 040243          381 HRQYACPS  388 (797)
Q Consensus       381 h~~~~cp~  388 (797)
                      -..+||++
T Consensus      2314 VIA~E~~~ 2321 (3151)
T PHA03247       2314 VVALRSDP 2321 (3151)
T ss_pred             EEEecCcc
Confidence            33444443

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.25  E-value=0.00063  Score=73.39  Aligned_cols=85  Identities=22%  Similarity=0.364  Sum_probs=66.9

Q ss_pred             CCCCcEEEEecCCCCCcHHH----H--HHHhhcCCCEEEEEEEecCCCCcc-cceE--EEEecCHHHHHHHHHhcCceee
Q 040243          488 ELDDTNLYIGYLPPTLDDDG----L--IRLFSTFGDIVMAKVIKDRVTGMS-KGYG--FVKYADIQMANNAIASMNGYRL  558 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~d----L--~~~Fs~fG~I~~v~v~~dk~TGks-rGfa--FV~F~s~e~A~~AI~~LnG~~l  558 (797)
                      -...+-+||-+|+..+..++    |  .++|.+||.|.+|.|-+......+ .+.+  ||+|.+.++|.+||...+|..+
T Consensus       111 VvQKNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~  190 (480)
T COG5175         111 VVQKNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLL  190 (480)
T ss_pred             eeecceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccc
Confidence            34566899999999887766    3  389999999999877554311111 2333  9999999999999999999999


Q ss_pred             ccceEEEEecCCCC
Q 040243          559 EGRTIAVRVAGKPP  572 (797)
Q Consensus       559 ~Gr~L~V~~A~~~~  572 (797)
                      +||.|+..|...+.
T Consensus       191 DGr~lkatYGTTKY  204 (480)
T COG5175         191 DGRVLKATYGTTKY  204 (480)
T ss_pred             cCceEeeecCchHH
Confidence            99999999876643

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

Probab=97.18  E-value=0.00074  Score=76.30  Aligned_cols=76  Identities=18%  Similarity=0.267  Sum_probs=63.4

Q ss_pred             CcEEEEecCCCCCcHHHHHHHhhcCCCEEE-EEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVM-AKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       491 ~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~-v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ...|.+++||+.|+++||.+||+-.--|.. |.++.|. .+++.|-|||.|++.++|++|+.. +...|+.|-|.|-.+
T Consensus       103 d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~-rgR~tGEAfVqF~sqe~ae~Al~r-hre~iGhRYIEvF~S  179 (510)
T KOG4211|consen  103 DGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQ-RGRPTGEAFVQFESQESAEIALGR-HRENIGHRYIEVFRS  179 (510)
T ss_pred             CceEEecCCCccCcHHHHHHHhcCCcccccceeeeccC-CCCcccceEEEecCHHHHHHHHHH-HHHhhccceEEeehh
Confidence            457999999999999999999998755544 5667776 688999999999999999999975 677788888888543

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

Probab=97.16  E-value=0.00032  Score=72.08  Aligned_cols=66  Identities=24%  Similarity=0.434  Sum_probs=54.1

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeec
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLE  559 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~  559 (797)
                      .-.||||.||..+++|++|+.+|+.|-....++|.. + .  .-..|||+|++.+.|..|+..|+|..|.
T Consensus       209 acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~-~-~--g~~vaf~~~~~~~~at~am~~lqg~~~s  274 (284)
T KOG1457|consen  209 ACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRA-R-G--GMPVAFADFEEIEQATDAMNHLQGNLLS  274 (284)
T ss_pred             hhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEec-C-C--CcceEeecHHHHHHHHHHHHHhhcceec
Confidence            456899999999999999999999997665555522 2 2  2358999999999999999999998663

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

Probab=97.10  E-value=0.0014  Score=67.89  Aligned_cols=77  Identities=22%  Similarity=0.434  Sum_probs=68.4

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeec-cceEEEEe
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLE-GRTIAVRV  567 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~-Gr~L~V~~  567 (797)
                      .....||+.||+..++.+.|..+|.+|....+|+++..+     ++.|||+|.+...|..|...|++..|- ...++|.+
T Consensus       144 ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~-----~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~  218 (221)
T KOG4206|consen  144 PPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPR-----SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITF  218 (221)
T ss_pred             CCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCC-----CceeEEecchhhhhHHHhhhhccceeccCceEEecc
Confidence            456789999999999999999999999999999988765     479999999999999999999998887 77888888


Q ss_pred             cCC
Q 040243          568 AGK  570 (797)
Q Consensus       568 A~~  570 (797)
                      +++
T Consensus       219 a~K  221 (221)
T KOG4206|consen  219 AKK  221 (221)
T ss_pred             cCC
Confidence            753

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

Probab=97.10  E-value=0.0046  Score=67.80  Aligned_cols=79  Identities=22%  Similarity=0.313  Sum_probs=70.3

Q ss_pred             CCCcEEEEecCCCC-CcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          489 LDDTNLYIGYLPPT-LDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       489 ~~~~tLfVgNLp~~-vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      ..++-+.|-+|... ++-+.|..+|-.||.|.+|++++.+.     |-|.|++.+..+.++|+..||+..+.|.+|.|.+
T Consensus       285 ~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk~-----gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~  359 (494)
T KOG1456|consen  285 APGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTKP-----GTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCV  359 (494)
T ss_pred             CCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeeccc-----ceeEEEcCcHHHHHHHHHHhccCccccceEEEee
Confidence            46778999999865 66678999999999999999999873     7999999999999999999999999999999999


Q ss_pred             cCCCC
Q 040243          568 AGKPP  572 (797)
Q Consensus       568 A~~~~  572 (797)
                      ++...
T Consensus       360 SkQ~~  364 (494)
T KOG1456|consen  360 SKQNF  364 (494)
T ss_pred             ccccc
Confidence            87543

>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]

Probab=97.04  E-value=0.0037  Score=67.68  Aligned_cols=104  Identities=29%  Similarity=0.350  Sum_probs=63.9

Q ss_pred             HHHHHHHHHHHHHHHHhCCCC-CCCCCCCCC----ceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEec
Q 040243          220 ERLNKERQEIISQIIKRNPAF-KPPADYRPP----KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRG  294 (797)
Q Consensus       220 ~~le~er~~li~~~~~~~p~~-~pp~dy~p~----~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrG  294 (797)
                      +.|......|.+++.+.--.- ++-+-+.|.    .++.||.+|.      --.|.|||.+|.|+|.|.+++||-|.|-=
T Consensus        96 eai~av~efI~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPN------stag~iigkggAtiK~~~Eqsga~iqisP  169 (402)
T KOG2191|consen   96 EALNAVHEFIADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPN------STAGMIIGKGGATIKAIQEQSGAWIQISP  169 (402)
T ss_pred             HHHHHHHHHHHHHHHHhHHhhcCCccccCCCCccccceeEEeccC------CcccceecCCcchHHHHHHhhCcceEecc
Confidence            455555555555554432222 211222332    3678999997      56799999999999999999999999972


Q ss_pred             cccccccccccccCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHhcCC
Q 040243          295 KGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQP  344 (797)
Q Consensus       295 kGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v~~A~~~I~~ll~~  344 (797)
                         .|+-+.          .+.|  .|.+...+.|.+.+|+++|-.-|++
T Consensus       170 ---qkpt~~----------sLqe--rvvt~sge~e~~~~A~~~IL~Ki~e  204 (402)
T KOG2191|consen  170 ---QKPTGI----------SLQE--RVVTVSGEPEQNMKAVSLILQKIQE  204 (402)
T ss_pred             ---cCCCCc----------ccee--EEEEecCCHHHHHHHHHHHHHHhhc
Confidence               111110          1111  3444445667777887777655543

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

Probab=97.02  E-value=0.0044  Score=72.37  Aligned_cols=76  Identities=16%  Similarity=0.324  Sum_probs=65.7

Q ss_pred             cEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       492 ~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      +-|-|.|++++++-+||.+||..|-.+-.-.+++-.+.|+..|-|.|.|++.++|.+|...|++..|..++|.|.+
T Consensus       868 ~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  868 RVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             eEEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            4788999999999999999999996554433344446899999999999999999999999999999999998875

>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=96.97  E-value=0.0016  Score=60.60  Aligned_cols=70  Identities=17%  Similarity=0.390  Sum_probs=44.3

Q ss_pred             cEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCce-----eeccceEEEE
Q 040243          492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGY-----RLEGRTIAVR  566 (797)
Q Consensus       492 ~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~-----~l~Gr~L~V~  566 (797)
                      +-|+|.++...++.++|+++|+.||.|..|.+.+.-      --|||-|.+.++|++|++.+.-.     .|.+..+.++
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~------~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~   75 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGD------TEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLE   75 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCC------CEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEE
Confidence            568999999999999999999999999998876643      38999999999999999876443     4556655554


Q ss_pred             e
Q 040243          567 V  567 (797)
Q Consensus       567 ~  567 (797)
                      +
T Consensus        76 v   76 (105)
T PF08777_consen   76 V   76 (105)
T ss_dssp             -
T ss_pred             E
Confidence            3

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

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

Probab=96.90  E-value=0.056  Score=59.62  Aligned_cols=38  Identities=21%  Similarity=0.332  Sum_probs=32.9

Q ss_pred             eEEEEecCHHHHHHHHHhcCceeec--cceEEEEecCCCC
Q 040243          535 YGFVKYADIQMANNAIASMNGYRLE--GRTIAVRVAGKPP  572 (797)
Q Consensus       535 faFV~F~s~e~A~~AI~~LnG~~l~--Gr~L~V~~A~~~~  572 (797)
                      -|.|+|++.+.|++|.+.|||..|.  --.|+|+||++..
T Consensus       161 QAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIeyAkP~r  200 (494)
T KOG1456|consen  161 QAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIEYAKPTR  200 (494)
T ss_pred             eeEEeechhHHHHHHHhhcccccccccceeEEEEecCcce
Confidence            6889999999999999999999875  3678999998754

>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]

Probab=96.84  E-value=0.0028  Score=68.58  Aligned_cols=37  Identities=38%  Similarity=0.551  Sum_probs=35.3

Q ss_pred             eEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEe
Q 040243          251 LQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIR  293 (797)
Q Consensus       251 ~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~Ir  293 (797)
                      +..||+||-      +-.|-|||-+|.||.+||+||||+|.+-
T Consensus        39 y~ikvLips------~AaGsIIGKGG~ti~~lqk~tgariklS   75 (402)
T KOG2191|consen   39 YFLKVLIPS------YAAGSIIGKGGQTIVQLQKETGARIKLS   75 (402)
T ss_pred             eEEEEEeec------ccccceeccchHHHHHHHhccCcEEEec
Confidence            788999998      8899999999999999999999999986

>PF12353 eIF3g: Eukaryotic translation initiation factor 3 subunit G ; InterPro: IPR024675 At least eleven different protein factors are involved in initiation of protein synthesis in eukaryotes

Probab=96.75  E-value=0.00058  Score=65.72  Aligned_cols=24  Identities=50%  Similarity=0.796  Sum_probs=21.8

Q ss_pred             cccccceecCCCCCCcccCCCCCcC
Q 040243          394 KSDVLCKICGDGGHPTIDCLVKGTT  418 (797)
Q Consensus       394 ~~~v~Cr~CG~~gH~t~dCp~k~~~  418 (797)
                      ...|+||+|+ ++|||..||||+++
T Consensus       104 ~~~v~CR~Ck-GdH~T~~CPyKd~~  127 (128)
T PF12353_consen  104 KSKVKCRICK-GDHWTSKCPYKDTL  127 (128)
T ss_pred             CceEEeCCCC-CCcccccCCccccc
Confidence            5789999997 99999999999875

Binding of initiator tRNA and mRNA to the 40S subunit requires the presence of the translation initiation factors eIF-2 and eIF-3, with eIF-3 being particularly important for 80S ribosome dissociation and mRNA binding []. eIF-3 is the most complex translation inititation factor, consisting of about 13 putative subunits and having a molecular weight of between 550 - 700 kDa in mammalian cells. Subunits are designated eIF-3a - eIF-3m; the large number of subunits means that the interactions between the individual subunits that make up the eIF-3 complex are complex and varied. Subunit G is required for eIF3 integrity. This entry represents a domain of approximately 130 amino acids in length found at the N terminus of eukaryotic translation initiation factor 3 subunit G. This domain is commonly found in association with the RNA recognition domain PF00076 from PFAM.

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

Probab=96.69  E-value=0.013  Score=64.47  Aligned_cols=78  Identities=17%  Similarity=0.279  Sum_probs=65.3

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCC-CEEE--EEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFG-DIVM--AKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG-~I~~--v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      ....|.+++|++..+-+||.++|..|. .|..  |+++.+. -|+..|-|||+|.+.++|..|..+.+.+....|-|.|-
T Consensus       279 ~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~-qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvf  357 (508)
T KOG1365|consen  279 SKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNG-QGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVF  357 (508)
T ss_pred             CCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcC-CCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEe
Confidence            355799999999999999999999986 3444  7888875 68999999999999999999998877776778888885


Q ss_pred             ec
Q 040243          567 VA  568 (797)
Q Consensus       567 ~A  568 (797)
                      -+
T Consensus       358 p~  359 (508)
T KOG1365|consen  358 PC  359 (508)
T ss_pred             ec
Confidence            43

>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]

Probab=96.66  E-value=0.0078  Score=69.90  Aligned_cols=103  Identities=22%  Similarity=0.332  Sum_probs=72.1

Q ss_pred             HHHHHHHHHHHHHHHHHhCCCCCCCCCCCCC-ceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEecccc
Q 040243          219 RERLNKERQEIISQIIKRNPAFKPPADYRPP-KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGS  297 (797)
Q Consensus       219 ~~~le~er~~li~~~~~~~p~~~pp~dy~p~-~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS  297 (797)
                      .+.|.+.-..||..+..-+-.+..-...... .++.++.||-      +-||-|||-+|+.||+|.++|||+|.|-++ .
T Consensus       105 ~~al~ka~~~iv~~~~~d~~~~~d~~~~~~~~~v~~RLlVp~------sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~-~  177 (485)
T KOG2190|consen  105 TDALFKAFDMIVFKLEEDDEAAEDNGEDASGPEVTCRLLVPS------SQVGSLIGKGGSLIKEIREETGAKIRVSSD-M  177 (485)
T ss_pred             HHHHHHHHHHHhhcccccccccccCCccccCCceEEEEEech------hheeeeeccCcHHHHHHHHhcCceEEecCC-C
Confidence            3667777777777654222222211111222 4788999998      889999999999999999999999999965 1


Q ss_pred             ccccccccccCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHhcCC
Q 040243          298 VKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQP  344 (797)
Q Consensus       298 ~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v~~A~~~I~~ll~~  344 (797)
                                    .+...|-+ |.|+|. .++|.+|+..|-.+|..
T Consensus       178 --------------lP~ster~-V~IsG~-~~av~~al~~Is~~L~~  208 (485)
T KOG2190|consen  178 --------------LPNSTERA-VTISGE-PDAVKKALVQISSRLLE  208 (485)
T ss_pred             --------------CCccccee-EEEcCc-hHHHHHHHHHHHHHHHh
Confidence                          12233333 777775 67899998888887764

>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional

Probab=96.66  E-value=0.0012  Score=64.86  Aligned_cols=43  Identities=35%  Similarity=0.697  Sum_probs=22.3

Q ss_pred             hhcccCCCCCccccCCCCCCCccccccceecCCCCCCcccCCC
Q 040243          372 YCRLCGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTIDCLV  414 (797)
Q Consensus       372 ~c~~cg~~gh~~~~cp~~~~~~~~~v~Cr~CG~~gH~t~dCp~  414 (797)
                      .|.+|++.||...+|++........++|.+||+.|||+.||+.
T Consensus       105 ~C~~Cg~~gH~~~~C~~~~~~~~~~~~C~~Cg~~gH~~~dCp~  147 (148)
T PTZ00368        105 ACYNCGGEGHISRDCPNAGKRPGGDKTCYNCGQTGHLSRDCPD  147 (148)
T ss_pred             hhcccCcCCcchhcCCCccccCCCCCccccCCCcCcccccCCC
Confidence            4555555555555555542222334555555555555555554

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=96.56  E-value=0.0032  Score=72.10  Aligned_cols=76  Identities=36%  Similarity=0.493  Sum_probs=61.6

Q ss_pred             CcEEEEecCCCCCc------HHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeec-cceE
Q 040243          491 DTNLYIGYLPPTLD------DDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLE-GRTI  563 (797)
Q Consensus       491 ~~tLfVgNLp~~vt------e~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~-Gr~L  563 (797)
                      ..-|+|.|+|---.      ..-|..+|+++|.|+.+.+..+..+| ++||.|++|.+..+|+.|++.|||+.|+ ...+
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            34688988885322      23466899999999999998887555 9999999999999999999999999987 4556


Q ss_pred             EEEe
Q 040243          564 AVRV  567 (797)
Q Consensus       564 ~V~~  567 (797)
                      .|..
T Consensus       137 ~v~~  140 (698)
T KOG2314|consen  137 FVRL  140 (698)
T ss_pred             Eeeh
Confidence            6653

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=96.51  E-value=0.0021  Score=71.31  Aligned_cols=74  Identities=31%  Similarity=0.479  Sum_probs=52.2

Q ss_pred             ecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHHHHHHHHH
Q 040243          257 IPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAA  336 (797)
Q Consensus       257 IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v~~A~~  336 (797)
                      ||.+-.-.-||+|||||-.|.+||+||.+||+||.|--   .-        +..   ..+-.-.+.|-| +-|.+..|-+
T Consensus       280 ~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~---lq--------els---~ynpERTItVkG-siEac~~AE~  344 (584)
T KOG2193|consen  280 IPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISK---LQ--------ELS---LYNPERTITVKG-SIEACVQAEA  344 (584)
T ss_pred             cchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeee---hh--------hhc---ccCccceEEecc-cHHHHHHHHH
Confidence            33333333499999999999999999999999999961   11        111   122344778888 7788888888


Q ss_pred             HHHHhcCCC
Q 040243          337 MVEKLLQPV  345 (797)
Q Consensus       337 ~I~~ll~~~  345 (797)
                      +|-+-|...
T Consensus       345 eImkKlre~  353 (584)
T KOG2193|consen  345 EIMKKLREC  353 (584)
T ss_pred             HHHHHHHHH
Confidence            877766643

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=96.45  E-value=0.002  Score=67.63  Aligned_cols=72  Identities=18%  Similarity=0.379  Sum_probs=62.2

Q ss_pred             CcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCC--------Ccccce----EEEEecCHHHHHHHHHhcCceee
Q 040243          491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVT--------GMSKGY----GFVKYADIQMANNAIASMNGYRL  558 (797)
Q Consensus       491 ~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~T--------GksrGf----aFV~F~s~e~A~~AI~~LnG~~l  558 (797)
                      .--||+++||..++-..|+++|++||+|-+|+|.....+        |.++.+    |.|+|.+...|.++.+.||+..|
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            347999999999999999999999999999999877655        334433    45999999999999999999999


Q ss_pred             ccce
Q 040243          559 EGRT  562 (797)
Q Consensus       559 ~Gr~  562 (797)
                      +|++
T Consensus       154 ggkk  157 (278)
T KOG3152|consen  154 GGKK  157 (278)
T ss_pred             CCCC
Confidence            9876

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=96.45  E-value=0.0026  Score=70.58  Aligned_cols=71  Identities=27%  Similarity=0.481  Sum_probs=53.7

Q ss_pred             eEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHHH
Q 040243          251 LQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQES  330 (797)
Q Consensus       251 ~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~  330 (797)
                      +-.+++||.      .|+|.|||+.|.|||.|-+.|-|||.|..+-  +.|            ..+..|.|+   .+.|.
T Consensus       199 ~PlR~lVpt------qyvgaIIGkeG~TIknItkqTqsriD~hrke--n~G------------aaek~itvh---~tpEg  255 (584)
T KOG2193|consen  199 WPLRLLVPT------QYVGAIIGKEGATIKNITKQTQSRIDVHRKE--NAG------------AAEKIITVH---STPEG  255 (584)
T ss_pred             cceeeeecc------ceeEEEecCCCccccCcchhhhheeeeeecc--cCC------------cccCceEEe---cCccc
Confidence            456788888      8999999999999999999999999998653  111            122233443   34567


Q ss_pred             HHHHHHHHHHhcCC
Q 040243          331 LEGAAAMVEKLLQP  344 (797)
Q Consensus       331 v~~A~~~I~~ll~~  344 (797)
                      ..+||++|-+++..
T Consensus       256 ~s~Ac~~ILeimqk  269 (584)
T KOG2193|consen  256 TSKACKMILEIMQK  269 (584)
T ss_pred             hHHHHHHHHHHHHH
Confidence            77899999998874

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

Probab=96.42  E-value=0.011  Score=64.50  Aligned_cols=79  Identities=16%  Similarity=0.287  Sum_probs=63.3

Q ss_pred             CCCCcEEEEecCCC----CCc-------HHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCce
Q 040243          488 ELDDTNLYIGYLPP----TLD-------DDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGY  556 (797)
Q Consensus       488 ~~~~~tLfVgNLp~----~vt-------e~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~  556 (797)
                      ....++|.|.||=.    ..+       +++|++-.++||.|.+|.|.-.    ...|.+-|.|.+.+.|..||+.|+|.
T Consensus       262 ~r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d~----hPdGvvtV~f~n~eeA~~ciq~m~GR  337 (382)
T KOG1548|consen  262 ARADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYDR----HPDGVVTVSFRNNEEADQCIQTMDGR  337 (382)
T ss_pred             ccCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEecc----CCCceeEEEeCChHHHHHHHHHhcCe
Confidence            35677899998732    222       3566777899999999977533    36799999999999999999999999


Q ss_pred             eeccceEEEEecCC
Q 040243          557 RLEGRTIAVRVAGK  570 (797)
Q Consensus       557 ~l~Gr~L~V~~A~~  570 (797)
                      .|+||.|...+...
T Consensus       338 ~fdgRql~A~i~DG  351 (382)
T KOG1548|consen  338 WFDGRQLTASIWDG  351 (382)
T ss_pred             eecceEEEEEEeCC
Confidence            99999999886543

>PRK00106 hypothetical protein; Provisional

Probab=96.41  E-value=0.022  Score=66.90  Aligned_cols=98  Identities=22%  Similarity=0.353  Sum_probs=73.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCCCCceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEec
Q 040243          215 EYRARERLNKERQEIISQIIKRNPAFKPPADYRPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRG  294 (797)
Q Consensus       215 e~r~~~~le~er~~li~~~~~~~p~~~pp~dy~p~~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrG  294 (797)
                      |..+++..+++-.+||..+++...     .+|.--..+--|.+|-+     ++-|+|||-.|.++|.||.-||+.|.|..
T Consensus       194 e~~a~~~a~~~a~~ii~~aiqr~a-----~~~~~e~tvs~v~lp~d-----emkGriIGreGrNir~~E~~tGvdliidd  263 (535)
T PRK00106        194 EREVKDRSDKMAKDLLAQAMQRLA-----GEYVTEQTITTVHLPDD-----NMKGRIIGREGRNIRTLESLTGIDVIIDD  263 (535)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhc-----chhhhhheeeeEEcCCh-----HhhcceeCCCcchHHHHHHHhCceEEEcC
Confidence            334555555555566665555543     25554566777888876     56699999999999999999999999984


Q ss_pred             cccccccccccccCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHhcCC
Q 040243          295 KGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQP  344 (797)
Q Consensus       295 kGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v~~A~~~I~~ll~~  344 (797)
                      .-                      =-|.|++.|.-.-+-|..-+++||..
T Consensus       264 tp----------------------~~v~lS~fdpvRReiAr~~le~Li~d  291 (535)
T PRK00106        264 TP----------------------EVVVLSGFDPIRREIARMTLESLIKD  291 (535)
T ss_pred             CC----------------------CeEEEeCCChHHHHHHHHHHHHHHHc
Confidence            32                      27999999998888888888888864

>KOG3671 consensus Actin regulatory protein (Wiskott-Aldrich syndrome protein) [Signal transduction mechanisms; Cytoskeleton]

Probab=96.35  E-value=0.13  Score=58.71  Aligned_cols=14  Identities=43%  Similarity=0.527  Sum_probs=10.2

Q ss_pred             CcHHHHHHHhhcCC
Q 040243          503 LDDDGLIRLFSTFG  516 (797)
Q Consensus       503 vte~dL~~~Fs~fG  516 (797)
                      -.+..|..+|++.|
T Consensus       264 ~~dp~~nn~~s~ag  277 (569)
T KOG3671|consen  264 NNDPPLNNLFSSAG  277 (569)
T ss_pred             CCChhhhcccccCC
Confidence            34567888888886

>PRK12704 phosphodiesterase; Provisional

Probab=96.35  E-value=0.024  Score=66.76  Aligned_cols=97  Identities=29%  Similarity=0.369  Sum_probs=71.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCCCCceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEec
Q 040243          215 EYRARERLNKERQEIISQIIKRNPAFKPPADYRPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRG  294 (797)
Q Consensus       215 e~r~~~~le~er~~li~~~~~~~p~~~pp~dy~p~~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrG  294 (797)
                      |..+++..+++-.+||-.+++...     .+|.--..+--|.||-+     ++-|+|||-.|.++|.||.-||+.|.|..
T Consensus       179 ~~~~~~~a~~~a~~i~~~a~qr~a-----~~~~~e~~~~~v~lp~d-----~mkgriigreGrnir~~e~~tgvd~iidd  248 (520)
T PRK12704        179 EEEAKEEADKKAKEILAQAIQRCA-----ADHVAETTVSVVNLPND-----EMKGRIIGREGRNIRALETLTGVDLIIDD  248 (520)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhc-----chhhhhhceeeeecCCc-----hhhcceeCCCcchHHHHHHHhCCeEEEcC
Confidence            334455555555566665555543     35555566667788876     56699999999999999999999999984


Q ss_pred             cccccccccccccCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHhcC
Q 040243          295 KGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQ  343 (797)
Q Consensus       295 kGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v~~A~~~I~~ll~  343 (797)
                      .                      |=-|+||+.+.-.-+.|...++.|+.
T Consensus       249 t----------------------p~~v~ls~~~~~rre~a~~~l~~l~~  275 (520)
T PRK12704        249 T----------------------PEAVILSGFDPIRREIARLALEKLVQ  275 (520)
T ss_pred             C----------------------CCeEEEecCChhhHHHHHHHHHHHHh
Confidence            3                      22799999998776677777777765

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

Probab=96.29  E-value=0.012  Score=64.80  Aligned_cols=74  Identities=18%  Similarity=0.193  Sum_probs=56.2

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcC----CCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEE
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTF----GDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAV  565 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~f----G~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V  565 (797)
                      +.-.|.+++|++++++.++.++|..-    |.+..|.+++. -+|+..|-|||.|..+++|+.||.+ +...|+-|-|.|
T Consensus       160 ~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~r-pdgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYIEl  237 (508)
T KOG1365|consen  160 NQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTR-PDGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYIEL  237 (508)
T ss_pred             cceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEEC-CCCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHHHH
Confidence            44568888999999999999999742    34445555554 3799999999999999999999975 444455555554

>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]

Probab=96.28  E-value=0.0043  Score=67.47  Aligned_cols=61  Identities=26%  Similarity=0.438  Sum_probs=53.2

Q ss_pred             ceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHhcCCC
Q 040243          266 NFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQPV  345 (797)
Q Consensus       266 NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v~~A~~~I~~ll~~~  345 (797)
                      -|+|.|||=+|.|.|+||+||+|+|.|=-.+..+                   =||.|++-..++|-+|.+.|..+|.++
T Consensus        66 ~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n~-------------------~~i~i~~~~~~~V~~a~~Ri~~~ids~  126 (345)
T KOG2814|consen   66 SFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNK-------------------EEIKIIGISRNCVIQALERIAKLIDSD  126 (345)
T ss_pred             HHhhhhhcccchHHHHHHHhhccceEccCCCCCc-------------------ceEEEeehhHHHHHHHHHHHHHHHHhh
Confidence            7899999999999999999999999987544211                   189999999999999999999998764

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=96.20  E-value=0.03  Score=65.83  Aligned_cols=96  Identities=26%  Similarity=0.358  Sum_probs=71.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCCCCCCCCCCceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccc
Q 040243          217 RARERLNKERQEIISQIIKRNPAFKPPADYRPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKG  296 (797)
Q Consensus       217 r~~~~le~er~~li~~~~~~~p~~~pp~dy~p~~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkG  296 (797)
                      .+++..+++-.+||..+++...     .+|.--..+.-|.||-+     ++-|+|||-.|.++|.||..||+.|.|...-
T Consensus       175 ~~~~~a~~~a~~i~~~aiqr~a-----~~~~~e~~~~~v~lp~d-----~~kgriigreGrnir~~e~~tgvd~iiddtp  244 (514)
T TIGR03319       175 EAKEEADKKAKEILATAIQRYA-----GDHVAETTVSVVNLPND-----EMKGRIIGREGRNIRALETLTGVDLIIDDTP  244 (514)
T ss_pred             HHHHHHHHHHHHHHHHHHHhcc-----chhhhhheeeeEEcCCh-----hhhccccCCCcchHHHHHHHhCceEEEcCCC
Confidence            4444445555555555555443     35555566777888887     5669999999999999999999999998532


Q ss_pred             cccccccccccCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHhcCC
Q 040243          297 SVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQP  344 (797)
Q Consensus       297 S~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v~~A~~~I~~ll~~  344 (797)
                                            =-|.|++.|.-.-+-|..-+++||..
T Consensus       245 ----------------------~~v~ls~fdp~rreia~~~l~~li~d  270 (514)
T TIGR03319       245 ----------------------EAVILSGFDPVRREIARMALEKLIQD  270 (514)
T ss_pred             ----------------------CeEEecCCchHHHHHHHHHHHHHHHc
Confidence                                  27899999998888888888888763

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=96.18  E-value=0.01  Score=48.41  Aligned_cols=52  Identities=27%  Similarity=0.511  Sum_probs=41.4

Q ss_pred             cEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHH
Q 040243          492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAI  550 (797)
Q Consensus       492 ~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI  550 (797)
                      +.|-|.+.+.+..+ ++..+|..||+|.++.+-..      .-+.||.|.++.+|++||
T Consensus         2 ~wI~V~Gf~~~~~~-~vl~~F~~fGeI~~~~~~~~------~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAE-EVLEHFASFGEIVDIYVPES------TNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHH-HHHHHHHhcCCEEEEEcCCC------CcEEEEEECCHHHHHhhC
Confidence            46778888876654 45568999999999887522      349999999999999985

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []

Probab=96.05  E-value=0.025  Score=52.31  Aligned_cols=78  Identities=22%  Similarity=0.351  Sum_probs=51.5

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEE-EEecC------CCCcccceEEEEecCHHHHHHHHHhcCceeeccc
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAK-VIKDR------VTGMSKGYGFVKYADIQMANNAIASMNGYRLEGR  561 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~-v~~dk------~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr  561 (797)
                      .+.+-|.|-+.+.. ....+.+.|++||.|++.. +.++.      ..-....+-.|+|++..+|.+||. .||..|.|.
T Consensus         4 ~~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~   81 (100)
T PF05172_consen    4 DSETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGS   81 (100)
T ss_dssp             GGCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTC
T ss_pred             cCCeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCc
Confidence            34566888898887 5567888999999998875 11100      001123588999999999999996 599999986


Q ss_pred             eE-EEEec
Q 040243          562 TI-AVRVA  568 (797)
Q Consensus       562 ~L-~V~~A  568 (797)
                      .| -|.+.
T Consensus        82 ~mvGV~~~   89 (100)
T PF05172_consen   82 LMVGVKPC   89 (100)
T ss_dssp             EEEEEEE-
T ss_pred             EEEEEEEc
Confidence            54 46654

This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A.

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=95.95  E-value=0.008  Score=67.12  Aligned_cols=81  Identities=21%  Similarity=0.288  Sum_probs=63.4

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEec---CCCCc----------ccceEEEEecCHHHHHHHHHhc
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKD---RVTGM----------SKGYGFVKYADIQMANNAIASM  553 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~d---k~TGk----------srGfaFV~F~s~e~A~~AI~~L  553 (797)
                      .+...++|.+-||+.+-.-+.|.++|+.||.|..|+|...   ..+.+          .+-+|||+|+..+.|.+|.+.|
T Consensus       227 eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~  306 (484)
T KOG1855|consen  227 EELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELL  306 (484)
T ss_pred             cccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhh
Confidence            4467899999999999888999999999999999999776   22221          2568999999999999999988


Q ss_pred             CceeeccceEEEEe
Q 040243          554 NGYRLEGRTIAVRV  567 (797)
Q Consensus       554 nG~~l~Gr~L~V~~  567 (797)
                      +-....-.-|+|++
T Consensus       307 ~~e~~wr~glkvkL  320 (484)
T KOG1855|consen  307 NPEQNWRMGLKVKL  320 (484)
T ss_pred             chhhhhhhcchhhh
Confidence            65443333355544

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

Probab=95.71  E-value=0.023  Score=64.93  Aligned_cols=64  Identities=23%  Similarity=0.383  Sum_probs=58.9

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhh-cCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHh
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFS-TFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS  552 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs-~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~  552 (797)
                      +..+|||||+|+.-++.++|..+|. -||.|.-+-|=.|..-+..||-|=|+|.+..+-.+||..
T Consensus       368 DprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  368 DPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             CccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            3567999999999999999999999 599999999999977889999999999999999999973

>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=95.70  E-value=0.005  Score=39.31  Aligned_cols=17  Identities=41%  Similarity=0.835  Sum_probs=15.2

Q ss_pred             ccceecCCCCCCcccCC
Q 040243          397 VLCKICGDGGHPTIDCL  413 (797)
Q Consensus       397 v~Cr~CG~~gH~t~dCp  413 (797)
                      ++|..||+.||+++||+
T Consensus         1 ~~C~~C~~~GH~~~~Cp   17 (18)
T PF00098_consen    1 RKCFNCGEPGHIARDCP   17 (18)
T ss_dssp             SBCTTTSCSSSCGCTSS
T ss_pred             CcCcCCCCcCcccccCc
Confidence            47999999999999997

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....

>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional

Probab=95.60  E-value=0.0077  Score=59.10  Aligned_cols=43  Identities=35%  Similarity=0.732  Sum_probs=21.6

Q ss_pred             hhcccCCCCCccccCCCCCCCccccccceecCCCCCCcccCCC
Q 040243          372 YCRLCGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTIDCLV  414 (797)
Q Consensus       372 ~c~~cg~~gh~~~~cp~~~~~~~~~v~Cr~CG~~gH~t~dCp~  414 (797)
                      .|.+|++.||...+|++........++|.+|+..||++.+|+.
T Consensus        79 ~C~~Cg~~GH~~~~C~~~~~~~~~~~~C~~Cg~~gH~~~~C~~  121 (148)
T PTZ00368         79 SCYNCGQTGHISRECPNRAKGGAARRACYNCGGEGHISRDCPN  121 (148)
T ss_pred             ccCcCCCCCcccccCCCcccccccchhhcccCcCCcchhcCCC
Confidence            4555555555555555543222334455555555555555553

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

Probab=95.50  E-value=0.029  Score=64.93  Aligned_cols=64  Identities=17%  Similarity=0.303  Sum_probs=52.8

Q ss_pred             HHHHHHhhcCCCEEEEEEEecC---CCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          506 DGLIRLFSTFGDIVMAKVIKDR---VTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       506 ~dL~~~Fs~fG~I~~v~v~~dk---~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      ++++.-+++||.|..|.+.++-   .-.-..|--||+|.+.+++++|.+.|+|..|.+|.+...|-.
T Consensus       424 Edvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYyd  490 (500)
T KOG0120|consen  424 EDVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYD  490 (500)
T ss_pred             HHHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecC
Confidence            3456667899999999988772   223355788999999999999999999999999999888753

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

Probab=95.21  E-value=0.015  Score=69.83  Aligned_cols=80  Identities=21%  Similarity=0.213  Sum_probs=72.9

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      ....|||.|+++..|.++|+.+|..+|.+.+++++..+ .|+.+|.|||.|.++.++.+++...+...+.-+.+.|.++.
T Consensus       735 gK~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r-~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsn  813 (881)
T KOG0128|consen  735 GKISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVR-AGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSN  813 (881)
T ss_pred             hhhhhheeCCCCCCchHHHHhhccccCCccccchhhhh-ccccccceeccCCCcchhhhhcccchhhhhhhcCccccccC
Confidence            45789999999999999999999999999999998887 79999999999999999999999888888888888888765


Q ss_pred             C
Q 040243          570 K  570 (797)
Q Consensus       570 ~  570 (797)
                      .
T Consensus       814 p  814 (881)
T KOG0128|consen  814 P  814 (881)
T ss_pred             C
Confidence            4

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

Probab=95.16  E-value=0.038  Score=61.58  Aligned_cols=77  Identities=17%  Similarity=0.269  Sum_probs=64.0

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccc-eEEEEec
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGR-TIAVRVA  568 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr-~L~V~~A  568 (797)
                      ...+|...|++.+++|++|+++|..-|-..+.+...    ++.+-++++.+.+.+.|..|+-.++.+.++.. .|+|+|+
T Consensus       413 psatlHlsnip~svsee~lk~~f~~~g~~vkafkff----~kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvSFS  488 (492)
T KOG1190|consen  413 PSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFF----QKDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVSFS  488 (492)
T ss_pred             chhheeeccCCcccchhHHHHhhhcCCceEEeeeec----CCCcceeecccCChhHhhhhccccccccCCCCceEEEEee
Confidence            356899999999999999999999988766554332    23445999999999999999999999888765 8999998


Q ss_pred             CC
Q 040243          569 GK  570 (797)
Q Consensus       569 ~~  570 (797)
                      +.
T Consensus       489 ks  490 (492)
T KOG1190|consen  489 KS  490 (492)
T ss_pred             cc
Confidence            64

>PF13696 zf-CCHC_2: Zinc knuckle

Probab=95.12  E-value=0.011  Score=43.27  Aligned_cols=21  Identities=33%  Similarity=0.771  Sum_probs=18.9

Q ss_pred             ccccceecCCCCCCcccCCCC
Q 040243          395 SDVLCKICGDGGHPTIDCLVK  415 (797)
Q Consensus       395 ~~v~Cr~CG~~gH~t~dCp~k  415 (797)
                      ...+|++|+..|||..|||.+
T Consensus         7 ~~Y~C~~C~~~GH~i~dCP~~   27 (32)
T PF13696_consen    7 PGYVCHRCGQKGHWIQDCPTN   27 (32)
T ss_pred             CCCEeecCCCCCccHhHCCCC
Confidence            567999999999999999984

>KOG3671 consensus Actin regulatory protein (Wiskott-Aldrich syndrome protein) [Signal transduction mechanisms; Cytoskeleton]

Probab=95.07  E-value=0.82  Score=52.57  Aligned_cols=58  Identities=10%  Similarity=0.166  Sum_probs=23.8

Q ss_pred             HHHHHHHHHHHHHHHH-HHHhCCCCCCCCCCCCCceEEEEEecCCCCCCCceeeeeeCCCc
Q 040243          217 RARERLNKERQEIISQ-IIKRNPAFKPPADYRPPKLQKKLYIPMKEYPGYNFIGLIIGPRG  276 (797)
Q Consensus       217 r~~~~le~er~~li~~-~~~~~p~~~pp~dy~p~~~~~Ki~IP~~~~P~~NfiG~iiGPrG  276 (797)
                      .+++.|-+ ...||.. ..++.-.|.....|+-.-+. -+..=||++..--|.=+|+.=.+
T Consensus        28 ~lf~~lgk-~~~~l~aAVVqLY~a~p~~~~W~~~~~~-Gal~lVkD~~~rsyFlrl~di~~   86 (569)
T KOG3671|consen   28 TLFKLLGK-KCKTLAAAVVQLYKAYPDPNHWNKTGLC-GALCLVKDNAQRSYFLRLVDIVN   86 (569)
T ss_pred             HHHHHhcc-chhhHHHHHHHHHhhcCChhhhccccCc-eeEEEeeccccceeeeEEeeecC
Confidence            34444444 3333332 34455555444455433221 12222345554334444544333

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=95.02  E-value=0.073  Score=52.25  Aligned_cols=74  Identities=27%  Similarity=0.550  Sum_probs=52.7

Q ss_pred             CcEEEEecCCC------CCcH---HHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccc
Q 040243          491 DTNLYIGYLPP------TLDD---DGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGR  561 (797)
Q Consensus       491 ~~tLfVgNLp~------~vte---~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr  561 (797)
                      ..||.|.=+.+      .+.+   .+|.+.|..||+|.-++++.+        .-+|+|.+-++|.+|+. |+|..+.|+
T Consensus        27 DaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals-~dg~~v~g~   97 (146)
T PF08952_consen   27 DATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALS-LDGIQVNGR   97 (146)
T ss_dssp             T-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHH-GCCSEETTE
T ss_pred             CceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHc-cCCcEECCE
Confidence            44788876661      2333   267788899999998888765        67899999999999995 899999999


Q ss_pred             eEEEEecCCCCC
Q 040243          562 TIAVRVAGKPPQ  573 (797)
Q Consensus       562 ~L~V~~A~~~~~  573 (797)
                      .|+|++..+.+.
T Consensus        98 ~l~i~LKtpdW~  109 (146)
T PF08952_consen   98 TLKIRLKTPDWL  109 (146)
T ss_dssp             EEEEEE------
T ss_pred             EEEEEeCCccHH
Confidence            999998766553

; PDB: 1UFW_A 2DNR_A.

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

Probab=94.98  E-value=0.035  Score=63.54  Aligned_cols=64  Identities=17%  Similarity=0.337  Sum_probs=47.7

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEe-cCC--CCcccc---eEEEEecCHHHHHHHHHhc
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIK-DRV--TGMSKG---YGFVKYADIQMANNAIASM  553 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~-dk~--TGksrG---faFV~F~s~e~A~~AI~~L  553 (797)
                      .-.++||||+|++.++|+.|...|..||.+. |.+.. ...  --..+|   |+|+.|+++.++..-|...
T Consensus       257 ~~S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC  326 (520)
T KOG0129|consen  257 RYSRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSAC  326 (520)
T ss_pred             ccccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHH
Confidence            3467899999999999999999999999764 22221 111  112567   9999999999888766543

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=94.94  E-value=0.011  Score=62.37  Aligned_cols=62  Identities=19%  Similarity=0.309  Sum_probs=51.5

Q ss_pred             HHHHHhh-cCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          507 GLIRLFS-TFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       507 dL~~~Fs-~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      +|...|+ +||+|.+++|-.+. .-.-+|-.||.|..+++|++|++.||+..+.|+.|...+.-
T Consensus        84 d~f~E~~~kygEiee~~Vc~Nl-~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~p  146 (260)
T KOG2202|consen   84 DVFTELEDKYGEIEELNVCDNL-GDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSP  146 (260)
T ss_pred             HHHHHHHHHhhhhhhhhhhccc-chhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecC
Confidence            4444445 89999999776654 44568999999999999999999999999999999998753

>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]

Probab=94.73  E-value=0.062  Score=57.25  Aligned_cols=85  Identities=25%  Similarity=0.371  Sum_probs=58.3

Q ss_pred             eeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHhcCCChHH
Q 040243          269 GLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQPVDEV  348 (797)
Q Consensus       269 G~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v~~A~~~I~~ll~~~~e~  348 (797)
                      -|||||.|+|||.||=-|.|-|.|.|.                        .|.+.|. ...|..+..+|+..+..++.-
T Consensus       161 qRLiGpng~TLKAlelLT~CYilVqG~------------------------TVsaiGp-fkGlkevr~IV~DcM~NiHPi  215 (356)
T KOG2874|consen  161 QRLIGPNGSTLKALELLTNCYILVQGN------------------------TVSAIGP-FKGLKEVRKIVEDCMKNIHPI  215 (356)
T ss_pred             HHhcCCCchhHHHHHHHhhcEEEeeCc------------------------EEEeecC-cchHHHHHHHHHHHHhccchH
Confidence            589999999999999999999999975                        3444443 346777777777777777766


Q ss_pred             HHHHHHHHHHHHHhhcCCcCccchhcccCCC
Q 040243          349 LNEHKRQQLRELAALNGTIRDEEYCRLCGEP  379 (797)
Q Consensus       349 ~n~~k~~Ql~ela~lnGt~r~~~~c~~cg~~  379 (797)
                      +|--.-.--|||+. +-+|.+++|.+.--.+
T Consensus       216 Y~IK~LmiKRel~k-d~~l~ne~W~rfLP~f  245 (356)
T KOG2874|consen  216 YNIKTLMIKRELAK-DPELANEDWSRFLPQF  245 (356)
T ss_pred             HHHHHHHHHHHhhc-ChhhccccHHHHhHHh
Confidence            54322233356654 4477777666554433

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

Probab=94.73  E-value=3.9  Score=49.53  Aligned_cols=35  Identities=17%  Similarity=0.228  Sum_probs=25.9

Q ss_pred             ccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          532 SKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       532 srGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      .+|+.+|=++...++.+|+.  .|.+|++-.+...|.
T Consensus       508 ~lGVt~IP~~kLt~dl~~~~--egam~d~~t~~p~~k  542 (894)
T KOG0132|consen  508 ELGVTYIPWEKLTDDLEAWC--EGAMLDGTTGPPEWK  542 (894)
T ss_pred             ccCeeEeehHhcCHHHHHhh--hhceecCccCCcccc
Confidence            45888998988888877764  588888776666553

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

Probab=94.54  E-value=0.0029  Score=75.60  Aligned_cols=70  Identities=19%  Similarity=0.361  Sum_probs=61.5

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeec
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLE  559 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~  559 (797)
                      +..++||.||+..+.+.+|...|..+|.+..+.+...+.+++.||+|||+|.+.+++.+||...++..++
T Consensus       666 ~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~g  735 (881)
T KOG0128|consen  666 DLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFG  735 (881)
T ss_pred             HHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhh
Confidence            4578999999999999999999999998888877766778999999999999999999999876665555

>PRK12705 hypothetical protein; Provisional

Probab=94.51  E-value=0.13  Score=60.22  Aligned_cols=101  Identities=24%  Similarity=0.284  Sum_probs=69.4

Q ss_pred             cChHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCCCCceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEE
Q 040243          211 INTREYRARERLNKERQEIISQIIKRNPAFKPPADYRPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKI  290 (797)
Q Consensus       211 ~ntre~r~~~~le~er~~li~~~~~~~p~~~pp~dy~p~~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI  290 (797)
                      +.-.|..+++..+++-.+||..+++....     +|.--...--|.+|-+     ++-|+|||-.|.++|.||..||+.|
T Consensus       163 i~~~e~~~~~~a~~~A~~ii~~aiqr~a~-----~~~~e~tvs~v~lp~d-----emkGriIGreGrNir~~E~~tGvdl  232 (508)
T PRK12705        163 VKKIEEEADLEAERKAQNILAQAMQRIAS-----ETASDLSVSVVPIPSD-----AMKGRIIGREGRNIRAFEGLTGVDL  232 (508)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhcc-----chhhhheeeeeecCCh-----HhhccccCccchhHHHHHHhhCCce
Confidence            33444455666666666676666655532     4444456667778866     5679999999999999999999999


Q ss_pred             EEeccccccccccccccCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHhcC
Q 040243          291 VIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQ  343 (797)
Q Consensus       291 ~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v~~A~~~I~~ll~  343 (797)
                      .|...-                      =-|.|++.+...-+.|...+++||.
T Consensus       233 iiddtp----------------------~~V~ls~fdp~rreia~~~l~~Li~  263 (508)
T PRK12705        233 IIDDTP----------------------EAVVISSFNPIRREIARLTLEKLLA  263 (508)
T ss_pred             EecCCc----------------------cchhhcccCccchHHHHHHHHHHHh
Confidence            998532                      1366777777666666555655554

>KOG0307 consensus Vesicle coat complex COPII, subunit SEC31 [Intracellular trafficking, secretion, and vesicular transport]

Probab=94.30  E-value=2.3  Score=53.14  Aligned_cols=39  Identities=18%  Similarity=0.403  Sum_probs=20.1

Q ss_pred             cccccceecCCCCCCcccCCCCCcCCCCcchHHHHHHhh
Q 040243          394 KSDVLCKICGDGGHPTIDCLVKGTTGKKMDDEYQNFLAE  432 (797)
Q Consensus       394 ~~~v~Cr~CG~~gH~t~dCp~k~~~g~~ld~eY~~~m~E  432 (797)
                      ...+.|.||.+.=|=...|-++..........|+.+++.
T Consensus       605 ~~a~lcYi~agsv~k~v~~w~~~~~~~~~~~~y~~~~e~  643 (1049)
T KOG0307|consen  605 SAAILCYICAGSVDKLVEIWLKALDLELAPTSYQDLAED  643 (1049)
T ss_pred             hhhhHHhhhccChhhhHHHHHHhcccccchHHHHHHHHH
Confidence            357889999755554455544432221223445554443

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

Probab=94.27  E-value=0.056  Score=65.34  Aligned_cols=77  Identities=30%  Similarity=0.412  Sum_probs=66.7

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeecc--ceEEEEe
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEG--RTIAVRV  567 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~G--r~L~V~~  567 (797)
                      ..+.+||++|..|+....|...|..||.|..|.+-..      --||+|.|.+...|+.|++.|.|..|++  ++|+|.|
T Consensus       454 ~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hg------q~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdl  527 (975)
T KOG0112|consen  454 PTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHG------QPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDL  527 (975)
T ss_pred             cceeeccCCCCCCChHHHHHHHhhccCcceeeecccC------CcceeeecccCccchhhHHHHhcCcCCCCCccccccc
Confidence            4678999999999999999999999999998765332      2499999999999999999999999986  6799999


Q ss_pred             cCCCC
Q 040243          568 AGKPP  572 (797)
Q Consensus       568 A~~~~  572 (797)
                      |....
T Consensus       528 a~~~~  532 (975)
T KOG0112|consen  528 ASPPG  532 (975)
T ss_pred             ccCCC
Confidence            87543

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=94.21  E-value=0.041  Score=63.73  Aligned_cols=78  Identities=14%  Similarity=0.178  Sum_probs=64.9

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhc-CCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceee---ccce
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFST-FGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRL---EGRT  562 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~-fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l---~Gr~  562 (797)
                      +....+.|||.||-.-+|.-.|++++.+ +|.|.+.  .+|+    -|..|||.|.+.++|.+.+..|+|...   +.+.
T Consensus       440 R~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~--WmDk----IKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~  513 (718)
T KOG2416|consen  440 RKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF--WMDK----IKSHCYVSYSSVEEAAATREALHNVQWPPSNPKH  513 (718)
T ss_pred             CCCccceEeeecccccchHHHHHHHHhhccCchHHH--HHHH----hhcceeEecccHHHHHHHHHHHhccccCCCCCce
Confidence            4556789999999999999999999995 5666665  3443    567999999999999999999999764   5788


Q ss_pred             EEEEecCC
Q 040243          563 IAVRVAGK  570 (797)
Q Consensus       563 L~V~~A~~  570 (797)
                      |.+.|+..
T Consensus       514 L~adf~~~  521 (718)
T KOG2416|consen  514 LIADFVRA  521 (718)
T ss_pred             eEeeecch
Confidence            99998764

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

Probab=94.03  E-value=0.12  Score=55.56  Aligned_cols=64  Identities=16%  Similarity=0.222  Sum_probs=52.3

Q ss_pred             HHHHHHhhcCCCEEEEEEEecCCCCccc-ceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          506 DGLIRLFSTFGDIVMAKVIKDRVTGMSK-GYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       506 ~dL~~~Fs~fG~I~~v~v~~dk~TGksr-GfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      +++++.+++||.|..|.|+.+..--..+ ---||+|...++|.+|+--|||..|+||.++..|-.
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            4677889999999999888875322222 246999999999999999999999999998877643

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=93.98  E-value=0.024  Score=61.97  Aligned_cols=84  Identities=20%  Similarity=0.358  Sum_probs=65.1

Q ss_pred             CCCcEEEEecCCCCCcHHH-HH--HHhhcCCCEEEEEEEecCC--CCc-ccceEEEEecCHHHHHHHHHhcCceeeccce
Q 040243          489 LDDTNLYIGYLPPTLDDDG-LI--RLFSTFGDIVMAKVIKDRV--TGM-SKGYGFVKYADIQMANNAIASMNGYRLEGRT  562 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~d-L~--~~Fs~fG~I~~v~v~~dk~--TGk-srGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~  562 (797)
                      ...+-+||-+|+..+.+++ |+  +.|.+||.|.+|.+.++..  .+. ...-++|+|...++|.+||...+|..++|+.
T Consensus        75 Vqknlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~  154 (327)
T KOG2068|consen   75 VQKNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRA  154 (327)
T ss_pred             hhhhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhh
Confidence            3456789999998765554 43  7899999999998888762  111 1123799999999999999999999999999


Q ss_pred             EEEEecCCCC
Q 040243          563 IAVRVAGKPP  572 (797)
Q Consensus       563 L~V~~A~~~~  572 (797)
                      |+..+...+.
T Consensus       155 lka~~gttky  164 (327)
T KOG2068|consen  155 LKASLGTTKY  164 (327)
T ss_pred             hHHhhCCCcc
Confidence            8887776544

>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]

Probab=93.88  E-value=0.058  Score=59.94  Aligned_cols=63  Identities=22%  Similarity=0.278  Sum_probs=50.9

Q ss_pred             CCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHhcCC
Q 040243          274 PRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQP  344 (797)
Q Consensus       274 PrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v~~A~~~I~~ll~~  344 (797)
                      =||.|+..||++||+.|..||+--.-        +.......+.+|..+|.+.|.|-+++|++.|+-++..
T Consensus       111 TRg~~~d~Ie~~~G~~~~~RGs~~~~--------El~~vg~~~~pLv~hI~~~T~Ei~~~Ai~RIkgv~~~  173 (531)
T KOG1960|consen  111 TRGTSYDHIEGITGTTSASRGSAPAP--------ELPPVGSSEGPLVDHIPPSTAEITSKAIERIKGVFMQ  173 (531)
T ss_pred             ccchhHHhhhhhccceeeccCCCCCc--------cCCCCCCCCCcceeecCCccHHHHHHHHhhCccceee
Confidence            38999999999999999999864221        1223446788999999999999999999999966553

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

Probab=93.53  E-value=0.13  Score=60.62  Aligned_cols=77  Identities=16%  Similarity=0.088  Sum_probs=65.1

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEE-EEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVM-AKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~-v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      .....|||-.|+..+++.++.++|...-.|++ |.|.+-. +++.++.|||.|..++++..|+..-..+.++.+.|+|.
T Consensus       432 ~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~P-~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~  509 (944)
T KOG4307|consen  432 GAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRLP-TDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVD  509 (944)
T ss_pred             CccceEEeccCCccccccchhhhhhhhhhhhheeEeccCC-cccccchhhheeccccccchhhhcccccccCceEEEee
Confidence            34568999999999999999999999877777 6666665 88899999999999999888886656667778889995

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=93.41  E-value=0.32  Score=41.19  Aligned_cols=55  Identities=20%  Similarity=0.230  Sum_probs=46.0

Q ss_pred             CcEEEEecCCCCCcHHHHHHHhhcC---CCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhc
Q 040243          491 DTNLYIGYLPPTLDDDGLIRLFSTF---GDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM  553 (797)
Q Consensus       491 ~~tLfVgNLp~~vte~dL~~~Fs~f---G~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~L  553 (797)
                      ..+|+|.+++. ++.++|+.+|..|   ....+|.++-|.       -|-|.|.+.+.|.+||..|
T Consensus         5 peavhirGvd~-lsT~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    5 PEAVHIRGVDE-LSTDDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eceEEEEcCCC-CCHHHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            45899999964 7778999999998   245688899886       6789999999999999765

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=93.27  E-value=0.085  Score=55.85  Aligned_cols=67  Identities=25%  Similarity=0.267  Sum_probs=57.6

Q ss_pred             cEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeec
Q 040243          492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLE  559 (797)
Q Consensus       492 ~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~  559 (797)
                      ..|||.||...++.+.|...|+.||.|.+..++.|- .++..+-++|.|...-.|.+|+..++-..|.
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~-r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~~   98 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDD-RGKPTREGIVEFAKKPNARKAARRCREGGFG   98 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecc-cccccccchhhhhcchhHHHHHHHhccCccc
Confidence            679999999999999999999999999987666663 6888899999999999999999877543333

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=93.11  E-value=0.12  Score=57.46  Aligned_cols=76  Identities=20%  Similarity=0.295  Sum_probs=61.8

Q ss_pred             EEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCC---CCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRV---TGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       493 tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~---TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      .|-|.||...++.+.++.||.-.|.|.++.|+-+..   -....-.|||.|.+...+..|- .|..++|-++-|.|..+.
T Consensus         9 vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQ-hLtntvfvdraliv~p~~   87 (479)
T KOG4676|consen    9 VIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQ-HLTNTVFVDRALIVRPYG   87 (479)
T ss_pred             eeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHh-hhccceeeeeeEEEEecC
Confidence            699999999999999999999999999998876332   2234459999999999999886 577777777777776543

>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]

Probab=92.44  E-value=0.078  Score=54.04  Aligned_cols=42  Identities=33%  Similarity=0.668  Sum_probs=35.8

Q ss_pred             chhcccCCCCCccccC-CCCCCCccccccceecCCCCCCcccCCCCC
Q 040243          371 EYCRLCGEPGHRQYAC-PSRTSTFKSDVLCKICGDGGHPTIDCLVKG  416 (797)
Q Consensus       371 ~~c~~cg~~gh~~~~c-p~~~~~~~~~v~Cr~CG~~gH~t~dCp~k~  416 (797)
                      ..|.+||+.||..-+| |.+.    ..+.|+.|....|.+++|+.-.
T Consensus        98 ~~C~~Cg~~GH~~~dC~P~~~----~~~~C~~C~s~~H~s~~Cp~~~  140 (190)
T COG5082          98 KKCYNCGETGHLSRDCNPSKD----QQKSCFDCNSTRHSSEDCPSIW  140 (190)
T ss_pred             cccccccccCccccccCcccc----cCcceeccCCCccccccCcccc
Confidence            4799999999999999 5554    5568999999999999998743

>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]

Probab=92.28  E-value=0.08  Score=56.88  Aligned_cols=38  Identities=42%  Similarity=0.867  Sum_probs=21.3

Q ss_pred             hcccCCCCCccccCCCCCCCccccccceecCCCCCCcccCCCC
Q 040243          373 CRLCGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTIDCLVK  415 (797)
Q Consensus       373 c~~cg~~gh~~~~cp~~~~~~~~~v~Cr~CG~~gH~t~dCp~k  415 (797)
                      |-+||+.||...+|++.     ....|..|+..+|+.+||+.+
T Consensus       146 Cy~Cg~~GH~s~~C~~~-----~~~~c~~c~~~~h~~~~C~~~  183 (261)
T KOG4400|consen  146 CYSCGEQGHISDDCPEN-----KGGTCFRCGKVGHGSRDCPSK  183 (261)
T ss_pred             cCCCCcCCcchhhCCCC-----CCCccccCCCcceecccCCcc
Confidence            55566666666555543     334555565556666666544

>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=92.06  E-value=0.45  Score=41.31  Aligned_cols=67  Identities=19%  Similarity=0.423  Sum_probs=40.0

Q ss_pred             EEEEe-cCCCCCcHHHHHHHhhcCC-----CEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          493 NLYIG-YLPPTLDDDGLIRLFSTFG-----DIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       493 tLfVg-NLp~~vte~dL~~~Fs~fG-----~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      +|||. +--..++..+|..++...+     .|-+|.|..+        |+||+... +.|+.+++.|++..+.|++|+|+
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 RLFINVGRKDGLTPRDIVGAICNEAGIPGRDIGRIDIFDN--------FSFVEVPE-EVAEKVLEALNGKKIKGKKVRVE   72 (74)
T ss_dssp             EEEES-SGGGT--HHHHHHHHHTCTTB-GGGEEEEEE-SS---------EEEEE-T-T-HHHHHHHHTT--SSS----EE
T ss_pred             EEEEEcccccCCCHHHHHHHHHhccCCCHHhEEEEEEeee--------EEEEEECH-HHHHHHHHHhcCCCCCCeeEEEE
Confidence            45552 2234578888888887764     5667776554        99998876 48889999999999999999998


Q ss_pred             ec
Q 040243          567 VA  568 (797)
Q Consensus       567 ~A  568 (797)
                      .|
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.

>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH)

Probab=91.69  E-value=0.28  Score=41.09  Aligned_cols=36  Identities=28%  Similarity=0.474  Sum_probs=31.7

Q ss_pred             eEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEE
Q 040243          251 LQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVI  292 (797)
Q Consensus       251 ~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~I  292 (797)
                      ...+|+|+.      .-+|+.||.+|.++|.+++.+|.+|.|
T Consensus        25 ~~~~v~V~~------~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          25 KRARVVVPD------DQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             cEEEEEECc------ccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            456777887      678999999999999999999999887

NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.

>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]

Probab=91.57  E-value=0.54  Score=48.28  Aligned_cols=69  Identities=26%  Similarity=0.383  Sum_probs=54.9

Q ss_pred             eEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEec----
Q 040243          251 LQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAE----  326 (797)
Q Consensus       251 ~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~----  326 (797)
                      ..+.|.||.      .-+|.|||..|.+.|.||+.++|+|.|..+..                      -|-|...    
T Consensus         8 ~~~~v~iPk------~R~~~lig~~g~v~k~ie~~~~~~~~iD~~~~----------------------~V~i~~~~~t~   59 (194)
T COG1094           8 SSEAVKIPK------DRIGVLIGKWGEVKKAIEEKTGVKLRIDSKTG----------------------SVTIRTTRKTE   59 (194)
T ss_pred             ceeeeecCc------hhheeeecccccchHHHHhhcCeEEEEECCCC----------------------eEEEEecCCCC
Confidence            345677887      77899999999999999999999999997620                      3334433    


Q ss_pred             CHHHHHHHHHHHHHhcCCChH
Q 040243          327 TQESLEGAAAMVEKLLQPVDE  347 (797)
Q Consensus       327 ~~e~v~~A~~~I~~ll~~~~e  347 (797)
                      |.-++.+|.++|+.|=..++.
T Consensus        60 Dp~~~~ka~d~VkAIgrGF~p   80 (194)
T COG1094          60 DPLALLKARDVVKAIGRGFPP   80 (194)
T ss_pred             ChHHHHHHHHHHHHHhcCCCH
Confidence            677899999999998776654

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

Probab=91.20  E-value=0.068  Score=64.68  Aligned_cols=81  Identities=16%  Similarity=0.242  Sum_probs=66.7

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      .....|||+|||...+++.+|+..|..||.|.+|.|-.-+ -++---|+||.|.+.+.+-+|+..+.+..|..-.+++.+
T Consensus       369 ~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~-~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~gl  447 (975)
T KOG0112|consen  369 FRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPH-IKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGL  447 (975)
T ss_pred             hhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCC-CCcccchhhhhhhccccCcccchhhcCCccccCcccccc
Confidence            3567899999999999999999999999999999875553 233345999999999999999998988887766666666


Q ss_pred             cC
Q 040243          568 AG  569 (797)
Q Consensus       568 A~  569 (797)
                      ..
T Consensus       448 G~  449 (975)
T KOG0112|consen  448 GQ  449 (975)
T ss_pred             cc
Confidence            54

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=90.91  E-value=0.92  Score=40.66  Aligned_cols=55  Identities=24%  Similarity=0.426  Sum_probs=42.4

Q ss_pred             CcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcC
Q 040243          491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMN  554 (797)
Q Consensus       491 ~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~Ln  554 (797)
                      .+-.||+ .|..+...||.++|+.||.|. |.++.|.       -|||....++.|..|+..+.
T Consensus         9 dHVFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~dT-------SAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen    9 DHVFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWINDT-------SAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             CCEEEEE---TT--HHHHHHHCCCCCCEE-EEEECTT-------EEEEEECCCHHHHHHHHHHT
T ss_pred             ceEEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcCC-------cEEEEeecHHHHHHHHHHhc
Confidence            4556666 899999999999999999874 6667764       89999999999999888765

; 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.

>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]

Probab=90.65  E-value=0.92  Score=48.03  Aligned_cols=86  Identities=20%  Similarity=0.326  Sum_probs=58.9

Q ss_pred             CCCCCceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEE
Q 040243          245 DYRPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVE  324 (797)
Q Consensus       245 dy~p~~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~  324 (797)
                      .|...+--.-|.|+.      .++=|+||.+|+-++-|.++|+|+|.|==.|                       .|+|.
T Consensus       140 ~~GkL~~G~iv~i~p------~kVpRvig~~~sm~~~l~~~~~~~I~VG~NG-----------------------~IWV~  190 (239)
T COG1097         140 GLGKLKNGQIVKIPP------SKVPRVIGKKGSMLNMLKEKTGCEIIVGQNG-----------------------RIWVD  190 (239)
T ss_pred             CCccccCCEEEEEch------hhcceEecCCCcHHHHhhhhcCeEEEEecCC-----------------------EEEec
Confidence            344444334566776      7777999999999999999999999997666                       78888


Q ss_pred             ecCHHHHHHHHHHHHHhcCCC-hHHHHHHHHHHHHH
Q 040243          325 AETQESLEGAAAMVEKLLQPV-DEVLNEHKRQQLRE  359 (797)
Q Consensus       325 a~~~e~v~~A~~~I~~ll~~~-~e~~n~~k~~Ql~e  359 (797)
                      +.++.....|++.|.++=... .+++-+..+.+|.+
T Consensus       191 ~~~~~~e~~~~~aI~~ie~ea~~~gltdr~~~~i~~  226 (239)
T COG1097         191 GENESLEELAIEAIRKIEREAHTSGLTDRIKEFLKK  226 (239)
T ss_pred             CCCcchHHHHHHHHHHHhhhhhhhhHHHHHHHHHHH
Confidence            888755555555565554433 24444444455443

>PF08920 SF3b1: Splicing factor 3B subunit 1; InterPro: IPR015016 This group of proteins consists of several eukaryotic splicing factor 3B subunit 1 proteins, which associate with p14 through a C terminus beta-strand that interacts with beta-3 of the p14 RNA recognition motif (RRM) beta-sheet, which is in turn connected to an alpha-helix by a loop that makes extensive contacts with both the shorter C-terminal helix and RRM of p14

Probab=90.47  E-value=0.087  Score=51.78  Aligned_cols=37  Identities=35%  Similarity=0.754  Sum_probs=2.9

Q ss_pred             hhhhcccCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCC
Q 040243          105 SRRRRRSRWDPPPSESGGTEGNGDSGSGTRKRRSRWADD  143 (797)
Q Consensus       105 ~~~~r~s~w~~~~~~~~~~~~~~~~~~~~~~r~srw~~~  143 (797)
                      +.+|||||||.-......  ..........+|||||+..
T Consensus         3 ~~~kkrsRWDetP~~~~~--~~~~t~~~~~~krsRWd~T   39 (144)
T PF08920_consen    3 SKKKKRSRWDETPAASEP--AGAATPGEPPKKRSRWDQT   39 (144)
T ss_dssp             ----------------------------------SBT--
T ss_pred             CcccccccccCCcccccc--cccccccCCCCCCCCcccC
Confidence            345799999987762111  0111111478899999974

This subunit is required for 'A' splicing complex assembly (formed by the stable binding of U2 snRNP to the branchpoint sequence in pre-mRNA) and 'E' splicing complex assembly []. ; PDB: 2FHO_A 3LQV_P 2PEH_D 2F9J_P 2F9D_Q.

>PF13917 zf-CCHC_3: Zinc knuckle

Probab=90.01  E-value=0.14  Score=39.90  Aligned_cols=20  Identities=40%  Similarity=0.831  Sum_probs=17.9

Q ss_pred             ccccceecCCCCCCcccCCC
Q 040243          395 SDVLCKICGDGGHPTIDCLV  414 (797)
Q Consensus       395 ~~v~Cr~CG~~gH~t~dCp~  414 (797)
                      ..+.|..|++.|||+..|+.
T Consensus         3 ~~~~CqkC~~~GH~tyeC~~   22 (42)
T PF13917_consen    3 ARVRCQKCGQKGHWTYECPN   22 (42)
T ss_pred             CCCcCcccCCCCcchhhCCC
Confidence            56789999999999999984

>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=89.83  E-value=0.39  Score=54.15  Aligned_cols=28  Identities=32%  Similarity=0.631  Sum_probs=27.4

Q ss_pred             ceeeeeeCCCchhHHHHHHHhCcEEEEe
Q 040243          266 NFIGLIIGPRGNTQKRMERETGAKIVIR  293 (797)
Q Consensus       266 NfiG~iiGPrG~t~K~le~eTgakI~Ir  293 (797)
                      +|||.+||=+|+.||+||..|+++|.|-
T Consensus        56 ~mvg~vigrggskik~iq~~tnt~iqii   83 (629)
T KOG0336|consen   56 EMVGKVIGRGGSKIKRIQNDTNTRIQII   83 (629)
T ss_pred             hhhheeeccCcchhhhhhcccceeEEEe
Confidence            8999999999999999999999999997

>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=89.81  E-value=0.63  Score=47.32  Aligned_cols=82  Identities=13%  Similarity=0.140  Sum_probs=51.2

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhc-CCCE---EEEEEEecC-CCCc-ccceEEEEecCHHHHHHHHHhcCceeecc--
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFST-FGDI---VMAKVIKDR-VTGM-SKGYGFVKYADIQMANNAIASMNGYRLEG--  560 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~-fG~I---~~v~v~~dk-~TGk-srGfaFV~F~s~e~A~~AI~~LnG~~l~G--  560 (797)
                      ....+|.|++||+++||+++.+.+.. ++..   ..+.-.... .... .-.-|||.|.+.+++..-++.++|+.|.+  
T Consensus         5 ~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~k   84 (176)
T PF03467_consen    5 KEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSK   84 (176)
T ss_dssp             ----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TT
T ss_pred             ccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCC
Confidence            45679999999999999999997776 6655   233211221 1121 23578999999999999999999988753  


Q ss_pred             ---ceEEEEecCC
Q 040243          561 ---RTIAVRVAGK  570 (797)
Q Consensus       561 ---r~L~V~~A~~  570 (797)
                         ....|++|--
T Consensus        85 g~~~~~~VE~Apy   97 (176)
T PF03467_consen   85 GNEYPAVVEFAPY   97 (176)
T ss_dssp             S-EEEEEEEE-SS
T ss_pred             CCCcceeEEEcch
Confidence               2356666643

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=89.45  E-value=12  Score=41.68  Aligned_cols=11  Identities=36%  Similarity=0.622  Sum_probs=8.1

Q ss_pred             CcchHHHHHHH
Q 040243          784 GADAEYEKFMA  794 (797)
Q Consensus       784 ~~~~~~~~~~~  794 (797)
                      ..|+|||..|.
T Consensus       357 lSeAEFEdiM~  367 (498)
T KOG4849|consen  357 LSEAEFEDIMT  367 (498)
T ss_pred             chHHHHHHHHh
Confidence            45788888874

>PF15288 zf-CCHC_6: Zinc knuckle

Probab=89.42  E-value=0.23  Score=38.28  Aligned_cols=24  Identities=38%  Similarity=0.628  Sum_probs=19.2

Q ss_pred             cccceecCCCCCCc--ccCCCCCcCC
Q 040243          396 DVLCKICGDGGHPT--IDCLVKGTTG  419 (797)
Q Consensus       396 ~v~Cr~CG~~gH~t--~dCp~k~~~g  419 (797)
                      .++|..||..||..  +.||++...+
T Consensus         1 k~kC~~CG~~GH~~t~k~CP~~~~~~   26 (40)
T PF15288_consen    1 KVKCKNCGAFGHMRTNKRCPMYCWSG   26 (40)
T ss_pred             CccccccccccccccCccCCCCCCCC
Confidence            36899999999998  4599987654

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=89.19  E-value=0.18  Score=59.43  Aligned_cols=71  Identities=11%  Similarity=0.172  Sum_probs=63.4

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ....+|||+|+...+.++-++.+...+|.|.+++.+.         |||..|.+.....+|+..|+-..++|+.+.+...
T Consensus        38 ~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~~d  108 (668)
T KOG2253|consen   38 PPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---------FGFCEFLKHIGDLRASRLLTELNIDDQKLIENVD  108 (668)
T ss_pred             CCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---------hcccchhhHHHHHHHHHHhcccCCCcchhhccch
Confidence            3566999999999999999999999999998876544         9999999999999999999999999999888764

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=88.93  E-value=0.35  Score=55.10  Aligned_cols=78  Identities=23%  Similarity=0.215  Sum_probs=61.4

Q ss_pred             CCCCcEEEEecCCCCC-cHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          488 ELDDTNLYIGYLPPTL-DDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~v-te~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      ..+.+.|-+.-.++.. +-++|...|.+||+|..|.|-...      -.|.|+|.+..+|-+|- ...+..|++|-|+|.
T Consensus       369 ~~dhs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~~------~~a~vTF~t~aeag~a~-~s~~avlnnr~iKl~  441 (526)
T KOG2135|consen  369 VVDHSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYSS------LHAVVTFKTRAEAGEAY-ASHGAVLNNRFIKLF  441 (526)
T ss_pred             hcccchhhhhccCCCCchHhhhhhhhhhcCccccccccCch------hhheeeeeccccccchh-ccccceecCceeEEE
Confidence            3456666666666654 457899999999999999875542      37899999999997776 468999999999999


Q ss_pred             ecCCCC
Q 040243          567 VAGKPP  572 (797)
Q Consensus       567 ~A~~~~  572 (797)
                      |-+...
T Consensus       442 whnps~  447 (526)
T KOG2135|consen  442 WHNPSP  447 (526)
T ss_pred             EecCCc
Confidence            987643

>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=88.03  E-value=0.92  Score=46.52  Aligned_cols=60  Identities=22%  Similarity=0.210  Sum_probs=45.6

Q ss_pred             cHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcC--ceeeccceEEEEecC
Q 040243          504 DDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMN--GYRLEGRTIAVRVAG  569 (797)
Q Consensus       504 te~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~Ln--G~~l~Gr~L~V~~A~  569 (797)
                      ....|+++|..|+.+..+.+++.      -+-..|.|.+.++|.+|...|+  +..+.|..|+|-|+.
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s------FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~   69 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS------FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQ   69 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT------TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE---
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC------CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcc
Confidence            34789999999999888876654      3567899999999999999999  999999999999983

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.

>KOG2893 consensus Zn finger protein [General function prediction only]

Probab=87.96  E-value=14  Score=39.19  Aligned_cols=9  Identities=33%  Similarity=0.914  Sum_probs=7.1

Q ss_pred             ccccceecC
Q 040243          395 SDVLCKICG  403 (797)
Q Consensus       395 ~~v~Cr~CG  403 (797)
                      ...+|.||.
T Consensus        33 khfkchich   41 (341)
T KOG2893|consen   33 KHFKCHICH   41 (341)
T ss_pred             ccceeeeeh
Confidence            467899996

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=87.77  E-value=2  Score=42.27  Aligned_cols=74  Identities=20%  Similarity=0.327  Sum_probs=55.0

Q ss_pred             CCCCCcEEEEecCCCCCc-HHHHH---HHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccce
Q 040243          487 KELDDTNLYIGYLPPTLD-DDGLI---RLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRT  562 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vt-e~dL~---~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~  562 (797)
                      .+..-.||.|+=|..++. .+||+   ..++.||.|.+|.+.-       |--|.|+|.+..+|-+|+.++.. ..-|..
T Consensus        82 kepPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cG-------rqsavVvF~d~~SAC~Av~Af~s-~~pgtm  153 (166)
T PF15023_consen   82 KEPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCG-------RQSAVVVFKDITSACKAVSAFQS-RAPGTM  153 (166)
T ss_pred             CCCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecC-------CceEEEEehhhHHHHHHHHhhcC-CCCCce
Confidence            344556899987766653 24444   5567799999997643       23799999999999999998865 566778


Q ss_pred             EEEEec
Q 040243          563 IAVRVA  568 (797)
Q Consensus       563 L~V~~A  568 (797)
                      +.+.|-
T Consensus       154 ~qCsWq  159 (166)
T PF15023_consen  154 FQCSWQ  159 (166)
T ss_pred             EEeecc
Confidence            888874

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=87.69  E-value=0.26  Score=53.78  Aligned_cols=82  Identities=17%  Similarity=0.098  Sum_probs=68.9

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ...+++||+++.+.+.+.++..+|..+|.+....+........++||+.|.|...+.+..|+.....+.+.+..+...+.
T Consensus        86 ~~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~  165 (285)
T KOG4210|consen   86 GSSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLN  165 (285)
T ss_pred             cccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCccc
Confidence            35779999999999999999999999998888888777778999999999999999999999754445777776666555


Q ss_pred             CC
Q 040243          569 GK  570 (797)
Q Consensus       569 ~~  570 (797)
                      ..
T Consensus       166 ~~  167 (285)
T KOG4210|consen  166 TR  167 (285)
T ss_pred             cc
Confidence            43

>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]

Probab=87.35  E-value=28  Score=40.59  Aligned_cols=20  Identities=35%  Similarity=0.875  Sum_probs=17.4

Q ss_pred             cccceecCCCCCCcccCCCC
Q 040243          396 DVLCKICGDGGHPTIDCLVK  415 (797)
Q Consensus       396 ~v~Cr~CG~~gH~t~dCp~k  415 (797)
                      .-.|+.||..||-..||+-+
T Consensus       261 ~~~c~~cg~~~H~q~~cp~r  280 (554)
T KOG0119|consen  261 NRACRNCGSTGHKQYDCPGR  280 (554)
T ss_pred             cccccccCCCccccccCCcc
Confidence            36899999999999999876

>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=86.98  E-value=0.39  Score=30.71  Aligned_cols=17  Identities=53%  Similarity=1.167  Sum_probs=15.4

Q ss_pred             hhcccCCCCCccccCCC
Q 040243          372 YCRLCGEPGHRQYACPS  388 (797)
Q Consensus       372 ~c~~cg~~gh~~~~cp~  388 (797)
                      .|-+||+.||.+.+||+
T Consensus         2 ~C~~C~~~GH~~~~Cp~   18 (18)
T PF00098_consen    2 KCFNCGEPGHIARDCPK   18 (18)
T ss_dssp             BCTTTSCSSSCGCTSSS
T ss_pred             cCcCCCCcCcccccCcc
Confidence            58899999999999984

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....

>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]

Probab=86.94  E-value=0.41  Score=51.44  Aligned_cols=44  Identities=36%  Similarity=0.786  Sum_probs=33.2

Q ss_pred             cchhcccCCCCCccccCCCCCCC-ccccccceecCCCCCCcccCCCC
Q 040243          370 EEYCRLCGEPGHRQYACPSRTST-FKSDVLCKICGDGGHPTIDCLVK  415 (797)
Q Consensus       370 ~~~c~~cg~~gh~~~~cp~~~~~-~~~~v~Cr~CG~~gH~t~dCp~k  415 (797)
                      +..|-.|+..||+.  |++.... +...+.|..||..|||..+|+..
T Consensus       118 ~~~~~~c~~~gh~~--~~~~~~~~~~~~~~Cy~Cg~~GH~s~~C~~~  162 (261)
T KOG4400|consen  118 ETSCYSCGKTGHRG--CPDADPVDGPKPAKCYSCGEQGHISDDCPEN  162 (261)
T ss_pred             cceeeccCCCcccc--CcccccccCCCCCccCCCCcCCcchhhCCCC
Confidence            44678899999998  5554422 22228999999999999999954

>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]

Probab=86.40  E-value=1.9  Score=45.99  Aligned_cols=69  Identities=26%  Similarity=0.398  Sum_probs=51.6

Q ss_pred             ceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHH
Q 040243          250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQE  329 (797)
Q Consensus       250 ~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e  329 (797)
                      ..+..|-||.      ++-|-|||-+|.-||+|-.|+||.|.|.---                 +-.|+--+.|++ +++
T Consensus       314 itTaQvtip~------dlggsiigkggqri~~ir~esGA~Ikidepl-----------------eGsedrIitItG-Tqd  369 (390)
T KOG2192|consen  314 ITTAQVTIPK------DLGGSIIGKGGQRIKQIRHESGASIKIDEPL-----------------EGSEDRIITITG-TQD  369 (390)
T ss_pred             eeeeeEeccc------ccCcceecccchhhhhhhhccCceEEecCcC-----------------CCCCceEEEEec-cHH
Confidence            5678899998      8899999999999999999999999998421                 112332444544 688


Q ss_pred             HHHHHHHHHHHhc
Q 040243          330 SLEGAAAMVEKLL  342 (797)
Q Consensus       330 ~v~~A~~~I~~ll  342 (797)
                      .|..|.=++++-+
T Consensus       370 QIqnAQYLlQn~V  382 (390)
T KOG2192|consen  370 QIQNAQYLLQNSV  382 (390)
T ss_pred             HHhhHHHHHHHHH
Confidence            8888866655443

>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=85.95  E-value=5.5  Score=37.60  Aligned_cols=68  Identities=21%  Similarity=0.256  Sum_probs=51.1

Q ss_pred             CcEEEEecCCCCCcHHHHHHHhhcC-CCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeecc
Q 040243          491 DTNLYIGYLPPTLDDDGLIRLFSTF-GDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEG  560 (797)
Q Consensus       491 ~~tLfVgNLp~~vte~dL~~~Fs~f-G~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~G  560 (797)
                      ...+.+...+..++.++|..+.+.+ ..|..++|++|.  ..++=.+.+.|.+.++|..-.+.+||+.+..
T Consensus        13 ~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~--~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   13 STLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDG--TPNRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             ceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCC--CCceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            3444555566666667777666665 467778999974  3467788999999999999999999988763

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

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

Probab=85.45  E-value=1  Score=52.39  Aligned_cols=57  Identities=14%  Similarity=0.178  Sum_probs=44.7

Q ss_pred             CCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCcee---ec-cceEEEEecCCC
Q 040243          515 FGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYR---LE-GRTIAVRVAGKP  571 (797)
Q Consensus       515 fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~---l~-Gr~L~V~~A~~~  571 (797)
                      .|.-..+++..|-.+....|||||.|.+.+++.++.+++||+.   |+ .+.+.+.||.-.
T Consensus       413 ~gtYDFlYLPiDF~nkcNvGYAFINm~sp~ai~~F~kAFnGk~W~~FnS~Kia~itYArIQ  473 (549)
T KOG4660|consen  413 KGTYDFLYLPIDFKNKCNVGYAFINMTSPEAIIRFYKAFNGKKWEKFNSEKIASITYARIQ  473 (549)
T ss_pred             cCccceEEeccccccccccceeEEeecCHHHHHHHHHHHcCCchhhhcceeeeeeehhhhh
Confidence            4555567788887788889999999999999999999999975   33 344677777543

>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]

Probab=84.80  E-value=2.4  Score=45.23  Aligned_cols=39  Identities=18%  Similarity=0.440  Sum_probs=33.7

Q ss_pred             ceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEec
Q 040243          250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRG  294 (797)
Q Consensus       250 ~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrG  294 (797)
                      +++.+|++-.|.      .|.|||-+|++||+|..+.+|.|+|-.
T Consensus        47 r~e~ril~~sk~------agavigkgg~nik~lr~d~na~v~vpd   85 (390)
T KOG2192|consen   47 RVELRILLQSKN------AGAVIGKGGKNIKALRTDYNASVSVPD   85 (390)
T ss_pred             ceeEEEEEeccc------ccceeccccccHHHHhhhccceeeccC
Confidence            577788887743      499999999999999999999999874

>KOG1984 consensus Vesicle coat complex COPII, subunit SFB3 [Intracellular trafficking, secretion, and vesicular transport]

Probab=84.72  E-value=1.2e+02  Score=38.09  Aligned_cols=7  Identities=14%  Similarity=0.496  Sum_probs=2.8

Q ss_pred             CcchHHH
Q 040243          784 GADAEYE  790 (797)
Q Consensus       784 ~~~~~~~  790 (797)
                      -.|.+|+
T Consensus       255 ~d~~~~r  261 (1007)
T KOG1984|consen  255 EDDSSFR  261 (1007)
T ss_pred             chhhhhh
Confidence            3344443

>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A

Probab=84.28  E-value=0.67  Score=40.00  Aligned_cols=39  Identities=28%  Similarity=0.441  Sum_probs=28.9

Q ss_pred             EEEecCCCCCCCceeeeeeCCCchhHHHHHHHh-CcEEEEe
Q 040243          254 KLYIPMKEYPGYNFIGLIIGPRGNTQKRMERET-GAKIVIR  293 (797)
Q Consensus       254 Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eT-gakI~Ir  293 (797)
                      ||.|-. ..+.+|-+|.+||.+|..+|.|+++. |-||.|=
T Consensus         6 kvaV~~-~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV   45 (69)
T PF13184_consen    6 KVAVKS-GDPNIDPVGACIGKKGSRIKAISEELNGEKIDVV   45 (69)
T ss_dssp             EEEEEE-SSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEE
T ss_pred             EEEEEc-CCCCcCcceecCccccHHHHHHHHHhCCCeEEEE
Confidence            444443 33789999999999999999999999 7777665

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=83.66  E-value=1.8  Score=50.38  Aligned_cols=73  Identities=12%  Similarity=0.215  Sum_probs=58.7

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhc--CCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCc--eeeccceE
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFST--FGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNG--YRLEGRTI  563 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~--fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG--~~l~Gr~L  563 (797)
                      ....|.|.++-|+..+-.++++.||..  |-.+.+|.+..+-       -=||+|++..+|+.|.+.|..  ++|.|+.|
T Consensus       172 ~~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~-------nWyITfesd~DAQqAykylreevk~fqgKpI  244 (684)
T KOG2591|consen  172 NHKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND-------NWYITFESDTDAQQAYKYLREEVKTFQGKPI  244 (684)
T ss_pred             CcceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC-------ceEEEeecchhHHHHHHHHHHHHHhhcCcch
Confidence            346778999999999999999999976  6788899877663       458999999999999887754  45777776


Q ss_pred             EEEe
Q 040243          564 AVRV  567 (797)
Q Consensus       564 ~V~~  567 (797)
                      ..++
T Consensus       245 mARI  248 (684)
T KOG2591|consen  245 MARI  248 (684)
T ss_pred             hhhh
Confidence            5544

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=83.59  E-value=1.9  Score=46.94  Aligned_cols=65  Identities=23%  Similarity=0.367  Sum_probs=48.3

Q ss_pred             CcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceE
Q 040243          491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTI  563 (797)
Q Consensus       491 ~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L  563 (797)
                      ..=|-|-+++..- -..|..+|++||+|++....      ..-.|-+|.|.++.+|++||. .||+.|+|..+
T Consensus       197 D~WVTVfGFppg~-~s~vL~~F~~cG~Vvkhv~~------~ngNwMhirYssr~~A~KALs-kng~ii~g~vm  261 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQ-VSIVLNLFSRCGEVVKHVTP------SNGNWMHIRYSSRTHAQKALS-KNGTIIDGDVM  261 (350)
T ss_pred             cceEEEeccCccc-hhHHHHHHHhhCeeeeeecC------CCCceEEEEecchhHHHHhhh-hcCeeeccceE
Confidence            3344455666643 35677899999999887543      223499999999999999996 59999998653

>PF13917 zf-CCHC_3: Zinc knuckle

Probab=83.42  E-value=0.5  Score=36.90  Aligned_cols=18  Identities=44%  Similarity=1.206  Sum_probs=16.7

Q ss_pred             chhcccCCCCCccccCCC
Q 040243          371 EYCRLCGEPGHRQYACPS  388 (797)
Q Consensus       371 ~~c~~cg~~gh~~~~cp~  388 (797)
                      ..|..|++.||-.|||+.
T Consensus         5 ~~CqkC~~~GH~tyeC~~   22 (42)
T PF13917_consen    5 VRCQKCGQKGHWTYECPN   22 (42)
T ss_pred             CcCcccCCCCcchhhCCC
Confidence            579999999999999995

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=82.84  E-value=0.7  Score=55.96  Aligned_cols=76  Identities=20%  Similarity=0.319  Sum_probs=64.8

Q ss_pred             CcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceee--ccceEEEEec
Q 040243          491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRL--EGRTIAVRVA  568 (797)
Q Consensus       491 ~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l--~Gr~L~V~~A  568 (797)
                      ..+.++.|..-..+...|..+|++||.|.+++.++|-      -.|.|+|.+.+.|-.|++.|+|+++  -|-..+|.+|
T Consensus       298 qp~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~------N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~a  371 (1007)
T KOG4574|consen  298 QPKQSLENNAVNLTSSSLATLCSDYGSVASAWTLRDL------NMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFA  371 (1007)
T ss_pred             cchhhhhcccccchHHHHHHHHHhhcchhhheecccc------cchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEec
Confidence            3467777888888999999999999999999988875      3899999999999999999999875  4777888888


Q ss_pred             CCCC
Q 040243          569 GKPP  572 (797)
Q Consensus       569 ~~~~  572 (797)
                      +.-.
T Consensus       372 k~~~  375 (1007)
T KOG4574|consen  372 KTLP  375 (1007)
T ss_pred             cccc
Confidence            7433

>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]

Probab=82.66  E-value=0.84  Score=53.42  Aligned_cols=40  Identities=35%  Similarity=0.630  Sum_probs=36.6

Q ss_pred             ceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEecc
Q 040243          250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGK  295 (797)
Q Consensus       250 ~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGk  295 (797)
                      .++.++.||.      ++||-|||..|+.+-.|++.|||.|.|-++
T Consensus       337 ~v~~~l~vps------~~igciiGk~G~~iseir~~tgA~I~I~~~  376 (485)
T KOG2190|consen  337 TVTQRLLVPS------DLIGCIIGKGGAKISEIRQRTGASISILNK  376 (485)
T ss_pred             eeeeeeccCc------cccceeecccccchHHHHHhcCCceEEccc
Confidence            3678888987      999999999999999999999999999864

>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A

Probab=81.95  E-value=0.61  Score=35.05  Aligned_cols=19  Identities=42%  Similarity=0.796  Sum_probs=12.4

Q ss_pred             cceecCCCCCCcccCCCCC
Q 040243          398 LCKICGDGGHPTIDCLVKG  416 (797)
Q Consensus       398 ~Cr~CG~~gH~t~dCp~k~  416 (797)
                      .|..||.+.||+++|..+-
T Consensus         4 ~CprC~kg~Hwa~~C~sk~   22 (36)
T PF14787_consen    4 LCPRCGKGFHWASECRSKT   22 (36)
T ss_dssp             C-TTTSSSCS-TTT---TC
T ss_pred             cCcccCCCcchhhhhhhhh
Confidence            6999999999999998763

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	797
1k1g_A	131	Structural Basis For Recognition Of The Intron Bran		4e-24
2bl5_A	140	Solution Structure Of The Kh-Qua2 Region Of The Xen		5e-24
2m0g_A	145	Structure, Phosphorylation And U2af65 Binding Of Th		1e-15
2m09_A	121	Structure, Phosphorylation And U2af65 Binding Of Th		1e-14
4fxx_A	112	Structure Of Sf1 Coiled-coil Domain Length = 112		4e-14
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		4e-13
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		6e-13
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		7e-13
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		9e-13
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		9e-13
4fxv_A	99	Crystal Structure Of An Elav-Like Protein 1 (Elavl1		1e-12
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		7e-12
2u2f_A	85	Solution Structure Of The Second Rna-Binding Domain		4e-11
3vaf_A	174	Structure Of U2af65 Variant With Bru3 Dna Length =		2e-10
2g4b_A	172	Structure Of U2af65 Variant With Polyuridine Tract		2e-10
2yh0_A	198	Solution Structure Of The Closed Conformation Of Hu		2e-10
2cpz_A	115	Solution Structure Of Rna Binding Domain 3 In Cug T		4e-10
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		1e-09
1sxl_A	97	Resonance Assignments And Solution Structure Of The		1e-09
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		2e-09
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		2e-09
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		3e-09
4fxw_B	124	Structure Of Phosphorylated Sf1 Complex With U2af65		4e-09
2dgp_A	106	Solution Structure Of The N-Terminal Rna Binding Do		5e-09
2div_A	99	Solution Structure Of The Rrm Domain Of Trna Seleno		7e-09
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		8e-09
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		2e-08
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		3e-08
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		3e-08
1d9a_A	85	Solution Structure Of The Second Rna-Binding Domain		5e-08
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		7e-08
2e5h_A	94	Solution Structure Of Rna Binding Domain In Zinc Fi		8e-08
2khc_A	118	Bruno Rrm3+ Length = 118		1e-07
1x5t_A	96	Solution Structure Of The Second Rrm Domain In Spli		2e-07
3md1_A	83	Crystal Structure Of The Second Rrm Domain Of Yeast		2e-07
2dgq_A	108	Solution Structure Of The N-Terminal Rna Binding Do		2e-07
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		2e-07
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		3e-07
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		6e-07
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		7e-07
2k8g_A	95	Solution Structure Of Rrm2 Domain Of Pabp1 Length =		7e-07
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		8e-07
4f25_A	115	Crystal Structure Of The Second Rrm Domain Of Human		8e-07
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		1e-06
2d9p_A	103	Solution Structure Of Rna Binding Domain 4 In Polya		2e-06
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		2e-06
2sxl_A	88	Sex-Lethal Rbd1, Nmr, Minimized Average Structure L		4e-06
1x5u_A	105	Solution Structure Of Rrm Domain In Splicing Factor		4e-06
2x1f_A	96	Structure Of Rna15 Rrm With Bound Rna (Gu) Length =		4e-06
2x1a_A	97	Structure Of Rna15 Rrm With Rna Bound (G) Length =		4e-06
2km8_B	84	Interdomain Rrm Packing Contributes To Rna Recognit		6e-06
3bs9_A	87	X-Ray Structure Of Human Tia-1 Rrm2 Length = 87		6e-06
1x5o_A	114	Solution Structure Of Rrm Domain In Rna Binding Mot		1e-05
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		2e-05
2ki2_A	90	Solution Structure Of Ss-Dna Binding Protein 12rnp2		3e-05
3lpy_A	79	Crystal Structure Of The Rrm Domain Of Cyp33 Length		3e-05
2ku7_A	140	Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric		3e-05
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		3e-05
3mdf_A	85	Crystal Structure Of The Rrm Domain Of Cyclophilin		3e-05
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		5e-05
2cqg_A	103	Solution Structure Of The Rna Binding Domain Of Tar		5e-05
2lea_A	135	Solution Structure Of Human Srsf2 (Sc35) Rrm Length		6e-05
2kn4_A	158	The Structure Of The Rrm Domain Of Sc35 Length = 15		8e-05
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		9e-05
4a8x_A	88	Structure Of The Core Asap Complex Length = 88		2e-04
2ywk_A	95	Crystal Structure Of Rrm-Domain Derived From Human		2e-04
1uaw_A	77	Solution Structure Of The N-Terminal Rna-Binding Do		5e-04
1x4e_A	85	Solution Structure Of Rrm Domain In Rna Binding Mot		5e-04
2jwn_A	124	Solution Nmr Structure Of The Protease-Resistent Do		7e-04

>pdb|1K1G|A Chain A, Structural Basis For Recognition Of The Intron Branch Site Rna By Splicing Factor 1 Length = 131

Iteration: 1
 Score =  110 bits (274), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 61/127 (48%), Positives = 88/127 (69%), Gaps = 8/127 (6%)
Query: 250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDL 309
           ++  K+ IP  EYP  NF+GL+IGPRGNT K +E+E  AKI+IRGKGSVKEG++ +K D 
Sbjct: 6   RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRK-DG 64
Query: 310 KPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQ-----PVDEVLNEHKRQQLRELAALN 364
           +  P E+E LH LV A T E+++ A   +  +L+     P D+  N+ ++ QLRELA LN
Sbjct: 65  QMLPGEDEPLHALVTANTMENVKKAVEQIRNILKQGIETPEDQ--NDLRKMQLRELARLN 122
Query: 365 GTIRDEE 371
           GT+R+++
Sbjct: 123 GTLREDD 129

>pdb|2BL5|A Chain A, Solution Structure Of The Kh-Qua2 Region Of The Xenopus Star-Gsg Quaking Protein Length = 140

Iteration: 1
 Score =  109 bits (273), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 60/126 (47%), Positives = 87/126 (69%), Gaps = 6/126 (4%)
Query: 250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDL 309
           +LQ+KLY+P+KEYP +NF+G I+GPRG T K++E ETG KI++RGKGS+++ + +++   
Sbjct: 1   QLQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRG 60
Query: 310 KPDPSE-NEDLHVLVEAETQES-----LEGAAAMVEKLLQPVDEVLNEHKRQQLRELAAL 363
           KP+    NEDLHVL+  E  ++     L+ A   V+KLL P  E  +  K+ +L ELA L
Sbjct: 61  KPNWEHLNEDLHVLITVEDAQNRAELKLKRAVEEVKKLLVPAAEGEDSLKKMKLMELAIL 120
Query: 364 NGTIRD 369
           NGT RD
Sbjct: 121 NGTYRD 126

>pdb|2M0G|A Chain A, Structure, Phosphorylation And U2af65 Binding Of The Nterminal Domain Of Splicing Factor 1 During 3 Splice Site Recognition Length = 145

Iteration: 1
 Score = 82.0 bits (201), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 50/129 (38%), Positives = 80/129 (62%), Gaps = 5/129 (3%)
Query: 134 RKRRSRWADDEPKPVIQLPDFMKDFTGGIEFDPEIQALNSRLLE-ISRMLQSG-LPLDDR 191
           +++RSRW  D  +    +P        G+  + E   +    +E ++R L++G L +   
Sbjct: 16  KRKRSRWNQDTMEQKTVIPGMPTVIPPGLTREQERAYIVQLQIEDLTRKLRTGDLGIPPN 75
Query: 192 PEGQRSPSPEPIYDNMGIRINTREYRARERLNKERQEIISQIIKRNPAFKPPADYRPP-- 249
           PE  RSPSPEPIY++ G R+NTRE+R R++L +ER  +I++++  NP FKPPADY+PP  
Sbjct: 76  PED-RSPSPEPIYNSEGKRLNTREFRTRKKLEEERHNLITEMVALNPDFKPPADYKPPAT 134
Query: 250 KLQKKLYIP 258
           ++  K+ IP
Sbjct: 135 RVCDKVMIP 143

>pdb|2M09|A Chain A, Structure, Phosphorylation And U2af65 Binding Of The Nterminal Domain Of Splicing Factor 1 During 3 Splice Site Recognition Length = 121

Iteration: 1
 Score = 78.6 bits (192), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 41/85 (48%), Positives = 63/85 (74%), Gaps = 4/85 (4%)
Query: 177 EISRMLQSG-LPLDDRPEGQRSPSPEPIYDNMGIRINTREYRARERLNKERQEIISQIIK 235
           +++R L++G L +   PE  RSPSPEPIY++ G R+NTRE+R R++L +ER  +I++++ 
Sbjct: 36  DLTRKLRTGDLGIPPNPE-DRSPSPEPIYNSEGKRLNTREFRTRKKLEEERHNLITEMVA 94
Query: 236 RNPAFKPPADYRPP--KLQKKLYIP 258
            NP FKPPADY+PP  ++  K+ IP
Sbjct: 95  LNPDFKPPADYKPPATRVSDKVMIP 119

>pdb|4FXX|A Chain A, Structure Of Sf1 Coiled-coil Domain Length = 112

Iteration: 1
 Score = 77.0 bits (188), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 38/74 (51%), Positives = 57/74 (77%), Gaps = 2/74 (2%)
Query: 177 EISRMLQSG-LPLDDRPEGQRSPSPEPIYDNMGIRINTREYRARERLNKERQEIISQIIK 235
           +++R L++G L +   PE  RSPSPEPIY++ G R+NTRE+R R++L +ER  +I++++ 
Sbjct: 40  DLTRKLRTGDLGIPPNPE-DRSPSPEPIYNSEGKRLNTREFRTRKKLEEERHNLITEMVA 98
Query: 236 RNPAFKPPADYRPP 249
            NP FKPPADY+PP
Sbjct: 99  LNPDFKPPADYKPP 112

>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition Motif (Rrm1) Of The Au-Rich Element (Are) Binding Protein Hur At 2.0 Angstrom Resolution Length = 84

Iteration: 1
 Score = 73.6 bits (179), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 36/77 (46%), Positives = 49/77 (63%)
Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           TNL + YLP  +  D L  LFS+ G++  AK+I+D+V G S GYGFV Y   + A  AI 
Sbjct: 5   TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 64
Query: 552 SMNGYRLEGRTIAVRVA 568
           ++NG RL+ +TI V  A
Sbjct: 65  TLNGLRLQSKTIKVSYA 81

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 72.8 bits (177), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 34/77 (44%), Positives = 49/77 (63%)
Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           TNL + YLP  +  D    LF + GDI   K+++D++TG S GYGFV Y+D   A+ AI 
Sbjct: 5   TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 552 SMNGYRLEGRTIAVRVA 568
           ++NG +L+ +TI V  A
Sbjct: 65  TLNGLKLQTKTIKVSYA 81

>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1) Of Hu Antigen C (Huc) Length = 89

Iteration: 1
 Score = 72.8 bits (177), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 34/77 (44%), Positives = 49/77 (63%)
Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           TNL + YLP  +  D    LF + GDI   K+++D++TG S GYGFV Y+D   A+ AI 
Sbjct: 5   TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 552 SMNGYRLEGRTIAVRVA 568
           ++NG +L+ +TI V  A
Sbjct: 65  TLNGLKLQTKTIKVSYA 81

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 72.4 bits (176), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 36/77 (46%), Positives = 49/77 (63%)
Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           TNL + YLP  +  D L  LFS+ G++  AK+I+D+V G S GYGFV Y   + A  AI 
Sbjct: 3   TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 552 SMNGYRLEGRTIAVRVA 568
           ++NG RL+ +TI V  A
Sbjct: 63  TLNGLRLQSKTIKVSYA 79

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 72.4 bits (176), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 36/77 (46%), Positives = 49/77 (63%)
Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           TNL + YLP  +  D L  LFS+ G++  AK+I+D+V G S GYGFV Y   + A  AI 
Sbjct: 3   TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 552 SMNGYRLEGRTIAVRVA 568
           ++NG RL+ +TI V  A
Sbjct: 63  TLNGLRLQSKTIKVSYA 79

>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From Homo Sapiens At 1.90 A Resolution Length = 99

Iteration: 1
 Score = 72.0 bits (175), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 36/77 (46%), Positives = 48/77 (62%)
Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           TNL + YLP     D L  LFS+ G++  AK+I+D+V G S GYGFV Y   + A  AI 
Sbjct: 20  TNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 79
Query: 552 SMNGYRLEGRTIAVRVA 568
           ++NG RL+ +TI V  A
Sbjct: 80  TLNGLRLQSKTIKVSYA 96

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 69.3 bits (168), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 33/77 (42%), Positives = 48/77 (62%)
Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           TNL + YLP  +  +    LF + G+I   K+++D++TG S GYGFV Y D + A  AI 
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 552 SMNGYRLEGRTIAVRVA 568
           ++NG RL+ +TI V  A
Sbjct: 63  TLNGLRLQTKTIKVSYA 79

>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of Hu2af65 Length = 85

Iteration: 1
 Score = 67.0 bits (162), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 31/75 (41%), Positives = 48/75 (64%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L+IG LP  L+DD +  L ++FG +    ++KD  TG+SKGY F +Y DI + + AIA +
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 554 NGYRLEGRTIAVRVA 568
           NG +L  + + V+ A
Sbjct: 64  NGMQLGDKKLLVQRA 78

>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna Length = 174

Iteration: 1
 Score = 65.1 bits (157), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 31/75 (41%), Positives = 48/75 (64%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L+IG LP  L+DD +  L ++FG +    ++KD  TG+SKGY F +Y DI + + AIA +
Sbjct: 99  LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 158
Query: 554 NGYRLEGRTIAVRVA 568
           NG +L  + + V+ A
Sbjct: 159 NGMQLGDKKLLVQRA 173

>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract Length = 172

Iteration: 1
 Score = 64.7 bits (156), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 31/75 (41%), Positives = 48/75 (64%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L+IG LP  L+DD +  L ++FG +    ++KD  TG+SKGY F +Y DI + + AIA +
Sbjct: 97  LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156
Query: 554 NGYRLEGRTIAVRVA 568
           NG +L  + + V+ A
Sbjct: 157 NGMQLGDKKLLVQRA 171

>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human U2af65 Tandem Rrm1 And Rrm2 Domains Length = 198

Iteration: 1
 Score = 64.7 bits (156), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 31/75 (41%), Positives = 48/75 (64%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L+IG LP  L+DD +  L ++FG +    ++KD  TG+SKGY F +Y DI + + AIA +
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 176
Query: 554 NGYRLEGRTIAVRVA 568
           NG +L  + + V+ A
Sbjct: 177 NGMQLGDKKLLVQRA 191

>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet Repeat Rna-Binding Protein 1 Length = 115

Iteration: 1
 Score = 63.5 bits (153), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 30/78 (38%), Positives = 49/78 (62%)
Query: 490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNA 549
           +  NL+I +LP    D  L+++F  FG++V AKV  D+ T +SK +GFV Y +   A  A
Sbjct: 24  EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA 83
Query: 550 IASMNGYRLEGRTIAVRV 567
           I SMNG+++  + + V++
Sbjct: 84  IQSMNGFQIGMKRLKVQL 101

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 62.4 bits (150), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 30/76 (39%), Positives = 46/76 (60%)
Query: 493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
           NL + Y+P T+D+  L +LF  +G I   K++ DR T  S+GYGFVK+     A  AIA 
Sbjct: 44  NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103
Query: 553 MNGYRLEGRTIAVRVA 568
           +NG+ +  + + V +A
Sbjct: 104 LNGFNILNKRLKVALA 119

>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second Rna-Binding Domain Of Sex-Lethal Determined By Multidimensional Heteronuclear Magnetic Resonance Spectroscopy Length = 97

Iteration: 1
 Score = 62.0 bits (149), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 31/82 (37%), Positives = 51/82 (62%), Gaps = 2/82 (2%)
Query: 489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANN 548
           + DTNLY+  LP T+ DD L  +F  +G IV   +++D++TG  +G  FV+Y   + A  
Sbjct: 11  IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQE 70
Query: 549 AIASMNGYRLEGRT--IAVRVA 568
           AI+++N    EG +  ++VR+A
Sbjct: 71  AISALNNVIPEGGSQPLSVRLA 92

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 61.6 bits (148), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 32/81 (39%), Positives = 50/81 (61%)
Query: 490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNA 549
           D+  L++G L    ++  L ++FS +G I    V+KDR T  S+G+GFV + +I  A +A
Sbjct: 11  DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 70
Query: 550 IASMNGYRLEGRTIAVRVAGK 570
           + +MNG  ++GR I V  AGK
Sbjct: 71  MMAMNGKSVDGRQIRVDQAGK 91

>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic Granule-Associated Rna Binding Protein 1 Length = 115

Iteration: 1
 Score = 61.2 bits (147), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 37/93 (39%), Positives = 52/93 (55%), Gaps = 4/93 (4%)
Query: 479 GSNGAKPIKELDDTN---LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGY 535
           GS+G+   K+ D +N   +++G L P +  + +   F+ FG I  A+V+KD  TG SKGY
Sbjct: 1   GSSGSSGQKK-DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGY 59
Query: 536 GFVKYADIQMANNAIASMNGYRLEGRTIAVRVA 568
           GFV + +   A NAI  M G  L GR I    A
Sbjct: 60  GFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA 92

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 60.8 bits (146), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 34/89 (38%), Positives = 54/89 (60%), Gaps = 5/89 (5%)
Query: 482 GAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYA 541
           G + IK   DTNLY+  LP T+ DD L  +F  +G IV   +++D++TG  +G  FV+Y 
Sbjct: 94  GGESIK---DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYN 150
Query: 542 DIQMANNAIASMNGYRLEGRT--IAVRVA 568
             + A  AI+++N    EG +  ++VR+A
Sbjct: 151 KREEAQEAISALNNVIPEGGSQPLSVRLA 179

>pdb|4FXW|B Chain B, Structure Of Phosphorylated Sf1 Complex With U2af65-uhm Domain Length = 124

Iteration: 1
 Score = 60.5 bits (145), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 25/47 (53%), Positives = 37/47 (78%)
Query: 203 IYDNMGIRINTREYRARERLNKERQEIISQIIKRNPAFKPPADYRPP 249
           IY++ G R+NTRE+R R++L +ER  +I++ +  NP FKPPADY+PP
Sbjct: 78  IYNSEGKRLNTREFRTRKKLEEERHNLITEXVALNPDFKPPADYKPP 124

>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Bruno-Like 4 Rna-Binding Protein Length = 106

Iteration: 1
 Score = 60.1 bits (144), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 30/76 (39%), Positives = 45/76 (59%)
Query: 479 GSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFV 538
           GS+G+  +K+ D   L+IG +P  LD+  L  LF  FG I    V+KDR TGM KG  F+
Sbjct: 1   GSSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFL 60
Query: 539 KYADIQMANNAIASMN 554
            Y + + A  A ++++
Sbjct: 61  TYCERESALKAQSALH 76

>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna Selenocysteine Associated Protein Length = 99

Iteration: 1
 Score = 59.7 bits (143), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 30/75 (40%), Positives = 50/75 (66%), Gaps = 1/75 (1%)
Query: 493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMA-KVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           +L++G L P +D++ + R F+T G+ VM+ K+I++R+TG+  GY FV++AD+  A   + 
Sbjct: 11  SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH 70
Query: 552 SMNGYRLEGRTIAVR 566
            +NG  L G T A R
Sbjct: 71  KINGKPLPGATPAKR 85

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 59.3 bits (142), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 31/84 (36%), Positives = 52/84 (61%), Gaps = 2/84 (2%)
Query: 487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMA 546
           + + DTNLY+  LP T+ DD L  +F  +G IV   +++D++TG  +G  FV+Y   + A
Sbjct: 85  ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 144
Query: 547 NNAIASMNGYRLEGRT--IAVRVA 568
             AI+++N    EG +  ++VR+A
Sbjct: 145 QEAISALNNVIPEGGSQPLSVRLA 168

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 58.2 bits (139), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 29/74 (39%), Positives = 44/74 (59%)
Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           + LY+G L   + +D L  +F  FG I    ++KD  TG SKGYGF+ ++D + A  A+ 
Sbjct: 6   SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65
Query: 552 SMNGYRLEGRTIAV 565
            +NG+ L GR + V
Sbjct: 66  QLNGFELAGRPMRV 79

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 57.4 bits (137), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 28/72 (38%), Positives = 43/72 (59%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           LY+G L   + +D L  +F  FG I   +++ D  TG SKGYGF+ ++D + A  A+  +
Sbjct: 29  LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 554 NGYRLEGRTIAV 565
           NG+ L GR + V
Sbjct: 89  NGFELAGRPMKV 100

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 57.4 bits (137), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 33/82 (40%), Positives = 44/82 (53%), Gaps = 1/82 (1%)
Query: 490 DDT-NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANN 548
           DDT NL++G L   +DD+ L   F  F   +   V+ D  TG S+GYGFV +     A N
Sbjct: 85  DDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQN 144
Query: 549 AIASMNGYRLEGRTIAVRVAGK 570
           A+ SM G  L GR + +  A K
Sbjct: 145 AMDSMQGQDLNGRPLRINWAAK 166

>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2) Of Hu Antigen C (Huc) Length = 85

Iteration: 1
 Score = 56.6 bits (135), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 24/67 (35%), Positives = 42/67 (62%)
Query: 491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAI 550
           D NLY+  LP T+    + +LFS +G I+ ++++ D+ TG+S+G GF+++     A  AI
Sbjct: 1   DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 60
Query: 551 ASMNGYR 557
             +NG +
Sbjct: 61  KGLNGQK 67

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 56.2 bits (134), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 36/88 (40%), Positives = 51/88 (57%), Gaps = 4/88 (4%)
Query: 479 GSNGAKPIKELDDTN---LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGY 535
           GS+G+   K+ D +N   +++G L P +  + +   F+ FG I  A+V+KD  TG SKGY
Sbjct: 1   GSSGSSGQKK-DTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGY 59
Query: 536 GFVKYADIQMANNAIASMNGYRLEGRTI 563
           GFV + +   A NAI  M G  L GR I
Sbjct: 60  GFVSFYNKLDAENAIVHMGGQWLGGRQI 87

>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger Cchc-Type And Rna Binding Motif 1 Length = 94

Iteration: 1
 Score = 55.8 bits (133), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 26/77 (33%), Positives = 44/77 (57%)
Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           + +Y+  LP +L ++ L R+FS +G +V   ++KD+ T  SKG  F+ + D   A N   
Sbjct: 17  STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76
Query: 552 SMNGYRLEGRTIAVRVA 568
           ++N  +L GR I   +A
Sbjct: 77  AINNKQLFGRVIKASIA 93

>pdb|2KHC|A Chain A, Bruno Rrm3+ Length = 118

Iteration: 1
 Score = 55.5 bits (132), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 29/85 (34%), Positives = 49/85 (57%)
Query: 483 AKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYAD 542
            K I+  +  NL+I +LP    D  L   F  FG+++ AKV  D+ T +SK +GFV + +
Sbjct: 32  GKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDN 91
Query: 543 IQMANNAIASMNGYRLEGRTIAVRV 567
              A  AI +MNG+++  + + V++
Sbjct: 92  PDSAQVAIKAMNGFQVGTKRLKVQL 116

>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing Factor 3b Length = 96

Iteration: 1
 Score = 55.1 bits (131), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 32/80 (40%), Positives = 46/80 (57%), Gaps = 1/80 (1%)
Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMA-KVIKDRVTGMSKGYGFVKYADIQMANNAI 550
           + ++IG L P +D+  L   FS FG I+   K+++D  TG SKGY F+ +A    ++ AI
Sbjct: 6   SGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAI 65
Query: 551 ASMNGYRLEGRTIAVRVAGK 570
            +MNG  L  R I V  A K
Sbjct: 66  EAMNGQYLCNRPITVSYAFK 85

>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast Poly(U)-Binding Protein (Pub1) Length = 83

Iteration: 1
 Score = 55.1 bits (131), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 30/78 (38%), Positives = 41/78 (52%)
Query: 493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
           NL++G L   +DD+ L   F  F   +   V+ D  TG S+GYGFV +     A NA+ S
Sbjct: 3   NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 553 MNGYRLEGRTIAVRVAGK 570
           M G  L GR + +  A K
Sbjct: 63  MQGQDLNGRPLRINWAAK 80

>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Bruno-Like 6 Rna-Binding Protein Length = 108

Iteration: 1
 Score = 54.7 bits (130), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 29/76 (38%), Positives = 44/76 (57%), Gaps = 1/76 (1%)
Query: 479 GSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFV 538
           GS+G  P+K+ D   L++G +P  LD+  L  LF  FG I    V+KDR+TG+ KG  F+
Sbjct: 4   GSSGV-PMKDHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFL 62
Query: 539 KYADIQMANNAIASMN 554
            Y     A  A ++++
Sbjct: 63  TYCARDSALKAQSALH 78

>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To Ssdna From A Portion Of Fuse Length = 216

Iteration: 1
 Score = 54.7 bits (130), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 26/72 (36%), Positives = 42/72 (58%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           +Y+  +   L DD +  +F  FG I  A + +D  TG  KGYGF++Y   Q + +A++SM
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187
Query: 554 NGYRLEGRTIAV 565
           N + L G+ + V
Sbjct: 188 NLFDLGGQYLRV 199

>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 = 53.9 bits (128), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 25/73 (34%), Positives = 44/73 (60%)
Query: 493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
           ++++G +P    ++ L  +FS  G +V  +++ DR TG  KGYGF +Y D + A +A+ +
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 553 MNGYRLEGRTIAV 565
           +NG    GR + V
Sbjct: 70  LNGREFSGRALRV 82

>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In Complex With Polyadenylate Rna Length = 190

Iteration: 1
 Score = 53.1 bits (126), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 29/73 (39%), Positives = 40/73 (54%), Gaps = 2/73 (2%)
Query: 493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
           N++I  L  ++D+  L   FS FG+I+  KV+ D     SKGYGFV +   + A  AI  
Sbjct: 100 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEK 157
Query: 553 MNGYRLEGRTIAV 565
           MNG  L  R + V
Sbjct: 158 MNGMLLNDRKVFV 170

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 53.1 bits (126), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 25/72 (34%), Positives = 41/72 (56%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           +Y+  +   L DD +  +F  FG I    + +D  TG  KGYGF++Y   Q + +A++SM
Sbjct: 113 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 172
Query: 554 NGYRLEGRTIAV 565
           N + L G+ + V
Sbjct: 173 NLFDLGGQYLRV 184

>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1 Length = 95

Iteration: 1
 Score = 53.1 bits (126), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 32/85 (37%), Positives = 46/85 (54%), Gaps = 3/85 (3%)
Query: 482 GAKP-IKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKY 540
           GA P +++    N++I  L  ++D+  L   FS FG+I+  KV+ D     SKGYGFV +
Sbjct: 1   GADPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHF 58
Query: 541 ADIQMANNAIASMNGYRLEGRTIAV 565
              + A  AI  MNG  L  R + V
Sbjct: 59  ETQEAAERAIEKMNGMLLNDRKVFV 83

>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In Complex With Rrm1-2 Of Pabp And Poly(A) Length = 213

Iteration: 1
 Score = 52.8 bits (125), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 29/73 (39%), Positives = 40/73 (54%), Gaps = 2/73 (2%)
Query: 493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
           N++I  L  ++D+  L   FS FG+I+  KV+ D     SKGYGFV +   + A  AI  
Sbjct: 105 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEK 162
Query: 553 MNGYRLEGRTIAV 565
           MNG  L  R + V
Sbjct: 163 MNGMLLNDRKVFV 175

>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1 At Ph 6.0 Length = 115

Iteration: 1
 Score = 52.8 bits (125), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 30/77 (38%), Positives = 41/77 (53%), Gaps = 2/77 (2%)
Query: 489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANN 548
           L   N++I  L  ++D+  L   FS FG+I+  KV+ D     SKGYGFV +   + A  
Sbjct: 3   LGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAER 60
Query: 549 AIASMNGYRLEGRTIAV 565
           AI  MNG  L  R + V
Sbjct: 61  AIEKMNGMLLNDRKVFV 77

>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna- Binding Region Containing Protein 1 Length = 116

Iteration: 1
 Score = 52.4 bits (124), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 34/82 (41%), Positives = 43/82 (52%), Gaps = 1/82 (1%)
Query: 487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMA 546
           K+   T +++G LP    D  L + F  FGDI  A VI DR TG S+GYGFV  AD   A
Sbjct: 13  KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAA 72
Query: 547 NNAIASMNGYRLEGRTIAVRVA 568
             A    N   ++GR   V +A
Sbjct: 73  ERACKDPNPI-IDGRKANVNLA 93

>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In Polyadenylation Binding Protein 3 Length = 103

Iteration: 1
 Score = 51.2 bits (121), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 31/77 (40%), Positives = 44/77 (57%), Gaps = 3/77 (3%)
Query: 479 GSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFV 538
           GS+G + I      NLY+  L   +DD+ L + FS FG I  AKV+ +   G SKG+GFV
Sbjct: 4   GSSGDR-ITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFV 60
Query: 539 KYADIQMANNAIASMNG 555
            ++  + A  A+  MNG
Sbjct: 61  CFSSPEEATKAVTEMNG 77

>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 = 51.2 bits (121), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/72 (33%), Positives = 40/72 (55%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           +Y+  +   L DD +  +F  FG I    + +D  TG  KGYGF++Y   Q + +A++S 
Sbjct: 112 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSX 171
Query: 554 NGYRLEGRTIAV 565
           N + L G+ + V
Sbjct: 172 NLFDLGGQYLRV 183

>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure Length = 88

Iteration: 1
 Score = 50.4 bits (119), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 26/78 (33%), Positives = 39/78 (50%)
Query: 491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAI 550
           +TNL + YLP  + D  L  LF   G I   ++++D  TG S GY FV +     +  AI
Sbjct: 3   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62
Query: 551 ASMNGYRLEGRTIAVRVA 568
             +NG  +  + + V  A
Sbjct: 63  KVLNGITVRNKRLKVSYA 80

>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b Length = 105

Iteration: 1
 Score = 50.4 bits (119), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 32/85 (37%), Positives = 47/85 (55%), Gaps = 1/85 (1%)
Query: 485 PIKELD-DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADI 543
           PI E + D  +Y+G L   + +  L  LF   G +V   + KDRVTG  +GYGFV++   
Sbjct: 8   PISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSE 67
Query: 544 QMANNAIASMNGYRLEGRTIAVRVA 568
           + A+ AI  M+  +L G+ I V  A
Sbjct: 68  EDADYAIKIMDMIKLYGKPIRVNKA 92

>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu) Length = 96

Iteration: 1
 Score = 50.4 bits (119), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 22/68 (32%), Positives = 44/68 (64%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           +Y+G +P    ++ ++ L S  G ++  K++ D  TG SKGY F+++ D++ + +A+ ++
Sbjct: 5   VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 554 NGYRLEGR 561
           NGY+L  R
Sbjct: 65  NGYQLGSR 72

>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G) Length = 97

Iteration: 1
 Score = 50.4 bits (119), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 22/68 (32%), Positives = 44/68 (64%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           +Y+G +P    ++ ++ L S  G ++  K++ D  TG SKGY F+++ D++ + +A+ ++
Sbjct: 6   VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 554 NGYRLEGR 561
           NGY+L  R
Sbjct: 66  NGYQLGSR 73

>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 = 49.7 bits (117), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 22/70 (31%), Positives = 45/70 (64%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           +Y+G +P    ++ ++ L S  G ++  K++ D  TG SKGY F+++ D++ + +A+ ++
Sbjct: 7   VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 554 NGYRLEGRTI 563
           NGY+L  R +
Sbjct: 67  NGYQLGSRFL 76

>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2 Length = 87

Iteration: 1
 Score = 49.7 bits (117), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 30/71 (42%), Positives = 41/71 (57%)
Query: 493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
           ++++G L P +    +   F+ FG I  A+V+KD  TG SKGYGFV + +   A NAI  
Sbjct: 8   HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67
Query: 553 MNGYRLEGRTI 563
           M G  L GR I
Sbjct: 68  MGGQWLGGRQI 78

>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif, Single-Stranded Interacting Protein 1 Length = 114

Iteration: 1
 Score = 48.9 bits (115), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 26/88 (29%), Positives = 45/88 (51%), Gaps = 5/88 (5%)
Query: 472 TPGHPGLGSNGAKPI----KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDR 527
           + G  GL ++G +      +E D TNLYI  LP ++D+  L  +   FG ++  ++++D 
Sbjct: 2   SSGSSGLKASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS 61
Query: 528 VTGMSKGYGFVKYADIQMANNAIASMNG 555
            +G S+G GF +    +     I   NG
Sbjct: 62  -SGTSRGVGFARMESTEKCEAVIGHFNG 88

>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 24/70 (34%), Positives = 40/70 (57%), Gaps = 1/70 (1%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L++G L  +   + L   FS +G++V   ++KD+ T  S+G+GFVK+ D       +AS 
Sbjct: 19  LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS- 77
Query: 554 NGYRLEGRTI 563
             + L+GR I
Sbjct: 78  RPHTLDGRNI 87

>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2 Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori Length = 90

Iteration: 1
 Score = 47.4 bits (111), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 28/76 (36%), Positives = 42/76 (55%), Gaps = 1/76 (1%)
Query: 493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
           N+Y+G L  +   + +  LFS FG +   K+I DR T   KG+GFV+  + +  + AIA 
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAK 61
Query: 553 MNGYRLEGRTIAVRVA 568
           ++     GRTI V  A
Sbjct: 62  LDNTDFMGRTIRVTEA 77

>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33 Length = 79

Iteration: 1
 Score = 47.4 bits (111), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 29/75 (38%), Positives = 40/75 (53%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           LY+G L   +DD  L   F  FGDI   ++  D  T   +G+ FV++   + A  AI +M
Sbjct: 5   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 554 NGYRLEGRTIAVRVA 568
           N   L GRTI V +A
Sbjct: 65  NESELFGRTIRVNLA 79

>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein Length = 140

Iteration: 1
 Score = 47.4 bits (111), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 29/75 (38%), Positives = 40/75 (53%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           LY+G L   +DD  L   F  FGDI   ++  D  T   +G+ FV++   + A  AI +M
Sbjct: 66  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 554 NGYRLEGRTIAVRVA 568
           N   L GRTI V +A
Sbjct: 126 NESELFGRTIRVNLA 140

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score = 47.4 bits (111), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 29/75 (38%), Positives = 40/75 (53%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           LY+G L   +DD  L   F  FGDI   ++  D  T   +G+ FV++   + A  AI +M
Sbjct: 8   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 554 NGYRLEGRTIAVRVA 568
           N   L GRTI V +A
Sbjct: 68  NESELFGRTIRVNLA 82

>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33 Length = 85

Iteration: 1
 Score = 47.4 bits (111), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 29/75 (38%), Positives = 40/75 (53%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           LY+G L   +DD  L   F  FGDI   ++  D  T   +G+ FV++   + A  AI +M
Sbjct: 10  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 554 NGYRLEGRTIAVRVA 568
           N   L GRTI V +A
Sbjct: 70  NESELFGRTIRVNLA 84

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 46.6 bits (109), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 33/90 (36%), Positives = 46/90 (51%), Gaps = 4/90 (4%)
Query: 479 GSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFV 538
           GS+G    K +    LY+G L   +DD  L   F  FGDI   ++  D  T   +G+ FV
Sbjct: 4   GSSGMATTKRV----LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFV 59
Query: 539 KYADIQMANNAIASMNGYRLEGRTIAVRVA 568
           ++   + A  AI +MN   L GRTI V +A
Sbjct: 60  EFELAEDAAAAIDNMNESELFGRTIRVNLA 89

>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna- Binding Protein-43 Length = 103

Iteration: 1
 Score = 46.6 bits (109), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 25/68 (36%), Positives = 41/68 (60%), Gaps = 2/68 (2%)
Query: 479 GSNGAKPIKEL--DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYG 536
           GS+G+  +K      ++L +  LP    +  L   FSTFG+++M +V KD  TG SKG+G
Sbjct: 1   GSSGSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFG 60
Query: 537 FVKYADIQ 544
           FV++ + +
Sbjct: 61  FVRFTEYE 68

>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm Length = 135

Iteration: 1
 Score = 46.6 bits (109), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 25/77 (32%), Positives = 45/77 (58%)
Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           T+L +  L      D L R+F  +G +    + +DR T  S+G+ FV++ D + A +A+ 
Sbjct: 48  TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107
Query: 552 SMNGYRLEGRTIAVRVA 568
           +M+G  L+GR + V++A
Sbjct: 108 AMDGAVLDGRELRVQMA 124

>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35 Length = 158

Iteration: 1
 Score = 46.2 bits (108), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 25/77 (32%), Positives = 45/77 (58%)
Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           T+L +  L      D L R+F  +G +    + +DR T  S+G+ FV++ D + A +A+ 
Sbjct: 71  TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130
Query: 552 SMNGYRLEGRTIAVRVA 568
           +M+G  L+GR + V++A
Sbjct: 131 AMDGAVLDGRELRVQMA 147

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 45.8 bits (107), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 28/77 (36%), Positives = 39/77 (50%), Gaps = 1/77 (1%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L+IG L    ++  L  +F   G I    +IKDR T  S+G+ F+ + +   A NA   M
Sbjct: 10  LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDM 68
Query: 554 NGYRLEGRTIAVRVAGK 570
           NG  L G+ I V  A K
Sbjct: 69  NGKSLHGKAIKVEQAKK 85

>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex Length = 88

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/74 (31%), Positives = 44/74 (59%), Gaps = 1/74 (1%)
Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVT-GMSKGYGFVKYADIQMANNAI 550
           T ++IG L   +  D ++ +FST+G I M  +  +R+   +SKGY +V++ +   A  A+
Sbjct: 5   TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64
Query: 551 ASMNGYRLEGRTIA 564
             M+G +++G+ I 
Sbjct: 65  KHMDGGQIDGQEIT 78

>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human Putative Rna-Binding Protein 11 Length = 95

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 28/81 (34%), Positives = 42/81 (51%), Gaps = 1/81 (1%)
Query: 485 PIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQ 544
           P +E  D  +++G L   + ++ L  LF   G +    + KDR  G  K +GFV +   +
Sbjct: 10  PAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPE 68
Query: 545 MANNAIASMNGYRLEGRTIAV 565
             + AIA +NG RL GR I V
Sbjct: 69  SVSYAIALLNGIRLYGRPINV 89

>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of Mouse Musashi1 Length = 77

Iteration: 1
 Score = 43.5 bits (101), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 23/75 (30%), Positives = 42/75 (56%), Gaps = 1/75 (1%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           ++IG L      +GL   F  FG++    V++D +T  S+G+GFV + D Q   + + + 
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMD-QAGVDKVLAQ 61
Query: 554 NGYRLEGRTIAVRVA 568
           + + L+ +TI  +VA
Sbjct: 62  SRHELDSKTIDPKVA 76

>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif, Single-Stranded Interacting Protein 2 Length = 85

Iteration: 1
 Score = 43.5 bits (101), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 23/62 (37%), Positives = 32/62 (51%)
Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           + LYI  L P   D  L++L   +G IV  K I D+ T   KGYGFV +     A  A+ 
Sbjct: 6   SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 65
Query: 552 SM 553
           ++
Sbjct: 66  AL 67

>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of Xenopus Laevis Epabp2 Length = 124

Iteration: 1
 Score = 43.1 bits (100), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 24/79 (30%), Positives = 42/79 (53%), Gaps = 1/79 (1%)
Query: 487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMA 546
           KE+D  ++Y+G +        L   FS+ G I    ++ D+ +G  KGY ++++A+    
Sbjct: 32  KEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSV 91
Query: 547 NNAIASMNGYRLEGRTIAV 565
           + A+A M+     GRTI V
Sbjct: 92  DAAVA-MDETVFRGRTIKV 109

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	797
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	1e-48
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	1e-47
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	2e-33
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	5e-32
1x4e_A	85	RNA binding motif, single-stranded interacting pro	2e-30
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	4e-30
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	5e-30
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	2e-28
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-29
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	3e-29
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	6e-28
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	1e-28
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	1e-28
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	1e-28
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	1e-28
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-28
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	5e-25
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	3e-28
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-19
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	8e-28
1x5o_A	114	RNA binding motif, single-stranded interacting pro	1e-27
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-27
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	9e-24
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-20
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-27
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	1e-19
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	8e-27
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-26
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-23
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	1e-26
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	2e-26
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	2e-26
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	3e-26
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	3e-26
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	4e-26
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	6e-26
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	8e-26
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	8e-26
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	9e-26
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-25
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	2e-25
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	3e-25
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	9e-22
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	4e-25
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	7e-25
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	7e-25
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	8e-25
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-24
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-23
2div_A	99	TRNA selenocysteine associated protein; structural	1e-24
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-24
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-21
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	2e-24
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	3e-24
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	3e-24
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	4e-24
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	5e-24
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	5e-24
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	5e-24
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	5e-24
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	1e-23
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	1e-23
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	2e-23
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	4e-23
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	6e-23
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	6e-23
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	6e-23
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	8e-23
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	1e-22
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	1e-22
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	2e-22
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	3e-22
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	4e-22
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	4e-22
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	4e-22
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	7e-22
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	8e-20
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	7e-17
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	1e-21
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	1e-21
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-21
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	1e-10
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-21
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	4e-17
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	2e-21
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	2e-21
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	2e-21
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	3e-21
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	3e-21
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-20
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	3e-21
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	3e-21
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	5e-21
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	6e-21
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	9e-21
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	9e-21
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	1e-20
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	2e-20
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-14
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	2e-20
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	2e-20
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	4e-20
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	4e-20
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	6e-20
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	6e-20
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	9e-20
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	1e-19
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	1e-19
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	1e-19
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	1e-19
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	2e-19
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-19
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	2e-19
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	3e-19
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	3e-19
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	4e-19
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	4e-19
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	7e-19
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	7e-19
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	1e-18
1x5p_A	97	Negative elongation factor E; structure genomics,	1e-18
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	2e-18
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	3e-18
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	4e-18
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	5e-18
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	5e-18
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	6e-18
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	9e-18
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	1e-17
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	1e-17
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-17
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	9e-14
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	2e-17
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	4e-17
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	4e-17
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	5e-17
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	1e-16
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	2e-16
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-16
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-11
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	4e-16
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	5e-16
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	5e-16
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	1e-15
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	1e-15
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-14
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	1e-15
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	3e-15
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	5e-15
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	7e-15
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	5e-14
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	3e-12
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	1e-11
2dis_A	109	Unnamed protein product; structural genomics, RRM	1e-14
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	2e-14
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	3e-14
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	6e-14
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	7e-14
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	1e-12
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	4e-12
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	2e-07
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	7e-14
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	1e-13
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	2e-13
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	9e-13
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	9e-13
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	1e-12
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	2e-12
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-12
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	4e-12
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	5e-12
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	8e-12
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	2e-11
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	5e-11
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	6e-11
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	9e-11
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	2e-10
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-10
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	2e-10
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-10
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	3e-10
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	9e-09
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	1e-08
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	9e-08
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	3e-07
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	1e-06
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	1e-09
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	3e-09
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	4e-09
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	1e-08
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	1e-08
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	1e-08
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-06
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-05
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-05
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	2e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-08
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	9e-08
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	1e-07
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	1e-07
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	3e-07
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	4e-07
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	5e-07
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	1e-06
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	2e-06
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	3e-06
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	5e-04
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	3e-06
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	8e-06
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	2e-05
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	7e-05
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	5e-06
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	5e-06
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	7e-05
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	1e-04
1deq_A	390	Fibrinogen (alpha chain); coiled-coil, blood clott	6e-06
1deq_A	390	Fibrinogen (alpha chain); coiled-coil, blood clott	3e-04
3v1v_A	433	2-MIB synthase, 2-methylisoborneol synthase; class	7e-06
3v1v_A	433	2-MIB synthase, 2-methylisoborneol synthase; class	1e-05
3v1v_A	433	2-MIB synthase, 2-methylisoborneol synthase; class	7e-05
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	8e-06
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	2e-05
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	2e-05
2z73_A	448	Rhodopsin; visual pigment, GQ-type, G-protein coup	2e-05
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	2e-05
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	3e-05
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	3e-05
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	5e-05
3tx7_B	352	Nuclear receptor subfamily 5 group A member 2; LRH	7e-05
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	7e-05
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	7e-05
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	9e-05
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	1e-04
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-04
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	2e-04
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	2e-04
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	3e-04
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	3e-04
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	3e-04
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	3e-04
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	3e-04
3nwa_A	703	GB, GB-1, GB1, envelope glycoprotein B; coiled-coi	5e-04
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	6e-04
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	6e-04
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	6e-04
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	7e-04
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	8e-04
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	8e-04
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	8e-04
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	8e-04

>1k1g_A SF1-BO isoform; splicing, branch point sequence, protein/RNA recognition, complex E, KH domain, QUA2 homology; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 131

 Score =  164 bits (416), Expect = 1e-47
 Identities = 60/128 (46%), Positives = 86/128 (67%), Gaps = 4/128 (3%)

Query: 247 RPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQK 306
              ++  K+ IP  EYP  NF+GL+IGPRGNT K +E+E  AKI+IRGKGSVKEG++ +K
Sbjct: 3   MATRVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRK 62

Query: 307 RDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQ---PVDEVLNEHKRQQLRELAAL 363
            D +  P E+E LH LV A T E+++ A   +  +L+      E  N+ ++ QLRELA L
Sbjct: 63  -DGQMLPGEDEPLHALVTANTMENVKKAVEQIRNILKQGIETPEDQNDLRKMQLRELARL 121

Query: 364 NGTIRDEE 371
           NGT+R+++
Sbjct: 122 NGTLREDD 129

>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 =  123 bits (310), Expect = 2e-33
 Identities = 38/102 (37%), Positives = 58/102 (56%), Gaps = 1/102 (0%)

Query: 468 GSSGTPGHPGLGSNGAKPIKELDD-TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKD 526
           GSSG+ G        A   KE  +  NL+I +LP    D  L+++F  FG++V AKV  D
Sbjct: 1   GSSGSSGLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFID 60

Query: 527 RVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA 568
           + T +SK +GFV Y +   A  AI SMNG+++  + + V++ 
Sbjct: 61  KQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK 102

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score =  119 bits (300), Expect = 5e-32
 Identities = 36/117 (30%), Positives = 59/117 (50%), Gaps = 6/117 (5%)

Query: 452 PGSGSSGSNPPWANNSGSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRL 511
            GS S+ S  P A+ + S+      G    G       +  NL+I +LP    D  L   
Sbjct: 7   FGSASALSTSPLASVALSAAAAAAAGKQIEGP------EGCNLFIYHLPQEFTDTDLAST 60

Query: 512 FSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA 568
           F  FG+++ AKV  D+ T +SK +GFV + +   A  AI +MNG+++  + + V++ 
Sbjct: 61  FLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLK 117

>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 =  113 bits (286), Expect = 2e-30
 Identities = 23/77 (29%), Positives = 35/77 (45%)

Query: 490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNA 549
             + LYI  L P   D  L++L   +G IV  K I D+ T   KGYGFV +     A  A
Sbjct: 4   GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKA 63

Query: 550 IASMNGYRLEGRTIAVR 566
           + ++    ++ +     
Sbjct: 64  VTALKASGVQAQMAKQS 80

>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 =  114 bits (288), Expect = 4e-30
 Identities = 33/132 (25%), Positives = 51/132 (38%), Gaps = 1/132 (0%)

Query: 457 SGSNPPWANNSGSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFG 516
           S  +P                         +     NL + Y+P T+D+  L +LF  +G
Sbjct: 8   SQYDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYG 67

Query: 517 DIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTV 576
            I   K++ DR T  S+GYGFVK+     A  AIA +NG+ +  + + V +A        
Sbjct: 68  PIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA-ASGHQRP 126

Query: 577 PPGPPTSTMPTY 588
                      Y
Sbjct: 127 GIAGAVGDGNGY 138

>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 =  115 bits (291), Expect = 5e-30
 Identities = 26/83 (31%), Positives = 40/83 (48%)

Query: 491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAI 550
           +TNL + YLP  + D  L  LF   G I   ++++D  TG S GY FV +     +  AI
Sbjct: 3   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62

Query: 551 ASMNGYRLEGRTIAVRVAGKPPQ 573
             +NG  +  + + V  A    +
Sbjct: 63  KVLNGITVRNKRLKVSYARPGGE 85

>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 =  111 bits (279), Expect = 2e-28
 Identities = 32/87 (36%), Positives = 51/87 (58%), Gaps = 1/87 (1%)

Query: 483 AKPIKE-LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYA 541
           A+P  E + DTNLY+  LP T+ DD L  +F  +G IV   +++D++TG  +G  FV+Y 
Sbjct: 80  ARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYN 139

Query: 542 DIQMANNAIASMNGYRLEGRTIAVRVA 568
             + A  AI+++N    EG +  + V 
Sbjct: 140 KREEAQEAISALNNVIPEGGSQPLSVR 166

>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 =  110 bits (277), Expect = 3e-29
 Identities = 30/82 (36%), Positives = 41/82 (50%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
            NL++G L   +DD+ L   F  F   +   V+ D  TG S+GYGFV +     A NA+ 
Sbjct: 2   FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61

Query: 552 SMNGYRLEGRTIAVRVAGKPPQ 573
           SM G  L GR + +  A K   
Sbjct: 62  SMQGQDLNGRPLRINWAAKLEH 83

>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 =  113 bits (284), Expect = 3e-29
 Identities = 33/77 (42%), Positives = 48/77 (62%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           TNL + YLP  +  +    LF + G+I   K+++D++TG S GYGFV Y D + A  AI 
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

Query: 552 SMNGYRLEGRTIAVRVA 568
           ++NG RL+ +TI V  A
Sbjct: 63  TLNGLRLQTKTIKVSYA 79

>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 =  109 bits (275), Expect = 6e-28
 Identities = 32/94 (34%), Positives = 51/94 (54%), Gaps = 9/94 (9%)

Query: 484 KPIK---------ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKG 534
           K IK          + D NLY+  LP T+    L +LFS +G I+ ++++ D+VTG+S+G
Sbjct: 72  KTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRG 131

Query: 535 YGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA 568
            GF+++     A  AI  +NG +  G T  + V 
Sbjct: 132 VGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVK 165

>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 =  109 bits (275), Expect = 1e-28
 Identities = 35/103 (33%), Positives = 53/103 (51%), Gaps = 3/103 (2%)

Query: 479 GSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFV 538
           GS+G+  +K+ D   L+IG +P  LD+  L  LF  FG I    V+KDR TGM KG  F+
Sbjct: 1   GSSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFL 60

Query: 539 KYADIQMANNAIASMNGYRL---EGRTIAVRVAGKPPQPTVPP 578
            Y + + A  A ++++  +      R I V+ A    +    P
Sbjct: 61  TYCERESALKAQSALHEQKTLPGMNRPIQVKPADSESRGGSGP 103

>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 =  109 bits (274), Expect = 1e-28
 Identities = 34/101 (33%), Positives = 53/101 (52%), Gaps = 8/101 (7%)

Query: 468 GSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDR 527
           GSSG+ G  G    G  P      + +Y+  LP +L ++ L R+FS +G +V   ++KD+
Sbjct: 1   GSSGSSGMSG----GLAP----SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDK 52

Query: 528 VTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA 568
            T  SKG  F+ + D   A N   ++N  +L GR I   +A
Sbjct: 53  DTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIA 93

>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 119

 Score =  110 bits (275), Expect = 1e-28
 Identities = 27/111 (24%), Positives = 47/111 (42%), Gaps = 8/111 (7%)

Query: 247 RPPKLQKKLYIPMKE-YPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQ 305
               +Q KL++ ++   P +N    + GP  +  + ++ ETGAK+ +RGKGS        
Sbjct: 8   GMHYVQDKLFVGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGS-------G 60

Query: 306 KRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQPVDEVLNEHKRQQ 356
             +        E +++ +     E L  A  + E LLQ V    +    Q 
Sbjct: 61  CIEPASGREAFEPMYIYISHPKPEGLAAAKKLCENLLQTVHAEYSRFVNQI 111

>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 =  109 bits (275), Expect = 1e-28
 Identities = 41/120 (34%), Positives = 60/120 (50%), Gaps = 7/120 (5%)

Query: 479 GSNGAKPIKE--LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYG 536
           GS+G+   K+   +  ++++G L P +  + +   F+ FG I  A+V+KD  TG SKGYG
Sbjct: 1   GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYG 60

Query: 537 FVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPGPPTSTMPTYPVSAPPVG 596
           FV + +   A NAI  M G  L GR I    A +      PP P ++       S P  G
Sbjct: 61  FVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK-----PPAPKSTYESNTKQSGPSSG 115

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score =  112 bits (283), Expect = 2e-28
 Identities = 32/90 (35%), Positives = 49/90 (54%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
             +Y+  +   L DD +  +F  FG I  A + +D  TG  KGYGF++Y   Q + +A++
Sbjct: 126 NRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVS 185

Query: 552 SMNGYRLEGRTIAVRVAGKPPQPTVPPGPP 581
           SMN + L G+ + V  A  PP P + P  P
Sbjct: 186 SMNLFDLGGQYLRVGKAVTPPMPLLTPATP 215

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score =  102 bits (257), Expect = 5e-25
 Identities = 30/110 (27%), Positives = 46/110 (41%)

Query: 464 ANNSGSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKV 523
            ++  S       G GS   +       + +Y+G +   L +D + + F+ FG I    +
Sbjct: 1   GSHMASMTGGQQMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDM 60

Query: 524 IKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQ 573
             D VT   KG+ FV+Y   + A  A+  MN   L GR I V       Q
Sbjct: 61  SWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQ 110

>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 =  111 bits (280), Expect = 3e-28
 Identities = 32/114 (28%), Positives = 52/114 (45%)

Query: 460 NPPWANNSGSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIV 519
             P         +             +       L+IG LP  L+DD +  L ++FG + 
Sbjct: 83  RRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLK 142

Query: 520 MAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQ 573
              ++KD  TG+SKGY F +Y DI + + AIA +NG +L  + + V+ A    +
Sbjct: 143 AFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAK 196

>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 = 86.2 bits (214), Expect = 2e-19
 Identities = 15/110 (13%), Positives = 41/110 (37%), Gaps = 6/110 (5%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDI-----VMAKVIKDRVTGMSKGYGFVKYADIQMANN 548
           LY+G +P  + ++ ++  F+    +          +        K + F+++  +     
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66

Query: 549 AIASMNGYRLEGRTIAVRVAGKPPQPTVPPGPPTSTMPTYPVSAPPVGGY 598
           A+A  +G   +G+++ +R              P+  +P    +  P   +
Sbjct: 67  AMA-FDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAH 115

>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 =  106 bits (268), Expect = 8e-28
 Identities = 33/92 (35%), Positives = 50/92 (54%), Gaps = 4/92 (4%)

Query: 479 GSNGAKP--IKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYG 536
           GS+G+    I      NLY+  L   +DD+ L + FS FG I  AKV+ +   G SKG+G
Sbjct: 1   GSSGSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFG 58

Query: 537 FVKYADIQMANNAIASMNGYRLEGRTIAVRVA 568
           FV ++  + A  A+  MNG  +  + + V +A
Sbjct: 59  FVCFSSPEEATKAVTEMNGRIVATKPLYVALA 90

>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 =  106 bits (268), Expect = 1e-27
 Identities = 22/83 (26%), Positives = 39/83 (46%), Gaps = 1/83 (1%)

Query: 486 IKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQM 545
            +E D TNLYI  LP ++D+  L  +   FG ++  ++++D  +G S+G GF +    + 
Sbjct: 20  QQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEK 78

Query: 546 ANNAIASMNGYRLEGRTIAVRVA 568
               I   NG  ++         
Sbjct: 79  CEAVIGHFNGKFIKTPPGVSAPT 101

>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 =  112 bits (282), Expect = 1e-27
 Identities = 25/84 (29%), Positives = 34/84 (40%)

Query: 491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAI 550
           D  L +  LPP+L       L   FG +    ++    TG SKGYGF +Y     A  A 
Sbjct: 95  DALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAK 154

Query: 551 ASMNGYRLEGRTIAVRVAGKPPQP 574
           + + G  L  RT+ V         
Sbjct: 155 SDLLGKPLGPRTLYVHWTDAGQLT 178

>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 =  101 bits (253), Expect = 9e-24
 Identities = 22/88 (25%), Positives = 33/88 (37%), Gaps = 2/88 (2%)

Query: 487 KELDDTNLYIGYLPPTLDD-DGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQM 545
             L    L +  LPP  +D D L R  S        ++   +  G  KG+  ++Y   +M
Sbjct: 180 ALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEM 238

Query: 546 ANNAIASMNGYRLEGRTIAVRVAGKPPQ 573
           A  A    +G  L G  + V      P 
Sbjct: 239 AEEAQQQADGLSLGGSHLRVSFCAPGPP 266

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 90.8 bits (226), Expect = 3e-20
 Identities = 17/79 (21%), Positives = 32/79 (40%), Gaps = 7/79 (8%)

Query: 490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNA 549
           +   + I  LP  + +  +  L S +        +K       KG  FV   + + A  A
Sbjct: 21  NRRKILIRGLPGDVTNQEVHDLLSDYE-------LKYCFVDKYKGTAFVTLLNGEQAEAA 73

Query: 550 IASMNGYRLEGRTIAVRVA 568
           I + +  RL  R ++V++ 
Sbjct: 74  INAFHQSRLRERELSVQLQ 92

>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 =  108 bits (272), Expect = 2e-27
 Identities = 32/89 (35%), Positives = 50/89 (56%), Gaps = 1/89 (1%)

Query: 481 NGAKPIKELDDT-NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVK 539
                 + L     L+IG LP  L+DD +  L ++FG +    ++KD  TG+SKGY F +
Sbjct: 83  RRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCE 142

Query: 540 YADIQMANNAIASMNGYRLEGRTIAVRVA 568
           Y DI + + AIA +NG +L  + + V+ A
Sbjct: 143 YVDINVTDQAIAGLNGMQLGDKKLLVQRA 171

>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 = 86.1 bits (214), Expect = 1e-19
 Identities = 12/89 (13%), Positives = 34/89 (38%), Gaps = 6/89 (6%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVM-----AKVIKDRVTGMSKGYGFVKYADIQMANN 548
           LY+G +P  + ++ ++  F+    +          +        K + F+++  +     
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66

Query: 549 AIASMNGYRLEGRTIAVRVAGKPPQPTVP 577
           A+A  +G   +G+++ +R           
Sbjct: 67  AMA-FDGIIFQGQSLKIRRPHDYQPLPGA 94

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score =  105 bits (264), Expect = 8e-27
 Identities = 37/132 (28%), Positives = 54/132 (40%), Gaps = 10/132 (7%)

Query: 439 ESASKQSTTLALGPGSGSSGSNPPWANNSGSSGTPGHPGLGSNGAKPIKEL--DDTNLYI 496
           E+ S +   +            P     +  + T  H   GS G+            LY+
Sbjct: 17  ENLSDEMYEILSNL--------PESVAYTCVNCTERHVDGGSGGSGGSGGSATTKRVLYV 68

Query: 497 GYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGY 556
           G L   +DD  L   F  FGDI   ++  D  T   +G+ FV++   + A  AI +MN  
Sbjct: 69  GGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNES 128

Query: 557 RLEGRTIAVRVA 568
            L GRTI V +A
Sbjct: 129 ELFGRTIRVNLA 140

>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 =  106 bits (266), Expect = 1e-26
 Identities = 30/78 (38%), Positives = 41/78 (52%)

Query: 493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
           NL++G L   +DD+ L   F  F   +   V+ D  TG S+GYGFV +     A NA+ S
Sbjct: 89  NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 148

Query: 553 MNGYRLEGRTIAVRVAGK 570
           M G  L GR + +  A K
Sbjct: 149 MQGQDLNGRPLRINWAAK 166

>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 = 96.8 bits (242), Expect = 2e-23
 Identities = 23/86 (26%), Positives = 41/86 (47%), Gaps = 1/86 (1%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           LY+G L   + +D L + F   G I   K++ D+    +  Y FV+Y     AN A+ ++
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTL 61

Query: 554 NGYRLEGRTIAVRVAGKPPQPTVPPG 579
           NG ++E   + +  A +  Q +    
Sbjct: 62  NGKQIENNIVKINWAFQSQQSSSDDT 87

>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 =  103 bits (259), Expect = 1e-26
 Identities = 36/101 (35%), Positives = 57/101 (56%), Gaps = 1/101 (0%)

Query: 479 GSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFV 538
           GS+G+  +   D+  L++G L    ++  L ++FS +G I    V+KDR T  S+G+GFV
Sbjct: 1   GSSGSSGMAS-DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFV 59

Query: 539 KYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPG 579
            + +I  A +A+ +MNG  ++GR I V  AGK       P 
Sbjct: 60  TFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDNRSGPS 100

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score =  103 bits (259), Expect = 2e-26
 Identities = 33/114 (28%), Positives = 47/114 (41%), Gaps = 5/114 (4%)

Query: 490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNA 549
               L+IG L    ++  L  +F   G I    +IKDR T  S+G+ F+ + +   A NA
Sbjct: 6   HPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNA 64

Query: 550 IASMNGYRLEGRTIAVRVAGKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQY 603
              MNG  L G+ I V  A KP   +     P    P    +  P G      +
Sbjct: 65  AKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRP----PASSRNRSPSGSLEHHHH 114

>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 =  107 bits (267), Expect = 2e-26
 Identities = 39/239 (16%), Positives = 64/239 (26%), Gaps = 12/239 (5%)

Query: 424 DEYQNFLAELGGTLPESASKQSTTLALGPGSGSSGSNPPWANNSGSSGTPGHPGLGSNGA 483
           D  + F  E      +        ++    +G +  +  + +    +         +   
Sbjct: 1   DVGEEFNQEAEYGGHDQIDLYDDVISPSANNGDAPEDRDYMDTLPPTVGDDVGKGAAPNV 60

Query: 484 KPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFG--DIVMAKVIKDRVTGMSKGYGFVKYA 541
                     LYIG L     D+ L     + G  DI+  K  ++R  G SKG+  V   
Sbjct: 61  VYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVG 120

Query: 542 DIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQ 601
               +   +  +    L G+   V    K                          G  S 
Sbjct: 121 SEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSR----------KTTQSGQMSG 170

Query: 602 QYAPGGPLPNPPAASYTGAPVPWGPPVPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQY 660
           +   G P  +  AA   G       P   P     P P G    PP        +   +
Sbjct: 171 EGKAGPPGGSSRAAFPQGGRGRGRFPGAVPGGDRFPGPAGPGGPPPPFPAGQTHHHHHH 229

>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 =  102 bits (257), Expect = 3e-26
 Identities = 31/101 (30%), Positives = 49/101 (48%), Gaps = 3/101 (2%)

Query: 479 GSNGAK-PIKELDD-TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYG 536
           GS+G+  P +  DD   + +  L     +  L  LF  FG I    + KD+ TG SKG+ 
Sbjct: 1   GSSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFA 60

Query: 537 FVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVP 577
           F+ +   + A  AIA ++G+  +   + V  A KP   + P
Sbjct: 61  FISFHRREDAARAIAGVSGFGYDHLILNVEWA-KPSTNSGP 100

>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 =  101 bits (255), Expect = 3e-26
 Identities = 32/82 (39%), Positives = 44/82 (53%)

Query: 491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAI 550
             ++++G L P +    +   F+ FG I  A+V+KD  TG SKGYGFV + +   A NAI
Sbjct: 6   HFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAI 65

Query: 551 ASMNGYRLEGRTIAVRVAGKPP 572
             M G  L GR I    A + P
Sbjct: 66  QQMGGQWLGGRQIRTNWATRKP 87

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score =  102 bits (257), Expect = 4e-26
 Identities = 29/77 (37%), Positives = 40/77 (51%), Gaps = 2/77 (2%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
            N++I  L  ++D+  L   FS FG+I+  KV+ D     SKGYGFV +   + A  AI 
Sbjct: 6   GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIE 63

Query: 552 SMNGYRLEGRTIAVRVA 568
            MNG  L  R + V   
Sbjct: 64  KMNGMLLNDRKVFVGRF 80

>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 =  101 bits (253), Expect = 6e-26
 Identities = 29/79 (36%), Positives = 40/79 (50%)

Query: 490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNA 549
               LY+G L   +DD  L   F  FGDI   ++  D  T   +G+ FV++   + A  A
Sbjct: 6   TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 65

Query: 550 IASMNGYRLEGRTIAVRVA 568
           I +MN   L GRTI V +A
Sbjct: 66  IDNMNESELFGRTIRVNLA 84

>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 =  101 bits (254), Expect = 8e-26
 Identities = 32/121 (26%), Positives = 52/121 (42%), Gaps = 12/121 (9%)

Query: 468 GSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDR 527
           GSSG+ G    G  G         + +++  L   +    L  +FS  G +V A +++D+
Sbjct: 1   GSSGSSGALQAGRLG---------STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK 51

Query: 528 VTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPP--QPTVPPGPPTSTM 585
             G S+G G V +     A  AI+  NG  L  R + V++  +        PP  P  + 
Sbjct: 52  -DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERALPKGDFFPPERPQQSG 110

Query: 586 P 586
           P
Sbjct: 111 P 111

>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 =  101 bits (253), Expect = 8e-26
 Identities = 23/91 (25%), Positives = 45/91 (49%), Gaps = 3/91 (3%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTG---MSKGYGFVKYADIQMANN 548
           + L+I  L  +  ++ L  +FS  G I    + K +      +S G+GFV+Y   + A  
Sbjct: 6   SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65

Query: 549 AIASMNGYRLEGRTIAVRVAGKPPQPTVPPG 579
           A+  + G+ ++G  + VR++ +  +P   P 
Sbjct: 66  ALKQLQGHTVDGHKLEVRISERATKPASGPS 96

>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 =  100 bits (252), Expect = 9e-26
 Identities = 31/90 (34%), Positives = 46/90 (51%), Gaps = 1/90 (1%)

Query: 479 GSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFV 538
           GS+G  P +E  D  +++G L   + ++ L  LF   G +    + KDR  G  K +GFV
Sbjct: 4   GSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFV 62

Query: 539 KYADIQMANNAIASMNGYRLEGRTIAVRVA 568
            +   +  + AIA +NG RL GR I V   
Sbjct: 63  CFKHPESVSYAIALLNGIRLYGRPINVSGP 92

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score =  100 bits (251), Expect = 1e-25
 Identities = 25/83 (30%), Positives = 38/83 (45%), Gaps = 2/83 (2%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
             +++  LP       L   F+  G ++ A +  +   G SKG G VK+   ++A  A  
Sbjct: 9   CQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACR 66

Query: 552 SMNGYRLEGRTIAVRVAGKPPQP 574
            MNG +L GR I VR+      P
Sbjct: 67  MMNGMKLSGREIDVRIDRNASGP 89

>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 =   99 bits (250), Expect = 2e-25
 Identities = 32/85 (37%), Positives = 46/85 (54%), Gaps = 1/85 (1%)

Query: 490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIV-MAKVIKDRVTGMSKGYGFVKYADIQMANN 548
             + ++IG L P +D+  L   FS FG I+   K+++D  TG SKGY F+ +A    ++ 
Sbjct: 4   GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDA 63

Query: 549 AIASMNGYRLEGRTIAVRVAGKPPQ 573
           AI +MNG  L  R I V  A K   
Sbjct: 64  AIEAMNGQYLCNRPITVSYAFKKDS 88

>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 =  102 bits (256), Expect = 3e-25
 Identities = 21/101 (20%), Positives = 37/101 (36%), Gaps = 2/101 (1%)

Query: 479 GSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFV 538
           GS+  +  +     NL+IG L P      L    S         V+ D  TG ++ +G+V
Sbjct: 1   GSHMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYV 59

Query: 539 KYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPG 579
            +   +    A+  + G ++ G  I +          V   
Sbjct: 60  DFESAEDLEKALE-LTGLKVFGNEIKLEKPKGRDSKKVRAA 99

>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 = 92.3 bits (230), Expect = 9e-22
 Identities = 15/79 (18%), Positives = 32/79 (40%), Gaps = 5/79 (6%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
             L    L   + +D L  +F    +I +         G SKG  ++++     A   + 
Sbjct: 100 RTLLAKNLSFNITEDELKEVFEDALEIRL-----VSQDGKSKGIAYIEFKSEADAEKNLE 154

Query: 552 SMNGYRLEGRTIAVRVAGK 570
              G  ++GR++++   G+
Sbjct: 155 EKQGAEIDGRSVSLYYTGE 173

>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 = 99.2 bits (248), Expect = 4e-25
 Identities = 36/102 (35%), Positives = 51/102 (50%), Gaps = 3/102 (2%)

Query: 479 GSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFV 538
           GS+G+  +       LY+G L   +DD  L   F  FGDI   ++  D  T   +G+ FV
Sbjct: 1   GSSGSSGMAT-TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFV 59

Query: 539 KYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPGP 580
           ++   + A  AI +MN   L GRTI V +A KP +     GP
Sbjct: 60  EFELAEDAAAAIDNMNESELFGRTIRVNLA-KPMRIK-ESGP 99

>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 = 98.5 bits (246), Expect = 7e-25
 Identities = 22/83 (26%), Positives = 46/83 (55%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
             +Y+G +P    ++ ++ L S  G ++  K++ D  TG SKGY F+++ D++ + +A+ 
Sbjct: 3   RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62

Query: 552 SMNGYRLEGRTIAVRVAGKPPQP 574
           ++NGY+L  R +    +      
Sbjct: 63  NLNGYQLGSRFLKCGYSSNSDIS 85

>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 = 98.4 bits (246), Expect = 7e-25
 Identities = 25/92 (27%), Positives = 42/92 (45%), Gaps = 2/92 (2%)

Query: 479 GSNGAKPIKELDD--TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYG 536
           GS+G+   +   D    L +  L     +  L  +FS +G I    ++ D+ +  S+G+ 
Sbjct: 1   GSSGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFA 60

Query: 537 FVKYADIQMANNAIASMNGYRLEGRTIAVRVA 568
           FV + ++  A  A    NG  L+GR I V   
Sbjct: 61  FVYFENVDDAKEAKERANGMELDGRRIRVSGP 92

>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 = 98.0 bits (245), Expect = 8e-25
 Identities = 30/91 (32%), Positives = 47/91 (51%), Gaps = 1/91 (1%)

Query: 490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNA 549
             + LY+G L   + +D L  +F  FG I    ++KD  TG SKGYGF+ ++D + A  A
Sbjct: 4   GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRA 63

Query: 550 IASMNGYRLEGRTIAVRVAG-KPPQPTVPPG 579
           +  +NG+ L GR + V     +    + P  
Sbjct: 64  LEQLNGFELAGRPMRVGHVTERLDGGSGPSS 94

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score =  101 bits (254), Expect = 1e-24
 Identities = 23/94 (24%), Positives = 43/94 (45%)

Query: 480 SNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVK 539
            +           +LY+G L P + +  L   FS  G I+  +V +D +T  S GY +V 
Sbjct: 4   GSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVN 63

Query: 540 YADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQ 573
           +     A  A+ +MN   ++G+ + +  + + P 
Sbjct: 64  FQQPADAERALDTMNFDVIKGKPVRIMWSQRDPS 97

>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 = 98.9 bits (247), Expect = 1e-23
 Identities = 35/122 (28%), Positives = 51/122 (41%), Gaps = 4/122 (3%)

Query: 480 SNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVK 539
           S     +++    N++I  L  ++D+  L   FS FG+I+  KV+ D     SKGYGFV 
Sbjct: 92  SQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVH 149

Query: 540 YADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPGPPTSTMPTYPVSAPPVGGYP 599
           +   + A  AI  MNG  L  R + V       +     G        YP   P   G  
Sbjct: 150 FETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEF--YPYDVPDYAGSS 207

Query: 600 SQ 601
            +
Sbjct: 208 GR 209

>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 = 97.8 bits (244), Expect = 1e-24
 Identities = 33/90 (36%), Positives = 55/90 (61%), Gaps = 5/90 (5%)

Query: 479 GSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVM-AKVIKDRVTGMSKGYGF 537
           GS+G+  +      +L++G L P +D++ + R F+T G+ VM  K+I++R+TG+  GY F
Sbjct: 1   GSSGSSGMA----ASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCF 56

Query: 538 VKYADIQMANNAIASMNGYRLEGRTIAVRV 567
           V++AD+  A   +  +NG  L G T A R 
Sbjct: 57  VEFADLATAEKCLHKINGKPLPGATPAKRF 86

>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 =  100 bits (251), Expect = 1e-24
 Identities = 18/81 (22%), Positives = 34/81 (41%), Gaps = 2/81 (2%)

Query: 490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTG--MSKGYGFVKYADIQMAN 547
           D   +++G +P T  +  L  LF  +G +    V++DR      SKG  FV +   + A 
Sbjct: 2   DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61

Query: 548 NAIASMNGYRLEGRTIAVRVA 568
            A  +++  ++          
Sbjct: 62  EAQNALHNMKVLPGMHHPIQM 82

>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 = 91.9 bits (229), Expect = 1e-21
 Identities = 21/85 (24%), Positives = 42/85 (49%), Gaps = 4/85 (4%)

Query: 487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMA 546
             ++D  L+IG +     ++ +  +FS+FG I   ++++    G+S+G  FV +    MA
Sbjct: 91  NAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMA 149

Query: 547 NNAIASMNGYRL---EGRTIAVRVA 568
             AI +M+  +        + V+ A
Sbjct: 150 QTAIKAMHQAQTMEGCSSPMVVKFA 174

>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 = 97.7 bits (244), Expect = 2e-24
 Identities = 28/102 (27%), Positives = 50/102 (49%), Gaps = 2/102 (1%)

Query: 479 GSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFV 538
           GS+G+          L +  L      D L R+F  +G +    + ++  T   +G+ FV
Sbjct: 1   GSSGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFV 60

Query: 539 KYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPGP 580
           ++ D + A +A A+M+G  L+GR + V+VA +  +     GP
Sbjct: 61  RFHDRRDAQDAEAAMDGAELDGRELRVQVA-RYGRRD-LSGP 100

>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 = 97.9 bits (244), Expect = 3e-24
 Identities = 27/124 (21%), Positives = 49/124 (39%), Gaps = 1/124 (0%)

Query: 451 GPGSGSSGSNPPWANNSGSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIR 510
                SSG  P  ++ +  +G         +         +  L +  L     +  L  
Sbjct: 6   HHHHHSSGLVPRGSHMASMTGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLRE 65

Query: 511 LFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGK 570
           +FS +G I    ++ D+ +  S+G+ FV + ++  A  A    NG  L+GR I V  +  
Sbjct: 66  VFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS-I 124

Query: 571 PPQP 574
             +P
Sbjct: 125 TKRP 128

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 97.9 bits (244), Expect = 3e-24
 Identities = 32/125 (25%), Positives = 63/125 (50%), Gaps = 2/125 (1%)

Query: 452 PGSGSSGSNPPWANNSGSSGTPGHPGLGSNGAKPIKELDD-TNLYIGYLPPTLDDDGLIR 510
               SSG  P  ++ +  +G         +  +P  +++  T+L +  L      D L R
Sbjct: 7   HHHHSSGLVPRGSHMASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRR 66

Query: 511 LFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGK 570
           +F  +G +    + +DR T  S+G+ FV++ D + A +A+ +M+G  L+GR + V++A +
Sbjct: 67  VFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA-R 125

Query: 571 PPQPT 575
             +P 
Sbjct: 126 YGRPP 130

>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 = 96.6 bits (241), Expect = 4e-24
 Identities = 30/101 (29%), Positives = 52/101 (51%), Gaps = 4/101 (3%)

Query: 485 PIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQ 544
           P  +    ++++G +P    ++ L  +FS  G +V  +++ DR TG  KGYGF +Y D +
Sbjct: 2   PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61

Query: 545 MANNAIASMNGYRLEGRTIAVRVA----GKPPQPTVPPGPP 581
            A +A+ ++NG    GR + V  A     K    ++  G P
Sbjct: 62  TALSAMRNLNGREFSGRALRVDNAASEKNKEELKSLGTGAP 102

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 96.2 bits (240), Expect = 5e-24
 Identities = 25/105 (23%), Positives = 47/105 (44%), Gaps = 8/105 (7%)

Query: 468 GSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDR 527
           GSSG+ G         +    L+   L+I  LP +   + L  +    G +   +++ +R
Sbjct: 1   GSSGSSGV-------FRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR 53

Query: 528 VTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPP 572
             G  KG  +V+Y +   A+ A+  M+G  ++   I V ++   P
Sbjct: 54  -AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAISNSGP 97

>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 = 95.7 bits (239), Expect = 5e-24
 Identities = 25/84 (29%), Positives = 46/84 (54%), Gaps = 2/84 (2%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRV-TGMSKGYGFVKYADIQMANNAI 550
           T ++IG L   +  D ++ +FST+G I M  +  +R+   +SKGY +V++ +   A  A+
Sbjct: 5   TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64

Query: 551 ASMNGYRLEGRTIAVRVAGKPPQP 574
             M+G +++G+ I        P P
Sbjct: 65  KHMDGGQIDGQEITATAV-LAPWP 87

>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 = 96.6 bits (241), Expect = 5e-24
 Identities = 41/107 (38%), Positives = 52/107 (48%), Gaps = 8/107 (7%)

Query: 468 GSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDR 527
           GSSG+ G  G         K+   T +++G LP    D  L + F  FGDI  A VI DR
Sbjct: 1   GSSGSSGMHG-------SQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDR 53

Query: 528 VTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQP 574
            TG S+GYGFV  AD   A  A    N   ++GR   V +A    +P
Sbjct: 54  QTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAYLGAKP 99

>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 = 96.2 bits (240), Expect = 5e-24
 Identities = 28/77 (36%), Positives = 43/77 (55%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
             LY+G L   + +D L  +F  FG I   +++ D  TG SKGYGF+ ++D + A  A+ 
Sbjct: 27  MRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALE 86

Query: 552 SMNGYRLEGRTIAVRVA 568
            +NG+ L GR + V   
Sbjct: 87  QLNGFELAGRPMKVGHV 103

>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 = 97.2 bits (242), Expect = 1e-23
 Identities = 32/140 (22%), Positives = 60/140 (42%), Gaps = 2/140 (1%)

Query: 436 TLPESASKQSTTLALGPGSGSSGSNPPWANNSGSSGTPGHPGLGSNGAKPIKELDDTNLY 495
           T  E+    +        +  +G +  W  +  +       G   +      E   T+L 
Sbjct: 16  TTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVE-GMTSLK 74

Query: 496 IGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNG 555
           +  L      D L R+F  +G +    + +DR T  S+G+ FV++ D + A +A+ +M+G
Sbjct: 75  VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 134

Query: 556 YRLEGRTIAVRVA-GKPPQP 574
             L+GR + V++A    P  
Sbjct: 135 AVLDGRELRVQMARYGRPPD 154

>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 = 95.0 bits (237), Expect = 1e-23
 Identities = 29/117 (24%), Positives = 46/117 (39%), Gaps = 11/117 (9%)

Query: 453 GSGSSGSNPPWANNSGSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLF 512
           GS        W ++   SG  G  G+ +             L +  L   + D  +  LF
Sbjct: 1   GSRPKQLPDKWQHDLFDSGFGGGAGVETG----------GKLLVSNLDFGVSDADIQELF 50

Query: 513 STFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG 569
           + FG +  A V  DR +G S G   V +     A  A+   NG  L+GR + +++  
Sbjct: 51  AEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT 106

>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 = 94.2 bits (235), Expect = 2e-23
 Identities = 32/97 (32%), Positives = 50/97 (51%), Gaps = 2/97 (2%)

Query: 479 GSNGAK--PIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYG 536
           GS+G+     +   D  +Y+G L   + +  L  LF   G +V   + KDRVTG  +GYG
Sbjct: 1   GSSGSSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYG 60

Query: 537 FVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQ 573
           FV++   + A+ AI  M+  +L G+ I V  A    +
Sbjct: 61  FVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNK 97

>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 = 96.1 bits (239), Expect = 4e-23
 Identities = 34/159 (21%), Positives = 58/159 (36%), Gaps = 4/159 (2%)

Query: 422 MD-DEYQNFLAELGGTLPESASKQSTTLALGPGSGSSGSNPPWANNSGSSGTPGHPGLGS 480
           +D D  + F  +  G       K+      G G GS  +     ++           L  
Sbjct: 5   LDIDNAEEFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEP 64

Query: 481 NGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKY 540
              + +   +   L++  +     +D +   F  +G+I    +  DR TG SKGY  V+Y
Sbjct: 65  GPQRSV---EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEY 121

Query: 541 ADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPG 579
              + A  A  ++NG  + G+TI V          V   
Sbjct: 122 ETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKRVKKS 160

>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 = 93.1 bits (232), Expect = 6e-23
 Identities = 28/111 (25%), Positives = 48/111 (43%), Gaps = 15/111 (13%)

Query: 468 GSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDR 527
           GSSG+ G     +           + L++G LPP + ++ + +LF  +G      + KD 
Sbjct: 1   GSSGSSGGEKTFTQR---------SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD- 50

Query: 528 VTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPP 578
                KG+GF++     +A  A   ++   L G+ + VR A      T  P
Sbjct: 51  -----KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSASLTSGP 96

>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 = 92.6 bits (231), Expect = 6e-23
 Identities = 29/82 (35%), Positives = 44/82 (53%), Gaps = 2/82 (2%)

Query: 493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
           N+Y+G L  +   + +  LFS FG +   K+I DR T   KG+GFV+  + +  + AIA 
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAK 61

Query: 553 MNGYRLEGRTIAVRVAGKPPQP 574
           ++     GRTI V  A  P + 
Sbjct: 62  LDNTDFMGRTIRVTEA-NPKKS 82

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score = 92.6 bits (231), Expect = 6e-23
 Identities = 21/80 (26%), Positives = 32/80 (40%), Gaps = 2/80 (2%)

Query: 493 NLYIGYLPPTLDDDGLIRLFSTFG--DIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAI 550
            LYIG L     D+ L     + G  DI+  K  ++R  G SKG+  V       +   +
Sbjct: 3   ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62

Query: 551 ASMNGYRLEGRTIAVRVAGK 570
             +    L G+   V  + K
Sbjct: 63  DLLPKRELHGQNPVVTPSNK 82

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 92.7 bits (231), Expect = 8e-23
 Identities = 23/95 (24%), Positives = 43/95 (45%)

Query: 480 SNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVK 539
            +   P + ++   L++  +     ++ +   F+ +G+I    +  DR TG  KGY  V+
Sbjct: 12  GDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVE 71

Query: 540 YADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQP 574
           Y   + A  A+  +NG  L G+ I+V        P
Sbjct: 72  YETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPP 106

>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 = 93.2 bits (232), Expect = 1e-22
 Identities = 29/119 (24%), Positives = 47/119 (39%), Gaps = 12/119 (10%)

Query: 453 GSGSSGSNPP-WANNSGSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRL 511
           G    G +P  W ++   SG  G  G+ +             L +  L   + D  +  L
Sbjct: 6   GGQQMGRDPDKWQHDLFDSGCGGGEGVETG----------AKLLVSNLDFGVSDADIQEL 55

Query: 512 FSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGK 570
           F+ FG +  A V  DR +G S G   V +     A  A+    G  L+GR + +++   
Sbjct: 56  FAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVAS 113

>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 = 92.0 bits (229), Expect = 1e-22
 Identities = 29/101 (28%), Positives = 46/101 (45%), Gaps = 3/101 (2%)

Query: 479 GSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFV 538
           GS+G    K      L++  +P    D  L ++F  FG I+  ++I +     SKG+GFV
Sbjct: 4   GSSGNSESKS-TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFV 60

Query: 539 KYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPG 579
            + +   A+ A   ++G  +EGR I V  A         P 
Sbjct: 61  TFENSADADRAREKLHGTVVEGRKIEVNNATARVMTNSGPS 101

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 92.0 bits (229), Expect = 2e-22
 Identities = 27/98 (27%), Positives = 48/98 (48%), Gaps = 5/98 (5%)

Query: 479 GSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFV 538
           GS+G++      D  L++G L     ++ ++RLF  FG I    V++    G SKG  FV
Sbjct: 4   GSSGSESRGG-RDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFV 61

Query: 539 KYADIQMANNAIASMNGYRLE---GRTIAVRVAGKPPQ 573
           K++    A  AI +++G +       ++ V+ A    +
Sbjct: 62  KFSSHTEAQAAIHALHGSQTMPGASSSLVVKFADTDKE 99

>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 = 91.6 bits (228), Expect = 3e-22
 Identities = 26/114 (22%), Positives = 49/114 (42%), Gaps = 1/114 (0%)

Query: 468 GSSGTPGHPGLGSNGAKPIKELDDT-NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKD 526
           GSSG+ G               +    LY+  L P + +  L+ LF+ F +     +   
Sbjct: 1   GSSGSSGEEIRKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFR 60

Query: 527 RVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPGP 580
            +TG  +G  F+ + + ++A  A+  +NGY+L G+ + +       Q +  P  
Sbjct: 61  MMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQRSSGPSS 114

>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 = 90.8 bits (226), Expect = 4e-22
 Identities = 31/115 (26%), Positives = 53/115 (46%), Gaps = 13/115 (11%)

Query: 468 GSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDR 527
           GSSG+ G         +  K+   + + +  +P   +   +  LFSTFG++   ++ K  
Sbjct: 1   GSSGSSG---------QVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKM 51

Query: 528 -VTGMSKGYGFVKYADIQMANNAIASM-NGYRLEGRTIAVRVAGKPPQPTVPPGP 580
             TG  +G+GFV +   Q A  A  ++ +   L GR + +  A    + TV  GP
Sbjct: 52  TGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWAD--SEVTVQSGP 104

>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 = 91.7 bits (228), Expect = 4e-22
 Identities = 23/97 (23%), Positives = 44/97 (45%), Gaps = 1/97 (1%)

Query: 479 GSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFV 538
             +   P + ++   L++  +     ++ +   F+ +G+I    +  DR TG  KGY  V
Sbjct: 10  DGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLV 69

Query: 539 KYADIQMANNAIASMNGYRLEGRTIAVRVAG-KPPQP 574
           +Y   + A  A+  +NG  L G+ I+V     + P  
Sbjct: 70  EYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPPK 106

>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 = 90.3 bits (225), Expect = 4e-22
 Identities = 18/87 (20%), Positives = 41/87 (47%), Gaps = 2/87 (2%)

Query: 488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMAN 547
           E D  ++Y+G +      + L   F   G +    ++ D+ +G  KG+ +++++D +   
Sbjct: 3   EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 62

Query: 548 NAIASMNGYRLEGRTIAVRVAGKPPQP 574
            ++A ++     GR I V    +  +P
Sbjct: 63  TSLA-LDESLFRGRQIKVIPK-RTNRP 87

>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 = 95.8 bits (239), Expect = 7e-22
 Identities = 14/93 (15%), Positives = 36/93 (38%), Gaps = 2/93 (2%)

Query: 484 KPIK--ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYA 541
             I    L +  L++   PP+     +  L      + ++  +       S+ + ++   
Sbjct: 108 NEIIVSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVT 167

Query: 542 DIQMANNAIASMNGYRLEGRTIAVRVAGKPPQP 574
             + A   +  +NG ++EG T+  +V+    + 
Sbjct: 168 SKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKS 200

>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 = 89.7 bits (223), Expect = 8e-20
 Identities = 22/83 (26%), Positives = 34/83 (40%), Gaps = 3/83 (3%)

Query: 492 TNLYIGYLPPTLDDDGLIR-LFSTFGDIVMAKVIKDR-VTGMSKGYGFVKYADIQMANNA 549
             + I  L   L D+ L+R  F  FG I    +   +     +    F+ + +   A  A
Sbjct: 211 REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA 270

Query: 550 IASMNGYRLEGRTIAVRVAGKPP 572
           +  MN   L  R I+V +A K P
Sbjct: 271 LQ-MNRSLLGNREISVSLADKKP 292

>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 = 80.8 bits (200), Expect = 7e-17
 Identities = 13/76 (17%), Positives = 29/76 (38%), Gaps = 3/76 (3%)

Query: 490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNA 549
           + T + +  LP + + + + + F   G I+   V        +  +  +++A    A  A
Sbjct: 40  ELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFRFARIEFARYDGALAA 97

Query: 550 IASMNGYRLEGRTIAV 565
           I   +   +    I V
Sbjct: 98  ITKTHKV-VGQNEIIV 112

>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 = 89.8 bits (223), Expect = 1e-21
 Identities = 28/112 (25%), Positives = 46/112 (41%), Gaps = 9/112 (8%)

Query: 477 GLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDI--------VMAKVIKDRV 528
           G   +   P ++ D++ +Y+  L  ++  D L   F   G +         M  +  D+ 
Sbjct: 1   GSSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKE 60

Query: 529 TGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG-KPPQPTVPPG 579
           TG  KG   V Y D   A  A+   +G   +G  + V +A  KPP  + P  
Sbjct: 61  TGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNSGPSS 112

>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 = 89.7 bits (223), Expect = 1e-21
 Identities = 26/107 (24%), Positives = 47/107 (43%), Gaps = 15/107 (14%)

Query: 468 GSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDR 527
           GSSG+ G          P    +   ++I  L    +++ L  +   FGD+   +V+   
Sbjct: 1   GSSGSSG---------LPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHP 51

Query: 528 VTGMSKGYGFVKYADIQMANNAIASMN------GYRLEGRTIAVRVA 568
            T  SKG  F ++   + A   +A+ +      G +L+GR + V +A
Sbjct: 52  DTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLA 98

>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 = 94.6 bits (234), Expect = 2e-21
 Identities = 36/181 (19%), Positives = 54/181 (29%), Gaps = 7/181 (3%)

Query: 493 NLYIGYLPPTLDDDGLIR----LFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANN 548
            +YI  L   +  D L +    +FS FG I+   V +   +   +G  FV + ++  A N
Sbjct: 11  TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 67

Query: 549 AIASMNGYRLEGRTIAVRVAGKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGP 608
           A+ SM G+    + + ++ A                         P              
Sbjct: 68  ALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQG 127

Query: 609 LPNPPAASYTGAPVPWGPPVPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAP 668
               P       PVP  PP+          P      PP    P P       PP    P
Sbjct: 128 GGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPP 187

Query: 669 P 669
            
Sbjct: 188 Q 188

>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 = 62.2 bits (150), Expect = 1e-10
 Identities = 19/135 (14%), Positives = 39/135 (28%), Gaps = 12/135 (8%)

Query: 434 GGTLPESASKQSTTLALGPGSGSSGSNPPWANNSGSSGTPGHPGLGSNGAKPIKELDDT- 492
           G      A +    +   P         P    +     PG           +       
Sbjct: 143 GMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLS 202

Query: 493 ------NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMA 546
                  L++  LP   ++  L  LF+ F      +++  R         FV++ +   A
Sbjct: 203 ENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQA 257

Query: 547 NNAIASMNGYRLEGR 561
             A  ++ G+++   
Sbjct: 258 GAARDALQGFKITQN 272

>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 = 90.7 bits (226), Expect = 2e-21
 Identities = 22/90 (24%), Positives = 41/90 (45%), Gaps = 3/90 (3%)

Query: 490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNA 549
           +   ++IG L     +D L   F  +G +   K++KD  TG S+G+GF+ +      +  
Sbjct: 2   ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61

Query: 550 IASMNGYRLEGRTIAVRVAGKPPQPTVPPG 579
           + + +   L+G+ I  + A  P       G
Sbjct: 62  VKTQH--ILDGKVIDPKRA-IPRDEQDKTG 88

>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 = 78.7 bits (195), Expect = 4e-17
 Identities = 24/87 (27%), Positives = 41/87 (47%), Gaps = 2/87 (2%)

Query: 483 AKPIKELDDTN-LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYA 541
           A P  E D T  +++G + P +        FS +G I+ A+++ D+ TG S+G+GFV Y 
Sbjct: 78  AIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYD 137

Query: 542 DIQMANNAIASMNGYRLEGRTIAVRVA 568
                +           + R I ++ A
Sbjct: 138 SADAVDRVCQ-NKFIDFKDRKIEIKRA 163

>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 = 88.9 bits (221), Expect = 2e-21
 Identities = 25/95 (26%), Positives = 42/95 (44%), Gaps = 1/95 (1%)

Query: 480 SNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVK 539
                P + ++   L++  +     +D +   F  +G+I    +  DR TG SKGY  V+
Sbjct: 15  ELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVE 74

Query: 540 YADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQP 574
           Y   + A  A  ++NG  + G+TI V        P
Sbjct: 75  YETHKQALAAKEALNGAEIMGQTIQVDWC-FVKGP 108

>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 = 88.5 bits (220), Expect = 2e-21
 Identities = 27/106 (25%), Positives = 46/106 (43%), Gaps = 7/106 (6%)

Query: 479 GSNGAKPIKELDD--TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYG 536
           GS+G+            L++  L     ++ L   F      V A+++ DR TG SKG+G
Sbjct: 1   GSSGSSGPNARSQPSKTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFG 57

Query: 537 FVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPGPPT 582
           FV +   + A  A  +M    ++G  + +  A   P+     GP +
Sbjct: 58  FVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAK--PKGEGGSGPSS 101

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 88.6 bits (220), Expect = 2e-21
 Identities = 13/106 (12%), Positives = 33/106 (31%), Gaps = 2/106 (1%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
             +    L   + +  L  +   +G++   +++    T    G   V +   + A   + 
Sbjct: 7   KEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVK 66

Query: 552 SMNGYRLEGRTIAVRVAGKPPQPTVPPGPPTSTMPTYPVSAPPVGG 597
           +++   + G  I  ++                   +Y     P GG
Sbjct: 67  NLHLTSVMGNIIHAQLD--IKGQQRMKYYELIVNGSYTPQTVPTGG 110

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 91.1 bits (226), Expect = 3e-21
 Identities = 25/120 (20%), Positives = 40/120 (33%), Gaps = 1/120 (0%)

Query: 451 GPGSGSSGSNPPWANNSGSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIR 510
               G      P++          H    S             L +  L   + D  +  
Sbjct: 48  AIARGGRNRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQE 107

Query: 511 LFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGK 570
           LF+ FG +  A V  DR +G S G   V +     A  A+    G  L+GR + +++   
Sbjct: 108 LFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVAS 166

>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 = 93.2 bits (232), Expect = 3e-21
 Identities = 21/82 (25%), Positives = 39/82 (47%), Gaps = 6/82 (7%)

Query: 491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAI 550
              L++G LP  + ++   RLF  +G+     + +DR      G+GF++     +A  A 
Sbjct: 22  RCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR------GFGFIRLESRTLAEIAK 75

Query: 551 ASMNGYRLEGRTIAVRVAGKPP 572
           A ++G  L+ R + +R A    
Sbjct: 76  AELDGTILKSRPLRIRFATHGA 97

>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 = 90.9 bits (226), Expect = 2e-20
 Identities = 29/130 (22%), Positives = 45/130 (34%), Gaps = 4/130 (3%)

Query: 491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAI 550
              L +  L P + ++ L + FS FG +  A V+ D   G + G GFV++A    A  A+
Sbjct: 96  GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD-RGRATGKGFVEFAAKPPARKAL 154

Query: 551 ASMN-GYRLEGRTIAVRVAGKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPL 609
                G  L   T    +     Q     G P   M                ++A  G  
Sbjct: 155 ERCGDGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLMQKTQQYHKE--REQPPRFAQPGTF 212

Query: 610 PNPPAASYTG 619
               A+ +  
Sbjct: 213 EFEYASRWKA 222

>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 = 88.1 bits (219), Expect = 3e-21
 Identities = 22/99 (22%), Positives = 34/99 (34%), Gaps = 9/99 (9%)

Query: 478 LGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMA--------KVIKDRVT 529
           +G +        D+  +++  L   +  + +   F   G I            +  DR T
Sbjct: 1   MGHHHHHH-SHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRET 59

Query: 530 GMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA 568
           G  KG   V + D   A  AI   +G    G  I V  A
Sbjct: 60  GKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 98

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 88.1 bits (219), Expect = 3e-21
 Identities = 24/77 (31%), Positives = 40/77 (51%), Gaps = 2/77 (2%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
             L++  +P    D  L ++F  FG I+  ++I +     SKG+GFV + +   A+ A  
Sbjct: 30  KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRARE 87

Query: 552 SMNGYRLEGRTIAVRVA 568
            ++G  +EGR I V  A
Sbjct: 88  KLHGTVVEGRKIEVNNA 104

>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 = 87.7 bits (218), Expect = 5e-21
 Identities = 31/111 (27%), Positives = 52/111 (46%), Gaps = 12/111 (10%)

Query: 468 GSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDR 527
           GSSG+ G        +          L +  LP    +  L   FSTFG+++M +V KD 
Sbjct: 1   GSSGSSGVKRAVQKTSD---------LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDL 51

Query: 528 VTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG-KPPQPTVP 577
            TG SKG+GFV++ + +     ++  +   ++GR    ++   K  Q + P
Sbjct: 52  KTGHSKGFGFVRFTEYETQVKVMSQRH--MIDGRWCDCKLPNSKQSQDSGP 100

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 87.3 bits (217), Expect = 6e-21
 Identities = 30/97 (30%), Positives = 46/97 (47%), Gaps = 4/97 (4%)

Query: 490 DDTNLYIGYLPPTLDDDGLIRLFS-TFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANN 548
            + +L++G L P +DD  L   F   +      KV+ D+ TG+SKGYGFVK+ D      
Sbjct: 8   PEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKR 66

Query: 549 AIASMNG-YRLEGRTIAVRVAG-KPPQPTVPPGPPTS 583
           A+    G   L  + + + VA  K  +       P+S
Sbjct: 67  ALTECQGAVGLGSKPVRLSVAIPKASRVKPVESGPSS 103

>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 = 86.9 bits (216), Expect = 9e-21
 Identities = 23/89 (25%), Positives = 40/89 (44%), Gaps = 1/89 (1%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
             L++  L  T  ++ L +LFS +G +       D +T   KG+ FV +   + A  A A
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 552 SMNGYRLEGRTIAVRVAGKPPQPTVPPGP 580
            ++G   +GR + V  +    +     GP
Sbjct: 69  EVDGQVFQGRMLHVLPS-TIKKEASQSGP 96

>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 = 86.9 bits (216), Expect = 9e-21
 Identities = 26/89 (29%), Positives = 48/89 (53%), Gaps = 4/89 (4%)

Query: 479 GSNGAKPIKELD--DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYG 536
           GS+G+  + E D     LY+G L   + +  +++LFS  G     K+I +  +     Y 
Sbjct: 1   GSSGSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYC 58

Query: 537 FVKYADIQMANNAIASMNGYRLEGRTIAV 565
           FV++ + + A  A+A+MNG ++ G+ + V
Sbjct: 59  FVEFYEHRDAAAALAAMNGRKILGKEVKV 87

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 88.1 bits (218), Expect = 1e-20
 Identities = 28/135 (20%), Positives = 42/135 (31%), Gaps = 2/135 (1%)

Query: 457 SGSNPPWANNSGSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFG 516
               PP       S  P +                  +Y+G       D  LI++  + G
Sbjct: 21  QSMEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIG 80

Query: 517 --DIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQP 574
             D+V  K  ++R  G SKGY  V  A     +  +  + G  L G  + VR A +    
Sbjct: 81  VYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLS 140

Query: 575 TVPPGPPTSTMPTYP 589
                         P
Sbjct: 141 QFEAQARKRECVRVP 155

>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 = 89.3 bits (222), Expect = 2e-20
 Identities = 26/104 (25%), Positives = 45/104 (43%), Gaps = 1/104 (0%)

Query: 480 SNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVK 539
           S    P +      L+IG L     D+ L   F  +G +    V++D  T  S+G+GFV 
Sbjct: 2   SKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVT 61

Query: 540 YADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPGPPTS 583
           YA ++  + A+     ++++GR +  + A        P    T 
Sbjct: 62  YATVEEVDAAMN-ARPHKVDGRVVEPKRAVSREDSQRPGAHLTV 104

>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 = 72.3 bits (178), Expect = 1e-14
 Identities = 18/101 (17%), Positives = 41/101 (40%), Gaps = 3/101 (2%)

Query: 481 NGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKY 540
           +  +P   L    +++G +    ++  L   F  +G I + +++ DR +G  +G+ FV +
Sbjct: 94  DSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153

Query: 541 ADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPGPP 581
            D    +  +     + + G    VR A    +  +     
Sbjct: 154 DDHDSVDKIVI-QKYHTVNGHNCEVRKA--LSKQEMASASS 191

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 85.8 bits (213), Expect = 2e-20
 Identities = 16/94 (17%), Positives = 34/94 (36%), Gaps = 5/94 (5%)

Query: 480 SNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVK 539
            +     K      L    L   + +D L  +F    +I +         G SKG  +++
Sbjct: 5   EDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRL-----VSQDGKSKGIAYIE 59

Query: 540 YADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQ 573
           +     A   +    G  ++GR++++   G+   
Sbjct: 60  FKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGG 93

>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 = 85.8 bits (213), Expect = 2e-20
 Identities = 25/113 (22%), Positives = 48/113 (42%), Gaps = 15/113 (13%)

Query: 468 GSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDR 527
           GSSG+ G     S+            LY+  L  +  ++ + + F+      + +V K  
Sbjct: 1   GSSGSSGDEDTMSSV---------KILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK-- 49

Query: 528 VTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPGP 580
                + Y FV +++ + A  A+ ++NG  L+G  I V +A    + +  P  
Sbjct: 50  ----IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDKDSSGPSS 98

>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 = 84.9 bits (211), Expect = 4e-20
 Identities = 25/104 (24%), Positives = 49/104 (47%), Gaps = 6/104 (5%)

Query: 479 GSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFV 538
           GS+G+   K      +++G +P    +  L   F  FG +    +I D      +G+GF+
Sbjct: 1   GSSGSSGSKS---NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFI 57

Query: 539 KYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPGPPT 582
            + D Q  + A+  M+ + + G+ + V+ A   P+ +   GP +
Sbjct: 58  TFEDEQSVDQAVN-MHFHDIMGKKVEVKRAE--PRDSKSSGPSS 98

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 84.1 bits (209), Expect = 4e-20
 Identities = 23/75 (30%), Positives = 41/75 (54%), Gaps = 1/75 (1%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           ++IG L      +GL   F  FG++    V++D +T  S+G+GFV + D    +  +A  
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-Q 61

Query: 554 NGYRLEGRTIAVRVA 568
           + + L+ +TI  +VA
Sbjct: 62  SRHELDSKTIDPKVA 76

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 84.4 bits (209), Expect = 6e-20
 Identities = 22/89 (24%), Positives = 36/89 (40%), Gaps = 5/89 (5%)

Query: 479 GSNGAKPI--KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYG 536
           GS+G+     K      L I  +PP L  + L  L   +G +   + +            
Sbjct: 1   GSSGSSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET---AVV 57

Query: 537 FVKYADIQMANNAIASMNGYRLEGRTIAV 565
            V Y+    A  A+  +NG++LE  T+ V
Sbjct: 58  NVTYSSKDQARQALDKLNGFQLENFTLKV 86

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 85.1 bits (211), Expect = 6e-20
 Identities = 22/95 (23%), Positives = 33/95 (34%), Gaps = 8/95 (8%)

Query: 487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDI--------VMAKVIKDRVTGMSKGYGFV 538
              D+  +++  L   +  + +   F   G I         M  +  DR TG  KG   V
Sbjct: 3   DNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATV 62

Query: 539 KYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQ 573
            + D   A  AI   +G    G  I V  A +   
Sbjct: 63  SFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRAD 97

>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 = 83.9 bits (208), Expect = 9e-20
 Identities = 24/92 (26%), Positives = 41/92 (44%), Gaps = 6/92 (6%)

Query: 490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNA 549
           +   L +  L  +  ++ L  +F     I     +     G SKGY F+++A  + A  A
Sbjct: 14  ESKTLVLSNLSYSATEETLQEVFEKATFIK----VPQNQNGKSKGYAFIEFASFEDAKEA 69

Query: 550 IASMNGYRLEGRTIAVRVAGKPPQPTVPPGPP 581
           + S N   +EGR I + + G  P+ +   GP 
Sbjct: 70  LNSCNKREIEGRAIRLELQG--PRGSPNSGPS 99

>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 = 84.3 bits (209), Expect = 1e-19
 Identities = 30/102 (29%), Positives = 46/102 (45%), Gaps = 2/102 (1%)

Query: 468 GSSGTPG-HPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKD 526
           GSSG+ G  P          +E D   ++   L   +    L   FS  G +   ++I D
Sbjct: 1   GSSGSSGKSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISD 60

Query: 527 RVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA 568
           R +  SKG  +V++ +IQ    AI  + G RL G  I V+ +
Sbjct: 61  RNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQAS 101

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 83.1 bits (206), Expect = 1e-19
 Identities = 16/83 (19%), Positives = 38/83 (45%), Gaps = 6/83 (7%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFG--DIVMAKVIKDRVTGMSKGYGFVKYADIQMANNA 549
             + +  + P    D ++   S +    +   ++IKD+ T  ++G+ FV+ +    A+  
Sbjct: 10  DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQL 69

Query: 550 IASMNG----YRLEGRTIAVRVA 568
           +  +       +++G+TI V  A
Sbjct: 70  LQILQSLHPPLKIDGKTIGVDFA 92

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A Length = 103

 Score = 83.5 bits (207), Expect = 1e-19
 Identities = 28/95 (29%), Positives = 46/95 (48%), Gaps = 10/95 (10%)

Query: 479 GSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFV 538
           GS+G+  + ++    L++  L  T+ ++ L + FS FG +   K +KD        Y F+
Sbjct: 1   GSSGSSGMAKV--KVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFI 50

Query: 539 KYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQ 573
            + +   A  A+  MNG  LEG  I +  A  P Q
Sbjct: 51  HFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQ 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 Length = 87

 Score = 83.0 bits (206), Expect = 1e-19
 Identities = 23/88 (26%), Positives = 38/88 (43%), Gaps = 2/88 (2%)

Query: 482 GAKPIKELDDTN-LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKY 540
           G    K  +D   +++G L        L   F+ FG++V   +  D  TG S+G+GF+ +
Sbjct: 1   GINASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILF 60

Query: 541 ADIQMANNAIASMNGYRLEGRTIAVRVA 568
            D       +       L+GR I  + A
Sbjct: 61  KDAASVEKVLDQKEHR-LDGRVIDPKKA 87

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 83.1 bits (206), Expect = 2e-19
 Identities = 32/113 (28%), Positives = 51/113 (45%), Gaps = 7/113 (6%)

Query: 468 GSSGTPGH-PGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKD 526
           GSSG+ G+   L            +  +Y G +   L D  + + FS FG I+  +V  +
Sbjct: 1   GSSGSSGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE 60

Query: 527 RVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPG 579
                 KGY FV+++  + A +AI S+NG  +EG  +      + P  T  P 
Sbjct: 61  ------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPDMTSGPS 107

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 82.7 bits (205), Expect = 2e-19
 Identities = 29/113 (25%), Positives = 41/113 (36%), Gaps = 18/113 (15%)

Query: 453 GSGSSGSNPPWANNSGSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLF 512
           GS + G  P           P         A P      T  YIG +P    +  LI LF
Sbjct: 1   GSQTIGLPPQ--------VNPQAVDHIIRSAPP----RVTTAYIGNIPHFATEADLIPLF 48

Query: 513 STFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAV 565
             FG I+  K   +      KG  F+KY   + A   I ++  +  +GR +  
Sbjct: 49  QNFGFILDFKHYPE------KGCCFIKYDTHEQAAVCIVALANFPFQGRNLRT 95

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 83.1 bits (206), Expect = 2e-19
 Identities = 33/115 (28%), Positives = 56/115 (48%), Gaps = 11/115 (9%)

Query: 468 GSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDR 527
           GSSG+ G    G++        +   L++G L  +   + L   FS +G++V   ++KD+
Sbjct: 1   GSSGSSGMNNSGAD--------EIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDK 52

Query: 528 VTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPGPPT 582
            T  S+G+GFVK+ D       +A    + L+GR I  +     P+   P GP +
Sbjct: 53  TTNQSRGFGFVKFKDPNCVGTVLA-SRPHTLDGRNIDPKPCT--PRGMQPSGPSS 104

>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 = 83.2 bits (206), Expect = 3e-19
 Identities = 27/110 (24%), Positives = 51/110 (46%), Gaps = 2/110 (1%)

Query: 465 NNSGSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVI 524
           ++  ++G           A+  KE+D  ++Y+G +        L   FS+ G I    ++
Sbjct: 10  HSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITIL 69

Query: 525 KDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQP 574
            D+ +G  KGY ++++A+    + A+A M+     GRTI V    +   P
Sbjct: 70  CDKFSGHPKGYAYIEFAERNSVDAAVA-MDETVFRGRTIKVLPK-RTNMP 117

>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 = 84.5 bits (209), Expect = 3e-19
 Identities = 26/87 (29%), Positives = 40/87 (45%)

Query: 479 GSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFV 538
           G N  +         LY+G L     ++ +  LFS  GDI    +  D++   + G+ FV
Sbjct: 27  GDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFV 86

Query: 539 KYADIQMANNAIASMNGYRLEGRTIAV 565
           +Y     A NA+  +NG RL+ R I  
Sbjct: 87  EYYSRADAENAMRYINGTRLDDRIIRT 113

>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 = 81.9 bits (203), Expect = 4e-19
 Identities = 24/101 (23%), Positives = 42/101 (41%), Gaps = 12/101 (11%)

Query: 479 GSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFV 538
           GS+G+      +   +++G +        L  LF   G ++   V+K         Y FV
Sbjct: 1   GSSGSSG----NTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFV 48

Query: 539 KYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPG 579
                  A  AIA +NG  ++G+ I V ++ K  + + P  
Sbjct: 49  HMEKEADAKAAIAQLNGKEVKGKRINVELSTKGQKKSGPSS 89

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 81.4 bits (202), Expect = 4e-19
 Identities = 13/75 (17%), Positives = 33/75 (44%), Gaps = 1/75 (1%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           +++G L      + +   F  FG +  A ++ D+ T   +G+GFV +    +       +
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-I 60

Query: 554 NGYRLEGRTIAVRVA 568
           + + +  + +  + A
Sbjct: 61  HFHEINNKMVECKKA 75

>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 = 81.5 bits (202), Expect = 7e-19
 Identities = 18/79 (22%), Positives = 31/79 (39%), Gaps = 2/79 (2%)

Query: 490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNA 549
              NL+IG L P      L    S         V+ D  TG ++ +G+V +   +    A
Sbjct: 16  TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAEDLEKA 74

Query: 550 IASMNGYRLEGRTIAVRVA 568
           +  + G ++ G  I +   
Sbjct: 75  LE-LTGLKVFGNEIKLEKP 92

>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 = 81.5 bits (202), Expect = 7e-19
 Identities = 30/108 (27%), Positives = 53/108 (49%), Gaps = 5/108 (4%)

Query: 471 GTPGHPGLGSNGAKPIKELDDTN---LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDR 527
           G+  H    S+G  P      ++   ++IG L      +GL   F  FG++    V++D 
Sbjct: 2   GSSHHHHHHSSGLVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDP 61

Query: 528 VTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG-KPPQP 574
           +T  S+G+GFV + D    +  +A  + + L+ +TI  +VA  +  QP
Sbjct: 62  LTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVAFPRRAQP 108

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 81.2 bits (201), Expect = 1e-18
 Identities = 19/87 (21%), Positives = 39/87 (44%), Gaps = 8/87 (9%)

Query: 487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMA 546
            EL +T L++   P  + +  L  +F  FG +   K++         G+ FV++ + + A
Sbjct: 27  GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESA 78

Query: 547 NNAIASMNGYRLEGRTIAVRVAGKPPQ 573
             AI  ++G     + + V  +  P +
Sbjct: 79  AKAIEEVHGKSFANQPLEVVYSKLPAK 105

>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 = 80.4 bits (199), Expect = 1e-18
 Identities = 25/103 (24%), Positives = 43/103 (41%), Gaps = 10/103 (9%)

Query: 479 GSNGAKPIKELDD--TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYG 536
           GS+G+   +        LY+      +    L   FS FG+I+   +         +   
Sbjct: 1   GSSGSSGERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPP------RNCA 52

Query: 537 FVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPG 579
           FV Y  ++ A+ A+A +NG ++E   + V +A K P     P 
Sbjct: 53  FVTYEKMESADQAVAELNGTQVESVQLKVNIARKQPMLDSGPS 95

>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 = 79.6 bits (197), Expect = 3e-18
 Identities = 19/77 (24%), Positives = 38/77 (49%), Gaps = 3/77 (3%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
             +++G +   +D+  +   F+ +G +   K+I DR TG+SKGYGFV + +       + 
Sbjct: 10  NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIV- 67

Query: 552 SMNGYRLEGRTIAVRVA 568
             +     G+ + +  A
Sbjct: 68  -ESQINFHGKKLKLGPA 83

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 79.2 bits (196), Expect = 4e-18
 Identities = 24/115 (20%), Positives = 45/115 (39%), Gaps = 24/115 (20%)

Query: 468 GSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDR 527
           GSSG+ G                 T L++G + PT  +  L   F  +G ++   ++K  
Sbjct: 1   GSSGSSGKAS--------------TKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK-- 44

Query: 528 VTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPGPPT 582
                  Y FV     + A  AI  ++    +G+ + V+++    +     GP +
Sbjct: 45  ------DYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLRT--ASGPSS 91

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 79.3 bits (196), Expect = 5e-18
 Identities = 29/113 (25%), Positives = 49/113 (43%), Gaps = 7/113 (6%)

Query: 468 GSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDR 527
           GSSG+ G  G G          +D  +Y+G LPP +    +  +F  +G I    +   R
Sbjct: 1   GSSGSSGMSGGGVIRGPAGN--NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR 58

Query: 528 VTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPGP 580
                  + FV++ D + A +A+   +GY  +G  + V    +  + T   GP
Sbjct: 59  ---GGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP-RSGRGT-GSGP 106

>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 = 78.8 bits (195), Expect = 5e-18
 Identities = 25/89 (28%), Positives = 39/89 (43%), Gaps = 9/89 (10%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
             L+IG LP    +  +  LF  +G ++   +IK         YGFV   D   A +AI 
Sbjct: 9   VKLFIGNLPREATEQEIRSLFEQYGKVLECDIIK--------NYGFVHIEDKTAAEDAIR 60

Query: 552 SMNGYRLEGRTIAVRVA-GKPPQPTVPPG 579
           +++ Y+L G  I V  +  K    + P  
Sbjct: 61  NLHHYKLHGVNINVEASKNKSKASSGPSS 89

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 79.2 bits (196), Expect = 6e-18
 Identities = 25/114 (21%), Positives = 50/114 (43%), Gaps = 1/114 (0%)

Query: 466 NSGSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIK 525
           +SGSSG            K  ++     L+IG L     ++ L   +  +G +    V++
Sbjct: 2   SSGSSGMEKTLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMR 61

Query: 526 DRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPG 579
           D  +  S+G+GFV ++ +   + A+A    + ++GR +  + A    +    P 
Sbjct: 62  DPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVAREESGSGPS 114

>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 = 77.7 bits (192), Expect = 9e-18
 Identities = 25/89 (28%), Positives = 42/89 (47%), Gaps = 8/89 (8%)

Query: 479 GSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFV 538
           GS+G+   ++   T LY+G L  T+ +  L   F  FG+I    V++       +   F+
Sbjct: 1   GSSGSSG-EDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFI 53

Query: 539 KYADIQMANNAI-ASMNGYRLEGRTIAVR 566
           ++A  Q A  A   S N   + GR + V+
Sbjct: 54  QFATRQAAEVAAEKSFNKLIVNGRRLNVK 82

>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 = 77.2 bits (191), Expect = 1e-17
 Identities = 12/75 (16%), Positives = 33/75 (44%), Gaps = 1/75 (1%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           +++G L P   ++ +   F  FG++   ++  D  T   +G+ F+ + + +     +   
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-K 60

Query: 554 NGYRLEGRTIAVRVA 568
             + +      ++VA
Sbjct: 61  KYHNVGLSKCEIKVA 75

>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 = 77.7 bits (192), Expect = 1e-17
 Identities = 31/100 (31%), Positives = 42/100 (42%), Gaps = 13/100 (13%)

Query: 468 GSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDR 527
           GSSG+ G  G G   A P      T L++G L P      L R F  FG I     +K  
Sbjct: 1   GSSGSSGKIGYGK--ANP-----TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD 53

Query: 528 VTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV 567
                  + +++Y  +  A  A A M G+ L G    +RV
Sbjct: 54  ------SFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRV 87

>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 = 80.7 bits (199), Expect = 1e-17
 Identities = 25/123 (20%), Positives = 48/123 (39%), Gaps = 7/123 (5%)

Query: 491 DTNLYIGYLPP-TLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNA 549
           ++ L +  L P  +    L  LF  +GD+   K++ +      K    V+ AD   A  A
Sbjct: 3   NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMADGNQAQLA 57

Query: 550 IASMNGYRLEGRTIAVRVAGKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPL 609
           ++ +NG++L G+ I + ++ K     +P         T      P+  +          +
Sbjct: 58  MSHLNGHKLHGKPIRITLS-KHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNI 116

Query: 610 PNP 612
             P
Sbjct: 117 FPP 119

>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 = 69.9 bits (171), Expect = 9e-14
 Identities = 23/140 (16%), Positives = 48/140 (34%), Gaps = 11/140 (7%)

Query: 434 GGTLPESASKQSTTLALGPGSGSSGSNPPWANNSGSSGTPGHPGLGSNGAKPIKELDDTN 493
           G  +  + SK         G    G    + N+              N   P        
Sbjct: 68  GKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSA-----T 122

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L++  +PP++ ++ L  LFS+ G +V       +     +    ++   ++ A  A+  +
Sbjct: 123 LHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK----DRKMALIQMGSVEEAVQALIDL 178

Query: 554 NGYRL-EGRTIAVRVAGKPP 572
           + + L E   + V  + K  
Sbjct: 179 HNHDLGENHHLRVSFS-KST 197

>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 = 78.7 bits (194), Expect = 2e-17
 Identities = 20/88 (22%), Positives = 36/88 (40%), Gaps = 6/88 (6%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKV-----IKDRVTGMSKGYGFVKYADIQMA 546
             +Y+  L   + +  L  +F  + D           I+    G  KG  F+   + + A
Sbjct: 46  CRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAA 105

Query: 547 NNAIASMNGYRLEGRTIAVRVAGKPPQP 574
             A+   NGY L G+ + V+ A +  +P
Sbjct: 106 AKALKEANGYVLFGKPMVVQFA-RSARP 132

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 76.3 bits (188), Expect = 4e-17
 Identities = 20/72 (27%), Positives = 32/72 (44%), Gaps = 1/72 (1%)

Query: 495 YIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMN 554
            I      +    L  LFS  G +V  +   D  TG +KG+ FV+   +  A   I S +
Sbjct: 16  VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75

Query: 555 GYRLEGR-TIAV 565
           G RL+ +  + +
Sbjct: 76  GKRLDLKHRLFL 87

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 76.1 bits (188), Expect = 4e-17
 Identities = 23/83 (27%), Positives = 33/83 (39%), Gaps = 7/83 (8%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
             LYIG L P +  D L +LF          +       +  GY FV Y D   A  AI 
Sbjct: 9   NKLYIGNLSPAVTADDLRQLFGDRK------LPLAGQVLLKSGYAFVDYPDQNWAIRAIE 62

Query: 552 SMNG-YRLEGRTIAVRVAGKPPQ 573
           +++G   L G+ + V  +     
Sbjct: 63  TLSGKVELHGKIMEVDYSVSKKL 85

>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 = 78.0 bits (192), Expect = 5e-17
 Identities = 19/83 (22%), Positives = 37/83 (44%), Gaps = 5/83 (6%)

Query: 490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNA 549
            D  +Y+G L    +   L R F  +G +    V ++       G+ FV++ D + A +A
Sbjct: 72  LDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADA 126

Query: 550 IASMNGYRLEGRTIAVRVAGKPP 572
           +  ++G  L G  + V ++    
Sbjct: 127 VRELDGRTLCGCRVRVELSNGEK 149

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 75.4 bits (186), Expect = 1e-16
 Identities = 21/104 (20%), Positives = 44/104 (42%), Gaps = 5/104 (4%)

Query: 493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
            +Y+G L        L R FS +G +    + ++       G+ FV++ D + A +A+  
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRG 56

Query: 553 MNGYRLEGRTIAVRVAGKPPQPTVPPGPPTSTMPTYPVSAPPVG 596
           ++G  + G  + V ++   P+ +    PP        +   P+ 
Sbjct: 57  LDGKVICGSRVRVELSTGMPRRSRFDRPPARRKLLEVLFNGPLE 100

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 75.1 bits (185), Expect = 2e-16
 Identities = 21/77 (27%), Positives = 36/77 (46%), Gaps = 3/77 (3%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
             LYI  LP  +  + +  +F  +G I   +V     T  ++G  +V Y DI  A NA+ 
Sbjct: 9   RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNAVD 65

Query: 552 SMNGYRLEGRTIAVRVA 568
            ++G+ +  R + V   
Sbjct: 66  HLSGFNVSNRYLVVLYY 82

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 77.7 bits (191), Expect = 3e-16
 Identities = 30/160 (18%), Positives = 54/160 (33%), Gaps = 17/160 (10%)

Query: 452 PGSGSSGSNPPWANNSGSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPP-TLDDDGLIR 510
                S    P  ++ G    PG  G G+           + L +  L P  +    L  
Sbjct: 6   HHHHHSSGLVPRGSHMGRIAIPGLAGAGN-----------SVLLVSNLNPERVTPQSLFI 54

Query: 511 LFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGK 570
           LF  +GD+   K++ +      K    V+ AD   A  A++ +NG++L G+ I + ++  
Sbjct: 55  LFGVYGDVQRVKILFN-----KKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKH 109

Query: 571 PPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLP 610
                   G     +     ++P                P
Sbjct: 110 QNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFP 149

>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 = 63.1 bits (153), Expect = 3e-11
 Identities = 14/75 (18%), Positives = 34/75 (45%), Gaps = 5/75 (6%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
             L++  +PP++ ++ L  LFS+ G +V       +     +    ++   ++ A  A+ 
Sbjct: 152 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK----DRKMALIQMGSVEEAVQALI 207

Query: 552 SMNGYRL-EGRTIAV 565
            ++ + L E   + V
Sbjct: 208 DLHNHDLGENHHLRV 222

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 73.5 bits (181), Expect = 4e-16
 Identities = 20/97 (20%), Positives = 41/97 (42%), Gaps = 2/97 (2%)

Query: 477 GLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYG 536
           G   +  K +        Y+G LP       +  +F     I   ++++D+ T   KG+ 
Sbjct: 1   GSSGSSGKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFC 59

Query: 537 FVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQ 573
           +V++ ++     A+   +G  L  R++ V +A    Q
Sbjct: 60  YVEFDEVDSLKEALT-YDGALLGDRSLRVDIAEGRKQ 95

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 73.6 bits (181), Expect = 5e-16
 Identities = 22/91 (24%), Positives = 42/91 (46%), Gaps = 9/91 (9%)

Query: 485 PIKELDDTNLYIGYLPPTLDD------DGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFV 538
              +  D+ + +  +P    D      + + ++FS FG I           G +KGY F+
Sbjct: 9   QEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKIT--NDFYPEEDGKTKGYIFL 66

Query: 539 KYADIQMANNAIASMNGYRLEGR-TIAVRVA 568
           +YA    A +A+ + +GY+L+ + T  V + 
Sbjct: 67  EYASPAHAVDAVKNADGYKLDKQHTFRVNLF 97

>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 = 73.6 bits (181), Expect = 5e-16
 Identities = 30/117 (25%), Positives = 51/117 (43%), Gaps = 12/117 (10%)

Query: 468 GSSGTPGHPGLGSNGAKPIK---ELDDTNLYIGYLPP-TLDDDGLIRLFSTFGDIVMAKV 523
           GSSG+ G            K   +  ++ ++IG L    +    +  +FS +G +    V
Sbjct: 1   GSSGSSGMSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV 60

Query: 524 IKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPGP 580
                    KGY FV+Y++ + A  A+   NG  L G+T+ + +AG+P      P  
Sbjct: 61  --------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEPKPDRSGPSS 109

>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 = 71.9 bits (177), Expect = 1e-15
 Identities = 21/80 (26%), Positives = 38/80 (47%), Gaps = 7/80 (8%)

Query: 493 NLYIGYLPPTLDDDGLIR----LFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANN 548
            +YI  L   +  D L +    +FS FG I+   V +   +   +G  FV + ++  A N
Sbjct: 10  TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 66

Query: 549 AIASMNGYRLEGRTIAVRVA 568
           A+ SM G+    + + ++ A
Sbjct: 67  ALRSMQGFPFYDKPMRIQYA 86

>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 = 75.5 bits (185), Expect = 1e-15
 Identities = 8/80 (10%), Positives = 24/80 (30%), Gaps = 4/80 (5%)

Query: 493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
            L+    P  + ++    +    G      V            G +++     A   +  
Sbjct: 125 VLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGF 184

Query: 553 MNGYRLEGRTI----AVRVA 568
           +N Y+++         +++ 
Sbjct: 185 LNHYQMKNPNGPYPYTLKLC 204

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 71.7 bits (175), Expect = 2e-14
 Identities = 24/123 (19%), Positives = 44/123 (35%), Gaps = 9/123 (7%)

Query: 490 DDTNLYIGYLPP-TLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANN 548
           D   L +  L    ++ D +  +F  +G++   K +K +      G   V+ AD    + 
Sbjct: 3   DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDR 57

Query: 549 AIASMNGYRLEGRTIAVRVAGKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGP 608
           AI  +N   + G+ + V V+    QP + PG                    ++   P   
Sbjct: 58  AITHLNNNFMFGQKMNVCVS---KQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQA 114

Query: 609 LPN 611
             N
Sbjct: 115 AKN 117

>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 = 72.0 bits (177), Expect = 1e-15
 Identities = 23/99 (23%), Positives = 44/99 (44%), Gaps = 9/99 (9%)

Query: 471 GTPGHPGLGSNGAKPIKELDDTNLYIGYLP-PTLDDDGLIRLFSTFGDIVMAKVIKDRVT 529
           G+  H    S+G  P      + L+IG LP   +  + L R+FS +G I+   +      
Sbjct: 2   GSSHHHHHHSSGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI------ 55

Query: 530 GMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA 568
                +GF+++ + Q   +AI   +     G+ + + V+
Sbjct: 56  --KNAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVS 92

>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 = 70.5 bits (173), Expect = 3e-15
 Identities = 17/91 (18%), Positives = 34/91 (37%), Gaps = 9/91 (9%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           + + +  LP   +   +  L   +        +K      +K   FV   + + A NAI 
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNAIQ 58

Query: 552 SMNGYRLEGRTIAVRVAGKPPQPTVPPGPPT 582
             + Y   G+ + V++   P    +  GP +
Sbjct: 59  MFHQYSFRGKDLIVQLQ--PTDALLCSGPSS 87

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 70.4 bits (173), Expect = 5e-15
 Identities = 21/102 (20%), Positives = 38/102 (37%), Gaps = 6/102 (5%)

Query: 471 GTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTG 530
           G+ G  G  S    P      T + +  +P T+  D ++  F  +  I  +  +K    G
Sbjct: 1   GSSGSSGASSGKPGP------TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKG 54

Query: 531 MSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPP 572
           M  G   V +     A  A+  +N   +  R + + +   P 
Sbjct: 55  MPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLGSGPS 96

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 77.9 bits (191), Expect = 7e-15
 Identities = 24/189 (12%), Positives = 35/189 (18%), Gaps = 10/189 (5%)

Query: 569 GKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGPPV 628
               +   P           P+  P     P    A G              P       
Sbjct: 2   SHHKKRVYPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQF 61

Query: 629 PPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATSSEA 688
             P                        +    P     A        P  P Q  T  + 
Sbjct: 62  LTPAQEQLHQQI-----DQATTSMNDMHLHNVPLVDPNAYM-----QPQVPVQMGTPLQQ 111

Query: 689 QQHSFPPGVQSESSSSAPAASANMYGSSMPPMPPNVQPAYATAPLGYSPYYNAVPPPPPP 748
           QQ         + S++       M       +   + P      L   P          P
Sbjct: 112 QQQPMAAPAYGQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPPPPLVIPPERMLVP 171

Query: 749 APVSAADHS 757
           + +S A   
Sbjct: 172 SELSNASPD 180

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 75.2 bits (184), Expect = 5e-14
 Identities = 26/204 (12%), Positives = 43/204 (21%), Gaps = 21/204 (10%)

Query: 590 VSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGPPVPPPYAPYAPPPPGSTMYPPVP 649
           +S      YP  Q   G        A+    P  + PP  P  A  +    G      VP
Sbjct: 1   MSHHKKRVYPQAQLQYGQN------ATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVP 54

Query: 650 GQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATSSEAQQHSFPPGVQSESSSSAPAAS 709
                 +       +      A T+            +   +  P               
Sbjct: 55  SMGQQQFLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQ--------VPVQMG 106

Query: 710 ANMYGSSMPPMPPNVQPAYATAPLGYSPYYNAVPPPPPPAPVSAADHSQNLGNVPWATNP 769
             +     P   P      A            + P     P+                 P
Sbjct: 107 TPLQQQQQPMAAPAYGQPSAAMG-------QNMRPMNQLYPIDLLTELPPPITDLTLPPP 159

Query: 770 PVQPPVSSAEKSNYGADAEYEKFM 793
           P+  P       +  ++A  +   
Sbjct: 160 PLVIPPERMLVPSELSNASPDYIR 183

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 69.5 bits (169), Expect = 3e-12
 Identities = 27/167 (16%), Positives = 37/167 (22%), Gaps = 1/167 (0%)

Query: 571 PPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGPPVPP 630
            P   +PP  P +   +Y     P  G            P                    
Sbjct: 25  QPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLHQQIDQATTSMNDMH 84

Query: 631 PYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATSSEAQQ 690
            +      P    M P VP Q   P   Q  P    A      A                
Sbjct: 85  LHNVPLVDPNAY-MQPQVPVQMGTPLQQQQQPMAAPAYGQPSAAMGQNMRPMNQLYPIDL 143

Query: 691 HSFPPGVQSESSSSAPAASANMYGSSMPPMPPNVQPAYATAPLGYSP 737
            +  P   ++ +   P          +P    N  P Y  + L   P
Sbjct: 144 LTELPPPITDLTLPPPPLVIPPERMLVPSELSNASPDYIRSTLNAVP 190

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 67.5 bits (164), Expect = 1e-11
 Identities = 35/193 (18%), Positives = 48/193 (24%), Gaps = 13/193 (6%)

Query: 571 PPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGPPVPP 630
           PPQ     G     M   P  A P  G   Q   P     +      T +         P
Sbjct: 31  PPQDPAAAGMSYGQMGMPPQGAVPSMGQQ-QFLTPAQEQLHQQIDQATTSMNDMHLHNVP 89

Query: 631 PYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATSSEAQ- 689
              P A   P   +    P Q              +A  G    P          +E   
Sbjct: 90  LVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYGQPSAAMGQNMRPMNQLYPIDLLTELPP 149

Query: 690 -----QHSFPPGVQSESSSSAPAASANM----YGSSMPPMPPNVQPAYATA-PLGYS-PY 738
                    PP V        P+  +N       S++  +P N      +  P G     
Sbjct: 150 PITDLTLPPPPLVIPPERMLVPSELSNASPDYIRSTLNAVPKNSSLLKKSKLPFGLVIRP 209

Query: 739 YNAVPPPPPPAPV 751
           Y  +     P P+
Sbjct: 210 YQHLYDDIDPPPL 222

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 69.4 bits (170), Expect = 1e-14
 Identities = 25/107 (23%), Positives = 41/107 (38%), Gaps = 12/107 (11%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVM-AKVIKD-RVTGMSKGYGFVKYADIQMANNAIA 551
           L+IG +P     + ++   +   + V+   V         ++G+ FV+Y   + A  A  
Sbjct: 11  LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 70

Query: 552 SMN--GYRLEGRTIAVRVAGKPPQPTVPPGPPTSTMPTYPVSAPPVG 596
            +     +L G  IAV  A +P             M T  VS P  G
Sbjct: 71  KLMPGRIQLWGHQIAVDWA-EP-----EIDVDEDVMET--VSGPSSG 109

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 68.6 bits (168), Expect = 2e-14
 Identities = 12/82 (14%), Positives = 30/82 (36%), Gaps = 2/82 (2%)

Query: 487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMA 546
            ++ + ++YI   P     D +       G ++  ++ +       KG  FV +  I+ A
Sbjct: 7   NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESA 65

Query: 547 NNAIASMNGYRLEGRTIAVRVA 568
              +    G + +   + +   
Sbjct: 66  KKFVE-TPGQKYKETDLLILFK 86

>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 = 68.1 bits (167), Expect = 3e-14
 Identities = 20/98 (20%), Positives = 36/98 (36%), Gaps = 9/98 (9%)

Query: 468 GSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDR 527
           GSSG+ G                 T + +  +P T+  D ++  F  +  I  +  +K  
Sbjct: 1   GSSGSSGSSSGKP---------GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYN 51

Query: 528 VTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAV 565
             GM  G   V +     A  A+  +N   +  R + +
Sbjct: 52  EKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKL 89

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 67.2 bits (165), Expect = 6e-14
 Identities = 20/98 (20%), Positives = 41/98 (41%), Gaps = 9/98 (9%)

Query: 483 AKPIKELDDTNLYIGYLPP-TLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYA 541
            +       + L+IG LP   +  + L R+FS +G I+   +           +GF+++ 
Sbjct: 2   TEMHNIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFD 53

Query: 542 DIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPG 579
           + Q   +AI   +     G+ + + V+    +P    G
Sbjct: 54  NPQSVRDAIECESQEMNFGKKLILEVSSSNARPQFDHG 91

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733

 Score = 75.1 bits (184), Expect = 7e-14
 Identities = 49/249 (19%), Positives = 74/249 (29%), Gaps = 20/249 (8%)

Query: 542  DIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQ 601
            D +     +       +E         G  P                 +   P+    S 
Sbjct: 1446 DEESLVKYMPEQKITEIEDGQ----DGGVTPYSNESGLVNADLDVKDELMFSPLVDSGSN 1501

Query: 602  QYAPGGPLPNPPAASYTGAPVPWGPPVPPPYAP-YAPPPPGSTMYPPVPGQPMPPYGVQY 660
                GG       A Y  A  P+G     P +P +    PG +   P      P Y    
Sbjct: 1502 DAMAGGFTA-YGGADYGEATSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSPTS 1560

Query: 661  PPPVQTAPPGALTAPPGAPTQTATSSEAQQHSFPPGVQSESSSSAPAASANMYGSSMPPM 720
            P    T+P  + T+P  +PT  + S  +  +S      S +S S    S + Y  + P  
Sbjct: 1561 PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS-YSPTSPSY 1619

Query: 721  PPNVQPAYATAPLGYSPYYNAVPPPPPPAPVSAADHSQNLGNVPWATNPPVQPPVSSAEK 780
             P   P+Y+     YSP   +  P  P    ++  +S            P  P  S    
Sbjct: 1620 SP-TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS------------PTSPAYSPTSP 1666

Query: 781  SNYGADAEY 789
            S       Y
Sbjct: 1667 SYSPTSPSY 1675

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733

 Score = 70.9 bits (173), Expect = 1e-12
 Identities = 52/192 (27%), Positives = 79/192 (41%), Gaps = 9/192 (4%)

Query: 574  PTVPPGPPTSTM--PTYPVSAPPVGGYP--SQQYAPGGPLPNPPAASYTGAPVPWGP--P 627
            PT P   PTS    PT P  +P    Y   S  Y+P  P  +P + SY+     + P  P
Sbjct: 1544 PTSPTYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSP 1603

Query: 628  VPPPYAP-YAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATSS 686
               P +P Y+P  P  +   P      P Y    P    T+P  + T+P  +PT  A S 
Sbjct: 1604 SYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSP 1663

Query: 687  EAQQHSFPPGVQSESSSSAPAASANMYGSSMPPMPPNVQPAYATAPLGYSPYYNAVPPPP 746
             +  +S P       +S + + ++  Y  + P   P   P+Y+    GYSP   A  P  
Sbjct: 1664 TSPSYS-PTSPSYSPTSPSYSPTSPSYSPTSPNYSPT-SPSYSPTSPGYSPGSPAYSPKQ 1721

Query: 747  PPAPVSAADHSQ 758
                 +  ++S+
Sbjct: 1722 DEQKHNENENSR 1733

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733

 Score = 69.4 bits (169), Expect = 4e-12
 Identities = 46/223 (20%), Positives = 74/223 (33%), Gaps = 6/223 (2%)

Query: 567  VAGKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGP 626
            +        +  G        Y  +  P G Y     +PG  + +P  +  +    P  P
Sbjct: 1495 LVDSGSNDAMAGGFTAYGGADYGEATSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSP 1554

Query: 627  PVPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATSS 686
               P    Y+P  P  +   P      P Y    P    T+P  + T+P  +PT  + S 
Sbjct: 1555 AYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP 1614

Query: 687  EAQQHS-----FPPGVQSESSSSAPAASANMYGSSMPPMPPNVQPAYATAPLGYSPYYNA 741
             +  +S     + P   S S +S   +  +   S   P      PAY+     YSP   +
Sbjct: 1615 TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPS 1674

Query: 742  VPPPPPP-APVSAADHSQNLGNVPWATNPPVQPPVSSAEKSNY 783
              P  P  +P S +    +    P + +     P  S     Y
Sbjct: 1675 YSPTSPSYSPTSPSYSPTSPNYSPTSPSYSPTSPGYSPGSPAY 1717

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733

 Score = 54.3 bits (130), Expect = 2e-07
 Identities = 33/121 (27%), Positives = 50/121 (41%), Gaps = 9/121 (7%)

Query: 573  QPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGPPVPPPY 632
             PT P   PTS  P+Y  ++P      S  Y+P  P  +P + +Y+     + P   P Y
Sbjct: 1620 SPTSPSYSPTS--PSYSPTSPSYSP-TSPSYSPTSPSYSPTSPAYSPTSPSYSPT-SPSY 1675

Query: 633  APYAPPP-PGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATSSEAQQH 691
            +P +P   P S  Y P      P Y    P    T+P  +  +P  +P Q        ++
Sbjct: 1676 SPTSPSYSPTSPSYSP----TSPNYSPTSPSYSPTSPGYSPGSPAYSPKQDEQKHNENEN 1731

Query: 692  S 692
            S
Sbjct: 1732 S 1732

>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 = 67.6 bits (165), Expect = 7e-14
 Identities = 17/78 (21%), Positives = 31/78 (39%), Gaps = 6/78 (7%)

Query: 494 LYIGYLPPTLDDDGLIR---LFSTFGDIVMAKVIKDRVTGMSK---GYGFVKYADIQMAN 547
           +++  L   L D  +++    F  FG I    +        S+      +V Y   + A 
Sbjct: 18  VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77

Query: 548 NAIASMNGYRLEGRTIAV 565
            AI  +N   ++GRT+  
Sbjct: 78  RAIQCVNNVVVDGRTLKA 95

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 67.6 bits (165), Expect = 1e-13
 Identities = 17/92 (18%), Positives = 35/92 (38%), Gaps = 7/92 (7%)

Query: 492 TNLYIGYLPPTLDDDGLIR----LFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMAN 547
             + I  + P +  + L      L S+ GDI+   V     +  + G  ++ +A  + A 
Sbjct: 30  QVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQ 86

Query: 548 NAIASMNGYRLEGRTIAVRVAGKPPQPTVPPG 579
             + +  GY  +G  + +  +  P       G
Sbjct: 87  AFVEAFQGYPFQGNPLVITFSETPQSQVAEDG 118

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 65.5 bits (160), Expect = 2e-13
 Identities = 22/82 (26%), Positives = 42/82 (51%), Gaps = 9/82 (10%)

Query: 491 DTNLYIGYLPPTLDD------DGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQ 544
           D+ + +  +P    D      + + ++FS FG I      ++   G +KGY F++YA   
Sbjct: 1   DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPA 58

Query: 545 MANNAIASMNGYRLEGR-TIAV 565
            A +A+ + +GY+L+ + T  V
Sbjct: 59  HAVDAVKNADGYKLDKQHTFRV 80

>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 = 64.2 bits (157), Expect = 9e-13
 Identities = 15/80 (18%), Positives = 34/80 (42%), Gaps = 1/80 (1%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
            ++G LP  + ++ +   F       +    +       KG+G+ ++ D+    +A++ +
Sbjct: 18  AFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-L 76

Query: 554 NGYRLEGRTIAVRVAGKPPQ 573
           N   L  + I V VA +   
Sbjct: 77  NEESLGNKRIRVDVADQAQD 96

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 63.8 bits (156), Expect = 9e-13
 Identities = 18/81 (22%), Positives = 37/81 (45%), Gaps = 4/81 (4%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVT-GMSKGYGFVKYADIQMANNAIAS 552
            ++G LP  + ++ +   F     I   ++ ++       KG+G+ ++ D+    +A++ 
Sbjct: 22  AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS- 79

Query: 553 MNGYRLEGRTIAVRVAGKPPQ 573
           +N   L  R I V VA    Q
Sbjct: 80  LNEESLGNRRIRVDVA-DQAQ 99

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 63.2 bits (154), Expect = 1e-12
 Identities = 12/78 (15%), Positives = 34/78 (43%), Gaps = 6/78 (7%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKV-----IKDRVTGMSKGYGFVKYADIQMANN 548
           LY+G +P  + ++ ++  F+    +          +        K + F+++  +     
Sbjct: 9   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68

Query: 549 AIASMNGYRLEGRTIAVR 566
           A+A  +G   +G+++ +R
Sbjct: 69  AMA-FDGIIFQGQSLKIR 85

>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 = 62.6 bits (153), Expect = 2e-12
 Identities = 19/93 (20%), Positives = 41/93 (44%), Gaps = 9/93 (9%)

Query: 490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNA 549
             + +++G     + +D L   FS +GD++   + K       + + FV +AD Q+A + 
Sbjct: 4   GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSL 58

Query: 550 IASMNGYRLEGRTIAVRVAGKPPQPTVPPGPPT 582
                   ++G ++ +  A   P+     GP +
Sbjct: 59  CG--EDLIIKGISVHISNA--EPKHNSNSGPSS 87

>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 = 62.9 bits (153), Expect = 3e-12
 Identities = 16/117 (13%), Positives = 30/117 (25%), Gaps = 7/117 (5%)

Query: 482 GAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYA 541
           G+        T +    LP       +   FS FG +         +         V++ 
Sbjct: 1   GSSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSL------GRVLLPEGGITAIVEFL 54

Query: 542 DIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPGPPTST-MPTYPVSAPPVGG 597
           +   A  A   +   +     + +  A        P    +    P     + P  G
Sbjct: 55  EPLEARKAFRHLAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAEKAESGPSSG 111

>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 = 61.9 bits (151), Expect = 4e-12
 Identities = 13/79 (16%), Positives = 35/79 (44%), Gaps = 7/79 (8%)

Query: 490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNA 549
             + +++G     +  + L + F  +G++V   + K       + + FV +AD ++A + 
Sbjct: 10  HGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQSL 64

Query: 550 IASMNGYRLEGRTIAVRVA 568
                   ++G ++ +  A
Sbjct: 65  CG--EDLIIKGISVHISNA 81

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 61.8 bits (150), Expect = 5e-12
 Identities = 25/101 (24%), Positives = 39/101 (38%), Gaps = 10/101 (9%)

Query: 468 GSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDR 527
           GSSG+ G       GA         ++Y+G LP       L R     G + +    +  
Sbjct: 1   GSSGSSGPGSPPGEGAPL-----AADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQG- 54

Query: 528 VTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA 568
                +   F+ Y D   A  A++ + G RL   T+ V +A
Sbjct: 55  ----PRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALA 91

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 61.2 bits (149), Expect = 8e-12
 Identities = 20/103 (19%), Positives = 42/103 (40%), Gaps = 11/103 (10%)

Query: 479 GSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFV 538
           GS+G+  ++     ++++   P  +D   L   F  FG +  A V+ D+  G    +  V
Sbjct: 1   GSSGSSGLR-----SVFVSGFPRGVDSAQLSEYFLAFGPV--ASVVMDKDKG---VFAIV 50

Query: 539 KYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPGPP 581
           +  D+      ++  + + L G  + VR   +    +     P
Sbjct: 51  EMGDVGAREAVLS-QSQHSLGGHRLRVRPREQKEFQSPASKSP 92

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 60.6 bits (147), Expect = 2e-11
 Identities = 23/119 (19%), Positives = 40/119 (33%), Gaps = 14/119 (11%)

Query: 479 GSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFV 538
           GS+G  P +  ++  + +  LPP+     L       GD+  A V +D       G G V
Sbjct: 4   GSSGGPPSRRSENR-VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVV 55

Query: 539 KYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPGPPTSTMPTYPVSAPPVGG 597
           ++   +    A+  ++  +                  V    P S       S+ P  G
Sbjct: 56  EFVRKEDMTYAVRKLDNTKFRSHEGETAYI------RVKVDGPRSPSYGRSRSSGPSSG 108

>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 = 64.9 bits (157), Expect = 5e-11
 Identities = 20/110 (18%), Positives = 42/110 (38%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L++  +     +  L R F  +G I    ++  + +G  +GY F++Y   +  ++A    
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164

Query: 554 NGYRLEGRTIAVRVAGKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQY 603
           +G +++GR + V V          P      +         V    S + 
Sbjct: 165 DGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRD 214

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 59.1 bits (143), Expect = 6e-11
 Identities = 18/109 (16%), Positives = 32/109 (29%), Gaps = 5/109 (4%)

Query: 466 NSGSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIK 525
           +     + G    GS+ +K   +     + +  LP       L  L              
Sbjct: 5   HHHHHHSSGLVPRGSHMSKLPAK--RYRITMKNLPEGCSWQDLKDLARENSLET---TFS 59

Query: 526 DRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQP 574
              T    G G +++   ++   A+  +N     G  I V     PP  
Sbjct: 60  SVNTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDDNPPPI 108

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 58.7 bits (142), Expect = 9e-11
 Identities = 18/116 (15%), Positives = 33/116 (28%), Gaps = 9/116 (7%)

Query: 474 GHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSK 533
           G    G  G    +   +  + +  LPP+     L       GD+  A V +D       
Sbjct: 1   GGAPRGRYGPPSRR--SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------- 51

Query: 534 GYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPGPPTSTMPTYP 589
           G G V++   +    A+  ++  +                    P    S   +  
Sbjct: 52  GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPSYGRSRSRSRS 107

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 58.2 bits (141), Expect = 2e-10
 Identities = 20/119 (16%), Positives = 38/119 (31%), Gaps = 10/119 (8%)

Query: 468 GSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDR 527
           GSSG+ G   + S              +I  +P ++    +++          A  +   
Sbjct: 1   GSSGSSGEGDVNSAK---------VCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVD 51

Query: 528 VTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPGPPTSTMP 586
             G   G   V++ +   A  +   ++  +L GR   V V        +   PP     
Sbjct: 52  NNGQGLGQALVQFKNEDDARKSE-RLHRKKLNGREAFVHVVTLEDMREIEKNPPAQGKS 109

>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 = 58.0 bits (140), Expect = 2e-10
 Identities = 21/114 (18%), Positives = 43/114 (37%), Gaps = 13/114 (11%)

Query: 457 SGSNPPWANNSGSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFG 516
             S+    ++SG      H G   +   P +      ++I  LP  + +  +I L   FG
Sbjct: 2   GSSHHHHHHSSGLVPRGSHMGDSRSAGVPSR-----VIHIRKLPIDVTEGEVISLGLPFG 56

Query: 517 DIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAI--ASMNGYRLEGRTIAVRVA 568
            +    ++K       K   F++    + AN  +   +     L G+ I ++ +
Sbjct: 57  KVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFS 104

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 57.5 bits (139), Expect = 2e-10
 Identities = 21/95 (22%), Positives = 33/95 (34%), Gaps = 8/95 (8%)

Query: 473 PGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMS 532
             H     N   P K      ++I  L   + +  L+     FG I    V+        
Sbjct: 3   HHHHHHMENYDDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP------K 56

Query: 533 KGYGFVKYADIQMANNAI--ASMNGYRLEGRTIAV 565
           K    V++ D+  A NA+  A+ N   + G    V
Sbjct: 57  KRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFV 91

>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 = 58.0 bits (140), Expect = 2e-10
 Identities = 21/107 (19%), Positives = 41/107 (38%), Gaps = 2/107 (1%)

Query: 459 SNPPWANNSGSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDI 518
           S+      S  +   G   +G  G+      +D  + +  LP     + +++ FS    +
Sbjct: 11  SSGLVPRGSHMASMTGGQQMGR-GSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIV 69

Query: 519 VMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAV 565
                +     G   G  FV++A  ++A  A+   +  R+  R I V
Sbjct: 70  PNGITLPVDPEGKITGEAFVQFASQELAEKAL-GKHKERIGHRYIEV 115

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score = 63.2 bits (153), Expect = 3e-10
 Identities = 50/222 (22%), Positives = 79/222 (35%), Gaps = 13/222 (5%)

Query: 568  AGKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAA--SYTGAPVPWG 625
              +  +     G   +  P   V +P      S   +PG  L +P  +  S   +  P  
Sbjct: 1512 GSEGREGFGDYGLLGAASPYKGVQSPGYTSPFSSAMSPGYGLTSPSYSPSSPGYSTSPAY 1571

Query: 626  PPVPPPYAP----YAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQ 681
             P  P Y+P    Y+P  P  +   P      P Y    P    T+P  + T+P  +PT 
Sbjct: 1572 MPSSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSATSPSYSPTSPSYSPTSPSYSPTS 1631

Query: 682  TATSSEAQQHS-FPPGVQSESSSSAPAASANMYGSSMPPMPPNVQPAYATAPL--GYSPY 738
             + S  +  +S   P     S S +P  ++  Y  + P   P       T+P     SP 
Sbjct: 1632 PSYSPTSPSYSPTSPSYSPTSPSYSP--TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS 1689

Query: 739  YNAVPPPPPPAPVSAADHSQNLGNVPWATNP--PVQPPVSSA 778
            Y+   P   P   S +  S +      + +P  P   P S +
Sbjct: 1690 YSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS 1731

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score = 58.5 bits (141), Expect = 9e-09
 Identities = 43/213 (20%), Positives = 68/213 (31%), Gaps = 11/213 (5%)

Query: 571  PPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGP--PV 628
            P       G           +A P  G  S  Y    P  +  +  Y      + P  P 
Sbjct: 1507 PLVQGGSEGREGFGDYGLLGAASPYKGVQSPGYTS--PFSSAMSPGYGLTSPSYSPSSPG 1564

Query: 629  PPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATSSEA 688
                  Y P  P  +   P      P Y    P    T+P  + T+P  +PT  + S  +
Sbjct: 1565 YSTSPAYMPSSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSATSPSYSPTSPSYSPTS 1624

Query: 689  QQHS-----FPPGVQSESSSSAPAASANMYGSSMPPMPPNVQPAYATAPLGYSPYYNAVP 743
              +S     + P   S S +S   +  +   S   P      P+Y+     YSP   +  
Sbjct: 1625 PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1684

Query: 744  PPPPPAPVSAADHSQNLGNVPWATNPPVQPPVS 776
            P  P    ++  +S    +  ++   P   P S
Sbjct: 1685 PTSPSYSPTSPSYSPT--SPSYSPTSPSYSPTS 1715

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score = 57.8 bits (139), Expect = 1e-08
 Identities = 46/254 (18%), Positives = 80/254 (31%), Gaps = 22/254 (8%)

Query: 540  YADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPGPPTSTMPTYPVSAPPVGGY- 598
            Y D  M  N         L G  +      + P+    P   +  + +  V +P    + 
Sbjct: 1450 YLDQDMLMNYSLGTAVPTLAGSGMG---TSQLPEGAGTPYERSPMVDSGFVGSPDAAAFS 1506

Query: 599  PSQQYAPGGPLPNPPAASYTGAPVPWGPPVPPPYAPYAPPPPGSTMYPPVPGQPMPPYGV 658
            P  Q    G            A    G   P   +P++               P  P   
Sbjct: 1507 PLVQGGSEGREGFGDYGLLGAASPYKGVQSPGYTSPFSSAMSPGYGLTSPSYSPSSPGYS 1566

Query: 659  QYPPPVQTAPPGALTAP---PGAPTQTATSSEAQQHSFPPGVQSES-----SSSAPAASA 710
              P  + ++P  + T+P   P +P+ + TS      S  P   + S     +S + + ++
Sbjct: 1567 TSPAYMPSSPSYSPTSPSYSPTSPSYSPTSPSYSPTS--PSYSATSPSYSPTSPSYSPTS 1624

Query: 711  NMYGSSMPPMPPNVQ------PAYATAPLGYSPYYNAVPPPPPPAPVSAADHSQNLGNVP 764
              Y  + P   P         P+Y+     YSP   +  P  P    S    S +  +  
Sbjct: 1625 PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY--SPTSPSYSPTSPS 1682

Query: 765  WATNPPVQPPVSSA 778
            ++   P   P S +
Sbjct: 1683 YSPTSPSYSPTSPS 1696

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score = 55.1 bits (132), Expect = 9e-08
 Identities = 47/185 (25%), Positives = 72/185 (38%), Gaps = 18/185 (9%)

Query: 571  PPQPTVPPGPPTST--MPTYPVSAPPVGGY--PSQQYAPGGPLPNPPAASYTGAPVPWGP 626
            P   T P   P+S    PT P  +P    Y   S  Y+P  P  +  + SY+    P   
Sbjct: 1563 PGYSTSPAYMPSSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSATSPSYSPTS-PSYS 1621

Query: 627  PVPPPYAP----YAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQT 682
            P  P Y+P    Y+P  P  +   P      P Y    P    T+P  + T+P  +PT  
Sbjct: 1622 PTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSP 1681

Query: 683  ATSSEAQQHSFPPGVQSESSSSAPAASANMYGSSMPPMPPNVQPAYATAPLGYSPYYNAV 742
            + S  +  +S         +S + + ++  Y  + P   P   P+Y+     YSP   + 
Sbjct: 1682 SYSPTSPSYS--------PTSPSYSPTSPSYSPTSPSYSPTS-PSYSPTSPSYSPTSPSY 1732

Query: 743  PPPPP 747
             P  P
Sbjct: 1733 SPTSP 1737

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score = 53.2 bits (127), Expect = 3e-07
 Identities = 40/149 (26%), Positives = 57/149 (38%), Gaps = 8/149 (5%)

Query: 572  PQPTVPPGPPTSTM--PTYPVSAPPVGGYP--SQQYAPGGPLPNPPAASYTGAPVPWGPP 627
              PT P    TS    PT P  +P    Y   S  Y+P  P  +P + SY+    P  P 
Sbjct: 1599 YSPTSPSYSATSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS----PTSPS 1654

Query: 628  VPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATSSE 687
              P    Y+P  P  +   P      P Y    P    T+P  + T+P  +PT  + S  
Sbjct: 1655 YSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPT 1714

Query: 688  AQQHSFPPGVQSESSSSAPAASANMYGSS 716
            +  +S      S +S S    S +   +S
Sbjct: 1715 SPSYSPTSPSYSPTSPSYSPTSPSYSPTS 1743

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score = 51.6 bits (123), Expect = 1e-06
 Identities = 38/139 (27%), Positives = 54/139 (38%), Gaps = 6/139 (4%)

Query: 571  PPQPTVPPGPPTSTMPTYPVSAP--PVGGYPSQQYAPGGPLPNPPAASYTGAPV---PWG 625
            P  P+  P  P S  PT P  +P  P     S  Y+P  P  +P + SY+       P  
Sbjct: 1615 PTSPSYSPTSP-SYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTS 1673

Query: 626  PPVPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATS 685
            P   P    Y+P  P  +   P      P Y    P    T+P  + T+P  +PT  + S
Sbjct: 1674 PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1733

Query: 686  SEAQQHSFPPGVQSESSSS 704
              +  +S      S +S S
Sbjct: 1734 PTSPSYSPTSPSYSPTSPS 1752

>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 = 55.1 bits (133), Expect = 1e-09
 Identities = 20/90 (22%), Positives = 39/90 (43%), Gaps = 2/90 (2%)

Query: 479 GSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFV 538
           GS+G  P    +D  + +  LP     + +++ FS    +     +     G S G  FV
Sbjct: 4   GSSGNSPDTA-NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFV 62

Query: 539 KYADIQMANNAIASMNGYRLEGRTIAVRVA 568
           ++A  ++A  A+   +  R+  R I +  +
Sbjct: 63  QFASQEIAEKAL-KKHKERIGHRYIEIFKS 91

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 54.1 bits (130), Expect = 3e-09
 Identities = 15/77 (19%), Positives = 32/77 (41%), Gaps = 8/77 (10%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAI--A 551
           ++I  LP  + +  +I L   FG +    ++K       K   F++    + AN  +   
Sbjct: 19  IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYY 72

Query: 552 SMNGYRLEGRTIAVRVA 568
           +     L G+ I ++ +
Sbjct: 73  TSVTPVLRGQPIYIQFS 89

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 53.6 bits (129), Expect = 4e-09
 Identities = 13/92 (14%), Positives = 31/92 (33%), Gaps = 10/92 (10%)

Query: 479 GSNGAKPIKELDDTN--LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYG 536
           GS+G+         +  +++  L  ++ +  L+     FG I    ++        K   
Sbjct: 1   GSSGSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQA 54

Query: 537 FVKYADIQMANNAIASM--NGYRLEGRTIAVR 566
            V++ +I  A   +         + G+     
Sbjct: 55  LVEFENIDSAKECVTFAADVPVYIAGQQAFFN 86

>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 = 52.5 bits (126), Expect = 1e-08
 Identities = 22/101 (21%), Positives = 38/101 (37%), Gaps = 17/101 (16%)

Query: 468 GSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDR 527
           GSSG+ G    G+             L+I  LP  + +  +I L   FG +    ++K  
Sbjct: 1   GSSGSSGDKMDGAPSR---------VLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG- 50

Query: 528 VTGMSKGYGFVKYADIQMANNAIA--SMNGYRLEGRTIAVR 566
                K   F++ A  + A   +   S     L  + I ++
Sbjct: 51  -----KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQ 86

>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 = 52.6 bits (126), Expect = 1e-08
 Identities = 17/91 (18%), Positives = 34/91 (37%), Gaps = 17/91 (18%)

Query: 479 GSNGAKPIKELDD---------TNLYI--GYLPPTLDDDGLIRLFSTFGDIVMAKVIKDR 527
           GS+GAK      +          +L +  G L   +  + L+ +    G +    +  + 
Sbjct: 4   GSSGAKHTLLRHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN- 62

Query: 528 VTGMSKGYGFVKYADIQMANNAIASMNGYRL 558
                K Y F +Y   + +  A  ++NG  +
Sbjct: 63  -----KPYSFARYRTTEESKRAYVTLNGKEV 88

>3pgw_B SM B; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_A Length = 231

 Score = 55.0 bits (132), Expect = 1e-08
 Identities = 32/144 (22%), Positives = 41/144 (28%), Gaps = 8/144 (5%)

Query: 563 IAVRVAGKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNP--------PA 614
           +++ V G PP+ T     P +     P      G                          
Sbjct: 78  VSMTVEGPPPKDTGIARVPLAGAAGGPGIGRAAGRGIPAGVPMPQAPAGLAGPVRGVGGP 137

Query: 615 ASYTGAPVPWGPPVPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTA 674
           +     P   G       A  A      T YPP  G P PP G   PPP    PP  +  
Sbjct: 138 SQQVMTPQGRGTVAAAAAAATASIAGAPTQYPPGRGGPPPPMGRGAPPPGMMGPPPGMRP 197

Query: 675 PPGAPTQTATSSEAQQHSFPPGVQ 698
           P G P              PPG++
Sbjct: 198 PMGPPMGIPPGRGTPMGMPPPGMR 221

>3pgw_B SM B; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_A Length = 231

 Score = 48.9 bits (116), Expect = 2e-06
 Identities = 32/116 (27%), Positives = 36/116 (31%), Gaps = 5/116 (4%)

Query: 569 GKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPV---PWG 625
           G P    +P  P     P   V  P       Q             AS  GAP    P  
Sbjct: 113 GIPAGVPMPQAPAGLAGPVRGVGGPSQQVMTPQGRGTVAAAAAAATASIAGAPTQYPPGR 172

Query: 626 PPVPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPP--PVQTAPPGALTAPPGAP 679
              PPP    APPP      P +     PP G+      P+   PPG    PPG  
Sbjct: 173 GGPPPPMGRGAPPPGMMGPPPGMRPPMGPPMGIPPGRGTPMGMPPPGMRPPPPGMR 228

>3pgw_B SM B; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_A Length = 231

 Score = 45.4 bits (107), Expect = 2e-05
 Identities = 20/92 (21%), Positives = 28/92 (30%), Gaps = 1/92 (1%)

Query: 568 AGKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGPP 627
           + +   P        +        A     YP  +  P  P+           P P   P
Sbjct: 138 SQQVMTPQGRGTVAAAAAAATASIAGAPTQYPPGRGGPPPPMGRGAPPPGMMGPPPGMRP 197

Query: 628 VPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQ 659
            P       PP  G+ M  P PG   PP G++
Sbjct: 198 -PMGPPMGIPPGRGTPMGMPPPGMRPPPPGMR 228

>3pgw_B SM B; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_A Length = 231

 Score = 45.0 bits (106), Expect = 3e-05
 Identities = 34/167 (20%), Positives = 43/167 (25%), Gaps = 17/167 (10%)

Query: 584 TMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGPPVPPPYAPYAPPPPGST 643
            + +  V  PP       +    G    P      G  +P G P+P   A  A P  G  
Sbjct: 76  NLVSMTVEGPPPKDTGIARVPLAGAAGGPGIGRAAGRGIPAGVPMPQAPAGLAGPVRGV- 134

Query: 644 MYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATSSEAQQHSFPPGVQSESSS 703
                  Q M P G         A   ++   P                 PPG       
Sbjct: 135 --GGPSQQVMTPQGRGTVAAAAAAATASIAGAPTQY--------------PPGRGGPPPP 178

Query: 704 SAPAASANMYGSSMPPMPPNVQPAYATAPLGYSPYYNAVPPPPPPAP 750
               A         P M P + P     P   +P     P   PP P
Sbjct: 179 MGRGAPPPGMMGPPPGMRPPMGPPMGIPPGRGTPMGMPPPGMRPPPP 225

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 52.1 bits (125), Expect = 2e-08
 Identities = 21/102 (20%), Positives = 39/102 (38%), Gaps = 2/102 (1%)

Query: 468 GSSGTPGHPGLGSNGAKPIKELDDTN-LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKD 526
           GSSG+ G    G   ++     +    +Y+  LP   ++  +I  F     +  +  I  
Sbjct: 1   GSSGSSGKSPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAY 60

Query: 527 RVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA 568
              G + G GFV++ +      A+   +   +  R I V   
Sbjct: 61  GPNGKATGEGFVEFRNEADYKAAL-CRHKQYMGNRFIQVHPI 101

>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 = 56.0 bits (134), Expect = 4e-08
 Identities = 60/375 (16%), Positives = 99/375 (26%), Gaps = 131/375 (34%)

Query: 146 KPVIQ--LPDFMKDF--------TGGI----EFDPEIQALNSRLLEISRMLQSGLPLDDR 191
           K ++      F+ +F           I    E D  I      +    R+  +   L  +
Sbjct: 19  KDILSVFEDAFVDNFDCKDVQDMPKSILSKEEID-HIIMSKDAVSGTLRLFWT---LLSK 74

Query: 192 PEG--QR--SPSPEPIYDNMGIRINTREYRARERLNKERQEIISQIIKRNPAFKPPADYR 247
            E   Q+         Y  +   I T E R    + +   E   ++   N  F      R
Sbjct: 75  QEEMVQKFVEEVLRINYKFLMSPIKT-EQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSR 133

Query: 248 PP---KLQKKLY--IPMKEYPGYNFIGLII-GPRGNTQKRMERETGAKIVIRGKGSV--- 298
                KL++ L    P K         ++I G        +    G+     GK +    
Sbjct: 134 LQPYLKLRQALLELRPAK--------NVLIDG--------V---LGS-----GK-TWVAL 168

Query: 299 ---KEGRLQQKRD-------LKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQPVDEV 348
                 ++Q K D       LK   S    L      E  + L     +        D  
Sbjct: 169 DVCLSYKVQCKMDFKIFWLNLKNCNSPETVL------EMLQKL--LYQIDPNWTSRSDHS 220

Query: 349 LN-----EHKRQQLRELAALNGTIRDEEYCRLCGEPGHRQYAC---------PSRTSTFK 394
            N        + +LR L      ++ + Y             C             + F 
Sbjct: 221 SNIKLRIHSIQAELRRL------LKSKPYEN-----------CLLVLLNVQNAKAWNAF- 262

Query: 395 SDVLCKI--------------CGDGGHPTIDCLVKGTTGKKMDDEYQNFLAE-LG---GT 436
            ++ CKI                   H ++D      T     DE ++ L + L      
Sbjct: 263 -NLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLT----PDEVKSLLLKYLDCRPQD 317

Query: 437 LPESASKQSTTLALG 451
           LP      +    L 
Sbjct: 318 LPREVLTTN-PRRLS 331

>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 = 50.1 bits (120), Expect = 9e-08
 Identities = 20/90 (22%), Positives = 36/90 (40%), Gaps = 3/90 (3%)

Query: 479 GSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFV 538
           GS+G       DD  + +  +P +  ++ +   F     +    ++KD   G + G G V
Sbjct: 4   GSSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH-VGRNNGNGLV 61

Query: 539 KYADIQMANNAIASMNGYRLEGRTIAVRVA 568
           K+   Q    A+   N   +  R + V  A
Sbjct: 62  KFLSPQDTFEAL-KRNRMLMIQRYVEVSPA 90

>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 = 51.3 bits (122), Expect = 1e-07
 Identities = 24/149 (16%), Positives = 47/149 (31%), Gaps = 17/149 (11%)

Query: 464 ANNSGSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKV 523
           +  SG+            G     +     + +  L   +  D L ++FS FG ++    
Sbjct: 19  SVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIIT 78

Query: 524 IKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA-GKPPQPTV------ 576
                   ++    ++YAD   A +A  S++G  +      +R+   K     V      
Sbjct: 79  FTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSLNVKYNNDK 134

Query: 577 ------PPGPPTSTMPTYPVSAPPVGGYP 599
                 P  P   + P+   +     G  
Sbjct: 135 SRDYTRPDLPSGDSQPSLDQTMAAAFGLS 163

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 52.5 bits (125), Expect = 1e-07
 Identities = 20/104 (19%), Positives = 34/104 (32%), Gaps = 15/104 (14%)

Query: 480 SNGAKPIKELDDTNLYIGYLPPTLDDDG---------LIRLFSTFGDIVMAKVIKDRVTG 530
             G        +  LY+G +   L+            +  +FS  GDI   + ++     
Sbjct: 123 DMGGIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE----- 177

Query: 531 MSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQP 574
            SK  GFVK+     A  A  +M+   L   +       +    
Sbjct: 178 -SKNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRREGTG 220

>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 = 48.1 bits (115), Expect = 3e-07
 Identities = 17/95 (17%), Positives = 37/95 (38%), Gaps = 6/95 (6%)

Query: 479 GSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFV 538
           GS+G+          + +   P  + +  ++   +     V  +++++   G   GY FV
Sbjct: 1   GSSGSSG---TTCHTVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNA-HGNKTGYIFV 55

Query: 539 KYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQ 573
            +++ +    A+   N   + GR I V      P 
Sbjct: 56  DFSNEEEVKQAL-KCNREYMGGRYIEVFREKSGPS 89

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 48.2 bits (115), Expect = 4e-07
 Identities = 13/102 (12%), Positives = 34/102 (33%), Gaps = 3/102 (2%)

Query: 477 GLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYG 536
           G   +     +      +++  LP    ++ +   FS     +   +      G   G  
Sbjct: 1   GSSGSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEA 58

Query: 537 FVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPP 578
            V++A  + A  A+ + +   ++ R + + +          P
Sbjct: 59  DVEFATHEDAVAAM-AKDKANMQHRYVELFLNSTAGTSGSGP 99

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 48.7 bits (116), Expect = 5e-07
 Identities = 19/124 (15%), Positives = 42/124 (33%), Gaps = 3/124 (2%)

Query: 456 SSGSNPPWANNSGSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTF 515
           SSG  P  ++ +  +G         +    ++      +++  LP    ++ +   FS  
Sbjct: 11  SSGLVPRGSHMASMTGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPL 70

Query: 516 GDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPT 575
              V   +      G   G   V++A  + A  A+ S +   ++ R I + +        
Sbjct: 71  N-PVRVHIEIGP-DGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNSTTGASN 127

Query: 576 VPPG 579
               
Sbjct: 128 GAYS 131

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 47.2 bits (112), Expect = 1e-06
 Identities = 24/101 (23%), Positives = 41/101 (40%), Gaps = 5/101 (4%)

Query: 468 GSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAK---VI 524
           GSSG+ G  G  +  A+ + + +   + +  LP T   + ++  F     I   K   + 
Sbjct: 1   GSSGSSG-GGTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILF 59

Query: 525 KDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAV 565
                G   G  FV +A  + A NA+   +   L  R I +
Sbjct: 60  VTYPDGRPTGDAFVLFACEEYAQNAL-RKHKDLLGKRYIEL 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 = 46.1 bits (109), Expect = 2e-06
 Identities = 15/87 (17%), Positives = 35/87 (40%), Gaps = 1/87 (1%)

Query: 490 DDTNLYIGYLPPTLDDDGLIR-LFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANN 548
           +  ++ +  +   L    L + L   F      K ++       +    V+  ++Q A  
Sbjct: 8   NGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIG 67

Query: 549 AIASMNGYRLEGRTIAVRVAGKPPQPT 575
           A+ S++ Y++  + I V +A     P+
Sbjct: 68  AVNSLHRYKIGSKKILVSLATGASGPS 94

>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens} Length = 163

 Score = 47.1 bits (112), Expect = 3e-06
 Identities = 24/130 (18%), Positives = 46/130 (35%), Gaps = 32/130 (24%)

Query: 227 QEIISQIIKRNPAFKPPADYRPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERET 286
           Q  I   +K    F P  +    KL+  + +P       +  G +IG  G T   ++  T
Sbjct: 64  QGRIYGKLKEENFFGPKEE---VKLETHIRVP------ASAAGRVIGKGGKTVNELQNLT 114

Query: 287 GAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQPVD 346
            A++V+                    P EN+ + V +         G     +   + + 
Sbjct: 115 AAEVVVPR---------------DQTPDENDQVIVKI--------IGHFYASQMAQRKIR 151

Query: 347 EVLNEHKRQQ 356
           ++L + K+Q 
Sbjct: 152 DILAQVKQQH 161

>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens} Length = 163

 Score = 40.5 bits (95), Expect = 5e-04
 Identities = 17/90 (18%), Positives = 34/90 (37%), Gaps = 23/90 (25%)

Query: 254 KLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDP 313
           +++IP +       +G IIG +G   K++ R   A I I                  P+ 
Sbjct: 6   QVFIPAQA------VGAIIGKKGQHIKQLSRFASASIKI----------------APPET 43

Query: 314 SENEDLHVLVEAETQESLEGAAAMVEKLLQ 343
            +++   V++     E+   A   +   L+
Sbjct: 44  PDSKVRMVIITG-PPEAQFKAQGRIYGKLK 72

>3dzy_A Retinoic acid receptor RXR-alpha; DNA-binding, HOST-virus interaction, metal-binding, nucleus, receptor, transcription, transcription regulation, zinc-FIN activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB: 3dzu_A* 3e00_A* Length = 467

 Score = 49.3 bits (117), Expect = 3e-06
 Identities = 26/149 (17%), Positives = 38/149 (25%), Gaps = 13/149 (8%)

Query: 598 YPSQQYAPGGPLPNPPAASYTGAPVPWGPPVPPPYAPYAPPPPGSTMYPPVPGQPMPPYG 657
           +          + +    S   +P   G    P   P   P  GS      PGQ   P  
Sbjct: 4   HHHHHVDDDDKMFSTQVNSSLTSPTGRGSMAAPSLHPSLGPGIGS------PGQLHSPIS 57

Query: 658 VQYPPPVQTAPPGALTAPPGAPTQTATSSEAQQHSFPPGVQSESSSSAPAASANMYGSSM 717
               P     PP ++ + P  P               P +   + S   ++  N   SS 
Sbjct: 58  TLSSPINGMGPPFSVISSPMGPHS-------MSVPTTPTLGFSTGSPQLSSPMNPVSSSE 110

Query: 718 PPMPPNVQPAYATAPLGYSPYYNAVPPPP 746
              PP         P   S    +     
Sbjct: 111 DIKPPLGLNGVLKVPAHPSGNMASFTKHI 139

>3dzy_A Retinoic acid receptor RXR-alpha; DNA-binding, HOST-virus interaction, metal-binding, nucleus, receptor, transcription, transcription regulation, zinc-FIN activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB: 3dzu_A* 3e00_A* Length = 467

 Score = 48.2 bits (114), Expect = 8e-06
 Identities = 25/116 (21%), Positives = 35/116 (30%)

Query: 572 PQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGPPVPPP 631
              T P G  +   P+   S  P  G P Q ++P   L +P         V   P  P  
Sbjct: 22  SSLTSPTGRGSMAAPSLHPSLGPGIGSPGQLHSPISTLSSPINGMGPPFSVISSPMGPHS 81

Query: 632 YAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATSSE 687
            +    P  G +   P    PM P              G L  P       A+ ++
Sbjct: 82  MSVPTTPTLGFSTGSPQLSSPMNPVSSSEDIKPPLGLNGVLKVPAHPSGNMASFTK 137

>3dzy_A Retinoic acid receptor RXR-alpha; DNA-binding, HOST-virus interaction, metal-binding, nucleus, receptor, transcription, transcription regulation, zinc-FIN activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB: 3dzu_A* 3e00_A* Length = 467

 Score = 47.0 bits (111), Expect = 2e-05
 Identities = 21/128 (16%), Positives = 31/128 (24%), Gaps = 7/128 (5%)

Query: 629 PPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATSSEA 688
               +    P    +M  P     + P      P    +P   L++P             
Sbjct: 18  TQVNSSLTSPTGRGSMAAPSLHPSLGP--GIGSPGQLHSPISTLSSP-----INGMGPPF 70

Query: 689 QQHSFPPGVQSESSSSAPAASANMYGSSMPPMPPNVQPAYATAPLGYSPYYNAVPPPPPP 748
              S P G  S S  + P    +     +      V  +    P         VP  P  
Sbjct: 71  SVISSPMGPHSMSVPTTPTLGFSTGSPQLSSPMNPVSSSEDIKPPLGLNGVLKVPAHPSG 130

Query: 749 APVSAADH 756
              S   H
Sbjct: 131 NMASFTKH 138

>3dzy_A Retinoic acid receptor RXR-alpha; DNA-binding, HOST-virus interaction, metal-binding, nucleus, receptor, transcription, transcription regulation, zinc-FIN activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB: 3dzu_A* 3e00_A* Length = 467

 Score = 45.1 bits (106), Expect = 7e-05
 Identities = 17/142 (11%), Positives = 35/142 (24%), Gaps = 15/142 (10%)

Query: 571 PPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGPPVPP 630
                      T    +           P+ + +   P  +P      G+P     P+  
Sbjct: 7   HHVDDDDKMFSTQVNSSLTS--------PTGRGSMAAPSLHPSLGPGIGSPGQLHSPIST 58

Query: 631 PYAP---YAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATSSE 687
             +P     PP          P  P        P    +     L++P    + +     
Sbjct: 59  LSSPINGMGPPFS----VISSPMGPHSMSVPTTPTLGFSTGSPQLSSPMNPVSSSEDIKP 114

Query: 688 AQQHSFPPGVQSESSSSAPAAS 709
               +    V +  S +  + +
Sbjct: 115 PLGLNGVLKVPAHPSGNMASFT 136

>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 = 5e-06
 Identities = 18/104 (17%), Positives = 38/104 (36%), Gaps = 4/104 (3%)

Query: 464 ANNSGSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKV 523
           +  SG+            G     +     + +  L   +  D L ++FS FG ++    
Sbjct: 1   SVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIIT 60

Query: 524 IKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV 567
                   ++    ++YAD   A +A  S++G  +      +R+
Sbjct: 61  FTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRI 100

>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae} Length = 124

 Score = 45.5 bits (107), Expect = 5e-06
 Identities = 12/56 (21%), Positives = 18/56 (32%), Gaps = 12/56 (21%)

Query: 373 CRLCGEPGHRQYACPSRTSTF------------KSDVLCKICGDGGHPTIDCLVKG 416
           C  C + GH +  CP    ++               + C  C + GH    C  K 
Sbjct: 7   CNNCSQRGHLKKDCPHIICSYCGATDDHYSRHCPKAIQCSKCDEVGHYRSQCPHKW 62

>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae} Length = 124

 Score = 42.1 bits (98), Expect = 7e-05
 Identities = 14/60 (23%), Positives = 18/60 (30%), Gaps = 15/60 (25%)

Query: 368 RDEEYCRLCGEPGHRQYACPSRTSTFK---------------SDVLCKICGDGGHPTIDC 412
             +  C LC    H +  CPS    +                  + C  CG  GH   DC
Sbjct: 62  WKKVQCTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDC 121

>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae} Length = 124

 Score = 41.7 bits (97), Expect = 1e-04
 Identities = 12/40 (30%), Positives = 15/40 (37%), Gaps = 4/40 (10%)

Query: 373 CRLCGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTIDC 412
           C  C E GH +  CP +       V C +C    H    C
Sbjct: 45  CSKCDEVGHYRSQCPHK----WKKVQCTLCKSKKHSKERC 80

>3v1v_A 2-MIB synthase, 2-methylisoborneol synthase; class I terpenoid cyclase fold, DDXXXXD motif, NDXXSXXXE MOT methylisoborneol biosynthesis; HET: GST; 1.80A {Streptomyces coelicolor} PDB: 3v1x_A* Length = 433

 Score = 48.2 bits (114), Expect = 7e-06
 Identities = 30/143 (20%), Positives = 40/143 (27%), Gaps = 13/143 (9%)

Query: 590 VSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGPPVPPPYAPYAPPPPGSTMYPPVP 649
           + +     + S    P G     P+AS T              A   PP       PP P
Sbjct: 1   MGSSHHHHHHSSGLVPRGSHMVIPSASVT-------SAASDFLAALHPPVTVPDPAPPPP 53

Query: 650 GQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATSSEAQQHSFPPGVQSESSSSAPAAS 709
             P         PP        L      PT   T+S A    +      E+ +SAP A+
Sbjct: 54  PAPAAGN-----PPDTVTGDSVLQRILRGPTGPGTTSLAPAVRYGRQPGPEAPASAPPAA 108

Query: 710 ANMY-GSSMPPMPPNVQPAYATA 731
                G    P+P          
Sbjct: 109 GRAVPGLYHHPVPEPDPVRVEEV 131

>3v1v_A 2-MIB synthase, 2-methylisoborneol synthase; class I terpenoid cyclase fold, DDXXXXD motif, NDXXSXXXE MOT methylisoborneol biosynthesis; HET: GST; 1.80A {Streptomyces coelicolor} PDB: 3v1x_A* Length = 433

 Score = 47.4 bits (112), Expect = 1e-05
 Identities = 17/102 (16%), Positives = 22/102 (21%)

Query: 568 AGKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGPP 627
               P  +V           +P    P    P       G  P+          +  GP 
Sbjct: 20  HMVIPSASVTSAASDFLAALHPPVTVPDPAPPPPPAPAAGNPPDTVTGDSVLQRILRGPT 79

Query: 628 VPPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPP 669
            P   +       G    P  P    P  G   P       P
Sbjct: 80  GPGTTSLAPAVRYGRQPGPEAPASAPPAAGRAVPGLYHHPVP 121

>3v1v_A 2-MIB synthase, 2-methylisoborneol synthase; class I terpenoid cyclase fold, DDXXXXD motif, NDXXSXXXE MOT methylisoborneol biosynthesis; HET: GST; 1.80A {Streptomyces coelicolor} PDB: 3v1x_A* Length = 433

 Score = 45.1 bits (106), Expect = 7e-05
 Identities = 16/111 (14%), Positives = 20/111 (18%), Gaps = 4/111 (3%)

Query: 569 GKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGPPV 628
           G                    + +  V    S   A   P    P      AP P   P 
Sbjct: 2   GSSHHHHHHSSGLVPRGSHMVIPSASVTSAASDFLAALHPPVTVPDP----APPPPPAPA 57

Query: 629 PPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAP 679
                               P  P            +   P A  + P A 
Sbjct: 58  AGNPPDTVTGDSVLQRILRGPTGPGTTSLAPAVRYGRQPGPEAPASAPPAA 108

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 44.6 bits (105), Expect = 8e-06
 Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 2/61 (3%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKD--RVTGMSKGYGFVKYADIQMANNAIA 551
           +++G LPP +D+D +   F  FG +V+    K   +     KGY F+ + +       I 
Sbjct: 11  VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALID 70

Query: 552 S 552
           +
Sbjct: 71  A 71

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens} Length = 85

 Score = 42.7 bits (101), Expect = 2e-05
 Identities = 20/105 (19%), Positives = 38/105 (36%), Gaps = 22/105 (20%)

Query: 239 AFKPPADYRPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSV 298
            F   A+       +++ IP          GL+IG  G T K+++   G K+++   G  
Sbjct: 2   QFHDNANGGQNGTVQEIMIP------AGKAGLVIGKGGETIKQLQERAGVKMILIQDG-- 53

Query: 299 KEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQ 343
                          + N D  + +       ++ A  MV  +L+
Sbjct: 54  -------------SQNTNVDKPLRIIG-DPYKVQQACEMVMDILR 84

>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus} Length = 61

 Score = 42.2 bits (99), Expect = 2e-05
 Identities = 15/40 (37%), Positives = 19/40 (47%)

Query: 373 CRLCGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTIDC 412
           C  CG PGH Q  CP +  +  S   C++C   GH    C
Sbjct: 7   CYTCGSPGHYQAQCPKKRKSGNSRERCQLCNGMGHNAKQC 46

>2z73_A Rhodopsin; visual pigment, GQ-type, G-protein coupled receptor, chromophore, glycoprotein, lipoprotein, membrane, palmitate phosphorylation; HET: BOG RET PLM TWT PC1; 2.50A {Todarodes pacificus} PDB: 3aym_A* 3ayn_A* 2ziy_A* Length = 448

 Score = 46.8 bits (111), Expect = 2e-05
 Identities = 35/121 (28%), Positives = 42/121 (34%), Gaps = 11/121 (9%)

Query: 569 GKPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGPPV 628
               + T       + +P    S        +Q       +           P  + PP 
Sbjct: 338 QFDDKETEDDKDAETEIPAGESSDAAPSADAAQMKEMMAMMQKMQQQQAAYPPQGYAPP- 396

Query: 629 PPPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATSSEA 688
           P  Y P   PP G   YPP   Q  PP G  YPPP Q APP    APP AP Q   +   
Sbjct: 397 PQGYPPQGYPPQG---YPP---QGYPPQG--YPPPPQGAPPQG--APPAAPPQGVDNQAY 446

Query: 689 Q 689
           Q
Sbjct: 447 Q 447

>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 = 45.2 bits (106), Expect = 2e-05
 Identities = 11/75 (14%), Positives = 27/75 (36%), Gaps = 2/75 (2%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
            ++YI   P     D +       G ++  ++ +       KG  FV +  I+ A   + 
Sbjct: 110 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE 168

Query: 552 SMNGYRLEGRTIAVR 566
           +    + +   + + 
Sbjct: 169 TPGQ-KYKETDLLIL 182

>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 = 43.0 bits (101), Expect = 3e-05
 Identities = 21/115 (18%), Positives = 44/115 (38%), Gaps = 10/115 (8%)

Query: 468 GSSGTPGHPGLGSNGAKPIKELDDTN-LYIGYLP-PTLDDDGLIRLFSTFGDIVMAKVIK 525
           GSSG+ G    G    K  ++ +    +++  LP     D  +++L   +G I    +++
Sbjct: 1   GSSGSSGKKPEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR 60

Query: 526 DRVTGMSKGYGFVKYADIQMANNAIA--SMNGYRLEGRTIAVRVAGKPPQPTVPP 578
                  K   F++    + A   +          +GR + V ++ K  +    P
Sbjct: 61  ------MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYKKLVSGP 109

>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens} Length = 164

 Score = 44.0 bits (104), Expect = 3e-05
 Identities = 18/120 (15%), Positives = 38/120 (31%), Gaps = 27/120 (22%)

Query: 227 QEIISQIIKRNPAFKPPADYRP---PKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRME 283
            E++  I++                      + +P       + +G++IG  G   K+++
Sbjct: 64  CEMVMDILRERDQGGFGDRNEYGSRIGGGIDVPVP------RHSVGVVIGRSGEMIKKIQ 117

Query: 284 RETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQ 343
            + G +I                   K D     +    +     +  E AA ++  LLQ
Sbjct: 118 NDAGVRIQF-----------------KQDDGTGPEKIAHIMG-PPDRCEHAARIINDLLQ 159

>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae} Length = 83

 Score = 41.5 bits (97), Expect = 5e-05
 Identities = 14/56 (25%), Positives = 17/56 (30%), Gaps = 15/56 (26%)

Query: 372 YCRLCGEPGHRQYACPSRTSTF---------------KSDVLCKICGDGGHPTIDC 412
            C LC    H +  CPS    +                  + C  CG  GH   DC
Sbjct: 7   QCTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDC 62

>3tx7_B Nuclear receptor subfamily 5 group A member 2; LRH-1, beta-catenin, armadillo repeat, nuclear receptor LIGA binding domain, protein binding; HET: P6L; 2.76A {Homo sapiens} Length = 352

 Score = 45.0 bits (106), Expect = 7e-05
 Identities = 21/158 (13%), Positives = 40/158 (25%), Gaps = 12/158 (7%)

Query: 570 KPPQPTVPPGPPTSTMPTYPVSAPPVGGYPSQQYAPGGPLPNPPAASYTGAPVPWGPPVP 629
           +     +   P         +S+     + + +  P      PP         P+     
Sbjct: 5   EAMSQVIQAMPSD-----LTISSAIQNIHSASKGLPLNHAALPPTDYDRS---PFVTSPI 56

Query: 630 PPYAPYAPPPPGSTMYPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGAPTQTATSSEAQ 689
               P      G   Y   P + +     +YP P  ++P   +        QT +S  + 
Sbjct: 57  SMTMPPHGSLQGYQTYGHFPSRAIK---SEYPDPYTSSPESIMGYSYMDSYQT-SSPASI 112

Query: 690 QHSFPPGVQSESSSSAPAASANMYGSSMPPMPPNVQPA 727
            H     ++ E       A    Y           +  
Sbjct: 113 PHLILELLKCEPDEPQVQAKIMAYLQQEQANRSKHEKL 150

>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 94

 Score = 41.3 bits (97), Expect = 7e-05
 Identities = 8/33 (24%), Positives = 12/33 (36%)

Query: 265 YNFIGLIIGPRGNTQKRMERETGAKIVIRGKGS 297
                 +IG  G   + +E +T  KI I     
Sbjct: 25  KEHHRFVIGKNGEKLQDLELKTATKIQIPRPDD 57

>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding, DNA-binding, nucleus, phosph ribonucleoprotein, RNA-binding, RNA binding protein; NMR {Homo sapiens} Length = 160

 Score = 42.8 bits (101), Expect = 7e-05
 Identities = 12/68 (17%), Positives = 26/68 (38%), Gaps = 8/68 (11%)

Query: 227 QEIISQIIKRNPAFKPPADYR--PPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMER 284
             +I   ++ + +           P +  +L +P       +  G +IG  G   K +  
Sbjct: 63  FAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVP------ASQCGSLIGKGGCKIKEIRE 116

Query: 285 ETGAKIVI 292
            TGA++ +
Sbjct: 117 STGAQVQV 124

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 42.0 bits (98), Expect = 9e-05
 Identities = 19/115 (16%), Positives = 39/115 (33%), Gaps = 9/115 (7%)

Query: 464 ANNSGSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKV 523
            ++  S      PG   + +   K L    L I      +  D L  + +  G +    +
Sbjct: 1   GSSGSSGKRITRPGNTDDPSGGNKVL---LLSIQNPLYPITVDVLYTVCNPVGKVQRIVI 57

Query: 524 IKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA-GKPPQPTVP 577
            K            V++  +  A  A A++NG  +      +++   +P +  V 
Sbjct: 58  FKRN-----GIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPTRLNVI 107

>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding protein, retrovirus, viral protein; NMR {Mason-pfizer monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A Length = 60

 Score = 39.9 bits (93), Expect = 1e-04
 Identities = 13/43 (30%), Positives = 15/43 (34%), Gaps = 3/43 (6%)

Query: 373 CRLCGEPGHRQYACPSRTS---TFKSDVLCKICGDGGHPTIDC 412
           C  CG+ GH    C          K   LC  C  G H   +C
Sbjct: 4   CFKCGKKGHFAKNCHEHAHNNAEPKVPGLCPRCKRGKHWANEC 46

>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 = 41.5 bits (97), Expect = 2e-04
 Identities = 16/120 (13%), Positives = 31/120 (25%), Gaps = 3/120 (2%)

Query: 448 LALGPGSGSSGSNPPWANNSGSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDG 507
           +          S      +  +S T G      +     +  +   + +  LP +   + 
Sbjct: 1   MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVED 60

Query: 508 LIRLFSTFG--DIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAV 565
           +    S     D            G   G  FV+         A+   +   +  R I V
Sbjct: 61  VQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMAL-KKDRESMGHRYIEV 119

>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 = 40.6 bits (95), Expect = 2e-04
 Identities = 16/87 (18%), Positives = 31/87 (35%), Gaps = 4/87 (4%)

Query: 482 GAKPIKELDDTN-LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIK--DRVTGMSKGYGFV 538
           G+K  +E+DD   +    LP +   + ++  FS          I       G  +G   +
Sbjct: 1   GSKLEEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALI 60

Query: 539 KYADIQMANNAIASMNGYRLEGRTIAV 565
           +    Q    A+   +   +  R + V
Sbjct: 61  EMESEQDVQKALE-KHRMYMGQRYVEV 86

>2axy_A Poly(RC)-binding protein 2; protein-DNA complex, DNA binding protein-DNA complex; 1.70A {Homo sapiens} SCOP: d.51.1.1 PDB: 2pqu_A 2py9_A 1ztg_A 3vke_A* Length = 73

 Score = 39.2 bits (92), Expect = 2e-04
 Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 6/46 (13%)

Query: 247 RPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVI 292
           +   L  +L +  KE      +G IIG +G + K+M  E+GA+I I
Sbjct: 1   KNVTLTIRLLMHGKE------VGSIIGKKGESVKKMREESGARINI 40

>2dgr_A Ring finger and KH domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 83

 Score = 39.5 bits (92), Expect = 3e-04
 Identities = 14/55 (25%), Positives = 27/55 (49%), Gaps = 6/55 (10%)

Query: 243 PADYRPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGS 297
            +     +   ++ +P      Y  +GL++GP+G T KR+++ T   IV  G+  
Sbjct: 2   SSGSSGGQTTIQVRVP------YRVVGLVVGPKGATIKRIQQRTHTYIVTPGRDK 50

>2ctk_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 104

 Score = 39.8 bits (93), Expect = 3e-04
 Identities = 17/94 (18%), Positives = 35/94 (37%), Gaps = 23/94 (24%)

Query: 265 YNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVE 324
           ++    +IG +G+  ++M  E    I +                  P P    D+ + + 
Sbjct: 25  FDLHRYVIGQKGSGIRKMMDEFEVNIHV------------------PAPELQSDI-IAIT 65

Query: 325 AETQESLEGAAAMVEKLLQPVDEVLNEHKRQQLR 358
                +L+ A A + +    V E+  E + + LR
Sbjct: 66  G-LAANLDRAKAGLLER---VKELQAEQEDRALR 95

>1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian, alpha-beta fold, DNA binding protein; 0.95A {Homo sapiens} SCOP: d.51.1.1 PDB: 1zzj_A 1zzi_A Length = 82

 Score = 39.2 bits (92), Expect = 3e-04
 Identities = 14/45 (31%), Positives = 21/45 (46%), Gaps = 6/45 (13%)

Query: 248 PPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVI 292
            P +  ++ IP       +  G IIG  G   K++  E+GA I I
Sbjct: 4   GPIITTQVTIP------KDLAGSIIGKGGQRIKQIRHESGASIKI 42

>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain, alpha-beta fold RNA-binding motif, immune system; 2.00A {Homo sapiens} SCOP: d.51.1.1 PDB: 1dt4_A Length = 76

 Score = 39.2 bits (92), Expect = 3e-04
 Identities = 15/48 (31%), Positives = 22/48 (45%), Gaps = 6/48 (12%)

Query: 254 KLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEG 301
           ++ +P       N +G I+G  G T    +  TGA+I I  KG    G
Sbjct: 6   EMAVP------ENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPG 47

>1x4m_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 Length = 94

 Score = 39.3 bits (92), Expect = 3e-04
 Identities = 15/54 (27%), Positives = 25/54 (46%), Gaps = 6/54 (11%)

Query: 248 PPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEG 301
           P    +++ IP       +  GL+IG  G T K+++   G K+V+   G    G
Sbjct: 12  PGNAVQEIMIP------ASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTG 59

>3nwa_A GB, GB-1, GB1, envelope glycoprotein B; coiled-coil, membrane fusion, viral P glycoprotein B, HSV-1, membrane; HET: NAG; 2.26A {Human herpesvirus 1} PDB: 3nwf_A* 3nw8_A* 3nwd_A* Length = 703

 Score = 42.6 bits (100), Expect = 5e-04
 Identities = 23/94 (24%), Positives = 26/94 (27%), Gaps = 1/94 (1%)

Query: 586 PTYPVSAPPVGGYPSQQYAPGGPL-PNPPAASYTGAPVPWGPPVPPPYAPYAPPPPGSTM 644
           P  P S    G   + Q A GGP  P PPA        P       P  P  P P G   
Sbjct: 2   PAAPTSPGTPGVAAATQAANGGPATPAPPALGAAPTGDPKPKKNKKPKNPTPPRPAGDNA 61

Query: 645 YPPVPGQPMPPYGVQYPPPVQTAPPGALTAPPGA 678
                   +  +          A       P GA
Sbjct: 62  TVAAGHATLREHLRDIKAENTDANFYVCPPPTGA 95

>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 = 39.1 bits (91), Expect = 6e-04
 Identities = 11/63 (17%), Positives = 24/63 (38%), Gaps = 1/63 (1%)

Query: 503 LDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRT 562
             ++    +   +G++    V  D +     G  +VK+   + A  A+  +N     G+ 
Sbjct: 39  FFEEVFTEMEEKYGEVEEMNV-CDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQP 97

Query: 563 IAV 565
           I  
Sbjct: 98  IHA 100

>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA binding protein/DNA complex; 1.60A {Homo sapiens} Length = 76

 Score = 38.0 bits (89), Expect = 6e-04
 Identities = 13/46 (28%), Positives = 21/46 (45%), Gaps = 6/46 (13%)

Query: 247 RPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVI 292
           +      +L IP       + IG IIG +G     + + +GA+I I
Sbjct: 1   KAQTTSHELTIP------NDLIGCIIGRQGAKINEIRQMSGAQIKI 40

>1ec6_A RNA-binding protein NOVA-2; KH domain, alpha-beta fold, RNA-binding motif, protein/RNA structure, RNA binding protein/RNA complex; 2.40A {Homo sapiens} SCOP: d.51.1.1 Length = 87

 Score = 38.5 bits (90), Expect = 6e-04
 Identities = 15/48 (31%), Positives = 22/48 (45%), Gaps = 6/48 (12%)

Query: 254 KLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEG 301
           ++ +P       N +G I+G  G T    +  TGA+I I  KG    G
Sbjct: 6   EIAVP------ENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPG 47

>1wvn_A Poly(RC)-binding protein 1; KH domain, RNA binding domain, RNA binding protein; 2.10A {Homo sapiens} SCOP: d.51.1.1 Length = 82

 Score = 38.0 bits (89), Expect = 7e-04
 Identities = 16/56 (28%), Positives = 23/56 (41%), Gaps = 6/56 (10%)

Query: 248 PPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRL 303
             +   +L IP       N IG IIG +G     + + +GA+I I        GR 
Sbjct: 3   GSQTTHELTIP------NNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQ 52

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A* Length = 178

 Score = 40.2 bits (94), Expect = 8e-04
 Identities = 14/69 (20%), Positives = 28/69 (40%), Gaps = 6/69 (8%)

Query: 224 KERQEIISQIIKRNPAFKPPADYRPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRME 283
           +E  + +++    +              Q K+ +P       +  GLIIG  G T K + 
Sbjct: 77  REMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVP------NSTAGLIIGKGGATVKAIM 130

Query: 284 RETGAKIVI 292
            ++GA + +
Sbjct: 131 EQSGAWVQL 139

>1j5k_A Heterogeneous nuclear ribonucleoprotein K; single-stranded DNA binding protein, transcription factor, hnRNP K, CT element, C-MYC oncogene; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1khm_A Length = 89

 Score = 38.1 bits (89), Expect = 8e-04
 Identities = 19/116 (16%), Positives = 41/116 (35%), Gaps = 31/116 (26%)

Query: 242 PPADYRPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEG 301
              D   P +  ++ IP       +  G IIG  G   K++  E+GA I I         
Sbjct: 5   SYGDLGGPIITTQVTIP------KDLAGSIIGKGGQRIKQIRHESGASIKID-------- 50

Query: 302 RLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQPVDEVLNEHKRQQL 357
                   +P     + + + +   TQ+ ++ A  +++         + ++  +  
Sbjct: 51  --------EPLEGSEDRI-ITITG-TQDQIQNAQYLLQ-------NSVKQYSGKFF 89

>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 = 39.1 bits (91), Expect = 8e-04
 Identities = 19/100 (19%), Positives = 30/100 (30%), Gaps = 10/100 (10%)

Query: 468 GSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFG--DIVMAKVIK 525
           GSSG+ G       G   +       + +  LP +   + +    S     D V      
Sbjct: 1   GSSGSSGMMLGPEGGEGYV-------VKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFI 53

Query: 526 DRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAV 565
               G   G  FV+         A+   +   +  R I V
Sbjct: 54  YTREGRQSGEAFVELESEDDVKLAL-KKDRESMGHRYIEV 92

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A Length = 105

 Score = 38.6 bits (90), Expect = 8e-04
 Identities = 14/77 (18%), Positives = 27/77 (35%), Gaps = 10/77 (12%)

Query: 500 PPTLDDDGLIRLF--------STFGDIVMAKVIK--DRVTGMSKGYGFVKYADIQMANNA 549
           P  L DD              S +G +   ++ +  D V     G  FV++  +     A
Sbjct: 16  PEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKA 75

Query: 550 IASMNGYRLEGRTIAVR 566
           +  + G +   R +  +
Sbjct: 76  MQGLTGRKFANRVVVTK 92

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	797
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	100.0
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	100.0
4fxw_B	124	Splicing factor 1; UHM, protein binding, phosphory	99.97
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	99.94
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.8
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.79
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.77
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.76
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.76
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.75
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.75
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.74
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.74
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.74
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.74
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.73
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.73
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.73
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.73
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.73
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.73
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.73
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.73
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.73
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.73
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.73
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.73
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.73
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.73
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.72
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.72
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.72
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.72
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.72
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.72
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.72
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.71
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.71
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.71
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.71
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.71
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.71
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.71
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.71
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.71
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.7
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.7
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.7
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.7
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.7
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.7
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.7
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.7
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.7
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.7
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.69
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.69
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.69
2div_A	99	TRNA selenocysteine associated protein; structural	99.69
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.69
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.69
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.69
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.69
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.68
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.68
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.68
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.68
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.68
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.68
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.67
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.67
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.67
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.67
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.67
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.67
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.67
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.67
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.67
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.67
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.67
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.66
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.66
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.66
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.66
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.66
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.66
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.66
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.66
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.66
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.66
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.65
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.65
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.65
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.65
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.65
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.65
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.65
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.64
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.63
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.63
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.63
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.63
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.62
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.62
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.62
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.62
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.62
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.61
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.61
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.61
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.61
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.61
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.61
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.61
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.61
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.61
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.6
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.6
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.6
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.6
1x5p_A	97	Negative elongation factor E; structure genomics,	99.6
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.6
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.59
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.38
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.59
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.59
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.59
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.59
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.59
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.58
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.58
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.58
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.58
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.58
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.58
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.57
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.57
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.57
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.57
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.57
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.57
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.57
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.57
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.57
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.56
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.56
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.56
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.56
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.56
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.56
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.55
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.55
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.54
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.54
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.53
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.53
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.53
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.53
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.52
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.52
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.52
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.51
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.5
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.5
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.49
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.49
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.49
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.49
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.48
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.48
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.48
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.48
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.47
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.47
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.47
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.47
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.46
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.45
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.45
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.45
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.45
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.45
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.44
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.42
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.42
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.39
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.39
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.38
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.38
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.37
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.37
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.36
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.35
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.33
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.3
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.28
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.27
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.25
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.25
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.25
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.25
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.25
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.24
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.24
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.21
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.2
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.11
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.1
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.05
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.04
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	98.98
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	98.96
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	98.94
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	98.93
1we8_A	104	Tudor and KH domain containing protein; structural	98.93
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	98.92
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	98.91
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	98.9
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	98.89
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	98.88
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.84
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	98.84
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	98.82
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	98.81
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	98.8
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	98.79
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	98.79
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	98.78
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	98.77
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.75
2cpq_A	91	FragIle X mental retardation syndrome related prot	98.7
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	98.7
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	98.69
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	98.69
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.68
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	98.59
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.57
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	98.5
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	98.46
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	98.42
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	98.32
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	98.3
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	98.29
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	98.22
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	98.21
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	98.17
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	98.13
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	98.01
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	97.95
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	97.87
1tua_A	191	Hypothetical protein APE0754; structural genomics,	97.83
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	97.63
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	97.63
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	97.61
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	97.6
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	97.54
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	97.54
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	97.49
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	97.49
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	97.34
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	97.31
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	97.25
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	97.18
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	96.84
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	96.73
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	96.71
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	96.61
1tua_A	191	Hypothetical protein APE0754; structural genomics,	96.42
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	96.4
1a6b_B	40	Momulv, zinc finger protein NCP10; nucleocapsid pr	96.35
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	96.14
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	96.13
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	96.0
1u6p_A	56	GAG polyprotein; MLV, A-minor K-turn, stem loop, b	95.67
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	95.53
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	95.28
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	95.08
1dsq_A	26	Nucleic acid binding protein P14; CCHC type zinc f	95.07
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	94.96
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	94.32
1nc8_A	29	Nucleocapsid protein; HIV-2, RNA recognition, zinc	93.66
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	93.12
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	92.2
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	92.15
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	92.02
2ysa_A	55	Retinoblastoma-binding protein 6; zinc finger, CCH	91.99
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	86.18
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	84.72
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	84.47
1a6b_B	40	Momulv, zinc finger protein NCP10; nucleocapsid pr	84.06
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	83.61
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	82.74
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	82.0
1u6p_A	56	GAG polyprotein; MLV, A-minor K-turn, stem loop, b	80.47

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=100.00  E-value=7.1e-39  Score=306.09  Aligned_cols=125  Identities=48%  Similarity=0.781  Sum_probs=113.3

Q ss_pred             ceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCC-CCCCCCceEEEEecCH
Q 040243          250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPD-PSENEDLHVLVEAETQ  328 (797)
Q Consensus       250 ~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~-~~~~e~LHv~I~a~~~  328 (797)
                      .+++|||||+++||+|||||+||||||+|+|+||+||||||.||||||+|+++.+......+. .+++|||||+|+|++.
T Consensus         1 ~~~~Ki~IP~~~~P~~NfiG~IiGPrG~t~K~ie~eTg~kI~IrGkGS~kd~~~e~~~~g~~~~~~~~epLHV~Isa~~~   80 (140)
T 2bl5_A            1 QLQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDA   80 (140)
T ss_dssp             CEEEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSC
T ss_pred             CceeEEEcCcccCCCCCeeeEEECCCcchHHHHHHHHCCeEEEecCCCcccccccccccCCCCccccCCCcEEEEEecCc
Confidence            368999999999999999999999999999999999999999999999999987654333332 2789999999999887


Q ss_pred             H-----HHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHhhcCCcCccchhc
Q 040243          329 E-----SLEGAAAMVEKLLQPVDEVLNEHKRQQLRELAALNGTIRDEEYCR  374 (797)
Q Consensus       329 e-----~v~~A~~~I~~ll~~~~e~~n~~k~~Ql~ela~lnGt~r~~~~c~  374 (797)
                      +     +|++|+++|++||.++++++|++|++||+|||.||||||++..|.
T Consensus        81 ~~~~~~~l~~A~~~I~~lL~p~~e~~de~K~~QL~eLA~lNGt~r~~~~~~  131 (140)
T 2bl5_A           81 QNRAELKLKRAVEEVKKLLVPAAEGEDSLKKMKLMELAILNGTYRDANLKS  131 (140)
T ss_dssp             CHHHHHHHHHHHHHHHHHSSCCSSSSSHHHHHHHTGGGSSSTTTSGGGGSC
T ss_pred             hhhHHHHHHHHHHHHHHHCCCCCcchhHHHHHHHHHHHHhcCCcCCCcccc
Confidence            5     899999999999999999999999999999999999999987653

>1k1g_A SF1-BO isoform; splicing, branch point sequence, protein/RNA recognition, complex E, KH domain, QUA2 homology; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=100.00  E-value=3.6e-36  Score=285.94  Aligned_cols=122  Identities=48%  Similarity=0.804  Sum_probs=110.4

Q ss_pred             CceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCH
Q 040243          249 PKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQ  328 (797)
Q Consensus       249 ~~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~  328 (797)
                      .|+++|||||+++||+|||||+||||||+|||+||+||||||.|||+||+|+++.+. .+.....+++|+|||+|+|++.
T Consensus         5 ~k~~~kv~IP~~~~P~~n~iG~IIGP~G~tiK~Iq~eTG~kI~IrgkgS~~~~~~~~-~~~~~~~~~~e~lhV~I~a~~~   83 (131)
T 1k1g_A            5 TRVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGR-KDGQMLPGEDEPLHALVTANTM   83 (131)
T ss_dssp             CCEEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSS-CCCCCSCCSSCCEEEEEEESSH
T ss_pred             ceEEEEEEECCccccCcceeeeEECCCcHHHHHHHHHHCCeEEecCCcccccccccc-cccccccccCCCeEEEEEECCH
Confidence            589999999999999999999999999999999999999999999999999987653 2444456889999999999999


Q ss_pred             HHHHHHHHHHHHhcCC---ChHHHHHHHHHHHHHHHhhcCCcCccc
Q 040243          329 ESLEGAAAMVEKLLQP---VDEVLNEHKRQQLRELAALNGTIRDEE  371 (797)
Q Consensus       329 e~v~~A~~~I~~ll~~---~~e~~n~~k~~Ql~ela~lnGt~r~~~  371 (797)
                      ++|++|+++|+.||..   +++++|++|++||+|||.||||||+++
T Consensus        84 e~~~~A~~~I~~ll~~~~~~p~~~d~~k~~Ql~eLa~~nGt~r~~~  129 (131)
T 1k1g_A           84 ENVKKAVEQIRNILKQGIETPEDQNDLRKMQLRELARLNGTLREDD  129 (131)
T ss_dssp             HHHHHHHHHHHHHHTTTTSCCTTSSGGGGGGGHHHHHHHTCCC---
T ss_pred             HHHHHHHHHHHHHHhccCCCCccHHHHHHHHHHHHHHHcCcCCCcC
Confidence            9999999999999975   778999999999999999999999874

>4fxw_B Splicing factor 1; UHM, protein binding, phosphorylat; HET: SEP; 2.29A {Homo sapiens} PDB: 4fxx_A

Probab=99.97  E-value=3.6e-32  Score=252.46  Aligned_cols=120  Identities=37%  Similarity=0.713  Sum_probs=87.8

Q ss_pred             CCCCCccCCCCCCCCCCCcccCCccccccCCCCcCCH-HHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCcccCCCC
Q 040243          130 GSGTRKRRSRWADDEPKPVIQLPDFMKDFTGGIEFDP-EIQALNSRLLEISRMLQSGLPLDDRPEGQRSPSPEPIYDNMG  208 (797)
Q Consensus       130 ~~~~~~r~srw~~~~~~~~~~~p~~~~~~~~~~~~~~-~~~~~~~r~~ei~~~l~~~~~~~~~~~~~rspsp~p~yd~~g  208 (797)
                      |.++||||||||.++++....||...+.++++++.++ +++++++|||||+++|++|++.....+++|||||+|+||++|
T Consensus         4 ~~~~~~r~srW~~~~~~~k~~ip~~pt~ip~~Lt~eq~~ay~~~~RieeIt~kL~~g~l~i~~~~~~RSPSPpP~Yd~~G   83 (124)
T 4fxw_B            4 GSSKKRKRSRWNQDTMEQKTVIPGMPTVIPPGLTREQERAYIVQLQIEDLTRKLRTGDLGIPPNPEDRSPSPEPIYNSEG   83 (124)
T ss_dssp             --------CCBCCC--------CCSCSBCCSSCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCSSTTSSCCCCCCCBCTTS
T ss_pred             CccccccccccCCCcccccccCCCCCeecCCCCCHHHHHHHHHHhhHHHHHHHHhcCCcCCCCCcccCCCCCCCccCccc
Confidence            5679999999998754433345555566677776555 335679999999999999987543346899999999999999


Q ss_pred             cccChHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCCCC
Q 040243          209 IRINTREYRARERLNKERQEIISQIIKRNPAFKPPADYRPP  249 (797)
Q Consensus       209 ~r~ntre~r~~~~le~er~~li~~~~~~~p~~~pp~dy~p~  249 (797)
                      +||||||+|+|++||+|||+||++|+++||.|++|+||||.
T Consensus        84 ~R~NTRE~R~r~~LE~ER~~lIe~~~k~~P~fkpP~DYkpp  124 (124)
T 4fxw_B           84 KRLNTREFRTRKKLEEERHNLITEMVALNPDFKPPADYKPP  124 (124)
T ss_dssp             CBSSCHHHHHHHHHHHHHHHHHHHGGGTCSSCCCCCC----
T ss_pred             cccchHHHHHHHHHHHHHHHHHHHHHHHCcCCCCCCCCCCC
Confidence            99999999999999999999999999999999999999974

>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.94  E-value=7.7e-27  Score=217.91  Aligned_cols=101  Identities=27%  Similarity=0.379  Sum_probs=91.9

Q ss_pred             CceEEEEEecCC-CCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecC
Q 040243          249 PKLQKKLYIPMK-EYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAET  327 (797)
Q Consensus       249 ~~~~~Ki~IP~~-~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~  327 (797)
                      .++++|||||++ +||+|||||+||||+|+|||+||+||||||.|||+||+|...       ....+++|+|||+|+|.+
T Consensus        10 ~~~~~ki~ip~~~~~p~fn~ig~IIGpgG~tiK~I~~eTG~kI~I~G~gS~~~e~-------~~~~e~~e~l~V~I~a~~   82 (119)
T 2yqr_A           10 HYVQDKLFVGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEP-------ASGREAFEPMYIYISHPK   82 (119)
T ss_dssp             SCEEEEEECCCTTSCTTTCHHHHHSCGGGHHHHHHHHHHCCEEEEESBTTTCCCT-------TTSSCCSSBCEEEEEESS
T ss_pred             eEEEEEEEcCCccCCCCCCeeeeEECCCChHHHHHHHHHCCEEEEecCCcccccc-------ccccccCCCcEEEEEeCC
Confidence            368999999999 699999999999999999999999999999999999987321       223478999999999999


Q ss_pred             HHHHHHHHHHHHHhcCCChHHHHHHHHHH
Q 040243          328 QESLEGAAAMVEKLLQPVDEVLNEHKRQQ  356 (797)
Q Consensus       328 ~e~v~~A~~~I~~ll~~~~e~~n~~k~~Q  356 (797)
                      .++|++|+++|+.||..+.+.++++|++|
T Consensus        83 ~e~i~~A~~~Ie~Ll~~v~~~~~~~~~q~  111 (119)
T 2yqr_A           83 PEGLAAAKKLCENLLQTVHAEYSRFVNQI  111 (119)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhchHHHHHHHHHhh
Confidence            99999999999999999999999999875

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.80  E-value=4.2e-19  Score=167.90  Aligned_cols=139  Identities=28%  Similarity=0.420  Sum_probs=103.8

Q ss_pred             cccceecCCCCCCcccCCCCCcCCCCcchHHHHHHhhhcCCCCcccccccccccCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 040243          396 DVLCKICGDGGHPTIDCLVKGTTGKKMDDEYQNFLAELGGTLPESASKQSTTLALGPGSGSSGSNPPWANNSGSSGTPGH  475 (797)
Q Consensus       396 ~v~Cr~CG~~gH~t~dCp~k~~~g~~ld~eY~~~m~Elg~~~pe~a~ka~~~~a~g~g~gg~G~~~p~~~~~g~~g~~g~  475 (797)
                      .|.|.+|++-.|.+  |       ..++++|.+++++|-....-.               ..........++++ +   .
T Consensus         2 mi~c~~c~~w~H~~--c-------~~~~~~~~~~l~~lp~~~~~~---------------c~~C~~~~~~~~~~-~---~   53 (140)
T 2ku7_A            2 MMQCGKCDRWVHSK--C-------ENLSDEMYEILSNLPESVAYT---------------CVNCTERHVDGGSG-G---S   53 (140)
T ss_dssp             CCCCSCCSSCHHHH--H-------CCCCHHHHHHHHSSCTTTTCC---------------SSCCTTTSCCCCSC-S---S
T ss_pred             ccccccCCCccCCc--c-------cccCHHHHHHHhhccccceee---------------CccccccccCCCCC-C---C
Confidence            57899999988865  5       248899999998754211000               00000000000000 0   0


Q ss_pred             CCCCCCCCCCCCCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCc
Q 040243          476 PGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNG  555 (797)
Q Consensus       476 ~g~g~~~~~~~~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG  555 (797)
                      +  +    ........++|||+||+.++++++|+++|++||.|.+|+|++++.+++++|||||+|.+.++|++||+.|||
T Consensus        54 ~--~----~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g  127 (140)
T 2ku7_A           54 G--G----SGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNE  127 (140)
T ss_dssp             C--S----SCSSCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTE
T ss_pred             C--C----CCCCCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCC
Confidence            0  0    011334678999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeeccceEEEEec
Q 040243          556 YRLEGRTIAVRVA  568 (797)
Q Consensus       556 ~~l~Gr~L~V~~A  568 (797)
                      ..|+|+.|+|+||
T Consensus       128 ~~~~g~~l~v~~A  140 (140)
T 2ku7_A          128 SELFGRTIRVNLA  140 (140)
T ss_dssp             EEETTEEEEEEC-
T ss_pred             CEECCEEEEEEeC
Confidence            9999999999986

>4fxv_A ELAV-like protein 1; RNA recognition motif, putative RNA-binding domain, transcri structural genomics, joint center for structural genomics; 1.90A {Homo sapiens}

Probab=99.79  E-value=2.9e-19  Score=161.36  Aligned_cols=82  Identities=44%  Similarity=0.753  Sum_probs=78.9

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ..+++|||+||++++|+++|+++|++||.|.+|+|++|+.||++||||||+|.+.++|++||+.|||..|+|+.|+|+||
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            45789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CC
Q 040243          569 GK  570 (797)
Q Consensus       569 ~~  570 (797)
                      ++
T Consensus        97 kP   98 (99)
T 4fxv_A           97 RP   98 (99)
T ss_dssp             CB
T ss_pred             eC
Confidence            63

>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=99.77  E-value=2.6e-18  Score=158.01  Aligned_cols=89  Identities=34%  Similarity=0.598  Sum_probs=83.0

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      .....++|||+||++++++++|+++|++||.|.+|+|++++.+++++|||||+|.+.++|++||+.||++.|+|+.|+|+
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            34567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCCCC
Q 040243          567 VAGKPPQPT  575 (797)
Q Consensus       567 ~A~~~~~~~  575 (797)
                      |++.+....
T Consensus       101 ~a~~~~~~~  109 (115)
T 2cpz_A          101 LKRSKNDSK  109 (115)
T ss_dssp             CCCCSCCCC
T ss_pred             EcCCCCcCC
Confidence            998765543

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=3.5e-18  Score=153.94  Aligned_cols=89  Identities=26%  Similarity=0.433  Sum_probs=83.6

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      +....++|||+||++++++++|+++|++||.|.+|+|++++.+++++|||||+|.+.++|++||+.|||+.|+|+.|+|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   90 (103)
T 2cq0_A           11 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVE   90 (103)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCCCC
Q 040243          567 VAGKPPQPT  575 (797)
Q Consensus       567 ~A~~~~~~~  575 (797)
                      |+..+....
T Consensus        91 ~a~~~~~~~   99 (103)
T 2cq0_A           91 WAKPSTNSG   99 (103)
T ss_dssp             ESSCCCCSC
T ss_pred             ECCCCCCCC
Confidence            998766544

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.76  E-value=1e-17  Score=153.85  Aligned_cols=89  Identities=36%  Similarity=0.598  Sum_probs=83.6

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      .....++|||+||++++++++|+++|++||.|.+|+|++++.+++++|||||+|.+.++|++||+.|+|+.|+|+.|+|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   90 (115)
T 2dgo_A           11 DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTN   90 (115)
T ss_dssp             CSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCCCC
Q 040243          567 VAGKPPQPT  575 (797)
Q Consensus       567 ~A~~~~~~~  575 (797)
                      |+..+....
T Consensus        91 ~a~~~~~~~   99 (115)
T 2dgo_A           91 WATRKPPAP   99 (115)
T ss_dssp             ESSCCCCCS
T ss_pred             EccCCCCCC
Confidence            998765543

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.75  E-value=5.7e-18  Score=149.66  Aligned_cols=82  Identities=32%  Similarity=0.553  Sum_probs=78.6

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      ....++|||+||+.++++++|+++|++||.|.+|+|+.++.+++++|||||+|.+.++|++||+.||+..|+|+.|+|+|
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   92 (94)
T 2e5h_A           13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASI   92 (94)
T ss_dssp             CCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEe
Confidence            34678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cC
Q 040243          568 AG  569 (797)
Q Consensus       568 A~  569 (797)
                      |+
T Consensus        93 ak   94 (94)
T 2e5h_A           93 AI   94 (94)
T ss_dssp             CC
T ss_pred             cC
Confidence            85

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.75  E-value=4.4e-18  Score=156.66  Aligned_cols=83  Identities=12%  Similarity=0.159  Sum_probs=79.3

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      ..++|||+||++++++++|+++|++||.|.+|+|++|+.||++||||||+|.+.++|++||+.|||..|+|+.|+|++|.
T Consensus         5 p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a~   84 (110)
T 3s8s_A            5 PLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDI   84 (110)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            46799999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             CCC
Q 040243          570 KPP  572 (797)
Q Consensus       570 ~~~  572 (797)
                      ...
T Consensus        85 ~~~   87 (110)
T 3s8s_A           85 KGQ   87 (110)
T ss_dssp             TTH
T ss_pred             CCc
Confidence            543

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=5.5e-18  Score=152.66  Aligned_cols=89  Identities=26%  Similarity=0.387  Sum_probs=83.1

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      .....++|||+||++++++++|+++|++||.|.+|+|+.++.|++++|||||+|.+.++|++||+.|||..|+|+.|+|+
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            44567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCCCC
Q 040243          567 VAGKPPQPT  575 (797)
Q Consensus       567 ~A~~~~~~~  575 (797)
                      ||+......
T Consensus        89 ~a~~~~~~~   97 (103)
T 2dnm_A           89 VARYGRRDL   97 (103)
T ss_dssp             ECSSCCSCC
T ss_pred             ECCcCCCCC
Confidence            998655443

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=2.2e-17  Score=151.96  Aligned_cols=88  Identities=40%  Similarity=0.565  Sum_probs=81.8

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      .+...++|||+||++++++++|+++|++||.|.+|+|++++.+++++|||||+|.+.++|++||+.|++ .|+|+.|+|+
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            556789999999999999999999999999999999999999999999999999999999999999998 8999999999


Q ss_pred             ecCCCCCCC
Q 040243          567 VAGKPPQPT  575 (797)
Q Consensus       567 ~A~~~~~~~  575 (797)
                      ||.......
T Consensus        92 ~a~~~~~~~  100 (116)
T 2cqd_A           92 LAYLGAKPR  100 (116)
T ss_dssp             ESTTTCCCC
T ss_pred             EcccCCCcc
Confidence            997654433

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=1e-17  Score=151.20  Aligned_cols=88  Identities=33%  Similarity=0.497  Sum_probs=82.7

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      .....++|||+||++++++++|+++|++||.|.+|+|+.++.+++++|||||+|.+.++|++||+.|+++.|+|+.|+|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   90 (105)
T 1x5u_A           11 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVN   90 (105)
T ss_dssp             CCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            44567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCCC
Q 040243          567 VAGKPPQP  574 (797)
Q Consensus       567 ~A~~~~~~  574 (797)
                      |+......
T Consensus        91 ~a~~~~~~   98 (105)
T 1x5u_A           91 KASAHNKN   98 (105)
T ss_dssp             ETTTTSCC
T ss_pred             ECCCCCcC
Confidence            99876543

>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=99.74  E-value=1.6e-18  Score=152.91  Aligned_cols=82  Identities=26%  Similarity=0.385  Sum_probs=73.2

Q ss_pred             cEEEEecCCCCCcHHHHHHHhhcCC--CEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          492 TNLYIGYLPPTLDDDGLIRLFSTFG--DIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       492 ~tLfVgNLp~~vte~dL~~~Fs~fG--~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      .+|||+||++++++++|+++|++||  .|.+|+|++|+.||++||||||+|.+.++|++||+.|||..|+|+.|+|+++.
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            5899999999999999999999999  99999999999999999999999999999999999999999999999999988


Q ss_pred             CCCC
Q 040243          570 KPPQ  573 (797)
Q Consensus       570 ~~~~  573 (797)
                      .+..
T Consensus        82 ~~~~   85 (90)
T 3p5t_L           82 KLEH   85 (90)
T ss_dssp             ----
T ss_pred             CCcc
Confidence            6544

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=1.4e-17  Score=147.35  Aligned_cols=83  Identities=25%  Similarity=0.374  Sum_probs=79.4

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      ....++|||+||++++++++|+++|++||.|.+|+|++++.+++++|||||+|.+.++|++||+.|||..|+|+.|+|+|
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (95)
T 2cqc_A           12 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSG   91 (95)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            34678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCC
Q 040243          568 AGK  570 (797)
Q Consensus       568 A~~  570 (797)
                      |+.
T Consensus        92 a~~   94 (95)
T 2cqc_A           92 PSS   94 (95)
T ss_dssp             CSC
T ss_pred             cCC
Confidence            874

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.73  E-value=3.6e-17  Score=149.76  Aligned_cols=84  Identities=25%  Similarity=0.359  Sum_probs=78.9

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      ....++|||+||++++++++|+++|++||.|.+|+|+.++ +++++|||||+|.+.++|++||+.||++.|+|+.|+|+|
T Consensus        12 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   90 (114)
T 2do0_A           12 GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKM   90 (114)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEE
Confidence            3467899999999999999999999999999999999998 699999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 040243          568 AGKPP  572 (797)
Q Consensus       568 A~~~~  572 (797)
                      +....
T Consensus        91 a~~~~   95 (114)
T 2do0_A           91 DERAL   95 (114)
T ss_dssp             CSCCC
T ss_pred             cccCC
Confidence            87543

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=1.7e-17  Score=148.36  Aligned_cols=87  Identities=21%  Similarity=0.421  Sum_probs=81.5

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      ....++|||+||++++++++|+++|++||.|.+|+|++++.+++++|||||+|.+.++|++||+ |+++.|+|+.|+|++
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            3567899999999999999999999999999999999999999999999999999999999998 999999999999999


Q ss_pred             cCCCCCCC
Q 040243          568 AGKPPQPT  575 (797)
Q Consensus       568 A~~~~~~~  575 (797)
                      +..+....
T Consensus        86 a~~~~~~~   93 (99)
T 2dgs_A           86 AEPRDSKS   93 (99)
T ss_dssp             CCCCCCCC
T ss_pred             CCCCcccC
Confidence            98765544

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.73  E-value=2.4e-17  Score=147.65  Aligned_cols=86  Identities=23%  Similarity=0.485  Sum_probs=80.9

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      .....++|||+||++++++++|+++|++||.|.+|+|+.++ +|+++|||||+|.+.++|++||+.|||..|+|+.|+|+
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            44567899999999999999999999999999999999998 99999999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 040243          567 VAGKPPQ  573 (797)
Q Consensus       567 ~A~~~~~  573 (797)
                      |+..+..
T Consensus        92 ~a~~~~~   98 (100)
T 2do4_A           92 ISNSGPS   98 (100)
T ss_dssp             ECCCCSC
T ss_pred             ECCCCCC
Confidence            9986543

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.73  E-value=2.1e-17  Score=150.51  Aligned_cols=89  Identities=22%  Similarity=0.426  Sum_probs=82.9

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcC------ceeecc
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMN------GYRLEG  560 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~Ln------G~~l~G  560 (797)
                      .....++|||+||++++++++|+++|++||.|.+|+|++|+.+++++|||||+|.+.++|++||+.|+      +..|+|
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             ceEEEEecCCCCCCC
Q 040243          561 RTIAVRVAGKPPQPT  575 (797)
Q Consensus       561 r~L~V~~A~~~~~~~  575 (797)
                      +.|+|+|+..+....
T Consensus        91 ~~l~v~~a~~~~~~~  105 (111)
T 1x4h_A           91 RQLKVDLAVTRDEAA  105 (111)
T ss_dssp             CEEEEECCCCCCCCC
T ss_pred             EEEEEEECCCCccCC
Confidence            999999998765443

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.73  E-value=2.7e-17  Score=148.31  Aligned_cols=87  Identities=21%  Similarity=0.390  Sum_probs=80.7

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      .....++|||+||++++++++|+++|++|| |.+|+|++|+.|++++|||||+|.+.++|++|| .||+..|+|+.|+|+
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 (103)
T 2dng_A           11 PTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVD   88 (103)
T ss_dssp             CSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEE
Confidence            445678999999999999999999999997 999999999999999999999999999999999 899999999999999


Q ss_pred             ecCCCCCCC
Q 040243          567 VAGKPPQPT  575 (797)
Q Consensus       567 ~A~~~~~~~  575 (797)
                      |+.......
T Consensus        89 ~a~~~~~~~   97 (103)
T 2dng_A           89 IAEGRKQDK   97 (103)
T ss_dssp             ECCCCCCCC
T ss_pred             EecCCCCCC
Confidence            998765443

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens}

Probab=99.73  E-value=1e-17  Score=145.69  Aligned_cols=83  Identities=37%  Similarity=0.587  Sum_probs=77.5

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ...++|||+||+.++++++|+++|++||.|.+|+++.++.+++++|||||+|.+.++|++||+.|||..|+|+.|+|+||
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            35789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCC
Q 040243          569 GKP  571 (797)
Q Consensus       569 ~~~  571 (797)
                      +.+
T Consensus        84 ~~k   86 (87)
T 3bs9_A           84 TRK   86 (87)
T ss_dssp             C--
T ss_pred             CCC
Confidence            864

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.73  E-value=3e-18  Score=152.12  Aligned_cols=83  Identities=16%  Similarity=0.434  Sum_probs=77.3

Q ss_pred             CcEEEEecCCCCCcHHHHHHHhhcCC-CEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhc-CceeeccceEEEEec
Q 040243          491 DTNLYIGYLPPTLDDDGLIRLFSTFG-DIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM-NGYRLEGRTIAVRVA  568 (797)
Q Consensus       491 ~~tLfVgNLp~~vte~dL~~~Fs~fG-~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~L-nG~~l~Gr~L~V~~A  568 (797)
                      +++|||+||+.++||++|+++|++|| .|.+|+|++|+.||++||||||+|.+.++|++||+.| ++..|+|+.|+|+||
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            36899999999999999999999999 8999999999999999999999999999999999987 567899999999999


Q ss_pred             CCCCC
Q 040243          569 GKPPQ  573 (797)
Q Consensus       569 ~~~~~  573 (797)
                      .++..
T Consensus        81 ~~~~~   85 (91)
T 2lxi_A           81 DPKPK   85 (91)
T ss_dssp             CSCCC
T ss_pred             CCCCC
Confidence            86654

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=2.1e-17  Score=148.82  Aligned_cols=87  Identities=33%  Similarity=0.550  Sum_probs=81.3

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      .....++|||+||++++++++|+++|++||.|.+|+|+.+  +++++|||||+|.+.++|++||+.|||..|+|+.|+|+
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 (103)
T 2d9p_A           11 TRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVA   88 (103)
T ss_dssp             CCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            4557889999999999999999999999999999999998  89999999999999999999999999999999999999


Q ss_pred             ecCCCCCCC
Q 040243          567 VAGKPPQPT  575 (797)
Q Consensus       567 ~A~~~~~~~  575 (797)
                      |+..+....
T Consensus        89 ~a~~~~~~~   97 (103)
T 2d9p_A           89 LAQRKEERQ   97 (103)
T ss_dssp             ECSSCCCCC
T ss_pred             EecccccCC
Confidence            998766544

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.73  E-value=1.9e-17  Score=146.55  Aligned_cols=86  Identities=34%  Similarity=0.592  Sum_probs=81.4

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      ..++|||+||+.++++++|+++|++||.|.+|+|++++.+++++|||||+|.+.++|++||+.|||+.|+|+.|+|+|+.
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   83 (95)
T 2dnz_A            4 GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVT   83 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEESS
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEcc
Confidence            46799999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCCCC
Q 040243          570 KPPQPT  575 (797)
Q Consensus       570 ~~~~~~  575 (797)
                      .+....
T Consensus        84 ~~~~~~   89 (95)
T 2dnz_A           84 ERLDGG   89 (95)
T ss_dssp             CCCCCC
T ss_pred             cccCCC
Confidence            766544

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.73  E-value=1.9e-17  Score=149.77  Aligned_cols=89  Identities=25%  Similarity=0.444  Sum_probs=83.0

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEec-CCCCcccceEEEEecCHHHHHHHHHhc-CceeeccceEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKD-RVTGMSKGYGFVKYADIQMANNAIASM-NGYRLEGRTIA  564 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~d-k~TGksrGfaFV~F~s~e~A~~AI~~L-nG~~l~Gr~L~  564 (797)
                      .+...++|||+||++++++++|+++|++||.|.+|+|+++ +.+++++|||||+|.+.++|++||+.| |++.|+|+.|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~   90 (107)
T 2cph_A           11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLV   90 (107)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEE
Confidence            4567889999999999999999999999999999999999 889999999999999999999999999 99999999999


Q ss_pred             EEecCCCCCCC
Q 040243          565 VRVAGKPPQPT  575 (797)
Q Consensus       565 V~~A~~~~~~~  575 (797)
                      |+|+.......
T Consensus        91 v~~a~~~~~~~  101 (107)
T 2cph_A           91 LEWADSEVTVQ  101 (107)
T ss_dssp             EEECCCCCCCC
T ss_pred             EEeCCCCCCCC
Confidence            99998765433

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.73  E-value=2.2e-17  Score=147.42  Aligned_cols=86  Identities=24%  Similarity=0.366  Sum_probs=81.8

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ...++|||+||++++++++|+++|++||.|.+|+|++++.+++++|||||+|.+.++|++||+.|||..|+|+.|+|+++
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            46789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 040243          569 GKPPQP  574 (797)
Q Consensus       569 ~~~~~~  574 (797)
                      ..+...
T Consensus        86 ~~~~~~   91 (99)
T 1whw_A           86 TIKKEA   91 (99)
T ss_dssp             CCCSTT
T ss_pred             CCCccc
Confidence            876654

>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=99.73  E-value=1.9e-17  Score=142.84  Aligned_cols=81  Identities=37%  Similarity=0.588  Sum_probs=78.2

Q ss_pred             cEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecCCC
Q 040243          492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKP  571 (797)
Q Consensus       492 ~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~~~  571 (797)
                      ++|||+||+.++++++|+++|++||.|.++++++++.+|+++|||||+|.+.++|++|++.|||..|+|+.|+|+|+..+
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   81 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKL   81 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCcC
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999865


Q ss_pred             C
Q 040243          572 P  572 (797)
Q Consensus       572 ~  572 (797)
                      .
T Consensus        82 ~   82 (83)
T 3md1_A           82 E   82 (83)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=1.4e-17  Score=150.59  Aligned_cols=87  Identities=28%  Similarity=0.458  Sum_probs=81.6

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      .....++|||+||++++++++|+++|++||.|.+|+|++++.+++++|||||+|.+.++|++||+. +++.|+|+.|+|+
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~   90 (105)
T 2dh8_A           12 GADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPK   90 (105)
T ss_dssp             CSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEE
Confidence            456778999999999999999999999999999999999999999999999999999999999998 9999999999999


Q ss_pred             ecCCCCCC
Q 040243          567 VAGKPPQP  574 (797)
Q Consensus       567 ~A~~~~~~  574 (797)
                      ++..+...
T Consensus        91 ~a~~~~~~   98 (105)
T 2dh8_A           91 PCTPRGMQ   98 (105)
T ss_dssp             CSCCSSCC
T ss_pred             EccCCCCC
Confidence            99866543

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=1.7e-17  Score=151.86  Aligned_cols=89  Identities=27%  Similarity=0.441  Sum_probs=83.1

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEE--------EEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceee
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIV--------MAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRL  558 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~--------~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l  558 (797)
                      +....++|||+||++++++++|+++|++||.|.        .|+|+.|+.+++++|||||+|.+.++|++||+.|||+.|
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            456789999999999999999999999999999        699999999999999999999999999999999999999


Q ss_pred             ccceEEEEecCCCCCCC
Q 040243          559 EGRTIAVRVAGKPPQPT  575 (797)
Q Consensus       559 ~Gr~L~V~~A~~~~~~~  575 (797)
                      +|+.|+|+|++.+....
T Consensus        91 ~g~~l~V~~a~~~~~~~  107 (113)
T 2cpe_A           91 QGSKLKVSLARKKPPMN  107 (113)
T ss_dssp             TTEECEEECSSCCCCST
T ss_pred             CCCEEEEEECCCCCCCC
Confidence            99999999998765543

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=1.4e-17  Score=149.55  Aligned_cols=87  Identities=33%  Similarity=0.418  Sum_probs=82.1

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ...++|||+||++++++++|+++|++||.|.+|+|+.|+.+++++|||||+|.+.++|++||+.||++.|+|+.|+|+|+
T Consensus        10 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   89 (102)
T 2cqb_A           10 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   89 (102)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEeC
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCC
Q 040243          569 GKPPQPT  575 (797)
Q Consensus       569 ~~~~~~~  575 (797)
                      .......
T Consensus        90 ~~~~~~~   96 (102)
T 2cqb_A           90 KPMRIKE   96 (102)
T ss_dssp             CCCCCCC
T ss_pred             CCCCCCC
Confidence            8766544

>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=99.72  E-value=1.5e-17  Score=150.39  Aligned_cols=89  Identities=35%  Similarity=0.573  Sum_probs=82.9

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceee---ccceE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRL---EGRTI  563 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l---~Gr~L  563 (797)
                      .+...++|||+||+.++++++|+++|++||.|.+|+|+.|+.++++||||||+|.+.++|++||+.||+..+   +|+.|
T Consensus         9 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l   88 (106)
T 2dgp_A            9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPI   88 (106)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceE
Confidence            456788999999999999999999999999999999999999999999999999999999999999999987   89999


Q ss_pred             EEEecCCCCCCC
Q 040243          564 AVRVAGKPPQPT  575 (797)
Q Consensus       564 ~V~~A~~~~~~~  575 (797)
                      +|+|+.......
T Consensus        89 ~v~~a~~~~~~~  100 (106)
T 2dgp_A           89 QVKPADSESRGG  100 (106)
T ss_dssp             EEEECCCCSCCC
T ss_pred             EEEECCcccccC
Confidence            999998766543

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A

Probab=99.72  E-value=5e-17  Score=146.67  Aligned_cols=87  Identities=28%  Similarity=0.481  Sum_probs=81.2

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeecc---ceEE
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEG---RTIA  564 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~G---r~L~  564 (797)
                      ....++|||+||++++++++|+++|++||.|.+|+|+.++ +|+++|||||+|.+.++|++||+.|||..|.|   +.|+
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~   90 (105)
T 2dnh_A           12 GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLV   90 (105)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEE
Confidence            3457899999999999999999999999999999999998 89999999999999999999999999999998   9999


Q ss_pred             EEecCCCCCCC
Q 040243          565 VRVAGKPPQPT  575 (797)
Q Consensus       565 V~~A~~~~~~~  575 (797)
                      |+||.......
T Consensus        91 V~~a~~~~~~~  101 (105)
T 2dnh_A           91 VKFADTDKESG  101 (105)
T ss_dssp             EEESCSSCCCS
T ss_pred             EEECccCcccC
Confidence            99998766544

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=1.8e-17  Score=148.75  Aligned_cols=87  Identities=37%  Similarity=0.643  Sum_probs=81.9

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ...++|||+||++++++++|+++|++||.|.+|+|++++.+++++|||||+|.+.++|++||+.||++.|+|+.|+|+|+
T Consensus        10 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   89 (102)
T 1x5s_A           10 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA   89 (102)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCC
Q 040243          569 GKPPQPT  575 (797)
Q Consensus       569 ~~~~~~~  575 (797)
                      +......
T Consensus        90 ~~~~~~~   96 (102)
T 1x5s_A           90 GKSSDNR   96 (102)
T ss_dssp             ECCCCCC
T ss_pred             CCCCCCC
Confidence            8765543

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=1.9e-17  Score=149.69  Aligned_cols=86  Identities=24%  Similarity=0.390  Sum_probs=81.2

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      .....++|||+||++++++++|+++|++||.|.+|+|+.++.+|+++|||||+|.+.++|++||+.|||..|+|+.|+|+
T Consensus        19 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   98 (106)
T 1p27_B           19 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD   98 (106)
T ss_dssp             CBTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEE
Confidence            44567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 040243          567 VAGKPP  572 (797)
Q Consensus       567 ~A~~~~  572 (797)
                      ||..+.
T Consensus        99 ~a~~~~  104 (106)
T 1p27_B           99 WCFVRG  104 (106)
T ss_dssp             ESEESS
T ss_pred             eecCCC
Confidence            997543

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=4.8e-17  Score=146.85  Aligned_cols=86  Identities=20%  Similarity=0.412  Sum_probs=80.3

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCC-CcccceEEEEecCHHHHHHHHHhcCceeeccceEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVT-GMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAV  565 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~T-GksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V  565 (797)
                      .....++|||+||++++++++|+++|++|| |.+|+|++++.+ |+++|||||+|.+.++|++|| .|++..|+|+.|+|
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            445678999999999999999999999999 999999999988 999999999999999999999 99999999999999


Q ss_pred             EecCCCCCC
Q 040243          566 RVAGKPPQP  574 (797)
Q Consensus       566 ~~A~~~~~~  574 (797)
                      +++..+...
T Consensus        89 ~~a~~~~~~   97 (104)
T 1wi8_A           89 DVADQAQDK   97 (104)
T ss_dssp             EECCCCCCC
T ss_pred             EEccCCCCC
Confidence            999876543

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.71  E-value=5.6e-17  Score=149.58  Aligned_cols=83  Identities=33%  Similarity=0.582  Sum_probs=79.0

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      .....++|||+||++++++++|+++|++||.|.+|+|++++.+|+++|||||+|.+.++|++||+.|||+.|+|+.|+|+
T Consensus        36 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~  115 (118)
T 2khc_A           36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQ  115 (118)
T ss_dssp             CCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            45677999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecC
Q 040243          567 VAG  569 (797)
Q Consensus       567 ~A~  569 (797)
                      |++
T Consensus       116 ~ak  118 (118)
T 2khc_A          116 LKK  118 (118)
T ss_dssp             EC-
T ss_pred             ecC
Confidence            974

>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=99.71  E-value=2.2e-17  Score=143.05  Aligned_cols=81  Identities=36%  Similarity=0.476  Sum_probs=78.2

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ...++|||+||++++++++|+++|++||.|.+|+|++++.+++++|||||+|.+.++|++|++.|||..|+|+.|+|+||
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            46789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             C
Q 040243          569 G  569 (797)
Q Consensus       569 ~  569 (797)
                      +
T Consensus        85 k   85 (85)
T 3mdf_A           85 K   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.71  E-value=2.8e-17  Score=146.47  Aligned_cols=86  Identities=26%  Similarity=0.516  Sum_probs=80.3

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCC---CCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRV---TGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~---TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      ..++|||+||++++++++|+++|++||.|.+|+|++++.   |++++|||||+|.+.++|++||+.|||..|+|+.|+|+
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   83 (98)
T 2cpf_A            4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVR   83 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            467899999999999999999999999999999999987   77999999999999999999999999999999999999


Q ss_pred             ecCCCCCCC
Q 040243          567 VAGKPPQPT  575 (797)
Q Consensus       567 ~A~~~~~~~  575 (797)
                      |+.......
T Consensus        84 ~a~~~~~~~   92 (98)
T 2cpf_A           84 ISERATKPA   92 (98)
T ss_dssp             CSSCSSCCC
T ss_pred             EccCCCCCC
Confidence            998766544

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.71  E-value=7.3e-18  Score=151.51  Aligned_cols=82  Identities=20%  Similarity=0.401  Sum_probs=76.4

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCC--EEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCce----eeccce
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGD--IVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGY----RLEGRT  562 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~--I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~----~l~Gr~  562 (797)
                      ..-.||||+||++++|+++|+++|++||.  |.+|+|++|+.||++||||||+|.+.++|++||+.|||.    .|+||.
T Consensus         7 ~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~   86 (95)
T 2lkz_A            7 HHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKT   86 (95)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEE
T ss_pred             CccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEE
Confidence            45569999999999999999999999995  678999999999999999999999999999999999986    599999


Q ss_pred             EEEEecCC
Q 040243          563 IAVRVAGK  570 (797)
Q Consensus       563 L~V~~A~~  570 (797)
                      |+|+||+.
T Consensus        87 i~V~~Aks   94 (95)
T 2lkz_A           87 IGVDFAKS   94 (95)
T ss_dssp             EEEEECCC
T ss_pred             EEEEEccC
Confidence            99999974

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=9.2e-17  Score=144.61  Aligned_cols=87  Identities=28%  Similarity=0.444  Sum_probs=79.7

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      .....++|||+||++++++++|+++|++||.|.+|+|+.++.  .++|||||+|.+.++|++||+.|+++.|+|+.|+|+
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            445678999999999999999999999999999999999864  389999999999999999999999999999999999


Q ss_pred             ecCCCCCCC
Q 040243          567 VAGKPPQPT  575 (797)
Q Consensus       567 ~A~~~~~~~  575 (797)
                      |+..+....
T Consensus        89 ~a~~~~~~~   97 (103)
T 2cq3_A           89 NATARVMTN   97 (103)
T ss_dssp             ECCSSCCCC
T ss_pred             EcccCCCCC
Confidence            998765544

>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=99.71  E-value=2.5e-17  Score=145.87  Aligned_cols=83  Identities=33%  Similarity=0.525  Sum_probs=78.3

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      .....++|||+||++++++++|+++|++||.|.+|+|..++. ++++|||||+|.+.++|++||+.||+..|+|+.|+|+
T Consensus        12 ~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   90 (95)
T 2ywk_A           12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVS   90 (95)
T ss_dssp             CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEE
Confidence            445678999999999999999999999999999999999985 9999999999999999999999999999999999999


Q ss_pred             ecCC
Q 040243          567 VAGK  570 (797)
Q Consensus       567 ~A~~  570 (797)
                      |++.
T Consensus        91 ~a~~   94 (95)
T 2ywk_A           91 GPSS   94 (95)
T ss_dssp             CCCC
T ss_pred             EcCC
Confidence            9864

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.71  E-value=3e-17  Score=154.87  Aligned_cols=87  Identities=21%  Similarity=0.429  Sum_probs=80.7

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEE--EEEEecCCCCcccceEEEEecCHHHHHHHHHhcCce----eecc
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVM--AKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGY----RLEG  560 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~--v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~----~l~G  560 (797)
                      .+...++|||+||++++++++|+++|++||.|..  |+|++|+.||++||||||+|.+. +|++||+.|||+    .|+|
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            4456789999999999999999999999999977  99999999999999999999999 999999999999    9999


Q ss_pred             ceEEEEecCCCCCC
Q 040243          561 RTIAVRVAGKPPQP  574 (797)
Q Consensus       561 r~L~V~~A~~~~~~  574 (797)
                      +.|+|+|++.....
T Consensus        98 r~l~V~~a~~~~~~  111 (131)
T 2m2b_A           98 KTINVEFAKGSKRD  111 (131)
T ss_dssp             CCCCCEECCCSCCC
T ss_pred             EEEEEEECCCCCCC
Confidence            99999999875443

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=2.8e-17  Score=145.76  Aligned_cols=86  Identities=37%  Similarity=0.606  Sum_probs=81.2

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEE-EEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMA-KVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v-~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ..++|||+||++++++++|+++|++||.|.+| +|++|+.+++++|||||+|.+.++|++||+.|||..|+|+.|+|+|+
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   83 (96)
T 1x5t_A            4 GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYA   83 (96)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            46799999999999999999999999999999 99999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCC
Q 040243          569 GKPPQPT  575 (797)
Q Consensus       569 ~~~~~~~  575 (797)
                      ..+....
T Consensus        84 ~~~~~~~   90 (96)
T 1x5t_A           84 FKKDSKG   90 (96)
T ss_dssp             CCCCCCC
T ss_pred             cccCCCC
Confidence            8766543

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=1.1e-16  Score=144.21  Aligned_cols=86  Identities=27%  Similarity=0.485  Sum_probs=79.0

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      .....++|||+||++++++++|+++|++||.|.+|+|++++.+  ++|||||+|.+.++|++||+.|++..|+|+.|+|+
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            4567889999999999999999999999999999999999643  79999999999999999999999999999999999


Q ss_pred             ecCCCCCC
Q 040243          567 VAGKPPQP  574 (797)
Q Consensus       567 ~A~~~~~~  574 (797)
                      |+..+...
T Consensus        89 ~a~~~~~~   96 (103)
T 2cqi_A           89 WATTPSSQ   96 (103)
T ss_dssp             ECCCTTCC
T ss_pred             ECCCCccc
Confidence            99876543

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=1.4e-16  Score=144.94  Aligned_cols=85  Identities=21%  Similarity=0.435  Sum_probs=77.3

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      .....++|||+||++++++++|+++|++||.|.+|+|..   +++++|||||+|.+.++|++||+.||++.|+|+.|+|+
T Consensus        18 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   94 (109)
T 1x4a_A           18 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN---RRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVE   94 (109)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECC---SSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEE---CCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            455678999999999999999999999999999999955   45689999999999999999999999999999999999


Q ss_pred             ecCCCCCC
Q 040243          567 VAGKPPQP  574 (797)
Q Consensus       567 ~A~~~~~~  574 (797)
                      |++.....
T Consensus        95 ~a~~~~~~  102 (109)
T 1x4a_A           95 FPRSGRGT  102 (109)
T ss_dssp             CCCCCCCC
T ss_pred             EcccCCCC
Confidence            99876543

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A

Probab=99.70  E-value=2.5e-17  Score=155.73  Aligned_cols=85  Identities=25%  Similarity=0.356  Sum_probs=80.6

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      ....++|||+||++++++++|+++|++||.|.+|+|++|+.+++++|||||+|.+.++|++||+.|||..|+|+.|+|+|
T Consensus        43 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~  122 (129)
T 2kxn_B           43 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF  122 (129)
T ss_dssp             CCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            34678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 040243          568 AGKPP  572 (797)
Q Consensus       568 A~~~~  572 (797)
                      +..+.
T Consensus       123 a~~~~  127 (129)
T 2kxn_B          123 SITKR  127 (129)
T ss_dssp             CSSSS
T ss_pred             ecCCC
Confidence            97654

>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=99.70  E-value=3.7e-17  Score=145.52  Aligned_cols=83  Identities=27%  Similarity=0.560  Sum_probs=79.4

Q ss_pred             CcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecCC
Q 040243          491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGK  570 (797)
Q Consensus       491 ~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~~  570 (797)
                      .++|||+||+.++++++|+++|++||.|.+|+|+.++.+|+++|||||+|.+.++|++||+.|+|..|+|+.|+|+||..
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   81 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSN   81 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCC
Confidence            46999999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CCC
Q 040243          571 PPQ  573 (797)
Q Consensus       571 ~~~  573 (797)
                      +..
T Consensus        82 ~~~   84 (96)
T 2x1f_A           82 SDI   84 (96)
T ss_dssp             SSG
T ss_pred             CCC
Confidence            653

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=1.4e-16  Score=143.34  Aligned_cols=87  Identities=26%  Similarity=0.466  Sum_probs=79.9

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      .....++|||+||++++++++|+++|++||.|.+|+|+.++.+|+++|||||+|.+.++|++||+  +++.|+|+.|+|+
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~   88 (103)
T 2cqg_A           11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCK   88 (103)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEE
T ss_pred             ccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEE
Confidence            44567899999999999999999999999999999999999999999999999999999999998  4789999999999


Q ss_pred             ecCCCCCCC
Q 040243          567 VAGKPPQPT  575 (797)
Q Consensus       567 ~A~~~~~~~  575 (797)
                      |+..+....
T Consensus        89 ~a~~~~~~~   97 (103)
T 2cqg_A           89 LPNSKQSQD   97 (103)
T ss_dssp             CCCTTCCCC
T ss_pred             ecCCCCcCC
Confidence            998765543

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.70  E-value=4.3e-17  Score=145.88  Aligned_cols=82  Identities=26%  Similarity=0.364  Sum_probs=78.6

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEE--------EEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeec
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVM--------AKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLE  559 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~--------v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~  559 (797)
                      ....++|||+||++++++++|+++|++||.|.+        |+|++|+.+|+++|||||+|.+.++|++||+.|||..|+
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~   89 (99)
T 2la6_A           10 HSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   89 (99)
T ss_dssp             CCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeC
Confidence            456789999999999999999999999999999        999999999999999999999999999999999999999


Q ss_pred             cceEEEEecC
Q 040243          560 GRTIAVRVAG  569 (797)
Q Consensus       560 Gr~L~V~~A~  569 (797)
                      |+.|+|++|+
T Consensus        90 g~~l~V~~A~   99 (99)
T 2la6_A           90 GNPIKVSFAT   99 (99)
T ss_dssp             SSBCEEEECC
T ss_pred             CcEEEEEecC
Confidence            9999999984

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens}

Probab=99.70  E-value=7.3e-17  Score=149.48  Aligned_cols=86  Identities=34%  Similarity=0.500  Sum_probs=80.8

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      ....++|||+||++++++++|+++|++||.|.+|+|+.++ +|+++|||||+|.+.++|++||+.|||..|+|+.|+|+|
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            4567899999999999999999999999999999999998 999999999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 040243          568 AGKPPQP  574 (797)
Q Consensus       568 A~~~~~~  574 (797)
                      ++.+...
T Consensus        83 a~~~~~~   89 (116)
T 2fy1_A           83 AKKPSFQ   89 (116)
T ss_dssp             CCCSSCS
T ss_pred             CCCCCCC
Confidence            9866543

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.70  E-value=9.5e-17  Score=152.24  Aligned_cols=89  Identities=35%  Similarity=0.563  Sum_probs=83.1

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      .....++|||+||++++++++|+++|++||.|.+|+|++++.++++||||||+|.+.++|++||+.|||..|+|+.|+|+
T Consensus        38 ~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  117 (139)
T 1u6f_A           38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA  117 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCCCC
Q 040243          567 VAGKPPQPT  575 (797)
Q Consensus       567 ~A~~~~~~~  575 (797)
                      |++......
T Consensus       118 ~a~~~~~~~  126 (139)
T 1u6f_A          118 LAASGHQRP  126 (139)
T ss_dssp             ESSCCCCCC
T ss_pred             ECCCCCCCC
Confidence            998765543

>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=99.70  E-value=3.3e-17  Score=146.01  Aligned_cols=83  Identities=19%  Similarity=0.304  Sum_probs=78.7

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ...++|||+||++++++++|+++|++||.|.+++++.++.+|+++|||||+|.+.++|++||+.|||..|+|+.|+|+++
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a   92 (98)
T 2cqp_A           13 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   92 (98)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEc
Confidence            45689999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCC
Q 040243          569 GKP  571 (797)
Q Consensus       569 ~~~  571 (797)
                      ..+
T Consensus        93 ~~~   95 (98)
T 2cqp_A           93 SGP   95 (98)
T ss_dssp             SCS
T ss_pred             CCC
Confidence            754

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.70  E-value=1.8e-17  Score=149.35  Aligned_cols=81  Identities=26%  Similarity=0.374  Sum_probs=77.8

Q ss_pred             CCcEEEEecCCC------CCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeecc-ce
Q 040243          490 DDTNLYIGYLPP------TLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEG-RT  562 (797)
Q Consensus       490 ~~~tLfVgNLp~------~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~G-r~  562 (797)
                      ..++|||+|||.      ++++++|+++|++||.|.+|+|++|+.||++||||||+|.+.++|++||+.|||+.|+| +.
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            467999999999      99999999999999999999999999999999999999999999999999999999999 99


Q ss_pred             EEEEecCC
Q 040243          563 IAVRVAGK  570 (797)
Q Consensus       563 L~V~~A~~  570 (797)
                      |+|.+|..
T Consensus        85 l~V~~a~~   92 (100)
T 3ns6_A           85 LFLYTMKD   92 (100)
T ss_dssp             CEEEESHH
T ss_pred             EEEEECch
Confidence            99999853

>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=99.70  E-value=4.3e-17  Score=148.53  Aligned_cols=86  Identities=27%  Similarity=0.410  Sum_probs=81.3

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      .....++|||+||++++++++|+++|++||.|.+|+|+.++.+|+++|||||+|.+.++|++||+.|+|..|+|+.|+|+
T Consensus        22 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  101 (110)
T 1oo0_B           22 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD  101 (110)
T ss_dssp             CBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            44567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 040243          567 VAGKPP  572 (797)
Q Consensus       567 ~A~~~~  572 (797)
                      |+..+.
T Consensus       102 ~a~~~~  107 (110)
T 1oo0_B          102 WCFVKG  107 (110)
T ss_dssp             ESEESS
T ss_pred             EcccCC
Confidence            997554

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.69  E-value=7.5e-17  Score=145.26  Aligned_cols=88  Identities=31%  Similarity=0.493  Sum_probs=81.5

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhc-CCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCcee-eccceEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFST-FGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYR-LEGRTIA  564 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~-fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~-l~Gr~L~  564 (797)
                      .....++|||+||++++++++|+++|++ ||.|.+|+|++|+ +|+++|||||+|.+.++|++||+.|++.. |+|+.|+
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~   83 (104)
T 2dhg_A            5 SSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVR   83 (104)
T ss_dssp             CSSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEE
Confidence            3456789999999999999999999999 9999999999999 99999999999999999999999999999 9999999


Q ss_pred             EEecCCCCCCC
Q 040243          565 VRVAGKPPQPT  575 (797)
Q Consensus       565 V~~A~~~~~~~  575 (797)
                      |+++..+....
T Consensus        84 v~~a~~~~~~~   94 (104)
T 2dhg_A           84 LSVAIPKASRV   94 (104)
T ss_dssp             CCBCCCCCSCC
T ss_pred             EEEccCCCcCC
Confidence            99997665443

>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=99.69  E-value=5.9e-17  Score=149.62  Aligned_cols=81  Identities=36%  Similarity=0.579  Sum_probs=75.6

Q ss_pred             CcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecCC
Q 040243          491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGK  570 (797)
Q Consensus       491 ~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~~  570 (797)
                      .++|||+||++++++++|+++|++||.|.+|+|++|+  +.+||||||+|.+.++|++||+.|+|+.|+|+.|+|+++..
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            4589999999999999999999999999999999996  55899999999999999999999999999999999999976


Q ss_pred             CCC
Q 040243          571 PPQ  573 (797)
Q Consensus       571 ~~~  573 (797)
                      +..
T Consensus        83 ~~~   85 (115)
T 4f25_A           83 RKE   85 (115)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            543

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.69  E-value=3.6e-16  Score=145.73  Aligned_cols=87  Identities=24%  Similarity=0.336  Sum_probs=81.0

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      ....++|||+||++++++++|+++|++||.|.+|+|+.++ +|+++|||||+|.+.++|++||+.|||..|+|+.|+|+|
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            3467899999999999999999999999999999999998 999999999999999999999999999999999999999


Q ss_pred             cCCCCCCC
Q 040243          568 AGKPPQPT  575 (797)
Q Consensus       568 A~~~~~~~  575 (797)
                      |.......
T Consensus       111 a~~~~~~~  118 (124)
T 2kt5_A          111 VASQIDLE  118 (124)
T ss_dssp             ECCTTCCC
T ss_pred             eCCCCCCC
Confidence            98655433

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=6.1e-17  Score=144.58  Aligned_cols=84  Identities=33%  Similarity=0.603  Sum_probs=79.8

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEE-EEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccce----E
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIV-MAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRT----I  563 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~-~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~----L  563 (797)
                      ...++|||+||++++++++|+++|++||.|. +|+|++|+.+++++|||||+|.+.++|++||+.|||..|+|+.    |
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~l   86 (99)
T 2div_A            7 GMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRF   86 (99)
T ss_dssp             SSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEEC
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcceeE
Confidence            4578999999999999999999999999999 9999999999999999999999999999999999999999999    9


Q ss_pred             EEEecCCCC
Q 040243          564 AVRVAGKPP  572 (797)
Q Consensus       564 ~V~~A~~~~  572 (797)
                      +|+||+...
T Consensus        87 ~v~~a~~~~   95 (99)
T 2div_A           87 KLNYATYSG   95 (99)
T ss_dssp             CEEETTCCS
T ss_pred             EEeecCCCC
Confidence            999997554

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.69  E-value=5.3e-17  Score=158.56  Aligned_cols=82  Identities=28%  Similarity=0.428  Sum_probs=77.3

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCC--CEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFG--DIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG--~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      ...++|||+||++++++++|+++|++||  .|.+|+|++|+.||++||||||+|.+.++|++||+.|||+.|+|+.|+|+
T Consensus        53 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~  132 (156)
T 3n9u_C           53 NRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVR  132 (156)
T ss_dssp             ---CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEE
Confidence            3568999999999999999999999999  99999999999999999999999999999999999999999999999999


Q ss_pred             ecCC
Q 040243          567 VAGK  570 (797)
Q Consensus       567 ~A~~  570 (797)
                      +|..
T Consensus       133 ~a~~  136 (156)
T 3n9u_C          133 PATR  136 (156)
T ss_dssp             ECCH
T ss_pred             EcCC
Confidence            9864

>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=99.69  E-value=9.3e-17  Score=140.02  Aligned_cols=81  Identities=28%  Similarity=0.518  Sum_probs=76.3

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      .+...++|||+||++++++++|+++|++||.|.+|+|++++.||+++|||||+|.+.++|++||+ +++..|+|+.|+|+
T Consensus         7 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~   85 (87)
T 3s7r_A            7 NEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPK   85 (87)
T ss_dssp             CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEE
Confidence            44577899999999999999999999999999999999999999999999999999999999996 58889999999999


Q ss_pred             ec
Q 040243          567 VA  568 (797)
Q Consensus       567 ~A  568 (797)
                      +|
T Consensus        86 ~A   87 (87)
T 3s7r_A           86 KA   87 (87)
T ss_dssp             EC
T ss_pred             eC
Confidence            86

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens}

Probab=99.69  E-value=8.4e-17  Score=147.21  Aligned_cols=84  Identities=33%  Similarity=0.612  Sum_probs=80.1

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      ....++|||+||+.++++++|+++|++||.|.+|+|++++.+|+++|||||+|.+.++|++||+.|+|..|+|+.|+|++
T Consensus        23 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~  102 (108)
T 2jrs_A           23 SAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGH  102 (108)
T ss_dssp             CSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 040243          568 AGKP  571 (797)
Q Consensus       568 A~~~  571 (797)
                      ++.+
T Consensus       103 a~~k  106 (108)
T 2jrs_A          103 VTER  106 (108)
T ss_dssp             SCSS
T ss_pred             cccC
Confidence            9765

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.69  E-value=1.1e-16  Score=146.88  Aligned_cols=87  Identities=18%  Similarity=0.279  Sum_probs=79.9

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHH---HHhhcCCCEEEEEEEecCCCC---cccceEEEEecCHHHHHHHHHhcCceeecc
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLI---RLFSTFGDIVMAKVIKDRVTG---MSKGYGFVKYADIQMANNAIASMNGYRLEG  560 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~---~~Fs~fG~I~~v~v~~dk~TG---ksrGfaFV~F~s~e~A~~AI~~LnG~~l~G  560 (797)
                      +....++|||+||++++++++|+   ++|++||.|.+|+|++++.++   +++|||||+|.+.++|++||+.|||+.|+|
T Consensus        11 r~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~g   90 (111)
T 2cpi_A           11 RVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDG   90 (111)
T ss_dssp             CCCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             cccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECC
Confidence            45567899999999999999999   999999999999999998755   456999999999999999999999999999


Q ss_pred             ceEEEEecCCCCC
Q 040243          561 RTIAVRVAGKPPQ  573 (797)
Q Consensus       561 r~L~V~~A~~~~~  573 (797)
                      +.|+|+||..+..
T Consensus        91 r~l~V~~a~~k~~  103 (111)
T 2cpi_A           91 RTLKASLGTTKYC  103 (111)
T ss_dssp             EEEEEESCCCCSC
T ss_pred             EEEEEEecccccc
Confidence            9999999987653

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.68  E-value=4.1e-17  Score=155.34  Aligned_cols=88  Identities=30%  Similarity=0.463  Sum_probs=82.5

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      .....++|||+||++++++++|+++|++||.|.+|+|+.++.+++++|||||+|.+.++|++||+.|||..|+|+.|+|+
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            45567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCCC
Q 040243          567 VAGKPPQP  574 (797)
Q Consensus       567 ~A~~~~~~  574 (797)
                      |++.....
T Consensus       123 ~a~~~~~~  130 (135)
T 2lea_A          123 MARYGRPP  130 (135)
T ss_dssp             ECCCCCCC
T ss_pred             ECCCCCCC
Confidence            99865543

>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=99.68  E-value=3.5e-17  Score=147.25  Aligned_cols=85  Identities=31%  Similarity=0.577  Sum_probs=80.6

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      +...++|||+||++++++++|+++|++||.|.+|+|+.++.+|+++|||||+|.+.++|++||+.|||..|+|+.|+|+|
T Consensus         5 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   84 (104)
T 1p1t_A            5 DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDN   84 (104)
T ss_dssp             HHHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEE
T ss_pred             CCCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Confidence            34568999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 040243          568 AGKPP  572 (797)
Q Consensus       568 A~~~~  572 (797)
                      +....
T Consensus        85 a~~~~   89 (104)
T 1p1t_A           85 AASEK   89 (104)
T ss_dssp             TTCTT
T ss_pred             CCCcc
Confidence            98655

>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=99.68  E-value=1.2e-16  Score=139.65  Aligned_cols=82  Identities=18%  Similarity=0.417  Sum_probs=78.1

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      .+.++|||+||++++++++|+++|++||.|.+|++..++.+++++|||||+|.+.++|++|+ .|+|..|+|+.|+|+++
T Consensus         4 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a   82 (89)
T 3ucg_A            4 ADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPK   82 (89)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEET
T ss_pred             CcCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEc
Confidence            35679999999999999999999999999999999999999999999999999999999999 89999999999999998


Q ss_pred             CCC
Q 040243          569 GKP  571 (797)
Q Consensus       569 ~~~  571 (797)
                      +..
T Consensus        83 ~~~   85 (89)
T 3ucg_A           83 RTN   85 (89)
T ss_dssp             TTT
T ss_pred             cCC
Confidence            753

>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=99.68  E-value=9e-17  Score=139.86  Aligned_cols=83  Identities=29%  Similarity=0.529  Sum_probs=78.0

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCc-ccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGM-SKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGk-srGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ..++|||+||+.++++++|+++|++||.|.+|+|+.++.++. ++|||||+|.+.++|++|++.|||..|+|+.|+|+++
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            467999999999999999999999999999999999988777 9999999999999999999999999999999999999


Q ss_pred             CCCC
Q 040243          569 GKPP  572 (797)
Q Consensus       569 ~~~~  572 (797)
                      ..+.
T Consensus        83 ~~~~   86 (88)
T 4a8x_A           83 LAPW   86 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7543

>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=99.68  E-value=1.6e-16  Score=143.89  Aligned_cols=80  Identities=28%  Similarity=0.397  Sum_probs=77.4

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ...++|||+||++++++++|+++|++||.|.+|+|+.++ +|+++|||||+|.+.++|++||+.|+|..|+|+.|+|+||
T Consensus        27 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  105 (107)
T 3ulh_A           27 ETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLV  105 (107)
T ss_dssp             CCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEe
Confidence            467899999999999999999999999999999999998 9999999999999999999999999999999999999998


Q ss_pred             C
Q 040243          569 G  569 (797)
Q Consensus       569 ~  569 (797)
                      .
T Consensus       106 ~  106 (107)
T 3ulh_A          106 T  106 (107)
T ss_dssp             C
T ss_pred             C
Confidence            5

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=2.1e-16  Score=145.48  Aligned_cols=87  Identities=21%  Similarity=0.416  Sum_probs=80.8

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      ....++|||+||++++++++|+++|++||.|.+|+|+.++.+++++|||||+|.+.++|++||+. +++.|+|+.|+|++
T Consensus        24 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~  102 (116)
T 1x4b_A           24 KEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKR  102 (116)
T ss_dssp             HHHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEEC
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEE
Confidence            34568999999999999999999999999999999999999999999999999999999999987 99999999999999


Q ss_pred             cCCCCCCC
Q 040243          568 AGKPPQPT  575 (797)
Q Consensus       568 A~~~~~~~  575 (797)
                      +..+....
T Consensus       103 a~~~~~~~  110 (116)
T 1x4b_A          103 AVAREESG  110 (116)
T ss_dssp             CSSCCCCC
T ss_pred             CCCCccCC
Confidence            98765543

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=2.7e-16  Score=141.03  Aligned_cols=84  Identities=29%  Similarity=0.453  Sum_probs=76.0

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      .....++|||+||++++++++|+++|++||.|   +++.+ .+++++|||||+|.+.++|++||+.||++.|+|+.|+|+
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            34567899999999999999999999999987   56666 589999999999999999999999999999999999999


Q ss_pred             ecCCCCCC
Q 040243          567 VAGKPPQP  574 (797)
Q Consensus       567 ~A~~~~~~  574 (797)
                      |++.+...
T Consensus        87 ~a~~~~~~   94 (101)
T 2fc9_A           87 LQGPRGSP   94 (101)
T ss_dssp             ECSSCCCC
T ss_pred             EcCCCCCC
Confidence            99876543

>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=99.67  E-value=1.6e-16  Score=141.80  Aligned_cols=82  Identities=16%  Similarity=0.232  Sum_probs=76.5

Q ss_pred             CCCcEEEEecCCCCCcHHHHH----HHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEE
Q 040243          489 LDDTNLYIGYLPPTLDDDGLI----RLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIA  564 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~----~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~  564 (797)
                      .+.++|||+||++++++++|+    ++|++||.|.+|+|+.|+.+   ||||||+|.+.++|++||+.|||..|+|+.|+
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~   83 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKIL   83 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            356899999999999999999    99999999999999999865   89999999999999999999999999999999


Q ss_pred             EEecCCCCC
Q 040243          565 VRVAGKPPQ  573 (797)
Q Consensus       565 V~~A~~~~~  573 (797)
                      |++|+....
T Consensus        84 V~~a~~~~~   92 (96)
T 2dgx_A           84 VSLATGASG   92 (96)
T ss_dssp             EEECCCSSC
T ss_pred             EEEcCCCCC
Confidence            999976544

>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=99.67  E-value=5e-17  Score=143.84  Aligned_cols=81  Identities=19%  Similarity=0.282  Sum_probs=76.6

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      ..++|||+||++++++++|+++|++||.|.+++++.++.+++++|||||+|.+.++|++||+.||++.|+|+.|+|+++.
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            45899999999999999999999999999999999999999999999999999999999999999999999999999976


Q ss_pred             C
Q 040243          570 K  570 (797)
Q Consensus       570 ~  570 (797)
                      .
T Consensus        94 s   94 (95)
T 2ek1_A           94 S   94 (95)
T ss_dssp             -
T ss_pred             C
Confidence            3

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*

Probab=99.67  E-value=1.1e-16  Score=149.23  Aligned_cols=88  Identities=25%  Similarity=0.409  Sum_probs=82.2

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      .....++|||+||++++++++|+++|++||.|.+|+|+.++.+++++|||||+|.+.++|++||+.|||..|+|+.|+|+
T Consensus        18 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   97 (126)
T 3ex7_B           18 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD   97 (126)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            44567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCCC
Q 040243          567 VAGKPPQP  574 (797)
Q Consensus       567 ~A~~~~~~  574 (797)
                      ||......
T Consensus        98 ~a~~~~~~  105 (126)
T 3ex7_B           98 WCFVRGPP  105 (126)
T ss_dssp             ESEESSSC
T ss_pred             EecCCCCC
Confidence            99765543

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=4.1e-16  Score=142.88  Aligned_cols=83  Identities=28%  Similarity=0.610  Sum_probs=78.0

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceee--------
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRL--------  558 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l--------  558 (797)
                      .+...++|||+||++++++++|+++|++||.|.+|+|+.++ +++++|||||+|.+.++|++||+.|||..|        
T Consensus        21 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~   99 (114)
T 1x5o_A           21 QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSA   99 (114)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccC
Confidence            44567899999999999999999999999999999999998 999999999999999999999999999999        


Q ss_pred             ccceEEEEecCC
Q 040243          559 EGRTIAVRVAGK  570 (797)
Q Consensus       559 ~Gr~L~V~~A~~  570 (797)
                      .++.|+|+||..
T Consensus       100 ~~~~l~v~~a~p  111 (114)
T 1x5o_A          100 PTEPLLCKFSGP  111 (114)
T ss_dssp             CSSCBEEEECCC
T ss_pred             CCCceeEEccCC
Confidence            578899999974

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.67  E-value=1.8e-16  Score=139.39  Aligned_cols=83  Identities=29%  Similarity=0.474  Sum_probs=77.8

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ...++|||+||++++++++|+++|++||.|.+|+|.++  +++++|||||+|.+.++|++||+.|++..|+|+.|+|+|+
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            45789999999999999999999999999999999985  8999999999999999999999999999999999999999


Q ss_pred             CCCCC
Q 040243          569 GKPPQ  573 (797)
Q Consensus       569 ~~~~~  573 (797)
                      +....
T Consensus        84 ~~~~~   88 (92)
T 2dgv_A           84 RNASG   88 (92)
T ss_dssp             SCCSS
T ss_pred             CCCCC
Confidence            86554

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=1.2e-16  Score=146.63  Aligned_cols=84  Identities=29%  Similarity=0.440  Sum_probs=79.1

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      +...++|||+||++++++++|+++|++||.|.+|+|+.|+.+++++|||||+|.+.++|++|| .|||+.|+|+.|+|+|
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~  100 (114)
T 2cq4_A           22 ERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQA  100 (114)
T ss_dssp             HHHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEe
Confidence            345689999999999999999999999999999999999999999999999999999999999 9999999999999999


Q ss_pred             cCCCC
Q 040243          568 AGKPP  572 (797)
Q Consensus       568 A~~~~  572 (797)
                      +....
T Consensus       101 a~~~~  105 (114)
T 2cq4_A          101 SQAEK  105 (114)
T ss_dssp             HHHHH
T ss_pred             cCCCc
Confidence            86543

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=3.3e-16  Score=137.81  Aligned_cols=82  Identities=17%  Similarity=0.324  Sum_probs=77.4

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      ....++|||+||++++++++|+++|+.| .|.+|+|+++ .+|+++|||||+|.+.++|++||+ |||..|+|+.|+|.+
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~   83 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFR   83 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEE
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEE
Confidence            3567899999999999999999999999 9999999999 699999999999999999999999 999999999999999


Q ss_pred             cCCCC
Q 040243          568 AGKPP  572 (797)
Q Consensus       568 A~~~~  572 (797)
                      +..+.
T Consensus        84 a~~~~   88 (91)
T 2dgw_A           84 EKSGP   88 (91)
T ss_dssp             ESSCC
T ss_pred             CCcCC
Confidence            98654

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.67  E-value=2.1e-16  Score=144.65  Aligned_cols=85  Identities=27%  Similarity=0.451  Sum_probs=76.8

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      ....++|||+||++++++++|+++|++||.|.+|+|++++.||++||||||+|.+.++|++||+.+ +..|+|+.|+|++
T Consensus        22 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~~  100 (109)
T 2rs2_A           22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPKV  100 (109)
T ss_dssp             ----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEEE
Confidence            345789999999999999999999999999999999999999999999999999999999999976 5999999999999


Q ss_pred             cCCCCC
Q 040243          568 AGKPPQ  573 (797)
Q Consensus       568 A~~~~~  573 (797)
                      +..+..
T Consensus       101 a~~~~~  106 (109)
T 2rs2_A          101 AFPRRA  106 (109)
T ss_dssp             CCCCCC
T ss_pred             ccCCCC
Confidence            986543

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=4.9e-17  Score=141.16  Aligned_cols=80  Identities=29%  Similarity=0.515  Sum_probs=76.7

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      ..++|||+||++++++++|+++|++||.|.+|+|+.++.+++++|||||+|.+.++|++||+.|||..|+|+.|+|+++.
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~~   83 (85)
T 1x4e_A            4 GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGPS   83 (85)
T ss_dssp             CCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCCC
Confidence            46799999999999999999999999999999999999999999999999999999999999999999999999988764

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C

Probab=99.67  E-value=5.7e-17  Score=167.84  Aligned_cols=81  Identities=26%  Similarity=0.393  Sum_probs=77.2

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCC--CEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFG--DIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG--~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      ..++|||+||++++++++|+++|++||  .|.+|+|++|+.||++||||||+|.+.++|++||+.||++.|+|+.|+|+|
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~  146 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTP  146 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEE
Confidence            567999999999999999999999999  999999999999999999999999999999999999999999999999999


Q ss_pred             cCC
Q 040243          568 AGK  570 (797)
Q Consensus       568 A~~  570 (797)
                      |+.
T Consensus       147 a~~  149 (229)
T 3q2s_C          147 VNK  149 (229)
T ss_dssp             CCH
T ss_pred             CCC
Confidence            865

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=2.9e-16  Score=142.59  Aligned_cols=85  Identities=20%  Similarity=0.287  Sum_probs=79.3

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCC-EEEEEEE-ecCCCCcccceEEEEecCHHHHHHHHHhcC--ceeeccceEE
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGD-IVMAKVI-KDRVTGMSKGYGFVKYADIQMANNAIASMN--GYRLEGRTIA  564 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~-I~~v~v~-~dk~TGksrGfaFV~F~s~e~A~~AI~~Ln--G~~l~Gr~L~  564 (797)
                      ...++|||+||++++++++|+++|++||. |.+|.|+ .++.+|++||||||+|.+.++|++||+.|+  +..|+|+.|+
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            46789999999999999999999999998 9999998 899999999999999999999999999996  5899999999


Q ss_pred             EEecCCCCC
Q 040243          565 VRVAGKPPQ  573 (797)
Q Consensus       565 V~~A~~~~~  573 (797)
                      |+||.....
T Consensus        86 V~~a~~~~~   94 (109)
T 2dis_A           86 VDWAEPEID   94 (109)
T ss_dssp             EEESCSSCS
T ss_pred             EEEcCCCCC
Confidence            999986654

>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=99.66  E-value=1.4e-16  Score=152.42  Aligned_cols=82  Identities=16%  Similarity=0.112  Sum_probs=76.9

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCC---EEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGD---IVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTI  563 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~---I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L  563 (797)
                      .....++|||+||++++|+++|+++|++||.   |.+|+|++|+. |++||||||+|.+.++|++||+ ||+..|+|+.|
T Consensus        40 ~~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i  117 (136)
T 2hgl_A           40 EGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRYI  117 (136)
T ss_dssp             SCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEE
Confidence            3456789999999999999999999999999   89999999986 9999999999999999999999 99999999999


Q ss_pred             EEEecCC
Q 040243          564 AVRVAGK  570 (797)
Q Consensus       564 ~V~~A~~  570 (797)
                      +|.++..
T Consensus       118 ~V~~a~~  124 (136)
T 2hgl_A          118 EVFKSHR  124 (136)
T ss_dssp             EEEECCH
T ss_pred             EEEECCh
Confidence            9999864

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=3.8e-16  Score=141.51  Aligned_cols=83  Identities=20%  Similarity=0.313  Sum_probs=76.9

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEE-EEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVM-AKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~-v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      ....++|||+||++++++++|+++|++||.|.+ |+|+.+ .+|+++|||||+|.+.++|++||+. ++..|+|+.|+|.
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~   89 (104)
T 1wg5_A           12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIF   89 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEE
Confidence            456789999999999999999999999999998 889898 6999999999999999999999987 9999999999999


Q ss_pred             ecCCCC
Q 040243          567 VAGKPP  572 (797)
Q Consensus       567 ~A~~~~  572 (797)
                      ++....
T Consensus        90 ~~~~~~   95 (104)
T 1wg5_A           90 KSSRAE   95 (104)
T ss_dssp             EECTTT
T ss_pred             ECCHHH
Confidence            987544

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.66  E-value=6.9e-17  Score=136.92  Aligned_cols=75  Identities=17%  Similarity=0.416  Sum_probs=72.8

Q ss_pred             EEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       493 tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      +|||+||++++++++|+++|++||.|.+|++..++.+|+++|||||+|.+.++|++|++ |++..|+|+.|+|++|
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            59999999999999999999999999999999999999999999999999999999997 9999999999999986

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=1.3e-16  Score=149.08  Aligned_cols=83  Identities=19%  Similarity=0.237  Sum_probs=76.8

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      ....++|||+||++++++++|+++|+.||.|.++.++.+..+|+++|||||+|.+.++|++||+ ||+..|+|+.|+|.+
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~  100 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHP  100 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEE
Confidence            3466899999999999999999999999999997777777899999999999999999999999 999999999999999


Q ss_pred             cCCC
Q 040243          568 AGKP  571 (797)
Q Consensus       568 A~~~  571 (797)
                      +..+
T Consensus       101 a~~~  104 (124)
T 1wel_A          101 ITKK  104 (124)
T ss_dssp             ECHH
T ss_pred             CCHH
Confidence            8653

>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=99.66  E-value=6.9e-16  Score=140.61  Aligned_cols=79  Identities=22%  Similarity=0.365  Sum_probs=73.8

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeecc-----ce
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEG-----RT  562 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~G-----r~  562 (797)
                      ....++|||+||++++++++|+++|++||.|.+|+|+.|       |||||+|.+.++|++||+.||++.|+|     +.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~   84 (108)
T 1x4c_A           12 RRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAY   84 (108)
T ss_dssp             CSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceE
Confidence            346789999999999999999999999999999999887       899999999999999999999999999     99


Q ss_pred             EEEEecCCCCC
Q 040243          563 IAVRVAGKPPQ  573 (797)
Q Consensus       563 L~V~~A~~~~~  573 (797)
                      |+|++|..+..
T Consensus        85 i~V~~a~~~~~   95 (108)
T 1x4c_A           85 IRVKVDGPRSP   95 (108)
T ss_dssp             EEEEESSCCSC
T ss_pred             EEEEeCCCCCC
Confidence            99999987544

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=2.8e-16  Score=142.48  Aligned_cols=82  Identities=15%  Similarity=0.186  Sum_probs=75.4

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      ....++|||+||++++++++|+++|++||. ++|+|++|+ +|++||||||+|.+.++|++||+ +|+..|+|+.|+|.+
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 STTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFL   88 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCc-eEEEEEECC-CCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEE
Confidence            346689999999999999999999999994 599999998 99999999999999999999995 799999999999999


Q ss_pred             cCCCC
Q 040243          568 AGKPP  572 (797)
Q Consensus       568 A~~~~  572 (797)
                      +....
T Consensus        89 ~~~~~   93 (102)
T 1wez_A           89 NSTAG   93 (102)
T ss_dssp             ECCCC
T ss_pred             CCCCC
Confidence            87554

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=2e-16  Score=145.70  Aligned_cols=83  Identities=16%  Similarity=0.194  Sum_probs=77.7

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCE-EEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDI-VMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I-~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      ....++|||+||++++++++|+++|+.||.| .+|+|++|+ +|++||||||+|.+.++|++||+. |+..|+|+.|+|.
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            4567899999999999999999999999999 899999999 999999999999999999999987 9999999999999


Q ss_pred             ecCCCC
Q 040243          567 VAGKPP  572 (797)
Q Consensus       567 ~A~~~~  572 (797)
                      ++..+.
T Consensus        90 ~a~~~~   95 (114)
T 2cpy_A           90 VVTLED   95 (114)
T ss_dssp             EECHHH
T ss_pred             ECCHHH
Confidence            987544

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori}

Probab=99.66  E-value=3.6e-17  Score=143.50  Aligned_cols=82  Identities=34%  Similarity=0.536  Sum_probs=74.6

Q ss_pred             cEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecCCC
Q 040243          492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKP  571 (797)
Q Consensus       492 ~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~~~  571 (797)
                      ++|||+||+.++++++|+++|++||.|.+|+|.+++.+|+++|||||+|.+.+ |++|++.|||..|+|+.|+|++|...
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            58999999999999999999999999999999999999999999999999999 99999999999999999999999865


Q ss_pred             CCC
Q 040243          572 PQP  574 (797)
Q Consensus       572 ~~~  574 (797)
                      ...
T Consensus        81 ~~~   83 (90)
T 2ki2_A           81 KSL   83 (90)
T ss_dssp             ---
T ss_pred             CCC
Confidence            543

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.66  E-value=3.6e-16  Score=145.36  Aligned_cols=83  Identities=25%  Similarity=0.462  Sum_probs=78.6

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ...++|||+||++++++++|+++|++||.|.+|+|++++.+|+++|||||+|.+.++|++|| .|+|..|+|+.|+|+|+
T Consensus        34 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a  112 (124)
T 2jwn_A           34 IDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPK  112 (124)
T ss_dssp             HHHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEEC
Confidence            35689999999999999999999999999999999999999999999999999999999999 79999999999999999


Q ss_pred             CCCC
Q 040243          569 GKPP  572 (797)
Q Consensus       569 ~~~~  572 (797)
                      +...
T Consensus       113 ~~~~  116 (124)
T 2jwn_A          113 RTNM  116 (124)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            7544

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.65  E-value=4.9e-16  Score=139.44  Aligned_cols=85  Identities=24%  Similarity=0.380  Sum_probs=77.9

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      .....++|||+||++++++++|+++|+.|+   +|+++.++.+++++|||||+|.+.++|++||+.||++.|+|+.|+|+
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   87 (102)
T 2fc8_A           11 RSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLD   87 (102)
T ss_dssp             SSCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            445678999999999999999999999874   67888999999999999999999999999999999999999999999


Q ss_pred             ecCCCCCC
Q 040243          567 VAGKPPQP  574 (797)
Q Consensus       567 ~A~~~~~~  574 (797)
                      |++.+...
T Consensus        88 ~a~~~~~~   95 (102)
T 2fc8_A           88 WAKPKGEG   95 (102)
T ss_dssp             ECCCCCSS
T ss_pred             EecCCCCC
Confidence            99876554

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=2.1e-16  Score=143.85  Aligned_cols=81  Identities=15%  Similarity=0.269  Sum_probs=76.3

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      .+...++|||+||++++|+++|+++|++||.|.+|+|++|+. |++||||||+|.+.++|++||+ +++..|+|+.|+|.
T Consensus         7 ~~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~   84 (103)
T 1s79_A            7 NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLIL   84 (103)
T ss_dssp             SCSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEE
T ss_pred             ccCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEE
Confidence            445678999999999999999999999999999999999986 9999999999999999999998 89999999999999


Q ss_pred             ecC
Q 040243          567 VAG  569 (797)
Q Consensus       567 ~A~  569 (797)
                      |+.
T Consensus        85 ~~~   87 (103)
T 1s79_A           85 FKD   87 (103)
T ss_dssp             EHH
T ss_pred             Ech
Confidence            864

>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=99.65  E-value=1e-16  Score=144.22  Aligned_cols=83  Identities=22%  Similarity=0.430  Sum_probs=75.8

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecC-CCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDR-VTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk-~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      ....++|||+||++++++++|+++|++|| |.+|+|++++ .+|+++|||||+|.+.++|++|| .|+|..|+|+.|+|+
T Consensus        16 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V~   93 (100)
T 2j76_E           16 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVD   93 (100)
T ss_dssp             ----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCCE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEEE
Confidence            35678999999999999999999999999 9999999998 69999999999999999999999 899999999999999


Q ss_pred             ecCCCC
Q 040243          567 VAGKPP  572 (797)
Q Consensus       567 ~A~~~~  572 (797)
                      +++...
T Consensus        94 ~a~~~~   99 (100)
T 2j76_E           94 VADQAQ   99 (100)
T ss_dssp             ECCCSC
T ss_pred             eccCCC
Confidence            997653

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X

Probab=99.65  E-value=4.3e-16  Score=150.88  Aligned_cols=85  Identities=28%  Similarity=0.388  Sum_probs=80.8

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ...++|||+||++++++++|+++|++||.|.+|+|+.++.|++++|||||+|.+.++|++||+.||++.|+|+.|+|+||
T Consensus        37 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  116 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD  116 (156)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCC
Q 040243          569 GKPPQ  573 (797)
Q Consensus       569 ~~~~~  573 (797)
                      .....
T Consensus       117 ~~~~~  121 (156)
T 1h2v_Z          117 AGFKE  121 (156)
T ss_dssp             SCCCT
T ss_pred             CCCCC
Confidence            86543

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.65  E-value=2.8e-16  Score=145.94  Aligned_cols=83  Identities=16%  Similarity=0.119  Sum_probs=77.3

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCC---EEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGD---IVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTI  563 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~---I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L  563 (797)
                      .....++|||+||++++++++|+++|+.||.   |.+|+|++|+. |++||||||+|.+.++|++||+ |+++.|+|+.|
T Consensus        13 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i   90 (118)
T 2db1_A           13 EGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDRESMGHRYI   90 (118)
T ss_dssp             CBCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEE
Confidence            3456789999999999999999999999999   89999999986 9999999999999999999998 99999999999


Q ss_pred             EEEecCCC
Q 040243          564 AVRVAGKP  571 (797)
Q Consensus       564 ~V~~A~~~  571 (797)
                      +|.++...
T Consensus        91 ~V~~a~~~   98 (118)
T 2db1_A           91 EVFKSHRT   98 (118)
T ss_dssp             EEEEECHH
T ss_pred             EEEECCHH
Confidence            99998654

>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=99.65  E-value=3.5e-16  Score=151.34  Aligned_cols=85  Identities=29%  Similarity=0.455  Sum_probs=80.5

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ...++|||+||++++++++|+++|++||.|.+|+|++|+.+|+++|||||+|.+.++|++||+.|||..|+|+.|+|+||
T Consensus        68 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  147 (158)
T 2kn4_A           68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA  147 (158)
T ss_dssp             CBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            35679999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCC
Q 040243          569 GKPPQ  573 (797)
Q Consensus       569 ~~~~~  573 (797)
                      .....
T Consensus       148 ~~~~~  152 (158)
T 2kn4_A          148 RYGRP  152 (158)
T ss_dssp             CCSSC
T ss_pred             CCCCC
Confidence            86543

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.65  E-value=9.5e-17  Score=136.42  Aligned_cols=76  Identities=30%  Similarity=0.554  Sum_probs=73.8

Q ss_pred             cEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       492 ~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ++|||+||++++++++|+++|++||.|.+|++..++.+|+++|||||+|.+.++|++|++.++ ..|+|+.|+|++|
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            479999999999999999999999999999999999999999999999999999999999999 9999999999997

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.64  E-value=5.8e-16  Score=141.06  Aligned_cols=81  Identities=16%  Similarity=0.130  Sum_probs=72.9

Q ss_pred             CCCCcEEEEecCCC-CCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCce--eeccceEE
Q 040243          488 ELDDTNLYIGYLPP-TLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGY--RLEGRTIA  564 (797)
Q Consensus       488 ~~~~~tLfVgNLp~-~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~--~l~Gr~L~  564 (797)
                      ....++|||+||++ .+++++|+++|++||.|.+|+|++++      |||||+|.+.++|++||+.|++.  .|+|+.|+
T Consensus        12 ~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~k------g~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~   85 (102)
T 1x4d_A           12 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI------NEAFIEMATTEDAQAAVDYYTTTPALVFGKPVR   85 (102)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS------SCEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcCC------CEEEEEECCHHHHHHHHHHHcCCCceECCcEEE
Confidence            34678999999999 99999999999999999999998764      89999999999999999999875  59999999


Q ss_pred             EEecCCCCCC
Q 040243          565 VRVAGKPPQP  574 (797)
Q Consensus       565 V~~A~~~~~~  574 (797)
                      |.||+.....
T Consensus        86 V~~a~~~~~~   95 (102)
T 1x4d_A           86 VHLSQKYKRI   95 (102)
T ss_dssp             EEEECCCTTS
T ss_pred             EEECCCCCCC
Confidence            9999865543

>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=99.63  E-value=6.1e-16  Score=151.56  Aligned_cols=87  Identities=26%  Similarity=0.404  Sum_probs=81.0

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      .....++|||+||++++++++|+++|++||.|..|.|+.++.||+++|||||+|.+.++|++||+.|||..|.|+.|+|.
T Consensus        68 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  147 (165)
T 1rk8_A           68 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD  147 (165)
T ss_dssp             CCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            45567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 040243          567 VAGKPPQ  573 (797)
Q Consensus       567 ~A~~~~~  573 (797)
                      |+.....
T Consensus       148 ~a~~~~~  154 (165)
T 1rk8_A          148 WCFVKGP  154 (165)
T ss_dssp             ESEECC-
T ss_pred             EecCCCC
Confidence            9976544

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.63  E-value=6.2e-16  Score=140.35  Aligned_cols=82  Identities=26%  Similarity=0.395  Sum_probs=75.6

Q ss_pred             CCCCcEEEEecCCCCC------cHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccc
Q 040243          488 ELDDTNLYIGYLPPTL------DDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGR  561 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~v------te~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr  561 (797)
                      +...++|||+||++.+      ++++|+++|++||.|.+|+|.  +.+|++||||||+|.+.++|++||+.|||+.|+|+
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~   89 (105)
T 2nlw_A           12 DGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ   89 (105)
T ss_dssp             CSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTT
T ss_pred             CCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCC
Confidence            3456899999999999      789999999999999999988  46899999999999999999999999999999999


Q ss_pred             -eEEEEecCCC
Q 040243          562 -TIAVRVAGKP  571 (797)
Q Consensus       562 -~L~V~~A~~~  571 (797)
                       .|+|++|...
T Consensus        90 ~~l~V~~a~~~  100 (105)
T 2nlw_A           90 HTFRVNLFTDF  100 (105)
T ss_dssp             CEEEEECSCCC
T ss_pred             ceEEEEEcchH
Confidence             9999998754

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=2.2e-15  Score=136.85  Aligned_cols=82  Identities=20%  Similarity=0.233  Sum_probs=73.0

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcC--ceeeccceEEE
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMN--GYRLEGRTIAV  565 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~Ln--G~~l~Gr~L~V  565 (797)
                      ....++|||+||++.+++++|+++|++||.|.+|.|+++      ||||||+|.+.++|++||+.|+  +..|.|+.|+|
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V   85 (101)
T 2cq1_A           12 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYI   85 (101)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEE
Confidence            345689999999999999999999999999999998875      6999999999999999999774  67899999999


Q ss_pred             EecCCCCCCC
Q 040243          566 RVAGKPPQPT  575 (797)
Q Consensus       566 ~~A~~~~~~~  575 (797)
                      +||+.+....
T Consensus        86 ~~a~~~~~~~   95 (101)
T 2cq1_A           86 QYSNHKELKT   95 (101)
T ss_dssp             EECSCSSCCC
T ss_pred             EEcCcccCcC
Confidence            9998665443

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=5.2e-16  Score=142.12  Aligned_cols=80  Identities=19%  Similarity=0.275  Sum_probs=72.6

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcC--ceeeccceEEEE
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMN--GYRLEGRTIAVR  566 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~Ln--G~~l~Gr~L~V~  566 (797)
                      ...++|||+||++.+++++|+++|++||.|.+|+|+++      ||||||+|.+.++|++||+.|+  +..|+|+.|+|+
T Consensus        14 ~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~   87 (105)
T 1sjq_A           14 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQ   87 (105)
T ss_dssp             CCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEE
Confidence            45789999999999999999999999999999999876      5999999999999999999886  478999999999


Q ss_pred             ecCCCCCC
Q 040243          567 VAGKPPQP  574 (797)
Q Consensus       567 ~A~~~~~~  574 (797)
                      ||+.+...
T Consensus        88 ~A~~~~~~   95 (105)
T 1sjq_A           88 FSNHKELK   95 (105)
T ss_dssp             CCSSSSCC
T ss_pred             EcCCCCCC
Confidence            99865543

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=6.3e-16  Score=141.38  Aligned_cols=83  Identities=29%  Similarity=0.485  Sum_probs=77.3

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      .....++|||+||+.++++++|+++|++||.|.+|+|++++  +.++|||||+|.+.++|++|++.|+|..|+|+.|+|+
T Consensus        25 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  102 (109)
T 2err_A           25 NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN  102 (109)
T ss_dssp             CTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999985  4599999999999999999999999999999999999


Q ss_pred             ecCCC
Q 040243          567 VAGKP  571 (797)
Q Consensus       567 ~A~~~  571 (797)
                      +++.+
T Consensus       103 ~a~~~  107 (109)
T 2err_A          103 NATAR  107 (109)
T ss_dssp             ECCCS
T ss_pred             ECCCC
Confidence            99764

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.62  E-value=1.9e-15  Score=134.65  Aligned_cols=79  Identities=29%  Similarity=0.512  Sum_probs=72.8

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeec--cceEEEE
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLE--GRTIAVR  566 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~--Gr~L~V~  566 (797)
                      ...++|||+||++++++++|+++|++||.|.+|++..+      +|||||+|.+.++|++||+.||+..|+  |+.|+|+
T Consensus        15 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~   88 (97)
T 1why_A           15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVD   88 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEE
Confidence            45679999999999999999999999999999998764      689999999999999999999999999  9999999


Q ss_pred             ecCCCCC
Q 040243          567 VAGKPPQ  573 (797)
Q Consensus       567 ~A~~~~~  573 (797)
                      |++.+..
T Consensus        89 ~a~~~~~   95 (97)
T 1why_A           89 FAKSGPS   95 (97)
T ss_dssp             ECCCCCC
T ss_pred             ECCCCCC
Confidence            9986543

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.62  E-value=1.8e-16  Score=142.25  Aligned_cols=83  Identities=20%  Similarity=0.292  Sum_probs=76.9

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ...++|||+||++++++++|+++|++||.|.. .++.++.+|++||||||+|.+.++|++||+ |||..|+|+.|+|+++
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            46789999999999999999999999999988 777888899999999999999999999998 9999999999999999


Q ss_pred             CCCCC
Q 040243          569 GKPPQ  573 (797)
Q Consensus       569 ~~~~~  573 (797)
                      ..+..
T Consensus        93 ~~~~~   97 (101)
T 1fj7_A           93 KGRDG   97 (101)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            86543

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.62  E-value=1.5e-15  Score=135.47  Aligned_cols=80  Identities=23%  Similarity=0.391  Sum_probs=72.5

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      ....++|||+||++++++++|+++|++||.|. +.++.+    +++|||||+|.+.++|++||+.|||..|+|+.|+|++
T Consensus        16 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~----~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   90 (97)
T 2e5j_A           16 APLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ----GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVAL   90 (97)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE----TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC----CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            34578999999999999999999999999996 666654    5889999999999999999999999999999999999


Q ss_pred             cCCCC
Q 040243          568 AGKPP  572 (797)
Q Consensus       568 A~~~~  572 (797)
                      ++.+.
T Consensus        91 a~~~~   95 (97)
T 2e5j_A           91 ARQQR   95 (97)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            98654

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.62  E-value=2.5e-15  Score=132.05  Aligned_cols=79  Identities=29%  Similarity=0.580  Sum_probs=73.3

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ...++|||+||++++++++|+++|++||.|.+|+|.        ||||||+|.+.++|++||+.|++..|+|+.|+|+|+
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            467899999999999999999999999999999987        589999999999999999999999999999999999


Q ss_pred             CCCCCCC
Q 040243          569 GKPPQPT  575 (797)
Q Consensus       569 ~~~~~~~  575 (797)
                      ..+....
T Consensus        78 ~~~~~~~   84 (90)
T 2dnq_A           78 KNKSKAS   84 (90)
T ss_dssp             SCCCCCC
T ss_pred             CCCCCCC
Confidence            8766543

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.61  E-value=5e-16  Score=134.02  Aligned_cols=74  Identities=28%  Similarity=0.484  Sum_probs=68.7

Q ss_pred             CcEEEEecCCCCC------cHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccc-eE
Q 040243          491 DTNLYIGYLPPTL------DDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGR-TI  563 (797)
Q Consensus       491 ~~tLfVgNLp~~v------te~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr-~L  563 (797)
                      +++|||+||+..+      ++++|+++|++||.|.+|+|.  +.+|++||||||+|.+.++|++||+.|||..|+|+ .|
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l   78 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF   78 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeE
Confidence            3689999999999      779999999999999999987  45899999999999999999999999999999999 88


Q ss_pred             EEE
Q 040243          564 AVR  566 (797)
Q Consensus       564 ~V~  566 (797)
                      +|.
T Consensus        79 ~V~   81 (81)
T 2krb_A           79 RVN   81 (81)
T ss_dssp             CCC
T ss_pred             EeC
Confidence            773

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.61  E-value=1.1e-15  Score=135.25  Aligned_cols=73  Identities=23%  Similarity=0.281  Sum_probs=69.2

Q ss_pred             CcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       491 ~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      ..-|||+||++.+||++|+++|.+||.|.++++..      +||||||+|.+.++|++||+.||+..|+|+.|+|++|.
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            45799999999999999999999999999999865      67999999999999999999999999999999999984

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.61  E-value=9e-16  Score=140.67  Aligned_cols=87  Identities=23%  Similarity=0.458  Sum_probs=75.6

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ...++|||+||++++++++|+++|++||.|.++.+..+..+++++|||||+|.+.++|++||+.|+|..|+|+.|+|+||
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a  102 (115)
T 2cpx_A           23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG  102 (115)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEc
Confidence            45689999999999999999999999999954433333338899999999999999999999999999999999999999


Q ss_pred             CCCCCCC
Q 040243          569 GKPPQPT  575 (797)
Q Consensus       569 ~~~~~~~  575 (797)
                      ..+....
T Consensus       103 ~~~~~~~  109 (115)
T 2cpx_A          103 KNKKQRS  109 (115)
T ss_dssp             CCCSCCC
T ss_pred             cCCCCCC
Confidence            8766544

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.61  E-value=1.2e-15  Score=140.39  Aligned_cols=79  Identities=23%  Similarity=0.322  Sum_probs=74.0

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      .+.++|||+||++++++++|+++|+.| .|.+|+|++|+. |++||||||+|.+.++|++|| .||+..|+||.|+|..+
T Consensus        14 ~~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~-g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a   90 (109)
T 2dnn_A           14 PDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPA   90 (109)
T ss_dssp             HHHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEEC
Confidence            456899999999999999999999999 899999999985 999999999999999999999 69999999999999887


Q ss_pred             CC
Q 040243          569 GK  570 (797)
Q Consensus       569 ~~  570 (797)
                      ..
T Consensus        91 ~~   92 (109)
T 2dnn_A           91 TE   92 (109)
T ss_dssp             CH
T ss_pred             Cc
Confidence            64

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.61  E-value=1.5e-15  Score=143.53  Aligned_cols=81  Identities=20%  Similarity=0.355  Sum_probs=73.6

Q ss_pred             CCCcEEEEecCCCCCcHHHHH----HHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEE
Q 040243          489 LDDTNLYIGYLPPTLDDDGLI----RLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIA  564 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~----~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~  564 (797)
                      ...++|||+||++.+++++|+    ++|++||.|.+|.+.+   ++++||||||+|.+.++|++||+.|||..|.|+.|+
T Consensus        27 ~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~  103 (127)
T 2a3j_A           27 EPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLV  103 (127)
T ss_dssp             SCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEE
Confidence            346799999999999999876    7999999999987743   789999999999999999999999999999999999


Q ss_pred             EEecCCCC
Q 040243          565 VRVAGKPP  572 (797)
Q Consensus       565 V~~A~~~~  572 (797)
                      |+||+.+.
T Consensus       104 V~~a~~~~  111 (127)
T 2a3j_A          104 ITFSETPQ  111 (127)
T ss_dssp             EEECCCCC
T ss_pred             EEEccCcc
Confidence            99998654

>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=99.61  E-value=2.5e-15  Score=137.09  Aligned_cols=80  Identities=13%  Similarity=0.177  Sum_probs=71.7

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCce--eeccceEEEE
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGY--RLEGRTIAVR  566 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~--~l~Gr~L~V~  566 (797)
                      ...++|||+||++.+++++|+++|++||.|.+|.|+++      ||||||+|.+.++|++||+.|++.  .|+|+.|+|+
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~   86 (104)
T 1wex_A           13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFN   86 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEE
Confidence            45679999999999999999999999999999998764      699999999999999999988765  4999999999


Q ss_pred             ecCCCCCC
Q 040243          567 VAGKPPQP  574 (797)
Q Consensus       567 ~A~~~~~~  574 (797)
                      |++.+...
T Consensus        87 ~a~~~~~~   94 (104)
T 1wex_A           87 YSTSKRIT   94 (104)
T ss_dssp             ECSSSSCC
T ss_pred             EccCcccc
Confidence            99865543

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.61  E-value=2.6e-15  Score=134.29  Aligned_cols=82  Identities=27%  Similarity=0.544  Sum_probs=74.8

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      ....++|||+||++++++++|+++|++||.|.+|+|.++      ||||||+|.+.++|++||+.|+|+.|+|+.|+|+|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~   85 (99)
T 2cpj_A           12 FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRF   85 (99)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEE
Confidence            356789999999999999999999999999999999864      68999999999999999999999999999999999


Q ss_pred             cCCCCCCC
Q 040243          568 AGKPPQPT  575 (797)
Q Consensus       568 A~~~~~~~  575 (797)
                      ++.+....
T Consensus        86 a~~~~~~~   93 (99)
T 2cpj_A           86 ACHSASLT   93 (99)
T ss_dssp             SSCCSCCC
T ss_pred             cCCCCCCC
Confidence            98765433

>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=99.61  E-value=2.5e-15  Score=136.89  Aligned_cols=82  Identities=30%  Similarity=0.547  Sum_probs=75.5

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      ....++|||+||+.++++++|+++|++||.|.+|+|+.+      +|||||+|.+.++|++||+.|+|+.|+|+.|+|+|
T Consensus        22 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   95 (109)
T 1x4g_A           22 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYW   95 (109)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEe
Confidence            345789999999999999999999999999999999886      68999999999999999999999999999999999


Q ss_pred             cCCCCCCC
Q 040243          568 AGKPPQPT  575 (797)
Q Consensus       568 A~~~~~~~  575 (797)
                      ++......
T Consensus        96 a~~~~~~~  103 (109)
T 1x4g_A           96 GKESPDMT  103 (109)
T ss_dssp             CCCCCSSC
T ss_pred             cCCCCCCC
Confidence            98766543

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.61  E-value=3.8e-15  Score=131.39  Aligned_cols=81  Identities=21%  Similarity=0.432  Sum_probs=73.9

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      .....++|||+||++++++++|+++|++||.|.+|+|++        +||||+|.+.++|++||+.||++.|+|+.|+|+
T Consensus         6 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   77 (92)
T 2dgt_A            6 SGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQ   77 (92)
T ss_dssp             CCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS--------SEEEEEESCHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEE
Confidence            445678999999999999999999999999999999874        499999999999999999999999999999999


Q ss_pred             ecCCCCCCC
Q 040243          567 VAGKPPQPT  575 (797)
Q Consensus       567 ~A~~~~~~~  575 (797)
                      |++.+....
T Consensus        78 ~a~~~~~~~   86 (92)
T 2dgt_A           78 LSTSRLRTA   86 (92)
T ss_dssp             ESSCCCSCC
T ss_pred             EccCCCCCC
Confidence            998765544

>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=99.60  E-value=3e-16  Score=132.76  Aligned_cols=75  Identities=16%  Similarity=0.387  Sum_probs=72.1

Q ss_pred             EEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       493 tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      +|||+||++++++++|+++|++||.|.+|++.+++.+|+++|||||+|.+.++|++||+. ++..|+|+.|+|++|
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-SSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEC
Confidence            599999999999999999999999999999999999999999999999999999999984 899999999999986

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.60  E-value=5e-15  Score=147.42  Aligned_cols=83  Identities=25%  Similarity=0.365  Sum_probs=78.7

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ...++|||+||++.+++++|+++|++||.|.+|+|+.++ +++++|||||+|.+.++|++||+.|||..|+|+.|+|+||
T Consensus        86 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a  164 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV  164 (177)
T ss_dssp             TTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            346899999999999999999999999999999999998 9999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 040243          569 GKPP  572 (797)
Q Consensus       569 ~~~~  572 (797)
                      ....
T Consensus       165 ~~~~  168 (177)
T 2f3j_A          165 ASQI  168 (177)
T ss_dssp             SSGG
T ss_pred             cCCC
Confidence            7543

>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=99.60  E-value=2.7e-15  Score=129.91  Aligned_cols=77  Identities=27%  Similarity=0.427  Sum_probs=71.8

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhc-CceeeccceEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM-NGYRLEGRTIAV  565 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~L-nG~~l~Gr~L~V  565 (797)
                      .+...++|||+||+.++++++|+++|++||.|.+|++.++      ||||||+|.+.++|++|++.| ++..|+|+.|+|
T Consensus         8 ~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v   81 (85)
T 2ytc_A            8 EDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNV   81 (85)
T ss_dssp             SCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTEECCE
T ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEE
Confidence            4456789999999999999999999999999999999874      699999999999999999999 999999999999


Q ss_pred             EecC
Q 040243          566 RVAG  569 (797)
Q Consensus       566 ~~A~  569 (797)
                      +||+
T Consensus        82 ~~ak   85 (85)
T 2ytc_A           82 KWGR   85 (85)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            9985

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A

Probab=99.60  E-value=9e-16  Score=145.02  Aligned_cols=80  Identities=24%  Similarity=0.348  Sum_probs=73.1

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEE--EEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEE
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIV--MAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAV  565 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~--~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V  565 (797)
                      ....++|||+||++++++++|+++|+.| .|.  +|+|++|+. |++||||||+|.+.++|++||+. ++..|+||.|+|
T Consensus        39 ~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~~-~~~~l~gR~I~V  115 (126)
T 2hgm_A           39 SANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALGK-HKERIGHRYIEV  115 (126)
T ss_dssp             SSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHTT-TTCCBTTBCCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHHH-CCCEECCEEEEE
Confidence            3467899999999999999999999999 677  899999986 99999999999999999999985 779999999999


Q ss_pred             EecCC
Q 040243          566 RVAGK  570 (797)
Q Consensus       566 ~~A~~  570 (797)
                      .++..
T Consensus       116 ~~a~~  120 (126)
T 2hgm_A          116 FKSSQ  120 (126)
T ss_dssp             EEECH
T ss_pred             EECCH
Confidence            88753

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=7.9e-15  Score=130.76  Aligned_cols=80  Identities=26%  Similarity=0.404  Sum_probs=72.1

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      ....++|||+||  ++++++|+++|++||.|.+|+|.      +++|||||+|.+.++|++||+.|+|..|+|+.|+|+|
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            346789999996  89999999999999999999984      5679999999999999999999999999999999999


Q ss_pred             cCCCCCCC
Q 040243          568 AGKPPQPT  575 (797)
Q Consensus       568 A~~~~~~~  575 (797)
                      +..+....
T Consensus        84 a~~~~~~~   91 (97)
T 1x5p_A           84 ARKQPMLD   91 (97)
T ss_dssp             CSSCCCCC
T ss_pred             CCCCCCCC
Confidence            98765443

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A

Probab=99.60  E-value=7.8e-15  Score=132.25  Aligned_cols=79  Identities=30%  Similarity=0.488  Sum_probs=72.4

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ...++|||+||++++++++|+++|++||.|.+|+|+        +|||||+|.+.++|++||+.|+++.|+|+.|+|+|+
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            356799999999999999999999999999999986        469999999999999999999999999999999999


Q ss_pred             CCCCCCC
Q 040243          569 GKPPQPT  575 (797)
Q Consensus       569 ~~~~~~~  575 (797)
                      ..+....
T Consensus        81 ~~~~~~~   87 (103)
T 2dgu_A           81 KPPDQKR   87 (103)
T ss_dssp             CCCCCCC
T ss_pred             CCCcccc
Confidence            8766543

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.59  E-value=1.5e-15  Score=136.11  Aligned_cols=76  Identities=29%  Similarity=0.450  Sum_probs=71.3

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ...++|||+||+.++++++|+++|++||.|.+|++.      ++||||||+|.+.++|++||+.|||..|+|+.|+|+||
T Consensus        25 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~------~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   98 (101)
T 2la4_A           25 PRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY------PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWG   98 (101)
T ss_dssp             SSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE------TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBC
T ss_pred             CCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe------cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEec
Confidence            346899999999999999999999999999999987      35799999999999999999999999999999999998


Q ss_pred             CC
Q 040243          569 GK  570 (797)
Q Consensus       569 ~~  570 (797)
                      +.
T Consensus        99 ~~  100 (101)
T 2la4_A           99 KE  100 (101)
T ss_dssp             CC
T ss_pred             cC
Confidence            75

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.38  E-value=7.8e-17  Score=148.47  Aligned_cols=87  Identities=24%  Similarity=0.342  Sum_probs=81.5

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEE--------EEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeec
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVM--------AKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLE  559 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~--------v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~  559 (797)
                      ....++|||+||++++++++|+++|++||.|.+        |+|+.|+.+++++|||||+|.+.++|++||+.|||..|+
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   83 (116)
T 2lcw_A            4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   83 (116)
Confidence            456789999999999999999999999999999        999999999999999999999999999999999999999


Q ss_pred             cceEEEEecCCCCCC
Q 040243          560 GRTIAVRVAGKPPQP  574 (797)
Q Consensus       560 Gr~L~V~~A~~~~~~  574 (797)
                      |+.|+|+|+..+...
T Consensus        84 g~~l~V~~a~~~~~~   98 (116)
T 2lcw_A           84 GNPIKVSFATRRADF   98 (116)
Confidence            999999999876543

>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=99.59  E-value=7.9e-16  Score=140.15  Aligned_cols=82  Identities=15%  Similarity=0.103  Sum_probs=76.7

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCC---EEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEE
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGD---IVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIA  564 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~---I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~  564 (797)
                      ....++|||+||++++++++|+++|+.||.   |.+|+|++|+. |+++|||||+|.+.++|++||+ |++..|+|+.|+
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            356789999999999999999999999998   89999999986 9999999999999999999998 999999999999


Q ss_pred             EEecCCC
Q 040243          565 VRVAGKP  571 (797)
Q Consensus       565 V~~A~~~  571 (797)
                      |.++...
T Consensus        86 V~~a~~~   92 (107)
T 2lmi_A           86 VYEINNE   92 (107)
T ss_dssp             CEECCHH
T ss_pred             EEECCHH
Confidence            9998753

>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=99.59  E-value=1.7e-15  Score=134.52  Aligned_cols=82  Identities=26%  Similarity=0.461  Sum_probs=75.5

Q ss_pred             CCCCcEEEEecCCCCCcHHHHH----HHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceE
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLI----RLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTI  563 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~----~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L  563 (797)
                      ....++|||+||++++++++|+    ++|++||.|.+|++.+   +|+++|||||+|.+.++|++|++.|+|..|+|+.|
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            4467899999999999999999    9999999999998873   68899999999999999999999999999999999


Q ss_pred             EEEecCCCC
Q 040243          564 AVRVAGKPP  572 (797)
Q Consensus       564 ~V~~A~~~~  572 (797)
                      +|+|+....
T Consensus        82 ~v~~a~~~~   90 (97)
T 1nu4_A           82 RIQYAKTDS   90 (97)
T ss_dssp             EEEECSSCC
T ss_pred             EEEEccCCC
Confidence            999998654

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.59  E-value=1.9e-15  Score=139.63  Aligned_cols=78  Identities=17%  Similarity=0.244  Sum_probs=71.6

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCC-CEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFG-DIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG-~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ..++|||+||++++++++|+++|++|| .|..+.|..+    +++|||||+|.+.++|++||+.|||..|+|+.|+|+++
T Consensus        27 ~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~----~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a  102 (111)
T 2jvr_A           27 KRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR----DFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERD  102 (111)
T ss_dssp             CCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC----SSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC----CCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            467999999999999999999999999 9999988543    48999999999999999999999999999999999998


Q ss_pred             CCC
Q 040243          569 GKP  571 (797)
Q Consensus       569 ~~~  571 (797)
                      ..+
T Consensus       103 ~~~  105 (111)
T 2jvr_A          103 DNP  105 (111)
T ss_dssp             CC-
T ss_pred             CCC
Confidence            754

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.59  E-value=1.4e-14  Score=129.48  Aligned_cols=79  Identities=24%  Similarity=0.380  Sum_probs=72.0

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcC--CCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEE
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTF--GDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAV  565 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~f--G~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V  565 (797)
                      ....++|||+||++++++++|+++|++|  |.|.+|++.        ||||||+|.+.++|++||+.|||+.|+|+.|+|
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            3467899999999999999999999999  999998863        579999999999999999999999999999999


Q ss_pred             EecCCCCCC
Q 040243          566 RVAGKPPQP  574 (797)
Q Consensus       566 ~~A~~~~~~  574 (797)
                      +|++.....
T Consensus        84 ~~a~~~~~~   92 (99)
T 2cpd_A           84 TLAKPVDKD   92 (99)
T ss_dssp             ECCCCCCCC
T ss_pred             EECCCCCCC
Confidence            999876543

>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=99.59  E-value=3.5e-15  Score=139.60  Aligned_cols=81  Identities=19%  Similarity=0.275  Sum_probs=73.2

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCc--eeeccceEEE
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNG--YRLEGRTIAV  565 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG--~~l~Gr~L~V  565 (797)
                      ....++|||+||++.+++++|+++|++||.|.+|+|+++      ||||||+|.+.++|++||+.|++  ..|.|+.|+|
T Consensus        28 ~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V  101 (119)
T 2ad9_A           28 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI  101 (119)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEE
Confidence            345789999999999999999999999999999999876      69999999999999999999885  5899999999


Q ss_pred             EecCCCCCC
Q 040243          566 RVAGKPPQP  574 (797)
Q Consensus       566 ~~A~~~~~~  574 (797)
                      +||+.+...
T Consensus       102 ~~a~~k~~~  110 (119)
T 2ad9_A          102 QFSNHKELK  110 (119)
T ss_dssp             EECSSSSCC
T ss_pred             EEccCCCCC
Confidence            999865543

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.58  E-value=2.3e-15  Score=134.99  Aligned_cols=78  Identities=23%  Similarity=0.478  Sum_probs=73.4

Q ss_pred             cEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecCCC
Q 040243          492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKP  571 (797)
Q Consensus       492 ~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~~~  571 (797)
                      ++|||+||++++++++|+++|++||.|.+|+|+.+     ++|||||+|.+.++|++||+.|+|..|+|+.|+|+|++..
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            58999999999999999999999999999999887     7899999999999999999999999999999999999876


Q ss_pred             CCC
Q 040243          572 PQP  574 (797)
Q Consensus       572 ~~~  574 (797)
                      ...
T Consensus        76 ~~~   78 (101)
T 2hvz_A           76 PRR   78 (101)
T ss_dssp             CCS
T ss_pred             CCc
Confidence            643

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.58  E-value=2.7e-15  Score=133.14  Aligned_cols=82  Identities=20%  Similarity=0.342  Sum_probs=74.1

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      .+...++|||+||++++++++|+++|++||.|..+     ..+++++|||||+|.+.++|++||+.|+|..|+|+.|+|+
T Consensus        12 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   86 (96)
T 1fjc_A           12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLY   86 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            34567899999999999999999999999988766     3489999999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 040243          567 VAGKPPQ  573 (797)
Q Consensus       567 ~A~~~~~  573 (797)
                      ++..+..
T Consensus        87 ~a~~~~~   93 (96)
T 1fjc_A           87 YTGEKGG   93 (96)
T ss_dssp             ECSSSCC
T ss_pred             EcCCCCC
Confidence            9976544

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.58  E-value=6.2e-15  Score=147.99  Aligned_cols=86  Identities=35%  Similarity=0.632  Sum_probs=80.9

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      ..++|||+||+..+++++|+++|++||.|.+|+|++++.+|+++|||||+|.+.++|.+||+.|||..|+|+.|+|+|+.
T Consensus       124 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a~  203 (216)
T 2qfj_A          124 AFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAV  203 (216)
T ss_dssp             TSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEECS
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEec
Confidence            45799999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCCCC
Q 040243          570 KPPQPT  575 (797)
Q Consensus       570 ~~~~~~  575 (797)
                      .+....
T Consensus       204 ~~~~~~  209 (216)
T 2qfj_A          204 TPPMPL  209 (216)
T ss_dssp             SCSSTT
T ss_pred             CCCCCC
Confidence            664433

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.58  E-value=6.1e-16  Score=145.51  Aligned_cols=81  Identities=20%  Similarity=0.191  Sum_probs=74.3

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCE----EEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceE
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDI----VMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTI  563 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I----~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L  563 (797)
                      ....++|||+||++++++++|+++|++||.|    .+|+|++|+ +|++||||||+|.+.++|++||+. ++..|+||.|
T Consensus        20 ~~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~-~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i   97 (123)
T 2dha_A           20 KENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP-DGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYI   97 (123)
T ss_dssp             CCSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECT-TSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECC-CCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEE
Confidence            3467899999999999999999999999976    689999995 899999999999999999999986 9999999999


Q ss_pred             EEEecCC
Q 040243          564 AVRVAGK  570 (797)
Q Consensus       564 ~V~~A~~  570 (797)
                      +|..+..
T Consensus        98 ~V~~a~~  104 (123)
T 2dha_A           98 ELFRSTA  104 (123)
T ss_dssp             CCEEECH
T ss_pred             EEEECCH
Confidence            9988754

>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=99.58  E-value=6e-16  Score=148.59  Aligned_cols=82  Identities=17%  Similarity=0.182  Sum_probs=74.9

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      ....++|||+||++++++++|+++|++|| |++|+|++|+. |++||||||+|.+.++|++|| .+|+..|+|+.|+|.+
T Consensus        43 ~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~  119 (139)
T 2hgn_A           43 STTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFL  119 (139)
T ss_dssp             --CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEE
Confidence            45678999999999999999999999999 77999999985 999999999999999999999 7899999999999999


Q ss_pred             cCCCC
Q 040243          568 AGKPP  572 (797)
Q Consensus       568 A~~~~  572 (797)
                      +....
T Consensus       120 a~~~~  124 (139)
T 2hgn_A          120 NSTTG  124 (139)
T ss_dssp             CCCSC
T ss_pred             CCCCC
Confidence            87554

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.58  E-value=1.2e-15  Score=136.99  Aligned_cols=83  Identities=23%  Similarity=0.509  Sum_probs=76.9

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      +...++|||+||++++++++|+++|++||.|.+|+|+.++ +|++||||||+|.+.++|++||+  ++..|+|+.|.|.+
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~   82 (102)
T 2xs2_A            6 KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGP   82 (102)
T ss_dssp             EEEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEE
Confidence            3456899999999999999999999999999999999998 99999999999999999999998  99999999999999


Q ss_pred             cCCCCC
Q 040243          568 AGKPPQ  573 (797)
Q Consensus       568 A~~~~~  573 (797)
                      +..+..
T Consensus        83 a~~~~~   88 (102)
T 2xs2_A           83 AIRKQN   88 (102)
T ss_dssp             EEECC-
T ss_pred             CCcCcc
Confidence            876543

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A

Probab=99.57  E-value=7e-15  Score=131.75  Aligned_cols=77  Identities=23%  Similarity=0.509  Sum_probs=71.4

Q ss_pred             CCCCcEEEEecCCC-CCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          488 ELDDTNLYIGYLPP-TLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       488 ~~~~~tLfVgNLp~-~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      ....++|||+||++ ++++++|+++|++||.|.+|+|        ++|||||+|.+.++|++||+.|||..|+|+.|+|+
T Consensus        19 ~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   90 (97)
T 2xnq_A           19 SHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILE   90 (97)
T ss_dssp             CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEE--------CSSEEEEEESSHHHHHHHHHHHTTSEETTEECEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34678999999998 9999999999999999999998        27999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 040243          567 VAGKPP  572 (797)
Q Consensus       567 ~A~~~~  572 (797)
                      |++...
T Consensus        91 ~a~~~~   96 (97)
T 2xnq_A           91 VSSSNA   96 (97)
T ss_dssp             ECCCCC
T ss_pred             ecCCCC
Confidence            997653

>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=99.57  E-value=3e-15  Score=137.49  Aligned_cols=79  Identities=14%  Similarity=0.089  Sum_probs=72.7

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      +.+.++|||+||++.+++++|+++|++||.|.+|.|..      ++|||||+|.+.++|++||+.|||+.|+|+.|+|+|
T Consensus         7 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   80 (111)
T 1whx_A            7 GRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEW   80 (111)
T ss_dssp             SEEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            44678999999999999999999999999999998864      568999999999999999999999999999999999


Q ss_pred             cCCCC
Q 040243          568 AGKPP  572 (797)
Q Consensus       568 A~~~~  572 (797)
                      |....
T Consensus        81 a~~~~   85 (111)
T 1whx_A           81 APIGV   85 (111)
T ss_dssp             EETTT
T ss_pred             CCCCc
Confidence            97644

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.57  E-value=6.5e-15  Score=149.56  Aligned_cols=84  Identities=27%  Similarity=0.462  Sum_probs=78.5

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ...++|||+||++++++++|+++|++||.|.+|+|++|+.|++++|||||+|.+.++|++||+.|++..+.|+.|+|.++
T Consensus        13 ~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~   92 (213)
T 4f02_A           13 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWS   92 (213)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccccc
Confidence            34679999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 040243          569 GKPP  572 (797)
Q Consensus       569 ~~~~  572 (797)
                      ....
T Consensus        93 ~~~~   96 (213)
T 4f02_A           93 QRDP   96 (213)
T ss_dssp             CCCT
T ss_pred             cccc
Confidence            6543

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A

Probab=99.57  E-value=1.5e-14  Score=131.81  Aligned_cols=76  Identities=30%  Similarity=0.609  Sum_probs=70.9

Q ss_pred             CCcEEEEecCCCC-CcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          490 DDTNLYIGYLPPT-LDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       490 ~~~tLfVgNLp~~-vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ..++|||+||+++ +++++|+++|++||.|.+|+|        ++|||||+|.+.++|++||+.|++..|+|+.|+|+|+
T Consensus        26 ~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   97 (110)
T 1wf1_A           26 INSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMA   97 (110)
T ss_dssp             CSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEES
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            4579999999999 999999999999999999998        5799999999999999999999999999999999999


Q ss_pred             CCCCC
Q 040243          569 GKPPQ  573 (797)
Q Consensus       569 ~~~~~  573 (797)
                      +.+..
T Consensus        98 ~~~~~  102 (110)
T 1wf1_A           98 GEPKP  102 (110)
T ss_dssp             CCCCS
T ss_pred             CCCCC
Confidence            75443

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.57  E-value=7.2e-15  Score=136.07  Aligned_cols=82  Identities=16%  Similarity=0.255  Sum_probs=72.6

Q ss_pred             CCCCcEEEEecCCCC-CcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCc--eeeccceEE
Q 040243          488 ELDDTNLYIGYLPPT-LDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNG--YRLEGRTIA  564 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~-vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG--~~l~Gr~L~  564 (797)
                      ....++|||+||+++ +++++|+++|++||.|.+|+|++      +||||||+|.+.++|++||+.|++  ..|+|+.|+
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~------~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~   95 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   95 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            345789999999998 99999999999999999999974      469999999999999999998865  569999999


Q ss_pred             EEecCCCCCCC
Q 040243          565 VRVAGKPPQPT  575 (797)
Q Consensus       565 V~~A~~~~~~~  575 (797)
                      |.||+.+....
T Consensus        96 V~~a~~~~~~~  106 (112)
T 1x4f_A           96 VDLSEKYKKLV  106 (112)
T ss_dssp             EEEECSCSSSS
T ss_pred             EEECccccccc
Confidence            99998765543

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.57  E-value=7e-15  Score=130.41  Aligned_cols=79  Identities=27%  Similarity=0.341  Sum_probs=73.0

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEE-EEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMA-KVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v-~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      ...++|||+||++++++++|+++|++||.|.+| .|+.++.+++    |||+|.+.++|++||+.|||+.|+|+.|+|++
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 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAV----VNVTYSSKDQARQALDKLNGFQLENFTLKVAY   88 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEE----EEEEESSHHHHHHHHHHHTTCBCSSCBCEEEE
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCE----EEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            456799999999999999999999999999999 5888876654    99999999999999999999999999999999


Q ss_pred             cCCC
Q 040243          568 AGKP  571 (797)
Q Consensus       568 A~~~  571 (797)
                      |..+
T Consensus        89 a~~~   92 (96)
T 2e44_A           89 IPDE   92 (96)
T ss_dssp             CCCC
T ss_pred             cCcc
Confidence            9866

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.57  E-value=7.5e-15  Score=133.27  Aligned_cols=77  Identities=19%  Similarity=0.240  Sum_probs=70.6

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCcee--eccceEEEE
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYR--LEGRTIAVR  566 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~--l~Gr~L~V~  566 (797)
                      ..+++|||+||++.+++++|+++|++||.|.+|++++      +||||||+|.+.++|.+||+.|++..  |.|+.|+|.
T Consensus        19 ~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~------~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~   92 (100)
T 3r27_A           19 PASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP------KKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVN   92 (100)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc------CCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEE
Confidence            3567999999999999999999999999999999975      36899999999999999999999875  789999999


Q ss_pred             ecCCC
Q 040243          567 VAGKP  571 (797)
Q Consensus       567 ~A~~~  571 (797)
                      |++.+
T Consensus        93 ~S~~k   97 (100)
T 3r27_A           93 YSTSQ   97 (100)
T ss_dssp             ECSCS
T ss_pred             ecccc
Confidence            99864

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.57  E-value=1.3e-14  Score=128.64  Aligned_cols=79  Identities=18%  Similarity=0.360  Sum_probs=71.4

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ...++|||+||++++++++|+++|++||.|.+|  +.++.+++   ||||+|.+.++|++||+ |+|+.|+|+.|+|+++
T Consensus         6 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a   79 (94)
T 2e5g_A            6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPR   79 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEEC
Confidence            345799999999999999999999999999987  67776776   99999999999999999 9999999999999998


Q ss_pred             CCCCC
Q 040243          569 GKPPQ  573 (797)
Q Consensus       569 ~~~~~  573 (797)
                      ..+..
T Consensus        80 ~~~~~   84 (94)
T 2e5g_A           80 EQKEF   84 (94)
T ss_dssp             CCSCC
T ss_pred             CcCCC
Confidence            75543

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.57  E-value=1e-14  Score=139.76  Aligned_cols=82  Identities=38%  Similarity=0.595  Sum_probs=78.6

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ...++|||+||+..+++++|+++|++||.|.+++++.++.+|+++|||||+|.+.++|.+|++.|||..|+|+.|+|+||
T Consensus        85 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  164 (166)
T 3md3_A           85 DDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA  164 (166)
T ss_dssp             TTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEec
Confidence            35679999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CC
Q 040243          569 GK  570 (797)
Q Consensus       569 ~~  570 (797)
                      ++
T Consensus       165 ~~  166 (166)
T 3md3_A          165 AK  166 (166)
T ss_dssp             CC
T ss_pred             CC
Confidence            63

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.56  E-value=6.8e-15  Score=134.61  Aligned_cols=78  Identities=24%  Similarity=0.553  Sum_probs=72.3

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      +...++|||+||++++++++|+++|++||.|.+|+|.        +|||||+|.+.++|++|++.|||..|+|+.|+|+|
T Consensus        28 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   99 (108)
T 2jvo_A           28 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVY   99 (108)
T ss_dssp             CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEES
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            4567899999999999999999999999999999987        68999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 040243          568 AGKPPQ  573 (797)
Q Consensus       568 A~~~~~  573 (797)
                      ++....
T Consensus       100 a~~~~~  105 (108)
T 2jvo_A          100 SKLPAK  105 (108)
T ss_dssp             CSCCC-
T ss_pred             ecCCCC
Confidence            986543

>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=99.56  E-value=1.2e-14  Score=139.47  Aligned_cols=82  Identities=40%  Similarity=0.726  Sum_probs=78.4

Q ss_pred             CcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecCC
Q 040243          491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGK  570 (797)
Q Consensus       491 ~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~~  570 (797)
                      .++|||+||+.++++++|+++|+.||.|.+|++++++.+|+++|||||+|.+.++|++|++.|+|..+.|+.|+|.++..
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            57999999999999999999999999999999999999999999999999999999999999999999999999999875


Q ss_pred             CC
Q 040243          571 PP  572 (797)
Q Consensus       571 ~~  572 (797)
                      ..
T Consensus        82 ~~   83 (167)
T 1fxl_A           82 SS   83 (167)
T ss_dssp             CC
T ss_pred             Cc
Confidence            43

>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=99.56  E-value=5.2e-15  Score=130.63  Aligned_cols=79  Identities=29%  Similarity=0.466  Sum_probs=69.9

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCC-EEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCc-eeeccceEEEE
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGD-IVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNG-YRLEGRTIAVR  566 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~-I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG-~~l~Gr~L~V~  566 (797)
                      ...++|||+||++++++++|+++|++||. |..+.+       .++|||||+|.+.++|++||+.||| ..|+|+.|+|+
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 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL-------LKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVD   78 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEE-------EETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEE-------cCCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEE
Confidence            35679999999999999999999999999 555555       2579999999999999999999999 99999999999


Q ss_pred             ecCCCCCC
Q 040243          567 VAGKPPQP  574 (797)
Q Consensus       567 ~A~~~~~~  574 (797)
                      |+..+...
T Consensus        79 ~a~~~~~~   86 (93)
T 2cqh_A           79 YSVSKKLR   86 (93)
T ss_dssp             ECCCCCCC
T ss_pred             EccCcccc
Confidence            99876543

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} SCOP: d.58.7.1 PDB: 2f9d_A 2f9j_A 2fho_B

Probab=99.56  E-value=1.1e-14  Score=133.60  Aligned_cols=80  Identities=25%  Similarity=0.426  Sum_probs=74.1

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ...++|||+||++++++++|+++|++||.|.+|+|+++   +.++|||||+|.+.++|++||+.|||..|+|+.|+|.|+
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            35679999999999999999999999999999999875   456999999999999999999999999999999999998


Q ss_pred             CCC
Q 040243          569 GKP  571 (797)
Q Consensus       569 ~~~  571 (797)
                      ...
T Consensus        83 ~~~   85 (115)
T 3lqv_A           83 NAN   85 (115)
T ss_dssp             CHH
T ss_pred             cCC
Confidence            753

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.56  E-value=1.4e-14  Score=127.18  Aligned_cols=78  Identities=26%  Similarity=0.452  Sum_probs=72.1

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      ....++|||+||++++++++|+++|++||.|.+|+|++        +||||+|.+.++|++||+.|||..|+|+.|+|+|
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   77 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEKEADAKAAIAQLNGKEVKGKRINVEL   77 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            45678999999999999999999999999999999873        4999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 040243          568 AGKPPQ  573 (797)
Q Consensus       568 A~~~~~  573 (797)
                      +.....
T Consensus        78 a~~~~~   83 (90)
T 2dnp_A           78 STKGQK   83 (90)
T ss_dssp             SCCCCC
T ss_pred             CCCCCC
Confidence            986644

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.56  E-value=5.1e-15  Score=139.54  Aligned_cols=79  Identities=18%  Similarity=0.262  Sum_probs=72.1

Q ss_pred             cEEEEecC----CCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecC----HHH----HHHHHH--hcCcee
Q 040243          492 TNLYIGYL----PPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYAD----IQM----ANNAIA--SMNGYR  557 (797)
Q Consensus       492 ~tLfVgNL----p~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s----~e~----A~~AI~--~LnG~~  557 (797)
                      ++|||+||    ++.+++.+|+++|+.||+|.+|.++.|+.||+++|||||+|.+    .++    |.+||+  .|+|..
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    322    899998  889999


Q ss_pred             eccceEEEEecCC
Q 040243          558 LEGRTIAVRVAGK  570 (797)
Q Consensus       558 l~Gr~L~V~~A~~  570 (797)
                      |+|+.|+|.+...
T Consensus        83 I~Gr~irV~ln~~   95 (136)
T 2j8a_A           83 IMGFKFEVILNKH   95 (136)
T ss_dssp             ETTEEEEEEECCT
T ss_pred             ecCcEEEEEECcc
Confidence            9999999998653

>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=99.55  E-value=1.1e-14  Score=140.36  Aligned_cols=83  Identities=31%  Similarity=0.552  Sum_probs=79.0

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      ..++|||+||+.++++++|+++|++||.|.+|++++++.+|+++|||||+|.+.++|++|++.|+|..++|+.|+|.|+.
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            35799999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CCC
Q 040243          570 KPP  572 (797)
Q Consensus       570 ~~~  572 (797)
                      ...
T Consensus        82 ~~~   84 (168)
T 1b7f_A           82 PGG   84 (168)
T ss_dssp             CCS
T ss_pred             CCc
Confidence            544

>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=99.55  E-value=1.2e-14  Score=139.71  Aligned_cols=80  Identities=24%  Similarity=0.413  Sum_probs=74.6

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      ....++|||+||++++++++|+++|++||.|.+|+|+++     ++|||||+|.+.++|++||+.|||..|+|+.|+|+|
T Consensus        70 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  144 (150)
T 2i2y_A           70 CPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVEL  144 (150)
T ss_dssp             STTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            346789999999999999999999999999999999887     589999999999999999999999999999999999


Q ss_pred             cCCCC
Q 040243          568 AGKPP  572 (797)
Q Consensus       568 A~~~~  572 (797)
                      +..+.
T Consensus       145 a~~~~  149 (150)
T 2i2y_A          145 SNGEK  149 (150)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            97653

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.54  E-value=8.4e-15  Score=130.48  Aligned_cols=79  Identities=24%  Similarity=0.519  Sum_probs=71.4

Q ss_pred             CCCCcEEEEecCCC-CCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          488 ELDDTNLYIGYLPP-TLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       488 ~~~~~tLfVgNLp~-~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      ....++|||+||++ ++++++|+++|++||.|.+|+|.        ||||||+|.+.++|++||+.|+|..|.|+.|+|+
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   78 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILE   78 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            45678999999998 99999999999999999999983        6899999999999999999999999999999999


Q ss_pred             ecCCCCCC
Q 040243          567 VAGKPPQP  574 (797)
Q Consensus       567 ~A~~~~~~  574 (797)
                      |+......
T Consensus        79 ~a~~~~~~   86 (96)
T 2kvi_A           79 VSSSNARP   86 (96)
T ss_dssp             EEECCCC-
T ss_pred             EcCcCCCC
Confidence            99765543

>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=99.54  E-value=1.2e-14  Score=127.50  Aligned_cols=76  Identities=20%  Similarity=0.333  Sum_probs=70.7

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      ..++|||+||++++++++|+++|++| .|.+++|.      ++||||||+|.+.++|++||+.|||..++|+.|+|+|+.
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            45789999999999999999999999 99999884      688999999999999999999999999999999999987


Q ss_pred             CCC
Q 040243          570 KPP  572 (797)
Q Consensus       570 ~~~  572 (797)
                      ...
T Consensus        77 ~~~   79 (88)
T 1wg1_A           77 TDA   79 (88)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            654

>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=99.53  E-value=3.2e-15  Score=142.67  Aligned_cols=83  Identities=23%  Similarity=0.413  Sum_probs=72.5

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEE--E---EecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEE
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAK--V---IKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIA  564 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~--v---~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~  564 (797)
                      ..++|||+||++++++++|+++|++||.|..+.  +   +....+|+++|||||+|.+.++|.+||+.|||+.|+|+.|+
T Consensus        44 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~  123 (143)
T 3egn_A           44 PNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMV  123 (143)
T ss_dssp             CCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEECE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcEEE
Confidence            457999999999999999999999999987741  1   11124799999999999999999999999999999999999


Q ss_pred             EEecCCCC
Q 040243          565 VRVAGKPP  572 (797)
Q Consensus       565 V~~A~~~~  572 (797)
                      |+||+...
T Consensus       124 V~~a~~~~  131 (143)
T 3egn_A          124 VQFARSAR  131 (143)
T ss_dssp             EEECCCSC
T ss_pred             EEECCCCC
Confidence            99997644

>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=99.53  E-value=9.5e-15  Score=134.92  Aligned_cols=75  Identities=23%  Similarity=0.399  Sum_probs=66.9

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccce-----E
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRT-----I  563 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~-----L  563 (797)
                      ...++|||+||++++++++|+++|++||.|.+|+|+.+       |||||+|.+.++|++||+.|||+.|+|+.     |
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i   86 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI   86 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEE
Confidence            45789999999999999999999999999999999876       89999999999999999999999999998     7


Q ss_pred             EEEecCC
Q 040243          564 AVRVAGK  570 (797)
Q Consensus       564 ~V~~A~~  570 (797)
                      +|..+..
T Consensus        87 ~v~~~~~   93 (115)
T 3beg_B           87 RVKVDGP   93 (115)
T ss_dssp             EEEECC-
T ss_pred             EeccCCC
Confidence            7776654

>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=99.53  E-value=2.2e-14  Score=141.80  Aligned_cols=85  Identities=26%  Similarity=0.443  Sum_probs=78.4

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      .....++|||+||++++++++|+++|++||.|.+|+|++++.+|+++|||||+|.+.++|++||+. ++..|+|+.|.|.
T Consensus         9 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~   87 (196)
T 1l3k_A            9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPK   87 (196)
T ss_dssp             CCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeee
Confidence            445678999999999999999999999999999999999999999999999999999999999976 8999999999999


Q ss_pred             ecCCCC
Q 040243          567 VAGKPP  572 (797)
Q Consensus       567 ~A~~~~  572 (797)
                      ++....
T Consensus        88 ~~~~~~   93 (196)
T 1l3k_A           88 RAVSRE   93 (196)
T ss_dssp             ECCC--
T ss_pred             cccCcc
Confidence            987543

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.53  E-value=2.8e-14  Score=141.26  Aligned_cols=85  Identities=36%  Similarity=0.658  Sum_probs=81.0

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ...++|||+||++++++++|+++|++||.|.+|++.+++.+|+++|||||+|.+.++|++||+.|||..|+|+.|+|+|+
T Consensus       112 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  191 (198)
T 2yh0_A          112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  191 (198)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCC
Q 040243          569 GKPPQ  573 (797)
Q Consensus       569 ~~~~~  573 (797)
                      ..+.+
T Consensus       192 ~~~~~  196 (198)
T 2yh0_A          192 SVGAK  196 (198)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87654

>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=99.52  E-value=1.7e-14  Score=139.70  Aligned_cols=80  Identities=39%  Similarity=0.720  Sum_probs=77.0

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      ..++|||+||+.++++++|+++|++||.|.++++.+++.+|+++|||||+|.+.++|++|++.|||..|+|+.|+|+||.
T Consensus        93 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~As  172 (172)
T 2g4b_A           93 GAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS  172 (172)
T ss_dssp             TTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeCC
Confidence            36789999999999999999999999999999999999999999999999999999999999999999999999999984

>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=99.52  E-value=3e-14  Score=160.71  Aligned_cols=84  Identities=20%  Similarity=0.410  Sum_probs=79.9

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      ..++|||+||+++|++++|+++|++||.|..|.|+.++.||+++|||||+|.+.++|++||+.|||+.|+|+.|.|.|+.
T Consensus       101 ~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a~  180 (437)
T 3pgw_S          101 AFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  180 (437)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            46799999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 040243          570 KPPQ  573 (797)
Q Consensus       570 ~~~~  573 (797)
                      ....
T Consensus       181 ~~~~  184 (437)
T 3pgw_S          181 GRTV  184 (437)
T ss_pred             CCCC
Confidence            6543

>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=99.52  E-value=1.5e-14  Score=139.35  Aligned_cols=81  Identities=23%  Similarity=0.486  Sum_probs=77.4

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      ..++|||+||+.++++++|+++|++||.|.+++|+.++.+|+++|||||+|.+.++|.+|++ +++..|+|+.|+|+||.
T Consensus        86 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~  164 (167)
T 2cjk_A           86 KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAE  164 (167)
T ss_dssp             HCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECC
T ss_pred             CCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecC
Confidence            46799999999999999999999999999999999999999999999999999999999998 89999999999999997


Q ss_pred             CC
Q 040243          570 KP  571 (797)
Q Consensus       570 ~~  571 (797)
                      ++
T Consensus       165 pk  166 (167)
T 2cjk_A          165 PR  166 (167)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.51  E-value=5.1e-15  Score=148.66  Aligned_cols=84  Identities=30%  Similarity=0.398  Sum_probs=76.2

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ...++|||+||+.++++++|+++|++||.|.+|+|++++.+|+++|||||+|.+.++|++||+.|++..|+|+.|+|.++
T Consensus        26 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~  105 (216)
T 2qfj_A           26 AIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRP  105 (216)
T ss_dssp             HHHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECC
T ss_pred             CcCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecC
Confidence            35689999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CCCC
Q 040243          569 GKPP  572 (797)
Q Consensus       569 ~~~~  572 (797)
                      ....
T Consensus       106 ~~~~  109 (216)
T 2qfj_A          106 SNIG  109 (216)
T ss_dssp             SCCG
T ss_pred             CCcc
Confidence            6543

>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=99.50  E-value=4.6e-14  Score=138.88  Aligned_cols=80  Identities=19%  Similarity=0.231  Sum_probs=72.4

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeecc--ceEEEE
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEG--RTIAVR  566 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~G--r~L~V~  566 (797)
                      ....+|||+||++.+++++|+++|++||.|.+|+|+.++    ++|||||+|.+.++|++|++.|||..|.|  +.|+|+
T Consensus        44 s~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~----~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~  119 (164)
T 1sjr_A           44 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID  119 (164)
T ss_dssp             CCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESS----SCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEE
T ss_pred             CceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCC----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEE
Confidence            345689999999999999999999999999999987543    57999999999999999999999999965  999999


Q ss_pred             ecCCCC
Q 040243          567 VAGKPP  572 (797)
Q Consensus       567 ~A~~~~  572 (797)
                      |++.+.
T Consensus       120 ~Ak~~~  125 (164)
T 1sjr_A          120 FSKLTS  125 (164)
T ss_dssp             ECSSSS
T ss_pred             EecCCc
Confidence            998654

>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=99.50  E-value=5.6e-14  Score=138.92  Aligned_cols=85  Identities=19%  Similarity=0.409  Sum_probs=76.0

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      ..++|||+||++++++++|+++|++||.|.+|+|+.++.+|+++|||||+|.+.++|.+||+. ++..|+|+.|.|+||.
T Consensus       103 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a~  181 (196)
T 1l3k_A          103 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKAL  181 (196)
T ss_dssp             CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEECC
T ss_pred             CcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEecC
Confidence            457999999999999999999999999999999999999999999999999999999999986 7999999999999998


Q ss_pred             CCCCCC
Q 040243          570 KPPQPT  575 (797)
Q Consensus       570 ~~~~~~  575 (797)
                      .+....
T Consensus       182 ~k~~~~  187 (196)
T 1l3k_A          182 SKQEMA  187 (196)
T ss_dssp             ------
T ss_pred             ChhHhc
Confidence            766543

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.49  E-value=5.4e-14  Score=142.80  Aligned_cols=80  Identities=36%  Similarity=0.565  Sum_probs=74.9

Q ss_pred             CcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecCC
Q 040243          491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGK  570 (797)
Q Consensus       491 ~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~~  570 (797)
                      .++|||+||++.+++++|+++|++||.|.+|+|++|+  +.+||||||+|.+.++|++||+.|||+.|+|+.|+|+||..
T Consensus       103 ~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~--~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~  180 (213)
T 4f02_A          103 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS  180 (213)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC--CCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            4589999999999999999999999999999999985  55899999999999999999999999999999999999976


Q ss_pred             CC
Q 040243          571 PP  572 (797)
Q Consensus       571 ~~  572 (797)
                      +.
T Consensus       181 ~~  182 (213)
T 4f02_A          181 RK  182 (213)
T ss_dssp             HH
T ss_pred             Cc
Confidence            43

>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=99.49  E-value=9e-14  Score=133.84  Aligned_cols=80  Identities=39%  Similarity=0.729  Sum_probs=76.5

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeecc--ceEEEE
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEG--RTIAVR  566 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~G--r~L~V~  566 (797)
                      ...++|||+||+..+++++|+++|++||.|.++++++++.+|+++|||||+|.+.++|.+|++.|||..|+|  +.|+|+
T Consensus        87 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~  166 (168)
T 1b7f_A           87 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR  166 (168)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEE
Confidence            356799999999999999999999999999999999999999999999999999999999999999999988  999999


Q ss_pred             ec
Q 040243          567 VA  568 (797)
Q Consensus       567 ~A  568 (797)
                      ||
T Consensus       167 ~A  168 (168)
T 1b7f_A          167 LA  168 (168)
T ss_dssp             EC
T ss_pred             eC
Confidence            86

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.49  E-value=7.4e-14  Score=133.70  Aligned_cols=81  Identities=28%  Similarity=0.456  Sum_probs=75.4

Q ss_pred             cEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecCCC
Q 040243          492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKP  571 (797)
Q Consensus       492 ~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~~~  571 (797)
                      ++|||+||+.++++++|+++|++||.|.+|+|++++ +++++|||||+|.+.++|++|++.|+|..+.|+.|+|.++...
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            489999999999999999999999999999999997 5889999999999999999999999999999999999998755


Q ss_pred             CC
Q 040243          572 PQ  573 (797)
Q Consensus       572 ~~  573 (797)
                      ..
T Consensus        80 ~~   81 (166)
T 3md3_A           80 QQ   81 (166)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.49  E-value=5.1e-14  Score=124.36  Aligned_cols=78  Identities=17%  Similarity=0.385  Sum_probs=62.9

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      ....++|||+||++++++++|+++|++||.|.+|+|+++     +||||||+|.+.++|+++..  ....+.|+.|.|.+
T Consensus         8 ~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~~~~--~~~~~~g~~v~v~~   80 (89)
T 3d2w_A            8 HHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQSLCG--EDLIIKGISVHISN   80 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHHHTT--CEEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHHHcC--CCcccCCEEEEEEE
Confidence            356789999999999999999999999999999999875     78999999999999984321  13345699999999


Q ss_pred             cCCCC
Q 040243          568 AGKPP  572 (797)
Q Consensus       568 A~~~~  572 (797)
                      |..+.
T Consensus        81 a~~k~   85 (89)
T 3d2w_A           81 AEPKH   85 (89)
T ss_dssp             CC---
T ss_pred             cCCCC
Confidence            87653

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.48  E-value=8.9e-14  Score=127.95  Aligned_cols=78  Identities=21%  Similarity=0.386  Sum_probs=68.2

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCC---CcccceEEEEecCHHHHHHHHHhcCceeeccceEEE
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVT---GMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAV  565 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~T---GksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V  565 (797)
                      ...++|||+||++++++++|+++|++||.|. +.++.++.+   |++||||||+|.+.++|++||+.|+  .++|+.|.|
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            3567899999999999999999999999999 888888877   7999999999999999999999883  366776666


Q ss_pred             EecC
Q 040243          566 RVAG  569 (797)
Q Consensus       566 ~~A~  569 (797)
                      ..+.
T Consensus        83 ~~~~   86 (114)
T 2dnl_A           83 VSSP   86 (114)
T ss_dssp             ECCS
T ss_pred             ccCC
Confidence            5543

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.48  E-value=1.1e-13  Score=131.38  Aligned_cols=78  Identities=19%  Similarity=0.288  Sum_probs=71.2

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccce-EEEEecCHHHHHHHHHhcCceeecc--ceEEEE
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGY-GFVKYADIQMANNAIASMNGYRLEG--RTIAVR  566 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGf-aFV~F~s~e~A~~AI~~LnG~~l~G--r~L~V~  566 (797)
                      ..-+|||+||++.+|+++|+++|++||.|.+|+|+.+     .+|| |||+|.+.++|++|++.|||..|.|  +.|+|+
T Consensus        27 ~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~-----~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~  101 (130)
T 3zzy_A           27 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID  101 (130)
T ss_dssp             SEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE-----TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEE
T ss_pred             ceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC-----CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEE
Confidence            4468999999999999999999999999999988764     3688 9999999999999999999999998  899999


Q ss_pred             ecCCCC
Q 040243          567 VAGKPP  572 (797)
Q Consensus       567 ~A~~~~  572 (797)
                      |++...
T Consensus       102 ~ak~~~  107 (130)
T 3zzy_A          102 FSKLTS  107 (130)
T ss_dssp             ECSCSS
T ss_pred             ecCCCc
Confidence            998654

>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=99.48  E-value=6.7e-13  Score=139.49  Aligned_cols=83  Identities=25%  Similarity=0.461  Sum_probs=76.3

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHH----HHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccce
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLI----RLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRT  562 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~----~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~  562 (797)
                      +....++|||+||++++++++|+    ++|++||.|.+|+|.+   ++++||||||+|.+.++|++||+.|||..|.|+.
T Consensus         5 ~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   81 (282)
T 3pgw_A            5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKP   81 (282)
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcE
Confidence            34568899999999999999976    8999999999999876   7889999999999999999999999999999999


Q ss_pred             EEEEecCCCC
Q 040243          563 IAVRVAGKPP  572 (797)
Q Consensus       563 L~V~~A~~~~  572 (797)
                      |+|+|++...
T Consensus        82 l~v~~a~~~~   91 (282)
T 3pgw_A           82 MRIQYAKTDS   91 (282)
T ss_pred             EEEEEeccCc
Confidence            9999997644

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.48  E-value=5.4e-14  Score=122.94  Aligned_cols=78  Identities=21%  Similarity=0.420  Sum_probs=67.7

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      ..++|||+||++++++++|+++|++||.|.+|+|+++     +||||||+|.+.++|++|+..  ...+.|+.|+|.++.
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~~--~~~~~g~~l~v~~a~   76 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGE--DLIIKGISVHISNAE   76 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTTC--EEEETTEEEEEECCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhcC--CceeCCEEEEEEecC
Confidence            4679999999999999999999999999999999865     789999999999999876432  456789999999998


Q ss_pred             CCCCC
Q 040243          570 KPPQP  574 (797)
Q Consensus       570 ~~~~~  574 (797)
                      .+...
T Consensus        77 ~~~~~   81 (88)
T 1wf0_A           77 PKHNS   81 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            66543

>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=99.47  E-value=1.1e-13  Score=132.73  Aligned_cols=79  Identities=39%  Similarity=0.727  Sum_probs=75.1

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccce--EEEEe
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRT--IAVRV  567 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~--L~V~~  567 (797)
                      ..++|||+||+..+++++|+++|++||.|.+++++.++.+|+++|||||+|.+.++|.+|++.|||..|+|+.  |+|+|
T Consensus        87 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~~  166 (167)
T 1fxl_A           87 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKF  166 (167)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEEe
Confidence            4578999999999999999999999999999999999999999999999999999999999999999999975  88888


Q ss_pred             c
Q 040243          568 A  568 (797)
Q Consensus       568 A  568 (797)
                      |
T Consensus       167 A  167 (167)
T 1fxl_A          167 A  167 (167)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.47  E-value=8.6e-14  Score=141.46  Aligned_cols=78  Identities=24%  Similarity=0.390  Sum_probs=72.5

Q ss_pred             CCcEEEEecCC-CCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          490 DDTNLYIGYLP-PTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       490 ~~~tLfVgNLp-~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      .+++|||+||+ +.+++++|+++|++||.|.+|+|+++     +||||||+|.+.++|++||+.|||..|.|+.|+|.++
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s   77 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVS   77 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT-----STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC-----CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEc
Confidence            46799999999 89999999999999999999999876     3799999999999999999999999999999999999


Q ss_pred             CCCC
Q 040243          569 GKPP  572 (797)
Q Consensus       569 ~~~~  572 (797)
                      +...
T Consensus        78 ~~~~   81 (205)
T 3tyt_A           78 KQPA   81 (205)
T ss_dssp             SCSC
T ss_pred             cCCc
Confidence            7543

>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=99.47  E-value=9.5e-14  Score=128.92  Aligned_cols=78  Identities=18%  Similarity=0.296  Sum_probs=69.9

Q ss_pred             CCCcEEEE--ecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceee-----ccc
Q 040243          489 LDDTNLYI--GYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRL-----EGR  561 (797)
Q Consensus       489 ~~~~tLfV--gNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l-----~Gr  561 (797)
                      ...++|||  |||++++++++|+++|++||.|.+|.|..      .||||||+|.+.++|++|++.|||..|     .|+
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~------~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~   96 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKI   96 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT------TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEE
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCc
Confidence            34678999  77999999999999999999999998754      369999999999999999999999998     689


Q ss_pred             eEEEEecCCCC
Q 040243          562 TIAVRVAGKPP  572 (797)
Q Consensus       562 ~L~V~~A~~~~  572 (797)
                      .|.|.|++...
T Consensus        97 ~l~v~~a~~~p  107 (114)
T 2cq2_A           97 TLYLNFVEKVQ  107 (114)
T ss_dssp             ECEEEEESCCC
T ss_pred             EEEEEecccCc
Confidence            99999987544

>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=99.46  E-value=1.3e-13  Score=133.32  Aligned_cols=79  Identities=27%  Similarity=0.561  Sum_probs=74.0

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeec---cceEEEE
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLE---GRTIAVR  566 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~---Gr~L~V~  566 (797)
                      ..++|||+||+..+++++|+++|++||.|.+|++++++ +|+++|||||+|.+.++|.+||+.|||..+.   ++.|+|+
T Consensus        94 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~  172 (175)
T 3nmr_A           94 EDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVK  172 (175)
T ss_dssp             GGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEE
T ss_pred             CCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECC-CCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEE
Confidence            56799999999999999999999999999999999996 6999999999999999999999999998776   4999999


Q ss_pred             ecC
Q 040243          567 VAG  569 (797)
Q Consensus       567 ~A~  569 (797)
                      ||.
T Consensus       173 ~ad  175 (175)
T 3nmr_A          173 FAD  175 (175)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            984

>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=99.45  E-value=1.2e-13  Score=119.92  Aligned_cols=72  Identities=18%  Similarity=0.575  Sum_probs=67.1

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcC----C-------CEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCcee
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTF----G-------DIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYR  557 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~f----G-------~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~  557 (797)
                      ...++|||+||++++++++|+++|++|    |       .|.++++.++      ||||||+|.+.++|++|+ .|||..
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~l~g~~   76 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDGII   76 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-GGTTCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-hcCCCE
Confidence            457899999999999999999999999    8       9999998765      699999999999999999 999999


Q ss_pred             eccceEEEEe
Q 040243          558 LEGRTIAVRV  567 (797)
Q Consensus       558 l~Gr~L~V~~  567 (797)
                      |+|+.|+|+.
T Consensus        77 ~~g~~l~V~r   86 (87)
T 2hzc_A           77 FQGQSLKIRR   86 (87)
T ss_dssp             ETTEECEEEC
T ss_pred             ECCeEEEEeC
Confidence            9999999974

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.45  E-value=2.5e-13  Score=121.50  Aligned_cols=75  Identities=25%  Similarity=0.333  Sum_probs=66.9

Q ss_pred             CcEEEEecCCCCCcHHH----HHHHhhcC-CCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEE
Q 040243          491 DTNLYIGYLPPTLDDDG----LIRLFSTF-GDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAV  565 (797)
Q Consensus       491 ~~tLfVgNLp~~vte~d----L~~~Fs~f-G~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V  565 (797)
                      .+.|||+||++.+++++    |+++|++| |.|.+|       |+   |||||+|.+.++|++|++.|+|..|.||.|+|
T Consensus         9 ~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v   78 (96)
T 2diu_A            9 HTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFGNRIIV   78 (96)
T ss_dssp             SEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             ceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCCceEEE
Confidence            34499999999999987    55899999 599998       34   99999999999999999999999999999999


Q ss_pred             EecCCCCCCC
Q 040243          566 RVAGKPPQPT  575 (797)
Q Consensus       566 ~~A~~~~~~~  575 (797)
                      .+|+......
T Consensus        79 ~~A~~~sd~~   88 (96)
T 2diu_A           79 SFTPKNRELC   88 (96)
T ss_dssp             ESSCCSCCCC
T ss_pred             EecCCCccee
Confidence            9998776543

>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=99.45  E-value=1.5e-13  Score=133.00  Aligned_cols=83  Identities=24%  Similarity=0.450  Sum_probs=75.8

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCC--cccceEEEEecCHHHHHHHHHhcCceeec---cceEE
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTG--MSKGYGFVKYADIQMANNAIASMNGYRLE---GRTIA  564 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TG--ksrGfaFV~F~s~e~A~~AI~~LnG~~l~---Gr~L~  564 (797)
                      +.++|||+||++++++++|+++|++||.|.+|+|++++.++  +++|||||+|.+.++|++|++.|++..+.   ++.+.
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            56899999999999999999999999999999999999887  99999999999999999999999998776   67788


Q ss_pred             EEecCCCC
Q 040243          565 VRVAGKPP  572 (797)
Q Consensus       565 V~~A~~~~  572 (797)
                      |.++....
T Consensus        82 ~~~~~~~~   89 (175)
T 3nmr_A           82 MKPADSEK   89 (175)
T ss_dssp             EEECGGGC
T ss_pred             Eccccccc
Confidence            88876443

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.45  E-value=2.5e-13  Score=127.97  Aligned_cols=76  Identities=21%  Similarity=0.246  Sum_probs=68.6

Q ss_pred             CcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccce-EEEEecCHHHHHHHHHhcCceeecc--ceEEEEe
Q 040243          491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGY-GFVKYADIQMANNAIASMNGYRLEG--RTIAVRV  567 (797)
Q Consensus       491 ~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGf-aFV~F~s~e~A~~AI~~LnG~~l~G--r~L~V~~  567 (797)
                      ...|||+||++.+++++|+++|++||.|.+|+|+. +     .|| |||+|.+.++|++|++.|||..|.|  +.|+|.+
T Consensus        25 vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~-~-----~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~   98 (124)
T 2e5i_A           25 VLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFK-R-----NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEY   98 (124)
T ss_dssp             EEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEE-S-----SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEEC
T ss_pred             EEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEe-C-----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEE
Confidence            34678999999999999999999999999999865 3     286 9999999999999999999999988  6899999


Q ss_pred             cCCCC
Q 040243          568 AGKPP  572 (797)
Q Consensus       568 A~~~~  572 (797)
                      |+.+.
T Consensus        99 Ak~~~  103 (124)
T 2e5i_A           99 ARPTR  103 (124)
T ss_dssp             CSCSC
T ss_pred             ecCCc
Confidence            98665

>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=99.45  E-value=9.9e-14  Score=133.63  Aligned_cols=79  Identities=25%  Similarity=0.497  Sum_probs=74.0

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      +.++|||+||++++++++|+++|++||.|.+|+|++++.+|+++|||||+|.+.++|++||+.  +..|+|+.|.|.++.
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            467999999999999999999999999999999999999999999999999999999999984  678999999999876


Q ss_pred             C
Q 040243          570 K  570 (797)
Q Consensus       570 ~  570 (797)
                      .
T Consensus        80 ~   80 (167)
T 2cjk_A           80 P   80 (167)
T ss_dssp             C
T ss_pred             c
Confidence            4

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.44  E-value=3.7e-13  Score=122.92  Aligned_cols=82  Identities=10%  Similarity=0.084  Sum_probs=72.9

Q ss_pred             CCCcEEEEecCCC-----CCcHHHHHHHhhcCCCEEEEEEEecCCC-CcccceEEEEecCHHHHHHHHHhcCceeeccce
Q 040243          489 LDDTNLYIGYLPP-----TLDDDGLIRLFSTFGDIVMAKVIKDRVT-GMSKGYGFVKYADIQMANNAIASMNGYRLEGRT  562 (797)
Q Consensus       489 ~~~~tLfVgNLp~-----~vte~dL~~~Fs~fG~I~~v~v~~dk~T-GksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~  562 (797)
                      ...++|+|.||-.     .-++++|+++|++||.|.+|+|++++.+ ++++|||||+|.+.++|.+|++.|||..|+||.
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            3567999999963     2368999999999999999999998754 689999999999999999999999999999999


Q ss_pred             EEEEecCC
Q 040243          563 IAVRVAGK  570 (797)
Q Consensus       563 L~V~~A~~  570 (797)
                      |+|.++..
T Consensus        86 i~v~~a~~   93 (105)
T 2pe8_A           86 VKACFYNL   93 (105)
T ss_dssp             CEEEECCH
T ss_pred             EEEEEcCH
Confidence            99999853

>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=99.42  E-value=3.1e-13  Score=131.51  Aligned_cols=78  Identities=19%  Similarity=0.365  Sum_probs=72.3

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ...++|||+||+..+++++|+++|++||.|..+     ..+++++|||||+|.+.++|.+||+.|||..|+|+.|+|+||
T Consensus        97 ~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  171 (175)
T 1fje_B           97 RAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT  171 (175)
T ss_dssp             GGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEEC
T ss_pred             ccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEec
Confidence            356799999999999999999999999988766     458999999999999999999999999999999999999999


Q ss_pred             CCC
Q 040243          569 GKP  571 (797)
Q Consensus       569 ~~~  571 (797)
                      ..+
T Consensus       172 ~~k  174 (175)
T 1fje_B          172 GEK  174 (175)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            754

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A

Probab=99.42  E-value=4.5e-13  Score=135.03  Aligned_cols=79  Identities=14%  Similarity=0.239  Sum_probs=73.2

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      ..++|||+||++.+++++|+++|++||.|.+|+|.++. ++++||||||+|.+.++|++||+.++ ..|+|+.|+|.|+.
T Consensus       108 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~~-~~~~Gr~l~V~~~~  185 (193)
T 2voo_A          108 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETPG-QKYKETDLLILFKD  185 (193)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCTT-CEETTEECEEEETT
T ss_pred             ccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhCC-CeECCEEEEEEEhH
Confidence            45899999999999999999999999999999999997 69999999999999999999998664 58999999999976


Q ss_pred             C
Q 040243          570 K  570 (797)
Q Consensus       570 ~  570 (797)
                      .
T Consensus       186 ~  186 (193)
T 2voo_A          186 D  186 (193)
T ss_dssp             T
T ss_pred             H
Confidence            4

>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=99.39  E-value=2.1e-12  Score=118.47  Aligned_cols=82  Identities=22%  Similarity=0.287  Sum_probs=70.5

Q ss_pred             CCCCcEEEEecCCCCCc-----------HHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCce
Q 040243          488 ELDDTNLYIGYLPPTLD-----------DDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGY  556 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vt-----------e~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~  556 (797)
                      ....++|+|.||-...+           +++|+++|++||.|.+|.| .++   .++|||||+|.+.++|++||+.|||+
T Consensus        12 ~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~lng~   87 (112)
T 2dit_A           12 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLDGR   87 (112)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHSTTC
T ss_pred             CCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcCCC
Confidence            34578999999954432           5799999999999999965 554   38999999999999999999999999


Q ss_pred             eeccceEEEEecCCCCC
Q 040243          557 RLEGRTIAVRVAGKPPQ  573 (797)
Q Consensus       557 ~l~Gr~L~V~~A~~~~~  573 (797)
                      .|+|+.|+|.|+.....
T Consensus        88 ~~~gr~l~v~~a~~~~~  104 (112)
T 2dit_A           88 WFGGRQITAQAWDGTTD  104 (112)
T ss_dssp             EETTEECEEEECCSCCC
T ss_pred             EECCcEEEEEEeCCCCC
Confidence            99999999999876543

>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=99.39  E-value=6e-13  Score=140.56  Aligned_cols=82  Identities=26%  Similarity=0.385  Sum_probs=76.2

Q ss_pred             CCCcEEEEecCCCC-CcHHHHHHHhhcCCCEEEEEEEecCC-CCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          489 LDDTNLYIGYLPPT-LDDDGLIRLFSTFGDIVMAKVIKDRV-TGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       489 ~~~~tLfVgNLp~~-vte~dL~~~Fs~fG~I~~v~v~~dk~-TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      ...++|||+||++. +++++|+++|++||.|.+|+|+.+.. ||+++|||||+|.+.++|.+|| .|||..|+|+.|+|.
T Consensus       208 ~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V~  286 (292)
T 2ghp_A          208 LEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVS  286 (292)
T ss_dssp             CTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEEE
T ss_pred             CCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEEE
Confidence            45679999999999 99999999999999999999999886 6999999999999999999999 999999999999999


Q ss_pred             ecCCC
Q 040243          567 VAGKP  571 (797)
Q Consensus       567 ~A~~~  571 (797)
                      ||..+
T Consensus       287 ~a~~k  291 (292)
T 2ghp_A          287 LADKK  291 (292)
T ss_dssp             ECCCC
T ss_pred             EecCC
Confidence            99865

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.38  E-value=5.1e-13  Score=139.15  Aligned_cols=80  Identities=30%  Similarity=0.445  Sum_probs=71.1

Q ss_pred             CCCCcEEEEecCCCCC---------cHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceee
Q 040243          488 ELDDTNLYIGYLPPTL---------DDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRL  558 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~v---------te~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l  558 (797)
                      +...++||||||+..+         +|++|+++|++||.|.+|+|+.      +||||||+|.+.++|+.|++.|+|..|
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~------~kG~AFV~F~~~~~Ae~A~~am~g~~l  204 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE------SKNCGFVKFKYQANAEFAKEAMSNQTL  204 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG------GGTEEEEEESSHHHHHHHHHHHTTCCC
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC------CCCEEEEEeCCHHHHHHHHHHhCCCEE
Confidence            3467899999999998         7999999999999999999985      469999999999999999999999999


Q ss_pred             ------------ccceEEEEecCCCCC
Q 040243          559 ------------EGRTIAVRVAGKPPQ  573 (797)
Q Consensus       559 ------------~Gr~L~V~~A~~~~~  573 (797)
                                  .|+.|.|+||+....
T Consensus       205 ~~~~~~e~~~~~~gr~L~V~wA~~~pn  231 (240)
T 3u1l_A          205 LLPSDKEWDDRREGTGLLVKWANEDPD  231 (240)
T ss_dssp             CCTTSTTGGGGGGSCCCEEEECC----
T ss_pred             eccccccccccCCCCEEEEEEccCCCC
Confidence                        899999999986554

>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=99.38  E-value=8e-13  Score=135.61  Aligned_cols=79  Identities=25%  Similarity=0.473  Sum_probs=74.0

Q ss_pred             CCCcEEEEecCCC-CCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          489 LDDTNLYIGYLPP-TLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       489 ~~~~tLfVgNLp~-~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      ...++|||+||++ ++++++|+++|++||.|.+|+|++++     +|||||+|.+.++|++||+.|+|..|.|+.|+|.+
T Consensus        32 ~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~  106 (229)
T 2adc_A           32 AGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITL  106 (229)
T ss_dssp             CCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEEC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            4678999999999 99999999999999999999999885     78999999999999999999999999999999999


Q ss_pred             cCCCC
Q 040243          568 AGKPP  572 (797)
Q Consensus       568 A~~~~  572 (797)
                      +....
T Consensus       107 a~~~~  111 (229)
T 2adc_A          107 SKHQN  111 (229)
T ss_dssp             CSCCC
T ss_pred             ecCcc
Confidence            97553

>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=99.37  E-value=2.2e-13  Score=132.57  Aligned_cols=84  Identities=20%  Similarity=0.298  Sum_probs=74.6

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      .....++|||+||++++++++|+++|..||.|.. .++.+..+|++||||||+|.+.++|++||+ |+|..|.|+.|+|.
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            4467899999999999999999999999998766 345555689999999999999999999994 99999999999999


Q ss_pred             ecCCCC
Q 040243          567 VAGKPP  572 (797)
Q Consensus       567 ~A~~~~  572 (797)
                      ++....
T Consensus        87 ~~~~~~   92 (175)
T 1fje_B           87 KPKGRD   92 (175)
T ss_dssp             CCCCSS
T ss_pred             cCCCcc
Confidence            987653

>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=99.37  E-value=1.3e-12  Score=137.38  Aligned_cols=78  Identities=19%  Similarity=0.383  Sum_probs=72.6

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeec-cceEEEE
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLE-GRTIAVR  566 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~-Gr~L~V~  566 (797)
                      ....++|||+||+..+++++|+++|++||.|.+|+|+.++     +|||||+|.+.++|++||+.|||+.|+ |+.|+|+
T Consensus       204 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~  278 (282)
T 3pgw_A          204 NPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKIS  278 (282)
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEE
Confidence            3457899999999999999999999999999999999765     589999999999999999999999999 9999999


Q ss_pred             ecCC
Q 040243          567 VAGK  570 (797)
Q Consensus       567 ~A~~  570 (797)
                      ||++
T Consensus       279 ~akk  282 (282)
T 3pgw_A          279 FAKK  282 (282)
T ss_pred             EecC
Confidence            9874

>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=99.36  E-value=1.7e-12  Score=136.60  Aligned_cols=83  Identities=30%  Similarity=0.460  Sum_probs=78.9

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      ..++|||+||++++++++|+++|+.||.|.+++++.++.+|+++|||||+|.+.++|.+|++.|+|..|+|+.|+|.|+.
T Consensus        94 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~  173 (284)
T 3smz_A           94 TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTD  173 (284)
T ss_dssp             CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECC
Confidence            34699999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             CCC
Q 040243          570 KPP  572 (797)
Q Consensus       570 ~~~  572 (797)
                      ...
T Consensus       174 ~~~  176 (284)
T 3smz_A          174 AGQ  176 (284)
T ss_dssp             GGG
T ss_pred             CCC
Confidence            654

>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=99.35  E-value=1.8e-12  Score=136.44  Aligned_cols=84  Identities=26%  Similarity=0.456  Sum_probs=78.7

Q ss_pred             CCCcEEEEecCCCCC-cHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          489 LDDTNLYIGYLPPTL-DDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       489 ~~~~tLfVgNLp~~v-te~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      ...++|||+||++.+ ++++|+++|+.||.|.+|+|+.+. +|+++|||||+|.+.++|.+|++.|||..|+|+.|+|.|
T Consensus       182 ~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  260 (284)
T 3smz_A          182 LHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSF  260 (284)
T ss_dssp             TSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECS-SCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECC-CCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEE
Confidence            456799999999995 999999999999999999999997 899999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 040243          568 AGKPPQ  573 (797)
Q Consensus       568 A~~~~~  573 (797)
                      +..+..
T Consensus       261 a~~~~~  266 (284)
T 3smz_A          261 CAPGPP  266 (284)
T ss_dssp             CCSSSC
T ss_pred             ecCCCc
Confidence            986553

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.33  E-value=9e-13  Score=131.16  Aligned_cols=78  Identities=26%  Similarity=0.485  Sum_probs=73.1

Q ss_pred             CCcEEEEecCCC-CCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          490 DDTNLYIGYLPP-TLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       490 ~~~tLfVgNLp~-~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      +.++|||+||++ .+++++|+++|++||.|.+|+|++++     +|||||+|.+.++|++||+.|+|..|.|+.|+|.|+
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a   76 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLS   76 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEEC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEe
Confidence            457999999999 99999999999999999999998875     789999999999999999999999999999999998


Q ss_pred             CCCC
Q 040243          569 GKPP  572 (797)
Q Consensus       569 ~~~~  572 (797)
                      ....
T Consensus        77 ~~~~   80 (198)
T 1qm9_A           77 KHQN   80 (198)
T ss_dssp             CCCS
T ss_pred             cCCC
Confidence            8654

>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=99.30  E-value=8.6e-13  Score=120.18  Aligned_cols=73  Identities=16%  Similarity=0.277  Sum_probs=65.1

Q ss_pred             EEecCCCCCcHHHHHHHh------------hcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccce
Q 040243          495 YIGYLPPTLDDDGLIRLF------------STFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRT  562 (797)
Q Consensus       495 fVgNLp~~vte~dL~~~F------------s~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~  562 (797)
                      ++.||++.+++++|+++|            ++||.|.+|+|.+++ ++++||||||+|.+.++|.+|++.|||..|+||.
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            367788888888777666            999999999999987 5899999999999999999999999999999999


Q ss_pred             EEEEec
Q 040243          563 IAVRVA  568 (797)
Q Consensus       563 L~V~~A  568 (797)
                      |+|+|+
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

>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=99.28  E-value=3.1e-12  Score=129.94  Aligned_cols=77  Identities=12%  Similarity=0.255  Sum_probs=69.7

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCE--EEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccc----eE
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDI--VMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGR----TI  563 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I--~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr----~L  563 (797)
                      ..++|||+||++.+++++|+++|++||.|  .+++++.++  ++++|||||+|.+.++|.+||..|||+.|.|+    .+
T Consensus       122 p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~  199 (205)
T 3tyt_A          122 PSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPY  199 (205)
T ss_dssp             CCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCE
T ss_pred             CcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcce
Confidence            35789999999999999999999999999  899998875  56779999999999999999999999999987    47


Q ss_pred             EEEec
Q 040243          564 AVRVA  568 (797)
Q Consensus       564 ~V~~A  568 (797)
                      .|+||
T Consensus       200 ~vk~~  204 (205)
T 3tyt_A          200 TLKLC  204 (205)
T ss_dssp             ECEEE
T ss_pred             EEEec
Confidence            77765

>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=99.27  E-value=7.4e-12  Score=131.03  Aligned_cols=81  Identities=27%  Similarity=0.351  Sum_probs=73.4

Q ss_pred             CcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCce-eec---cceEEEE
Q 040243          491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGY-RLE---GRTIAVR  566 (797)
Q Consensus       491 ~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~-~l~---Gr~L~V~  566 (797)
                      .++|||+||+..+++++|+++|+.||.|.+|+|+.| .+|+++|||||+|.+.++|.+||+.|++. .+.   ++.|.|+
T Consensus        96 ~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~  174 (261)
T 3sde_A           96 GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVE  174 (261)
T ss_dssp             SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE-TTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEE
T ss_pred             CCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeC-CCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEe
Confidence            458999999999999999999999999999999999 49999999999999999999999999554 444   9999999


Q ss_pred             ecCCCC
Q 040243          567 VAGKPP  572 (797)
Q Consensus       567 ~A~~~~  572 (797)
                      ++....
T Consensus       175 ~~~~~~  180 (261)
T 3sde_A          175 PMEQFD  180 (261)
T ss_dssp             ECCCEE
T ss_pred             eccccC
Confidence            987643

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.25  E-value=6.1e-12  Score=125.16  Aligned_cols=77  Identities=17%  Similarity=0.342  Sum_probs=71.6

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCC-CEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeec-cceEEEEe
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFG-DIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLE-GRTIAVRV  567 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG-~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~-Gr~L~V~~  567 (797)
                      ..++|||+||+..+++++|+++|++|| .|.+|+|+.+     .+|||||+|.+.++|.+|++.|||..|+ |+.|+|.|
T Consensus       119 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~  193 (198)
T 1qm9_A          119 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF  193 (198)
T ss_dssp             CCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST-----TSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC-----CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEe
Confidence            468999999999999999999999999 9999998764     2799999999999999999999999999 99999999


Q ss_pred             cCCC
Q 040243          568 AGKP  571 (797)
Q Consensus       568 A~~~  571 (797)
                      ++.+
T Consensus       194 a~~~  197 (198)
T 1qm9_A          194 SKST  197 (198)
T ss_dssp             ECCC
T ss_pred             eccc
Confidence            8753

>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=99.25  E-value=7.9e-12  Score=131.98  Aligned_cols=83  Identities=16%  Similarity=0.382  Sum_probs=70.9

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCC-CEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFG-DIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG-~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ..++|||+||++.+++++|+++|+.|| .|.+|+|+.++. |+++|||||+|.+.++|.+||+.|+|..|+|+.|+|.|+
T Consensus       116 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  194 (292)
T 2ghp_A          116 TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRF-NTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVS  194 (292)
T ss_dssp             CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCC-CCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence            467999999999999999999999999 999999999974 889999999999999999999999999999999999998


Q ss_pred             CCCCC
Q 040243          569 GKPPQ  573 (797)
Q Consensus       569 ~~~~~  573 (797)
                      .....
T Consensus       195 ~~~~~  199 (292)
T 2ghp_A          195 NPLEK  199 (292)
T ss_dssp             CCC--
T ss_pred             CCCcc
Confidence            75543

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.25  E-value=5.3e-11  Score=107.85  Aligned_cols=76  Identities=20%  Similarity=0.335  Sum_probs=64.0

Q ss_pred             CcEEEEecCC-------CCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceE
Q 040243          491 DTNLYIGYLP-------PTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTI  563 (797)
Q Consensus       491 ~~tLfVgNLp-------~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L  563 (797)
                      .++|.|.-..       ..+++++|+++|++||.|.+|+|+     +++||||||+|.+.++|++||+.+++  +.|+.|
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            4466666443       458999999999999999999987     46899999999999999999998555  689999


Q ss_pred             EEEecCCCCC
Q 040243          564 AVRVAGKPPQ  573 (797)
Q Consensus       564 ~V~~A~~~~~  573 (797)
                      +|+|++.+..
T Consensus        83 ~V~~a~~~~~   92 (100)
T 2d9o_A           83 KISWLEGQPQ   92 (100)
T ss_dssp             EEECSSCCCC
T ss_pred             EEEEccCCCC
Confidence            9999986654

>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=99.25  E-value=1.1e-11  Score=113.10  Aligned_cols=79  Identities=13%  Similarity=0.169  Sum_probs=69.1

Q ss_pred             CcEEEEecCC--CCC--------cHHHHHHHhhcCCCEEEEEEEecCCC--CcccceEEEEecCHHHHHHHHHhcCceee
Q 040243          491 DTNLYIGYLP--PTL--------DDDGLIRLFSTFGDIVMAKVIKDRVT--GMSKGYGFVKYADIQMANNAIASMNGYRL  558 (797)
Q Consensus       491 ~~tLfVgNLp--~~v--------te~dL~~~Fs~fG~I~~v~v~~dk~T--GksrGfaFV~F~s~e~A~~AI~~LnG~~l  558 (797)
                      .+.|.|.|+=  ..+        .+++|+++|++||.|.+|+|.+++.+  ++++||+||+|.+.++|.+|++.|||..|
T Consensus         5 s~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~f   84 (105)
T 3v4m_A            5 TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKF   84 (105)
T ss_dssp             CSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTCEE
T ss_pred             CeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCCEe
Confidence            5579999983  223        23689999999999999999999865  47899999999999999999999999999


Q ss_pred             ccceEEEEecC
Q 040243          559 EGRTIAVRVAG  569 (797)
Q Consensus       559 ~Gr~L~V~~A~  569 (797)
                      +||.|+|.++.
T Consensus        85 ~GR~i~v~~~~   95 (105)
T 3v4m_A           85 ANRVVVTKYCD   95 (105)
T ss_dssp             TTEECEEEEEC
T ss_pred             CCCEEEEEEeC
Confidence            99999999874

>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=99.25  E-value=1.5e-11  Score=114.70  Aligned_cols=80  Identities=15%  Similarity=0.214  Sum_probs=70.8

Q ss_pred             CCcEEEEecCCCC-----CcHHHHHHHhhcCCCEEEEEEEecCC----CCcccceEEEEecCHHHHHHHHHhcCceeecc
Q 040243          490 DDTNLYIGYLPPT-----LDDDGLIRLFSTFGDIVMAKVIKDRV----TGMSKGYGFVKYADIQMANNAIASMNGYRLEG  560 (797)
Q Consensus       490 ~~~tLfVgNLp~~-----vte~dL~~~Fs~fG~I~~v~v~~dk~----TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~G  560 (797)
                      ..++|+|.|+-..     -.++||++.|++||.|.+|+|.+++.    +++++||+||+|.+.++|.+|++.|||..|+|
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            4678999998421     23689999999999999999999875    46889999999999999999999999999999


Q ss_pred             ceEEEEecC
Q 040243          561 RTIAVRVAG  569 (797)
Q Consensus       561 r~L~V~~A~  569 (797)
                      |.|+|.++.
T Consensus        99 R~i~v~~~~  107 (118)
T 3ue2_A           99 RKVVAEVYD  107 (118)
T ss_dssp             EECEEEEEC
T ss_pred             cEEEEEEcC
Confidence            999999864

>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=99.24  E-value=1.4e-11  Score=126.26  Aligned_cols=77  Identities=17%  Similarity=0.342  Sum_probs=71.4

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCC-CEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeec-cceEEEEe
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFG-DIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLE-GRTIAVRV  567 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG-~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~-Gr~L~V~~  567 (797)
                      ..++|||+||+..+++++|+++|++|| .|.+|+|+.+     .+|||||+|.+.++|.+||+.|+|..|+ |+.|+|+|
T Consensus       150 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~  224 (229)
T 2adc_A          150 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF  224 (229)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS-----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEE
T ss_pred             CCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC-----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEE
Confidence            468999999999999999999999999 9999998663     3699999999999999999999999999 99999999


Q ss_pred             cCCC
Q 040243          568 AGKP  571 (797)
Q Consensus       568 A~~~  571 (797)
                      ++.+
T Consensus       225 a~~~  228 (229)
T 2adc_A          225 SKST  228 (229)
T ss_dssp             CSSC
T ss_pred             ecCC
Confidence            9753

>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=99.24  E-value=1.5e-11  Score=128.74  Aligned_cols=76  Identities=26%  Similarity=0.585  Sum_probs=71.0

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ...++|||+||++++|+++|+++|++||.|.+|+|.++      +|||||+|.+.++|.+||+.|+|..|.|+.|+|.++
T Consensus        20 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a   93 (261)
T 3sde_A           20 TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFA   93 (261)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeec
Confidence            45689999999999999999999999999999998654      699999999999999999999999999999999998


Q ss_pred             CC
Q 040243          569 GK  570 (797)
Q Consensus       569 ~~  570 (797)
                      ..
T Consensus        94 ~~   95 (261)
T 3sde_A           94 TH   95 (261)
T ss_dssp             CC
T ss_pred             cc
Confidence            64

>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=99.21  E-value=2.5e-11  Score=117.27  Aligned_cols=75  Identities=16%  Similarity=0.526  Sum_probs=67.3

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcC----C-------CEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceee
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTF----G-------DIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRL  558 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~f----G-------~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l  558 (797)
                      +.++|||+||+.++++++|+++|++|    |       .|.++++.      +++|||||+|.+.++|++|+ .|+|..|
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~------~~~g~afV~f~~~~~A~~A~-~~~~~~~   75 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN------QDKNFAFLEFRSVDETTQAM-AFDGIIF   75 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEE------TTTTEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEec------CCCCEEEEEeCCHHHHHHHH-HhCCcEe
Confidence            46799999999999999999999999    6       77777764      35799999999999999999 8999999


Q ss_pred             ccceEEEEecCCC
Q 040243          559 EGRTIAVRVAGKP  571 (797)
Q Consensus       559 ~Gr~L~V~~A~~~  571 (797)
                      +|+.|+|.++...
T Consensus        76 ~g~~i~v~~~~~~   88 (172)
T 2g4b_A           76 QGQSLKIRRPHDY   88 (172)
T ss_dssp             TTEECEEECCSSC
T ss_pred             cCceeeecCCccc
Confidence            9999999987644

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.20  E-value=3.7e-11  Score=118.76  Aligned_cols=76  Identities=16%  Similarity=0.517  Sum_probs=66.8

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcC----C-------CEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceee
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTF----G-------DIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRL  558 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~f----G-------~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l  558 (797)
                      ..++|||+||++++++++|+++|++|    |       .|.++++      ++++|||||+|.+.++|++|| .|||..|
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            46799999999999999999999999    5       5666654      456899999999999999999 8999999


Q ss_pred             ccceEEEEecCCCC
Q 040243          559 EGRTIAVRVAGKPP  572 (797)
Q Consensus       559 ~Gr~L~V~~A~~~~  572 (797)
                      +|+.|+|.++....
T Consensus        76 ~g~~i~v~~~~~~~   89 (198)
T 2yh0_A           76 QGQSLKIRRPHDYQ   89 (198)
T ss_dssp             TTEEEEEECCCCCC
T ss_pred             cCceEEEeCCCCCC
Confidence            99999999987543

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*

Probab=99.11  E-value=1e-10  Score=127.84  Aligned_cols=76  Identities=17%  Similarity=0.319  Sum_probs=65.6

Q ss_pred             CCCCcEEEEec--CCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeec---cc-
Q 040243          488 ELDDTNLYIGY--LPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLE---GR-  561 (797)
Q Consensus       488 ~~~~~tLfVgN--Lp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~---Gr-  561 (797)
                      +....+|||||  |++.++|++|+++|++||+|.+|.+..      +||||||+|.+.++|++||+.|||+.+.   |+ 
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~   88 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQK   88 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCccccccCCc
Confidence            34567999999  578999999999999999999987643      5799999999999999999999999874   44 


Q ss_pred             -eEEEEecC
Q 040243          562 -TIAVRVAG  569 (797)
Q Consensus       562 -~L~V~~A~  569 (797)
                       .|.|.++.
T Consensus        89 ~~ly~~~~~   97 (345)
T 3tht_A           89 ITLYLNFVE   97 (345)
T ss_dssp             EECEEEECS
T ss_pred             eEEEEEEee
Confidence             57888875

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens}

Probab=99.10  E-value=1.2e-10  Score=102.23  Aligned_cols=72  Identities=26%  Similarity=0.439  Sum_probs=61.4

Q ss_pred             ceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHH
Q 040243          250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQE  329 (797)
Q Consensus       250 ~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e  329 (797)
                      ....+|.||.      ++||+|||++|+|+|+|+++|||+|.|...|+.               ....+-+|.|+| +.+
T Consensus        13 ~~~~~i~Ip~------~~ig~IIGkgG~~Ik~I~~~tga~I~i~~~~~~---------------~~~~er~v~I~G-~~~   70 (85)
T 2opv_A           13 GTVQEIMIPA------GKAGLVIGKGGETIKQLQERAGVKMILIQDGSQ---------------NTNVDKPLRIIG-DPY   70 (85)
T ss_dssp             SEEEEEEECT------TTHHHHHTTTTHHHHHHHHHHTCEEEECSSSCS---------------STTSCEEEEEEE-CHH
T ss_pred             CEEEEEEeCh------hheeeeECCCCHHHHHHHHHHCCEEEEcCCCCC---------------CCCCceEEEEEe-CHH
Confidence            4567889998      899999999999999999999999999976631               112344899999 999


Q ss_pred             HHHHHHHHHHHhcC
Q 040243          330 SLEGAAAMVEKLLQ  343 (797)
Q Consensus       330 ~v~~A~~~I~~ll~  343 (797)
                      ++++|+++|+.|+.
T Consensus        71 ~v~~A~~~I~~i~~   84 (85)
T 2opv_A           71 KVQQACEMVMDILR   84 (85)
T ss_dssp             HHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHhc
Confidence            99999999999875

>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain, alpha-beta fold RNA-binding motif, immune system; 2.00A {Homo sapiens} SCOP: d.51.1.1 PDB: 1dt4_A

Probab=99.05  E-value=2.9e-10  Score=97.47  Aligned_cols=73  Identities=25%  Similarity=0.410  Sum_probs=61.0

Q ss_pred             ceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHH
Q 040243          250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQE  329 (797)
Q Consensus       250 ~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e  329 (797)
                      +.+.+|.||.      ++||+|||++|+|+|+|+++|||+|.|...+....+              ..+-.|.|+|. .+
T Consensus         2 ~~~~~i~Ip~------~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~--------------~~~~~v~I~G~-~~   60 (76)
T 1dtj_A            2 KELVEMAVPE------NLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPG--------------TRNRRVTITGS-PA   60 (76)
T ss_dssp             CEEEEEEEET------TTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTT--------------CCEEEEEEEES-HH
T ss_pred             ceEEEEEECh------HHcceEECCCchHHHHHHHHhCCEEEECcCCCCCCC--------------CceeEEEEEeC-HH
Confidence            5678899998      899999999999999999999999999865421111              12348999997 89


Q ss_pred             HHHHHHHHHHHhcC
Q 040243          330 SLEGAAAMVEKLLQ  343 (797)
Q Consensus       330 ~v~~A~~~I~~ll~  343 (797)
                      .+++|.++|+.+|.
T Consensus        61 ~v~~A~~~I~~~i~   74 (76)
T 1dtj_A           61 ATQAAQYLISQRVT   74 (76)
T ss_dssp             HHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHHHh
Confidence            99999999999986

>1x4m_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1

Probab=99.04  E-value=1.5e-10  Score=103.77  Aligned_cols=78  Identities=24%  Similarity=0.408  Sum_probs=65.9

Q ss_pred             CCCCceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEe
Q 040243          246 YRPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEA  325 (797)
Q Consensus       246 y~p~~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a  325 (797)
                      +.|-..+.+|.||.      ++||+|||.+|+|+|+|+++|||+|.|...+...               ...+-.|.|++
T Consensus        10 ~~p~~~~~~i~Ip~------~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~---------------~~~~r~v~I~G   68 (94)
T 1x4m_A           10 DGPGNAVQEIMIPA------SKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQN---------------TGADKPLRITG   68 (94)
T ss_dssp             CCCCCEEEEEEECH------HHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCS---------------SCSCEEEEEEE
T ss_pred             CCCCcEEEEEEECh------hhcceEECCCCHHHHHHHHHHCCeEEecCCCCCC---------------CCCceEEEEEe
Confidence            34677899999998      8999999999999999999999999998665211               12345899999


Q ss_pred             cCHHHHHHHHHHHHHhcCCC
Q 040243          326 ETQESLEGAAAMVEKLLQPV  345 (797)
Q Consensus       326 ~~~e~v~~A~~~I~~ll~~~  345 (797)
                       +.+++++|+++|+.+|...
T Consensus        69 -~~~~v~~A~~~I~~~i~~~   87 (94)
T 1x4m_A           69 -DPYKVQQAKEMVLELIRDQ   87 (94)
T ss_dssp             -CTTTHHHHHHHHHHHHCCC
T ss_pred             -CHHHHHHHHHHHHHHHhcc
Confidence             8899999999999999764

>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=98.98  E-value=4.1e-10  Score=104.39  Aligned_cols=77  Identities=18%  Similarity=0.251  Sum_probs=64.7

Q ss_pred             CCcEEEEecCCCCC----------cHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeec
Q 040243          490 DDTNLYIGYLPPTL----------DDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLE  559 (797)
Q Consensus       490 ~~~tLfVgNLp~~v----------te~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~  559 (797)
                      ..+.|.+.|+=.--          .++||++.|++||.|.+|+|.++.    .+||+||+|.+.++|.+|++.|||..|+
T Consensus         6 ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~f~   81 (114)
T 3s6e_A            6 ATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRWFA   81 (114)
T ss_dssp             CCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCEET
T ss_pred             CCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCEEC
Confidence            34578888874321          135789999999999999986653    5899999999999999999999999999


Q ss_pred             cceEEEEecCC
Q 040243          560 GRTIAVRVAGK  570 (797)
Q Consensus       560 Gr~L~V~~A~~  570 (797)
                      ||.|+|.|+..
T Consensus        82 GR~i~v~~~~~   92 (114)
T 3s6e_A           82 GKMITAAYVPL   92 (114)
T ss_dssp             TEECEEEEECH
T ss_pred             CEEEEEEEEcH
Confidence            99999999753

>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens}

Probab=98.96  E-value=6.9e-10  Score=101.77  Aligned_cols=74  Identities=19%  Similarity=0.321  Sum_probs=60.5

Q ss_pred             eEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHHH
Q 040243          251 LQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQES  330 (797)
Q Consensus       251 ~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~  330 (797)
                      .+.+|.||.      ++||+|||.+|+|||+|+++|||+|.|.......              ....+-.|.|++ +.++
T Consensus         7 ~~~~i~IP~------~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~~--------------~~~~~r~V~I~G-~~e~   65 (107)
T 2hh2_A            7 GEMTFSIPT------HKCGLVIGRGGENVKAINQQTGAFVEISRQLPPN--------------GDPNFKLFIIRG-SPQQ   65 (107)
T ss_dssp             CCEEEEEEG------GGTTTTSTTTTCHHHHHHHHSSSEEEECCCCCTT--------------CCTTEEEEEEES-CHHH
T ss_pred             CeEEEEECH------HHcCccCCCCcHHHHHHHHHhCCEEEEcCccCCC--------------CCCCceEEEEEC-CHHH
Confidence            367889998      8999999999999999999999999998643100              011234789999 8999


Q ss_pred             HHHHHHHHHHhcCCC
Q 040243          331 LEGAAAMVEKLLQPV  345 (797)
Q Consensus       331 v~~A~~~I~~ll~~~  345 (797)
                      |++|+++|+.+|...
T Consensus        66 v~~A~~~I~~~i~e~   80 (107)
T 2hh2_A           66 IDHAKQLIEEKIEGP   80 (107)
T ss_dssp             HHHHHHHHHHHSCSC
T ss_pred             HHHHHHHHHHHHhcc
Confidence            999999999998753

>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA binding protein/DNA complex; 1.60A {Homo sapiens}

Probab=98.94  E-value=7.9e-10  Score=94.95  Aligned_cols=73  Identities=26%  Similarity=0.387  Sum_probs=61.2

Q ss_pred             CCceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecC
Q 040243          248 PPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAET  327 (797)
Q Consensus       248 p~~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~  327 (797)
                      +..++.+|.||.      ++||+|||.+|+|+|+|+++|||+|.|....   .              ...+-.|.|+|. 
T Consensus         2 ~~~~~~~i~Ip~------~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~---~--------------~~~~~~v~I~G~-   57 (76)
T 2p2r_A            2 AQTTSHELTIPN------DLIGCIIGRQGAKINEIRQMSGAQIKIANPV---E--------------GSTDRQVTITGS-   57 (76)
T ss_dssp             -CCEEEEEEEEH------HHHHHHHCGGGHHHHHHHHHHCCEEEECCCC---T--------------TCSEEEEEEEEC-
T ss_pred             CCceEEEEEECh------HHcceEECCCChHHHHHHHHHCCEEEEcCCC---C--------------CCCeEEEEEEeC-
Confidence            456788999998      8999999999999999999999999998521   1              112338999997 


Q ss_pred             HHHHHHHHHHHHHhcCC
Q 040243          328 QESLEGAAAMVEKLLQP  344 (797)
Q Consensus       328 ~e~v~~A~~~I~~ll~~  344 (797)
                      .+.+++|.++|+.+|..
T Consensus        58 ~~~v~~A~~~I~~~i~~   74 (76)
T 2p2r_A           58 AASISLAQYLINVRLSS   74 (76)
T ss_dssp             HHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHc
Confidence            99999999999999864

>1ec6_A RNA-binding protein NOVA-2; KH domain, alpha-beta fold, RNA-binding motif, protein/RNA structure, RNA binding protein/RNA complex; 2.40A {Homo sapiens} SCOP: d.51.1.1

Probab=98.93  E-value=6.1e-10  Score=98.21  Aligned_cols=74  Identities=24%  Similarity=0.391  Sum_probs=61.2

Q ss_pred             ceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHH
Q 040243          250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQE  329 (797)
Q Consensus       250 ~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e  329 (797)
                      +.+.+|.||.      ++||+|||.+|+|+|+|+++|||+|.|...+....|              ..+-.|.|+|. .+
T Consensus         2 k~t~~i~IP~------~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~g--------------~~~r~v~I~G~-~~   60 (87)
T 1ec6_A            2 KELVEIAVPE------NLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPG--------------TRNRRVTITGS-PA   60 (87)
T ss_dssp             CSEEEEEEEH------HHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBSTT--------------SCEEEEEEESS-HH
T ss_pred             ceEEEEEECh------HHcCeeECCCcHhHHHHHHHhCCEEEEccCCCCCCC--------------CCceEEEEEcC-HH
Confidence            5678899998      899999999999999999999999999865421111              12238999997 89


Q ss_pred             HHHHHHHHHHHhcCC
Q 040243          330 SLEGAAAMVEKLLQP  344 (797)
Q Consensus       330 ~v~~A~~~I~~ll~~  344 (797)
                      .+++|..+|+.+|..
T Consensus        61 ~v~~A~~~I~~~i~~   75 (87)
T 1ec6_A           61 ATQAAQYLISQRVTY   75 (87)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhc
Confidence            999999999999864

>1we8_A Tudor and KH domain containing protein; structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.51.1.1

Probab=98.93  E-value=1.2e-09  Score=99.60  Aligned_cols=81  Identities=17%  Similarity=0.254  Sum_probs=63.8

Q ss_pred             CCCCCCCCCCceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCc
Q 040243          240 FKPPADYRPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDL  319 (797)
Q Consensus       240 ~~pp~dy~p~~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~L  319 (797)
                      +...++|.|  ++.+|.||.      ++||+|||++|+|+|+|+++|||+|.|......               ...++-
T Consensus         6 ~~~~s~~ap--~~~~i~Ip~------~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~~---------------~~~~~~   62 (104)
T 1we8_A            6 SGILTENTP--VFEQLSVPQ------RSVGRIIGRGGETIRSICKASGAKITCDKESEG---------------TLLLSR   62 (104)
T ss_dssp             CCCCSSSCE--EEEEEEEET------TTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCC---------------SSSSEE
T ss_pred             ccccCCCCC--EEEEEEECh------hheeeeECCCCHHHHHHHHHHCCEEEEecCCCC---------------CCCCcc
Confidence            345566666  455677998      899999999999999999999999999864310               012334


Q ss_pred             eEEEEecCHHHHHHHHHHHHHhcCC
Q 040243          320 HVLVEAETQESLEGAAAMVEKLLQP  344 (797)
Q Consensus       320 Hv~I~a~~~e~v~~A~~~I~~ll~~  344 (797)
                      .|.|+|... .+++|+++|+.+|..
T Consensus        63 ~V~I~G~~~-~v~~A~~~I~~~i~e   86 (104)
T 1we8_A           63 LIKISGTQK-EVAAAKHLILEKVSE   86 (104)
T ss_dssp             EEEEEEEHH-HHHHHHHHHHHHHHH
T ss_pred             eEEEEcCHH-HHHHHHHHHHHHHhh
Confidence            899999766 799999999999864

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens}

Probab=98.92  E-value=5.6e-10  Score=102.25  Aligned_cols=70  Identities=20%  Similarity=0.413  Sum_probs=58.8

Q ss_pred             EEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHHHH
Q 040243          252 QKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESL  331 (797)
Q Consensus       252 ~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v  331 (797)
                      +.+|.||.      ++||+|||++|+|||+|+++|||+|.|....                 ....+-+|.|++. .|++
T Consensus        12 ~~~i~Ip~------~~iG~IIGkgG~~Ik~I~~~TGakI~I~~~~-----------------~~~~er~V~I~G~-~e~v   67 (106)
T 2hh3_A           12 GIDVPVPR------HSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD-----------------GTGPEKIAHIMGP-PDRC   67 (106)
T ss_dssp             CEEEEEET------TTHHHHHTTTTHHHHHHHHHHTCEEEECSSC-----------------SSSSEEEEEEESS-HHHH
T ss_pred             EEEEEECH------HHcCccCCCCcHHHHHHHHHHCcEEEEecCC-----------------CCCceeEEEEEeC-HHHH
Confidence            56788998      8999999999999999999999999998432                 0122348999987 8999


Q ss_pred             HHHHHHHHHhcCCC
Q 040243          332 EGAAAMVEKLLQPV  345 (797)
Q Consensus       332 ~~A~~~I~~ll~~~  345 (797)
                      ++|+++|+.+|...
T Consensus        68 ~~A~~~I~~ii~~~   81 (106)
T 2hh3_A           68 EHAARIINDLLQSL   81 (106)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcc
Confidence            99999999998643

>1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian, alpha-beta fold, DNA binding protein; 0.95A {Homo sapiens} SCOP: d.51.1.1 PDB: 1zzj_A 1zzi_A

Probab=98.91  E-value=2e-09  Score=93.83  Aligned_cols=72  Identities=29%  Similarity=0.511  Sum_probs=60.0

Q ss_pred             CceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCH
Q 040243          249 PKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQ  328 (797)
Q Consensus       249 ~~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~  328 (797)
                      ..++.+|.||.      +++|+|||++|+|+|+|+++|||+|.|...-   .+              ..+-.|.|++ +.
T Consensus         5 ~~~~~~i~Vp~------~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~---~~--------------~~~~~v~I~G-~~   60 (82)
T 1zzk_A            5 PIITTQVTIPK------DLAGSIIGKGGQRIKQIRHESGASIKIDEPL---EG--------------SEDRIITITG-TQ   60 (82)
T ss_dssp             CCEEEEEEEET------TTGGGGTCGGGHHHHHHHHHHCCEEEECCTT---SC--------------SSEEEEEEEE-CH
T ss_pred             CeEEEEEEECh------HhcCeeECCCchHHHHHHHHHCCEEEEcCCC---CC--------------CCceEEEEEe-CH
Confidence            35788999998      8999999999999999999999999997421   01              1223799999 59


Q ss_pred             HHHHHHHHHHHHhcCC
Q 040243          329 ESLEGAAAMVEKLLQP  344 (797)
Q Consensus       329 e~v~~A~~~I~~ll~~  344 (797)
                      +.+++|.++|+.+|..
T Consensus        61 ~~v~~A~~~I~~~i~~   76 (82)
T 1zzk_A           61 DQIQNAQYLLQNSVKQ   76 (82)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHh
Confidence            9999999999999864

>1x4n_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 PDB: 2opu_A

Probab=98.90  E-value=1.1e-09  Score=97.66  Aligned_cols=72  Identities=22%  Similarity=0.495  Sum_probs=61.1

Q ss_pred             CceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCH
Q 040243          249 PKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQ  328 (797)
Q Consensus       249 ~~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~  328 (797)
                      ..++.+|.||.      ++||+|||++|+|+|+|+++|||+|.|.....   +              ..+-.|.|++. .
T Consensus        13 ~~~~~~i~Ip~------~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~---g--------------~~~r~v~I~G~-~   68 (92)
T 1x4n_A           13 SVMTEEYKVPD------GMVGFIIGRGGEQISRIQQESGCKIQIAPDSG---G--------------LPERSCMLTGT-P   68 (92)
T ss_dssp             CCEEEEEEEEH------HHHHHHHCSSSHHHHHHHHHSCCEEEECSCCT---T--------------CSEEEEEEEEC-H
T ss_pred             CCEEEEEEECh------HHcceeECCCchHHHHHHHHhCCEEEEcCCCC---C--------------CCccEEEEEeC-H
Confidence            45788999998      89999999999999999999999999986431   1              12237999997 8


Q ss_pred             HHHHHHHHHHHHhcCC
Q 040243          329 ESLEGAAAMVEKLLQP  344 (797)
Q Consensus       329 e~v~~A~~~I~~ll~~  344 (797)
                      +.|++|+++|+.+|..
T Consensus        69 e~v~~A~~~I~~~i~~   84 (92)
T 1x4n_A           69 ESVQSAKRLLDQIVEK   84 (92)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHh
Confidence            9999999999999864

>1wvn_A Poly(RC)-binding protein 1; KH domain, RNA binding domain, RNA binding protein; 2.10A {Homo sapiens} SCOP: d.51.1.1

Probab=98.89  E-value=1.6e-09  Score=94.43  Aligned_cols=71  Identities=28%  Similarity=0.436  Sum_probs=59.6

Q ss_pred             ceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHH
Q 040243          250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQE  329 (797)
Q Consensus       250 ~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e  329 (797)
                      .++.+|.||.      ++||+|||++|+|+|+|+++|||+|.|....   ++              ..+-.|.|+|.. +
T Consensus         5 ~~~~~i~Ip~------~~vg~IIGkgG~~Ik~I~~~sga~I~i~~~~---~~--------------~~~r~v~I~G~~-~   60 (82)
T 1wvn_A            5 QTTHELTIPN------NLIGCIIGRQGANINEIRQMSGAQIKIANPV---EG--------------SSGRQVTITGSA-A   60 (82)
T ss_dssp             CEEEEEEEEG------GGHHHHHCGGGHHHHHHHHHHCCEEEECCCC---TT--------------CSEEEEEEEECH-H
T ss_pred             cEEEEEEEch------HhccceeCCCchhHHHHHHHhCCEEEEecCC---CC--------------CCceEEEEEcCH-H
Confidence            5678999998      8999999999999999999999999998531   11              123389999965 9


Q ss_pred             HHHHHHHHHHHhcCC
Q 040243          330 SLEGAAAMVEKLLQP  344 (797)
Q Consensus       330 ~v~~A~~~I~~ll~~  344 (797)
                      .+++|+++|+.+|..
T Consensus        61 ~v~~A~~~I~~~i~~   75 (82)
T 1wvn_A           61 SISLAQYLINARLSS   75 (82)
T ss_dssp             HHHHHHHHHHHHTC-
T ss_pred             HHHHHHHHHHHHHHh
Confidence            999999999999875

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}

Probab=98.88  E-value=2e-09  Score=125.89  Aligned_cols=96  Identities=19%  Similarity=0.268  Sum_probs=84.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHhCCCC-CCCCCCCCCceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEecc
Q 040243          217 RARERLNKERQEIISQIIKRNPAF-KPPADYRPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGK  295 (797)
Q Consensus       217 r~~~~le~er~~li~~~~~~~p~~-~pp~dy~p~~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGk  295 (797)
                      .+.++-.+.+.+|++.|.+.+... ...+.|.|+..+.|  ||.      ++||.||||+|+|+|.|+++|||+|.|...
T Consensus       534 ~aL~~A~~g~~~I~~~m~~al~~~~~~~~~~ap~~~~~~--I~~------~kI~~vIG~gG~~Ik~I~e~tg~~I~I~d~  605 (630)
T 3u1k_A          534 EAIQQASVAKKEILQIMNKTISKPRASRKENGPVVETVQ--VPL------SKRAKFVGPGGYNLKKLQAETGVTISQVDE  605 (630)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHCSSCCSSCCTTCCEEEEEE--CCH------HHHHHHHCGGGHHHHHHHHHHCCEEEECSS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhhhcccCCeEEEEE--eCh------hHhheeECCCChhHHHHHHHHCCEEEEcCC
Confidence            456667778999999999999988 45789999988877  998      999999999999999999999999999876


Q ss_pred             ccccccccccccCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHhcC
Q 040243          296 GSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQ  343 (797)
Q Consensus       296 GS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v~~A~~~I~~ll~  343 (797)
                      |                       .|.|+|.+.+++++|+++|+.|+.
T Consensus       606 G-----------------------~V~I~~~~~~~~~~A~~~I~~i~~  630 (630)
T 3u1k_A          606 E-----------------------TFSVFAPTPSAMHEARDFITEICK  630 (630)
T ss_dssp             S-----------------------EEEEEESSHHHHHHHHHHTTC---
T ss_pred             c-----------------------EEEEEeCCHHHHHHHHHHHHHHhC
Confidence            6                       899999999999999999998863

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.84  E-value=7.5e-09  Score=91.80  Aligned_cols=74  Identities=23%  Similarity=0.509  Sum_probs=63.4

Q ss_pred             CcEEEEecCCC----C-CcH---HHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccce
Q 040243          491 DTNLYIGYLPP----T-LDD---DGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRT  562 (797)
Q Consensus       491 ~~tLfVgNLp~----~-vte---~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~  562 (797)
                      ..||+|.-++.    + .++   .+|.+.|++||+|..++|+.|+        +||+|.+.++|.+||+ |||..++||.
T Consensus         7 d~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~-mnG~~v~Gr~   77 (91)
T 2dnr_A            7 GGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLS-LNGKELLNRT   77 (91)
T ss_dssp             SCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGG-GTTCEETTEE
T ss_pred             CCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHh-cCCeEeCCeE
Confidence            45899988762    2 332   5789999999999999999874        8999999999999998 9999999999


Q ss_pred             EEEEecCCCCC
Q 040243          563 IAVRVAGKPPQ  573 (797)
Q Consensus       563 L~V~~A~~~~~  573 (797)
                      |+|+++++...
T Consensus        78 LkV~lkt~dW~   88 (91)
T 2dnr_A           78 ITIALKSPSGP   88 (91)
T ss_dssp             EEEEECCCSSC
T ss_pred             EEEEeCCCCcc
Confidence            99999987654

>2axy_A Poly(RC)-binding protein 2; protein-DNA complex, DNA binding protein-DNA complex; 1.70A {Homo sapiens} SCOP: d.51.1.1 PDB: 2pqu_A 2py9_A 1ztg_A 3vke_A*

Probab=98.84  E-value=2.6e-09  Score=91.17  Aligned_cols=70  Identities=26%  Similarity=0.370  Sum_probs=60.3

Q ss_pred             CceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCH
Q 040243          249 PKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQ  328 (797)
Q Consensus       249 ~~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~  328 (797)
                      ..+..+|.||.      +++|.|||++|+|+|+|+++|||+|.|...|+                   .+-.|.|+|. .
T Consensus         3 ~~~~~~i~ip~------~~ig~iIGkgG~~Ik~I~~~tga~I~i~~~~~-------------------~er~v~I~G~-~   56 (73)
T 2axy_A            3 VTLTIRLLMHG------KEVGSIIGKKGESVKKMREESGARINISEGNC-------------------PERIITLAGP-T   56 (73)
T ss_dssp             CCEEEEEEEEH------HHHHHHHCGGGHHHHHHHHHHCCEEEECSSCC-------------------SEEEEEEEEC-H
T ss_pred             ceEEEEEEECh------hHeeeEECCCCHHHHHHHHHHCCEEEEecCCC-------------------CcEEEEEEeC-H
Confidence            45778999998      99999999999999999999999999986541                   1126899998 9


Q ss_pred             HHHHHHHHHHHHhcCC
Q 040243          329 ESLEGAAAMVEKLLQP  344 (797)
Q Consensus       329 e~v~~A~~~I~~ll~~  344 (797)
                      +.+.+|+++|..+|..
T Consensus        57 ~~v~~A~~~I~~~l~e   72 (73)
T 2axy_A           57 NAIFKAFAMIIDKLEE   72 (73)
T ss_dssp             HHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHhc
Confidence            9999999999998753

>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1vih_A

Probab=98.82  E-value=4.7e-09  Score=89.15  Aligned_cols=68  Identities=15%  Similarity=0.205  Sum_probs=58.0

Q ss_pred             ceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHH
Q 040243          250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQE  329 (797)
Q Consensus       250 ~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e  329 (797)
                      ..+..|.||.      .++|+|||++|+|+|+|+++|||+|.|-..|.                  ++ =.|.|+|. .+
T Consensus         4 ~~~~~i~I~~------~~ig~iIG~gG~~I~~I~e~tg~~I~i~~~g~------------------~~-~~V~I~G~-~~   57 (71)
T 1vig_A            4 MDYVEINIDH------KFHRHLIGKSGANINRIKDQYKVSVRIPPDSE------------------KS-NLIRIEGD-PQ   57 (71)
T ss_dssp             CEEEEEEECS------SHHHHHTCSSCCHHHHHHHHTCCEEECCCCCS------------------SS-EEEEEEES-SH
T ss_pred             eEEEEEEECH------HHhhhhcCCCCccHHHHHHHHCCEEEECCCCC------------------cc-cEEEEEcC-HH
Confidence            4567888998      89999999999999999999999999986652                  00 17999998 58


Q ss_pred             HHHHHHHHHHHhcC
Q 040243          330 SLEGAAAMVEKLLQ  343 (797)
Q Consensus       330 ~v~~A~~~I~~ll~  343 (797)
                      ++++|.++|+.|+.
T Consensus        58 ~v~~A~~~I~~i~~   71 (71)
T 1vig_A           58 GVQQAKRELLELAS   71 (71)
T ss_dssp             HHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHHHHhC
Confidence            99999999999863

>1j5k_A Heterogeneous nuclear ribonucleoprotein K; single-stranded DNA binding protein, transcription factor, hnRNP K, CT element, C-MYC oncogene; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1khm_A

Probab=98.81  E-value=3.4e-09  Score=93.90  Aligned_cols=72  Identities=26%  Similarity=0.464  Sum_probs=60.3

Q ss_pred             CceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCH
Q 040243          249 PKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQ  328 (797)
Q Consensus       249 ~~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~  328 (797)
                      ..++.+|.||.      ++||+|||.+|+|+|+|+++|||+|.|...-   .              ...+-.|.|++. .
T Consensus        12 ~~~~~~i~Ip~------~~vg~IIGkgG~~Ik~I~~~tga~I~I~~~~---~--------------~~~~~~v~I~G~-~   67 (89)
T 1j5k_A           12 PIITTQVTIPK------DLAGSIIGKGGQRIKQIRHESGASIKIDEPL---E--------------GSEDRIITITGT-Q   67 (89)
T ss_dssp             CEEEEEEEEEH------HHHHHHHCGGGHHHHHHHHHTCCEEEECSCC---S--------------SSSEEEEEEEEE-H
T ss_pred             CeEEEEEEECh------hhcceeECCCCHhHHHHHHHhCCeEEecCCC---C--------------CCCccEEEEEcC-H
Confidence            46788999998      8999999999999999999999999997421   0              012237999997 8


Q ss_pred             HHHHHHHHHHHHhcCC
Q 040243          329 ESLEGAAAMVEKLLQP  344 (797)
Q Consensus       329 e~v~~A~~~I~~ll~~  344 (797)
                      +.+++|+++|+.+|..
T Consensus        68 e~v~~A~~~I~~~i~e   83 (89)
T 1j5k_A           68 DQIQNAQYLLQNSVKQ   83 (89)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHh
Confidence            9999999999999854

>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens}

Probab=98.80  E-value=9.7e-09  Score=100.21  Aligned_cols=101  Identities=24%  Similarity=0.369  Sum_probs=77.2

Q ss_pred             HHHHHHHHHHHHHHHHhCCCCCCCCCCCCCceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEecccccc
Q 040243          220 ERLNKERQEIISQIIKRNPAFKPPADYRPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVK  299 (797)
Q Consensus       220 ~~le~er~~li~~~~~~~p~~~pp~dy~p~~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k  299 (797)
                      +.+++.+..|++.|.+.. .+.+ .  ....++.+|.||.      +++|+|||.+|+|+|+|+++|||+|.|...+.  
T Consensus        58 e~v~~A~~~I~~~~~e~~-~~~~-~--~~~~~~~~i~vp~------~~~g~iIGkgG~~I~~i~~~tga~I~i~~~~~--  125 (163)
T 3krm_A           58 EAQFKAQGRIYGKLKEEN-FFGP-K--EEVKLETHIRVPA------SAAGRVIGKGGKTVNELQNLTAAEVVVPRDQT--  125 (163)
T ss_dssp             HHHHHHHHHHHHHHHHTT-SSCS-S--CCCCEEEEEEEET------TTHHHHHCGGGHHHHHHHHHHCCEEECCTTCC--
T ss_pred             HHHHHHHHHHHHHHhccc-cccc-c--cCCceEEEEEcCh------hheeeEEcCCChHHHHHHHHhCCeEEECCCCC--
Confidence            566777777877776652 1211 1  1235667899998      99999999999999999999999999986552  


Q ss_pred             ccccccccCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHhcCCCh
Q 040243          300 EGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQPVD  346 (797)
Q Consensus       300 ~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v~~A~~~I~~ll~~~~  346 (797)
                                   ++.++.-.|.|+| +.++|++|.++|+.+|..+.
T Consensus       126 -------------~~~~~~~~v~I~G-~~~~v~~A~~~I~~~i~~~~  158 (163)
T 3krm_A          126 -------------PDENDQVIVKIIG-HFYASQMAQRKIRDILAQVK  158 (163)
T ss_dssp             -------------CCTTSEEEEEEEE-CHHHHHHHHHHHHHHHHHHT
T ss_pred             -------------CCCCCceEEEEEe-CHHHHHHHHHHHHHHHHHHH
Confidence                         1234445799999 78999999999999997543

>2ctk_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=98.79  E-value=3.9e-09  Score=96.31  Aligned_cols=74  Identities=15%  Similarity=0.233  Sum_probs=61.3

Q ss_pred             CCCCCCCceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEE
Q 040243          243 PADYRPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVL  322 (797)
Q Consensus       243 p~dy~p~~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~  322 (797)
                      ...|.|  +...|.||.      ++||+|||++|+|+|+|+++|||+|.|-..|+.                   .=.|.
T Consensus        11 i~~~ap--~~~~i~Ip~------~~ig~IIG~gG~~Ir~I~eetg~~I~I~~~g~~-------------------~~~V~   63 (104)
T 2ctk_A           11 LEALVP--VTIEVEVPF------DLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQ-------------------SDIIA   63 (104)
T ss_dssp             CCCSSC--EEEEEECCH------HHHHHHHCSSSHHHHHHHHHTCCEEECCCTTTT-------------------CCEEE
T ss_pred             HHhhCC--EEEEEEECh------HHccceeCCCchHHHHHHHHHCCEEEecCCCCC-------------------cceEE
Confidence            445666  455666998      999999999999999999999999999866520                   01899


Q ss_pred             EEecCHHHHHHHHHHHHHhcCC
Q 040243          323 VEAETQESLEGAAAMVEKLLQP  344 (797)
Q Consensus       323 I~a~~~e~v~~A~~~I~~ll~~  344 (797)
                      |+|.. +++++|+++|+.++..
T Consensus        64 I~G~~-e~v~~A~~~I~~i~~e   84 (104)
T 2ctk_A           64 ITGLA-ANLDRAKAGLLERVKE   84 (104)
T ss_dssp             EEECH-HHHHHHHHHHHHHHHH
T ss_pred             EEcCH-HHHHHHHHHHHHHHhh
Confidence            99985 8999999999999864

>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=98.79  E-value=3.3e-09  Score=94.96  Aligned_cols=69  Identities=20%  Similarity=0.281  Sum_probs=59.2

Q ss_pred             ceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHH
Q 040243          250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQE  329 (797)
Q Consensus       250 ~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e  329 (797)
                      .++.+|.||.      +++|.|||++|+|+|+|+++|||+|.|-..++                   ++-.|.|+|. .+
T Consensus        16 ~~t~~i~Ip~------~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~~~-------------------~~~~V~I~G~-~e   69 (94)
T 2cte_A           16 QASATVAIPK------EHHRFVIGKNGEKLQDLELKTATKIQIPRPDD-------------------PSNQIKITGT-KE   69 (94)
T ss_dssp             CEEEEEECCT------TTHHHHHCSSSCHHHHHHHHTTCCCBCCCTTS-------------------SCCEEEEEEC-HH
T ss_pred             ceEEEEEECh------HHeeeeECCCChhHHHHHHHHCCEEEeCCCCC-------------------CCCeEEEEEC-HH
Confidence            4678899998      89999999999999999999999999974321                   1128999998 99


Q ss_pred             HHHHHHHHHHHhcCC
Q 040243          330 SLEGAAAMVEKLLQP  344 (797)
Q Consensus       330 ~v~~A~~~I~~ll~~  344 (797)
                      .+++|.++|+.++..
T Consensus        70 ~v~~A~~~I~~i~~~   84 (94)
T 2cte_A           70 GIEKARHEVLLISAE   84 (94)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhc
Confidence            999999999999753

>2dgr_A Ring finger and KH domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.78  E-value=3.1e-09  Score=93.13  Aligned_cols=69  Identities=26%  Similarity=0.471  Sum_probs=57.1

Q ss_pred             CCceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecC
Q 040243          248 PPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAET  327 (797)
Q Consensus       248 p~~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~  327 (797)
                      +...+.+|.||.      +++|+|||++|+|+|+||++|||+|.|-.++                   +|. .|.|+++.
T Consensus         7 ~~~~~~~i~VP~------~~vG~IIGkgG~tIk~Iqe~Tga~I~I~~~~-------------------~~~-~v~ItG~~   60 (83)
T 2dgr_A            7 GGQTTIQVRVPY------RVVGLVVGPKGATIKRIQQRTHTYIVTPGRD-------------------KEP-VFAVTGMP   60 (83)
T ss_dssp             CCSEEEEEECCH------HHHHHHHTTTTSSHHHHHHHTTCEEECCCSS-------------------SCC-EEEEEECT
T ss_pred             CCceEEEEEeCh------HHeeeeECCCchHHHHHHHHhCCeEEecCCC-------------------CCC-eEEEEcCH
Confidence            345778889997      9999999999999999999999999997432                   111 57788875


Q ss_pred             HHHHHHHHHHHHHhcC
Q 040243          328 QESLEGAAAMVEKLLQ  343 (797)
Q Consensus       328 ~e~v~~A~~~I~~ll~  343 (797)
                       +++++|.++|+.++.
T Consensus        61 -e~v~~A~~~I~~~i~   75 (83)
T 2dgr_A           61 -ENVDRAREEIEAHIT   75 (83)
T ss_dssp             -TTHHHHHHHHHHHHH
T ss_pred             -HHHHHHHHHHHHHHh
Confidence             899999999998753

>2ctl_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=98.77  E-value=4.8e-09  Score=94.52  Aligned_cols=72  Identities=13%  Similarity=0.221  Sum_probs=60.2

Q ss_pred             ceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHH
Q 040243          250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQE  329 (797)
Q Consensus       250 ~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e  329 (797)
                      .++.+|.||.      .+||+|||++|+|+|+|+++|||+|.|-..|...                ...-.|.|+|. .+
T Consensus        16 ~~~~~i~Ip~------~~ig~IIGkgG~~Ik~I~~etg~~I~i~~~g~~~----------------~~~~~V~I~G~-~e   72 (97)
T 2ctl_A           16 SFKLSVTVDP------KYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGN----------------QPQDQITITGY-EK   72 (97)
T ss_dssp             TCEEEEECCT------TTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTCS----------------SCSSEEEEESC-HH
T ss_pred             ceeEEEEECH------HHhhhcCCCCchhHHHHHHHHCCEEEecCCCCCC----------------CCccEEEEEeC-HH
Confidence            4677888998      8999999999999999999999999998665211                01227999997 89


Q ss_pred             HHHHHHHHHHHhcCC
Q 040243          330 SLEGAAAMVEKLLQP  344 (797)
Q Consensus       330 ~v~~A~~~I~~ll~~  344 (797)
                      .+++|.++|+.|+..
T Consensus        73 ~v~~A~~~I~~iv~e   87 (97)
T 2ctl_A           73 NTEAARDAILRIVGE   87 (97)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH
Confidence            999999999999754

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.75  E-value=1.8e-08  Score=94.25  Aligned_cols=75  Identities=17%  Similarity=0.173  Sum_probs=67.8

Q ss_pred             CCCCcEEEEecCCCC-CcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecC-HHHHHHHHHhcC--ceeeccceE
Q 040243          488 ELDDTNLYIGYLPPT-LDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYAD-IQMANNAIASMN--GYRLEGRTI  563 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~-vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s-~e~A~~AI~~Ln--G~~l~Gr~L  563 (797)
                      -..++-|||+||++. +++++|+++|++||.|..|.++++..      .|||.|.+ ..+|..|++.|+  +..|.|..+
T Consensus        15 ~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~   88 (121)
T 1owx_A           15 EKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRNKEV   88 (121)
T ss_dssp             CCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSE
T ss_pred             ccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeCcEE
Confidence            356889999999999 99999999999999999999998874      59999999 899999999995  788999998


Q ss_pred             EEEec
Q 040243          564 AVRVA  568 (797)
Q Consensus       564 ~V~~A  568 (797)
                      +|++.
T Consensus        89 ~~evL   93 (121)
T 1owx_A           89 TWEVL   93 (121)
T ss_dssp             EEEEC
T ss_pred             EEEEC
Confidence            88764

>2cpq_A FragIle X mental retardation syndrome related protein 1, isoform B'; KH domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=98.70  E-value=7.9e-09  Score=91.82  Aligned_cols=66  Identities=17%  Similarity=0.368  Sum_probs=58.4

Q ss_pred             ceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcE-EEEecc-ccccccccccccCCCCCCCCCCCceEEEEecC
Q 040243          250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAK-IVIRGK-GSVKEGRLQQKRDLKPDPSENEDLHVLVEAET  327 (797)
Q Consensus       250 ~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgak-I~IrGk-GS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~  327 (797)
                      .+...|.||.      ++||.||||+|+|+|+|+++|||+ |.|... |                       .|.|+|.+
T Consensus        14 ~~i~~i~I~~------dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~eddG-----------------------~V~I~g~~   64 (91)
T 2cpq_A           14 AFHEEFVVRE------DLMGLAIGTHGSNIQQARKVPGVTAIELDEDTG-----------------------TFRIYGES   64 (91)
T ss_dssp             SEEEEEECCH------HHHHHHHTTTTHHHHHHHTSTTEEEEEEETTTT-----------------------EEEEEESS
T ss_pred             ceEEEEEECh------HHhhhhcCCCcHHHHHHHHHhCCeEEEEEcCCC-----------------------EEEEEECC
Confidence            3566777998      999999999999999999999998 999742 3                       89999999


Q ss_pred             HHHHHHHHHHHHHhcCC
Q 040243          328 QESLEGAAAMVEKLLQP  344 (797)
Q Consensus       328 ~e~v~~A~~~I~~ll~~  344 (797)
                      .+++++|.++|+.+-..
T Consensus        65 ~ea~~~A~~~I~~ie~~   81 (91)
T 2cpq_A           65 ADAVKKARGFLEFVEDF   81 (91)
T ss_dssp             HHHHHHHHHHHSCCCCC
T ss_pred             HHHHHHHHHHHHhhheE
Confidence            99999999999987654

>2ctm_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=98.70  E-value=1.2e-08  Score=91.58  Aligned_cols=70  Identities=20%  Similarity=0.233  Sum_probs=59.4

Q ss_pred             ceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHH
Q 040243          250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQE  329 (797)
Q Consensus       250 ~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e  329 (797)
                      .++..|.||.      .++|+|||++|+|+|+|+++|||+|.|-.+|+..                  .-.|.|+|. .+
T Consensus        16 ~vt~~i~Ip~------~~ig~IIG~gG~~Ir~I~e~tg~~I~i~~~g~~~------------------~~~V~I~G~-~e   70 (95)
T 2ctm_A           16 MVSEDVPLDH------RVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPD------------------PNCVTVTGL-PE   70 (95)
T ss_dssp             CCCEEEECCT------TTHHHHHCSSSCHHHHHHHHHTCEEECCCTTCSC------------------TTEEEEESC-HH
T ss_pred             cEEEEEEECH------HHccccCCCCcchHHHHHHHHCCeEEecCCCCCC------------------CcEEEEEcC-HH
Confidence            4567888998      8999999999999999999999999998766311                  127999998 69


Q ss_pred             HHHHHHHHHHHhcCC
Q 040243          330 SLEGAAAMVEKLLQP  344 (797)
Q Consensus       330 ~v~~A~~~I~~ll~~  344 (797)
                      ++++|+++|+.|+..
T Consensus        71 ~v~~A~~~I~~i~~e   85 (95)
T 2ctm_A           71 NVEEAIDHILNLEEE   85 (95)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH
Confidence            999999999998753

>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens}

Probab=98.69  E-value=1.1e-08  Score=99.64  Aligned_cols=102  Identities=17%  Similarity=0.356  Sum_probs=75.6

Q ss_pred             HHHHHHHHHHHHHHHHhCC-CCCCCCCCCCC-ceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEecccc
Q 040243          220 ERLNKERQEIISQIIKRNP-AFKPPADYRPP-KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGS  297 (797)
Q Consensus       220 ~~le~er~~li~~~~~~~p-~~~pp~dy~p~-~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS  297 (797)
                      +.+++.+..|.+.+.+... .|.+..+|.+. ..+.+|.||.      +++|+|||.+|+|+|+|+++|||+|.|.....
T Consensus        58 ~~v~~A~~~I~~ii~e~~~~~~~~~~~~~~~~~~~~~i~vp~------~~~g~iIGk~G~~I~~i~~~tg~~I~i~~~~~  131 (164)
T 2jvz_A           58 YKVQQACEMVMDILRERDQGGFGDRNEYGSRIGGGIDVPVPR------HSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDG  131 (164)
T ss_dssp             HHHHHHHHHHHHHTTCSSSCCCSSCSSCTTSCSSSBCCEEET------TTHHHHHCSSSHHHHHHHHHTCCEEEECCCCT
T ss_pred             HHHHHHHHHHHHHHHhccCCCCCCccccCCCCCceEEEEECh------hhccccCCCCcHhHHHHHHHHCCeEEEeCCCC
Confidence            5666667666666554332 34444566543 2456778997      89999999999999999999999999985431


Q ss_pred             ccccccccccCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHhcCCC
Q 040243          298 VKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQPV  345 (797)
Q Consensus       298 ~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v~~A~~~I~~ll~~~  345 (797)
                                       ...+-.|.|+|. .+.+++|..+|+.+|..+
T Consensus       132 -----------------~~~~~~v~I~G~-~~~v~~A~~~I~~~i~~~  161 (164)
T 2jvz_A          132 -----------------TGPEKIAHIMGP-PDRCEHAARIINDLLQSL  161 (164)
T ss_dssp             -----------------TSSEEEEEEESC-HHHHHHHHHHHHHHHHHH
T ss_pred             -----------------CCCcEEEEEEcC-HHHHHHHHHHHHHHHhhh
Confidence                             112237999997 899999999999998653

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=98.69  E-value=8.9e-09  Score=121.69  Aligned_cols=101  Identities=23%  Similarity=0.312  Sum_probs=41.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHhCCCC-CCCCCCCCCceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEecc
Q 040243          217 RARERLNKERQEIISQIIKRNPAF-KPPADYRPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGK  295 (797)
Q Consensus       217 r~~~~le~er~~li~~~~~~~p~~-~pp~dy~p~~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGk  295 (797)
                      .+.++..+.+.+|++.|.+.+... ...+.|+|+..+.|  |+.      ++||.||||+|+|||.|+++||++|.|...
T Consensus       537 ~aL~~A~~g~~~I~~~m~~al~~~r~~~~~~ap~~~~~~--i~~------~ki~~vig~gg~~i~~i~~~tg~~idi~dd  608 (726)
T 4aid_A          537 QALAQAKEGRAHILGEMNKAMDAPRADVGDFAPKIETIN--IPT------DKIREVIGSGGKVIREIVATTGAKVDINDD  608 (726)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTCSSCCSSCCSSCCC----------------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhhhhcccCCeEEEEe--CCH------HHHHhhcCCCchhHHHHHHHHCCceeEECC
Confidence            466667778999999999999887 45789999988877  888      899999999999999999999999999977


Q ss_pred             ccccccccccccCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHhcCCChHH
Q 040243          296 GSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQPVDEV  348 (797)
Q Consensus       296 GS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v~~A~~~I~~ll~~~~e~  348 (797)
                      |                       .|.|.+.+.+++++|+++|+.|+.....|
T Consensus       609 G-----------------------~v~I~~~~~~~~~~A~~~i~~i~~~~~vG  638 (726)
T 4aid_A          609 G-----------------------VVKVSASDGAKIKAAIDWIKSITDEAEVG  638 (726)
T ss_dssp             ----------------------------CCSCHHHHHHHHHC-----------
T ss_pred             c-----------------------eEEEEeCCHHHHHHHHHHHHHHhhhhcCC
Confidence            6                       78899999999999999999999765544

>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=98.68  E-value=2.8e-08  Score=101.23  Aligned_cols=67  Identities=16%  Similarity=0.224  Sum_probs=60.8

Q ss_pred             CcHHHHHHHhhcCCCEEEEEEEecC----CCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          503 LDDDGLIRLFSTFGDIVMAKVIKDR----VTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       503 vte~dL~~~Fs~fG~I~~v~v~~dk----~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      -.+++|++.|++||.|.+++|.++.    .+++++||+||+|.+.++|.+||+.|||..++||.|+|.+..
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~  211 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYD  211 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECC
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcC
Confidence            3568999999999999999998554    455999999999999999999999999999999999999864

>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding, DNA-binding, nucleus, phosph ribonucleoprotein, RNA-binding, RNA binding protein; NMR {Homo sapiens}

Probab=98.59  E-value=9.3e-08  Score=92.95  Aligned_cols=101  Identities=16%  Similarity=0.249  Sum_probs=73.2

Q ss_pred             HHHHHHHHHHHHHHHHhCCCCCCCCC-CCCCceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccc
Q 040243          220 ERLNKERQEIISQIIKRNPAFKPPAD-YRPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSV  298 (797)
Q Consensus       220 ~~le~er~~li~~~~~~~p~~~pp~d-y~p~~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~  298 (797)
                      +.+++.+..|++.|.+......+... ..-...+.+|.||.      +++|+|||.+|.|+|+|+++|||+|.|.+..  
T Consensus        57 ~~v~~A~~~I~~~i~e~~~~~~~~~~~~~~~~~~~~i~vp~------~~~g~iIGkgG~~Ik~i~~~tga~I~i~~~~--  128 (160)
T 2jzx_A           57 NAIFKAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPA------SQCGSLIGKGGCKIKEIRESTGAQVQVAGDM--  128 (160)
T ss_dssp             HHHHHHHHHHHHHHHHHHTSCCCSSSCCCCCSEEEEEEEEH------HHHHHHHCGGGHHHHHHHHHHSSEECCCCCC--
T ss_pred             HHHHHHHHHHHHHHHhhccccCCCCccCCCCCEEEEEEECh------hheeeEECCCCHHHHHHHHHhCCeEEECCCC--
Confidence            66777777777777664332211111 01123677889998      8999999999999999999999999997532  


Q ss_pred             cccccccccCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHhcC
Q 040243          299 KEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQ  343 (797)
Q Consensus       299 k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v~~A~~~I~~ll~  343 (797)
                      .              ....+=.|.|+| +.+.+++|+++|..+|.
T Consensus       129 ~--------------~~~~~~~v~I~G-~~~~v~~A~~~I~~~i~  158 (160)
T 2jzx_A          129 L--------------PNSTERAITIAG-IPQSIIECVKQICVVML  158 (160)
T ss_dssp             S--------------TTCCEEEEEEEE-CHHHHHHHHHHHHHHHH
T ss_pred             C--------------CCCCceEEEEEc-CHHHHHHHHHHHHHHHh
Confidence            0              011234799999 79999999999998874

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.57  E-value=7.8e-08  Score=85.77  Aligned_cols=71  Identities=20%  Similarity=0.483  Sum_probs=61.2

Q ss_pred             CCcEEEEecCCCC------CcH---HHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeecc
Q 040243          490 DDTNLYIGYLPPT------LDD---DGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEG  560 (797)
Q Consensus       490 ~~~tLfVgNLp~~------vte---~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~G  560 (797)
                      ...||+|.-++..      ..+   .+|.+.|.+||+|..++|+.|+        +||+|.+.++|.+||+ |||..++|
T Consensus        14 pD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~-ldG~~v~G   84 (95)
T 1ufw_A           14 LDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDGMKVKG   84 (95)
T ss_dssp             TTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGGSEETT
T ss_pred             CCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHh-cCCeeeCC
Confidence            3458999988642      332   4688999999999999999985        9999999999999998 99999999


Q ss_pred             ceEEEEecC
Q 040243          561 RTIAVRVAG  569 (797)
Q Consensus       561 r~L~V~~A~  569 (797)
                      |.|+|++-.
T Consensus        85 r~L~V~~k~   93 (95)
T 1ufw_A           85 RAVKISGPS   93 (95)
T ss_dssp             EEEEEECCC
T ss_pred             eEEEEeccC
Confidence            999999753

>2ctj_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=98.50  E-value=5.1e-08  Score=87.54  Aligned_cols=69  Identities=20%  Similarity=0.303  Sum_probs=58.8

Q ss_pred             ceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHh-CcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCH
Q 040243          250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERET-GAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQ  328 (797)
Q Consensus       250 ~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eT-gakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~  328 (797)
                      ..+..|.||.      .|++.|||++|+|+|+|+++| ||+|.|-..|+.                   .-.|.|+|.+.
T Consensus        16 ~vt~~i~Ip~------~~i~~iIG~gGk~Ir~I~eetggv~I~i~~~g~~-------------------~~~V~I~G~~~   70 (95)
T 2ctj_A           16 IAEVEVSIPA------KLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSG-------------------SDTVVIRGPSS   70 (95)
T ss_dssp             SCCEEEECCH------HHHHHHHCSSSHHHHHHHHHHTSCEEECCCTTTT-------------------CCEEEEESCHH
T ss_pred             cEEEEEEECH------HHHhhhCCCCchhHHHHHHHcCCCEEEeCCCCCC-------------------cceEEEEcCHH
Confidence            3567788998      899999999999999999999 999999876631                   01799999877


Q ss_pred             HHHHHHHHHHHHhcCC
Q 040243          329 ESLEGAAAMVEKLLQP  344 (797)
Q Consensus       329 e~v~~A~~~I~~ll~~  344 (797)
                       .|++|+++|+.|+..
T Consensus        71 -~v~~A~~~I~~iv~e   85 (95)
T 2ctj_A           71 -DVEKAKKQLLHLAEE   85 (95)
T ss_dssp             -HHHHHHHHHHHHHHH
T ss_pred             -HHHHHHHHHHHHHhh
Confidence             999999999999753

>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1

Probab=98.46  E-value=1.9e-07  Score=92.12  Aligned_cols=72  Identities=21%  Similarity=0.369  Sum_probs=58.0

Q ss_pred             ceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHH
Q 040243          250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQE  329 (797)
Q Consensus       250 ~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e  329 (797)
                      ..+.+|.||.      +++|+|||.+|+|+|+|+++|||+|.|.......              ....+-.|.|+| +.+
T Consensus       103 ~~~~~i~vp~------~~~g~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~--------------~~~~~~~v~I~G-~~~  161 (174)
T 1j4w_A          103 LQEFNFIVPT------GKTGLIIGKGGETIKSISQQSGARIELQRNPPPN--------------ADPNMKLFTIRG-TPQ  161 (174)
T ss_dssp             -CEEEEEEET------TTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTT--------------SCTTEEEEEEEC-CHH
T ss_pred             cEEEEEEECh------HHcCeeECCCchHHHHHHHHHCCEEEECCCCCCC--------------CCCCceEEEEEC-CHH
Confidence            3577889997      8999999999999999999999999998643100              011223789999 789


Q ss_pred             HHHHHHHHHHHhc
Q 040243          330 SLEGAAAMVEKLL  342 (797)
Q Consensus       330 ~v~~A~~~I~~ll  342 (797)
                      .+++|.++|+++|
T Consensus       162 ~v~~A~~~I~~~i  174 (174)
T 1j4w_A          162 QIDYARQLIEEKI  174 (174)
T ss_dssp             HHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHhC
Confidence            9999999999876

>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens}

Probab=98.42  E-value=3.6e-07  Score=88.89  Aligned_cols=73  Identities=26%  Similarity=0.426  Sum_probs=59.3

Q ss_pred             eEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHHH
Q 040243          251 LQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQES  330 (797)
Q Consensus       251 ~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~  330 (797)
                      .+.+|.||.      +++|+|||.+|+|+|+|+++|||+|.|...+..               ....+-.|.|+| +.+.
T Consensus         2 ~~~~~~Vp~------~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~---------------~~~~~r~v~I~G-~~~~   59 (164)
T 2jvz_A            2 TVQEIMIPA------GKAGLVIGKGGETIKQLQERAGVKMILIQDGSQ---------------NTNVDKPLRIIG-DPYK   59 (164)
T ss_dssp             EEEEEEECT------TCHHHHTCTTTHHHHHHHHTSCSEEEECCCTTS---------------SSSSCEEEEEEE-CHHH
T ss_pred             eEEEEEech------hheeEEECCChHHHHHHHHHhCCeEEEecCCCC---------------CCCCceEEEEEc-CHHH
Confidence            467899998      899999999999999999999999999643311               012233788999 7899


Q ss_pred             HHHHHHHHHHhcCCC
Q 040243          331 LEGAAAMVEKLLQPV  345 (797)
Q Consensus       331 v~~A~~~I~~ll~~~  345 (797)
                      |++|..+|..++...
T Consensus        60 v~~A~~~I~~ii~e~   74 (164)
T 2jvz_A           60 VQQACEMVMDILRER   74 (164)
T ss_dssp             HHHHHHHHHHHTTCS
T ss_pred             HHHHHHHHHHHHHhc
Confidence            999999999998754

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B

Probab=98.32  E-value=3.7e-07  Score=93.77  Aligned_cols=71  Identities=24%  Similarity=0.344  Sum_probs=57.0

Q ss_pred             CCCCCCCceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEe-ccccccccccccccCCCCCCCCCCCceE
Q 040243          243 PADYRPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIR-GKGSVKEGRLQQKRDLKPDPSENEDLHV  321 (797)
Q Consensus       243 p~dy~p~~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~Ir-GkGS~k~g~~~~~~~~~~~~~~~e~LHv  321 (797)
                      .++|+|...  +|.||.      +.||.|||++|+|+|.|+++|||+|.|. ..|                       .|
T Consensus        28 ~s~~aP~i~--~i~IP~------~kig~lIG~gGk~Ik~I~e~tgvkI~I~~~~g-----------------------~V   76 (219)
T 2e3u_A           28 WEEFFKQEE--YVKIPK------DRIAVLIGKKGQTKKEIEKRTKTKITIDSETG-----------------------EV   76 (219)
T ss_dssp             -----CCEE--EEECCH------HHHHHHHCGGGHHHHHHHHHHTEEEEECTTTC-----------------------EE
T ss_pred             cCCCCCEEE--EEEeCH------HHhhhhhcccHHHHHHHHHHHCcEEEEEcCCC-----------------------EE
Confidence            467888765  566998      9999999999999999999999999997 323                       57


Q ss_pred             EEEecC----HHHHHHHHHHHHHhcCC
Q 040243          322 LVEAET----QESLEGAAAMVEKLLQP  344 (797)
Q Consensus       322 ~I~a~~----~e~v~~A~~~I~~ll~~  344 (797)
                      .|.+.+    .+++++|.++|+.|+..
T Consensus        77 ~I~~~~~t~d~~~i~kA~~~I~~i~rg  103 (219)
T 2e3u_A           77 WITSTKETEDPLAVWKARDIVLAIGRG  103 (219)
T ss_dssp             EEEECTTCCSHHHHHHHHHHHHHHHTT
T ss_pred             EEecCCCCCCHHHHHHHHHHHHHHhcc
Confidence            788876    89999999999999843

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A*

Probab=98.30  E-value=5.2e-07  Score=89.22  Aligned_cols=75  Identities=23%  Similarity=0.364  Sum_probs=59.5

Q ss_pred             ceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHH
Q 040243          250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQE  329 (797)
Q Consensus       250 ~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e  329 (797)
                      .++.+|.||.      +++|+|||.+|+|+|+|+++|||+|.|...+....             ... +=.|.|+|. .+
T Consensus         5 ~~~~~i~vp~------~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~-------------~~~-er~v~I~G~-~~   63 (178)
T 2anr_A            5 QYFLKVLIPS------YAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYP-------------GTT-ERVCLIQGT-IE   63 (178)
T ss_dssp             CEEEEEEEEH------HHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBCT-------------TSS-EEEEEEEEC-HH
T ss_pred             CEEEEEEECh------hHeeeeECCCcHHHHHHHHHhCCeEEEecCCCCCC-------------CCC-CceEEEEeC-HH
Confidence            4678999998      89999999999999999999999999975431110             111 125788886 88


Q ss_pred             HHHHHHHHHHHhcCCC
Q 040243          330 SLEGAAAMVEKLLQPV  345 (797)
Q Consensus       330 ~v~~A~~~I~~ll~~~  345 (797)
                      .+.+|.++|..++...
T Consensus        64 ~v~~A~~~I~~~~~~~   79 (178)
T 2anr_A           64 ALNAVHGFIAEKIREM   79 (178)
T ss_dssp             HHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHHHHHhcc
Confidence            9999999999988653

>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1

Probab=98.29  E-value=5.5e-07  Score=88.80  Aligned_cols=70  Identities=20%  Similarity=0.411  Sum_probs=57.4

Q ss_pred             eEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHHH
Q 040243          251 LQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQES  330 (797)
Q Consensus       251 ~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~  330 (797)
                      .+.+|.||.      +++|+|||.+|+|+|+|+++|||+|.|...-    +             ...+-.|.|++. .+.
T Consensus         3 ~~~~~~vp~------~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~----~-------------~~~~r~v~I~G~-~~~   58 (174)
T 1j4w_A            3 HMIDVPIPR------FAVGIVIGRNGEMIKKIQNDAGVRIQFKPDD----G-------------TTPERIAQITGP-PDR   58 (174)
T ss_dssp             EEEEEEEEH------HHHHHHHCGGGHHHHHHHHHHCCEEEEECCT----T-------------SCSEEEEEEEEC-HHH
T ss_pred             eEEEEEECh------hheeeeecCCchHHHHHHHHhCCEEEEecCC----C-------------CCCccEEEEEeC-HHH
Confidence            357888998      8999999999999999999999999997421    0             112237889988 899


Q ss_pred             HHHHHHHHHHhcCC
Q 040243          331 LEGAAAMVEKLLQP  344 (797)
Q Consensus       331 v~~A~~~I~~ll~~  344 (797)
                      |++|+++|+.+|..
T Consensus        59 v~~A~~~I~~~~~~   72 (174)
T 1j4w_A           59 AQHAAEIITDLLRS   72 (174)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHh
Confidence            99999999988753

>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding, DNA-binding, nucleus, phosph ribonucleoprotein, RNA-binding, RNA binding protein; NMR {Homo sapiens}

Probab=98.22  E-value=1.1e-06  Score=85.42  Aligned_cols=69  Identities=26%  Similarity=0.378  Sum_probs=57.9

Q ss_pred             CceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCH
Q 040243          249 PKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQ  328 (797)
Q Consensus       249 ~~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~  328 (797)
                      ..++.+|.||.      +++|+|||.+|.|+|+|+++|||+|.|...|+                   .+-.|.|+|. .
T Consensus         3 ~~~~~~~~vp~------~~~g~iIGkgG~~Ik~i~~~tg~~I~i~~~~~-------------------~~r~v~I~G~-~   56 (160)
T 2jzx_A            3 VTLTIRLLMHG------KEVGSIIGKKGESVKKMREESGARINISEGNC-------------------PERIITLAGP-T   56 (160)
T ss_dssp             CEEEEEEEEEH------HHHHHHHCGGGHHHHHHHHHHCSEEEEECCTT-------------------TEEEEEEEEE-H
T ss_pred             ccEEEEEEEch------hheeeeECCCcHHHHHHHHHHCCEEEEcCCCC-------------------CceEEEEEeC-H
Confidence            45678999998      89999999999999999999999999986431                   1127889997 7


Q ss_pred             HHHHHHHHHHHHhcC
Q 040243          329 ESLEGAAAMVEKLLQ  343 (797)
Q Consensus       329 e~v~~A~~~I~~ll~  343 (797)
                      +.+.+|..+|..++.
T Consensus        57 ~~v~~A~~~I~~~i~   71 (160)
T 2jzx_A           57 NAIFKAFAMIIDKLE   71 (160)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH
Confidence            899999999987653

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A*

Probab=98.21  E-value=5.3e-07  Score=89.20  Aligned_cols=73  Identities=27%  Similarity=0.321  Sum_probs=59.0

Q ss_pred             ceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHH
Q 040243          250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQE  329 (797)
Q Consensus       250 ~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e  329 (797)
                      ..+.+|.||.      +++|+|||.+|+|+|+|+++|||+|.|.......               ...+-.|.|+|.. +
T Consensus       103 ~~~~~i~Vp~------~~vg~iIGkgG~~Ik~i~~~tga~I~i~~~~~~~---------------~~~~~~v~I~G~~-~  160 (178)
T 2anr_A          103 ANQVKIIVPN------STAGLIIGKGGATVKAIMEQSGAWVQLSQKPDGI---------------NLQNRVVTVSGEP-E  160 (178)
T ss_dssp             GGEEEEEEEH------HHHHHHHCGGGHHHHHHHHHSSCEEEECCCC-------------------CCEEEEEEESSH-H
T ss_pred             ceEEEEEEch------hheeeeECCCcHHHHHHHHHHCCEEEEeCCCCCC---------------CCCceEEEEEcCH-H
Confidence            3678999998      9999999999999999999999999998543100               0122378899975 8


Q ss_pred             HHHHHHHHHHHhcCC
Q 040243          330 SLEGAAAMVEKLLQP  344 (797)
Q Consensus       330 ~v~~A~~~I~~ll~~  344 (797)
                      ++++|+.+|..+|..
T Consensus       161 ~v~~A~~~I~~~i~e  175 (178)
T 2anr_A          161 QNRKAVELIIQKIQE  175 (178)
T ss_dssp             HHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHh
Confidence            999999999998864

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=98.17  E-value=6.6e-07  Score=106.21  Aligned_cols=100  Identities=22%  Similarity=0.267  Sum_probs=18.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHhCCCC-CCCCCCCCCceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEecc
Q 040243          217 RARERLNKERQEIISQIIKRNPAF-KPPADYRPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGK  295 (797)
Q Consensus       217 r~~~~le~er~~li~~~~~~~p~~-~pp~dy~p~~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGk  295 (797)
                      .+.++-.+.+.+|++.|.+.+... ...+.|.|+..+.+  |+.      ++||.||||+|+|+|.|.++||++|.|.+.
T Consensus       527 ~~l~~A~~~~~~I~~~m~~al~~~~~~~~~~ap~~~~~~--i~~------~ki~~~ig~gGk~I~~I~~~~G~~IdI~~d  598 (723)
T 3cdi_A          527 VALNQAKGARLHILGVMEQAINAPRGDISEFAPRIHTIK--INP------DKIKDVIGKGGSVIRALTEETGTTIEIEDD  598 (723)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHCC----------------------------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhhcchhccccCceEEEEE--ECH------HHhcccccccceeeeeeehhhCceEEecCC
Confidence            456666778889999999988877 55789999998888  787      899999999999999999999999999976


Q ss_pred             ccccccccccccCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHhcCCChH
Q 040243          296 GSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQPVDE  347 (797)
Q Consensus       296 GS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v~~A~~~I~~ll~~~~e  347 (797)
                      |                       .|+|++.+.+.+++|.++|+.++.....
T Consensus       599 g-----------------------~v~I~~~~~~~~~~a~~~i~~i~~~~~v  627 (723)
T 3cdi_A          599 G-----------------------TVKIAATDGEKAKHAIRRIEEITAEIEV  627 (723)
T ss_dssp             ----------------------------------------------------
T ss_pred             c-----------------------cEEEecCCHHHHHHHHHHHHHHhhhhhc
Confidence            6                       6889999999999999999988754433

>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens}

Probab=98.13  E-value=2.6e-06  Score=82.96  Aligned_cols=69  Identities=23%  Similarity=0.348  Sum_probs=56.3

Q ss_pred             EEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHHHH
Q 040243          252 QKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESL  331 (797)
Q Consensus       252 ~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v  331 (797)
                      +.+|.||.      +++|+|||.+|.|+|+|+++|||+|.|...+.                ....+-.|.|+| +.+.+
T Consensus         4 ~~~~~ip~------~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~----------------~~~~~r~v~I~G-~~e~v   60 (163)
T 3krm_A            4 MVQVFIPA------QAVGAIIGKKGQHIKQLSRFASASIKIAPPET----------------PDSKVRMVIITG-PPEAQ   60 (163)
T ss_dssp             EEEEEEEG------GGHHHHHCGGGHHHHHHHHHHTCEEEECCCSS----------------TTCSEEEEEEEE-CHHHH
T ss_pred             EEEEEech------hhcceeECCCcHHHHHHHHHHCCeEEEcCCCC----------------CCCCceEEEEEc-CHHHH
Confidence            56788998      89999999999999999999999999986441                011223688999 78999


Q ss_pred             HHHHHHHHHhcC
Q 040243          332 EGAAAMVEKLLQ  343 (797)
Q Consensus       332 ~~A~~~I~~ll~  343 (797)
                      .+|..+|..++.
T Consensus        61 ~~A~~~I~~~~~   72 (163)
T 3krm_A           61 FKAQGRIYGKLK   72 (163)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHh
Confidence            999998887764

>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A

Probab=98.01  E-value=8.3e-07  Score=105.75  Aligned_cols=95  Identities=23%  Similarity=0.395  Sum_probs=51.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCCCCCCCCCCceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccc
Q 040243          217 RARERLNKERQEIISQIIKRNPAFKPPADYRPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKG  296 (797)
Q Consensus       217 r~~~~le~er~~li~~~~~~~p~~~pp~dy~p~~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkG  296 (797)
                      .+.++-.+.|.+|++.|.+.+......+.|.|+..+.+  ||.      ++||.||||+|+++|.|+++||++|.|.+.|
T Consensus       566 ~aL~~A~~~~~~I~~~m~~al~~~~~~~~~ap~~~~~~--I~~------~ki~~vIG~gGk~Ik~I~~~~G~~IdI~~dG  637 (757)
T 1e3p_A          566 AALKQARDARLHILDVMMEAIDTPDEMSPNAPRIITVK--IPV------DKIGEVIGPKRQMINQIQEDTGAEITIEDDG  637 (757)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHCSSCCCCCTTSCBCCCC--------------------------CTTCCCCCSCC------
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcccccccccCceeEEEE--ECh------HHeehcccccceeeehhhHhhCCEEEecCCc
Confidence            45666677888999999998876666789999998877  887      8899999999999999999999999998766


Q ss_pred             cccccccccccCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHhc
Q 040243          297 SVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLL  342 (797)
Q Consensus       297 S~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v~~A~~~I~~ll  342 (797)
                                             .|+|++.+.+++++|.++|+.|+
T Consensus       638 -----------------------~v~Is~~~~~~~~~a~~~i~~i~  660 (757)
T 1e3p_A          638 -----------------------TIYIGAADGPAAEAARATINGIA  660 (757)
T ss_dssp             -------------------------CCCBSSHHHHCC---------
T ss_pred             -----------------------eEEEecCCHHHHHHHHHHHHHhc
Confidence                                   67888999999999988888876

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=97.95  E-value=2e-05  Score=71.85  Aligned_cols=72  Identities=15%  Similarity=0.206  Sum_probs=66.9

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcC-----CCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceE
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTF-----GDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTI  563 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~f-----G~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L  563 (797)
                      .+.++|-+-||+..+++..|+.++..+     |.|++|.+..|.      +-|+|+|.+...|-+|.-.|+|.+|+|++|
T Consensus        19 ~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH------~GAivef~d~~~AgKasLaL~G~ef~gr~L   92 (117)
T 2l9w_A           19 ELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF------NGAIIIFRDSKFAAKMLMILNGSQFQGKVI   92 (117)
T ss_dssp             TTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT------TEEEEECSCHHHHHHHHHHHSSEEETTEEE
T ss_pred             cCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC------CceEEEEccchhhHHHHhhcCCeeecCeEE
Confidence            456788899999999999999999999     999999999886      689999999999999998999999999999


Q ss_pred             EEE
Q 040243          564 AVR  566 (797)
Q Consensus       564 ~V~  566 (797)
                      +|.
T Consensus        93 r~g   95 (117)
T 2l9w_A           93 RSG   95 (117)
T ss_dssp             EEE
T ss_pred             Eec
Confidence            985

>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}

Probab=97.87  E-value=7.5e-06  Score=67.38  Aligned_cols=47  Identities=32%  Similarity=0.762  Sum_probs=38.7

Q ss_pred             cchhcccCCCCCccccCCCCCCCccccccceecCCCCCCcccCCCCC
Q 040243          370 EEYCRLCGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTIDCLVKG  416 (797)
Q Consensus       370 ~~~c~~cg~~gh~~~~cp~~~~~~~~~v~Cr~CG~~gH~t~dCp~k~  416 (797)
                      ...|-+|++.||.+.+|+.....-...++|.+||+.||+++||+.+.
T Consensus         4 ~~~C~~Cg~~GH~a~~C~~~~~~~~~~~~C~~Cg~~GH~ar~C~~~~   50 (61)
T 2ihx_A            4 RGLCYTCGSPGHYQAQCPKKRKSGNSRERCQLCNGMGHNAKQCRKRD   50 (61)
T ss_dssp             TTBCSSSCCBTCCGGGCTTTTSSSCCCSBCTTTCCBSSCGGGCCCCC
T ss_pred             CCcccccCCCCeehhhCcCCcCCCCCCCeeCCCCCCCCCcCCCcCCC
Confidence            45799999999999999987532123588999999999999998754

>1tua_A Hypothetical protein APE0754; structural genomics, protein structure initiative, MCSG, four layers alpha-beta sandwich, PSI; 1.50A {Aeropyrum pernix} SCOP: d.51.1.1 d.51.1.1

Probab=97.83  E-value=2.3e-05  Score=78.71  Aligned_cols=54  Identities=24%  Similarity=0.289  Sum_probs=47.4

Q ss_pred             ceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHhcCC
Q 040243          266 NFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQP  344 (797)
Q Consensus       266 NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v~~A~~~I~~ll~~  344 (797)
                      ..+|+|||++|.|+|.||..|||+|.|.|+                        .|.|.| +.+.++.|...|++||..
T Consensus       107 r~~GrIIGk~G~tik~iE~~Tg~~I~v~~~------------------------~v~i~G-~~~~i~~Ar~~i~~li~g  160 (191)
T 1tua_A          107 RIKGRIIGEGGRARRTIEEMTDTYINVGEY------------------------EVAIIG-DYERAMAAKQAIEMLAEG  160 (191)
T ss_dssp             HHHHHHHCGGGHHHHHHHHHHTCEEEECSS------------------------EEEEEE-EHHHHHHHHHHHHHHHTT
T ss_pred             HHhhheeCCCccHHHHHHHHHCceEEEcCC------------------------EEEEEe-ChHHHHHHHHHHHHHHcC
Confidence            368999999999999999999999999753                        577777 588899999999999875

>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains, type I domains, fragIle X mental retardation protein, RNA BI protein; 1.90A {Homo sapiens} PDB: 2fmr_A

Probab=97.63  E-value=5.5e-05  Score=72.69  Aligned_cols=72  Identities=18%  Similarity=0.406  Sum_probs=56.6

Q ss_pred             EEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCc-EEEEeccccccccccccccCCCCCCCCCCC-ceEEEEecCHHH
Q 040243          253 KKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGA-KIVIRGKGSVKEGRLQQKRDLKPDPSENED-LHVLVEAETQES  330 (797)
Q Consensus       253 ~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTga-kI~IrGkGS~k~g~~~~~~~~~~~~~~~e~-LHv~I~a~~~e~  330 (797)
                      ..|.||.      +.+|++||-+|.|+|.|+++||| +|.|.+.....             ...++. --|.|+| +.++
T Consensus        69 ~~v~Vp~------~~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~-------------~~~~~~~~~vtI~G-~~~~  128 (144)
T 2qnd_A           69 DVIQVPR------NLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKN-------------VPQEEGMVPFVFVG-TKDS  128 (144)
T ss_dssp             EEEEEEG------GGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTC-------------CCCCTTEEEEEEEE-EHHH
T ss_pred             EEEEECH------HHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCC-------------ccccCCeeEEEEEe-CHHH
Confidence            7888998      88999999999999999999997 99998643100             011222 2477888 4789


Q ss_pred             HHHHHHHHHHhcCC
Q 040243          331 LEGAAAMVEKLLQP  344 (797)
Q Consensus       331 v~~A~~~I~~ll~~  344 (797)
                      +++|..+|+.+|..
T Consensus       129 v~~Ak~li~~~l~~  142 (144)
T 2qnd_A          129 IANATVLLDYHLNY  142 (144)
T ss_dssp             HHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHh
Confidence            99999999998864

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B

Probab=97.63  E-value=5.5e-05  Score=77.63  Aligned_cols=54  Identities=31%  Similarity=0.450  Sum_probs=47.8

Q ss_pred             eeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHhcCCC
Q 040243          267 FIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQPV  345 (797)
Q Consensus       267 fiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v~~A~~~I~~ll~~~  345 (797)
                      .+|+|||.+|.|+|.||+.|||+|.|.|+                        .|.|.| +.+.++.|..+|++||...
T Consensus       139 ~~GriIGk~G~tik~ie~~Tg~~I~v~~~------------------------~v~i~G-~~~~i~~A~~~i~~li~g~  192 (219)
T 2e3u_A          139 VRGRIIGRKGRTRQIIEEMSGASVSVYGK------------------------TVAIIG-NPIQIEIAKTAIEKLARGS  192 (219)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHCCEEEEETT------------------------EEEEEE-CHHHHHHHHHHHHHHHTTC
T ss_pred             hhheeECCCchHHHHHHHHhCceEEECCe------------------------EEEEEe-CHHHHHHHHHHHHHHHcCC
Confidence            59999999999999999999999999741                        588888 5789999999999999753

>2ec7_A GAG polyprotein (PR55GAG); nucleocapsid protein, HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus type 2} SCOP: g.40.1.1

Probab=97.61  E-value=3.4e-05  Score=60.67  Aligned_cols=41  Identities=29%  Similarity=0.635  Sum_probs=35.7

Q ss_pred             chhcccCCCCCccccCCCCCCCccccccceecCCCCCCcccCCCCC
Q 040243          371 EYCRLCGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTIDCLVKG  416 (797)
Q Consensus       371 ~~c~~cg~~gh~~~~cp~~~~~~~~~v~Cr~CG~~gH~t~dCp~k~  416 (797)
                      ..|-+||+.||...+|+...     .+.|.+||+.||+++||+.+.
T Consensus         7 ~~C~~Cg~~GH~a~~C~~~~-----~~~C~~Cg~~GH~~~~C~~~~   47 (49)
T 2ec7_A            7 IRCWNCGKEGHSARQCRAPR-----RQGCWKCGKTGHVMAKCPERQ   47 (49)
T ss_dssp             CBCTTTCCBTCCTTTCCCSS-----CCSCSSSCCSSCCGGGCCSSC
T ss_pred             CeeeecCCCCcChhhCcCCC-----CCeeCcCCCcCCccCCCcCCC
Confidence            47999999999999999742     468999999999999998753

>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}

Probab=97.60  E-value=2.7e-05  Score=58.26  Aligned_cols=37  Identities=32%  Similarity=0.706  Sum_probs=32.9

Q ss_pred             hhcccCCCCCccccCCCCCCCccccccceecCCCCCCcccCC
Q 040243          372 YCRLCGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTIDCL  413 (797)
Q Consensus       372 ~c~~cg~~gh~~~~cp~~~~~~~~~v~Cr~CG~~gH~t~dCp  413 (797)
                      .|-+||+.||.+.+|+..     ..+.|..||+.||+++||+
T Consensus         2 ~C~~Cg~~GH~a~~C~~~-----~~~~C~~Cg~~GH~~~~C~   38 (39)
T 2a51_A            2 TCFNCGKPGHTARMCRQP-----RQEGCWNCGSKEHRFAQCP   38 (39)
T ss_dssp             BCTTTCCBSSCTTTCCSC-----CCSSCTTTCCSSSCTTTSC
T ss_pred             eeeccCCCCcccccCCCC-----CCCccccCCCCCCccCcCc
Confidence            488999999999999964     2468999999999999997

>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}

Probab=97.54  E-value=3.2e-05  Score=57.17  Aligned_cols=35  Identities=34%  Similarity=0.812  Sum_probs=31.7

Q ss_pred             hhcccCCCCCccccCCCCCCCccccccceecCCCCCCcccCC
Q 040243          372 YCRLCGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTIDCL  413 (797)
Q Consensus       372 ~c~~cg~~gh~~~~cp~~~~~~~~~v~Cr~CG~~gH~t~dCp  413 (797)
                      .|-+||+.||.+.+|+..       +.|.+||+.||+++||+
T Consensus         2 ~C~~Cg~~GH~~~~C~~~-------~~C~~Cg~~GH~a~~C~   36 (37)
T 2bl6_A            2 TCYNCGKPGHLSSQCRAP-------KVCFKCKQPGHFSKQCR   36 (37)
T ss_dssp             CBSSSCCSSCCTTTSSCB-------TTCSSCCCTTGGGGTTC
T ss_pred             cccccCCCCcchhhCcCc-------CeEccCCCcCCccCcCc
Confidence            488999999999999853       68999999999999997

>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.54  E-value=3.6e-05  Score=63.73  Aligned_cols=42  Identities=24%  Similarity=0.546  Sum_probs=36.5

Q ss_pred             chhcccCCCCCccccCCCCCCCccccccceecCCCCCCcccCCCCC
Q 040243          371 EYCRLCGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTIDCLVKG  416 (797)
Q Consensus       371 ~~c~~cg~~gh~~~~cp~~~~~~~~~v~Cr~CG~~gH~t~dCp~k~  416 (797)
                      ..|-+|++.||.+.+|+...    ..+.|.+||+.||+++||+.+.
T Consensus         8 ~~C~~Cg~~GH~a~~C~~~~----~~~~C~~Cg~~GH~ar~Cp~~~   49 (63)
T 2cqf_A            8 DRCYNCGGLDHHAKECKLPP----QPKKCHFCQSISHMVASCPLKA   49 (63)
T ss_dssp             CCCSSSCCSSSCTTTCCSCC----CSSCCTTTCCSSSCTTTCTGGG
T ss_pred             CcccccCCCCcChhhCCCCC----CCCccCCcCCcCCccCcCCCcc
Confidence            46999999999999999653    4578999999999999998753

>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding protein, retrovirus, viral protein; NMR {Mason-pfizer monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A

Probab=97.49  E-value=2.9e-05  Score=63.53  Aligned_cols=45  Identities=31%  Similarity=0.572  Sum_probs=19.4

Q ss_pred             hhcccCCCCCccccCCCCCCCc---cccccceecCCCCCCcccCCCCC
Q 040243          372 YCRLCGEPGHRQYACPSRTSTF---KSDVLCKICGDGGHPTIDCLVKG  416 (797)
Q Consensus       372 ~c~~cg~~gh~~~~cp~~~~~~---~~~v~Cr~CG~~gH~t~dCp~k~  416 (797)
                      .|-+|++.||.+.+|+......   ...++|..||+.||+++||+.+.
T Consensus         3 ~Cf~Cg~~GH~a~~C~~~~~~~~~~~~~~~C~~Cg~~GH~ar~C~~~~   50 (60)
T 1cl4_A            3 SCFKCGKKGHFAKNCHEHAHNNAEPKVPGLCPRCKRGKHWANECKSKT   50 (60)
T ss_dssp             --------------------------CCCSCSSCSSCSSCSTTCCCTT
T ss_pred             ccccCCCCCcCHhhCcCCCCCccccCCCcceeECCCCCCccCcCCCcc
Confidence            4889999999999999864211   13688999999999999998764

>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}

Probab=97.49  E-value=5e-05  Score=64.93  Aligned_cols=42  Identities=24%  Similarity=0.546  Sum_probs=36.6

Q ss_pred             chhcccCCCCCccccCCCCCCCccccccceecCCCCCCcccCCCCC
Q 040243          371 EYCRLCGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTIDCLVKG  416 (797)
Q Consensus       371 ~~c~~cg~~gh~~~~cp~~~~~~~~~v~Cr~CG~~gH~t~dCp~k~  416 (797)
                      ..|-+||+.||...+|+...    ..+.|.+||+.||+++||+.+.
T Consensus        25 ~~C~~Cg~~GH~a~~C~~~~----~~~~C~~Cg~~GH~ar~Cp~~~   66 (74)
T 2li8_A           25 DRCYNCGGLDHHAKECKLPP----QPKKCHFCQSISHMVASCPLKA   66 (74)
T ss_dssp             SCCTTTCCSSSCTTTCSSCC----CCCCCTTTCCTTSCGGGCTTGG
T ss_pred             CcccccCCcCcCcccCCCCC----CCCccCCcCCcCCccCcCcCCc
Confidence            47999999999999998643    4578999999999999998754

>1a1t_A Nucleocapsid protein; stem-loop RNA, viral protein/RNA complex; NMR {Human immunodeficiency virus 1} SCOP: g.40.1.1 PDB: 1mfs_A 1f6u_A* 1aaf_A 2l4l_A 2exf_A 2jzw_A* 1bj6_A* 1esk_A 1q3y_A 1q3z_A 2e1x_A 2iwj_A

Probab=97.34  E-value=9.8e-05  Score=59.28  Aligned_cols=40  Identities=33%  Similarity=0.682  Sum_probs=35.2

Q ss_pred             chhcccCCCCCccccCCCCCCCccccccceecCCCCCCcccCCCC
Q 040243          371 EYCRLCGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTIDCLVK  415 (797)
Q Consensus       371 ~~c~~cg~~gh~~~~cp~~~~~~~~~v~Cr~CG~~gH~t~dCp~k  415 (797)
                      ..|-+||+.||.+.+|+..     ....|..||+.||+++||+.+
T Consensus        13 ~~C~~Cg~~GH~a~~C~~~-----~~~~C~~Cg~~GH~~~~C~~~   52 (55)
T 1a1t_A           13 VKCFNCGKEGHIAKNCRAP-----RKKGCWKCGKEGHQMKDCTER   52 (55)
T ss_dssp             CBCTTTCCBSSCGGGCSSC-----SCCBCTTTCCBSSCGGGCSSS
T ss_pred             cceeeeCCCCcChhhcCCC-----CCCEeCCCCCcCCccCCCcCc
Confidence            4799999999999999874     346899999999999999864

>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}

Probab=97.31  E-value=0.00011  Score=64.28  Aligned_cols=47  Identities=32%  Similarity=0.629  Sum_probs=37.4

Q ss_pred             chhcccCCCCCccccCCCCCCCc---------------cccccceecCCCCCCcccCCCCCc
Q 040243          371 EYCRLCGEPGHRQYACPSRTSTF---------------KSDVLCKICGDGGHPTIDCLVKGT  417 (797)
Q Consensus       371 ~~c~~cg~~gh~~~~cp~~~~~~---------------~~~v~Cr~CG~~gH~t~dCp~k~~  417 (797)
                      ..|.+|++.||.+-+||+.+.-|               ...+.|..||+.|||.+||+....
T Consensus         6 ~~C~~Cg~~GH~~~~Cp~~~rcY~c~~~gh~~~~c~~p~~~~~CYnCG~~GH~~rdC~~~r~   67 (83)
T 3nyb_B            6 VQCTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCKEKRS   67 (83)
T ss_dssp             -CCSSSCCSSSCGGGCGGGTCCCCBC-------------CCCBCSSSSCBSSCGGGCSSCCS
T ss_pred             CCCCCCCCCCCccccCCCcccccccccCCcccccccCCCCCCeecccCCCCcCcccCCcccc
Confidence            47999999999999999863211               134889999999999999998653

>2ctf_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=97.25  E-value=0.0003  Score=63.72  Aligned_cols=65  Identities=18%  Similarity=0.321  Sum_probs=54.7

Q ss_pred             eEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHH-hCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHH
Q 040243          251 LQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERE-TGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQE  329 (797)
Q Consensus       251 ~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~e-TgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e  329 (797)
                      .+.+|.||.      .|-+.|||.+|.|+|+|+++ ++++|.+-..                     ++ .|.|+|. .+
T Consensus        27 ~t~~i~vp~------~~h~~IIG~~G~~Ik~i~~~~~~v~I~fp~~---------------------~~-~ItI~G~-~~   77 (102)
T 2ctf_A           27 TVSSVAAPS------WLHRFIIGKKGQNLAKITQQMPKVHIEFTEG---------------------ED-KITLEGP-TE   77 (102)
T ss_dssp             EEEEEECCS------TTHHHHHTTTTCHHHHHHHHCSSSEEEECSS---------------------SC-EEEEEEC-HH
T ss_pred             EEEEEEeCH------HHHhhhcCCCCccHHHHHHHcCCcEEEeCCC---------------------CC-EEEEECC-HH
Confidence            678899998      67789999999999999997 5898877630                     01 6999999 88


Q ss_pred             HHHHHHHHHHHhcCC
Q 040243          330 SLEGAAAMVEKLLQP  344 (797)
Q Consensus       330 ~v~~A~~~I~~ll~~  344 (797)
                      .|++|.++|+.++..
T Consensus        78 ~V~~a~~~I~~~v~e   92 (102)
T 2ctf_A           78 DVSVAQEQIEGMVKD   92 (102)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH
Confidence            999999999998864

>3ts2_A Protein LIN-28 homolog A; microrna biogenesis, protein-RNA complex, PRE-element, CCHC knuckle; HET: GMP; 2.01A {Mus musculus} PDB: 3trz_A* 3ts0_A*

Probab=97.18  E-value=0.00016  Score=69.77  Aligned_cols=42  Identities=24%  Similarity=0.546  Sum_probs=36.5

Q ss_pred             chhcccCCCCCccccCCCCCCCccccccceecCCCCCCcccCCCCC
Q 040243          371 EYCRLCGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTIDCLVKG  416 (797)
Q Consensus       371 ~~c~~cg~~gh~~~~cp~~~~~~~~~v~Cr~CG~~gH~t~dCp~k~  416 (797)
                      ..|-+||+.||.+-+|+...    ....|.+||+.||+++||+.+.
T Consensus        98 ~~C~~Cg~~GH~a~~C~~~~----~~~~C~~Cg~~GH~~r~Cp~~~  139 (148)
T 3ts2_A           98 DRCYNCGGLDHHAKECKLPP----QPKKCHFCQSINHMVASCPLKA  139 (148)
T ss_dssp             CCCTTTCCSSCCGGGCCSCC----CCCCCTTTCCSSCCGGGCTTTT
T ss_pred             CcccEeCCccchhhhCCCCC----CCCcccccCCcCCEeccCcCCC
Confidence            46999999999999999744    3568999999999999999763

>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=96.84  E-value=0.0017  Score=58.89  Aligned_cols=73  Identities=12%  Similarity=0.137  Sum_probs=62.0

Q ss_pred             CcEEEEecCCCCC-cH----HHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEE
Q 040243          491 DTNLYIGYLPPTL-DD----DGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAV  565 (797)
Q Consensus       491 ~~tLfVgNLp~~v-te----~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V  565 (797)
                      .++|+|.||+..+ ..    +.++++|..|+.+.....++.-      .-..|.|.+.++|.+|-..|++..++|++|+|
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSF------RRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~   78 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF------KRVRINFSNPLSAADARLRLHKTEFLGKEMKL   78 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT------TEEEEECSSTTHHHHHHHTSTTSEETTEECEE
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcc------eEEEEEeCChHHHHHHHHHhccceecCceeEE
Confidence            4689999998765 22    4678999999999887766642      35679999999999999999999999999999


Q ss_pred             EecC
Q 040243          566 RVAG  569 (797)
Q Consensus       566 ~~A~  569 (797)
                      -++.
T Consensus        79 YFgq   82 (104)
T 1wey_A           79 YFAQ   82 (104)
T ss_dssp             ECCC
T ss_pred             EecC
Confidence            9987

>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA binding, cell cycle; 2.79A {Caenorhabditis elegans}

Probab=96.73  E-value=0.0024  Score=70.30  Aligned_cols=83  Identities=13%  Similarity=0.240  Sum_probs=63.0

Q ss_pred             CCCCCCCCCceEEEEEecCCCCCCCceeeeeeCCCc--hhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCC
Q 040243          241 KPPADYRPPKLQKKLYIPMKEYPGYNFIGLIIGPRG--NTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENED  318 (797)
Q Consensus       241 ~pp~dy~p~~~~~Ki~IP~~~~P~~NfiG~iiGPrG--~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~  318 (797)
                      .+.-+-+.-.++.++.||.      .|.+.|||.+|  .+||+|.+||||+|.+=..+.  ++..       .  ... .
T Consensus        20 ~~~le~~~~~VTl~v~Ip~------~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~--~~~~-------~--~~k-s   81 (376)
T 3n89_A           20 IPMIEINPTRVTLNMEFES------QYYSLMTSDNGDHENVASIMAETNTLIQLPDRSV--GGTT-------P--DPF-A   81 (376)
T ss_dssp             SCCCCCCTTEEEEEEECCG------GGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCC--CSSS-------C--CTT-T
T ss_pred             ceEEEecCCEEEEEEEEch------hhhhhhccCCChHHHHHHHHHHhCCeEECCCCcc--cccC-------C--cCC-C
Confidence            4555667778999999998      78889999999  999999999999999965431  0100       0  000 0


Q ss_pred             ceEEEEecCHHHHHHHHHHHHHhc
Q 040243          319 LHVLVEAETQESLEGAAAMVEKLL  342 (797)
Q Consensus       319 LHv~I~a~~~e~v~~A~~~I~~ll  342 (797)
                      =-|.|+|. .++|++|.+.|..++
T Consensus        82 ~~VtItG~-~enVE~AR~~I~~l~  104 (376)
T 3n89_A           82 QQVTITGY-FGDVDRARMLMRRNC  104 (376)
T ss_dssp             TEEEEEEE-HHHHHHHHHHHHHSC
T ss_pred             CeEEEEcC-HHHHHHHHHHHHhcC
Confidence            15899997 789999999999863

>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}

Probab=96.71  E-value=0.00084  Score=62.60  Aligned_cols=44  Identities=32%  Similarity=0.643  Sum_probs=32.2

Q ss_pred             chhcccCCCCCccccCCCCCCCc---------------cccccceecCCCCCCcccCCC
Q 040243          371 EYCRLCGEPGHRQYACPSRTSTF---------------KSDVLCKICGDGGHPTIDCLV  414 (797)
Q Consensus       371 ~~c~~cg~~gh~~~~cp~~~~~~---------------~~~v~Cr~CG~~gH~t~dCp~  414 (797)
                      ..|.+||+.||...+||+.+..|               ...+.|..||+.|||++||+.
T Consensus        65 ~~C~~Cg~~GH~~~~Cp~~~~~y~~~~~~~~~~~~~~~~~~~~Cy~Cg~~GH~a~dCp~  123 (124)
T 2lli_A           65 VQCTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCKE  123 (124)
T ss_dssp             CSSSSSCSSCCCTTTCCCSTTSCCSSSCCCCCCCSCCCCCCCCTTTTSSSCTTTTTSCC
T ss_pred             ccCCCCCcCCcchhhCCCccccccccCccccccccccCCCCCCcCCCCCCCcCcccCcC
Confidence            46888888888888888764321               135788888888888888874

>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA binding, cell cycle; 2.79A {Caenorhabditis elegans}

Probab=96.61  E-value=0.0031  Score=69.33  Aligned_cols=96  Identities=14%  Similarity=0.188  Sum_probs=66.3

Q ss_pred             HHHHHHHHHHHHHHHHhCCCCCCCCCCC-CCceEEEEEecCCCCCCCceeeeeeCCCc--hhHHHHHHHhCcEEEEeccc
Q 040243          220 ERLNKERQEIISQIIKRNPAFKPPADYR-PPKLQKKLYIPMKEYPGYNFIGLIIGPRG--NTQKRMERETGAKIVIRGKG  296 (797)
Q Consensus       220 ~~le~er~~li~~~~~~~p~~~pp~dy~-p~~~~~Ki~IP~~~~P~~NfiG~iiGPrG--~t~K~le~eTgakI~IrGkG  296 (797)
                      +.+++++..|++++.+.        .++ -..++..|-|+.      .++..|||-+|  .+|++|.++|||+|.+-..+
T Consensus       162 ~~akeA~~~Ll~~l~~~--------e~~~~~~~s~~v~V~~------~~H~~IIGk~G~n~~IkkIr~eTGv~I~FP~~~  227 (376)
T 3n89_A          162 HELIEAAKRLNEILFRE--------SPAPENNFTLHFTLST------YYVDQVLGSSSTAQLMPVIERETTTIISYPCYN  227 (376)
T ss_dssp             HHHHHHHHHHHHHHCC----------CCCSSCEEEEEEEEG------GGHHHHTCCTTSCCHHHHHHHHHTCEEECC---
T ss_pred             HHHHHHHHHHHHHHHhh--------hcccccceEEEEEeCH------HHHHHhhcCCCcchHHHHHHHhhCCEEECCCCC
Confidence            56777888888887432        222 234667777887      66789999999  56799999999999987766


Q ss_pred             cccccccccccCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHhcC
Q 040243          297 SVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQ  343 (797)
Q Consensus       297 S~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v~~A~~~I~~ll~  343 (797)
                      +..+..             ...-.|.|+| +.++|.+|.+.|+.||=
T Consensus       228 d~~d~~-------------~~~~~ItItG-s~e~V~~Ark~I~~lLP  260 (376)
T 3n89_A          228 NRNETR-------------GNIYEIKVVG-NIDNVLKARRYIMDLLP  260 (376)
T ss_dssp             -------------------CCEEEEEEES-CHHHHHHHHHHHHHTSE
T ss_pred             Cccccc-------------CCceEEEEEe-CHHHHHHHHHHHHhhCC
Confidence            432211             1122789999 78999999999999873

>1tua_A Hypothetical protein APE0754; structural genomics, protein structure initiative, MCSG, four layers alpha-beta sandwich, PSI; 1.50A {Aeropyrum pernix} SCOP: d.51.1.1 d.51.1.1

Probab=96.42  E-value=0.0031  Score=63.31  Aligned_cols=69  Identities=26%  Similarity=0.377  Sum_probs=55.8

Q ss_pred             ceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEE----e
Q 040243          250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVE----A  325 (797)
Q Consensus       250 ~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~----a  325 (797)
                      +.+.+|.||.      +-+|.|||-.|.|+|.|++++||+|.|..+    ++                  -|.|.    .
T Consensus         3 ~~~~~i~VP~------~rvg~liGk~g~~~k~i~e~~g~~i~id~~----~~------------------~V~i~t~~~t   54 (191)
T 1tua_A            3 KPRIYVKVKP------ERLGAVIGPRGEVKAEIMRRTGTVITVDTE----NS------------------MVIVEPEAEG   54 (191)
T ss_dssp             CCCEEEECCG------GGHHHHHCGGGHHHHHHHHHHTEEEEEETT----TT------------------EEEEEESSTT
T ss_pred             CcceEEECCH------HHhhHHHhcCHhHHHHHHHHHCcEEEEEcC----CC------------------eEEEEeCCCC
Confidence            4457899998      889999999999999999999999999743    11                  33444    2


Q ss_pred             cCHHHHHHHHHHHHHhcCCCh
Q 040243          326 ETQESLEGAAAMVEKLLQPVD  346 (797)
Q Consensus       326 ~~~e~v~~A~~~I~~ll~~~~  346 (797)
                      .+...+.+|.++|+.+...+.
T Consensus        55 ~dp~~i~KA~dlI~ai~rgf~   75 (191)
T 1tua_A           55 IPPVNLMKAAEVVKAISLGFP   75 (191)
T ss_dssp             SCHHHHHHHHHHHHHHHHTCC
T ss_pred             CCHHHHHHHHHHHHHHHcCCC
Confidence            466799999999999887654

>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains, type I domains, fragIle X mental retardation protein, RNA BI protein; 1.90A {Homo sapiens} PDB: 2fmr_A

Probab=96.40  E-value=0.0028  Score=60.74  Aligned_cols=62  Identities=15%  Similarity=0.393  Sum_probs=46.7

Q ss_pred             ceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHH
Q 040243          250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQE  329 (797)
Q Consensus       250 ~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e  329 (797)
                      .++++|.||.      +++|++||.+|.++|+|++|+|  |.|---                   .+++--+.+.+-+.+
T Consensus         3 ~~~~~~~Vp~------~~vG~~IG~~G~~I~~i~~e~g--I~ii~~-------------------~~~~~~~i~~~~~p~   55 (144)
T 2qnd_A            3 RFHEQFIVRE------DLMGLAIGTHGANIQQARKVPG--VTAIDL-------------------DEDTCTFHIYGEDQD   55 (144)
T ss_dssp             -CEEEEECCG------GGHHHHHCGGGHHHHHHHTSTT--EEEEEE-------------------ETTTTEEEEEESSHH
T ss_pred             ceEEEEEECC------cceeeEECCChhHHHHHHHHHC--CeEecc-------------------CCCchheeeccCCHH
Confidence            4678999998      9999999999999999999999  443210                   012225678888899


Q ss_pred             HHHHHHHHH
Q 040243          330 SLEGAAAMV  338 (797)
Q Consensus       330 ~v~~A~~~I  338 (797)
                      ++.+|.+++
T Consensus        56 ~v~~~~~~l   64 (144)
T 2qnd_A           56 AVKKARSFL   64 (144)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHhh
Confidence            888886544

>1a6b_B Momulv, zinc finger protein NCP10; nucleocapsid protein, intercalation, nucleic acid, retrovirus, viral protein/DNA complex; HET: DNA; NMR {Synthetic} SCOP: g.40.1.1

Probab=96.35  E-value=0.0018  Score=48.70  Aligned_cols=24  Identities=29%  Similarity=0.497  Sum_probs=21.0

Q ss_pred             cccccceecCCCCCCcccCCCCCc
Q 040243          394 KSDVLCKICGDGGHPTIDCLVKGT  417 (797)
Q Consensus       394 ~~~v~Cr~CG~~gH~t~dCp~k~~  417 (797)
                      ...+.|++||+.|||++|||.+..
T Consensus         8 ~~~~~C~~Cgk~GH~ardCP~~~~   31 (40)
T 1a6b_B            8 LDRDQCAYCKEKGHWAKDCPKKPR   31 (40)
T ss_dssp             CCSSSCSSSCCTTCCTTSCSSSCC
T ss_pred             CCCCeeeECCCCCcchhhCcCCcc
Confidence            467899999999999999998654

>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}

Probab=96.14  E-value=0.0028  Score=59.07  Aligned_cols=40  Identities=30%  Similarity=0.703  Sum_probs=25.5

Q ss_pred             hhcccCCCCCccccCCCCCCCccccccceecCCCCCCcccCCCC
Q 040243          372 YCRLCGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTIDCLVK  415 (797)
Q Consensus       372 ~c~~cg~~gh~~~~cp~~~~~~~~~v~Cr~CG~~gH~t~dCp~k  415 (797)
                      .|.+|++.||.+.+||...    ..+.|.+||+.||+++||+..
T Consensus        44 ~C~~Cg~~GH~~~~C~~~~----~~~~C~~Cg~~GH~~~~Cp~~   83 (124)
T 2lli_A           44 QCSKCDEVGHYRSQCPHKW----KKVQCTLCKSKKHSKERCPSI   83 (124)
T ss_dssp             CSSSSSCSSSSTTTSCCCC----CCCSSSSSCSSCCCTTTCCCS
T ss_pred             cccccCCCCCccccCcCcc----cCccCCCCCcCCcchhhCCCc
Confidence            4666666666666666542    235677777777777777653

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.13  E-value=0.023  Score=51.30  Aligned_cols=70  Identities=20%  Similarity=0.307  Sum_probs=58.3

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhc-----CCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEE
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFST-----FGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIA  564 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~-----fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~  564 (797)
                      ...+|.|.||+..+.++.|.-+|+.     -|+|.+|....        +-|+|+|.+.+.|++.|+. ..+.|++..|.
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            4568999999999999999999987     26888887643        4789999999999999963 46788888888


Q ss_pred             EEec
Q 040243          565 VRVA  568 (797)
Q Consensus       565 V~~A  568 (797)
                      |.-.
T Consensus        78 V~P~   81 (104)
T 2dhx_A           78 LRPA   81 (104)
T ss_dssp             EEEC
T ss_pred             EEcC
Confidence            8653

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=96.00  E-value=0.023  Score=50.87  Aligned_cols=56  Identities=25%  Similarity=0.386  Sum_probs=47.7

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMN  554 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~Ln  554 (797)
                      ..+-++| ++|..+...||..+|+.|| -..|+++-|.       -|||.|.+.+.|..|+..+.
T Consensus        15 r~HVf~l-~FP~ewKt~DI~~lFs~fg-gv~I~WidDT-------sAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           15 RDHVLHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDDT-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCSEEEE-ECCTTCCHHHHHHHHTTTC-SCCCEEEETT-------EEEEECSCHHHHHHHHHHHH
T ss_pred             CCeEEEE-eCChhhhhHHHHHHhhccC-CEEEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            3455666 9999999999999999999 4567888885       89999999999999998653

>1u6p_A GAG polyprotein; MLV, A-minor K-turn, stem loop, bulge, G-U mismatch, G-A MIS U mismatch, A-C mismatch, zinc finger, NC, viral protein-RN; HET: AP7; NMR {Moloney murine leukemia virus} SCOP: g.40.1.1 PDB: 1wwd_A 1wwe_A 1wwf_A 1wwg_A

Probab=95.67  E-value=0.0041  Score=50.22  Aligned_cols=25  Identities=28%  Similarity=0.442  Sum_probs=21.6

Q ss_pred             ccccccceecCCCCCCcccCCCCCc
Q 040243          393 FKSDVLCKICGDGGHPTIDCLVKGT  417 (797)
Q Consensus       393 ~~~~v~Cr~CG~~gH~t~dCp~k~~  417 (797)
                      ....+.|++||+.|||++||+.+..
T Consensus        20 ~~~~~~C~~Cge~GH~ardCp~~~~   44 (56)
T 1u6p_A           20 QLDRDQCAYCKEKGHWAKDCPKKPR   44 (56)
T ss_dssp             TCCTTBCSSSCCBSSCGGGCTTCCC
T ss_pred             CCCCCcceeCCCCCcccccCcCCcc
Confidence            3578899999999999999998654

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=95.53  E-value=0.042  Score=48.64  Aligned_cols=69  Identities=13%  Similarity=0.211  Sum_probs=57.3

Q ss_pred             cEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCc--ccceEEEEecCHHHHHHHHHhcCceeecc
Q 040243          492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGM--SKGYGFVKYADIQMANNAIASMNGYRLEG  560 (797)
Q Consensus       492 ~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGk--srGfaFV~F~s~e~A~~AI~~LnG~~l~G  560 (797)
                      ++|.|++||..+||+++.+.++....+....++..+.+.+  .-.-|||.|.+.+++..-.+.++|+.+.+
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D   72 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLD   72 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEEC
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEc
Confidence            5899999999999999999999998877776665554333  23678999999999999999999998753

>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=95.28  E-value=0.022  Score=51.15  Aligned_cols=54  Identities=24%  Similarity=0.374  Sum_probs=46.9

Q ss_pred             cEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcC
Q 040243          492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMN  554 (797)
Q Consensus       492 ~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~Ln  554 (797)
                      +-++| ++|..+...||..+|+.|| -..|+++-|.       -|||.|.+.+.|..|+..+.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fg-gv~I~WidDT-------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDDT-------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSE-EEEEEEEETT-------EEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccC-CEEEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            34555 9999999999999999999 5678888885       89999999999999998664

>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=95.08  E-value=0.06  Score=49.94  Aligned_cols=73  Identities=19%  Similarity=0.308  Sum_probs=56.9

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeecc-ceEEEE
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEG-RTIAVR  566 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~G-r~L~V~  566 (797)
                      ..+.+-|.|-+.+... -..|...|++||+|++.....      ...+-.|.|.+..+|++||. .||..|+| -.|-|.
T Consensus        21 ~~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~~------~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~   92 (119)
T 1wwh_A           21 HLDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMSN------TGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVK   92 (119)
T ss_dssp             CGGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECS------SSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEE
T ss_pred             CCCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCC------CCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEE
Confidence            3456788888998874 567788999999999987621      23599999999999999996 59999985 455565


Q ss_pred             ec
Q 040243          567 VA  568 (797)
Q Consensus       567 ~A  568 (797)
                      ..
T Consensus        93 p~   94 (119)
T 1wwh_A           93 PC   94 (119)
T ss_dssp             EC
T ss_pred             EC
Confidence            53

>1dsq_A Nucleic acid binding protein P14; CCHC type zinc finger, virus/viral protein; NMR {Mouse mammary tumor virus} SCOP: g.40.1.1

Probab=95.07  E-value=0.0069  Score=41.21  Aligned_cols=20  Identities=35%  Similarity=0.752  Sum_probs=17.5

Q ss_pred             cccceecCCCCCCcccCCCC
Q 040243          396 DVLCKICGDGGHPTIDCLVK  415 (797)
Q Consensus       396 ~v~Cr~CG~~gH~t~dCp~k  415 (797)
                      .+.|..||+.|||++||+..
T Consensus         2 ~~~Cf~CG~~GH~ardC~~~   21 (26)
T 1dsq_A            2 GPVCFSCGKTGHIKRDCKEE   21 (26)
T ss_dssp             CCBCTTTCCBSSCTTTTTCC
T ss_pred             CCeeEeCCCCCcccccCCCc
Confidence            36799999999999999865

>3v69_A Protein filia; RNA-binding, embryogenesis, KH domain, RNA binding, P binding; 2.20A {Mus musculus}

Probab=94.96  E-value=0.027  Score=53.20  Aligned_cols=91  Identities=19%  Similarity=0.266  Sum_probs=58.1

Q ss_pred             CCCCCCCCCCCCCceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCC
Q 040243          237 NPAFKPPADYRPPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSEN  316 (797)
Q Consensus       237 ~p~~~pp~dy~p~~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~  316 (797)
                      +|-+..+.+.+.+.   .+||..      ..+|.||||+|+.|+.||..|++.|.|.--.|                  .
T Consensus        45 ~PwW~~~e~L~dPl---VF~vE~------~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~~s------------------~   97 (140)
T 3v69_A           45 LPKWFHVECLEDPK---RLYVEP------RLLEIMFGKDGEHIPHLESMLHTLIHVNVWGP------------------E   97 (140)
T ss_dssp             CCTTCCGGGGSSCE---EEEECG------GGHHHHHCGGGTTHHHHHHHHTSEEEEECCCT------------------T
T ss_pred             CCCccCHHHCCCCe---EEEEeh------hhhhcccCCCcCccchHHhhcceeEEEeccCC------------------C
Confidence            34455555555443   345666      89999999999999999999999999982221                  1


Q ss_pred             CCceEEEEecCHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHhh
Q 040243          317 EDLHVLVEAETQESLEGAAAMVEKLLQPVDEVLNEHKRQQLRELAAL  363 (797)
Q Consensus       317 e~LHv~I~a~~~e~v~~A~~~I~~ll~~~~e~~n~~k~~Ql~ela~l  363 (797)
                      .---|.|.|... .=.+|+.+|..|.        +.-|+.|.|...|
T Consensus        98 g~tEVtIfG~~~-~Q~rak~MI~sLA--------~~hr~~~~~~~~~  135 (140)
T 3v69_A           98 RRAEIWIFGPPP-FRRDVDRMLTDLA--------HYCRMKLMEIEAL  135 (140)
T ss_dssp             SCEEEEEESCHH-HHHHHHHHHHHHH--------HHHHHHHHHHC--
T ss_pred             CcEEEEEECCHH-HHHHHHHHHHHHH--------HHHHHHHHHHHHH
Confidence            112688888754 2234555565554        3345556665444

>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=94.32  E-value=0.034  Score=52.76  Aligned_cols=36  Identities=17%  Similarity=0.090  Sum_probs=30.3

Q ss_pred             EEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCcee
Q 040243          520 MAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYR  557 (797)
Q Consensus       520 ~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~  557 (797)
                      .++|+++.  .+++|||||+|.+.++|++|++.+++..
T Consensus         2 ~~kl~ln~--~~~~G~~fV~f~~~~~A~~al~~~~~~~   37 (158)
T 2kn4_A            2 QYKLILNG--KTLKGETTTEAVDAATAEKVFKQYANDN   37 (158)
T ss_dssp             EEEEEEEC--SSCEEEEEEECSSHHHHHHHHHHHHHHH
T ss_pred             cEEEEecC--ccccchhHHHHHHHHhHHHHHHhhcccC
Confidence            46788875  3799999999999999999998887643

>1nc8_A Nucleocapsid protein; HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus 2} SCOP: g.40.1.1 PDB: 2di2_A

Probab=93.66  E-value=0.022  Score=39.64  Aligned_cols=20  Identities=30%  Similarity=0.710  Sum_probs=17.9

Q ss_pred             ccccceecCCCCCCcccCCC
Q 040243          395 SDVLCKICGDGGHPTIDCLV  414 (797)
Q Consensus       395 ~~v~Cr~CG~~gH~t~dCp~  414 (797)
                      ..+.|..||..||++++|+.
T Consensus         5 ~~~~C~nCgk~GH~ar~C~~   24 (29)
T 1nc8_A            5 KVIRCWNCGKEGHSARQCRA   24 (29)
T ss_dssp             CCCBCTTTSCBSSCGGGCCS
T ss_pred             CCCEEEECCccccCHhHCcc
Confidence            45789999999999999975

>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=93.12  E-value=0.054  Score=51.08  Aligned_cols=42  Identities=19%  Similarity=0.141  Sum_probs=38.1

Q ss_pred             CCcccceEEEEecCHHHHHHHHHhc-CceeeccceEEEEecCCC
Q 040243          529 TGMSKGYGFVKYADIQMANNAIASM-NGYRLEGRTIAVRVAGKP  571 (797)
Q Consensus       529 TGksrGfaFV~F~s~e~A~~AI~~L-nG~~l~Gr~L~V~~A~~~  571 (797)
                      ..+.+|+++|+|.+.++|++|++.| ||..++| .++|.++...
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 9999988753

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=92.20  E-value=0.12  Score=48.76  Aligned_cols=78  Identities=21%  Similarity=0.288  Sum_probs=53.6

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEE-EEec------------CCCC-cccceEEEEecCHHHHHHHHHhcCc
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAK-VIKD------------RVTG-MSKGYGFVKYADIQMANNAIASMNG  555 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~-v~~d------------k~TG-ksrGfaFV~F~s~e~A~~AI~~LnG  555 (797)
                      ..+-|.|-+.+... ...+.+.|++||.|++-. +.++            +.-. ....+-.|+|++..+|.+||. .||
T Consensus         6 ~e~~VtVFGFp~~~-~~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG   83 (132)
T 3p3d_A            6 GELAILVFGYPETM-ANQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENG   83 (132)
T ss_dssp             --CEEEEECCCGGG-HHHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTT
T ss_pred             CceEEEEEecCHHH-HHHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCC
Confidence            34567777887654 466778999999987722 1110            0000 124678999999999999996 599


Q ss_pred             eeeccceEEEEecC
Q 040243          556 YRLEGRTIAVRVAG  569 (797)
Q Consensus       556 ~~l~Gr~L~V~~A~  569 (797)
                      ..|+|..|-|....
T Consensus        84 ~ii~G~mIGV~Py~   97 (132)
T 3p3d_A           84 AVFNGVLLGVIPYT   97 (132)
T ss_dssp             CEETTEECEEEECC
T ss_pred             eEeCcEEEEEEECC
Confidence            99999877776543

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=92.15  E-value=0.22  Score=44.59  Aligned_cols=79  Identities=13%  Similarity=0.134  Sum_probs=56.0

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCC-c-ccceEEEEecCHHHHHHHHHhcCceeeccc-----e
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTG-M-SKGYGFVKYADIQMANNAIASMNGYRLEGR-----T  562 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TG-k-srGfaFV~F~s~e~A~~AI~~LnG~~l~Gr-----~  562 (797)
                      ..-+|.|+.||+.+||+++.+.++..-++....++..+.+. . .-.-|||.|.+.++...-.+.++|+.+-+.     +
T Consensus         8 ~~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~~~   87 (97)
T 2l08_A            8 HSHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLEYP   87 (97)
T ss_dssp             CCCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCEEE
T ss_pred             cceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCEee
Confidence            34579999999999999998888776554332322222221 1 225789999999999999999999987532     3


Q ss_pred             EEEEec
Q 040243          563 IAVRVA  568 (797)
Q Consensus       563 L~V~~A  568 (797)
                      ..|++|
T Consensus        88 a~VE~A   93 (97)
T 2l08_A           88 AVVEFA   93 (97)
T ss_dssp             EEEEEC
T ss_pred             eEEEec
Confidence            456665

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=92.02  E-value=0.067  Score=60.48  Aligned_cols=57  Identities=16%  Similarity=0.314  Sum_probs=43.3

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHh
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS  552 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~  552 (797)
                      ..++|||. .+..+++.+|.++|++||.|.++.+.+++  |   -|+.|+|.+.+++..++..
T Consensus        52 a~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~--g---~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           52 AQRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF--G---LYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             HHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS--S---EEEEEECC---CCHHHHSS
T ss_pred             hcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC--C---eEEEEEeCCHHHHHHHHhc
Confidence            45789997 78899999999999999999999887654  2   5999999999999987653

>2ysa_A Retinoblastoma-binding protein 6; zinc finger, CCHC, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=91.99  E-value=0.049  Score=43.78  Aligned_cols=22  Identities=36%  Similarity=0.732  Sum_probs=18.7

Q ss_pred             ccccceecCCCCCCcccCCCCC
Q 040243          395 SDVLCKICGDGGHPTIDCLVKG  416 (797)
Q Consensus       395 ~~v~Cr~CG~~gH~t~dCp~k~  416 (797)
                      ...+|..||..|||.++|+.++
T Consensus         6 ~~~~C~kCGk~GH~~k~Cp~~~   27 (55)
T 2ysa_A            6 SGYTCFRCGKPGHYIKNCPTNG   27 (55)
T ss_dssp             SSCCCTTTCCTTSCGGGCSGGG
T ss_pred             CCCccccCCCcCcccccCCCCC
Confidence            4568999999999999998543

>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}

Probab=86.18  E-value=0.2  Score=36.99  Aligned_cols=19  Identities=32%  Similarity=0.667  Sum_probs=17.0

Q ss_pred             ccceecCCCCCCcccCCCC
Q 040243          397 VLCKICGDGGHPTIDCLVK  415 (797)
Q Consensus       397 v~Cr~CG~~gH~t~dCp~k  415 (797)
                      |.|..||+.||++++|+..
T Consensus         1 i~C~~Cg~~GH~a~~C~~~   19 (39)
T 2a51_A            1 LTCFNCGKPGHTARMCRQP   19 (39)
T ss_dssp             CBCTTTCCBSSCTTTCCSC
T ss_pred             CeeeccCCCCcccccCCCC
Confidence            5799999999999999863

>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}

Probab=84.72  E-value=0.36  Score=40.96  Aligned_cols=36  Identities=17%  Similarity=0.267  Sum_probs=19.5

Q ss_pred             CCCccccCCCCCCC-----ccccccceecCCCCCCcccCCC
Q 040243          379 PGHRQYACPSRTST-----FKSDVLCKICGDGGHPTIDCLV  414 (797)
Q Consensus       379 ~gh~~~~cp~~~~~-----~~~~v~Cr~CG~~gH~t~dCp~  414 (797)
                      .||..=+|+.....     -...+.|..||+.||++++|+.
T Consensus         2 ~gh~~rdc~~~~~~~~~~~~~r~~~C~~Cg~~GH~a~~C~~   42 (74)
T 2li8_A            2 SGLVPRGSHMPKGKSMQKRRSKGDRCYNCGGLDHHAKECKL   42 (74)
T ss_dssp             ----------CCCCCCCSCCSTTSCCTTTCCSSSCTTTCSS
T ss_pred             CccccCcCCCCCcCccccccCCCCcccccCCcCcCcccCCC
Confidence            46666677654311     1245789999999999999985

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=84.47  E-value=0.19  Score=64.98  Aligned_cols=18  Identities=28%  Similarity=0.283  Sum_probs=10.5

Q ss_pred             hHHHHHHHhCcEEEEecc
Q 040243          278 TQKRMERETGAKIVIRGK  295 (797)
Q Consensus       278 t~K~le~eTgakI~IrGk  295 (797)
                      .|++||+..=-+|.|+|-
T Consensus      1265 ~l~~l~~~~l~~~~i~Gi 1282 (1752)
T 3h0g_A         1265 FLKTIEGHMLESISLRGV 1282 (1752)
T ss_dssp             HHHHHHHHHTTCCCSSCC
T ss_pred             HHHHHHHhhccceEEecC
Confidence            477777554445666663

>1a6b_B Momulv, zinc finger protein NCP10; nucleocapsid protein, intercalation, nucleic acid, retrovirus, viral protein/DNA complex; HET: DNA; NMR {Synthetic} SCOP: g.40.1.1

Probab=84.06  E-value=0.51  Score=35.39  Aligned_cols=26  Identities=31%  Similarity=0.733  Sum_probs=21.6

Q ss_pred             CCcCccchhcccCCCCCccccCCCCC
Q 040243          365 GTIRDEEYCRLCGEPGHRQYACPSRT  390 (797)
Q Consensus       365 Gt~r~~~~c~~cg~~gh~~~~cp~~~  390 (797)
                      +...+...|.+||+.||-+.+||...
T Consensus         5 ~~~~~~~~C~~Cgk~GH~ardCP~~~   30 (40)
T 1a6b_B            5 RSQLDRDQCAYCKEKGHWAKDCPKKP   30 (40)
T ss_dssp             CCSCCSSSCSSSCCTTCCTTSCSSSC
T ss_pred             cCCCCCCeeeECCCCCcchhhCcCCc
Confidence            34445678999999999999999875

>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}

Probab=83.61  E-value=0.38  Score=35.09  Aligned_cols=19  Identities=32%  Similarity=0.711  Sum_probs=16.6

Q ss_pred             ccceecCCCCCCcccCCCC
Q 040243          397 VLCKICGDGGHPTIDCLVK  415 (797)
Q Consensus       397 v~Cr~CG~~gH~t~dCp~k  415 (797)
                      +.|..||+.||++++|+..
T Consensus         1 ~~C~~Cg~~GH~~~~C~~~   19 (37)
T 2bl6_A            1 QTCYNCGKPGHLSSQCRAP   19 (37)
T ss_dssp             CCBSSSCCSSCCTTTSSCB
T ss_pred             CcccccCCCCcchhhCcCc
Confidence            4699999999999999863

>2ec7_A GAG polyprotein (PR55GAG); nucleocapsid protein, HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus type 2} SCOP: g.40.1.1

Probab=82.74  E-value=0.39  Score=37.30  Aligned_cols=21  Identities=29%  Similarity=0.667  Sum_probs=18.4

Q ss_pred             ccccceecCCCCCCcccCCCC
Q 040243          395 SDVLCKICGDGGHPTIDCLVK  415 (797)
Q Consensus       395 ~~v~Cr~CG~~gH~t~dCp~k  415 (797)
                      ..+.|..||+.||++++|+..
T Consensus         5 r~~~C~~Cg~~GH~a~~C~~~   25 (49)
T 2ec7_A            5 KVIRCWNCGKEGHSARQCRAP   25 (49)
T ss_dssp             CCCBCTTTCCBTCCTTTCCCS
T ss_pred             CcCeeeecCCCCcChhhCcCC
Confidence            457899999999999999864

>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}

Probab=82.00  E-value=0.53  Score=38.23  Aligned_cols=22  Identities=36%  Similarity=0.706  Sum_probs=18.8

Q ss_pred             ccccceecCCCCCCcccCCCCC
Q 040243          395 SDVLCKICGDGGHPTIDCLVKG  416 (797)
Q Consensus       395 ~~v~Cr~CG~~gH~t~dCp~k~  416 (797)
                      ..+.|..||+.||++++|+...
T Consensus         3 ~~~~C~~Cg~~GH~a~~C~~~~   24 (61)
T 2ihx_A            3 ARGLCYTCGSPGHYQAQCPKKR   24 (61)
T ss_dssp             CTTBCSSSCCBTCCGGGCTTTT
T ss_pred             CCCcccccCCCCeehhhCcCCc
Confidence            3568999999999999998753

>1u6p_A GAG polyprotein; MLV, A-minor K-turn, stem loop, bulge, G-U mismatch, G-A MIS U mismatch, A-C mismatch, zinc finger, NC, viral protein-RN; HET: AP7; NMR {Moloney murine leukemia virus} SCOP: g.40.1.1 PDB: 1wwd_A 1wwe_A 1wwf_A 1wwg_A

Probab=80.47  E-value=0.77  Score=36.93  Aligned_cols=26  Identities=31%  Similarity=0.733  Sum_probs=21.4

Q ss_pred             CCcCccchhcccCCCCCccccCCCCC
Q 040243          365 GTIRDEEYCRLCGEPGHRQYACPSRT  390 (797)
Q Consensus       365 Gt~r~~~~c~~cg~~gh~~~~cp~~~  390 (797)
                      +...+...|.+||+.||-+++||...
T Consensus        18 ~~~~~~~~C~~Cge~GH~ardCp~~~   43 (56)
T 1u6p_A           18 RSQLDRDQCAYCKEKGHWAKDCPKKP   43 (56)
T ss_dssp             STTCCTTBCSSSCCBSSCGGGCTTCC
T ss_pred             CCCCCCCcceeCCCCCcccccCcCCc
Confidence            33445578999999999999999875

---

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	797
d2bl5a1	134	d.51.1.1 (A:1-134) Quaking protein A (Xqua) {Afric	1e-48
d1k1ga_	122	d.51.1.1 (A:) RNA splicing factor 1 {Human (Homo s	1e-44
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	2e-21
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	2e-20
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	1e-19
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	2e-19
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	4e-19
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	1e-17
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	4e-17
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	1e-16
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	1e-16
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-16
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	2e-16
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	2e-16
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	2e-16
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-16
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	3e-16
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	4e-16
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-15
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	2e-15
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	2e-15
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	2e-15
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	4e-15
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	2e-14
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	3e-14
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	5e-14
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	6e-14
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	1e-13
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	1e-13
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	2e-13
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	2e-13
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	2e-13
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	3e-13
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	3e-13
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	4e-13
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	4e-13
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 5e-13
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	5e-13
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	5e-13
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	6e-13
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	7e-13
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	1e-12
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	1e-12
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	2e-12
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	2e-12
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-12
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	2e-12
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	2e-12
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	4e-12
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	5e-12
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-09
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	1e-11
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	2e-11
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	6e-11
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	8e-11
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	1e-10
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	1e-10
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	2e-10
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	6e-10
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	6e-10
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	8e-10
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	2e-09
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	3e-09
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	3e-09
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	3e-09
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	6e-09
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	7e-09
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	9e-09
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	9e-09
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	1e-08
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	2e-08
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	3e-08
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	5e-08
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	6e-08
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	7e-08
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-07
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-07
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	2e-07
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-07
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	8e-07
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	1e-06
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	3e-06
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	4e-06
d2je6i3	69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	4e-06
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	4e-06
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	6e-06
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	7e-06
d2cpqa1	78	d.51.1.1 (A:212-289) Fragile X mental retardation	8e-06
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	1e-05
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	1e-05
d2exfa1	42	g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod	2e-05
d1tuaa2	104	d.51.1.1 (A:85-188) Hypothetical protein APE0754 {	2e-05
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	3e-05
d2z0sa2	87	d.51.1.1 (A:148-234) Exosome complex RNA-binding p	3e-05
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	4e-05
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	4e-05
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	5e-05
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	6e-05
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	6e-05
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	7e-05
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	7e-05
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	8e-05
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	9e-05
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	1e-04
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	2e-04
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	2e-04
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	6e-04
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	0.001
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	0.004

>d2bl5a1 d.51.1.1 (A:1-134) Quaking protein A (Xqua) {African clawed frog (Xenopus laevis) [TaxId: 8355]} Length = 134

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Quaking protein A (Xqua)
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

 Score =  166 bits (421), Expect = 1e-48
 Identities = 60/128 (46%), Positives = 84/128 (65%), Gaps = 6/128 (4%)

Query: 250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRL-QQKRD 308
           +LQ+KLY+P+KEYP +NF+G I+GPRG T K++E ETG KI++RGKGS+++ +  +Q R 
Sbjct: 1   QLQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRG 60

Query: 309 LKPDPSENEDLHVLVEAETQES-----LEGAAAMVEKLLQPVDEVLNEHKRQQLRELAAL 363
                  NEDLHVL+  E  ++     L+ A   V+KLL P  E  +  K+ +L ELA L
Sbjct: 61  KPNWEHLNEDLHVLITVEDAQNRAELKLKRAVEEVKKLLVPAAEGEDSLKKMKLMELAIL 120

Query: 364 NGTIRDEE 371
           NGT RD  
Sbjct: 121 NGTYRDAN 128

>d1k1ga_ d.51.1.1 (A:) RNA splicing factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 122

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: RNA splicing factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  154 bits (391), Expect = 1e-44
 Identities = 59/122 (48%), Positives = 82/122 (67%), Gaps = 4/122 (3%)

Query: 250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDL 309
           ++  K+ IP  EYP  NF+GL+IGPRGNT K +E+E  AKI+IRGKGSVKEG+   ++D 
Sbjct: 2   RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGK-VGRKDG 60

Query: 310 KPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQ---PVDEVLNEHKRQQLRELAALNGT 366
           +  P E+E LH LV A T E+++ A   +  +L+      E  N+ ++ QLRELA LNGT
Sbjct: 61  QMLPGEDEPLHALVTANTMENVKKAVEQIRNILKQGIETPEDQNDLRKMQLRELARLNGT 120

Query: 367 IR 368
           +R
Sbjct: 121 LR 122

>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 = 86.9 bits (215), Expect = 2e-21
 Identities = 31/83 (37%), Positives = 51/83 (61%), Gaps = 2/83 (2%)

Query: 488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMAN 547
            + DTNLY+  LP T+ DD L  +F  +G IV   +++D++TG  +G  FV+Y   + A 
Sbjct: 3   SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQ 62

Query: 548 NAIASMNGYRLEG--RTIAVRVA 568
            AI+++N    EG  + ++VR+A
Sbjct: 63  EAISALNNVIPEGGSQPLSVRLA 85

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 84.3 bits (208), Expect = 2e-20
 Identities = 29/79 (36%), Positives = 48/79 (60%)

Query: 489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANN 548
           + D NLY+  LP T+    L +LFS +G I+ ++++ D+VTG+S+G GF+++     A  
Sbjct: 4   IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEE 63

Query: 549 AIASMNGYRLEGRTIAVRV 567
           AI  +NG +  G T  + V
Sbjct: 64  AIKGLNGQKPSGATEPITV 82

>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 = 81.2 bits (200), Expect = 1e-19
 Identities = 23/75 (30%), Positives = 41/75 (54%), Gaps = 1/75 (1%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           ++IG L      +GL   F  FG++    V++D +T  S+G+GFV + D    +  +A  
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-Q 61

Query: 554 NGYRLEGRTIAVRVA 568
           + + L+ +TI  +VA
Sbjct: 62  SRHELDSKTIDPKVA 76

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 81.1 bits (200), Expect = 2e-19
 Identities = 22/78 (28%), Positives = 41/78 (52%)

Query: 493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
           +LY+G L P + +  L   FS  G I+  +V +D +T  S GY +V +     A  A+ +
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 553 MNGYRLEGRTIAVRVAGK 570
           MN   ++G+ + +  + +
Sbjct: 62  MNFDVIKGKPVRIMWSQR 79

>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 = 80.8 bits (199), Expect = 4e-19
 Identities = 22/84 (26%), Positives = 41/84 (48%), Gaps = 2/84 (2%)

Query: 487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDR-VTGMSKGYGFVKYADIQM 545
           K+   + + +  +P   +   +  LFSTFG++   ++ K    TG  +G+GFV +   Q 
Sbjct: 4   KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQD 63

Query: 546 ANNAIASM-NGYRLEGRTIAVRVA 568
           A  A  ++ +   L GR + +  A
Sbjct: 64  AKKAFNALCHSTHLYGRRLVLEWA 87

>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 = 76.2 bits (187), Expect = 1e-17
 Identities = 27/81 (33%), Positives = 41/81 (50%), Gaps = 1/81 (1%)

Query: 491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAI 550
           +TNL + YLP  + D  L  LF   G I   ++++D  TG S GY FV +     +  AI
Sbjct: 2   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 61

Query: 551 ASMNGYRLEGRTIAVRVAGKP 571
             +NG  +  + + V  A +P
Sbjct: 62  KVLNGITVRNKRLKVSYA-RP 81

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 74.7 bits (183), Expect = 4e-17
 Identities = 18/90 (20%), Positives = 36/90 (40%), Gaps = 4/90 (4%)

Query: 479 GSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFV 538
           G++  KP      T + +  +P T+  D ++  F  +  I  +  +K    GM  G   V
Sbjct: 1   GASSGKP----GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMV 56

Query: 539 KYADIQMANNAIASMNGYRLEGRTIAVRVA 568
            +     A  A+  +N   +  R + + + 
Sbjct: 57  AFESRDEATAAVIDLNDRPIGSRKVKLVLG 86

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 72.7 bits (178), Expect = 1e-16
 Identities = 12/75 (16%), Positives = 33/75 (44%), Gaps = 1/75 (1%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           +++G L P   ++ +   F  FG++   ++  D  T   +G+ F+ + + +     +   
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-K 60

Query: 554 NGYRLEGRTIAVRVA 568
             + +      ++VA
Sbjct: 61  KYHNVGLSKCEIKVA 75

>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 = 73.1 bits (179), Expect = 1e-16
 Identities = 23/77 (29%), Positives = 43/77 (55%), Gaps = 2/77 (2%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           ++L +  LP    +  L   FSTFG+++M +V KD  TG SKG+GFV++ + +     ++
Sbjct: 9   SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS 68

Query: 552 SMNGYRLEGRTIAVRVA 568
             +   ++GR    ++ 
Sbjct: 69  QRHM--IDGRWCDCKLP 83

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 73.1 bits (179), Expect = 2e-16
 Identities = 31/75 (41%), Positives = 48/75 (64%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L+IG LP  L+DD +  L ++FG +    ++KD  TG+SKGY F +Y DI + + AIA +
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 554 NGYRLEGRTIAVRVA 568
           NG +L  + + V+ A
Sbjct: 64  NGMQLGDKKLLVQRA 78

>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 = 72.4 bits (177), Expect = 2e-16
 Identities = 24/83 (28%), Positives = 43/83 (51%), Gaps = 2/83 (2%)

Query: 487 KELDDTN-LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQM 545
           KE +    L+IG L     D+ L   F  +G +    V++D  T  S+G+GFV YA ++ 
Sbjct: 1   KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 60

Query: 546 ANNAIASMNGYRLEGRTIAVRVA 568
            + A+     ++++GR +  + A
Sbjct: 61  VDAAMN-ARPHKVDGRVVEPKRA 82

>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 = 72.3 bits (177), Expect = 2e-16
 Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 1/75 (1%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L +  L   + D  +  LF+ FG +  A V  DR +G S G   V +     A  A+   
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQY 61

Query: 554 NGYRLEGRTIAVRVA 568
           NG  L+GR + +++ 
Sbjct: 62  NGVPLDGRPMNIQLV 76

>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 = 72.7 bits (178), Expect = 2e-16
 Identities = 24/77 (31%), Positives = 37/77 (48%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
             LY+G L     ++ +  LFS  GDI    +  D++   + G+ FV+Y     A NA+ 
Sbjct: 8   CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 67

Query: 552 SMNGYRLEGRTIAVRVA 568
            +NG RL+ R I     
Sbjct: 68  YINGTRLDDRIIRTDWD 84

>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 = 71.9 bits (176), Expect = 3e-16
 Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 1/75 (1%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           ++IG L        L   FS FG++V   +  D +TG S+G+GFV + + +  +  +   
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-Q 60

Query: 554 NGYRLEGRTIAVRVA 568
             ++L G+ I  + A
Sbjct: 61  KEHKLNGKVIDPKRA 75

>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 = 72.4 bits (177), Expect = 3e-16
 Identities = 22/84 (26%), Positives = 43/84 (51%), Gaps = 3/84 (3%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDR---VTGMSKGYGFVKYADIQMANNAI 550
           L+I  L  +  ++ L  +FS  G I    + K +      +S G+GFV+Y   + A  A+
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 551 ASMNGYRLEGRTIAVRVAGKPPQP 574
             + G+ ++G  + VR++ +  +P
Sbjct: 61  KQLQGHTVDGHKLEVRISERATKP 84

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 71.7 bits (175), Expect = 4e-16
 Identities = 34/80 (42%), Positives = 50/80 (62%), Gaps = 1/80 (1%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           TNL + YLP  +  +    LF + G+I   K+++D++TG S GYGFV Y D + A  AI 
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

Query: 552 SMNGYRLEGRTIAVRVAGKP 571
           ++NG RL+ +TI V  A +P
Sbjct: 63  TLNGLRLQTKTIKVSYA-RP 81

>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 = 70.7 bits (173), Expect = 1e-15
 Identities = 28/113 (24%), Positives = 49/113 (43%), Gaps = 18/113 (15%)

Query: 468 GSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPP-TLDDDGLIRLFSTFGDIVMAKVIKD 526
           GSSG+ G         K      ++ ++IG L    +    +  +FS +G IV   V K 
Sbjct: 1   GSSGSSG---------KTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHK- 50

Query: 527 RVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPG 579
                  G+ FV+Y + + A  A+A  +G  + G+ + + +A +P      P 
Sbjct: 51  -------GFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEPKVNRSGPS 96

>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 = 69.8 bits (170), Expect = 2e-15
 Identities = 31/76 (40%), Positives = 44/76 (57%), Gaps = 1/76 (1%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMA-KVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
           ++IG L P +D+  L   FS FG I+   K+++D  TG SKGY F+ +A    ++ AI +
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 553 MNGYRLEGRTIAVRVA 568
           MNG  L  R I V  A
Sbjct: 61  MNGQYLCNRPITVSYA 76

>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 = 70.5 bits (172), Expect = 2e-15
 Identities = 18/79 (22%), Positives = 39/79 (49%), Gaps = 1/79 (1%)

Query: 490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNA 549
               L+IG L     ++ L   +  +G +    V++D  +  S+G+GFV ++ +   + A
Sbjct: 19  QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAA 78

Query: 550 IASMNGYRLEGRTIAVRVA 568
           +A    + ++GR +  + A
Sbjct: 79  MA-ARPHSIDGRVVEPKRA 96

>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 = 69.7 bits (170), Expect = 2e-15
 Identities = 31/81 (38%), Positives = 43/81 (53%), Gaps = 1/81 (1%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           LY+G L   +DD  L   F  FGDI   ++  D  T   +G+ FV++   + A  AI +M
Sbjct: 8   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67

Query: 554 NGYRLEGRTIAVRVAGKPPQP 574
           N   L GRTI V +A KP + 
Sbjct: 68  NESELFGRTIRVNLA-KPMRI 87

>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 = 69.3 bits (169), Expect = 4e-15
 Identities = 32/85 (37%), Positives = 47/85 (55%), Gaps = 1/85 (1%)

Query: 485 PIKELD-DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADI 543
           PI E + D  +Y+G L   + +  L  LF   G +V   + KDRVTG  +GYGFV++   
Sbjct: 2   PISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSE 61

Query: 544 QMANNAIASMNGYRLEGRTIAVRVA 568
           + A+ AI  M+  +L G+ I V  A
Sbjct: 62  EDADYAIKIMDMIKLYGKPIRVNKA 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 = 66.7 bits (162), Expect = 2e-14
 Identities = 13/75 (17%), Positives = 33/75 (44%), Gaps = 1/75 (1%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           +++G L      + +   F  FG +  A ++ D+ T   +G+GFV +    +       +
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-I 60

Query: 554 NGYRLEGRTIAVRVA 568
           + + +  + +  + A
Sbjct: 61  HFHEINNKMVECKKA 75

>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 = 66.9 bits (163), Expect = 3e-14
 Identities = 23/86 (26%), Positives = 41/86 (47%), Gaps = 6/86 (6%)

Query: 490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNA 549
            +  +Y G +   L D  + + FS FG I+  +V  ++       Y FV+++  + A +A
Sbjct: 17  KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG------YSFVRFSTHESAAHA 70

Query: 550 IASMNGYRLEGRTIAVRVAGKPPQPT 575
           I S+NG  +EG  +      + P  T
Sbjct: 71  IVSVNGTTIEGHVVKCYWGKESPDMT 96

>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 = 65.9 bits (160), Expect = 5e-14
 Identities = 32/83 (38%), Positives = 50/83 (60%)

Query: 490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNA 549
           D+  L++G L    ++  L ++FS +G I    V+KDR T  S+G+GFV + +I  A +A
Sbjct: 4   DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 63

Query: 550 IASMNGYRLEGRTIAVRVAGKPP 572
           + +MNG  ++GR I V  AGK  
Sbjct: 64  MMAMNGKSVDGRQIRVDQAGKSS 86

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 66.6 bits (162), Expect = 6e-14
 Identities = 21/78 (26%), Positives = 37/78 (47%), Gaps = 3/78 (3%)

Query: 491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAI 550
           +  LYI  LP  +  + +  +F  +G I   + I+   T  ++G  +V Y DI  A NA 
Sbjct: 7   NRILYIRNLPYKITAEEMYDIFGKYGPI---RQIRVGNTPETRGTAYVVYEDIFDAKNAC 63

Query: 551 ASMNGYRLEGRTIAVRVA 568
             ++G+ +  R + V   
Sbjct: 64  DHLSGFNVCNRYLVVLYY 81

>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 = 65.1 bits (158), Expect = 1e-13
 Identities = 21/74 (28%), Positives = 35/74 (47%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
             L +  L     +  L  +FS +G I    ++ D+ +  S+G+ FV + ++  A  A  
Sbjct: 10  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 69

Query: 552 SMNGYRLEGRTIAV 565
             NG  L+GR I V
Sbjct: 70  RANGMELDGRRIRV 83

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.4 bits (156), Expect = 1e-13
 Identities = 17/75 (22%), Positives = 36/75 (48%), Gaps = 1/75 (1%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           +++G +    ++  L   F  +G I + +++ DR +G  +G+ FV + D   + + I   
Sbjct: 5   IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD-SVDKIVIQ 63

Query: 554 NGYRLEGRTIAVRVA 568
             + + G    VR A
Sbjct: 64  KYHTVNGHNCEVRKA 78

>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 = 65.1 bits (158), Expect = 2e-13
 Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 1/82 (1%)

Query: 487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMA 546
           +E D   ++   L   +    L   FS  G +   ++I DR +  SKG  +V++ +IQ  
Sbjct: 14  EERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSV 73

Query: 547 NNAIASMNGYRLEGRTIAVRVA 568
             AI  + G RL G  I V+ +
Sbjct: 74  PLAIG-LTGQRLLGVPIIVQAS 94

>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 = 64.4 bits (156), Expect = 2e-13
 Identities = 24/84 (28%), Positives = 41/84 (48%)

Query: 485 PIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQ 544
           P + ++   L++  +     +D +   F  +G+I    +  DR TG SKGY  V+Y   +
Sbjct: 1   PQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHK 60

Query: 545 MANNAIASMNGYRLEGRTIAVRVA 568
            A  A  ++NG  + G+TI V   
Sbjct: 61  QALAAKEALNGAEIMGQTIQVDWC 84

>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 = 64.3 bits (156), Expect = 2e-13
 Identities = 25/82 (30%), Positives = 40/82 (48%), Gaps = 1/82 (1%)

Query: 490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNA 549
           D+  + +  L     +  L  LF  FG I    + KD+ TG SKG+ F+ +   + A  A
Sbjct: 7   DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA 66

Query: 550 IASMNGYRLEGRTIAVRVAGKP 571
           IA ++G+  +   + V  A KP
Sbjct: 67  IAGVSGFGYDHLILNVEWA-KP 87

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.9 bits (155), Expect = 3e-13
 Identities = 26/77 (33%), Positives = 37/77 (48%), Gaps = 2/77 (2%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
            N++I  L  ++D+  L   FS FG+I+  KV+ D        YGFV +   + A  AI 
Sbjct: 9   GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKG--YGFVHFETQEAAERAIE 66

Query: 552 SMNGYRLEGRTIAVRVA 568
            MNG  L  R + V   
Sbjct: 67  KMNGMLLNDRKVFVGRF 83

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.5 bits (154), Expect = 3e-13
 Identities = 19/79 (24%), Positives = 38/79 (48%), Gaps = 7/79 (8%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           LY+  L  +  ++ + + F+      + +V         + Y FV +++ + A  A+ ++
Sbjct: 11  LYVRNLMLSTSEEMIEKEFNNIKPGAVERV------KKIRDYAFVHFSNREDAVEAMKAL 64

Query: 554 NGYRLEGRTIAVRVAGKPP 572
           NG  L+G  I V +A KP 
Sbjct: 65  NGKVLDGSPIEVTLA-KPV 82

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.5 bits (154), Expect = 4e-13
 Identities = 20/86 (23%), Positives = 39/86 (45%), Gaps = 4/86 (4%)

Query: 490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNA 549
           +D  +Y+G LPP +    +  +F  +G I    +   R       + FV++ D + A +A
Sbjct: 13  NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR---GGPPFAFVEFEDPRDAEDA 69

Query: 550 IASMNGYRLEGRTIAVRVAGKPPQPT 575
           +   +GY  +G  + V    +  + T
Sbjct: 70  VYGRDGYDYDGYRLRVEFP-RSGRGT 94

>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 = 63.1 bits (153), Expect = 4e-13
 Identities = 20/84 (23%), Positives = 38/84 (45%), Gaps = 6/84 (7%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           + L++G LPP + ++ + +LF  +G      +         KG+GF++     +A  A  
Sbjct: 9   SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH------KDKGFGFIRLETRTLAEIAKV 62

Query: 552 SMNGYRLEGRTIAVRVAGKPPQPT 575
            ++   L G+ + VR A      T
Sbjct: 63  ELDNMPLRGKQLRVRFACHSASLT 86

>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 = 63.9 bits (155), Expect = 5e-13
 Identities = 10/74 (13%), Positives = 27/74 (36%), Gaps = 1/74 (1%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           +++ +        ++    +   +G++    V  +       G  +VK+   + A  A+ 
Sbjct: 28  SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVI 86

Query: 552 SMNGYRLEGRTIAV 565
            +N     G+ I  
Sbjct: 87  DLNNRWFNGQPIHA 100

>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 = 63.6 bits (154), Expect = 5e-13
 Identities = 28/113 (24%), Positives = 46/113 (40%), Gaps = 17/113 (15%)

Query: 468 GSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDR 527
           GSSG+ G                   L++  L  T  ++ L +LFS +G +       D 
Sbjct: 1   GSSGSSG----------------SGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDS 44

Query: 528 VTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPGP 580
           +T   KG+ FV +   + A  A A ++G   +GR + V  +    +     GP
Sbjct: 45  LTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS-TIKKEASQSGP 96

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.6 bits (154), Expect = 5e-13
 Identities = 35/88 (39%), Positives = 45/88 (51%), Gaps = 1/88 (1%)

Query: 487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMA 546
           K+   T +++G LP    D  L + F  FGDI  A VI DR TG S+GYGFV  AD   A
Sbjct: 6   KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAA 65

Query: 547 NNAIASMNGYRLEGRTIAVRVAGKPPQP 574
             A    N   ++GR   V +A    +P
Sbjct: 66  ERACKDPNPI-IDGRKANVNLAYLGAKP 92

>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 = 63.6 bits (154), Expect = 6e-13
 Identities = 32/92 (34%), Positives = 56/92 (60%), Gaps = 1/92 (1%)

Query: 477 GLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYG 536
            +G+ G++  +  +  NL+I +LP    D  L+++F  FG++V AKV  D+ T +SK +G
Sbjct: 5   SIGAAGSQK-EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFG 63

Query: 537 FVKYADIQMANNAIASMNGYRLEGRTIAVRVA 568
           FV Y +   A  AI SMNG+++  + + V++ 
Sbjct: 64  FVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK 95

>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 = 63.2 bits (153), Expect = 7e-13
 Identities = 17/87 (19%), Positives = 32/87 (36%), Gaps = 4/87 (4%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMA--KVIKDRVTGMSKGYGFVKYADIQMANNA 549
             L+IG +P     + ++   +   + V+             ++G+ FV+Y   + A  A
Sbjct: 2   CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 61

Query: 550 IASMNG--YRLEGRTIAVRVAGKPPQP 574
              +     +L G  IAV  A      
Sbjct: 62  RRKLMPGRIQLWGHQIAVDWAEPEIDV 88

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.0 bits (150), Expect = 1e-12
 Identities = 23/84 (27%), Positives = 42/84 (50%), Gaps = 2/84 (2%)

Query: 490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNA 549
               LY+G L   + +  +++LFS  G     K+I +     +  Y FV++ + + A  A
Sbjct: 7   QPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH--TSNDPYCFVEFYEHRDAAAA 64

Query: 550 IASMNGYRLEGRTIAVRVAGKPPQ 573
           +A+MNG ++ G+ + V  A  P  
Sbjct: 65  LAAMNGRKILGKEVKVNWATTPSS 88

>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 = 62.1 bits (150), Expect = 1e-12
 Identities = 27/97 (27%), Positives = 42/97 (43%), Gaps = 9/97 (9%)

Query: 485 PIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVI--------KDRVTGMSKGYG 536
           P ++ D++ +Y+  L  ++  D L   F   G + M K           D+ TG  KG  
Sbjct: 2   PDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDA 61

Query: 537 FVKYADIQMANNAIASMNGYRLEGRTIAVRVA-GKPP 572
            V Y D   A  A+   +G   +G  + V +A  KPP
Sbjct: 62  TVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPP 98

>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 = 62.0 bits (150), Expect = 2e-12
 Identities = 16/84 (19%), Positives = 33/84 (39%), Gaps = 5/84 (5%)

Query: 487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMA 546
           K      L    L   + +D L  +F    +I +         G SKG  ++++     A
Sbjct: 12  KVRAARTLLAKNLSFNITEDELKEVFEDALEIRL-----VSQDGKSKGIAYIEFKSEADA 66

Query: 547 NNAIASMNGYRLEGRTIAVRVAGK 570
              +    G  ++GR++++   G+
Sbjct: 67  EKNLEEKQGAEIDGRSVSLYYTGE 90

>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 = 61.4 bits (148), Expect = 2e-12
 Identities = 13/81 (16%), Positives = 34/81 (41%), Gaps = 1/81 (1%)

Query: 491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAI 550
           +  L++   PP+     +  L      + ++  +       S+ + ++     + A   +
Sbjct: 1   ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCV 60

Query: 551 ASMNGYRLEGRTIAVRVAGKP 571
             +NG ++EG T+  +V+  P
Sbjct: 61  EKLNGLKIEGYTLVTKVS-NP 80

>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 = 61.7 bits (149), Expect = 2e-12
 Identities = 14/91 (15%), Positives = 38/91 (41%), Gaps = 9/91 (9%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKV-----IKDRVTGMSKGYGFVKYADIQMANN 548
           LY+G +P  + ++ ++  F+    +          +        K + F+++  +     
Sbjct: 4   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 63

Query: 549 AIASMNGYRLEGRTIAVRVAGKPPQPTVPPG 579
           A+ + +G   +G+++ +R   +P      PG
Sbjct: 64  AM-AFDGIIFQGQSLKIR---RPHDYQPLPG 90

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.6 bits (149), Expect = 2e-12
 Identities = 27/89 (30%), Positives = 44/89 (49%), Gaps = 3/89 (3%)

Query: 480 SNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVK 539
           S+G    K      L++  +P    D  L ++F  FG I+  ++I +     SKG+GFV 
Sbjct: 1   SSGNSESKS-TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVT 57

Query: 540 YADIQMANNAIASMNGYRLEGRTIAVRVA 568
           + +   A+ A   ++G  +EGR I V  A
Sbjct: 58  FENSADADRAREKLHGTVVEGRKIEVNNA 86

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 61.4 bits (148), Expect = 2e-12
 Identities = 15/89 (16%), Positives = 33/89 (37%), Gaps = 8/89 (8%)

Query: 486 IKELDDTNLYIGYLPPTLDDDGLIRLF---STFGDIVMAKVIKDRVTG---MSKGYGFVK 539
           ++ +    +++  L   L D  +++       FG I    +                +V 
Sbjct: 3   VRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVT 62

Query: 540 YADIQMANNAIASMNGYRLEGRTIAVRVA 568
           Y   + A  AI  +N   ++GRT+  + +
Sbjct: 63  YIRSEDALRAIQCVNNVVVDGRTL--KAS 89

>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 = 60.4 bits (146), Expect = 4e-12
 Identities = 17/76 (22%), Positives = 32/76 (42%), Gaps = 1/76 (1%)

Query: 494 LYIGYLPPTLDDDGLIRL-FSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
           +YI  L   +  D L +   + F        I    +   +G  FV + ++  A NA+ S
Sbjct: 6   IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 65

Query: 553 MNGYRLEGRTIAVRVA 568
           M G+    + + ++ A
Sbjct: 66  MQGFPFYDKPMRIQYA 81

>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 = 63.1 bits (152), Expect = 5e-12
 Identities = 16/82 (19%), Positives = 36/82 (43%), Gaps = 1/82 (1%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
             +++G +    ++  L   F  +G I + +++ DR +G  +G+ FV + D    +  + 
Sbjct: 98  KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 157

Query: 552 SMNGYRLEGRTIAVRVAGKPPQ 573
               + + G    VR A    +
Sbjct: 158 -QKYHTVNGHNCEVRKALSKQE 178

>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 = 56.2 bits (134), Expect = 1e-09
 Identities = 20/97 (20%), Positives = 35/97 (36%)

Query: 490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNA 549
               L+IG L     D+ L   F  +G +    V++D  T  S+G+GFV YA ++  + A
Sbjct: 5   QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 64

Query: 550 IASMNGYRLEGRTIAVRVAGKPPQPTVPPGPPTSTMP 586
           + +             R   +              + 
Sbjct: 65  MNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIF 101

>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 = 58.9 bits (142), Expect = 1e-11
 Identities = 23/76 (30%), Positives = 33/76 (43%), Gaps = 7/76 (9%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           LYIG L P +  D L +LF      +           +  GY FV Y D   A  AI ++
Sbjct: 4   LYIGNLSPAVTADDLRQLFGDRKLPL------AGQVLLKSGYAFVDYPDQNWAIRAIETL 57

Query: 554 NG-YRLEGRTIAVRVA 568
           +G   L G+ + V  +
Sbjct: 58  SGKVELHGKIMEVDYS 73

>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 = 59.0 bits (142), Expect = 2e-11
 Identities = 17/91 (18%), Positives = 33/91 (36%), Gaps = 9/91 (9%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           + + +  LP   +   +  L   +         K      +K   FV   + + A NAI 
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYDL-------KYCYVDRNKRTAFVTLLNGEQAQNAIQ 58

Query: 552 SMNGYRLEGRTIAVRVAGKPPQPTVPPGPPT 582
             + Y   G+ + V++   P    +  GP +
Sbjct: 59  MFHQYSFRGKDLIVQLQ--PTDALLCSGPSS 87

>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 = 57.8 bits (139), Expect = 6e-11
 Identities = 30/101 (29%), Positives = 52/101 (51%), Gaps = 4/101 (3%)

Query: 485 PIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQ 544
           P  +    ++++G +P    ++ L  +FS  G +V  +++ DR TG  KGYGF +Y D +
Sbjct: 2   PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61

Query: 545 MANNAIASMNGYRLEGRTIAVRVA----GKPPQPTVPPGPP 581
            A +A+ ++NG    GR + V  A     K    ++  G P
Sbjct: 62  TALSAMRNLNGREFSGRALRVDNAASEKNKEELKSLGTGAP 102

>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 = 56.5 bits (136), Expect = 8e-11
 Identities = 16/86 (18%), Positives = 32/86 (37%), Gaps = 11/86 (12%)

Query: 489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANN 548
           LDDT + +   P       ++  F+ +G+I+   +           +  ++Y     A  
Sbjct: 2   LDDTWVTVFGFPQASASY-ILLQFAQYGNILKHVMSNT------GNWMHIRYQSKLQARK 54

Query: 549 AIASMNGYRLEGRTIAVRVAGKPPQP 574
           A+ S +G       + + V  KP   
Sbjct: 55  AL-SKDGRIFGESIM-IGV--KPCID 76

>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 = 55.5 bits (133), Expect = 1e-10
 Identities = 23/70 (32%), Positives = 34/70 (48%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           LYI  L P   D  L++L   +G IV  K I D+ T   KGYGFV +     A  A+ ++
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 554 NGYRLEGRTI 563
               ++ +  
Sbjct: 61  KASGVQAQMA 70

>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 = 56.2 bits (135), Expect = 1e-10
 Identities = 17/88 (19%), Positives = 37/88 (42%), Gaps = 7/88 (7%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           + +++G     + +D L   FS +GD++   + K       + + FV +AD Q+A +   
Sbjct: 6   SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQSLC- 59

Query: 552 SMNGYRLEGRTIAVRVAGKPPQPTVPPG 579
                 ++G ++ +  A         P 
Sbjct: 60  -GEDLIIKGISVHISNAEPKHNSNSGPS 86

>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 = 55.7 bits (133), Expect = 2e-10
 Identities = 20/90 (22%), Positives = 36/90 (40%), Gaps = 2/90 (2%)

Query: 479 GSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFV 538
           GS+  +  +     NL+IG L P      L    S         V+  R TG ++ +G+V
Sbjct: 1   GSHMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYV 59

Query: 539 KYADIQMANNAIASMNGYRLEGRTIAVRVA 568
            +   +    A+  + G ++ G  I +   
Sbjct: 60  DFESAEDLEKAL-ELTGLKVFGNEIKLEKP 88

>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 = 54.7 bits (131), Expect = 6e-10
 Identities = 30/108 (27%), Positives = 42/108 (38%), Gaps = 13/108 (12%)

Query: 468 GSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDR 527
           GSSG+ G  G G       K    T L++G L P      L R F  FG I     +   
Sbjct: 1   GSSGSSGKIGYG-------KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHV--- 50

Query: 528 VTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPT 575
                  + +++Y  +  A  A A M G+ L G    +RV      P+
Sbjct: 51  ---KGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGPS 95

>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 = 54.4 bits (130), Expect = 6e-10
 Identities = 22/86 (25%), Positives = 35/86 (40%), Gaps = 3/86 (3%)

Query: 489 LDDTNLYIGYLPP-TLDDDGLIRLFSTFGDIVMAKVIKD-RVTGMSKGYGFVKYADIQMA 546
           L+   + I  L    LD++ L   F  FG I    +    +    +    F+ + +   A
Sbjct: 2   LEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSA 61

Query: 547 NNAIASMNGYRLEGRTIAVRVAGKPP 572
             A+  MN   L  R I+V +A K P
Sbjct: 62  ERALQ-MNRSLLGNREISVSLADKKP 86

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.4 bits (130), Expect = 8e-10
 Identities = 19/77 (24%), Positives = 39/77 (50%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
             LY+  L P + +  L+ LF+ F +     +    +TG  +G  F+ + + ++A  A+ 
Sbjct: 19  KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 78

Query: 552 SMNGYRLEGRTIAVRVA 568
            +NGY+L G+ + +   
Sbjct: 79  LVNGYKLYGKILVIEFG 95

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.7 bits (128), Expect = 2e-09
 Identities = 14/92 (15%), Positives = 30/92 (32%), Gaps = 1/92 (1%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
              +I  +P ++    +++          A  +     G   G   V++ +   A  +  
Sbjct: 9   VCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER 68

Query: 552 SMNGYRLEGRTIAVRVAGKPPQPTVPPGPPTS 583
            ++  +L GR   V V        +   PP  
Sbjct: 69  -LHRKKLNGREAFVHVVTLEDMREIEKNPPAQ 99

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.6 bits (126), Expect = 3e-09
 Identities = 17/82 (20%), Positives = 30/82 (36%), Gaps = 9/82 (10%)

Query: 487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMA 546
            + +D  L +      + +D L    S FG I    +          G   V + D + A
Sbjct: 20  MDFEDDPLVLN----EIRED-LRVECSKFGQIRKLLLFDRHP----DGVASVSFRDPEEA 70

Query: 547 NNAIASMNGYRLEGRTIAVRVA 568
           +  I +++G    GR I  +  
Sbjct: 71  DYCIQTLDGRWFGGRQITAQAW 92

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.9 bits (126), Expect = 3e-09
 Identities = 21/90 (23%), Positives = 41/90 (45%), Gaps = 6/90 (6%)

Query: 485 PIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQ 544
           P    +   ++I  L    +++ L  +   FGD+   +V+    T  SKG  F ++   +
Sbjct: 2   PSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQE 61

Query: 545 MANNAIASMN------GYRLEGRTIAVRVA 568
            A   +A+ +      G +L+GR + V +A
Sbjct: 62  AAQKCLAAASLEAEGGGLKLDGRQLKVDLA 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 = 52.8 bits (126), Expect = 3e-09
 Identities = 20/104 (19%), Positives = 42/104 (40%), Gaps = 5/104 (4%)

Query: 479 GSNGA--KPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYG 536
           GS+G+    + +      ++G LP  + ++ +   F       +    +       KG+G
Sbjct: 1   GSSGSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFG 60

Query: 537 FVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPGP 580
           + ++ D+    +A++ +N   L  + I V VA          GP
Sbjct: 61  YAEFEDLDSLLSALS-LNEESLGNKRIRVDVA--DQAQDKDSGP 101

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.7 bits (123), Expect = 6e-09
 Identities = 12/82 (14%), Positives = 29/82 (35%), Gaps = 2/82 (2%)

Query: 487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMA 546
            ++ + ++YI   P     D +          V+   ++  +    KG  FV +  I+ A
Sbjct: 2   NDVKNRSVYIKGFPTDATLDDIKEWLEDK-GQVLNIQMRRTLHKAFKGSIFVVFDSIESA 60

Query: 547 NNAIASMNGYRLEGRTIAVRVA 568
              +    G + +   + +   
Sbjct: 61  KKFVE-TPGQKYKETDLLILFK 81

>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 = 51.7 bits (123), Expect = 7e-09
 Identities = 25/92 (27%), Positives = 40/92 (43%), Gaps = 2/92 (2%)

Query: 477 GLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYG 536
           G+ +  AK  +E D TNLYI  LP ++D+  L  +   FG ++    I    +G S+G G
Sbjct: 5   GVQAQMAKQ-QEQDPTNLYISNLPLSMDEQELENMLKPFGQVIS-TRILRDSSGTSRGVG 62

Query: 537 FVKYADIQMANNAIASMNGYRLEGRTIAVRVA 568
           F +    +     I   NG  ++         
Sbjct: 63  FARMESTEKCEAVIGHFNGKFIKTPPGVSAPT 94

>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 = 50.8 bits (121), Expect = 9e-09
 Identities = 23/81 (28%), Positives = 35/81 (43%), Gaps = 8/81 (9%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
             LY+     T     L   FS FG+I       D      +   FV Y  ++ A+ A+A
Sbjct: 6   NTLYVYGEDMT--PTLLRGAFSPFGNI------IDLSMDPPRNCAFVTYEKMESADQAVA 57

Query: 552 SMNGYRLEGRTIAVRVAGKPP 572
            +NG ++E   + V +A K P
Sbjct: 58  ELNGTQVESVQLKVNIARKQP 78

>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 = 51.7 bits (123), Expect = 9e-09
 Identities = 14/112 (12%), Positives = 30/112 (26%), Gaps = 17/112 (15%)

Query: 491 DTNLYIGYLPP-----TLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQM 545
            + L            +        LF T+      +         S     + +++   
Sbjct: 5   SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYF------KSFKRVRINFSNPLS 58

Query: 546 ANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPGPPTSTMPTYPVSAPPVGG 597
           A +A   ++     G+ + +  A      +    PP       P  + P  G
Sbjct: 59  AADARLRLHKTEFLGKEMKLYFAQTLHIGSSHLAPPN------PDKSGPSSG 104

>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 = 51.6 bits (123), Expect = 1e-08
 Identities = 17/87 (19%), Positives = 34/87 (39%), Gaps = 5/87 (5%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
             + +  L   +  D L ++FS FG ++            ++    ++YAD   A +A  
Sbjct: 8   LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKL 63

Query: 552 SMNGYRLEGRTIAVRVA-GKPPQPTVP 577
           S++G  +      +R+   K     V 
Sbjct: 64  SLDGQNIYNACCTLRIDFSKLTSLNVK 90

>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 = 50.5 bits (120), Expect = 2e-08
 Identities = 11/75 (14%), Positives = 28/75 (37%), Gaps = 7/75 (9%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           +  G L   +  + L+ +    G +    +        +K Y F +Y   + +  A  ++
Sbjct: 23  VANGGLGNGVSRNQLLPVLEKCGLVDALLMP------PNKPYSFARYRTTEESKRAYVTL 76

Query: 554 NGYRL-EGRTIAVRV 567
           NG  + +     + +
Sbjct: 77  NGKEVVDDLGQKITL 91

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 51.1 bits (121), Expect = 3e-08
 Identities = 32/88 (36%), Positives = 48/88 (54%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
            NL + Y+P T+D+  L +LF  +G I   K++ DR T  S+GYGFVK+     A  AIA
Sbjct: 43  RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIA 102

Query: 552 SMNGYRLEGRTIAVRVAGKPPQPTVPPG 579
            +NG+ +  + + V +A    Q     G
Sbjct: 103 GLNGFNILNKRLKVALAASGHQRPGIAG 130

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.8 bits (118), Expect = 5e-08
 Identities = 24/104 (23%), Positives = 42/104 (40%), Gaps = 7/104 (6%)

Query: 492 TNLYIGYLPP-TLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAI 550
           + L +  L P  +    L  LF  +GD+   K++        K    V+ AD   A  A+
Sbjct: 3   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILF-----NKKENALVQMADGNQAQLAM 57

Query: 551 ASMNGYRLEGRTIAVRVAGKPPQPTVPPGPPTSTMPTYPVSAPP 594
           + +NG++L G+ I + ++ K     +P         T      P
Sbjct: 58  SHLNGHKLHGKPIRITLS-KHQNVQLPREGQEDQGLTKDYGNSP 100

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.7 bits (116), Expect = 6e-08
 Identities = 15/93 (16%), Positives = 32/93 (34%), Gaps = 23/93 (24%)

Query: 266 NFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEA 325
           +    +IG +G+  ++M  E    I +                    P+      ++   
Sbjct: 19  DLHRYVIGQKGSGIRKMMDEFEVNIHV--------------------PAPELQSDIIAIT 58

Query: 326 ETQESLEGAAAMVEKLLQPVDEVLNEHKRQQLR 358
               +L+ A A + +    V E+  E + + LR
Sbjct: 59  GLAANLDRAKAGLLER---VKELQAEQEDRALR 88

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 48.3 bits (114), Expect = 7e-08
 Identities = 11/75 (14%), Positives = 26/75 (34%), Gaps = 3/75 (4%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           T + +  LP + + + + + F   G I+   V        +  +  +++A       A  
Sbjct: 1   TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK--KNFRFARIEFAR-YDGALAAI 57

Query: 552 SMNGYRLEGRTIAVR 566
           +     +    I V 
Sbjct: 58  TKTHKVVGQNEIIVS 72

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.3 bits (114), Expect = 1e-07
 Identities = 22/100 (22%), Positives = 42/100 (42%), Gaps = 2/100 (2%)

Query: 479 GSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFV 538
           GS+G  P    +D  + +  LP     + +++ FS    +     +     G S G  FV
Sbjct: 4   GSSGNSPDTA-NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFV 62

Query: 539 KYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPP 578
           ++A  ++A  A+   +  R+  R I +  + +    T  P
Sbjct: 63  QFASQEIAEKAL-KKHKERIGHRYIEIFKSSRAEVRTSGP 101

>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 = 47.7 bits (113), Expect = 2e-07
 Identities = 14/81 (17%), Positives = 30/81 (37%), Gaps = 8/81 (9%)

Query: 487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDR--VTGMSKGYGFVKYADIQ 544
           +EL D   Y       + +D +    S +G +   ++ +    V     G  FV++  + 
Sbjct: 16  EELLDDEEYE-----EIVED-VRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVF 69

Query: 545 MANNAIASMNGYRLEGRTIAV 565
               A+  + G +   R +  
Sbjct: 70  DCQKAMQGLTGRKFANRVVVT 90

>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 = 47.5 bits (112), Expect = 2e-07
 Identities = 21/105 (20%), Positives = 34/105 (32%), Gaps = 11/105 (10%)

Query: 479 GSNGAK--PIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYG 536
           GS+G+   P     D  + +  LPP+     L       GD+  A V          G G
Sbjct: 1   GSSGSSGGPPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADV-------QKDGMG 53

Query: 537 FVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPGPP 581
            V+Y   +    A+  ++  +              P+     GP 
Sbjct: 54  MVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYPER--SSGPS 96

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.4 bits (112), Expect = 3e-07
 Identities = 17/111 (15%), Positives = 37/111 (33%), Gaps = 12/111 (10%)

Query: 468 GSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDR 527
           GSSG         +     +      +++  LP    ++ +   FS    + +       
Sbjct: 1   GSSG---------SSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIE--IG 49

Query: 528 VTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPP 578
             G   G   V++A  + A  A+A  +   ++ R + + +          P
Sbjct: 50  PDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNSTAGTSGSGP 99

>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 = 44.9 bits (105), Expect = 8e-07
 Identities = 17/75 (22%), Positives = 31/75 (41%), Gaps = 7/75 (9%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           + I  LP  + +  +  L S +        +K       KG  FV   + + A  AI + 
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDY-------ELKYCFVDKYKGTAFVTLLNGEQAEAAINTF 53

Query: 554 NGYRLEGRTIAVRVA 568
           +  RL  R ++V++ 
Sbjct: 54  HQSRLRERELSVQLQ 68

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.1 bits (106), Expect = 1e-06
 Identities = 14/78 (17%), Positives = 34/78 (43%), Gaps = 5/78 (6%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
             L++  +PP++ ++ L  LFS+ G +V             +    ++   ++ A  A+ 
Sbjct: 11  ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALI 66

Query: 552 SMNGYRL-EGRTIAVRVA 568
            ++ + L E   + V  +
Sbjct: 67  DLHNHDLGENHHLRVSFS 84

>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.5 bits (103), Expect = 3e-06
 Identities = 15/78 (19%), Positives = 26/78 (33%), Gaps = 20/78 (25%)

Query: 266 NFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEA 325
                +IG  G   + +E +T  KI I                  P P +  +  + +  
Sbjct: 19  EHHRFVIGKNGEKLQDLELKTATKIQI------------------PRPDDPSNQ-IKITG 59

Query: 326 ETQESLEGAAAMVEKLLQ 343
            T+E +E A   V  +  
Sbjct: 60  -TKEGIEKARHEVLLISA 76

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.5 bits (102), Expect = 4e-06
 Identities = 14/84 (16%), Positives = 31/84 (36%), Gaps = 11/84 (13%)

Query: 494 LYIGYLPP--TLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
           ++I        L    L++L   FG I    ++            F++ A  + A  A+ 
Sbjct: 11  VHIMDFQRGKNLRYQ-LLQLVEPFGVISNHLIL------NKINEAFIEMATTEDAQAAVD 63

Query: 552 --SMNGYRLEGRTIAVRVAGKPPQ 573
             +     + G+ + V ++ K  +
Sbjct: 64  YYTTTPALVFGKPVRVHLSQKYKR 87

>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]} Length = 69

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 42.8 bits (101), Expect = 4e-06
 Identities = 8/76 (10%), Positives = 21/76 (27%), Gaps = 23/76 (30%)

Query: 266 NFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEA 325
             +  +IG   +  + +  ++G  I +   G +                           
Sbjct: 10  VKVPRVIGKNKSMYETLTSKSGCSIFVANNGRIW-----------------------ATC 46

Query: 326 ETQESLEGAAAMVEKL 341
            ++ S E     + K+
Sbjct: 47  PSRFSEEILIEAIRKI 62

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.3 bits (102), Expect = 4e-06
 Identities = 16/78 (20%), Positives = 31/78 (39%), Gaps = 18/78 (23%)

Query: 266 NFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEA 325
             +G IIG  G    R+++E+G KI I                     S        +  
Sbjct: 17  GMVGFIIGRGGEQISRIQQESGCKIQI------------------APDSGGLPERSCMLT 58

Query: 326 ETQESLEGAAAMVEKLLQ 343
            T ES++ A  +++++++
Sbjct: 59  GTPESVQSAKRLLDQIVE 76

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.6 bits (102), Expect = 6e-06
 Identities = 14/83 (16%), Positives = 24/83 (28%), Gaps = 7/83 (8%)

Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYAD-IQMANNAI 550
              + G L      + L  LFS  G+I     +           G + + +  + A    
Sbjct: 12  LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFV------RGAKEGIILFKEKAKEALGKA 65

Query: 551 ASMNGYRLEGRTIAVRVAGKPPQ 573
              N   L+ R   V       +
Sbjct: 66  KDANNGNLQLRNKEVTWEVLEGE 88

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.5 bits (100), Expect = 7e-06
 Identities = 11/83 (13%), Positives = 31/83 (37%), Gaps = 17/83 (20%)

Query: 266 NFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEA 325
            +   IIG +G    ++  E    I                   K D ++ +D  + +  
Sbjct: 19  KYHPKIIGRKGAVITQIRLEHDVNIQF---------------PDKDDGNQPQD-QITITG 62

Query: 326 ETQESLEGAAAMVEKLLQPVDEV 348
             +++ E A   + +++  ++++
Sbjct: 63  -YEKNTEAARDAILRIVGELEQM 84

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Fragile X mental retardation syndrome related protein 1, FXR1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.2 bits (99), Expect = 8e-06
 Identities = 9/93 (9%), Positives = 29/93 (31%), Gaps = 27/93 (29%)

Query: 249 PKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRD 308
               ++  +        + +GL IG  G+  ++  +  G   +                 
Sbjct: 6   AAFHEEFVVR------EDLMGLAIGTHGSNIQQARKVPGVTAIE---------------- 43

Query: 309 LKPDPSENEDLHVLVEAETQESLEGAAAMVEKL 341
                 + +     +  E+ ++++ A   +E +
Sbjct: 44  -----LDEDTGTFRIYGESADAVKKARGFLEFV 71

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.6 bits (99), Expect = 1e-05
 Identities = 10/86 (11%), Positives = 21/86 (24%), Gaps = 7/86 (8%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           + +  LPP+     L        D +              G G V++   +    A+  +
Sbjct: 3   VVVSGLPPSGSWQDLK-------DHMREAGDVCYADVYRDGTGVVEFVRKEDMTYAVRKL 55

Query: 554 NGYRLEGRTIAVRVAGKPPQPTVPPG 579
           +  +                    P 
Sbjct: 56  DNTKFRSHEGETAYIRVKVDGPRSPS 81

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.7 bits (98), Expect = 1e-05
 Identities = 10/76 (13%), Positives = 25/76 (32%), Gaps = 20/76 (26%)

Query: 266 NFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEA 325
            F   +IG  G    R++ +    + I                    P ++E  +++   
Sbjct: 14  KFHRHLIGKSGANINRIKDQYKVSVRI--------------------PPDSEKSNLIRIE 53

Query: 326 ETQESLEGAAAMVEKL 341
              + ++ A   + +L
Sbjct: 54  GDPQGVQQAKRELLEL 69

>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]} Length = 42

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 1, different isolates [TaxId: 11676]

 Score = 40.6 bits (95), Expect = 2e-05
 Identities = 13/40 (32%), Positives = 15/40 (37%), Gaps = 5/40 (12%)

Query: 373 CRLCGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTIDC 412
           C  CG+ GH    C +          C  CG  GH   DC
Sbjct: 4   CFNCGKEGHTARNCRA-----PRKKGCWKCGKEGHQMKDC 38

>d1tuaa2 d.51.1.1 (A:85-188) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

 Score = 42.0 bits (99), Expect = 2e-05
 Identities = 10/43 (23%), Positives = 16/43 (37%)

Query: 268 IGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLK 310
            G IIG  G  ++ +E  T   I +        G  ++    K
Sbjct: 24  KGRIIGEGGRARRTIEEMTDTYINVGEYEVAIIGDYERAMAAK 66

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Neuro-oncological ventral antigen 2, nova-2, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.6 bits (95), Expect = 3e-05
 Identities = 14/77 (18%), Positives = 28/77 (36%), Gaps = 15/77 (19%)

Query: 266 NFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEA 325
           N +G I+G  G T    +  TGA+I I              +  +  P       V +  
Sbjct: 12  NLVGAILGKGGKTLVEYQELTGARIQI-------------SKKGEFLPGTRNRR-VTITG 57

Query: 326 ETQESLEGAAAMVEKLL 342
            +  + + A  ++ + +
Sbjct: 58  -SPAATQAAQYLISQRV 73

>d2z0sa2 d.51.1.1 (A:148-234) Exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

 Score = 40.9 bits (96), Expect = 3e-05
 Identities = 9/76 (11%), Positives = 24/76 (31%), Gaps = 23/76 (30%)

Query: 266 NFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEA 325
             +  +IG + +  K +E +T  KI +                         +  + +E 
Sbjct: 10  AKVPRVIGRKMSMLKTLEEKTECKIFV-----------------------ARNGRIHLEC 46

Query: 326 ETQESLEGAAAMVEKL 341
             ++    A   ++ +
Sbjct: 47  PNEDLEAIAVMAIKII 62

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: HnRNP K, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.2 bits (94), Expect = 4e-05
 Identities = 19/95 (20%), Positives = 37/95 (38%), Gaps = 24/95 (25%)

Query: 249 PKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRD 308
           P +  ++ IP       +  G IIG  G   K++  E+GA I I                
Sbjct: 2   PIITTQVTIP------KDLAGSIIGKGGQRIKQIRHESGASIKI---------------- 39

Query: 309 LKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQ 343
                  +ED  + +   TQ+ ++ A  +++  ++
Sbjct: 40  -DEPLEGSEDRIITITG-TQDQIQNAQYLLQNSVK 72

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.5 bits (96), Expect = 4e-05
 Identities = 18/120 (15%), Positives = 33/120 (27%), Gaps = 10/120 (8%)

Query: 479 GSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFV 538
           GS+G+        T +    LP       +   FS FG +         +         V
Sbjct: 1   GSSGSS---GRSKTVILAKNLPAGTLAAEIQETFSRFGSLG------RVLLPEGGITAIV 51

Query: 539 KYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPGPPTST-MPTYPVSAPPVGG 597
           ++ +   A  A   +   +     + +  A        P    +    P     + P  G
Sbjct: 52  EFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAEKAESGPSSG 111

>d1j4wa2 d.51.1.1 (A:104-174) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.9 bits (93), Expect = 5e-05
 Identities = 16/77 (20%), Positives = 34/77 (44%), Gaps = 15/77 (19%)

Query: 266 NFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEA 325
              GLIIG  G T K + +++GA+I +                  P P+ + ++ +    
Sbjct: 10  GKTGLIIGKGGETIKSISQQSGARIEL---------------QRNPPPNADPNMKLFTIR 54

Query: 326 ETQESLEGAAAMVEKLL 342
            T + ++ A  ++E+ +
Sbjct: 55  GTPQQIDYARQLIEEKI 71

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.6 bits (94), Expect = 6e-05
 Identities = 17/112 (15%), Positives = 33/112 (29%), Gaps = 15/112 (13%)

Query: 468 GSSGTPGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDR 527
           GSSG+ G            K      +++  L  ++ +  L+     FG I    ++   
Sbjct: 1   GSSGSSG---------SHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMM--- 48

Query: 528 VTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPPQPTVPPG 579
                K    V++ +I  A   +       +              +    PG
Sbjct: 49  ---PFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRITRPG 97

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.9 bits (93), Expect = 6e-05
 Identities = 18/96 (18%), Positives = 36/96 (37%), Gaps = 22/96 (22%)

Query: 248 PPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKR 307
           P    +++ IP       +  GL+IG  G T K+++   G K+V+               
Sbjct: 5   PGNAVQEIMIP------ASKAGLVIGKGGETIKQLQERAGVKMVM--------------- 43

Query: 308 DLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQ 343
                 +   D  + +       ++ A  MV +L++
Sbjct: 44  IQDGPQNTGADKPLRITG-DPYKVQQAKEMVLELIR 78

>d2ba0a3 d.51.1.1 (A:136-219) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 39.7 bits (93), Expect = 7e-05
 Identities = 14/79 (17%), Positives = 30/79 (37%), Gaps = 10/79 (12%)

Query: 266 NFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEA 325
             +  +IG +G+  K ++ E   +IV+   G +          +  D  +       +  
Sbjct: 10  ARVPRVIGKKGSMIKLLKSELDVQIVVGQNGLIW---------VNGDRRKVSIAEEAIYL 60

Query: 326 ETQES-LEGAAAMVEKLLQ 343
             QE+  EG    V + ++
Sbjct: 61  IEQEAHTEGLTDRVAEFIK 79

>d1we8a_ d.51.1.1 (A:) Tudor and KH domain containing protein, Tdrkh {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Tudor and KH domain containing protein, Tdrkh
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.3 bits (94), Expect = 7e-05
 Identities = 15/90 (16%), Positives = 33/90 (36%), Gaps = 16/90 (17%)

Query: 266 NFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEA 325
             +G IIG  G T + + + +GAKI                 D + + +      + +  
Sbjct: 24  RSVGRIIGRGGETIRSICKASGAKITC---------------DKESEGTLLLSRLIKISG 68

Query: 326 ETQESLEGAAAMVEKLLQPVDEVLNEHKRQ 355
            TQ+ +  A  ++ + +   +E+       
Sbjct: 69  -TQKEVAAAKHLILEKVSEDEELRKRIAHS 97

>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.4 bits (92), Expect = 8e-05
 Identities = 14/79 (17%), Positives = 23/79 (29%), Gaps = 19/79 (24%)

Query: 265 YNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVE 324
           +     IIG RG   +++  E    I                    P     +   V V 
Sbjct: 18  HRVHARIIGARGKAIRKIMDEFKVDIRF------------------PQSGAPDPNCVTVT 59

Query: 325 AETQESLEGAAAMVEKLLQ 343
               E++E A   +  L +
Sbjct: 60  G-LPENVEEAIDHILNLEE 77

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.1 bits (91), Expect = 9e-05
 Identities = 14/78 (17%), Positives = 29/78 (37%), Gaps = 18/78 (23%)

Query: 266 NFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEA 325
             +G++IG  G   K+++ + G +I                   KPD     +    +  
Sbjct: 12  FAVGIVIGRNGEMIKKIQNDAGVRI-----------------QFKPDDGTTPERIAQITG 54

Query: 326 ETQESLEGAAAMVEKLLQ 343
              +  + AA ++  LL+
Sbjct: 55  -PPDRAQHAAEIITDLLR 71

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

 Score = 39.0 bits (91), Expect = 1e-04
 Identities = 15/78 (19%), Positives = 28/78 (35%), Gaps = 22/78 (28%)

Query: 266 NFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEA 325
             +G +IGPRG  +  + R TG  I +                      + E+  V+VE 
Sbjct: 12  ERLGAVIGPRGEVKAEIMRRTGTVITV----------------------DTENSMVIVEP 49

Query: 326 ETQESLEGAAAMVEKLLQ 343
           E +           ++++
Sbjct: 50  EAEGIPPVNLMKAAEVVK 67

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 70

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.3 bits (89), Expect = 2e-04
 Identities = 16/77 (20%), Positives = 27/77 (35%), Gaps = 18/77 (23%)

Query: 266 NFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEA 325
           N IG IIG +G     + + +GA+I I                   +P E      +   
Sbjct: 11  NLIGCIIGRQGANINEIRQMSGAQIKI------------------ANPVEGSSGRQVTIT 52

Query: 326 ETQESLEGAAAMVEKLL 342
            +  S+  A  ++   L
Sbjct: 53  GSAASISLAQYLINARL 69

>d1e3ha4 d.52.3.1 (A:579-632) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6 {Streptomyces antibioticus [TaxId: 1890]} Length = 54

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6
species: Streptomyces antibioticus [TaxId: 1890]

 Score = 37.3 bits (87), Expect = 2e-04
 Identities = 11/32 (34%), Positives = 20/32 (62%)

Query: 268 IGLIIGPRGNTQKRMERETGAKIVIRGKGSVK 299
           IG +IGP+     +++ +TGA+I I   G++ 
Sbjct: 14  IGEVIGPKRQMINQIQEDTGAEITIEDDGTIY 45

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.1 bits (86), Expect = 6e-04
 Identities = 17/78 (21%), Positives = 32/78 (41%), Gaps = 20/78 (25%)

Query: 266 NFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEA 325
             +G IIG +G + K+M  E+GA+I I                   + +  E + + +  
Sbjct: 13  KEVGSIIGKKGESVKKMREESGARINI------------------SEGNCPERI-ITLAG 53

Query: 326 ETQESLEGAAAMVEKLLQ 343
               ++  A AM+   L+
Sbjct: 54  -PTNAIFKAFAMIIDKLE 70

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 36.8 bits (84), Expect = 0.001
 Identities = 15/78 (19%), Positives = 31/78 (39%), Gaps = 6/78 (7%)

Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
           L++  LP   ++  L  LF+ F           R+        FV++     +N A  ++
Sbjct: 11  LFLTNLPEETNEMMLSMLFNQFPGFKE-----VRLVPNRHDIAFVEFTTELQSNAAKEAL 65

Query: 554 NGYRL-EGRTIAVRVAGK 570
            G+++     + +  A K
Sbjct: 66  QGFKITPTHAMKITFAKK 83

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.2 bits (80), Expect = 0.004
 Identities = 14/78 (17%), Positives = 28/78 (35%), Gaps = 8/78 (10%)

Query: 493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
            L+I  LP  + +  +I L   FG +         +    K   F++ A  + A   +  
Sbjct: 10  VLHIRKLPGEVTETEVIALGLPFGKVTN------ILMLKGKNQAFLELATEEAAITMVNY 63

Query: 553 M--NGYRLEGRTIAVRVA 568
                  L  + I ++ +
Sbjct: 64  YSAVTPHLRNQPIYIQYS 81

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	797
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	100.0
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	100.0
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.78
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.78
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.77
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.77
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.77
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.77
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.77
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.76
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.76
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.76
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.76
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.76
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.75
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.75
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.75
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.74
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.73
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.73
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.73
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.73
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.73
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.73
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.73
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.73
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.72
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.72
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.72
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.72
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.71
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.71
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.71
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.7
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.7
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.7
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.7
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.7
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.7
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.68
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.68
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.68
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.67
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.67
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.66
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.65
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.65
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.64
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.63
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.63
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.63
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.63
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.63
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.62
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.62
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.62
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.61
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.61
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.61
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.61
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.6
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.6
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.6
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.59
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.58
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.58
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.57
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.57
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.57
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.57
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.56
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.56
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.53
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.53
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.52
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.5
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.5
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.49
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.47
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.46
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.45
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.44
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	99.38
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.26
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.22
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.21
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.16
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.11
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.98
d2cpqa1	78	Fragile X mental retardation syndrome related prot	98.97
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	98.94
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	98.9
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	98.89
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	98.88
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	98.87
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.83
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	98.83
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	98.79
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	98.76
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.76
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	98.73
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.71
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	98.61
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	98.57
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.57
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	98.56
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.55
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	98.49
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	98.42
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	98.38
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	98.21
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	98.19
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	98.03
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	96.32
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	96.25
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	95.82
d1nc8a_	29	HIV nucleocapsid {Human immunodeficiency virus typ	94.14
d1dsqa_	26	Nucleic acid binding protein p14 {Mouse mammary tu	93.83
d1a6bb_	40	Zinc finger protein ncp10 {Moloney murine leukemia	92.41
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	90.96
d2ja9a2	85	Ribosomal RNA-processing protein 40, RRP40 {Saccha	90.74
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	87.99
d3etja1	79	N5-carboxyaminoimidazole ribonucleotide synthetase	85.55
d1cl4a_	32	Nucleocapsid protein from mason-pfizer monkey viru	82.53
d1dsva_	31	Nucleic acid binding protein p14 {Mouse mammary tu	80.34

>d2bl5a1 d.51.1.1 (A:1-134) Quaking protein A (Xqua) {African clawed frog (Xenopus laevis) [TaxId: 8355]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Quaking protein A (Xqua)
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

Probab=100.00  E-value=2.3e-40  Score=311.32  Aligned_cols=122  Identities=49%  Similarity=0.788  Sum_probs=111.2

Q ss_pred             ceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCC-CCCCCCCceEEEEecCH
Q 040243          250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKP-DPSENEDLHVLVEAETQ  328 (797)
Q Consensus       250 ~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~-~~~~~e~LHv~I~a~~~  328 (797)
                      |+++|||||+++||+|||||+||||||+|+|+||+||||||.||||||+|+++.+....... ..+++|+|||+|+|++.
T Consensus         1 kl~eKv~IP~~~~P~~NfvG~IiGPrG~t~K~le~eTg~kI~IrGrGS~k~~~~~~~~~~~~~~~~~~epLHv~I~a~~~   80 (134)
T d2bl5a1           1 QLQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDA   80 (134)
T ss_dssp             CEEEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSC
T ss_pred             CcceEEeCCCCCCCCCCeeEEEECCCCchHHHHHHHHCCEEEEEecCCCcCccccccccCCCCCcCCCCCCEEEEEecCc
Confidence            58999999999999999999999999999999999999999999999999988765432222 24789999999999985


Q ss_pred             H-----HHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHhhcCCcCccc
Q 040243          329 E-----SLEGAAAMVEKLLQPVDEVLNEHKRQQLRELAALNGTIRDEE  371 (797)
Q Consensus       329 e-----~v~~A~~~I~~ll~~~~e~~n~~k~~Ql~ela~lnGt~r~~~  371 (797)
                      +     +|++|+++|++||.++.+++|++||+||+|||.||||||+++
T Consensus        81 ~~~a~~kl~~A~~~I~~lL~p~~e~~de~k~~QL~eLa~lNGt~r~~~  128 (134)
T d2bl5a1          81 QNRAELKLKRAVEEVKKLLVPAAEGEDSLKKMKLMELAILNGTYRDAN  128 (134)
T ss_dssp             CHHHHHHHHHHHHHHHHHSSCCSSSSSHHHHHHHTGGGSSSTTTSGGG
T ss_pred             HHHHHHHHHHHHHHHHHHcCCCccchHHHHHHHHHHHHHhcCcccccc
Confidence            4     699999999999999999999999999999999999999986

>d1k1ga_ d.51.1.1 (A:) RNA splicing factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: RNA splicing factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=6.6e-39  Score=298.33  Aligned_cols=119  Identities=50%  Similarity=0.801  Sum_probs=109.6

Q ss_pred             CceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCH
Q 040243          249 PKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQ  328 (797)
Q Consensus       249 ~~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~  328 (797)
                      .|+++|||||+++||+|||||+||||||+|+|+||+||||||+||||||+|+++.+. .+.....+++|+|||+|+|+++
T Consensus         1 ~k~~~Ki~iP~~~~P~fNfvG~IlGPrG~t~K~Le~eTgckI~IrGrGS~kd~~~~~-~~~~~~~~~~epLHv~I~a~~~   79 (122)
T d1k1ga_           1 TRVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGR-KDGQMLPGEDEPLHALVTANTM   79 (122)
T ss_dssp             CCEEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSS-CCCCCSCCSSCCEEEEEEESSH
T ss_pred             CceeEEEecCCccCCCCCeeeeEeCCCCchHHHHHHHHCCEEEEEecCCcccccccc-cCCCCCCCCCCCceEEEecCCh
Confidence            378999999999999999999999999999999999999999999999999988654 3555566899999999999999


Q ss_pred             HHHHHHHHHHHHhcC---CChHHHHHHHHHHHHHHHhhcCCcC
Q 040243          329 ESLEGAAAMVEKLLQ---PVDEVLNEHKRQQLRELAALNGTIR  368 (797)
Q Consensus       329 e~v~~A~~~I~~ll~---~~~e~~n~~k~~Ql~ela~lnGt~r  368 (797)
                      ++|++|+++|++||.   .+.+++|++||+||+|||.||||||
T Consensus        80 ~~~~~A~~~i~~ll~~~~~~~e~~d~~k~~Ql~eLa~lnGt~r  122 (122)
T d1k1ga_          80 ENVKKAVEQIRNILKQGIETPEDQNDLRKMQLRELARLNGTLR  122 (122)
T ss_dssp             HHHHHHHHHHHHHHTTTTSCCTTSSGGGGGGGHHHHHHHTCCC
T ss_pred             hhHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHhcCcCC
Confidence            999999999999996   4567889999999999999999997

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.78  E-value=1.9e-19  Score=157.21  Aligned_cols=85  Identities=27%  Similarity=0.421  Sum_probs=80.2

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      +..++++|||+||+.++++++|+++|++||.|.+|+|++|+.||++||||||+|.+.++|++|++.|||..|+|+.|+|+
T Consensus         3 ~s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~   82 (88)
T d1rk8a_           3 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD   82 (88)
T ss_dssp             CCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            45678899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCC
Q 040243          567 VAGKP  571 (797)
Q Consensus       567 ~A~~~  571 (797)
                      ||..+
T Consensus        83 ~a~~k   87 (88)
T d1rk8a_          83 WCFVK   87 (88)
T ss_dssp             ESEEC
T ss_pred             EecCC
Confidence            99754

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.78  E-value=2.1e-19  Score=154.34  Aligned_cols=80  Identities=33%  Similarity=0.583  Sum_probs=77.6

Q ss_pred             CcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecCC
Q 040243          491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGK  570 (797)
Q Consensus       491 ~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~~  570 (797)
                      +++|||+||+.++++++|+++|++||.|.+|+|++|+.+|++||||||+|.+.++|++||+.|||..|+|+.|+|+||++
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            56899999999999999999999999999999999999999999999999999999999999999999999999999964

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=4.6e-19  Score=155.24  Aligned_cols=85  Identities=27%  Similarity=0.453  Sum_probs=80.7

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      +..+.++|||+||+.++++++|+++|++||.|.+|+|++|+.||++||||||+|.+.++|++||+.|+|..|+|+.|+|+
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             ecCCC
Q 040243          567 VAGKP  571 (797)
Q Consensus       567 ~A~~~  571 (797)
                      ||+++
T Consensus        84 ~akp~   88 (90)
T d2cq0a1          84 WAKPS   88 (90)
T ss_dssp             ESSCC
T ss_pred             eeeCC
Confidence            99754

>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=99.77  E-value=5.2e-19  Score=156.02  Aligned_cols=84  Identities=35%  Similarity=0.512  Sum_probs=80.2

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ...++|||+||+.++++++|+++|++||.|.+|+|++|+.||++||||||+|.+.++|++||+.|||+.|+|+.|+|+||
T Consensus         7 ~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A   86 (93)
T d1x5ua1           7 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKA   86 (93)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEET
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            44679999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCC
Q 040243          569 GKPP  572 (797)
Q Consensus       569 ~~~~  572 (797)
                      ..+.
T Consensus        87 ~~~~   90 (93)
T d1x5ua1          87 SAHN   90 (93)
T ss_dssp             TTTS
T ss_pred             CCCC
Confidence            8654

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=3.2e-19  Score=154.80  Aligned_cols=82  Identities=38%  Similarity=0.698  Sum_probs=78.5

Q ss_pred             cEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecCCC
Q 040243          492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKP  571 (797)
Q Consensus       492 ~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~~~  571 (797)
                      ++|||+||++++++++|+++|++||.|.+|+|++|+.||++||||||+|.+.++|++|++.|||+.|+|+.|+|+||...
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            57999999999999999999999999999999999999999999999999999999999999999999999999999865


Q ss_pred             CC
Q 040243          572 PQ  573 (797)
Q Consensus       572 ~~  573 (797)
                      ..
T Consensus        82 ~~   83 (85)
T d2u2fa_          82 AK   83 (85)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.77  E-value=6e-19  Score=151.20  Aligned_cols=78  Identities=28%  Similarity=0.481  Sum_probs=76.2

Q ss_pred             EEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecCC
Q 040243          493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGK  570 (797)
Q Consensus       493 tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~~  570 (797)
                      +|||+||+.++++++|+++|++||.|.+|+|++|+.||+++|||||+|.+.++|++||+.|+|..|+|+.|+|.||+.
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~~   79 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQR   79 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECCC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            699999999999999999999999999999999999999999999999999999999999999999999999999964

>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=99.77  E-value=7e-19  Score=150.87  Aligned_cols=80  Identities=41%  Similarity=0.741  Sum_probs=77.3

Q ss_pred             CcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecCC
Q 040243          491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGK  570 (797)
Q Consensus       491 ~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~~  570 (797)
                      .++|||+||+.++++++|+++|++||.|.+|+|++|..+|+++|||||+|.+.++|++|++.|||..|+|+.|+|+||++
T Consensus         2 ~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           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999863

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.76  E-value=1.2e-18  Score=155.03  Aligned_cols=84  Identities=25%  Similarity=0.382  Sum_probs=80.2

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      ..++|||+||++++++++|+++|++||.|.+|+|++|+.|+++||||||+|.+.++|++||+.||++.|+|+.|+|++|.
T Consensus         7 ~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a~   86 (99)
T d1whwa_           7 GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPST   86 (99)
T ss_dssp             SCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECC
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            46689999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 040243          570 KPPQ  573 (797)
Q Consensus       570 ~~~~  573 (797)
                      .+..
T Consensus        87 ~~~~   90 (99)
T d1whwa_          87 IKKE   90 (99)
T ss_dssp             CCST
T ss_pred             CCCc
Confidence            7654

>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=99.76  E-value=1.2e-18  Score=153.62  Aligned_cols=83  Identities=29%  Similarity=0.393  Sum_probs=79.2

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ..++||||+||++++++++|+++|++||.|.+|.|++++.++++||||||+|.+.++|++||+.|||..|+|+.|+|+||
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            35679999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCC
Q 040243          569 GKP  571 (797)
Q Consensus       569 ~~~  571 (797)
                      ...
T Consensus        85 ~~~   87 (93)
T d1h2vz_          85 AGF   87 (93)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            643

>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=99.76  E-value=1.2e-18  Score=150.99  Aligned_cols=82  Identities=38%  Similarity=0.717  Sum_probs=77.6

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeecc--ceEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEG--RTIA  564 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~G--r~L~  564 (797)
                      ++.+.++|||+||++++++++|+++|++||.|.+++|++|+.+|++||||||+|.+.++|++||+.|||..+.|  ++|+
T Consensus         2 ~~~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~   81 (85)
T d1b7fa2           2 ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLS   81 (85)
T ss_dssp             STTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEE
Confidence            34567889999999999999999999999999999999999999999999999999999999999999999976  8899


Q ss_pred             EEec
Q 040243          565 VRVA  568 (797)
Q Consensus       565 V~~A  568 (797)
                      |+||
T Consensus        82 V~~A   85 (85)
T d1b7fa2          82 VRLA   85 (85)
T ss_dssp             EEEC
T ss_pred             EEEC
Confidence            9997

>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=99.76  E-value=5.4e-19  Score=154.48  Aligned_cols=82  Identities=35%  Similarity=0.463  Sum_probs=78.6

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      ..++|||+||++++++++|+++|++||.|.+|+|++|+.+|++||||||+|.+.++|++||+.|||..|+|+.|+|+||+
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            45699999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             CC
Q 040243          570 KP  571 (797)
Q Consensus       570 ~~  571 (797)
                      +.
T Consensus        84 p~   85 (89)
T d2cqba1          84 PM   85 (89)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.76  E-value=2e-18  Score=162.76  Aligned_cols=85  Identities=36%  Similarity=0.590  Sum_probs=80.3

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ...++|||+||++++++++|+++|++||.|.+|+|++|+.||++||||||+|.+.++|++||+.|||+.|+|+.|+|+||
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             CCCCC
Q 040243          569 GKPPQ  573 (797)
Q Consensus       569 ~~~~~  573 (797)
                      .....
T Consensus       120 ~~~~~  124 (139)
T d1u6fa1         120 ASGHQ  124 (139)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            76554

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=2.7e-18  Score=154.13  Aligned_cols=86  Identities=40%  Similarity=0.549  Sum_probs=79.6

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      ++...++|||+||++++++++|+++|++||.|.+|+|++|+.||++||||||+|.+.++|++||+.+++ .|+|+.|+|+
T Consensus         6 ~d~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~   84 (103)
T d2cqda1           6 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVN   84 (103)
T ss_dssp             CSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEE
Confidence            445567899999999999999999999999999999999999999999999999999999999999876 6999999999


Q ss_pred             ecCCCCC
Q 040243          567 VAGKPPQ  573 (797)
Q Consensus       567 ~A~~~~~  573 (797)
                      ||.....
T Consensus        85 ~a~~~~~   91 (103)
T d2cqda1          85 LAYLGAK   91 (103)
T ss_dssp             ESTTTCC
T ss_pred             EcCCCCC
Confidence            9986544

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=1.5e-18  Score=150.54  Aligned_cols=80  Identities=38%  Similarity=0.724  Sum_probs=75.8

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeecc--ceEEEE
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEG--RTIAVR  566 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~G--r~L~V~  566 (797)
                      ..+++|||+||+.++++++|+++|++||.|.+++|++|+.+|++||||||+|.+.++|++|++.|||..++|  ++|+|+
T Consensus         4 ~k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~   83 (85)
T d1fxla2           4 IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVK   83 (85)
T ss_dssp             GTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEE
Confidence            356789999999999999999999999999999999999999999999999999999999999999999998  559999


Q ss_pred             ec
Q 040243          567 VA  568 (797)
Q Consensus       567 ~A  568 (797)
                      ||
T Consensus        84 ~A   85 (85)
T d1fxla2          84 FA   85 (85)
T ss_dssp             EC
T ss_pred             eC
Confidence            87

>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=99.75  E-value=1.7e-18  Score=155.22  Aligned_cols=84  Identities=36%  Similarity=0.639  Sum_probs=79.9

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      .+++|||+||++++++++|+++|++||.|.+++++.++.+|++||||||+|.+.++|++||+.|||+.|+|+.|+|+||.
T Consensus        17 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a~   96 (102)
T d2cpza1          17 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKR   96 (102)
T ss_dssp             TTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEeC
Confidence            45689999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 040243          570 KPPQ  573 (797)
Q Consensus       570 ~~~~  573 (797)
                      .+..
T Consensus        97 ~k~~  100 (102)
T d2cpza1          97 SKND  100 (102)
T ss_dssp             CSCC
T ss_pred             CCCC
Confidence            7653

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.74  E-value=3.1e-18  Score=151.30  Aligned_cols=86  Identities=24%  Similarity=0.448  Sum_probs=79.3

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecC-CCCcccceEEEEecCHHHHHHHHHhc-CceeeccceEEE
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDR-VTGMSKGYGFVKYADIQMANNAIASM-NGYRLEGRTIAV  565 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk-~TGksrGfaFV~F~s~e~A~~AI~~L-nG~~l~Gr~L~V  565 (797)
                      ....++|||+||++++++++|+++|++||.|.+|+|++++ .+|++||||||+|.+.++|++||+.| ||..|+|+.|+|
T Consensus         5 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V   84 (94)
T d2cpha1           5 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL   84 (94)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEE
Confidence            4466789999999999999999999999999999999885 48999999999999999999999998 899999999999


Q ss_pred             EecCCCCC
Q 040243          566 RVAGKPPQ  573 (797)
Q Consensus       566 ~~A~~~~~  573 (797)
                      +||.....
T Consensus        85 ~~A~~~~~   92 (94)
T d2cpha1          85 EWADSEVT   92 (94)
T ss_dssp             EECCCCCC
T ss_pred             EEcCCCCC
Confidence            99986543

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=1.1e-18  Score=156.53  Aligned_cols=84  Identities=31%  Similarity=0.573  Sum_probs=79.4

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      .+.++|||+||++++++++|+++|++||.|.+|+|++++.||++||||||+|.+.++|++||+.|||..|+|+.|+|+||
T Consensus         6 ~~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a   85 (104)
T d1p1ta_           6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNA   85 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEET
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            34568999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 040243          569 GKPP  572 (797)
Q Consensus       569 ~~~~  572 (797)
                      ....
T Consensus        86 ~~~~   89 (104)
T d1p1ta_          86 ASEK   89 (104)
T ss_dssp             TCTT
T ss_pred             CCCC
Confidence            7643

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.73  E-value=3.8e-18  Score=147.42  Aligned_cols=80  Identities=26%  Similarity=0.531  Sum_probs=74.8

Q ss_pred             EEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCC---cccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecCC
Q 040243          494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTG---MSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGK  570 (797)
Q Consensus       494 LfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TG---ksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~~  570 (797)
                      |||+||++++++++|+++|++||.|.+|+|++++.++   ++||||||+|.+.++|++||+.|||+.|+|+.|+|+||..
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            8999999999999999999999999999999998776   5799999999999999999999999999999999999875


Q ss_pred             CCC
Q 040243          571 PPQ  573 (797)
Q Consensus       571 ~~~  573 (797)
                      ..+
T Consensus        81 ~~k   83 (85)
T d2cpfa1          81 ATK   83 (85)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            443

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=2.5e-18  Score=150.23  Aligned_cols=84  Identities=38%  Similarity=0.679  Sum_probs=79.6

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      +..+|||+||++++++++|+++|++||.|..+.++.+..+|+++|||||+|.+.++|++||+.|+|+.|+|+.|+|+||.
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            56689999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             CCCC
Q 040243          570 KPPQ  573 (797)
Q Consensus       570 ~~~~  573 (797)
                      ++..
T Consensus        84 ~~~~   87 (90)
T d1x5sa1          84 KSSD   87 (90)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6543

>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=99.73  E-value=8.4e-18  Score=147.56  Aligned_cols=81  Identities=28%  Similarity=0.515  Sum_probs=75.7

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      ..++|||+||++++|+++|+++|++||.|.+|+|++|+.||++||||||+|.+.++|++||+.  .+.|+|+.|.|++|.
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            457899999999999999999999999999999999999999999999999999999999984  458999999999997


Q ss_pred             CCC
Q 040243          570 KPP  572 (797)
Q Consensus       570 ~~~  572 (797)
                      .+.
T Consensus        85 ~k~   87 (90)
T d2cqga1          85 SKQ   87 (90)
T ss_dssp             TTC
T ss_pred             CCC
Confidence            654

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=6.1e-18  Score=146.37  Aligned_cols=79  Identities=28%  Similarity=0.483  Sum_probs=75.3

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      ..++|||+||++++++++|+++|++||.|.+++|++|+.||++||||||+|.+.++|++||+ ++++.|+|+.|+|+.|.
T Consensus         5 ~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            45799999999999999999999999999999999999999999999999999999999997 68999999999999885

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.73  E-value=1.1e-18  Score=148.89  Aligned_cols=76  Identities=30%  Similarity=0.553  Sum_probs=73.6

Q ss_pred             cEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       492 ~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ++|||+||++++++++|+++|++||.|.+++|++|+.||++||||||+|.+.++|++||+ ++++.|+|+.|+|++|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            579999999999999999999999999999999999999999999999999999999997 7999999999999987

>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=99.73  E-value=6.1e-18  Score=145.61  Aligned_cols=76  Identities=28%  Similarity=0.439  Sum_probs=73.7

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEE
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAV  565 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V  565 (797)
                      ..++|||+||++++++++|+++|++||.|.+|+|++|+.||+++|||||+|.+.++|++||+.|||+.|+|++|+|
T Consensus         8 ~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           8 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             GGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            4578999999999999999999999999999999999999999999999999999999999999999999999987

>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=99.73  E-value=2.6e-18  Score=147.22  Aligned_cols=80  Identities=15%  Similarity=0.392  Sum_probs=70.2

Q ss_pred             CcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecCC
Q 040243          491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGK  570 (797)
Q Consensus       491 ~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~~  570 (797)
                      .+||||+||++++++++|+++|++||.|..++++.+..+|++||||||+|.+.++|++||+.|||+.|+|+.|+|++|++
T Consensus         1 d~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           1 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CcEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            36999999999999999999999999999999998888999999999999999999999999999999999999999874

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=4.1e-18  Score=146.62  Aligned_cols=80  Identities=40%  Similarity=0.648  Sum_probs=75.5

Q ss_pred             EEEecCCCCCcHHHHHHHhhcCCCEEEE-EEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecCCCC
Q 040243          494 LYIGYLPPTLDDDGLIRLFSTFGDIVMA-KVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPP  572 (797)
Q Consensus       494 LfVgNLp~~vte~dL~~~Fs~fG~I~~v-~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~~~~  572 (797)
                      |||+||++++++++|+++|++||.|.++ +|++|+.||+++|||||+|.+.++|++||+.|+|..|+|+.|+|+||..+.
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            8999999999999999999999999775 889999999999999999999999999999999999999999999998654


Q ss_pred             C
Q 040243          573 Q  573 (797)
Q Consensus       573 ~  573 (797)
                      .
T Consensus        81 ~   81 (83)
T d1x5ta1          81 S   81 (83)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=99.72  E-value=1e-17  Score=148.09  Aligned_cols=86  Identities=23%  Similarity=0.435  Sum_probs=79.6

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcC------ceeeccc
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMN------GYRLEGR  561 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~Ln------G~~l~Gr  561 (797)
                      ..++++|||+||++++++++|+++|++||.|.++.++.++.+++++|||||+|.+.++|.+||+.|+      |..|+|+
T Consensus         5 ~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr   84 (98)
T d1x4ha1           5 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR   84 (98)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSC
T ss_pred             CCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCE
Confidence            3457799999999999999999999999999999999999999999999999999999999999876      6789999


Q ss_pred             eEEEEecCCCCC
Q 040243          562 TIAVRVAGKPPQ  573 (797)
Q Consensus       562 ~L~V~~A~~~~~  573 (797)
                      .|+|+||..+..
T Consensus        85 ~l~v~~a~~k~~   96 (98)
T d1x4ha1          85 QLKVDLAVTRDE   96 (98)
T ss_dssp             EEEEECCCCCCC
T ss_pred             EEEEEECCCCCc
Confidence            999999987554

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.72  E-value=5.5e-18  Score=144.49  Aligned_cols=76  Identities=29%  Similarity=0.434  Sum_probs=74.0

Q ss_pred             EEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       493 tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      +|||+||++++++++|+++|++||.|.+|+|..++ +|+++|||||+|.+.++|++||+.|||+.|+|+.|+|++|.
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            69999999999999999999999999999999997 89999999999999999999999999999999999999986

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=1.3e-17  Score=145.85  Aligned_cols=84  Identities=27%  Similarity=0.493  Sum_probs=77.3

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      +...++|||+||+.++++++|+++|++||.|.+|+|+.|+.++  +|||||+|.+.++|++|++.|+|..|.|+.|+|.|
T Consensus         5 ~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~--~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~   82 (90)
T d2cqia1           5 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNW   82 (90)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS--CCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc--ceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            4556799999999999999999999999999999999997654  79999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 040243          568 AGKPPQ  573 (797)
Q Consensus       568 A~~~~~  573 (797)
                      |+.+..
T Consensus        83 a~~~~~   88 (90)
T d2cqia1          83 ATTPSS   88 (90)
T ss_dssp             CCCTTC
T ss_pred             cCCCCC
Confidence            986543

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=1.1e-17  Score=150.37  Aligned_cols=83  Identities=22%  Similarity=0.438  Sum_probs=78.1

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      ..++|||+||++++++++|+++|++||.|.+++|.+|+.|+++||||||+|.+.++|++||+ ++++.|+|+.|.|++|.
T Consensus        19 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~   97 (103)
T d1x4ba1          19 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAV   97 (103)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCS
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECc
Confidence            34799999999999999999999999999999999999999999999999999999999995 79999999999999998


Q ss_pred             CCCC
Q 040243          570 KPPQ  573 (797)
Q Consensus       570 ~~~~  573 (797)
                      .+..
T Consensus        98 ~ke~  101 (103)
T d1x4ba1          98 AREE  101 (103)
T ss_dssp             SCCC
T ss_pred             ccCC
Confidence            7654

>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=99.71  E-value=6e-18  Score=143.27  Aligned_cols=75  Identities=28%  Similarity=0.531  Sum_probs=71.9

Q ss_pred             EEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       493 tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      +|||+||++++++++|+++|++||.|.+|+|++|+.|+++||||||+|.+.++|++||+ +++..|+|+.|+|+.|
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            49999999999999999999999999999999999999999999999999999999997 7999999999999765

>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=99.71  E-value=1.2e-17  Score=148.61  Aligned_cols=87  Identities=28%  Similarity=0.458  Sum_probs=79.8

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEE--------EEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceee
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIV--------MAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRL  558 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~--------~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l  558 (797)
                      ++...++|||+||++++++++|+++|++||.|.        .+++.+|+.+|+++|||||+|.+.++|.+||+.|||+.|
T Consensus         4 ~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~   83 (101)
T d2cpea1           4 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   83 (101)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEE
Confidence            456778999999999999999999999999874        577888999999999999999999999999999999999


Q ss_pred             ccceEEEEecCCCCC
Q 040243          559 EGRTIAVRVAGKPPQ  573 (797)
Q Consensus       559 ~Gr~L~V~~A~~~~~  573 (797)
                      +|+.|+|+||+.+..
T Consensus        84 ~gr~i~V~~a~~~~p   98 (101)
T d2cpea1          84 QGSKLKVSLARKKPP   98 (101)
T ss_dssp             TTEECEEECSSCCCC
T ss_pred             CCEEEEEEEcCCCCC
Confidence            999999999986543

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=1.3e-17  Score=145.69  Aligned_cols=81  Identities=36%  Similarity=0.558  Sum_probs=75.3

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      ...+|||+||++++++++|+++|++||.|.+++|+.++  +.+||||||+|.+.++|++||+.|||+.|+|+.|+|++|+
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~   84 (89)
T d1cvja2           7 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK   84 (89)
T ss_dssp             TTTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT--TBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec--CCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            34589999999999999999999999999999999986  4578999999999999999999999999999999999998


Q ss_pred             CCC
Q 040243          570 KPP  572 (797)
Q Consensus       570 ~~~  572 (797)
                      .+.
T Consensus        85 ~~~   87 (89)
T d1cvja2          85 SRK   87 (89)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            654

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=3.7e-17  Score=143.91  Aligned_cols=84  Identities=29%  Similarity=0.462  Sum_probs=77.3

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      .....++|||+||++++++++|+++|++||.|.+|+|+.++.  .+||||||+|.+.++|++||+.|||..|+|+.|+|+
T Consensus         7 ~~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~--~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~   84 (93)
T d2cq3a1           7 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN   84 (93)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhhcceeeecccccccc--CCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            345677899999999999999999999999999999999863  479999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 040243          567 VAGKPP  572 (797)
Q Consensus       567 ~A~~~~  572 (797)
                      ||+.+.
T Consensus        85 ~A~~r~   90 (93)
T d2cq3a1          85 NATARV   90 (93)
T ss_dssp             ECCSSC
T ss_pred             ecCcCC
Confidence            998654

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=9.5e-18  Score=150.29  Aligned_cols=80  Identities=29%  Similarity=0.453  Sum_probs=76.2

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      .+.++|||+||++++++++|+++|+.||.|.+|+|++|+.||++||||||+|.+.++|++||+ |||..|+|+.|+|++|
T Consensus        16 ~~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a   94 (101)
T d2cq4a1          16 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQAS   94 (101)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEH
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEEC
Confidence            345799999999999999999999999999999999999999999999999999999999995 9999999999999987


Q ss_pred             C
Q 040243          569 G  569 (797)
Q Consensus       569 ~  569 (797)
                      .
T Consensus        95 ~   95 (101)
T d2cq4a1          95 Q   95 (101)
T ss_dssp             H
T ss_pred             C
Confidence            5

>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=99.70  E-value=1.2e-17  Score=145.10  Aligned_cols=81  Identities=23%  Similarity=0.344  Sum_probs=71.2

Q ss_pred             CCcEEEEecCCCCCc-HHHHHHHhhcCCCEEEEEEEe-cCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          490 DDTNLYIGYLPPTLD-DDGLIRLFSTFGDIVMAKVIK-DRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       490 ~~~tLfVgNLp~~vt-e~dL~~~Fs~fG~I~~v~v~~-dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      +.++|||+||+++++ +++|+++|++||.|.+|+|.. ++.++++||||||+|.+.++|++||+ |||+.|+|+.|+|+|
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            567999999999876 566999999999999999876 45789999999999999999999996 999999999999999


Q ss_pred             cCCC
Q 040243          568 AGKP  571 (797)
Q Consensus       568 A~~~  571 (797)
                      |+++
T Consensus        82 a~~k   85 (86)
T d2ghpa3          82 ADKK   85 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9865

>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=99.70  E-value=2.5e-17  Score=140.21  Aligned_cols=77  Identities=21%  Similarity=0.469  Sum_probs=73.8

Q ss_pred             CcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       491 ~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      .++|||+||++++|+++|+++|++||.|..+++..++.+++++|||||+|.+.++|++|++ |+|+.|+|+.|+|+.|
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            3589999999999999999999999999999999999999999999999999999999995 8999999999999987

>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=99.70  E-value=7e-18  Score=143.20  Aligned_cols=75  Identities=16%  Similarity=0.380  Sum_probs=71.8

Q ss_pred             EEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       493 tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      +||||||++++|+++|+++|++||.|.+|+|++|+.|+++||||||+|.+.++|++||+ ++++.|+|+.|+|++|
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            69999999999999999999999999999999999999999999999999999999996 4778999999999876

>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=99.68  E-value=1.2e-16  Score=141.10  Aligned_cols=80  Identities=23%  Similarity=0.474  Sum_probs=73.3

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ...++|||+||+.++++++|+++|++||.|..+.+..+   +.+||||||+|.+.++|++||+.|||+.|+|++|+|+||
T Consensus        12 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a   88 (95)
T d1x4aa1          12 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP   88 (95)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEec
Confidence            45679999999999999999999999999999887554   567899999999999999999999999999999999998


Q ss_pred             CCC
Q 040243          569 GKP  571 (797)
Q Consensus       569 ~~~  571 (797)
                      +..
T Consensus        89 ~~~   91 (95)
T d1x4aa1          89 RSG   91 (95)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            753

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=1.4e-16  Score=142.61  Aligned_cols=84  Identities=20%  Similarity=0.413  Sum_probs=74.5

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecC-CCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDR-VTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk-~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      ...++|||+||++++++++|+++|++|| |++++++.++ .++++||||||+|.+.++|++|+ .||++.|+|+.|+|+|
T Consensus        13 ~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~gr~l~V~~   90 (104)
T d1wi8a_          13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEECCEEEEEEE
Confidence            3568999999999999999999999999 7788877765 57899999999999999998777 5999999999999999


Q ss_pred             cCCCCCC
Q 040243          568 AGKPPQP  574 (797)
Q Consensus       568 A~~~~~~  574 (797)
                      |..+...
T Consensus        91 a~~~~~~   97 (104)
T d1wi8a_          91 ADQAQDK   97 (104)
T ss_dssp             CCCCCCC
T ss_pred             CCCCCCC
Confidence            9865543

>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=99.68  E-value=9e-18  Score=147.53  Aligned_cols=83  Identities=20%  Similarity=0.306  Sum_probs=76.0

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      .....++|||+||++++++++|+++|++||.|.+++|+.+ .+|++||||||+|.+.++|++||+ |||..|+|+.|+|+
T Consensus         9 ~~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~   86 (91)
T d1fjeb1           9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLE   86 (91)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEE
T ss_pred             CCCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEE
Confidence            3456779999999999999999999999999999988765 589999999999999999999996 99999999999999


Q ss_pred             ecCCC
Q 040243          567 VAGKP  571 (797)
Q Consensus       567 ~A~~~  571 (797)
                      +|+.+
T Consensus        87 ~ak~k   91 (91)
T d1fjeb1          87 KPKGR   91 (91)
T ss_dssp             CCCCS
T ss_pred             ecCCC
Confidence            99753

>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=99.67  E-value=2.2e-17  Score=138.90  Aligned_cols=75  Identities=17%  Similarity=0.416  Sum_probs=72.7

Q ss_pred             EEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       493 tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      +|||+||+.++|+++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++ |||+.|+|+.|+|++|
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            59999999999999999999999999999999999999999999999999999999996 9999999999999986

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=1.2e-16  Score=142.19  Aligned_cols=77  Identities=27%  Similarity=0.554  Sum_probs=69.6

Q ss_pred             CCCCcEEEEecCC-CCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          488 ELDDTNLYIGYLP-PTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       488 ~~~~~tLfVgNLp-~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      ....++|||+||+ ..+++++|+++|++||.|.+|+|        +||||||+|.+.++|++||+.|||+.|+|+.|+|+
T Consensus        12 ~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i--------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~   83 (98)
T d1wf2a_          12 RSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDIN   83 (98)
T ss_dssp             SSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE--------ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEE
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE--------eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            3456789999997 57889999999999999999998        46899999999999999999999999999999999


Q ss_pred             ecCCCC
Q 040243          567 VAGKPP  572 (797)
Q Consensus       567 ~A~~~~  572 (797)
                      ||..+.
T Consensus        84 ~a~~~~   89 (98)
T d1wf2a_          84 LAAEPK   89 (98)
T ss_dssp             ETTSCC
T ss_pred             ECCCCC
Confidence            997543

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=2e-17  Score=147.40  Aligned_cols=85  Identities=24%  Similarity=0.474  Sum_probs=80.1

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      ..++|||+||+.++++++|+++|++||.|..+.+..+..+|+++|||||+|.+.++|++||+.|||..|.|+.|+|+||+
T Consensus        17 ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~ak   96 (102)
T d2cpxa1          17 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGK   96 (102)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeCC
Confidence            45799999999999999999999999999999999998899999999999999999999999999999999999999998


Q ss_pred             CCCCC
Q 040243          570 KPPQP  574 (797)
Q Consensus       570 ~~~~~  574 (797)
                      .+...
T Consensus        97 ~k~~r  101 (102)
T d2cpxa1          97 NKKQR  101 (102)
T ss_dssp             CCSCC
T ss_pred             CcccC
Confidence            76543

>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=99.65  E-value=1.2e-16  Score=142.78  Aligned_cols=82  Identities=27%  Similarity=0.540  Sum_probs=76.5

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      .+.+.++|||+||+.++++++|+++|++||.|..+.+..+. +++++|||||+|.+.++|.+||+.|||..|.|+.+.|.
T Consensus        14 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~   92 (101)
T d1x5oa1          14 QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSA   92 (101)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCC
T ss_pred             ccCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccc-ccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccC
Confidence            44567899999999999999999999999999999999885 89999999999999999999999999999999999887


Q ss_pred             ecC
Q 040243          567 VAG  569 (797)
Q Consensus       567 ~A~  569 (797)
                      +++
T Consensus        93 ~~~   95 (101)
T d1x5oa1          93 PTE   95 (101)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            765

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=1.7e-16  Score=144.28  Aligned_cols=78  Identities=27%  Similarity=0.431  Sum_probs=72.8

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      .+++|||+||+.++++++|+++|++||.|.+|++..   ++.+||||||+|.+.++|..||+.|||+.|+|+.|+|.|+.
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            467999999999999999999999999999999875   46789999999999999999999999999999999999985


Q ss_pred             C
Q 040243          570 K  570 (797)
Q Consensus       570 ~  570 (797)
                      .
T Consensus        83 ~   83 (114)
T d2f9da1          83 A   83 (114)
T ss_dssp             H
T ss_pred             C
Confidence            3

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=2.9e-16  Score=139.08  Aligned_cols=77  Identities=31%  Similarity=0.588  Sum_probs=72.2

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      ..++|||+||+.++++++|+++|++||.|.+|+|+.|      ||||||+|.+.++|++||+.|||..|+|+.|+|.|++
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            4578999999999999999999999999999999876      5899999999999999999999999999999999997


Q ss_pred             CCC
Q 040243          570 KPP  572 (797)
Q Consensus       570 ~~~  572 (797)
                      ..+
T Consensus        91 ~~p   93 (96)
T d1x4ga1          91 ESP   93 (96)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            643

>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=99.63  E-value=3.3e-16  Score=140.04  Aligned_cols=86  Identities=14%  Similarity=0.174  Sum_probs=76.2

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      +....++|||+|||+++|+++|+++|..|| |.+|.++++. +++++|||||+|.+.++|++||+ ||++.|+||.|+|.
T Consensus        11 ~~~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~   87 (102)
T d1weza_          11 QSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELF   87 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEec-CCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEE
Confidence            445678999999999999999999999998 5578888886 78999999999999999999996 89999999999999


Q ss_pred             ecCCCCCCC
Q 040243          567 VAGKPPQPT  575 (797)
Q Consensus       567 ~A~~~~~~~  575 (797)
                      |+.......
T Consensus        88 ~s~~~~~~~   96 (102)
T d1weza_          88 LNSTAGTSG   96 (102)
T ss_dssp             EECCCCCCC
T ss_pred             EcCCCCCCC
Confidence            988665433

>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=99.63  E-value=2.3e-16  Score=139.40  Aligned_cols=84  Identities=20%  Similarity=0.290  Sum_probs=74.9

Q ss_pred             CcEEEEecCCCCCcHHHHHHHhhcCCC-EEEEEEEecC-CCCcccceEEEEecCHHHHHHHHHhcCc--eeeccceEEEE
Q 040243          491 DTNLYIGYLPPTLDDDGLIRLFSTFGD-IVMAKVIKDR-VTGMSKGYGFVKYADIQMANNAIASMNG--YRLEGRTIAVR  566 (797)
Q Consensus       491 ~~tLfVgNLp~~vte~dL~~~Fs~fG~-I~~v~v~~dk-~TGksrGfaFV~F~s~e~A~~AI~~LnG--~~l~Gr~L~V~  566 (797)
                      +++|||+||+.++++++|+++|++||. |.+++|++|. .++++||||||+|.+.++|.+||+.|++  ..++|+.|+|+
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            478999999999999999999999995 9999999885 4789999999999999999999999964  45679999999


Q ss_pred             ecCCCCCC
Q 040243          567 VAGKPPQP  574 (797)
Q Consensus       567 ~A~~~~~~  574 (797)
                      ||+++...
T Consensus        81 ~A~p~~~~   88 (96)
T d2disa1          81 WAEPEIDV   88 (96)
T ss_dssp             ESCSSCST
T ss_pred             EcCCCCCC
Confidence            99765543

>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=99.63  E-value=4.1e-16  Score=135.03  Aligned_cols=78  Identities=15%  Similarity=0.264  Sum_probs=73.5

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      ..++|||+||+.++++++|+++|+.||.|.+|+|.+++ +|++||||||+|.+.++|++||+ +++..+.|+.|+|.|+.
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            45799999999999999999999999999999998886 89999999999999999999995 79999999999999864

>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=99.63  E-value=8.2e-16  Score=137.80  Aligned_cols=86  Identities=19%  Similarity=0.273  Sum_probs=77.2

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      ..+..+|||+|||+++++++|+++|..||.|..+.++.+..+++++|||||+|.+.++|++|++ |++..|+||.|+|.+
T Consensus        12 ~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~   90 (104)
T d1wg5a_          12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFK   90 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEE
Confidence            3456689999999999999999999999999987777777799999999999999999999996 899999999999999


Q ss_pred             cCCCCCC
Q 040243          568 AGKPPQP  574 (797)
Q Consensus       568 A~~~~~~  574 (797)
                      +......
T Consensus        91 ~~~~~~~   97 (104)
T d1wg5a_          91 SSRAEVR   97 (104)
T ss_dssp             ECTTTSC
T ss_pred             CCHHHhc
Confidence            9866543

>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=99.63  E-value=2.2e-16  Score=142.48  Aligned_cols=79  Identities=14%  Similarity=0.076  Sum_probs=72.1

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      .+..++|||+||++++++++|+++|++||.|.+|.|.      ++||||||+|.+.++|++||+.|||+.|.|+.|+|+|
T Consensus         7 ~r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~------~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~   80 (111)
T d1whxa_           7 GRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP------EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEW   80 (111)
T ss_dssp             SEEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC------SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEee------ccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEE
Confidence            3466899999999999999999999999999999873      3579999999999999999999999999999999999


Q ss_pred             cCCCC
Q 040243          568 AGKPP  572 (797)
Q Consensus       568 A~~~~  572 (797)
                      +....
T Consensus        81 a~~~~   85 (111)
T d1whxa_          81 APIGV   85 (111)
T ss_dssp             EETTT
T ss_pred             CCCCc
Confidence            86544

>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=99.62  E-value=1.2e-16  Score=133.51  Aligned_cols=71  Identities=32%  Similarity=0.588  Sum_probs=69.0

Q ss_pred             EEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEE
Q 040243          494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIA  564 (797)
Q Consensus       494 LfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~  564 (797)
                      |||+||+.++++++|+++|++||.|.++++.+++.+++++|||||+|.+.++|++||+.|||..|+|+.|+
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            89999999999999999999999999999999999999999999999999999999999999999998864

>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=99.62  E-value=2.8e-16  Score=137.22  Aligned_cols=78  Identities=22%  Similarity=0.319  Sum_probs=72.0

Q ss_pred             CCCcEEEEecCCCCCcHHHH---HHHhhcCCCEEEEEEEecCCCCccc---ceEEEEecCHHHHHHHHHhcCceeeccce
Q 040243          489 LDDTNLYIGYLPPTLDDDGL---IRLFSTFGDIVMAKVIKDRVTGMSK---GYGFVKYADIQMANNAIASMNGYRLEGRT  562 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL---~~~Fs~fG~I~~v~v~~dk~TGksr---GfaFV~F~s~e~A~~AI~~LnG~~l~Gr~  562 (797)
                      ...++|||+||++++++++|   +++|++||.|.+|.|++|+.++.++   |||||+|.+.++|.+||+.|||+.|+|+.
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            45668999999999999999   6789999999999999998877655   99999999999999999999999999999


Q ss_pred             EEEE
Q 040243          563 IAVR  566 (797)
Q Consensus       563 L~V~  566 (797)
                      |+|+
T Consensus        86 lkvS   89 (89)
T d2cpia1          86 LKAS   89 (89)
T ss_dssp             EEEE
T ss_pred             EEEC
Confidence            9985

>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=99.62  E-value=3.8e-16  Score=138.00  Aligned_cols=81  Identities=19%  Similarity=0.334  Sum_probs=73.6

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      ..+.++|||+||++++++++|+++|++||.|..++     .+++++|||||+|.+.++|++||+.|||..|+|+.|+|+|
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~-----~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~   87 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY   87 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEE-----ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeee-----ecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34578999999999999999999999999887654     3789999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 040243          568 AGKPPQ  573 (797)
Q Consensus       568 A~~~~~  573 (797)
                      +..+..
T Consensus        88 a~~k~~   93 (96)
T d1fjca_          88 TGEKGG   93 (96)
T ss_dssp             CSSSCC
T ss_pred             eCCCCC
Confidence            987654

>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=99.61  E-value=7.8e-16  Score=132.38  Aligned_cols=78  Identities=18%  Similarity=0.380  Sum_probs=71.0

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeec-cceEEEE
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLE-GRTIAVR  566 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~-Gr~L~V~  566 (797)
                      +..+++|||+||+.++++++|+++|++||.|.+|+++++     .+|||||+|.+.++|.+|++.|+|+.|. |+.|+|+
T Consensus         5 ~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~   79 (83)
T d2b0ga1           5 QPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN-----RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKIT   79 (83)
T ss_dssp             CSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT-----TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc-----cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEE
Confidence            345679999999999999999999999999999999765     3689999999999999999999999884 6899999


Q ss_pred             ecCC
Q 040243          567 VAGK  570 (797)
Q Consensus       567 ~A~~  570 (797)
                      ||++
T Consensus        80 ~akk   83 (83)
T d2b0ga1          80 FAKK   83 (83)
T ss_dssp             ECCC
T ss_pred             EecC
Confidence            9974

>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=99.61  E-value=8.3e-16  Score=138.27  Aligned_cols=77  Identities=26%  Similarity=0.490  Sum_probs=71.0

Q ss_pred             CcEEEEecCCC-CCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          491 DTNLYIGYLPP-TLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       491 ~~tLfVgNLp~-~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      +++|||+||++ .+++++|+++|++||.|.+|+|++++     ||||||+|.+.++|.+||+.|||..|+|+.|+|+|++
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            46999999965 69999999999999999999999874     7999999999999999999999999999999999987


Q ss_pred             CCC
Q 040243          570 KPP  572 (797)
Q Consensus       570 ~~~  572 (797)
                      ...
T Consensus        77 ~~~   79 (109)
T d2adca1          77 HQN   79 (109)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=99.61  E-value=3.6e-16  Score=135.12  Aligned_cols=79  Identities=19%  Similarity=0.299  Sum_probs=71.6

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ..++|||+|||+++++++|+++|+.||.|....++.+..+|+++|||||+|.+.++|++||+.||++.|+|++|+|++|
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            4568999999999999999999999999877544444468999999999999999999999999999999999999986

>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=99.61  E-value=4.8e-16  Score=134.84  Aligned_cols=77  Identities=27%  Similarity=0.600  Sum_probs=71.8

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      ..++|||+||+.++++++|+++|++||.|.+|++.++      ||||||+|.+.++|++|++.|||..|+|+.|+|+||.
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            3568999999999999999999999999999999866      4899999999999999999999999999999999997


Q ss_pred             CCC
Q 040243          570 KPP  572 (797)
Q Consensus       570 ~~~  572 (797)
                      ...
T Consensus        81 ~~~   83 (86)
T d2cpja1          81 HSA   83 (86)
T ss_dssp             CCS
T ss_pred             CcC
Confidence            654

>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=99.60  E-value=1.2e-15  Score=135.71  Aligned_cols=78  Identities=21%  Similarity=0.285  Sum_probs=71.4

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEe
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV  567 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~  567 (797)
                      ....++|||+||++++++++|+++|++||.|.+++|..       +|||||+|.+.++|++||+.|||..|+|+.|+|.+
T Consensus        12 ~~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~   84 (98)
T d1wg4a_          12 RRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSY   84 (98)
T ss_dssp             CSCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEE
Confidence            34677999999999999999999999999999999854       48999999999999999999999999999999999


Q ss_pred             cCCCC
Q 040243          568 AGKPP  572 (797)
Q Consensus       568 A~~~~  572 (797)
                      ++...
T Consensus        85 ~~~~~   89 (98)
T d1wg4a_          85 IRVYP   89 (98)
T ss_dssp             EEEEC
T ss_pred             EecCC
Confidence            86544

>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=99.60  E-value=6.4e-16  Score=131.79  Aligned_cols=74  Identities=27%  Similarity=0.429  Sum_probs=68.3

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      .+++|||+||+  +|+++|+++|++||.|.+|++.++      +|||||+|.+.++|.+||+.|||..|+|+.|+|+||+
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            46799999995  899999999999999999998754      5899999999999999999999999999999999997


Q ss_pred             CC
Q 040243          570 KP  571 (797)
Q Consensus       570 ~~  571 (797)
                      .+
T Consensus        76 ~~   77 (79)
T d2bz2a1          76 KQ   77 (79)
T ss_dssp             SS
T ss_pred             CC
Confidence            54

>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=99.60  E-value=7.2e-16  Score=134.15  Aligned_cols=78  Identities=19%  Similarity=0.398  Sum_probs=69.5

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      ..++|||+||++++++++|+++|++||.|.+|++.     ..++|||||+|.+.++|++||.  +++.|+|+.|+|++|.
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~-----~~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~   76 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIP-----KPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAE   76 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECC-----SSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEe-----eccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCC
Confidence            45699999999999999999999999999999764     4578999999999999999985  8899999999999997


Q ss_pred             CCCCC
Q 040243          570 KPPQP  574 (797)
Q Consensus       570 ~~~~~  574 (797)
                      .+...
T Consensus        77 ~k~~~   81 (88)
T d1wf0a_          77 PKHNS   81 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            65543

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=4.6e-16  Score=133.12  Aligned_cols=77  Identities=31%  Similarity=0.506  Sum_probs=69.2

Q ss_pred             cEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCce-eeccceEEEEecCC
Q 040243          492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGY-RLEGRTIAVRVAGK  570 (797)
Q Consensus       492 ~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~-~l~Gr~L~V~~A~~  570 (797)
                      ++|||+||+.++++++|+++|++||.|.++++..      +||||||+|.+.++|++||+.|||. .|+|+.|+|+||..
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            3799999999999999999999999988777665      4689999999999999999999995 69999999999987


Q ss_pred             CCCC
Q 040243          571 PPQP  574 (797)
Q Consensus       571 ~~~~  574 (797)
                      +.+.
T Consensus        76 k~~r   79 (80)
T d2cqha1          76 KKLR   79 (80)
T ss_dssp             CCCC
T ss_pred             cCcC
Confidence            6543

>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=99.58  E-value=8.8e-16  Score=134.33  Aligned_cols=79  Identities=27%  Similarity=0.491  Sum_probs=71.7

Q ss_pred             CcEEEEecCCCCCcHHHHH----HHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          491 DTNLYIGYLPPTLDDDGLI----RLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       491 ~~tLfVgNLp~~vte~dL~----~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      .++|||+||++++++++|+    ++|++||.|.+|++..   +++++|||||+|.+.++|.+|++.|||..|+|+.|+|+
T Consensus         3 ~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~   79 (91)
T d1nu4a_           3 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ   79 (91)
T ss_dssp             CSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            5799999999999999886    4689999999988754   57899999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 040243          567 VAGKPP  572 (797)
Q Consensus       567 ~A~~~~  572 (797)
                      ||+.+.
T Consensus        80 ~ak~~~   85 (91)
T d1nu4a_          80 YAKTDS   85 (91)
T ss_dssp             ECSSCC
T ss_pred             EeCCCc
Confidence            998654

>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=99.58  E-value=4.1e-15  Score=131.59  Aligned_cols=77  Identities=31%  Similarity=0.565  Sum_probs=70.1

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeecc--ceEEEEe
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEG--RTIAVRV  567 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~G--r~L~V~~  567 (797)
                      ..++|||+||+.++++++|+++|++||.|..|++.++      ++||||+|.+.++|++|++.||+..|+|  ++|+|+|
T Consensus        16 Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~   89 (97)
T d1whya_          16 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDF   89 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEE
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEe
Confidence            4578999999999999999999999999999998765      5799999999999999999999999986  5799999


Q ss_pred             cCCCC
Q 040243          568 AGKPP  572 (797)
Q Consensus       568 A~~~~  572 (797)
                      |+..+
T Consensus        90 ak~~~   94 (97)
T d1whya_          90 AKSGP   94 (97)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            98543

>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=99.57  E-value=4.1e-15  Score=128.46  Aligned_cols=77  Identities=22%  Similarity=0.343  Sum_probs=70.0

Q ss_pred             CcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecCC
Q 040243          491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGK  570 (797)
Q Consensus       491 ~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~~  570 (797)
                      .++|||+||++++++++|+++|++||.|..+.+.      ++||||||+|.+.++|.+||..|||..|+|+.|+|+||++
T Consensus         8 ~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~------~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP   81 (86)
T d2cpda1           8 VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKP   81 (86)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEE------ECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCC
T ss_pred             CCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEc------cccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccC
Confidence            4689999999999999999999999998877763      4579999999999999999999999999999999999986


Q ss_pred             CCC
Q 040243          571 PPQ  573 (797)
Q Consensus       571 ~~~  573 (797)
                      +.+
T Consensus        82 ~~~   84 (86)
T d2cpda1          82 VDK   84 (86)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=2.7e-15  Score=130.22  Aligned_cols=76  Identities=18%  Similarity=0.364  Sum_probs=69.4

Q ss_pred             CcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceee-ccceEEEEecC
Q 040243          491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRL-EGRTIAVRVAG  569 (797)
Q Consensus       491 ~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l-~Gr~L~V~~A~  569 (797)
                      .++|||+||+.++++++|+++|++||.|.++.+..+    +++|||||+|.+.++|.+|+..|+|+.| +|+.|+|+|++
T Consensus        10 s~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~----~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk   85 (88)
T d2adca2          10 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSK   85 (88)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS----SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECS
T ss_pred             CCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee----cccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCC
Confidence            569999999999999999999999999998876554    4689999999999999999999999988 58999999987


Q ss_pred             C
Q 040243          570 K  570 (797)
Q Consensus       570 ~  570 (797)
                      .
T Consensus        86 ~   86 (88)
T d2adca2          86 S   86 (88)
T ss_dssp             S
T ss_pred             C
Confidence            5

>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=99.57  E-value=1.6e-15  Score=132.12  Aligned_cols=77  Identities=17%  Similarity=0.293  Sum_probs=67.0

Q ss_pred             CcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecCC
Q 040243          491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGK  570 (797)
Q Consensus       491 ~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~~  570 (797)
                      .++|||+||++++++++|+++|++|| +..+.      ++++||||||+|.+.++|++||+.||++.|+|++|+|+|+..
T Consensus         5 s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~------~~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~   77 (88)
T d1wg1a_           5 SSGILVKNLPQDSNCQEVHDLLKDYD-LKYCY------VDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPT   77 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSC-CCCEE------EEGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcC-ceeee------eeccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            45799999999999999999999999 22233      245789999999999999999999999999999999999976


Q ss_pred             CCCC
Q 040243          571 PPQP  574 (797)
Q Consensus       571 ~~~~  574 (797)
                      ....
T Consensus        78 ~~~~   81 (88)
T d1wg1a_          78 DALL   81 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            5443

>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=99.57  E-value=6.7e-16  Score=134.05  Aligned_cols=73  Identities=18%  Similarity=0.274  Sum_probs=67.8

Q ss_pred             cEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecCCC
Q 040243          492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKP  571 (797)
Q Consensus       492 ~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~~~  571 (797)
                      ++|||+||++++++++|+++|++||.|.+++|..|       |||||+|.+.++|++||+.|||..|+|+.|+|.++...
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            36999999999999999999999999999998654       79999999999999999999999999999999887543

>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=99.56  E-value=4.3e-15  Score=125.57  Aligned_cols=74  Identities=18%  Similarity=0.246  Sum_probs=68.3

Q ss_pred             cEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       492 ~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ++|||+||++++++++|+++|+.||.|.+|++..++.+  .+|||||+|.+.++|++||. |+++.|+|+.|.|+.+
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 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK--NFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS--SSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccc--cceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            58999999999999999999999999999999998743  45799999999999999995 8999999999999865

>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=99.56  E-value=1.8e-15  Score=135.18  Aligned_cols=81  Identities=15%  Similarity=0.150  Sum_probs=72.6

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ....+|||+||++++++++|+++|..||.|..+.++.+..+|+++|||||+|.+.++|++||+ ||+..|+|+.|.|.++
T Consensus         6 ~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~   84 (103)
T d2cpya1           6 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVV   84 (103)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEEC
Confidence            345689999999999999999999999998875555555699999999999999999999996 8999999999999987


Q ss_pred             CC
Q 040243          569 GK  570 (797)
Q Consensus       569 ~~  570 (797)
                      ..
T Consensus        85 ~~   86 (103)
T d2cpya1          85 TL   86 (103)
T ss_dssp             CH
T ss_pred             CH
Confidence            54

>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=99.53  E-value=5.2e-15  Score=133.40  Aligned_cols=79  Identities=19%  Similarity=0.244  Sum_probs=71.7

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceee--ccceEEEEe
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRL--EGRTIAVRV  567 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l--~Gr~L~V~~  567 (797)
                      ...+|||+||++.+|+++|+++|++||.|.+|.|+.++    ++|||||+|.+.++|++||+.|||..|  .+++|+|.|
T Consensus         6 ~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~   81 (108)
T d2adba1           6 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF   81 (108)
T ss_dssp             CEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEE
T ss_pred             CeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEe
Confidence            45689999999999999999999999999999998875    589999999999999999999999998  578899999


Q ss_pred             cCCCC
Q 040243          568 AGKPP  572 (797)
Q Consensus       568 A~~~~  572 (797)
                      ++...
T Consensus        82 s~~~~   86 (108)
T d2adba1          82 SKLTS   86 (108)
T ss_dssp             CSSCS
T ss_pred             cCCcc
Confidence            87544

>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=99.53  E-value=3.5e-14  Score=127.05  Aligned_cols=81  Identities=14%  Similarity=0.165  Sum_probs=71.4

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhc--CceeeccceEE
Q 040243          487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM--NGYRLEGRTIA  564 (797)
Q Consensus       487 ~~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~L--nG~~l~Gr~L~  564 (797)
                      ......+|||+||+..++|++|+++|++||.|.++++.++      ||||||+|.+.++|++||+.|  ++..+.|++|+
T Consensus        11 ~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~   84 (104)
T d1wexa_          11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAF   84 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEE
Confidence            3346779999999999999999999999999999998764      589999999999999999987  45678899999


Q ss_pred             EEecCCCCC
Q 040243          565 VRVAGKPPQ  573 (797)
Q Consensus       565 V~~A~~~~~  573 (797)
                      |.|++.+..
T Consensus        85 v~~s~~~~~   93 (104)
T d1wexa_          85 FNYSTSKRI   93 (104)
T ss_dssp             EEECSSSSC
T ss_pred             EEEcCCCcc
Confidence            999976543

>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=99.52  E-value=2.1e-14  Score=121.24  Aligned_cols=72  Identities=24%  Similarity=0.344  Sum_probs=64.8

Q ss_pred             EEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecCCCC
Q 040243          494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGKPP  572 (797)
Q Consensus       494 LfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~~~~  572 (797)
                      |||+|||.++++++|+++|++|| +..+++      +++||||||+|.+.++|++|++.|||+.++|+.|+|+|+....
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~------~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d~   72 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTDA   72 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCSTT
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee------cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCCC
Confidence            79999999999999999999999 554443      4578999999999999999999999999999999999997543

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.50  E-value=4.1e-14  Score=122.67  Aligned_cols=79  Identities=19%  Similarity=0.228  Sum_probs=70.7

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhc--CceeeccceEEE
Q 040243          488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM--NGYRLEGRTIAV  565 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~L--nG~~l~Gr~L~V  565 (797)
                      ....++|||+||+.++++++|+++|++||.|.++++..+      +|||||+|.+.++|++|++.|  ++..++|+.|+|
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v   78 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYI   78 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEE
Confidence            346779999999999999999999999999999998765      479999999999999999865  567899999999


Q ss_pred             EecCCCC
Q 040243          566 RVAGKPP  572 (797)
Q Consensus       566 ~~A~~~~  572 (797)
                      +|++.+.
T Consensus        79 ~~sk~~~   85 (88)
T d2cq1a1          79 QYSNHKE   85 (88)
T ss_dssp             EECSCSS
T ss_pred             EECCCCC
Confidence            9997654

>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=99.50  E-value=1.1e-14  Score=132.17  Aligned_cols=81  Identities=20%  Similarity=0.244  Sum_probs=73.4

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ...++|||+||++++++++|+++|+.||.|..+.++.+..+|+++|||||+|.+.++|++|++ ||+..|+|+.|.|.++
T Consensus        16 ~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~~   94 (112)
T d1wela1          16 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPI   94 (112)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEE
T ss_pred             CCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEEc
Confidence            356799999999999999999999999999876666666799999999999999999999995 8999999999999887


Q ss_pred             CC
Q 040243          569 GK  570 (797)
Q Consensus       569 ~~  570 (797)
                      ..
T Consensus        95 ~~   96 (112)
T d1wela1          95 TK   96 (112)
T ss_dssp             CH
T ss_pred             Ch
Confidence            53

>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=99.49  E-value=4.6e-14  Score=137.01  Aligned_cols=82  Identities=21%  Similarity=0.437  Sum_probs=77.2

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       489 ~~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      ...++|||+||++.+++++|+++|+.||.|..+.|+.|+.+|+++|||||+|.+.++|.+||+ ++++.|+|+.|+|++|
T Consensus        95 ~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~A  173 (183)
T d1u1qa_          95 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA  173 (183)
T ss_dssp             CCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEEC
T ss_pred             cccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEec
Confidence            456799999999999999999999999999999999999999999999999999999999996 7899999999999998


Q ss_pred             CCC
Q 040243          569 GKP  571 (797)
Q Consensus       569 ~~~  571 (797)
                      .++
T Consensus       174 ~~k  176 (183)
T d1u1qa_         174 LSK  176 (183)
T ss_dssp             CCH
T ss_pred             CCc
Confidence            754

>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=99.47  E-value=4.1e-14  Score=127.02  Aligned_cols=78  Identities=13%  Similarity=0.083  Sum_probs=68.9

Q ss_pred             CCcEEEEecCCCCCcH-----HHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEE
Q 040243          490 DDTNLYIGYLPPTLDD-----DGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIA  564 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte-----~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~  564 (797)
                      ..++|||+||+..+.+     ++|+++|++||.|.++++++      ++|||||+|.+.++|.+||+.|||+.|+|+.|+
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k------~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~   77 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK------SFKRVRINFSNPLSAADARLRLHKTEFLGKEMK   77 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET------TTTEEEEECSSTTHHHHHHHTSTTSEETTEECE
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec------CCCEEEEEECCHHHHHHHHHHhcccccCCCEeE
Confidence            4568999999988633     56999999999999999875      468999999999999999999999999999999


Q ss_pred             EEecCCCCC
Q 040243          565 VRVAGKPPQ  573 (797)
Q Consensus       565 V~~A~~~~~  573 (797)
                      |.||+....
T Consensus        78 v~~a~~~~~   86 (104)
T d1weya_          78 LYFAQTLHI   86 (104)
T ss_dssp             EECCCCSSC
T ss_pred             EeecccCCC
Confidence            999976544

>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=99.46  E-value=5.6e-14  Score=124.84  Aligned_cols=79  Identities=16%  Similarity=0.262  Sum_probs=70.5

Q ss_pred             CCCCcEEEEecCCC-CCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHH--hcCceeeccceEE
Q 040243          488 ELDDTNLYIGYLPP-TLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA--SMNGYRLEGRTIA  564 (797)
Q Consensus       488 ~~~~~tLfVgNLp~-~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~--~LnG~~l~Gr~L~  564 (797)
                      ...+++|||+||+. .+|+++|+++|++||.|.+|+++++      ||||||+|.+.++|.+||+  .+++..|+|+.|+
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~   88 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   88 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEEEE
Confidence            34568999999997 4899999999999999999999865      4899999999999999998  5678899999999


Q ss_pred             EEecCCCC
Q 040243          565 VRVAGKPP  572 (797)
Q Consensus       565 V~~A~~~~  572 (797)
                      |.||+.+.
T Consensus        89 V~~s~~~~   96 (99)
T d1x4fa1          89 VDLSEKYK   96 (99)
T ss_dssp             EEEECSCS
T ss_pred             EEEcCCcc
Confidence            99997654

>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=99.45  E-value=1.8e-15  Score=131.82  Aligned_cols=77  Identities=16%  Similarity=0.418  Sum_probs=68.3

Q ss_pred             cEEEEecCCCCCcHHHHHHHhhcCCCEEEEEE-----EecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEE
Q 040243          492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKV-----IKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVR  566 (797)
Q Consensus       492 ~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v-----~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~  566 (797)
                      ++|||+||+++++|++|+++|++||.|..+.+     +.+..++++||||||+|.+.++|++|++ |||+.|+|+.|+|+
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            58999999999999999999999998766544     3456788999999999999999999995 99999999999997


Q ss_pred             ecC
Q 040243          567 VAG  569 (797)
Q Consensus       567 ~A~  569 (797)
                      .++
T Consensus        81 r~k   83 (90)
T d1u2fa_          81 RPH   83 (90)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            544

>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=99.44  E-value=1.2e-13  Score=120.33  Aligned_cols=79  Identities=16%  Similarity=0.129  Sum_probs=70.1

Q ss_pred             CCCCcEEEEecCCCC-CcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhc--CceeeccceEE
Q 040243          488 ELDDTNLYIGYLPPT-LDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM--NGYRLEGRTIA  564 (797)
Q Consensus       488 ~~~~~tLfVgNLp~~-vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~L--nG~~l~Gr~L~  564 (797)
                      ....++|||+||+.. +|+++|.++|+.||.|.+|.++.++      +||||+|++.++|+.|++.|  ++..+.|++|+
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 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI------NEAFIEMATTEDAQAAVDYYTTTPALVFGKPVR   78 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS------SCEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccc------eEEEEEEcchhhHHHHHHHHhhCCCccCCceEE
Confidence            346678999999986 8899999999999999999998764      69999999999999999966  67789999999


Q ss_pred             EEecCCCC
Q 040243          565 VRVAGKPP  572 (797)
Q Consensus       565 V~~A~~~~  572 (797)
                      |+||+...
T Consensus        79 V~~s~~~~   86 (89)
T d1x4da1          79 VHLSQKYK   86 (89)
T ss_dssp             EEEECCCT
T ss_pred             EEECCCcc
Confidence            99997543

>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=99.38  E-value=2.8e-14  Score=128.14  Aligned_cols=76  Identities=13%  Similarity=0.226  Sum_probs=71.9

Q ss_pred             cEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEec
Q 040243          492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA  568 (797)
Q Consensus       492 ~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A  568 (797)
                      +.++|.++...++|++|+++|++||.|.+|+|+++. +|++||||||+|.+.++|.+||+.|||+.|+||.|+|+|+
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~-~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCC-CCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            468899999999999999999999999999998875 8999999999999999999999999999999999999985

>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=99.26  E-value=7.2e-12  Score=121.16  Aligned_cols=80  Identities=28%  Similarity=0.478  Sum_probs=72.1

Q ss_pred             CcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecCC
Q 040243          491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGK  570 (797)
Q Consensus       491 ~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~~  570 (797)
                      .++|||+||++++|+++|+++|++||.|.++.++++..++.++|||||+|.+.++|++|+.. ++..++++.+.+.+...
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~-~~~~~~~~~~~~~~~~~   84 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVS   84 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHh-cCCcccccchhhhhhhh
Confidence            37999999999999999999999999999999999999999999999999999999999975 56668888888876544


Q ss_pred             C
Q 040243          571 P  571 (797)
Q Consensus       571 ~  571 (797)
                      .
T Consensus        85 ~   85 (183)
T d1u1qa_          85 R   85 (183)
T ss_dssp             T
T ss_pred             c
Confidence            3

>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=99.22  E-value=6.1e-12  Score=114.08  Aligned_cols=73  Identities=19%  Similarity=0.170  Sum_probs=64.5

Q ss_pred             CcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCH-HHHHHHHHhcCceeeccceEEEEecC
Q 040243          491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADI-QMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       491 ~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~-e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      ...+|||||++.+|+++|+++|++||.|.+|.|+++      +|||||.|.+. ++|..|+..|++..|.++.+.|.|+.
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            346699999999999999999999999999999865      58999999985 78999999999999888887777754

>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=99.21  E-value=8.6e-12  Score=111.01  Aligned_cols=64  Identities=17%  Similarity=0.327  Sum_probs=57.6

Q ss_pred             CCCcEEEEec--CCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceee
Q 040243          489 LDDTNLYIGY--LPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRL  558 (797)
Q Consensus       489 ~~~~tLfVgN--Lp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l  558 (797)
                      ....+|||.|  |+.++|+++|+++|++||.|.+|++..+      ||||||+|.+.++|++|++.|||+.|
T Consensus        16 ~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            3456888955  9999999999999999999999988765      47999999999999999999999886

>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=99.16  E-value=3.1e-11  Score=106.92  Aligned_cols=81  Identities=20%  Similarity=0.280  Sum_probs=68.5

Q ss_pred             CCCCCcEEEEecC--CCCC---------cHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCc
Q 040243          487 KELDDTNLYIGYL--PPTL---------DDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNG  555 (797)
Q Consensus       487 ~~~~~~tLfVgNL--p~~v---------te~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG  555 (797)
                      +....++|+|.||  +..+         .++||++.|++||.|..|++..+    ..+||+||+|.+.++|.+|+..|||
T Consensus         4 ~~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~lng   79 (99)
T d2dita1           4 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDG   79 (99)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHSTT
T ss_pred             CCCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhCC
Confidence            3456789999999  4332         13689999999999999988665    3679999999999999999999999


Q ss_pred             eeeccceEEEEecCCC
Q 040243          556 YRLEGRTIAVRVAGKP  571 (797)
Q Consensus       556 ~~l~Gr~L~V~~A~~~  571 (797)
                      ..|+||.|+|+++..+
T Consensus        80 ~~~~gr~i~v~~~~g~   95 (99)
T d2dita1          80 RWFGGRQITAQAWDGT   95 (99)
T ss_dssp             CEETTEECEEEECCSC
T ss_pred             cEECCEEEEEEEeCCc
Confidence            9999999999997543

>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=99.11  E-value=4.3e-11  Score=102.33  Aligned_cols=73  Identities=19%  Similarity=0.244  Sum_probs=62.0

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccce-EEEEec
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRT-IAVRVA  568 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~-L~V~~A  568 (797)
                      +.+.|+|++|+++++++.| ++|++||.|.++++.      +.+|||||+|.+.++|++||+ |||..|+|+. |.|+.+
T Consensus         3 ~~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~------~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~   74 (81)
T d1wwha1           3 DDTWVTVFGFPQASASYIL-LQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPC   74 (81)
T ss_dssp             GGGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEEC------SSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEEC
T ss_pred             cccEEEEECCChHHHHHHH-HHHHhhhhhheEEec------CCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeC
Confidence            4678999999999987656 579999999999864      346899999999999999995 8999999985 568766


Q ss_pred             CC
Q 040243          569 GK  570 (797)
Q Consensus       569 ~~  570 (797)
                      ..
T Consensus        75 ~~   76 (81)
T d1wwha1          75 ID   76 (81)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=98.98  E-value=2e-10  Score=102.38  Aligned_cols=79  Identities=14%  Similarity=0.209  Sum_probs=67.3

Q ss_pred             CcEEEEecC--CCCC--------cHHHHHHHhhcCCCEEEEEEEecCCCC--cccceEEEEecCHHHHHHHHHhcCceee
Q 040243          491 DTNLYIGYL--PPTL--------DDDGLIRLFSTFGDIVMAKVIKDRVTG--MSKGYGFVKYADIQMANNAIASMNGYRL  558 (797)
Q Consensus       491 ~~tLfVgNL--p~~v--------te~dL~~~Fs~fG~I~~v~v~~dk~TG--ksrGfaFV~F~s~e~A~~AI~~LnG~~l  558 (797)
                      .+.|.|.||  +..+        ..+||++.|++||.|.+|+|.++..+.  ..+|++||+|.+.++|.+|+..|+|..+
T Consensus         4 s~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~f   83 (104)
T d1o0pa_           4 TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKF   83 (104)
T ss_dssp             CSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCCS
T ss_pred             CcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCEE
Confidence            457999999  3333        235789999999999999998876553  3569999999999999999999999999


Q ss_pred             ccceEEEEecC
Q 040243          559 EGRTIAVRVAG  569 (797)
Q Consensus       559 ~Gr~L~V~~A~  569 (797)
                      +||.|+|.++.
T Consensus        84 ~gR~v~v~f~~   94 (104)
T d1o0pa_          84 ANRVVVTKYCD   94 (104)
T ss_dssp             SSSCCEEEEEC
T ss_pred             CCeEEEEEEcC
Confidence            99999999875

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Fragile X mental retardation syndrome related protein 1, FXR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.97  E-value=1.2e-10  Score=98.92  Aligned_cols=70  Identities=13%  Similarity=0.285  Sum_probs=60.3

Q ss_pred             CceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCH
Q 040243          249 PKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQ  328 (797)
Q Consensus       249 ~~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~  328 (797)
                      ..+++.|-||.      ++||+|||++|+|||+|+++|||+|.|...-                     .-.|.|+|.+.
T Consensus         6 ~~~t~~i~Ip~------~~ig~vIG~gG~~I~~I~~~tGa~i~i~~~~---------------------~g~v~I~g~~~   58 (78)
T d2cpqa1           6 AAFHEEFVVRE------DLMGLAIGTHGSNIQQARKVPGVTAIELDED---------------------TGTFRIYGESA   58 (78)
T ss_dssp             CSEEEEEECCH------HHHHHHHTTTTHHHHHHHTSTTEEEEEEETT---------------------TTEEEEEESSH
T ss_pred             CCceEEEEECH------HHHHHHcCCChHHHHHHHHhcCcEEEEecCC---------------------CceEEEEECCH
Confidence            35788999998      9999999999999999999999999986321                     11799999999


Q ss_pred             HHHHHHHHHHHHhcCCC
Q 040243          329 ESLEGAAAMVEKLLQPV  345 (797)
Q Consensus       329 e~v~~A~~~I~~ll~~~  345 (797)
                      +++++|.++|+.+...+
T Consensus        59 eav~~A~~~Ie~~~~~~   75 (78)
T d2cpqa1          59 DAVKKARGFLEFVEDFI   75 (78)
T ss_dssp             HHHHHHHHHHSCCCCCC
T ss_pred             HHHHHHHHHHHHhheee
Confidence            99999999999877653

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Neuro-oncological ventral antigen 2, nova-2, KH3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.94  E-value=6.8e-10  Score=92.97  Aligned_cols=73  Identities=25%  Similarity=0.416  Sum_probs=58.5

Q ss_pred             ceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHH
Q 040243          250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQE  329 (797)
Q Consensus       250 ~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e  329 (797)
                      +...+|.||.      +++|.|||.+|+|+|+|+++|||+|.|...+....+              ..+-.|.|+| +.+
T Consensus         2 k~~i~i~VP~------~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~--------------~~~r~v~I~G-~~~   60 (74)
T d1dtja_           2 KELVEMAVPE------NLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPG--------------TRNRRVTITG-SPA   60 (74)
T ss_dssp             CEEEEEEEET------TTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTT--------------CCEEEEEEEE-SHH
T ss_pred             cEEEEEEeCH------HHcceeECCCChhHHHHHHHcCCEEEEccCCCCCCC--------------CCceEEEEEe-CHH
Confidence            4456889998      899999999999999999999999999865421111              1123688999 589


Q ss_pred             HHHHHHHHHHHhcC
Q 040243          330 SLEGAAAMVEKLLQ  343 (797)
Q Consensus       330 ~v~~A~~~I~~ll~  343 (797)
                      ++++|.++|+++|.
T Consensus        61 ~v~~A~~~I~~~is   74 (74)
T d1dtja_          61 ATQAAQYLISQRVT   74 (74)
T ss_dssp             HHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHHcC
Confidence            99999999998873

>d1we8a_ d.51.1.1 (A:) Tudor and KH domain containing protein, Tdrkh {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Tudor and KH domain containing protein, Tdrkh
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.90  E-value=7e-10  Score=98.96  Aligned_cols=73  Identities=21%  Similarity=0.293  Sum_probs=59.4

Q ss_pred             ceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHH
Q 040243          250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQE  329 (797)
Q Consensus       250 ~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e  329 (797)
                      .++++|+||.      +++|+|||.+|.|||+|+++|||+|.|.-.+....               ..+=.|.|+| +.+
T Consensus        14 ~v~~~i~IP~------~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~~~~---------------~~~r~v~I~G-~~~   71 (104)
T d1we8a_          14 PVFEQLSVPQ------RSVGRIIGRGGETIRSICKASGAKITCDKESEGTL---------------LLSRLIKISG-TQK   71 (104)
T ss_dssp             EEEEEEEEET------TTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSS---------------SSEEEEEEEE-EHH
T ss_pred             CEEEEEEECH------HHhcceECCCCcchHHHHHHcCCEEEECCCCCCCC---------------CCccEEEEEe-CHH
Confidence            4668899998      89999999999999999999999999965431110               1112688999 788


Q ss_pred             HHHHHHHHHHHhcCC
Q 040243          330 SLEGAAAMVEKLLQP  344 (797)
Q Consensus       330 ~v~~A~~~I~~ll~~  344 (797)
                      .|++|+++|+++|..
T Consensus        72 ~v~~A~~~I~~~i~e   86 (104)
T d1we8a_          72 EVAAAKHLILEKVSE   86 (104)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhC
Confidence            999999999999964

>d1j4wa2 d.51.1.1 (A:104-174) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.89  E-value=1e-09  Score=91.10  Aligned_cols=70  Identities=21%  Similarity=0.392  Sum_probs=55.1

Q ss_pred             EEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHHHH
Q 040243          252 QKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESL  331 (797)
Q Consensus       252 ~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v  331 (797)
                      +..+.||.      +++|+|||.+|+|+|+|+++|||+|.|........              ...+=.|.|+| +.+++
T Consensus         2 ~~~~~IP~------~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~--------------~~~~r~v~I~G-~~~~v   60 (71)
T d1j4wa2           2 EFNFIVPT------GKTGLIIGKGGETIKSISQQSGARIELQRNPPPNA--------------DPNMKLFTIRG-TPQQI   60 (71)
T ss_dssp             EEEEEEET------TTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTTS--------------CTTEEEEEEEC-CHHHH
T ss_pred             EEEEEECh------HhcceEECCCCcChHHHHhhcCcEEEEeecCCCCC--------------CCCeEEEEEEe-CHHHH
Confidence            35678997      89999999999999999999999999964331111              11122578999 58999


Q ss_pred             HHHHHHHHHhc
Q 040243          332 EGAAAMVEKLL  342 (797)
Q Consensus       332 ~~A~~~I~~ll  342 (797)
                      ++|.++|+++|
T Consensus        61 ~~A~~~I~e~i   71 (71)
T d1j4wa2          61 DYARQLIEEKI   71 (71)
T ss_dssp             HHHHHHHHHHC
T ss_pred             HHHHHHHHhhC
Confidence            99999999875

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.88  E-value=7.9e-10  Score=94.19  Aligned_cols=75  Identities=25%  Similarity=0.460  Sum_probs=61.0

Q ss_pred             CCceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecC
Q 040243          248 PPKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAET  327 (797)
Q Consensus       248 p~~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~  327 (797)
                      +-..+++|.||.      +++|.|||++|+|+|+|+++|||+|.|.-.....               .+.+=+|.|+|. 
T Consensus         5 ~~~~~~~i~Vp~------~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~~---------------~~~~r~v~I~G~-   62 (81)
T d1x4ma1           5 PGNAVQEIMIPA------SKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQN---------------TGADKPLRITGD-   62 (81)
T ss_dssp             CCCEEEEEEECH------HHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCS---------------SCSCEEEEEEEC-
T ss_pred             CccEEEEEEECH------HHcCeeECCCCchHHHHHHHhCCeEEEccCCCCC---------------CCCceEEEEEeC-
Confidence            557889999998      8999999999999999999999999997332110               112237899995 


Q ss_pred             HHHHHHHHHHHHHhcCC
Q 040243          328 QESLEGAAAMVEKLLQP  344 (797)
Q Consensus       328 ~e~v~~A~~~I~~ll~~  344 (797)
                      .++|++|.++|+.+|..
T Consensus        63 ~~~v~~A~~~I~~~i~e   79 (81)
T d1x4ma1          63 PYKVQQAKEMVLELIRD   79 (81)
T ss_dssp             TTTHHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHHHHHHh
Confidence            68999999999999863

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: HnRNP K, KH3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.87  E-value=1.7e-09  Score=90.57  Aligned_cols=70  Identities=26%  Similarity=0.439  Sum_probs=57.7

Q ss_pred             ceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHH
Q 040243          250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQE  329 (797)
Q Consensus       250 ~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e  329 (797)
                      .++.+|.||.      +++|.|||.+|+|+|+|+++|||+|.|.....                 ...+-.|.|+| +.+
T Consensus         3 ~~t~~i~VP~------~~vg~iIG~~G~~I~~I~~~sga~I~i~~~~~-----------------~~~~r~i~I~G-~~~   58 (75)
T d1zzka1           3 IITTQVTIPK------DLAGSIIGKGGQRIKQIRHESGASIKIDEPLE-----------------GSEDRIITITG-TQD   58 (75)
T ss_dssp             CEEEEEEEET------TTGGGGTCGGGHHHHHHHHHHCCEEEECCTTS-----------------CSSEEEEEEEE-CHH
T ss_pred             cEEEEEEECh------HhcCeeECCCCchHHHHHhhcCCeEEEccCCC-----------------CCCceEEEEEe-CHH
Confidence            5678999998      89999999999999999999999999963220                 11122578888 589


Q ss_pred             HHHHHHHHHHHhcC
Q 040243          330 SLEGAAAMVEKLLQ  343 (797)
Q Consensus       330 ~v~~A~~~I~~ll~  343 (797)
                      .+++|.++|+.+|.
T Consensus        59 ~v~~A~~~I~~~i~   72 (75)
T d1zzka1          59 QIQNAQYLLQNSVK   72 (75)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH
Confidence            99999999999875

>d2z0sa2 d.51.1.1 (A:148-234) Exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.83  E-value=1.4e-09  Score=93.71  Aligned_cols=62  Identities=18%  Similarity=0.233  Sum_probs=56.4

Q ss_pred             EEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHHHHHHH
Q 040243          255 LYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGA  334 (797)
Q Consensus       255 i~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v~~A  334 (797)
                      |-||.      +.||+|||++|+++|+|+++|||+|.|-..|                       .|.|.|.+.+.+++|
T Consensus         5 i~I~~------~ki~~vIG~gG~~ik~i~~~t~~~I~I~d~G-----------------------~V~I~g~~~~~~~~A   55 (87)
T d2z0sa2           5 VEISP------AKVPRVIGRKMSMLKTLEEKTECKIFVARNG-----------------------RIHLECPNEDLEAIA   55 (87)
T ss_dssp             EECCG------GGSGGGTCGGGHHHHHHHHHHCCEEEEETTT-----------------------EEEEECSCHHHHHHH
T ss_pred             EEECh------hhcceeECCCCcHHHHHHHHHCCEEEECCCc-----------------------EEEEEeCCHHHHHHH
Confidence            45887      9999999999999999999999999997655                       799999999999999


Q ss_pred             HHHHHHhcCCC
Q 040243          335 AAMVEKLLQPV  345 (797)
Q Consensus       335 ~~~I~~ll~~~  345 (797)
                      +++|+.|....
T Consensus        56 ~~~I~~I~~ea   66 (87)
T d2z0sa2          56 VMAIKIIDEEA   66 (87)
T ss_dssp             HHHHHHHHHCS
T ss_pred             HHHHHHHHHhc
Confidence            99999997654

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.83  E-value=9.2e-10  Score=92.06  Aligned_cols=70  Identities=19%  Similarity=0.382  Sum_probs=57.5

Q ss_pred             eEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHHH
Q 040243          251 LQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQES  330 (797)
Q Consensus       251 ~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~  330 (797)
                      ...+|.||.      +++|+|||.+|+|+|+|+++|||+|.|....+.                 ..+--|.|+|+ .++
T Consensus         3 ~~~~i~VP~------~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~~-----------------~~~r~v~I~G~-~~~   58 (74)
T d1j4wa1           3 HMIDVPIPR------FAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGT-----------------TPERIAQITGP-PDR   58 (74)
T ss_dssp             EEEEEEEEH------HHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTS-----------------CSEEEEEEEEC-HHH
T ss_pred             eEEEEEeCH------HHCCeeECCCCcHHHHHHHHcCCEEEeccCCCC-----------------CCeeEEEEEeC-HHH
Confidence            456888998      999999999999999999999999999854311                 11225788885 789


Q ss_pred             HHHHHHHHHHhcCC
Q 040243          331 LEGAAAMVEKLLQP  344 (797)
Q Consensus       331 v~~A~~~I~~ll~~  344 (797)
                      +++|.++|+.+|..
T Consensus        59 v~~A~~~I~~~i~~   72 (74)
T d1j4wa1          59 AQHAAEIITDLLRS   72 (74)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHh
Confidence            99999999999864

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.79  E-value=2.5e-09  Score=90.45  Aligned_cols=71  Identities=23%  Similarity=0.482  Sum_probs=59.1

Q ss_pred             CceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCH
Q 040243          249 PKLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQ  328 (797)
Q Consensus       249 ~~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~  328 (797)
                      ..++.+|.||.      +++|.|||.+|.|||+|+++|||+|.|.....                 ...+-.|.|+| +.
T Consensus         6 ~~~t~~i~IP~------~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~~~-----------------~~~~r~v~I~G-~~   61 (79)
T d1x4na1           6 SVMTEEYKVPD------GMVGFIIGRGGEQISRIQQESGCKIQIAPDSG-----------------GLPERSCMLTG-TP   61 (79)
T ss_dssp             CCEEEEEEEEH------HHHHHHHCSSSHHHHHHHHHSCCEEEECSCCT-----------------TCSEEEEEEEE-CH
T ss_pred             CcEEEEEEECh------HhhcceECCCchhHHHHHHHhCCEEEEcCCCC-----------------CCCceEEEEEe-CH
Confidence            46789999999      99999999999999999999999999963210                 11122688999 58


Q ss_pred             HHHHHHHHHHHHhcC
Q 040243          329 ESLEGAAAMVEKLLQ  343 (797)
Q Consensus       329 e~v~~A~~~I~~ll~  343 (797)
                      +.|++|.++|..+|.
T Consensus        62 ~~v~~A~~~I~~~i~   76 (79)
T d1x4na1          62 ESVQSAKRLLDQIVE   76 (79)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH
Confidence            999999999999885

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.76  E-value=5.4e-09  Score=86.48  Aligned_cols=69  Identities=26%  Similarity=0.390  Sum_probs=56.2

Q ss_pred             eEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHHH
Q 040243          251 LQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQES  330 (797)
Q Consensus       251 ~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~  330 (797)
                      .+.+|.||.      +++|.|||.+|+++|+|+++|||+|.|.....                + ..+--|.|+|. .+.
T Consensus         2 ~T~~i~VP~------~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~----------------~-~~~r~v~I~G~-~~~   57 (70)
T d1wvna1           2 TTHELTIPN------NLIGCIIGRQGANINEIRQMSGAQIKIANPVE----------------G-SSGRQVTITGS-AAS   57 (70)
T ss_dssp             EEEEEEEEG------GGHHHHHCGGGHHHHHHHHHHCCEEEECCCCT----------------T-CSEEEEEEEEC-HHH
T ss_pred             eEEEEEECh------HhcceeECCCChHHHHHHHHcCcEEEEcCCCC----------------C-CCcEEEEEEeC-HHH
Confidence            577899998      99999999999999999999999999964210                0 11124788885 899


Q ss_pred             HHHHHHHHHHhcC
Q 040243          331 LEGAAAMVEKLLQ  343 (797)
Q Consensus       331 v~~A~~~I~~ll~  343 (797)
                      +++|..+|+..|.
T Consensus        58 v~~A~~~I~~~is   70 (70)
T d1wvna1          58 ISLAQYLINARLS   70 (70)
T ss_dssp             HHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHcC
Confidence            9999999998763

>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=98.76  E-value=2.3e-10  Score=94.86  Aligned_cols=62  Identities=15%  Similarity=0.193  Sum_probs=47.0

Q ss_pred             EEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHHHHHHH
Q 040243          255 LYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGA  334 (797)
Q Consensus       255 i~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v~~A  334 (797)
                      |.||.      ++||+|||++|.|+|+||++|||+|.|-..|                       .|.|+|.+.+.+++|
T Consensus         5 i~Ip~------~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~g-----------------------~v~I~g~~~~~v~~A   55 (69)
T d2je6i3           5 IDIMP------VKVPRVIGKNKSMYETLTSKSGCSIFVANNG-----------------------RIWATCPSRFSEEIL   55 (69)
T ss_dssp             EECCG------GGHHHHHCGGGHHHHHHHTTC---CEECTTS-----------------------EEEC-----CTTCCT
T ss_pred             EEECh------hhccceECCchhHHHHHHHHHCCEEEEcCCC-----------------------EEEEEeCCHHHHHHH
Confidence            55787      9999999999999999999999999995333                       689999999999999


Q ss_pred             HHHHHHhcCCC
Q 040243          335 AAMVEKLLQPV  345 (797)
Q Consensus       335 ~~~I~~ll~~~  345 (797)
                      .++|+.|+...
T Consensus        56 ~~~I~~i~~ea   66 (69)
T d2je6i3          56 IEAIRKIENES   66 (69)
T ss_dssp             HHHHTTTTTTT
T ss_pred             HHHHHHHHHhh
Confidence            99999888754

>d2ba0a3 d.51.1.1 (A:136-219) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=98.73  E-value=5e-09  Score=89.88  Aligned_cols=63  Identities=19%  Similarity=0.262  Sum_probs=54.4

Q ss_pred             EEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHHHHH
Q 040243          253 KKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLE  332 (797)
Q Consensus       253 ~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v~  332 (797)
                      +-|.||.      ++||+|||++|+|+|+|+++|||+|.|-..|                       .|.|+| +.++++
T Consensus         3 ~vi~Ip~------~~ig~IIG~gG~~I~~I~~~tg~~I~i~~~g-----------------------~v~I~G-~~e~v~   52 (84)
T d2ba0a3           3 RIVAINP------ARVPRVIGKKGSMIKLLKSELDVQIVVGQNG-----------------------LIWVNG-DRRKVS   52 (84)
T ss_dssp             EEEECCG------GGHHHHHCGGGHHHHHHHHHHTCEEEECTTS-----------------------EEEEES-CHHHHH
T ss_pred             EEEEECh------hhcceeeCCcHHHHHHHHHHHCCEEEECCCC-----------------------EEEEEe-CHHHHH
Confidence            3466887      9999999999999999999999999995332                       689999 568999


Q ss_pred             HHHHHHHHhcCCC
Q 040243          333 GAAAMVEKLLQPV  345 (797)
Q Consensus       333 ~A~~~I~~ll~~~  345 (797)
                      +|.++|+.++...
T Consensus        53 ~A~~~I~~i~~ea   65 (84)
T d2ba0a3          53 IAEEAIYLIEQEA   65 (84)
T ss_dssp             HHHHHHHHHHHCS
T ss_pred             HHHHHHHHHHHhc
Confidence            9999999998753

>d1tuaa2 d.51.1.1 (A:85-188) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.71  E-value=6.6e-09  Score=92.37  Aligned_cols=55  Identities=24%  Similarity=0.248  Sum_probs=48.1

Q ss_pred             eeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHhcCCChH
Q 040243          268 IGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQPVDE  347 (797)
Q Consensus       268 iG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v~~A~~~I~~ll~~~~e  347 (797)
                      +|+|||++|.|+|.||++|||+|.|.++                        +|.|.+ +.+.++.|.++|+.|+...+.
T Consensus        24 ~GrIIG~gGktik~Ie~~Tg~~I~I~d~------------------------~v~iig-~~e~i~~A~~~Ie~li~~~e~   78 (104)
T d1tuaa2          24 KGRIIGEGGRARRTIEEMTDTYINVGEY------------------------EVAIIG-DYERAMAAKQAIEMLAEGRMH   78 (104)
T ss_dssp             HHHHHCGGGHHHHHHHHHHTCEEEECSS------------------------EEEEEE-EHHHHHHHHHHHHHHHTTCCH
T ss_pred             hcceeCCCcHHHHHHHHHHCCeEEEeCC------------------------eEEEEE-CchhHHHHHHHHHHHHcCCCc
Confidence            6899999999999999999999999754                        466667 678999999999999987553

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.61  E-value=1.5e-08  Score=84.00  Aligned_cols=68  Identities=28%  Similarity=0.398  Sum_probs=57.3

Q ss_pred             ceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHH
Q 040243          250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQE  329 (797)
Q Consensus       250 ~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e  329 (797)
                      .++.+|.||.      +++|.|||.+|+|+|+|+++|||+|.|-..++                  .| =-|.|+| +.+
T Consensus         3 ~vt~~i~vp~------~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~------------------~e-r~v~I~G-~~~   56 (71)
T d2axya1           3 TLTIRLLMHG------KEVGSIIGKKGESVKKMREESGARINISEGNC------------------PE-RIITLAG-PTN   56 (71)
T ss_dssp             CEEEEEEEEH------HHHHHHHCGGGHHHHHHHHHHCCEEEECSSCC------------------SE-EEEEEEE-CHH
T ss_pred             cEEEEEEECH------HHcCeEECCCChhHHHHHHHhCCEEEEcCCCC------------------Cc-ceEEEEE-CHH
Confidence            4678999998      99999999999999999999999999964331                  11 1577888 689


Q ss_pred             HHHHHHHHHHHhcC
Q 040243          330 SLEGAAAMVEKLLQ  343 (797)
Q Consensus       330 ~v~~A~~~I~~ll~  343 (797)
                      .+.+|..+|..+|.
T Consensus        57 ~v~~A~~~I~~~l~   70 (71)
T d2axya1          57 AIFKAFAMIIDKLE   70 (71)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhc
Confidence            99999999998875

>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.57  E-value=2.3e-08  Score=84.89  Aligned_cols=69  Identities=20%  Similarity=0.255  Sum_probs=56.8

Q ss_pred             ceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHH
Q 040243          250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQE  329 (797)
Q Consensus       250 ~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e  329 (797)
                      .+++.|.||.      +|+|.|||++|.|+|+|+++|||+|.|-..++.                 ++ -.|.|+| +.+
T Consensus         9 ~~t~~i~Vp~------~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~~-----------------~~-~~v~I~G-~~~   63 (81)
T d2ctma1           9 MVSEDVPLDH------RVHARIIGARGKAIRKIMDEFKVDIRFPQSGAP-----------------DP-NCVTVTG-LPE   63 (81)
T ss_dssp             CCCEEEECCT------TTHHHHHCSSSCHHHHHHHHHTCEEECCCTTCS-----------------CT-TEEEEES-CHH
T ss_pred             CEEEEEEECH------HHHhhccCCCCccHHHHHHHhCCEEEeCCccCC-----------------CC-CEEEEeC-CHH
Confidence            4567899998      899999999999999999999999999643310                 11 1688998 578


Q ss_pred             HHHHHHHHHHHhcC
Q 040243          330 SLEGAAAMVEKLLQ  343 (797)
Q Consensus       330 ~v~~A~~~I~~ll~  343 (797)
                      .|++|.++|+.|+.
T Consensus        64 ~V~~A~~~I~~i~~   77 (81)
T d2ctma1          64 NVEEAIDHILNLEE   77 (81)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH
Confidence            89999999998875

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.57  E-value=1e-08  Score=87.86  Aligned_cols=61  Identities=30%  Similarity=0.467  Sum_probs=47.4

Q ss_pred             EEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecC----HHH
Q 040243          255 LYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAET----QES  330 (797)
Q Consensus       255 i~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~----~e~  330 (797)
                      |.||.      +.||+|||++|+|+|+||++|||+|.|....                      -.|.|.+.+    ..+
T Consensus         7 i~ip~------~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~d~----------------------g~v~i~~~~~~~~~~a   58 (84)
T d1tuaa1           7 VKVKP------ERLGAVIGPRGEVKAEIMRRTGTVITVDTEN----------------------SMVIVEPEAEGIPPVN   58 (84)
T ss_dssp             EECCG------GGHHHHHCGGGHHHHHHHHHHTEEEEEETTT----------------------TEEEEEESSTTSCHHH
T ss_pred             EEeCH------HHcCeeecCCchhHHHHHHHHCCEEEEEcCC----------------------CeEEEecCCccccHHH
Confidence            45887      9999999999999999999999999996432                      156666654    456


Q ss_pred             HHHHHHHHHHhcC
Q 040243          331 LEGAAAMVEKLLQ  343 (797)
Q Consensus       331 v~~A~~~I~~ll~  343 (797)
                      +++|.++|+.|..
T Consensus        59 ~~~a~~iI~aI~r   71 (84)
T d1tuaa1          59 LMKAAEVVKAISL   71 (84)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhC
Confidence            6777777776653

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.56  E-value=2.5e-08  Score=86.53  Aligned_cols=70  Identities=14%  Similarity=0.245  Sum_probs=58.7

Q ss_pred             ceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHH
Q 040243          250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQE  329 (797)
Q Consensus       250 ~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e  329 (797)
                      .++..|.||.      +|+|.|||.+|.+||+|+++|||+|.|-..++                  + .-.|.|+|+ .+
T Consensus         9 ~vt~~i~Vp~------~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~------------------~-~~~v~I~G~-~~   62 (91)
T d2ctka1           9 PVTIEVEVPF------DLHRYVIGQKGSGIRKMMDEFEVNIHVPAPEL------------------Q-SDIIAITGL-AA   62 (91)
T ss_dssp             CEEEEEECCH------HHHHHHHCSSSHHHHHHHHHTCCEEECCCTTT------------------T-CCEEEEEEC-HH
T ss_pred             CEEEEEEECH------HHHhHhcCCCchhHHHHHHHhCCEEEECCCCC------------------C-cceEEEECC-HH
Confidence            4678888998      89999999999999999999999999954331                  1 116889985 78


Q ss_pred             HHHHHHHHHHHhcCCC
Q 040243          330 SLEGAAAMVEKLLQPV  345 (797)
Q Consensus       330 ~v~~A~~~I~~ll~~~  345 (797)
                      .|++|.++|..++...
T Consensus        63 ~V~~A~~~I~~~v~e~   78 (91)
T d2ctka1          63 NLDRAKAGLLERVKEL   78 (91)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            9999999999999753

>d1e3ha4 d.52.3.1 (A:579-632) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6 {Streptomyces antibioticus [TaxId: 1890]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6
species: Streptomyces antibioticus [TaxId: 1890]

Probab=98.55  E-value=2.4e-09  Score=84.25  Aligned_cols=38  Identities=34%  Similarity=0.705  Sum_probs=10.0

Q ss_pred             EEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEecccc
Q 040243          254 KLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGS  297 (797)
Q Consensus       254 Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS  297 (797)
                      +|.||.      ++||.||||+|+|+|.|+++|||+|.|...|.
T Consensus         6 ~i~Ip~------~kig~vIG~GG~~Ik~I~~~tga~I~i~ddg~   43 (54)
T d1e3ha4           6 TVKIPV------DKIGEVIGPKRQMINQIQEDTGAEITIEDDGT   43 (54)
T ss_dssp             ---------------------------CHHHHSCCCC-------
T ss_pred             EEEeCH------HHeeEEECCccHHHHHHHHHHCCEEEEeCCeE
Confidence            345888      89999999999999999999999999987763

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.49  E-value=5.2e-08  Score=83.15  Aligned_cols=73  Identities=14%  Similarity=0.272  Sum_probs=58.0

Q ss_pred             ceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHH
Q 040243          250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQE  329 (797)
Q Consensus       250 ~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e  329 (797)
                      .++..|.||.      .|+|.|||.+|.|+|+|+++|||+|.|-..++.               +.++. -|.|+|. .+
T Consensus         9 ~~~~~i~Vp~------~~~~~iIG~~G~~i~~I~~~t~~~I~~~~~~~~---------------~~~~~-~i~I~G~-~e   65 (84)
T d2ctla1           9 SFKLSVTVDP------KYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDG---------------NQPQD-QITITGY-EK   65 (84)
T ss_dssp             TCEEEEECCT------TTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTC---------------SSCSS-EEEEESC-HH
T ss_pred             cEEEEEEECH------HHHhhhcCCCchhHHHHHHHhCCEEEECCCCCC---------------CCCcc-eEEEECC-HH
Confidence            3566788998      889999999999999999999999999544321               11122 4788887 88


Q ss_pred             HHHHHHHHHHHhcCCC
Q 040243          330 SLEGAAAMVEKLLQPV  345 (797)
Q Consensus       330 ~v~~A~~~I~~ll~~~  345 (797)
                      .|++|..+|..++..+
T Consensus        66 ~v~~A~~~I~~~i~e~   81 (84)
T d2ctla1          66 NTEAARDAILRIVGEL   81 (84)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhH
Confidence            9999999999998643

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.42  E-value=1.5e-07  Score=77.87  Aligned_cols=66  Identities=15%  Similarity=0.204  Sum_probs=54.3

Q ss_pred             eEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHHH
Q 040243          251 LQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQES  330 (797)
Q Consensus       251 ~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~  330 (797)
                      ....|-||.      .|+|+|||.+|.|+|+|+++|||+|.|-..++.                  + =.|.|+|. .+.
T Consensus         5 ~~~ei~V~~------~~~~~iIG~~G~~i~~I~~~tg~~I~i~~~~~~------------------~-~~v~I~G~-~~~   58 (71)
T d1viga_           5 DYVEINIDH------KFHRHLIGKSGANINRIKDQYKVSVRIPPDSEK------------------S-NLIRIEGD-PQG   58 (71)
T ss_dssp             EEEEEEECS------SHHHHHTCSSCCHHHHHHHHTCCEEECCCCCSS------------------S-EEEEEEES-SHH
T ss_pred             EEEEEEECH------HHhcccCCCCCchHHHHHHHhCCEEEeCCCCCC------------------C-CEEEEECC-HHH
Confidence            455777887      899999999999999999999999999644310                  1 15889985 789


Q ss_pred             HHHHHHHHHHhc
Q 040243          331 LEGAAAMVEKLL  342 (797)
Q Consensus       331 v~~A~~~I~~ll  342 (797)
                      |++|.++|++|.
T Consensus        59 v~~A~~~I~~i~   70 (71)
T d1viga_          59 VQQAKRELLELA   70 (71)
T ss_dssp             HHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHh
Confidence            999999999875

>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.38  E-value=9.1e-08  Score=81.12  Aligned_cols=69  Identities=22%  Similarity=0.311  Sum_probs=56.6

Q ss_pred             ceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHH
Q 040243          250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQE  329 (797)
Q Consensus       250 ~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e  329 (797)
                      ..+..|.||.      .|+|+|||.+|.++++|+++|||+|.|-..++.                  ++ -|.|+| +.+
T Consensus         9 ~~t~~i~Ip~------~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~~------------------~~-~v~I~G-~~~   62 (81)
T d2ctea1           9 QASATVAIPK------EHHRFVIGKNGEKLQDLELKTATKIQIPRPDDP------------------SN-QIKITG-TKE   62 (81)
T ss_dssp             CEEEEEECCT------TTHHHHHCSSSCHHHHHHHHTTCCCBCCCTTSS------------------CC-EEEEEE-CHH
T ss_pred             ceEEEEEECH------HHHhhccCCCChhHHHHHHHhCCEEEECCCCCC------------------CC-EEEEEe-CHH
Confidence            4678899998      889999999999999999999999999644421                  11 367777 567


Q ss_pred             HHHHHHHHHHHhcCC
Q 040243          330 SLEGAAAMVEKLLQP  344 (797)
Q Consensus       330 ~v~~A~~~I~~ll~~  344 (797)
                      .|++|.++|..|+..
T Consensus        63 ~v~~A~~~I~~iv~e   77 (81)
T d2ctea1          63 GIEKARHEVLLISAE   77 (81)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH
Confidence            999999999998853

>d2ctja1 d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.21  E-value=4.3e-07  Score=76.94  Aligned_cols=68  Identities=21%  Similarity=0.320  Sum_probs=55.4

Q ss_pred             ceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHH-hCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCH
Q 040243          250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERE-TGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQ  328 (797)
Q Consensus       250 ~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~e-TgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~  328 (797)
                      ..+..|.||.      +|+|+|||++|.++|+|+++ ++|+|.+--.++                  ++ =-|.|+| +.
T Consensus         9 ~~t~~i~Vp~------~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~~~~------------------~~-~~v~I~G-~~   62 (82)
T d2ctja1           9 IAEVEVSIPA------KLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGS------------------GS-DTVVIRG-PS   62 (82)
T ss_dssp             SCCEEEECCH------HHHHHHHCSSSHHHHHHHHHHTSCEEECCCTTT------------------TC-CEEEEES-CH
T ss_pred             cEEEEEEECH------HHHhhcCCCCCccHHHHHHHcCCcEEEEeCCCC------------------CC-ceEEEeC-CH
Confidence            3567888998      99999999999999999987 599998864331                  11 1588988 58


Q ss_pred             HHHHHHHHHHHHhcC
Q 040243          329 ESLEGAAAMVEKLLQ  343 (797)
Q Consensus       329 e~v~~A~~~I~~ll~  343 (797)
                      +.|++|.++|+.++.
T Consensus        63 ~~v~~A~~~I~~~v~   77 (82)
T d2ctja1          63 SDVEKAKKQLLHLAE   77 (82)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHh
Confidence            899999999999875

>d2ctfa1 d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.19  E-value=6.9e-07  Score=77.20  Aligned_cols=66  Identities=15%  Similarity=0.236  Sum_probs=55.4

Q ss_pred             ceEEEEEecCCCCCCCceeeeeeCCCchhHHHHHHH-hCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCH
Q 040243          250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERE-TGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQ  328 (797)
Q Consensus       250 ~~~~Ki~IP~~~~P~~NfiG~iiGPrG~t~K~le~e-TgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~  328 (797)
                      .++..|.||.      .|.++|||++|.|+|+|+++ +||+|.+-...                      =.|.|+| +.
T Consensus        20 ~~t~~v~VP~------~~h~~iIG~~G~~I~~i~~~~~~v~I~~~~~~----------------------~~v~i~G-~~   70 (90)
T d2ctfa1          20 FTVSSVAAPS------WLHRFIIGKKGQNLAKITQQMPKVHIEFTEGE----------------------DKITLEG-PT   70 (90)
T ss_dssp             CEEEEEECCS------TTHHHHHTTTTCHHHHHHHHCSSSEEEECSSS----------------------CEEEEEE-CH
T ss_pred             cEEEEEEcCH------HHHhhcCCCCchhHHHHHHHcCCcEEeeCCCC----------------------ceEEEeC-CH
Confidence            4688999998      77899999999999999999 58999885211                      0589999 57


Q ss_pred             HHHHHHHHHHHHhcCC
Q 040243          329 ESLEGAAAMVEKLLQP  344 (797)
Q Consensus       329 e~v~~A~~~I~~ll~~  344 (797)
                      +.|++|.++|+.|+..
T Consensus        71 ~~ve~Ak~~I~~iv~e   86 (90)
T d2ctfa1          71 EDVSVAQEQIEGMVKD   86 (90)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            8999999999999864

>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 1, different isolates [TaxId: 11676]

Probab=98.03  E-value=1.2e-06  Score=65.10  Aligned_cols=40  Identities=33%  Similarity=0.703  Sum_probs=34.7

Q ss_pred             chhcccCCCCCccccCCCCCCCccccccceecCCCCCCcccCCCC
Q 040243          371 EYCRLCGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTIDCLVK  415 (797)
Q Consensus       371 ~~c~~cg~~gh~~~~cp~~~~~~~~~v~Cr~CG~~gH~t~dCp~k  415 (797)
                      ..|-+||+.||.+.+||...     ...|..||..||+++|||.+
T Consensus         2 i~C~~Cg~~GH~~~~Cp~~~-----~~~C~~Cg~~GH~~~~Cp~r   41 (42)
T d2exfa1           2 VKCFNCGKEGHTARNCRAPR-----KKGCWKCGKEGHQMKDCTER   41 (42)
T ss_dssp             CCCTTTCCSSSCTTTCSSCC-----CSSCSSSCCSSSCTTTCCSS
T ss_pred             CccccCCCcCcCcccCcCCC-----cCccccCCCCCeecccCCCC
Confidence            36999999999999999742     35799999999999999865

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.32  E-value=0.006  Score=49.28  Aligned_cols=61  Identities=20%  Similarity=0.260  Sum_probs=52.2

Q ss_pred             HHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccceEEEEecC
Q 040243          506 DGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG  569 (797)
Q Consensus       506 ~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr~L~V~~A~  569 (797)
                      +.|.+.|.++|.|.++.|.... .|.  -.|-|...+.++|..|+..|+.+.|++++|.|.++.
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~-dg~--~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHT-DYQ--LKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCC-STT--CCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHhheeEEEEEEEecc-CCc--EEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            3466889999999999986653 232  378999999999999999999999999999999975

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.25  E-value=0.0035  Score=53.07  Aligned_cols=69  Identities=22%  Similarity=0.525  Sum_probs=56.2

Q ss_pred             CcEEEEecCCCCCcH---------HHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcCceeeccc
Q 040243          491 DTNLYIGYLPPTLDD---------DGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGR  561 (797)
Q Consensus       491 ~~tLfVgNLp~~vte---------~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~LnG~~l~Gr  561 (797)
                      ..||.|.=+.+...+         .+|.+.|..||+|.-|+++.|        -..|+|.+-++|.+|++ |+|..+.|+
T Consensus        15 DgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~-l~g~~v~G~   85 (95)
T d1ufwa_          15 DATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLD-VDGMKVKGR   85 (95)
T ss_dssp             TCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHH-GGGSEETTE
T ss_pred             CcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhc-cCCeEEcce
Confidence            347888655543332         357788999999999999887        57899999999999995 899999999


Q ss_pred             eEEEEec
Q 040243          562 TIAVRVA  568 (797)
Q Consensus       562 ~L~V~~A  568 (797)
                      .|+|...
T Consensus        86 ~l~It~~   92 (95)
T d1ufwa_          86 AVKISGP   92 (95)
T ss_dssp             EEEEECC
T ss_pred             EEEEecC
Confidence            9999753

>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=95.82  E-value=0.017  Score=49.00  Aligned_cols=77  Identities=14%  Similarity=0.219  Sum_probs=62.2

Q ss_pred             cEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcc--cceEEEEecCHHHHHHHHHhcCceeeccc-----eEE
Q 040243          492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMS--KGYGFVKYADIQMANNAIASMNGYRLEGR-----TIA  564 (797)
Q Consensus       492 ~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGks--rGfaFV~F~s~e~A~~AI~~LnG~~l~Gr-----~L~  564 (797)
                      ++|.|+.||..+||+++.+.+...|++........+.+-+.  -.-|+|.|.+.+++..-.+.++|+.+.+.     +-.
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            58999999999999999999999999888777665544332  25789999999999999999999987532     235


Q ss_pred             EEec
Q 040243          565 VRVA  568 (797)
Q Consensus       565 V~~A  568 (797)
                      |++|
T Consensus        82 VE~A   85 (91)
T d1uw4a_          82 VEFA   85 (91)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            6665

>d1nc8a_ g.40.1.1 (A:) HIV nucleocapsid {Human immunodeficiency virus type 2 [TaxId: 11709]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 2 [TaxId: 11709]

Probab=94.14  E-value=0.0078  Score=39.55  Aligned_cols=21  Identities=29%  Similarity=0.719  Sum_probs=18.6

Q ss_pred             cccccceecCCCCCCcccCCC
Q 040243          394 KSDVLCKICGDGGHPTIDCLV  414 (797)
Q Consensus       394 ~~~v~Cr~CG~~gH~t~dCp~  414 (797)
                      +..|+|..||..||++++|.-
T Consensus         4 r~~ikCfNCGkeGH~ar~CrA   24 (29)
T d1nc8a_           4 RKVIRCWNCGKEGHSARQCRA   24 (29)
T ss_dssp             CCCCBCTTTSCBSSCGGGCCS
T ss_pred             cceeEeecCCccchhhhhccC
Confidence            367899999999999999964

>d1dsqa_ g.40.1.1 (A:) Nucleic acid binding protein p14 {Mouse mammary tumor virus [TaxId: 11757]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: Nucleic acid binding protein p14
species: Mouse mammary tumor virus [TaxId: 11757]

Probab=93.83  E-value=0.0075  Score=37.98  Aligned_cols=18  Identities=39%  Similarity=0.811  Sum_probs=15.9

Q ss_pred             ccceecCCCCCCcccCCC
Q 040243          397 VLCKICGDGGHPTIDCLV  414 (797)
Q Consensus       397 v~Cr~CG~~gH~t~dCp~  414 (797)
                      -+|..||..||+.+||..
T Consensus         3 pvcfscgktghikkdck~   20 (26)
T d1dsqa_           3 PVCFSCGKTGHIKRDCKE   20 (26)
T ss_dssp             CBCTTTCCBSSCTTTTTC
T ss_pred             CEEEecCCcccchhhhhh
Confidence            379999999999999964

>d1a6bb_ g.40.1.1 (B:) Zinc finger protein ncp10 {Moloney murine leukemia virus, MoMLV [TaxId: 11801]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: Zinc finger protein ncp10
species: Moloney murine leukemia virus, MoMLV [TaxId: 11801]

Probab=92.41  E-value=0.021  Score=40.22  Aligned_cols=21  Identities=33%  Similarity=0.596  Sum_probs=17.9

Q ss_pred             cccceecCCCCCCcccCCCCC
Q 040243          396 DVLCKICGDGGHPTIDCLVKG  416 (797)
Q Consensus       396 ~v~Cr~CG~~gH~t~dCp~k~  416 (797)
                      .-.|..|.+.|||.+|||-+-
T Consensus        10 kDQCAyCke~GHW~~dCPkkp   30 (40)
T d1a6bb_          10 RDQCAYCKEKGHWAKDCPKKP   30 (40)
T ss_dssp             SSSCSSSCCTTCCTTSCSSSC
T ss_pred             chhhHHHhhcCchhhhCccCC
Confidence            346999999999999999763

>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 1, different isolates [TaxId: 11676]

Probab=90.96  E-value=0.032  Score=40.54  Aligned_cols=20  Identities=35%  Similarity=0.810  Sum_probs=18.0

Q ss_pred             cccceecCCCCCCcccCCCC
Q 040243          396 DVLCKICGDGGHPTIDCLVK  415 (797)
Q Consensus       396 ~v~Cr~CG~~gH~t~dCp~k  415 (797)
                      +|+|..||+.||+++||+..
T Consensus         1 ni~C~~Cg~~GH~~~~Cp~~   20 (42)
T d2exfa1           1 NVKCFNCGKEGHTARNCRAP   20 (42)
T ss_dssp             CCCCTTTCCSSSCTTTCSSC
T ss_pred             CCccccCCCcCcCcccCcCC
Confidence            47899999999999999864

>d2ja9a2 d.51.1.1 (A:152-236) Ribosomal RNA-processing protein 40, RRP40 {Saccharomyces cerevisiae [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Ribosomal RNA-processing protein 40, RRP40
species: Saccharomyces cerevisiae [TaxId: 4932]

Probab=90.74  E-value=0.052  Score=45.40  Aligned_cols=52  Identities=15%  Similarity=0.140  Sum_probs=41.3

Q ss_pred             ceeeeeeCCCch-hHHHHHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHH
Q 040243          266 NFIGLIIGPRGN-TQKRMERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEK  340 (797)
Q Consensus       266 NfiG~iiGPrG~-t~K~le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v~~A~~~I~~  340 (797)
                      +|+-+|||.++. -++.|.+.++|.|.|=-.|                       .|+|.+++.+..-++.+.|++
T Consensus        10 ~~~rrll~~~~~~ml~~l~~~~~~eI~VG~NG-----------------------rIWi~~~~~~~~i~i~~aI~~   62 (85)
T d2ja9a2          10 NFARQLLFNNDFPLLKVLAAHTKFEVAIGLNG-----------------------KIWVKCEELSNTLACYRTIME   62 (85)
T ss_dssp             HHHHHHHHCTTCCHHHHHHTTCCCEEEEETTT-----------------------EEEEECSSHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCChHHHHHHhhcCceEEEecCc-----------------------EEEEECCCHHHHHHHHHHHHH
Confidence            889999999998 6888999999999997666                       799999987654444443433

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=87.99  E-value=0.86  Score=38.63  Aligned_cols=57  Identities=23%  Similarity=0.358  Sum_probs=46.4

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHhhcCCCEEEEEEEecCCCCcccceEEEEecCHHHHHHHHHhcC
Q 040243          490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMN  554 (797)
Q Consensus       490 ~~~tLfVgNLp~~vte~dL~~~Fs~fG~I~~v~v~~dk~TGksrGfaFV~F~s~e~A~~AI~~Ln  554 (797)
                      ...-||.-..|..+...||.++|+.||.|. |.++-|.       -|||...+.++|+.++..+.
T Consensus        14 ~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~-VswIddT-------Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          14 KRDHVLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDDT-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCSEEEEECCTTCCHHHHHHHHTTTCSCC-CEEEETT-------EEEEECSCHHHHHHHHHHHH
T ss_pred             CcceeEEEeCCcccchhHHHHHhcCCCceE-EEEecCc-------eEEEEecCHHHHHHHHHHhc
Confidence            344688889999999999999999999764 4445553       89999999999999886543

>d3etja1 b.84.2.1 (A:277-355) N5-carboxyaminoimidazole ribonucleotide synthetase PurK (AIRC), C-domain {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: Barrel-sandwich hybrid
superfamily: Rudiment single hybrid motif
family: BC C-terminal domain-like
domain: N5-carboxyaminoimidazole ribonucleotide synthetase PurK (AIRC), C-domain
species: Escherichia coli [TaxId: 562]

Probab=85.55  E-value=0.7  Score=37.73  Aligned_cols=48  Identities=19%  Similarity=0.203  Sum_probs=40.1

Q ss_pred             HHHHhCcEEEEeccccccccccccccCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHhcCC
Q 040243          282 MERETGAKIVIRGKGSVKEGRLQQKRDLKPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQP  344 (797)
Q Consensus       282 le~eTgakI~IrGkGS~k~g~~~~~~~~~~~~~~~e~LHv~I~a~~~e~v~~A~~~I~~ll~~  344 (797)
                      +-+..+++|-+.|| ..|.|++-.              ||.|.+++.+.+.+.++.++.+|.+
T Consensus        18 ~l~~p~~~~H~YGK-~~RpgRKmG--------------Hitl~~~~~~~l~~~~~~l~~~L~~   65 (79)
T d3etja1          18 WLKLPLVHLHWYDK-EVRPGRKVG--------------HLNLTDSDTSRLTATLEALIPLLPP   65 (79)
T ss_dssp             GGGSTTCEEEECCC-CCCTTCEEE--------------EEEEECSCHHHHHHHHHHHGGGSCG
T ss_pred             HHhCCCcEEEecCC-CCCCCCcEE--------------EEEeecCCHHHHHHHHHHHHHhCCH
Confidence            44567999999999 578777643              9999999999999998888888874

>d1cl4a_ g.40.1.1 (A:) Nucleocapsid protein from mason-pfizer monkey virus (MPMV) {Mason-pfizer monkey virus [TaxId: 11855]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: Nucleocapsid protein from mason-pfizer monkey virus (MPMV)
species: Mason-pfizer monkey virus [TaxId: 11855]

Probab=82.53  E-value=0.23  Score=33.39  Aligned_cols=20  Identities=35%  Similarity=0.669  Sum_probs=17.3

Q ss_pred             cceecCCCCCCcccCCCCCc
Q 040243          398 LCKICGDGGHPTIDCLVKGT  417 (797)
Q Consensus       398 ~Cr~CG~~gH~t~dCp~k~~  417 (797)
                      +|-.|+.+-||++||..|-.
T Consensus         4 lCPrC~kG~HWa~~Crsk~~   23 (32)
T d1cl4a_           4 LCPRCKRGKHWANECKSKTD   23 (32)
T ss_dssp             SCSSCSSCSSCSTTCCCTTS
T ss_pred             cCccccCcchHHHHhhhhhc
Confidence            68899999999999988743

>d1dsva_ g.40.1.1 (A:) Nucleic acid binding protein p14 {Mouse mammary tumor virus [TaxId: 11757]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: Nucleic acid binding protein p14
species: Mouse mammary tumor virus [TaxId: 11757]

Probab=80.34  E-value=0.26  Score=32.98  Aligned_cols=19  Identities=37%  Similarity=0.604  Sum_probs=16.8

Q ss_pred             cceecCCCCCCcccCCCCC
Q 040243          398 LCKICGDGGHPTIDCLVKG  416 (797)
Q Consensus       398 ~Cr~CG~~gH~t~dCp~k~  416 (797)
                      +|-.|+.+-||+++|..|-
T Consensus         4 lCPrC~kG~HWa~~Crsk~   22 (31)
T d1dsva_           4 LCPRCKKGYHWKSECKSKF   22 (31)
T ss_dssp             BCTTTCSSBSCTTTCCCSE
T ss_pred             cCccccCcchHHHHhhhhh
Confidence            6889999999999998763